---
_id: '356'
abstract:
- lang: eng
text: Cu2ZnSnS4, based on abundant and environmental friendly elements and with
a direct band gap of 1.5 eV, is a main candidate material for solar energy conversion
through both photovoltaics and photocatalysis. We detail here the synthesis of
quasi-spherical Cu 2ZnSnS4 nanoparticles with unprecedented narrow size distributions.
We further detail their use as seeds to produce CZTS-Au and CZTS-Pt heterostructured
nanoparticles. Such heterostructured nanoparticles are shown to have excellent
photocatalytic properties toward degradation of Rhodamine B and hydrogen generation
by water splitting.
acknowledgement: This work was supported by the European Regional Development Funds
and the Framework 7 program under project SCALENANO (FP7-NMP-ENERGY-2011-284486).
article_processing_charge: No
article_type: original
author:
- first_name: Xuelian
full_name: Yu, Xuelian
last_name: Yu
- first_name: Alexey
full_name: Shavel, Alexey
last_name: Shavel
- first_name: Xiaoqiang
full_name: An, Xiaoqiang
last_name: An
- first_name: Zhishan
full_name: Luo, Zhishan
last_name: Luo
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: Yu X, Shavel A, An X, Luo Z, Ibáñez M, Cabot A. Cu2ZnSnS4-Pt and Cu2ZnSnS4-Au
heterostructured nanoparticles for photocatalytic water splitting and pollutant
degradation. Journal of the American Chemical Society. 2014;136(26):9236-9239.
doi:10.1021/ja502076b
apa: Yu, X., Shavel, A., An, X., Luo, Z., Ibáñez, M., & Cabot, A. (2014). Cu2ZnSnS4-Pt
and Cu2ZnSnS4-Au heterostructured nanoparticles for photocatalytic water splitting
and pollutant degradation. Journal of the American Chemical Society. American
Chemical Society. https://doi.org/10.1021/ja502076b
chicago: Yu, Xuelian, Alexey Shavel, Xiaoqiang An, Zhishan Luo, Maria Ibáñez, and
Andreu Cabot. “Cu2ZnSnS4-Pt and Cu2ZnSnS4-Au Heterostructured Nanoparticles for
Photocatalytic Water Splitting and Pollutant Degradation.” Journal of the American
Chemical Society. American Chemical Society, 2014. https://doi.org/10.1021/ja502076b.
ieee: X. Yu, A. Shavel, X. An, Z. Luo, M. Ibáñez, and A. Cabot, “Cu2ZnSnS4-Pt and
Cu2ZnSnS4-Au heterostructured nanoparticles for photocatalytic water splitting
and pollutant degradation,” Journal of the American Chemical Society, vol.
136, no. 26. American Chemical Society, pp. 9236–9239, 2014.
ista: Yu X, Shavel A, An X, Luo Z, Ibáñez M, Cabot A. 2014. Cu2ZnSnS4-Pt and Cu2ZnSnS4-Au
heterostructured nanoparticles for photocatalytic water splitting and pollutant
degradation. Journal of the American Chemical Society. 136(26), 9236–9239.
mla: Yu, Xuelian, et al. “Cu2ZnSnS4-Pt and Cu2ZnSnS4-Au Heterostructured Nanoparticles
for Photocatalytic Water Splitting and Pollutant Degradation.” Journal of the
American Chemical Society, vol. 136, no. 26, American Chemical Society, 2014,
pp. 9236–39, doi:10.1021/ja502076b.
short: X. Yu, A. Shavel, X. An, Z. Luo, M. Ibáñez, A. Cabot, Journal of the American
Chemical Society 136 (2014) 9236–9239.
date_created: 2018-12-11T11:46:00Z
date_published: 2014-07-02T00:00:00Z
date_updated: 2021-01-12T07:44:18Z
day: '02'
doi: 10.1021/ja502076b
extern: '1'
intvolume: ' 136'
issue: '26'
language:
- iso: eng
month: '07'
oa_version: None
page: 9236 - 9239
publication: Journal of the American Chemical Society
publication_status: published
publisher: American Chemical Society
publist_id: '7472'
quality_controlled: '1'
status: public
title: Cu2ZnSnS4-Pt and Cu2ZnSnS4-Au heterostructured nanoparticles for photocatalytic
water splitting and pollutant degradation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 136
year: '2014'
...
---
_id: '358'
abstract:
- lang: eng
text: Monodispersed Pt3Sn nanoparticles were prepared through a mild thermal synthesis
in the presence of surfactants. The performance of Pt3Sn for the electrooxidation
of ethanol and adsorbed carbon monoxide (COad) in acid medium was studied by a
combination of electrochemical and insitu spectroscopic methods, namely, infrared
reflection absorption spectroscopy and differential electrochemical mass spectrometry
(DEMS), and the results were compared to those obtained with the use of Pt black.
The formation of the Pt3Sn solid solution promoted the oxidation of COad at less-positive
potentials than those required for Pt black. Also, the electrooxidation of ethanol,
especially at lower potentials, was more favorable with Pt3Sn, as deduced from
the higher faradaic currents recorded during the ethanol oxidation reaction (EOR).
However, the distribution of products as deduced by DEMS analysis suggested that
the formation of C1 products, CO2 inclusive, is less significant on Pt3Sn than
on Pt. In fact, the higher faradaic current recorded with the former catalyst
can be attributed to the greater amounts of acetaldehyde and acetic acid formed.
After the EOR, the surface of both Pt and Pt3Sn remained covered by ethanol adsorbates.
Whereas C2 fragments were the main adsorbates at the surface of Pt3Sn after the
EOR, both C1 and C2 species remained adsorbed at Pt black.
acknowledgement: The Spanish Ministry of Science and Innovation (Project ENE2010–15381)
and the CSIC (Project 201080E116) are acknowledged for financial support.
article_processing_charge: No
article_type: original
author:
- first_name: Tirma
full_name: Herranz, Tirma
last_name: Herranz
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: José
full_name: Gómez De La Fuente, José
last_name: Gómez De La Fuente
- first_name: Francisco
full_name: Pérez Alonso, Francisco
last_name: Pérez Alonso
- first_name: Miguel
full_name: Peña, Miguel
last_name: Peña
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
- first_name: Sergio
full_name: Rojas, Sergio
last_name: Rojas
citation:
ama: Herranz T, Ibáñez M, Gómez De La Fuente J, et al. In situ study of ethanol
electrooxidation on monodispersed Pt inf 3 inf Sn nanoparticles. ChemElectroChem.
2014;1(5):885-895. doi:10.1002/celc.201300254
apa: Herranz, T., Ibáñez, M., Gómez De La Fuente, J., Pérez Alonso, F., Peña, M.,
Cabot, A., & Rojas, S. (2014). In situ study of ethanol electrooxidation on
monodispersed Pt inf 3 inf Sn nanoparticles. ChemElectroChem. Wiley-Blackwell.
https://doi.org/10.1002/celc.201300254
chicago: Herranz, Tirma, Maria Ibáñez, José Gómez De La Fuente, Francisco Pérez
Alonso, Miguel Peña, Andreu Cabot, and Sergio Rojas. “In Situ Study of Ethanol
Electrooxidation on Monodispersed Pt Inf 3 Inf Sn Nanoparticles.” ChemElectroChem.
Wiley-Blackwell, 2014. https://doi.org/10.1002/celc.201300254.
ieee: T. Herranz et al., “In situ study of ethanol electrooxidation on monodispersed
Pt inf 3 inf Sn nanoparticles,” ChemElectroChem, vol. 1, no. 5. Wiley-Blackwell,
pp. 885–895, 2014.
ista: Herranz T, Ibáñez M, Gómez De La Fuente J, Pérez Alonso F, Peña M, Cabot A,
Rojas S. 2014. In situ study of ethanol electrooxidation on monodispersed Pt inf
3 inf Sn nanoparticles. ChemElectroChem. 1(5), 885–895.
mla: Herranz, Tirma, et al. “In Situ Study of Ethanol Electrooxidation on Monodispersed
Pt Inf 3 Inf Sn Nanoparticles.” ChemElectroChem, vol. 1, no. 5, Wiley-Blackwell,
2014, pp. 885–95, doi:10.1002/celc.201300254.
short: T. Herranz, M. Ibáñez, J. Gómez De La Fuente, F. Pérez Alonso, M. Peña, A.
Cabot, S. Rojas, ChemElectroChem 1 (2014) 885–895.
date_created: 2018-12-11T11:46:00Z
date_published: 2014-03-03T00:00:00Z
date_updated: 2021-01-12T07:44:26Z
day: '03'
doi: 10.1002/celc.201300254
extern: '1'
intvolume: ' 1'
issue: '5'
language:
- iso: eng
month: '03'
oa_version: None
page: 885 - 895
publication: ChemElectroChem
publication_status: published
publisher: Wiley-Blackwell
publist_id: '7474'
quality_controlled: '1'
status: public
title: In situ study of ethanol electrooxidation on monodispersed Pt inf 3 inf Sn
nanoparticles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2014'
...
---
_id: '451'
abstract:
- lang: eng
text: We introduce algorithms for the computation of homology, cohomology, and related
operations on cubical cell complexes, using the technique based on a chain contraction
from the original chain complex to a reduced one that represents its homology.
This work is based on previous results for simplicial complexes, and uses Serre’s
diagonalization for cubical cells. An implementation in C++ of the introduced
algorithms is available at http://www.pawelpilarczyk.com/chaincon/ together with
some examples. The paper is self-contained as much as possible, and is written
at a very elementary level, so that basic knowledge of algebraic topology should
be sufficient to follow it.
acknowledgement: 'This research was partially supported from Fundo Europeu de Desenvolvimento
Regional (FEDER) through COMPETE – Programa Operacional Factores de Compe titividade
(POFC) and from the Portuguese national funds through Fundacaoparaa Ciencia e a
Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645(ref.
FCT PTDC/MAT/098871/2008), as well as from the funds distributed through the European
Science Foundation (ESF) Research Networking Programme on “Applied and Computational
Algebraic Topology” (ACAT). P.Real was additionally supported by the Spanish Ministry
of Science and Innovation, project no. MTM2009-12716. '
author:
- first_name: Pawel
full_name: Pawel Pilarczyk
id: 3768D56A-F248-11E8-B48F-1D18A9856A87
last_name: Pilarczyk
- first_name: Pedro
full_name: Real, Pedro
last_name: Real
citation:
ama: Pilarczyk P, Real P. Computation of cubical homology, cohomology, and (co)homological
operations via chain contraction. Advances in Computational Mathematics.
2014;41(1):253-275. doi:10.1007/s10444-014-9356-1
apa: Pilarczyk, P., & Real, P. (2014). Computation of cubical homology, cohomology,
and (co)homological operations via chain contraction. Advances in Computational
Mathematics. Kluwer. https://doi.org/10.1007/s10444-014-9356-1
chicago: Pilarczyk, Pawel, and Pedro Real. “Computation of Cubical Homology, Cohomology,
and (Co)Homological Operations via Chain Contraction.” Advances in Computational
Mathematics. Kluwer, 2014. https://doi.org/10.1007/s10444-014-9356-1.
ieee: P. Pilarczyk and P. Real, “Computation of cubical homology, cohomology, and
(co)homological operations via chain contraction,” Advances in Computational
Mathematics, vol. 41, no. 1. Kluwer, pp. 253–275, 2014.
ista: Pilarczyk P, Real P. 2014. Computation of cubical homology, cohomology, and
(co)homological operations via chain contraction. Advances in Computational Mathematics.
41(1), 253–275.
mla: Pilarczyk, Pawel, and Pedro Real. “Computation of Cubical Homology, Cohomology,
and (Co)Homological Operations via Chain Contraction.” Advances in Computational
Mathematics, vol. 41, no. 1, Kluwer, 2014, pp. 253–75, doi:10.1007/s10444-014-9356-1.
short: P. Pilarczyk, P. Real, Advances in Computational Mathematics 41 (2014) 253–275.
date_created: 2018-12-11T11:46:33Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T07:59:20Z
day: '01'
doi: 10.1007/s10444-014-9356-1
extern: 1
intvolume: ' 41'
issue: '1'
main_file_link:
- open_access: '1'
url: https://idus.us.es/xmlui/handle/11441/38719
month: '01'
oa: 1
page: 253 - 275
publication: Advances in Computational Mathematics
publication_status: published
publisher: Kluwer
publist_id: '7371'
quality_controlled: 0
status: public
title: Computation of cubical homology, cohomology, and (co)homological operations
via chain contraction
type: journal_article
volume: 41
year: '2014'
...
---
_id: '468'
abstract:
- lang: eng
text: Invasive alien parasites and pathogens are a growing threat to biodiversity
worldwide, which can contribute to the extinction of endemic species. On the Galápagos
Islands, the invasive parasitic fly Philornis downsi poses a major threat to the
endemic avifauna. Here, we investigated the influence of this parasite on the
breeding success of two Darwin's finch species, the warbler finch (Certhidea olivacea)
and the sympatric small tree finch (Camarhynchus parvulus), on Santa Cruz Island
in 2010 and 2012. While the population of the small tree finch appeared to be
stable, the warbler finch has experienced a dramatic decline in population size
on Santa Cruz Island since 1997. We aimed to identify whether warbler finches
are particularly vulnerable during different stages of the breeding cycle. Contrary
to our prediction, breeding success was lower in the small tree finch than in
the warbler finch. In both species P. downsi had a strong negative impact on breeding
success and our data suggest that heavy rain events also lowered the fledging
success. On the one hand parents might be less efficient in compensating their
chicks' energy loss due to parasitism as they might be less efficient in foraging
on days of heavy rain. On the other hand, intense rainfalls might lead to increased
humidity and more rapid cooling of the nests. In the case of the warbler finch
we found that the control of invasive plant species with herbicides had a significant
additive negative impact on the breeding success. It is very likely that the availability
of insects (i.e. food abundance) is lower in such controlled areas, as herbicide
usage led to the removal of the entire understory. Predation seems to be a minor
factor in brood loss.
acknowledgement: The study was funded by the University of Vienna (Focus of Excellence
grant), the Galápagos Conservation Trust, and the Ethologische Gesellschaft e.V.
article_number: '0107518'
author:
- first_name: Arno
full_name: Cimadom, Arno
last_name: Cimadom
- first_name: Angel
full_name: Ulloa, Angel
last_name: Ulloa
- first_name: Patrick
full_name: Meidl, Patrick
id: 4709BCE6-F248-11E8-B48F-1D18A9856A87
last_name: Meidl
- first_name: Markus
full_name: Zöttl, Markus
last_name: Zöttl
- first_name: Elisabet
full_name: Zöttl, Elisabet
last_name: Zöttl
- first_name: Birgit
full_name: Fessl, Birgit
last_name: Fessl
- first_name: Erwin
full_name: Nemeth, Erwin
last_name: Nemeth
- first_name: Michael
full_name: Dvorak, Michael
last_name: Dvorak
- first_name: Francesca
full_name: Cunninghame, Francesca
last_name: Cunninghame
- first_name: Sabine
full_name: Tebbich, Sabine
last_name: Tebbich
citation:
ama: Cimadom A, Ulloa A, Meidl P, et al. Invasive parasites habitat change and heavy
rainfall reduce breeding success in Darwin’s finches. PLoS One. 2014;9(9).
doi:10.1371/journal.pone.0107518
apa: Cimadom, A., Ulloa, A., Meidl, P., Zöttl, M., Zöttl, E., Fessl, B., … Tebbich,
S. (2014). Invasive parasites habitat change and heavy rainfall reduce breeding
success in Darwin’s finches. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0107518
chicago: Cimadom, Arno, Angel Ulloa, Patrick Meidl, Markus Zöttl, Elisabet Zöttl,
Birgit Fessl, Erwin Nemeth, Michael Dvorak, Francesca Cunninghame, and Sabine
Tebbich. “Invasive Parasites Habitat Change and Heavy Rainfall Reduce Breeding
Success in Darwin’s Finches.” PLoS One. Public Library of Science, 2014.
https://doi.org/10.1371/journal.pone.0107518.
ieee: A. Cimadom et al., “Invasive parasites habitat change and heavy rainfall
reduce breeding success in Darwin’s finches,” PLoS One, vol. 9, no. 9.
Public Library of Science, 2014.
ista: Cimadom A, Ulloa A, Meidl P, Zöttl M, Zöttl E, Fessl B, Nemeth E, Dvorak M,
Cunninghame F, Tebbich S. 2014. Invasive parasites habitat change and heavy rainfall
reduce breeding success in Darwin’s finches. PLoS One. 9(9), 0107518.
mla: Cimadom, Arno, et al. “Invasive Parasites Habitat Change and Heavy Rainfall
Reduce Breeding Success in Darwin’s Finches.” PLoS One, vol. 9, no. 9,
0107518, Public Library of Science, 2014, doi:10.1371/journal.pone.0107518.
short: A. Cimadom, A. Ulloa, P. Meidl, M. Zöttl, E. Zöttl, B. Fessl, E. Nemeth,
M. Dvorak, F. Cunninghame, S. Tebbich, PLoS One 9 (2014).
date_created: 2018-12-11T11:46:38Z
date_published: 2014-09-23T00:00:00Z
date_updated: 2021-01-12T08:00:48Z
day: '23'
ddc:
- '576'
department:
- _id: CampIT
doi: 10.1371/journal.pone.0107518
file:
- access_level: open_access
checksum: b24e7518ccd41effed0d7d9e2498f67f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:48Z
date_updated: 2020-07-14T12:46:34Z
file_id: '5103'
file_name: IST-2018-954-v1+1_2014_Meidl_Invasive_parasites.PDF
file_size: 489387
relation: main_file
file_date_updated: 2020-07-14T12:46:34Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '9'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '09'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '7352'
pubrep_id: '954'
quality_controlled: '1'
scopus_import: 1
status: public
title: Invasive parasites habitat change and heavy rainfall reduce breeding success
in Darwin's finches
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2014'
...
---
_id: '475'
abstract:
- lang: eng
text: 'First cycle games (FCG) are played on a finite graph by two players who push
a token along the edges until a vertex is repeated, and a simple cycle is formed.
The winner is determined by some fixed property Y of the sequence of labels of
the edges (or nodes) forming this cycle. These games are traditionally of interest
because of their connection with infinite-duration games such as parity and mean-payoff
games. We study the memory requirements for winning strategies of FCGs and certain
associated infinite duration games. We exhibit a simple FCG that is not memoryless
determined (this corrects a mistake in Memoryless determinacy of parity and mean
payoff games: a simple proof by Bj⋯orklund, Sandberg, Vorobyov (2004) that claims
that FCGs for which Y is closed under cyclic permutations are memoryless determined).
We show that θ (n)! memory (where n is the number of nodes in the graph), which
is always sufficient, may be necessary to win some FCGs. On the other hand, we
identify easy to check conditions on Y (i.e., Y is closed under cyclic permutations,
and both Y and its complement are closed under concatenation) that are sufficient
to ensure that the corresponding FCGs and their associated infinite duration games
are memoryless determined. We demonstrate that many games considered in the literature,
such as mean-payoff, parity, energy, etc., satisfy these conditions. On the complexity
side, we show (for efficiently computable Y) that while solving FCGs is in PSPACE,
solving some families of FCGs is PSPACE-hard. '
alternative_title:
- EPTCS
author:
- first_name: Benjamin
full_name: Aminof, Benjamin
id: 4A55BD00-F248-11E8-B48F-1D18A9856A87
last_name: Aminof
- first_name: Sasha
full_name: Rubin, Sasha
id: 2EC51194-F248-11E8-B48F-1D18A9856A87
last_name: Rubin
citation:
ama: 'Aminof B, Rubin S. First cycle games. In: Electronic Proceedings in Theoretical
Computer Science, EPTCS. Vol 146. Open Publishing Association; 2014:83-90.
doi:10.4204/EPTCS.146.11'
apa: 'Aminof, B., & Rubin, S. (2014). First cycle games. In Electronic Proceedings
in Theoretical Computer Science, EPTCS (Vol. 146, pp. 83–90). Grenoble, France:
Open Publishing Association. https://doi.org/10.4204/EPTCS.146.11'
chicago: Aminof, Benjamin, and Sasha Rubin. “First Cycle Games.” In Electronic
Proceedings in Theoretical Computer Science, EPTCS, 146:83–90. Open Publishing
Association, 2014. https://doi.org/10.4204/EPTCS.146.11.
ieee: B. Aminof and S. Rubin, “First cycle games,” in Electronic Proceedings
in Theoretical Computer Science, EPTCS, Grenoble, France, 2014, vol. 146,
pp. 83–90.
ista: 'Aminof B, Rubin S. 2014. First cycle games. Electronic Proceedings in Theoretical
Computer Science, EPTCS. SR: Strategic Reasoning, EPTCS, vol. 146, 83–90.'
mla: Aminof, Benjamin, and Sasha Rubin. “First Cycle Games.” Electronic Proceedings
in Theoretical Computer Science, EPTCS, vol. 146, Open Publishing Association,
2014, pp. 83–90, doi:10.4204/EPTCS.146.11.
short: B. Aminof, S. Rubin, in:, Electronic Proceedings in Theoretical Computer
Science, EPTCS, Open Publishing Association, 2014, pp. 83–90.
conference:
end_date: 2014-04-06
location: Grenoble, France
name: 'SR: Strategic Reasoning'
start_date: 2014-04-05
date_created: 2018-12-11T11:46:41Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2021-01-12T08:00:53Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.4204/EPTCS.146.11
ec_funded: 1
file:
- access_level: open_access
checksum: 4d7b4ab82980cca2b96ac7703992a8c8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:08Z
date_updated: 2020-07-14T12:46:35Z
file_id: '5260'
file_name: IST-2018-952-v1+1_2014_Rubin_First_cycle.pdf
file_size: 100115
relation: main_file
file_date_updated: 2020-07-14T12:46:35Z
has_accepted_license: '1'
intvolume: ' 146'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 83 - 90
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication: Electronic Proceedings in Theoretical Computer Science, EPTCS
publication_status: published
publisher: Open Publishing Association
publist_id: '7345'
pubrep_id: '952'
quality_controlled: '1'
scopus_import: 1
status: public
title: First cycle games
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 146
year: '2014'
...
---
_id: '10892'
abstract:
- lang: eng
text: "In this paper, we introduce planar matchings on directed pseudo-line arrangements,
which yield a planar set of pseudo-line segments such that only matching-partners
are adjacent. By translating the planar matching problem into a corresponding
stable roommates problem we show that such matchings always exist.\r\nUsing our
new framework, we establish, for the first time, a complete, rigorous definition
of weighted straight skeletons, which are based on a so-called wavefront propagation
process. We present a generalized and unified approach to treat structural changes
in the wavefront that focuses on the restoration of weak planarity by finding
planar matchings."
acknowledgement: 'T. Biedl was supported by NSERC and the Ross and Muriel Cheriton
Fellowship. P. Palfrader was supported by Austrian Science Fund (FWF): P25816-N15.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Therese
full_name: Biedl, Therese
last_name: Biedl
- first_name: Stefan
full_name: Huber, Stefan
id: 4700A070-F248-11E8-B48F-1D18A9856A87
last_name: Huber
orcid: 0000-0002-8871-5814
- first_name: Peter
full_name: Palfrader, Peter
last_name: Palfrader
citation:
ama: 'Biedl T, Huber S, Palfrader P. Planar matchings for weighted straight skeletons.
In: 25th International Symposium, ISAAC 2014. Vol 8889. Springer Nature;
2014:117-127. doi:10.1007/978-3-319-13075-0_10'
apa: 'Biedl, T., Huber, S., & Palfrader, P. (2014). Planar matchings for weighted
straight skeletons. In 25th International Symposium, ISAAC 2014 (Vol. 8889,
pp. 117–127). Jeonju, Korea: Springer Nature. https://doi.org/10.1007/978-3-319-13075-0_10'
chicago: Biedl, Therese, Stefan Huber, and Peter Palfrader. “Planar Matchings for
Weighted Straight Skeletons.” In 25th International Symposium, ISAAC 2014,
8889:117–27. Springer Nature, 2014. https://doi.org/10.1007/978-3-319-13075-0_10.
ieee: T. Biedl, S. Huber, and P. Palfrader, “Planar matchings for weighted straight
skeletons,” in 25th International Symposium, ISAAC 2014, Jeonju, Korea,
2014, vol. 8889, pp. 117–127.
ista: 'Biedl T, Huber S, Palfrader P. 2014. Planar matchings for weighted straight
skeletons. 25th International Symposium, ISAAC 2014. ISAAC: International Symposium
on Algorithms and Computation, LNCS, vol. 8889, 117–127.'
mla: Biedl, Therese, et al. “Planar Matchings for Weighted Straight Skeletons.”
25th International Symposium, ISAAC 2014, vol. 8889, Springer Nature, 2014,
pp. 117–27, doi:10.1007/978-3-319-13075-0_10.
short: T. Biedl, S. Huber, P. Palfrader, in:, 25th International Symposium, ISAAC
2014, Springer Nature, 2014, pp. 117–127.
conference:
end_date: 2014-12-17
location: Jeonju, Korea
name: 'ISAAC: International Symposium on Algorithms and Computation'
start_date: 2014-12-15
date_created: 2022-03-21T07:09:03Z
date_published: 2014-11-08T00:00:00Z
date_updated: 2023-02-23T12:20:55Z
day: '08'
department:
- _id: HeEd
doi: 10.1007/978-3-319-13075-0_10
intvolume: ' 8889'
language:
- iso: eng
month: '11'
oa_version: None
page: 117-127
publication: 25th International Symposium, ISAAC 2014
publication_identifier:
eisbn:
- '9783319130750'
eissn:
- 1611-3349
isbn:
- '9783319130743'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '481'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Planar matchings for weighted straight skeletons
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8889
year: '2014'
...
---
_id: '537'
abstract:
- lang: eng
text: Transgenerational effects are broader than only parental relationships. Despite
mounting evidence that multigenerational effects alter phenotypic and life-history
traits, our understanding of how they combine to determine fitness is not well
developed because of the added complexity necessary to study them. Here, we derive
a quantitative genetic model of adaptation to an extraordinary new environment
by an additive genetic component, phenotypic plasticity, maternal and grandmaternal
effects. We show how, at equilibrium, negative maternal and negative grandmaternal
effects maximize expected population mean fitness. We define negative transgenerational
effects as those that have a negative effect on trait expression in the subsequent
generation, that is, they slow, or potentially reverse, the expected evolutionary
dynamic. When maternal effects are positive, negative grandmaternal effects are
preferred. As expected under Mendelian inheritance, the grandmaternal effects
have a lower impact on fitness than the maternal effects, but this dual inheritance
model predicts a more complex relationship between maternal and grandmaternal
effects to constrain phenotypic variance and so maximize expected population mean
fitness in the offspring.
author:
- first_name: Roshan
full_name: Prizak, Roshan
id: 4456104E-F248-11E8-B48F-1D18A9856A87
last_name: Prizak
- first_name: Thomas
full_name: Ezard, Thomas
last_name: Ezard
- first_name: Rebecca
full_name: Hoyle, Rebecca
last_name: Hoyle
citation:
ama: Prizak R, Ezard T, Hoyle R. Fitness consequences of maternal and grandmaternal
effects. Ecology and Evolution. 2014;4(15):3139-3145. doi:10.1002/ece3.1150
apa: Prizak, R., Ezard, T., & Hoyle, R. (2014). Fitness consequences of maternal
and grandmaternal effects. Ecology and Evolution. Wiley-Blackwell. https://doi.org/10.1002/ece3.1150
chicago: Prizak, Roshan, Thomas Ezard, and Rebecca Hoyle. “Fitness Consequences
of Maternal and Grandmaternal Effects.” Ecology and Evolution. Wiley-Blackwell,
2014. https://doi.org/10.1002/ece3.1150.
ieee: R. Prizak, T. Ezard, and R. Hoyle, “Fitness consequences of maternal and grandmaternal
effects,” Ecology and Evolution, vol. 4, no. 15. Wiley-Blackwell, pp. 3139–3145,
2014.
ista: Prizak R, Ezard T, Hoyle R. 2014. Fitness consequences of maternal and grandmaternal
effects. Ecology and Evolution. 4(15), 3139–3145.
mla: Prizak, Roshan, et al. “Fitness Consequences of Maternal and Grandmaternal
Effects.” Ecology and Evolution, vol. 4, no. 15, Wiley-Blackwell, 2014,
pp. 3139–45, doi:10.1002/ece3.1150.
short: R. Prizak, T. Ezard, R. Hoyle, Ecology and Evolution 4 (2014) 3139–3145.
date_created: 2018-12-11T11:47:02Z
date_published: 2014-07-19T00:00:00Z
date_updated: 2021-01-12T08:01:30Z
day: '19'
ddc:
- '530'
- '571'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1002/ece3.1150
file:
- access_level: open_access
checksum: e32abf75a248e7a11811fd7f60858769
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:31Z
date_updated: 2020-07-14T12:46:38Z
file_id: '4886'
file_name: IST-2018-934-v1+1_Prizak_et_al-2014-Ecology_and_Evolution.pdf
file_size: 621582
relation: main_file
file_date_updated: 2020-07-14T12:46:38Z
has_accepted_license: '1'
intvolume: ' 4'
issue: '15'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 3139 - 3145
publication: Ecology and Evolution
publication_status: published
publisher: Wiley-Blackwell
publist_id: '7280'
pubrep_id: '934'
scopus_import: 1
status: public
title: Fitness consequences of maternal and grandmaternal effects
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2014'
...
---
_id: '1903'
abstract:
- lang: eng
text: 'We consider two-player zero-sum partial-observation stochastic games on graphs.
Based on the information available to the players these games can be classified
as follows: (a) general partial-observation (both players have partial view of
the game); (b) one-sided partial-observation (one player has partial-observation
and the other player has complete-observation); and (c) perfect-observation (both
players have complete view of the game). The one-sided partial-observation games
subsumes the important special case of one-player partial-observation stochastic
games (or partial-observation Markov decision processes (POMDPs)). Based on the
randomization available for the strategies, (a) the players may not be allowed
to use randomization (pure strategies), or (b) they may choose a probability distribution
over actions but the actual random choice is external and not visible to the player
(actions invisible), or (c) they may use full randomization. We consider all these
classes of games with reachability, and parity objectives that can express all
ω-regular objectives. The analysis problems are classified into the qualitative
analysis that asks for the existence of a strategy that ensures the objective
with probability 1; and the quantitative analysis that asks for the existence
of a strategy that ensures the objective with probability at least λ (0,1). In
this talk we will cover a wide range of results: for perfect-observation games;
for POMDPs; for one-sided partial-observation games; and for general partial-observation
games.'
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: 'Chatterjee K. Partial-observation stochastic reachability and parity games.
In: Vol 8634. Springer; 2014:1-4. doi:10.1007/978-3-662-44522-8_1'
apa: 'Chatterjee, K. (2014). Partial-observation stochastic reachability and parity
games (Vol. 8634, pp. 1–4). Presented at the MFCS: Mathematical Foundations of
Computer Science, Budapest, Hungary: Springer. https://doi.org/10.1007/978-3-662-44522-8_1'
chicago: Chatterjee, Krishnendu. “Partial-Observation Stochastic Reachability and
Parity Games,” 8634:1–4. Springer, 2014. https://doi.org/10.1007/978-3-662-44522-8_1.
ieee: 'K. Chatterjee, “Partial-observation stochastic reachability and parity games,”
presented at the MFCS: Mathematical Foundations of Computer Science, Budapest,
Hungary, 2014, vol. 8634, no. PART 1, pp. 1–4.'
ista: 'Chatterjee K. 2014. Partial-observation stochastic reachability and parity
games. MFCS: Mathematical Foundations of Computer Science, LNCS, vol. 8634, 1–4.'
mla: Chatterjee, Krishnendu. Partial-Observation Stochastic Reachability and
Parity Games. Vol. 8634, no. PART 1, Springer, 2014, pp. 1–4, doi:10.1007/978-3-662-44522-8_1.
short: K. Chatterjee, in:, Springer, 2014, pp. 1–4.
conference:
end_date: 2014-08-29
location: Budapest, Hungary
name: 'MFCS: Mathematical Foundations of Computer Science'
start_date: 2014-08-25
date_created: 2018-12-11T11:54:38Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-02-23T12:23:43Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-662-44522-8_1
ec_funded: 1
intvolume: ' 8634'
issue: PART 1
language:
- iso: eng
month: '01'
oa_version: None
page: 1 - 4
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication_status: published
publisher: Springer
publist_id: '5192'
pubrep_id: '141'
quality_controlled: '1'
related_material:
record:
- id: '2211'
relation: later_version
status: public
- id: '5381'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Partial-observation stochastic reachability and parity games
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8634
year: '2014'
...
---
_id: '2211'
abstract:
- lang: eng
text: 'In two-player finite-state stochastic games of partial observation on graphs,
in every state of the graph, the players simultaneously choose an action, and
their joint actions determine a probability distribution over the successor states.
The game is played for infinitely many rounds and thus the players construct an
infinite path in the graph. We consider reachability objectives where the first
player tries to ensure a target state to be visited almost-surely (i.e., with
probability 1) or positively (i.e., with positive probability), no matter the
strategy of the second player. We classify such games according to the information
and to the power of randomization available to the players. On the basis of information,
the game can be one-sided with either (a) player 1, or (b) player 2 having partial
observation (and the other player has perfect observation), or two-sided with
(c) both players having partial observation. On the basis of randomization, (a)
the players may not be allowed to use randomization (pure strategies), or (b)
they may choose a probability distribution over actions but the actual random
choice is external and not visible to the player (actions invisible), or (c) they
may use full randomization. Our main results for pure strategies are as follows:
(1) For one-sided games with player 2 having perfect observation we show that
(in contrast to full randomized strategies) belief-based (subset-construction
based) strategies are not sufficient, and we present an exponential upper bound
on memory both for almost-sure and positive winning strategies; we show that the
problem of deciding the existence of almost-sure and positive winning strategies
for player 1 is EXPTIME-complete and present symbolic algorithms that avoid the
explicit exponential construction. (2) For one-sided games with player 1 having
perfect observation we show that nonelementarymemory is both necessary and sufficient
for both almost-sure and positive winning strategies. (3) We show that for the
general (two-sided) case finite-memory strategies are sufficient for both positive
and almost-sure winning, and at least nonelementary memory is required. We establish
the equivalence of the almost-sure winning problems for pure strategies and for
randomized strategies with actions invisible. Our equivalence result exhibit serious
flaws in previous results of the literature: we show a nonelementary memory lower
bound for almost-sure winning whereas an exponential upper bound was previously
claimed.'
article_number: '16'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
citation:
ama: 'Chatterjee K, Doyen L. Partial-observation stochastic games: How to win when
belief fails. ACM Transactions on Computational Logic (TOCL). 2014;15(2).
doi:10.1145/2579821'
apa: 'Chatterjee, K., & Doyen, L. (2014). Partial-observation stochastic games:
How to win when belief fails. ACM Transactions on Computational Logic (TOCL).
ACM. https://doi.org/10.1145/2579821'
chicago: 'Chatterjee, Krishnendu, and Laurent Doyen. “Partial-Observation Stochastic
Games: How to Win When Belief Fails.” ACM Transactions on Computational Logic
(TOCL). ACM, 2014. https://doi.org/10.1145/2579821.'
ieee: 'K. Chatterjee and L. Doyen, “Partial-observation stochastic games: How to
win when belief fails,” ACM Transactions on Computational Logic (TOCL),
vol. 15, no. 2. ACM, 2014.'
ista: 'Chatterjee K, Doyen L. 2014. Partial-observation stochastic games: How to
win when belief fails. ACM Transactions on Computational Logic (TOCL). 15(2),
16.'
mla: 'Chatterjee, Krishnendu, and Laurent Doyen. “Partial-Observation Stochastic
Games: How to Win When Belief Fails.” ACM Transactions on Computational Logic
(TOCL), vol. 15, no. 2, 16, ACM, 2014, doi:10.1145/2579821.'
short: K. Chatterjee, L. Doyen, ACM Transactions on Computational Logic (TOCL) 15
(2014).
date_created: 2018-12-11T11:56:21Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2023-02-23T12:23:43Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/2579821
external_id:
arxiv:
- '1107.2141'
intvolume: ' 15'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1107.2141
month: '04'
oa: 1
oa_version: Preprint
publication: ACM Transactions on Computational Logic (TOCL)
publication_status: published
publisher: ACM
publist_id: '4759'
quality_controlled: '1'
related_material:
record:
- id: '1903'
relation: earlier_version
status: public
- id: '2955'
relation: earlier_version
status: public
- id: '5381'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: 'Partial-observation stochastic games: How to win when belief fails'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2014'
...
---
_id: '2038'
abstract:
- lang: eng
text: Recently, there has been an effort to add quantitative objectives to formal
verification and synthesis. We introduce and investigate the extension of temporal
logics with quantitative atomic assertions. At the heart of quantitative objectives
lies the accumulation of values along a computation. It is often the accumulated
sum, as with energy objectives, or the accumulated average, as with mean-payoff
objectives. We investigate the extension of temporal logics with the prefix-accumulation
assertions Sum(v) ≥ c and Avg(v) ≥ c, where v is a numeric (or Boolean) variable
of the system, c is a constant rational number, and Sum(v) and Avg(v) denote the
accumulated sum and average of the values of v from the beginning of the computation
up to the current point in time. We also allow the path-accumulation assertions
LimInfAvg(v) ≥ c and LimSupAvg(v) ≥ c, referring to the average value along an
entire infinite computation. We study the border of decidability for such quantitative
extensions of various temporal logics. In particular, we show that extending the
fragment of CTL that has only the EX, EF, AX, and AG temporal modalities with
both prefix-accumulation assertions, or extending LTL with both path-accumulation
assertions, results in temporal logics whose model-checking problem is decidable.
Moreover, the prefix-accumulation assertions may be generalized with "controlled
accumulation," allowing, for example, to specify constraints on the average
waiting time between a request and a grant. On the negative side, we show that
this branching-time logic is, in a sense, the maximal logic with one or both of
the prefix-accumulation assertions that permits a decidable model-checking procedure.
Extending a temporal logic that has the EG or EU modalities, such as CTL or LTL,
makes the problem undecidable.
acknowledgement: The research was supported in part by ERC Starting grant 278410 (QUALITY).
article_number: '27'
article_processing_charge: No
article_type: original
author:
- first_name: Udi
full_name: Boker, Udi
id: 31E297B6-F248-11E8-B48F-1D18A9856A87
last_name: Boker
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Orna
full_name: Kupferman, Orna
last_name: Kupferman
citation:
ama: Boker U, Chatterjee K, Henzinger TA, Kupferman O. Temporal specifications with
accumulative values. ACM Transactions on Computational Logic (TOCL). 2014;15(4).
doi:10.1145/2629686
apa: Boker, U., Chatterjee, K., Henzinger, T. A., & Kupferman, O. (2014). Temporal
specifications with accumulative values. ACM Transactions on Computational
Logic (TOCL). ACM. https://doi.org/10.1145/2629686
chicago: Boker, Udi, Krishnendu Chatterjee, Thomas A Henzinger, and Orna Kupferman.
“Temporal Specifications with Accumulative Values.” ACM Transactions on Computational
Logic (TOCL). ACM, 2014. https://doi.org/10.1145/2629686.
ieee: U. Boker, K. Chatterjee, T. A. Henzinger, and O. Kupferman, “Temporal specifications
with accumulative values,” ACM Transactions on Computational Logic (TOCL),
vol. 15, no. 4. ACM, 2014.
ista: Boker U, Chatterjee K, Henzinger TA, Kupferman O. 2014. Temporal specifications
with accumulative values. ACM Transactions on Computational Logic (TOCL). 15(4),
27.
mla: Boker, Udi, et al. “Temporal Specifications with Accumulative Values.” ACM
Transactions on Computational Logic (TOCL), vol. 15, no. 4, 27, ACM, 2014,
doi:10.1145/2629686.
short: U. Boker, K. Chatterjee, T.A. Henzinger, O. Kupferman, ACM Transactions on
Computational Logic (TOCL) 15 (2014).
date_created: 2018-12-11T11:55:21Z
date_published: 2014-09-16T00:00:00Z
date_updated: 2023-02-23T12:23:54Z
day: '16'
ddc:
- '000'
- '004'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1145/2629686
ec_funded: 1
file:
- access_level: open_access
checksum: 354c41d37500b56320afce94cf9a99c2
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:59Z
date_updated: 2020-07-14T12:45:26Z
file_id: '4851'
file_name: IST-2014-192-v1+1_AccumulativeValues.pdf
file_size: 346184
relation: main_file
file_date_updated: 2020-07-14T12:45:26Z
has_accepted_license: '1'
intvolume: ' 15'
issue: '4'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: ACM Transactions on Computational Logic (TOCL)
publication_status: published
publisher: ACM
publist_id: '5013'
pubrep_id: '192'
quality_controlled: '1'
related_material:
record:
- id: '3356'
relation: earlier_version
status: public
- id: '5385'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Temporal specifications with accumulative values
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2014'
...
---
_id: '2162'
abstract:
- lang: eng
text: 'We study two-player (zero-sum) concurrent mean-payoff games played on a finite-state
graph. We focus on the important sub-class of ergodic games where all states are
visited infinitely often with probability 1. The algorithmic study of ergodic
games was initiated in a seminal work of Hoffman and Karp in 1966, but all basic
complexity questions have remained unresolved. Our main results for ergodic games
are as follows: We establish (1) an optimal exponential bound on the patience
of stationary strategies (where patience of a distribution is the inverse of the
smallest positive probability and represents a complexity measure of a stationary
strategy); (2) the approximation problem lies in FNP; (3) the approximation problem
is at least as hard as the decision problem for simple stochastic games (for which
NP ∩ coNP is the long-standing best known bound). We present a variant of the
strategy-iteration algorithm by Hoffman and Karp; show that both our algorithm
and the classical value-iteration algorithm can approximate the value in exponential
time; and identify a subclass where the value-iteration algorithm is a FPTAS.
We also show that the exact value can be expressed in the existential theory of
the reals, and establish square-root sum hardness for a related class of games.'
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
citation:
ama: 'Chatterjee K, Ibsen-Jensen R. The complexity of ergodic mean payoff games.
In: Vol 8573. Springer; 2014:122-133. doi:10.1007/978-3-662-43951-7_11'
apa: 'Chatterjee, K., & Ibsen-Jensen, R. (2014). The complexity of ergodic mean
payoff games (Vol. 8573, pp. 122–133). Presented at the ICST: International Conference
on Software Testing, Verification and Validation, Copenhagen, Denmark: Springer.
https://doi.org/10.1007/978-3-662-43951-7_11'
chicago: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Complexity of Ergodic
Mean Payoff Games,” 8573:122–33. Springer, 2014. https://doi.org/10.1007/978-3-662-43951-7_11.
ieee: 'K. Chatterjee and R. Ibsen-Jensen, “The complexity of ergodic mean payoff
games,” presented at the ICST: International Conference on Software Testing, Verification
and Validation, Copenhagen, Denmark, 2014, vol. 8573, no. Part 2, pp. 122–133.'
ista: 'Chatterjee K, Ibsen-Jensen R. 2014. The complexity of ergodic mean payoff
games. ICST: International Conference on Software Testing, Verification and Validation,
LNCS, vol. 8573, 122–133.'
mla: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. The Complexity of Ergodic
Mean Payoff Games. Vol. 8573, no. Part 2, Springer, 2014, pp. 122–33, doi:10.1007/978-3-662-43951-7_11.
short: K. Chatterjee, R. Ibsen-Jensen, in:, Springer, 2014, pp. 122–133.
conference:
end_date: 2014-07-11
location: Copenhagen, Denmark
name: 'ICST: International Conference on Software Testing, Verification and Validation'
start_date: 2014-07-08
date_created: 2018-12-11T11:56:04Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-02-23T12:24:48Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-662-43951-7_11
ec_funded: 1
external_id:
arxiv:
- '1404.5734'
intvolume: ' 8573'
issue: Part 2
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1404.5734
month: '01'
oa: 1
oa_version: Preprint
page: 122 - 133
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication_status: published
publisher: Springer
publist_id: '4822'
quality_controlled: '1'
related_material:
record:
- id: '5404'
relation: earlier_version
status: public
status: public
title: The complexity of ergodic mean payoff games
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8573
year: '2014'
...
---
_id: '2213'
abstract:
- lang: eng
text: We consider two-player partial-observation stochastic games on finitestate
graphs where player 1 has partial observation and player 2 has perfect observation.
The winning condition we study are ε-regular conditions specified as parity objectives.
The qualitative-analysis problem given a partial-observation stochastic game and
a parity objective asks whether there is a strategy to ensure that the objective
is satisfied with probability 1 (resp. positive probability). These qualitative-analysis
problems are known to be undecidable. However in many applications the relevant
question is the existence of finite-memory strategies, and the qualitative-analysis
problems under finite-memory strategies was recently shown to be decidable in
2EXPTIME.We improve the complexity and show that the qualitative-analysis problems
for partial-observation stochastic parity games under finite-memory strategies
are EXPTIME-complete; and also establish optimal (exponential) memory bounds for
finite-memory strategies required for qualitative analysis.
acknowledgement: 'This research was supported by European project Cassting (FP7-601148),
NSF grants CNS 1049862 and CCF-1139011, by NSF Expe ditions in Computing project
“ExCAPE: Expeditions in Computer Augmented Program Engineering”, by BSF grant 9800096,
and by gift from Intel.'
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
- first_name: Sumit
full_name: Nain, Sumit
last_name: Nain
- first_name: Moshe
full_name: Vardi, Moshe
last_name: Vardi
citation:
ama: 'Chatterjee K, Doyen L, Nain S, Vardi M. The complexity of partial-observation
stochastic parity games with finite-memory strategies. In: Vol 8412. Springer;
2014:242-257. doi:10.1007/978-3-642-54830-7_16'
apa: 'Chatterjee, K., Doyen, L., Nain, S., & Vardi, M. (2014). The complexity
of partial-observation stochastic parity games with finite-memory strategies (Vol.
8412, pp. 242–257). Presented at the FoSSaCS: Foundations of Software Science
and Computation Structures, Grenoble, France: Springer. https://doi.org/10.1007/978-3-642-54830-7_16'
chicago: Chatterjee, Krishnendu, Laurent Doyen, Sumit Nain, and Moshe Vardi. “The
Complexity of Partial-Observation Stochastic Parity Games with Finite-Memory Strategies,”
8412:242–57. Springer, 2014. https://doi.org/10.1007/978-3-642-54830-7_16.
ieee: 'K. Chatterjee, L. Doyen, S. Nain, and M. Vardi, “The complexity of partial-observation
stochastic parity games with finite-memory strategies,” presented at the FoSSaCS:
Foundations of Software Science and Computation Structures, Grenoble, France,
2014, vol. 8412, pp. 242–257.'
ista: 'Chatterjee K, Doyen L, Nain S, Vardi M. 2014. The complexity of partial-observation
stochastic parity games with finite-memory strategies. FoSSaCS: Foundations of
Software Science and Computation Structures, LNCS, vol. 8412, 242–257.'
mla: Chatterjee, Krishnendu, et al. The Complexity of Partial-Observation Stochastic
Parity Games with Finite-Memory Strategies. Vol. 8412, Springer, 2014, pp.
242–57, doi:10.1007/978-3-642-54830-7_16.
short: K. Chatterjee, L. Doyen, S. Nain, M. Vardi, in:, Springer, 2014, pp. 242–257.
conference:
end_date: 2014-04-13
location: Grenoble, France
name: 'FoSSaCS: Foundations of Software Science and Computation Structures'
start_date: 2014-04-05
date_created: 2018-12-11T11:56:21Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2023-02-23T12:24:58Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-642-54830-7_16
ec_funded: 1
external_id:
arxiv:
- '1401.3289'
intvolume: ' 8412'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1401.3289
month: '04'
oa: 1
oa_version: Preprint
page: 242 - 257
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication_status: published
publisher: Springer
publist_id: '4757'
quality_controlled: '1'
related_material:
record:
- id: '5408'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: The complexity of partial-observation stochastic parity games with finite-memory
strategies
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8412
year: '2014'
...
---
_id: '2212'
abstract:
- lang: eng
text: 'The theory of graph games is the foundation for modeling and synthesizing
reactive processes. In the synthesis of stochastic processes, we use 2 1/2-player
games where some transitions of the game graph are controlled by two adversarial
players, the System and the Environment, and the other transitions are determined
probabilistically. We consider 2 1/2-player games where the objective of the System
is the conjunction of a qualitative objective (specified as a parity condition)
and a quantitative objective (specified as a mean-payoff condition). We establish
that the problem of deciding whether the System can ensure that the probability
to satisfy the mean-payoff parity objective is at least a given threshold is in
NP ∩ coNP, matching the best known bound in the special case of 2-player games
(where all transitions are deterministic). We present an algorithm running in
time O(d·n2d·MeanGame) to compute the set of almost-sure winning states from which
the objective can be ensured with probability 1, where n is the number of states
of the game, d the number of priorities of the parity objective, and MeanGame
is the complexity to compute the set of almost-sure winning states in 2 1/2-player
mean-payoff games. Our results are useful in the synthesis of stochastic reactive
systems with both functional requirement (given as a qualitative objective) and
performance requirement (given as a quantitative objective). '
acknowledgement: "This research was supported by European project Cassting (FP7-601148).\r\nA
Technical Report of this paper is available at: \r\nhttps://repository.ist.ac.at/id/eprint/128."
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
- first_name: Hugo
full_name: Gimbert, Hugo
last_name: Gimbert
- first_name: Youssouf
full_name: Oualhadj, Youssouf
last_name: Oualhadj
citation:
ama: 'Chatterjee K, Doyen L, Gimbert H, Oualhadj Y. Perfect-information stochastic
mean-payoff parity games. In: Vol 8412. Springer; 2014:210-225. doi:10.1007/978-3-642-54830-7_14'
apa: 'Chatterjee, K., Doyen, L., Gimbert, H., & Oualhadj, Y. (2014). Perfect-information
stochastic mean-payoff parity games (Vol. 8412, pp. 210–225). Presented at the
FoSSaCS: Foundations of Software Science and Computation Structures, Grenoble,
France: Springer. https://doi.org/10.1007/978-3-642-54830-7_14'
chicago: Chatterjee, Krishnendu, Laurent Doyen, Hugo Gimbert, and Youssouf Oualhadj.
“Perfect-Information Stochastic Mean-Payoff Parity Games,” 8412:210–25. Springer,
2014. https://doi.org/10.1007/978-3-642-54830-7_14.
ieee: 'K. Chatterjee, L. Doyen, H. Gimbert, and Y. Oualhadj, “Perfect-information
stochastic mean-payoff parity games,” presented at the FoSSaCS: Foundations of
Software Science and Computation Structures, Grenoble, France, 2014, vol. 8412,
pp. 210–225.'
ista: 'Chatterjee K, Doyen L, Gimbert H, Oualhadj Y. 2014. Perfect-information stochastic
mean-payoff parity games. FoSSaCS: Foundations of Software Science and Computation
Structures, LNCS, vol. 8412, 210–225.'
mla: Chatterjee, Krishnendu, et al. Perfect-Information Stochastic Mean-Payoff
Parity Games. Vol. 8412, Springer, 2014, pp. 210–25, doi:10.1007/978-3-642-54830-7_14.
short: K. Chatterjee, L. Doyen, H. Gimbert, Y. Oualhadj, in:, Springer, 2014, pp.
210–225.
conference:
end_date: 2014-04-13
location: Grenoble, France
name: 'FoSSaCS: Foundations of Software Science and Computation Structures'
start_date: 2014-04-05
date_created: 2018-12-11T11:56:21Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2023-02-23T12:24:50Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-642-54830-7_14
ec_funded: 1
intvolume: ' 8412'
language:
- iso: eng
month: '04'
oa_version: None
page: 210 - 225
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication_status: published
publisher: Springer
publist_id: '4758'
quality_controlled: '1'
related_material:
record:
- id: '5405'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Perfect-information stochastic mean-payoff parity games
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8412
year: '2014'
...
---
_id: '2216'
abstract:
- lang: eng
text: The edit distance between two (untimed) traces is the minimum cost of a sequence
of edit operations (insertion, deletion, or substitution) needed to transform
one trace to the other. Edit distances have been extensively studied in the untimed
setting, and form the basis for approximate matching of sequences in different
domains such as coding theory, parsing, and speech recognition. In this paper,
we lift the study of edit distances from untimed languages to the timed setting.
We define an edit distance between timed words which incorporates both the edit
distance between the untimed words and the absolute difference in time stamps.
Our edit distance between two timed words is computable in polynomial time. Further,
we show that the edit distance between a timed word and a timed language generated
by a timed automaton, defined as the edit distance between the word and the closest
word in the language, is PSPACE-complete. While computing the edit distance between
two timed automata is undecidable, we show that the approximate version, where
we decide if the edit distance between two timed automata is either less than
a given parameter or more than δ away from the parameter, for δ > 0, can be
solved in exponential space and is EXPSPACE-hard. Our definitions and techniques
can be generalized to the setting of hybrid systems, and analogous decidability
results hold for rectangular automata.
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Ritankar
full_name: Majumdar, Ritankar
last_name: Majumdar
citation:
ama: 'Chatterjee K, Ibsen-Jensen R, Majumdar R. Edit distance for timed automata.
In: Springer; 2014:303-312. doi:10.1145/2562059.2562141'
apa: 'Chatterjee, K., Ibsen-Jensen, R., & Majumdar, R. (2014). Edit distance
for timed automata (pp. 303–312). Presented at the HSCC: Hybrid Systems - Computation
and Control, Berlin, Germany: Springer. https://doi.org/10.1145/2562059.2562141'
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Ritankar Majumdar. “Edit
Distance for Timed Automata,” 303–12. Springer, 2014. https://doi.org/10.1145/2562059.2562141.
ieee: 'K. Chatterjee, R. Ibsen-Jensen, and R. Majumdar, “Edit distance for timed
automata,” presented at the HSCC: Hybrid Systems - Computation and Control, Berlin,
Germany, 2014, pp. 303–312.'
ista: 'Chatterjee K, Ibsen-Jensen R, Majumdar R. 2014. Edit distance for timed automata.
HSCC: Hybrid Systems - Computation and Control, 303–312.'
mla: Chatterjee, Krishnendu, et al. Edit Distance for Timed Automata. Springer,
2014, pp. 303–12, doi:10.1145/2562059.2562141.
short: K. Chatterjee, R. Ibsen-Jensen, R. Majumdar, in:, Springer, 2014, pp. 303–312.
conference:
end_date: 2017-04-17
location: Berlin, Germany
name: 'HSCC: Hybrid Systems - Computation and Control'
start_date: 2017-04-15
date_created: 2018-12-11T11:56:22Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-02-23T12:25:01Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/2562059.2562141
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://dl.acm.org/citation.cfm?doid=2562059.2562141
month: '01'
oa: 1
oa_version: Submitted Version
page: 303 - 312
publication_status: published
publisher: Springer
publist_id: '4752'
quality_controlled: '1'
related_material:
record:
- id: '5409'
relation: earlier_version
status: public
status: public
title: Edit distance for timed automata
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '5411'
abstract:
- lang: eng
text: "Model-based testing is a promising technology for black-box software and
hardware testing, in which test cases are generated automatically from high-level
specifications. Nowadays, systems typically consist of multiple interacting components
and, due to their complexity, testing presents a considerable portion of the effort
and cost in the design process. Exploiting the compositional structure of system
specifications can considerably reduce the effort in model-based testing. Moreover,
inferring properties about the system from testing its individual components allows
the designer to reduce the amount of integration testing.\r\nIn this paper, we
study compositional properties of the IOCO-testing theory. We propose a new approach
to composition and hiding operations, inspired by contract-based design and interface
theories. These operations preserve behaviors that are compatible under composition
and hiding, and prune away incompatible ones. The resulting specification characterizes
the input sequences for which the unit testing of components is sufficient to
infer the correctness of component integration without the need for further tests.
We provide a methodology that uses these results to minimize integration testing
effort, but also to detect potential weaknesses in specifications. While we focus
on asynchronous models and the IOCO conformance relation, the resulting methodology
can be applied to a broader class of systems."
alternative_title:
- IST Austria Technical Report
author:
- first_name: Przemyslaw
full_name: Daca, Przemyslaw
id: 49351290-F248-11E8-B48F-1D18A9856A87
last_name: Daca
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Willibald
full_name: Krenn, Willibald
last_name: Krenn
- first_name: Dejan
full_name: Nickovic, Dejan
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
citation:
ama: Daca P, Henzinger TA, Krenn W, Nickovic D. Compositional Specifications
for IOCO Testing. IST Austria; 2014. doi:10.15479/AT:IST-2014-148-v2-1
apa: Daca, P., Henzinger, T. A., Krenn, W., & Nickovic, D. (2014). Compositional
specifications for IOCO testing. IST Austria. https://doi.org/10.15479/AT:IST-2014-148-v2-1
chicago: Daca, Przemyslaw, Thomas A Henzinger, Willibald Krenn, and Dejan Nickovic.
Compositional Specifications for IOCO Testing. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-148-v2-1.
ieee: P. Daca, T. A. Henzinger, W. Krenn, and D. Nickovic, Compositional specifications
for IOCO testing. IST Austria, 2014.
ista: Daca P, Henzinger TA, Krenn W, Nickovic D. 2014. Compositional specifications
for IOCO testing, IST Austria, 20p.
mla: Daca, Przemyslaw, et al. Compositional Specifications for IOCO Testing.
IST Austria, 2014, doi:10.15479/AT:IST-2014-148-v2-1.
short: P. Daca, T.A. Henzinger, W. Krenn, D. Nickovic, Compositional Specifications
for IOCO Testing, IST Austria, 2014.
date_created: 2018-12-12T11:39:11Z
date_published: 2014-01-28T00:00:00Z
date_updated: 2023-02-23T10:31:07Z
day: '28'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.15479/AT:IST-2014-148-v2-1
file:
- access_level: open_access
checksum: 0e03aba625cc334141a3148432aa5760
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:21Z
date_updated: 2020-07-14T12:46:46Z
file_id: '5543'
file_name: IST-2014-148-v2+1_main_tr.pdf
file_size: 534732
relation: main_file
file_date_updated: 2020-07-14T12:46:46Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: '20'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '152'
related_material:
record:
- id: '2167'
relation: later_version
status: public
status: public
title: Compositional specifications for IOCO testing
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '5413'
abstract:
- lang: eng
text: "We consider Markov decision processes (MDPs) which are a standard model for
probabilistic systems. We focus on qualitative properties for MDPs that can express
that desired behaviors of the system arise almost-surely (with probability 1)
or with positive probability.\r\nWe introduce a new simulation relation to capture
the refinement relation of MDPs with respect to qualitative properties, and present
discrete graph theoretic algorithms with quadratic complexity to compute the simulation
relation.\r\nWe present an automated technique for assume-guarantee style reasoning
for compositional analysis of MDPs with qualitative properties by giving a counter-example
guided abstraction-refinement approach to compute our new simulation relation.
We have implemented our algorithms and show that the compositional analysis leads
to significant improvements. "
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Przemyslaw
full_name: Daca, Przemyslaw
id: 49351290-F248-11E8-B48F-1D18A9856A87
last_name: Daca
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
citation:
ama: Chatterjee K, Daca P, Chmelik M. CEGAR for Qualitative Analysis of Probabilistic
Systems. IST Austria; 2014. doi:10.15479/AT:IST-2014-153-v2-2
apa: Chatterjee, K., Daca, P., & Chmelik, M. (2014). CEGAR for qualitative
analysis of probabilistic systems. IST Austria. https://doi.org/10.15479/AT:IST-2014-153-v2-2
chicago: Chatterjee, Krishnendu, Przemyslaw Daca, and Martin Chmelik. CEGAR for
Qualitative Analysis of Probabilistic Systems. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-153-v2-2.
ieee: K. Chatterjee, P. Daca, and M. Chmelik, CEGAR for qualitative analysis
of probabilistic systems. IST Austria, 2014.
ista: Chatterjee K, Daca P, Chmelik M. 2014. CEGAR for qualitative analysis of probabilistic
systems, IST Austria, 33p.
mla: Chatterjee, Krishnendu, et al. CEGAR for Qualitative Analysis of Probabilistic
Systems. IST Austria, 2014, doi:10.15479/AT:IST-2014-153-v2-2.
short: K. Chatterjee, P. Daca, M. Chmelik, CEGAR for Qualitative Analysis of Probabilistic
Systems, IST Austria, 2014.
date_created: 2018-12-12T11:39:11Z
date_published: 2014-02-06T00:00:00Z
date_updated: 2023-02-23T12:25:18Z
day: '06'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2014-153-v2-2
file:
- access_level: open_access
checksum: ce4967a184d84863eec76c66cbac1614
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:17Z
date_updated: 2020-07-14T12:46:47Z
file_id: '5539'
file_name: IST-2014-153-v2+2_main.pdf
file_size: 606049
relation: main_file
file_date_updated: 2020-07-14T12:46:47Z
has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '33'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '164'
related_material:
record:
- id: '2063'
relation: later_version
status: public
- id: '5412'
relation: earlier_version
status: public
- id: '5414'
relation: later_version
status: public
status: public
title: CEGAR for qualitative analysis of probabilistic systems
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '5414'
abstract:
- lang: eng
text: "We consider Markov decision processes (MDPs) which are a standard model for
probabilistic systems. We focus on qualitative properties for MDPs that can express
that desired behaviors of the system arise almost-surely (with probability 1)
or with positive probability.\r\nWe introduce a new simulation relation to capture
the refinement relation of MDPs with respect to qualitative properties, and present
discrete graph theoretic algorithms with quadratic complexity to compute the simulation
relation.\r\nWe present an automated technique for assume-guarantee style reasoning
for compositional analysis of MDPs with qualitative properties by giving a counter-example
guided abstraction-refinement approach to compute our new simulation relation.
\r\nWe have implemented our algorithms and show that the compositional analysis
leads to significant improvements. "
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Przemyslaw
full_name: Daca, Przemyslaw
id: 49351290-F248-11E8-B48F-1D18A9856A87
last_name: Daca
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
citation:
ama: Chatterjee K, Daca P, Chmelik M. CEGAR for Qualitative Analysis of Probabilistic
Systems. IST Austria; 2014. doi:10.15479/AT:IST-2014-153-v3-1
apa: Chatterjee, K., Daca, P., & Chmelik, M. (2014). CEGAR for qualitative
analysis of probabilistic systems. IST Austria. https://doi.org/10.15479/AT:IST-2014-153-v3-1
chicago: Chatterjee, Krishnendu, Przemyslaw Daca, and Martin Chmelik. CEGAR for
Qualitative Analysis of Probabilistic Systems. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-153-v3-1.
ieee: K. Chatterjee, P. Daca, and M. Chmelik, CEGAR for qualitative analysis
of probabilistic systems. IST Austria, 2014.
ista: Chatterjee K, Daca P, Chmelik M. 2014. CEGAR for qualitative analysis of probabilistic
systems, IST Austria, 33p.
mla: Chatterjee, Krishnendu, et al. CEGAR for Qualitative Analysis of Probabilistic
Systems. IST Austria, 2014, doi:10.15479/AT:IST-2014-153-v3-1.
short: K. Chatterjee, P. Daca, M. Chmelik, CEGAR for Qualitative Analysis of Probabilistic
Systems, IST Austria, 2014.
date_created: 2018-12-12T11:39:12Z
date_published: 2014-02-07T00:00:00Z
date_updated: 2023-02-23T12:25:15Z
day: '07'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2014-153-v3-1
file:
- access_level: open_access
checksum: 87b93fe9af71fc5c94b0eb6151537e11
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:03Z
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has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '33'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '165'
related_material:
record:
- id: '2063'
relation: later_version
status: public
- id: '5412'
relation: earlier_version
status: public
- id: '5413'
relation: earlier_version
status: public
status: public
title: CEGAR for qualitative analysis of probabilistic systems
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '5412'
abstract:
- lang: eng
text: "We consider Markov decision processes (MDPs) which are a standard model for
probabilistic systems. We focus on qualitative properties for MDPs that can express
that desired behaviors of the system arise almost-surely (with probability 1)
or with positive probability.\r\nWe introduce a new simulation relation to capture
the refinement relation of MDPs with respect to qualitative properties, and present
discrete graph theoretic algorithms with quadratic complexity to compute the simulation
relation.\r\nWe present an automated technique for assume-guarantee style reasoning
for compositional analysis of MDPs with qualitative properties by giving a counter-example
guided abstraction-refinement approach to compute our new simulation relation.
We have implemented our algorithms and show that the compositional analysis leads
to significant improvements. "
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Przemyslaw
full_name: Daca, Przemyslaw
id: 49351290-F248-11E8-B48F-1D18A9856A87
last_name: Daca
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
citation:
ama: Chatterjee K, Daca P, Chmelik M. CEGAR for Qualitative Analysis of Probabilistic
Systems. IST Austria; 2014. doi:10.15479/AT:IST-2014-153-v1-1
apa: Chatterjee, K., Daca, P., & Chmelik, M. (2014). CEGAR for qualitative
analysis of probabilistic systems. IST Austria. https://doi.org/10.15479/AT:IST-2014-153-v1-1
chicago: Chatterjee, Krishnendu, Przemyslaw Daca, and Martin Chmelik. CEGAR for
Qualitative Analysis of Probabilistic Systems. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-153-v1-1.
ieee: K. Chatterjee, P. Daca, and M. Chmelik, CEGAR for qualitative analysis
of probabilistic systems. IST Austria, 2014.
ista: Chatterjee K, Daca P, Chmelik M. 2014. CEGAR for qualitative analysis of probabilistic
systems, IST Austria, 31p.
mla: Chatterjee, Krishnendu, et al. CEGAR for Qualitative Analysis of Probabilistic
Systems. IST Austria, 2014, doi:10.15479/AT:IST-2014-153-v1-1.
short: K. Chatterjee, P. Daca, M. Chmelik, CEGAR for Qualitative Analysis of Probabilistic
Systems, IST Austria, 2014.
date_created: 2018-12-12T11:39:11Z
date_published: 2014-01-29T00:00:00Z
date_updated: 2023-02-23T12:25:18Z
day: '29'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2014-153-v1-1
file:
- access_level: open_access
checksum: 4d6cda4bebed970926403ad6ad8c745f
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:39Z
date_updated: 2020-07-14T12:46:47Z
file_id: '5500'
file_name: IST-2014-153-v1+1_main.pdf
file_size: 423322
relation: main_file
file_date_updated: 2020-07-14T12:46:47Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: '31'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '153'
related_material:
record:
- id: '2063'
relation: later_version
status: public
- id: '5413'
relation: later_version
status: public
- id: '5414'
relation: later_version
status: public
status: public
title: CEGAR for qualitative analysis of probabilistic systems
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '2163'
abstract:
- lang: eng
text: We consider multi-player graph games with partial-observation and parity objective.
While the decision problem for three-player games with a coalition of the first
and second players against the third player is undecidable in general, we present
a decidability result for partial-observation games where the first and third
player are in a coalition against the second player, thus where the second player
is adversarial but weaker due to partial-observation. We establish tight complexity
bounds in the case where player 1 is less informed than player 2, namely 2-EXPTIME-completeness
for parity objectives. The symmetric case of player 1 more informed than player
2 is much more complicated, and we show that already in the case where player
1 has perfect observation, memory of size non-elementary is necessary in general
for reachability objectives, and the problem is decidable for safety and reachability
objectives. From our results we derive new complexity results for partial-observation
stochastic games.
acknowledgement: "This research was partly supported by European project Cassting
(FP7-601148).\r\nTechnical Report under https://research-explorer.app.ist.ac.at/record/5418\r\n"
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
citation:
ama: 'Chatterjee K, Doyen L. Games with a weak adversary. In: Lecture Notes in
Computer Science. Vol 8573. Springer; 2014:110-121. doi:10.1007/978-3-662-43951-7_10'
apa: 'Chatterjee, K., & Doyen, L. (2014). Games with a weak adversary. In Lecture
Notes in Computer Science (Vol. 8573, pp. 110–121). Copenhagen, Denmark: Springer.
https://doi.org/10.1007/978-3-662-43951-7_10'
chicago: Chatterjee, Krishnendu, and Laurent Doyen. “Games with a Weak Adversary.”
In Lecture Notes in Computer Science, 8573:110–21. Springer, 2014. https://doi.org/10.1007/978-3-662-43951-7_10.
ieee: K. Chatterjee and L. Doyen, “Games with a weak adversary,” in Lecture Notes
in Computer Science, Copenhagen, Denmark, 2014, vol. 8573, no. Part 2, pp.
110–121.
ista: 'Chatterjee K, Doyen L. 2014. Games with a weak adversary. Lecture Notes in
Computer Science. ICALP: Automata, Languages and Programming, LNCS, vol. 8573,
110–121.'
mla: Chatterjee, Krishnendu, and Laurent Doyen. “Games with a Weak Adversary.” Lecture
Notes in Computer Science, vol. 8573, no. Part 2, Springer, 2014, pp. 110–21,
doi:10.1007/978-3-662-43951-7_10.
short: K. Chatterjee, L. Doyen, in:, Lecture Notes in Computer Science, Springer,
2014, pp. 110–121.
conference:
end_date: 2014-07-11
location: Copenhagen, Denmark
name: 'ICALP: Automata, Languages and Programming'
start_date: 2014-07-08
date_created: 2018-12-11T11:56:04Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-02-23T12:25:29Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-662-43951-7_10
ec_funded: 1
external_id:
arxiv:
- '1404.5453'
intvolume: ' 8573'
issue: Part 2
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1404.5453
month: '01'
oa: 1
oa_version: Preprint
page: 110 - 121
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Lecture Notes in Computer Science
publication_status: published
publisher: Springer
publist_id: '4821'
quality_controlled: '1'
related_material:
record:
- id: '5418'
relation: earlier_version
status: public
status: public
title: Games with a weak adversary
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8573
year: '2014'
...
---
_id: '5419'
abstract:
- lang: eng
text: "We consider the reachability and shortest path problems on low tree-width
graphs, with n nodes, m edges, and tree-width t, on a standard RAM with wordsize
W. We use O to hide polynomial factors of the inverse of the Ackermann function.
Our main contributions are three fold:\r\n1. For reachability, we present an algorithm
that requires O(n·t2·log(n/t)) preprocessing time, O(n·(t·log(n/t))/W) space,
and O(t/W) time for pair queries and O((n·t)/W) time for single-source queries.
Note that for constant t our algorithm uses O(n·logn) time for preprocessing;
and O(n/W) time for single-source queries, which is faster than depth first search/breath
first search (after the preprocessing).\r\n2. We present an algorithm for shortest
path that requires O(n·t2) preprocessing time, O(n·t) space, and O(t2) time for
pair queries and O(n·t) time single-source queries.\r\n3. We give a space versus
query time trade-off algorithm for shortest path that, given any constant >0,
requires O(n·t2) preprocessing time, O(n·t2) space, and O(n1−·t2) time for pair
queries.\r\nOur algorithms improve all existing results, and use very simple data
structures."
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Improved Algorithms for Reachability
and Shortest Path on Low Tree-Width Graphs. IST Austria; 2014. doi:10.15479/AT:IST-2014-187-v1-1
apa: Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2014). Improved
algorithms for reachability and shortest path on low tree-width graphs. IST
Austria. https://doi.org/10.15479/AT:IST-2014-187-v1-1
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis.
Improved Algorithms for Reachability and Shortest Path on Low Tree-Width Graphs.
IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-187-v1-1.
ieee: K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, Improved algorithms
for reachability and shortest path on low tree-width graphs. IST Austria,
2014.
ista: Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2014. Improved algorithms for
reachability and shortest path on low tree-width graphs, IST Austria, 34p.
mla: Chatterjee, Krishnendu, et al. Improved Algorithms for Reachability and
Shortest Path on Low Tree-Width Graphs. IST Austria, 2014, doi:10.15479/AT:IST-2014-187-v1-1.
short: K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, Improved Algorithms for
Reachability and Shortest Path on Low Tree-Width Graphs, IST Austria, 2014.
date_created: 2018-12-12T11:39:13Z
date_published: 2014-04-14T00:00:00Z
date_updated: 2021-01-12T08:02:03Z
day: '14'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2014-187-v1-1
file:
- access_level: open_access
checksum: c608e66030a4bf51d2d99b451f539b99
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:25Z
date_updated: 2020-07-14T12:46:50Z
file_id: '5548'
file_name: IST-2014-187-v1+1_main_full_tech.pdf
file_size: 670031
relation: main_file
file_date_updated: 2020-07-14T12:46:50Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '34'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '187'
status: public
title: Improved algorithms for reachability and shortest path on low tree-width graphs
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '2217'
abstract:
- lang: eng
text: "As hybrid systems involve continuous behaviors, they should be evaluated
by quantitative methods, rather than qualitative methods. In this paper we adapt
a quantitative framework, called model measuring, to the hybrid systems domain.
The model-measuring problem asks, given a model M and a specification, what is
the maximal distance such that all models within that distance from M satisfy
(or violate) the specification. A distance function on models is given as part
of the input of the problem. Distances, especially related to continuous behaviors
are more natural in the hybrid case than the discrete case. We are interested
in distances represented by monotonic hybrid automata, a hybrid counterpart of
(discrete) weighted automata, whose recognized timed languages are monotone (w.r.t.
inclusion) in the values of parameters.\r\n\r\nThe contributions of this paper
are twofold. First, we give sufficient conditions under which the model-measuring
problem can be solved. Second, we discuss the modeling of distances and applications
of the model-measuring problem."
acknowledgement: "This work was supported in part by the Austrian Science
Fund NFN RiSE (Rigorous Systems Engineering) and by the ERC Advanced Grant
QUAREM (Quantitative Reactive Modeling).\r\nA Technical Report of this paper is
available at: \r\nhttps://repository.ist.ac.at/id/eprint/171"
article_processing_charge: No
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: 'Henzinger TA, Otop J. Model measuring for hybrid systems. In: Proceedings
of the 17th International Conference on Hybrid Systems: Computation and Control.
Springer; 2014:213-222. doi:10.1145/2562059.2562130'
apa: 'Henzinger, T. A., & Otop, J. (2014). Model measuring for hybrid systems.
In Proceedings of the 17th international conference on Hybrid systems: computation
and control (pp. 213–222). Berlin, Germany: Springer. https://doi.org/10.1145/2562059.2562130'
chicago: 'Henzinger, Thomas A, and Jan Otop. “Model Measuring for Hybrid Systems.”
In Proceedings of the 17th International Conference on Hybrid Systems: Computation
and Control, 213–22. Springer, 2014. https://doi.org/10.1145/2562059.2562130.'
ieee: 'T. A. Henzinger and J. Otop, “Model measuring for hybrid systems,” in Proceedings
of the 17th international conference on Hybrid systems: computation and control,
Berlin, Germany, 2014, pp. 213–222.'
ista: 'Henzinger TA, Otop J. 2014. Model measuring for hybrid systems. Proceedings
of the 17th international conference on Hybrid systems: computation and control.
HSCC: Hybrid Systems - Computation and Control, 213–222.'
mla: 'Henzinger, Thomas A., and Jan Otop. “Model Measuring for Hybrid Systems.”
Proceedings of the 17th International Conference on Hybrid Systems: Computation
and Control, Springer, 2014, pp. 213–22, doi:10.1145/2562059.2562130.'
short: 'T.A. Henzinger, J. Otop, in:, Proceedings of the 17th International Conference
on Hybrid Systems: Computation and Control, Springer, 2014, pp. 213–222.'
conference:
end_date: 2014-04-17
location: Berlin, Germany
name: 'HSCC: Hybrid Systems - Computation and Control'
start_date: 2014-04-15
date_created: 2018-12-11T11:56:23Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2023-02-23T12:25:23Z
day: '01'
department:
- _id: ToHe
doi: 10.1145/2562059.2562130
ec_funded: 1
language:
- iso: eng
month: '04'
oa_version: None
page: 213 - 222
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: 'Proceedings of the 17th international conference on Hybrid systems:
computation and control'
publication_status: published
publisher: Springer
publist_id: '4751'
quality_controlled: '1'
related_material:
record:
- id: '5416'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Model measuring for hybrid systems
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '5417'
abstract:
- lang: eng
text: "We define the model-measuring problem: given a model M and specification
φ, what is the maximal distance ρ such that all models M'within distance ρ from
M satisfy (or violate)φ. The model measuring problem presupposes a distance function
on models. We concentrate on automatic distance functions, which are defined by
weighted automata.\r\nThe model-measuring problem subsumes several generalizations
of the classical model-checking problem, in particular, quantitative model-checking
problems that measure the degree of satisfaction of a specification, and robustness
problems that measure how much a model can be perturbed without violating the
specification.\r\nWe show that for automatic distance functions, and ω-regular
linear-time and branching-time specifications, the model-measuring problem can
be solved.\r\nWe use automata-theoretic model-checking methods for model measuring,
replacing the emptiness question for standard word and tree automata by the optimal-weight
question for the weighted versions of these automata. We consider weighted automata
that accumulate weights by maximizing, summing, discounting, and limit averaging.
\r\nWe give several examples of using the model-measuring problem to compute various
notions of robustness and quantitative satisfaction for temporal specifications."
alternative_title:
- IST Austria Technical Report
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: Henzinger TA, Otop J. From Model Checking to Model Measuring. IST Austria;
2014. doi:10.15479/AT:IST-2014-172-v1-1
apa: Henzinger, T. A., & Otop, J. (2014). From model checking to model measuring.
IST Austria. https://doi.org/10.15479/AT:IST-2014-172-v1-1
chicago: Henzinger, Thomas A, and Jan Otop. From Model Checking to Model Measuring.
IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-172-v1-1.
ieee: T. A. Henzinger and J. Otop, From model checking to model measuring.
IST Austria, 2014.
ista: Henzinger TA, Otop J. 2014. From model checking to model measuring, IST Austria,
14p.
mla: Henzinger, Thomas A., and Jan Otop. From Model Checking to Model Measuring.
IST Austria, 2014, doi:10.15479/AT:IST-2014-172-v1-1.
short: T.A. Henzinger, J. Otop, From Model Checking to Model Measuring, IST Austria,
2014.
date_created: 2018-12-12T11:39:13Z
date_published: 2014-02-19T00:00:00Z
date_updated: 2023-02-23T10:38:10Z
day: '19'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.15479/AT:IST-2014-172-v1-1
file:
- access_level: open_access
checksum: fcc3eab903cfcd3778b338d2d0d44d18
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:20Z
date_updated: 2020-07-14T12:46:49Z
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language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '14'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '175'
related_material:
record:
- id: '2327'
relation: later_version
status: public
status: public
title: From model checking to model measuring
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '5416'
abstract:
- lang: eng
text: As hybrid systems involve continuous behaviors, they should be evaluated by
quantitative methods, rather than qualitative methods. In this paper we adapt
a quantitative framework, called model measuring, to the hybrid systems domain.
The model-measuring problem asks, given a model M and a specification, what is
the maximal distance such that all models within that distance from M satisfy
(or violate) the specification. A distance function on models is given as part
of the input of the problem. Distances, especially related to continuous behaviors
are more natural in the hybrid case than the discrete case. We are interested
in distances represented by monotonic hybrid automata, a hybrid counterpart of
(discrete) weighted automata, whose recognized timed languages are monotone (w.r.t.
inclusion) in the values of parameters.The contributions of this paper are twofold.
First, we give sufficient conditions under which the model-measuring problem can
be solved. Second, we discuss the modeling of distances and applications of the
model-measuring problem.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: Henzinger TA, Otop J. Model Measuring for Hybrid Systems. IST Austria;
2014. doi:10.15479/AT:IST-2014-171-v1-1
apa: Henzinger, T. A., & Otop, J. (2014). Model measuring for hybrid systems.
IST Austria. https://doi.org/10.15479/AT:IST-2014-171-v1-1
chicago: Henzinger, Thomas A, and Jan Otop. Model Measuring for Hybrid Systems.
IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-171-v1-1.
ieee: T. A. Henzinger and J. Otop, Model measuring for hybrid systems. IST
Austria, 2014.
ista: Henzinger TA, Otop J. 2014. Model measuring for hybrid systems, IST Austria,
22p.
mla: Henzinger, Thomas A., and Jan Otop. Model Measuring for Hybrid Systems.
IST Austria, 2014, doi:10.15479/AT:IST-2014-171-v1-1.
short: T.A. Henzinger, J. Otop, Model Measuring for Hybrid Systems, IST Austria,
2014.
date_created: 2018-12-12T11:39:12Z
date_published: 2014-02-19T00:00:00Z
date_updated: 2023-02-23T10:33:21Z
day: '19'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.15479/AT:IST-2014-171-v1-1
file:
- access_level: open_access
checksum: 445456d22371e4e49aad2b9a0c13bf80
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:32Z
date_updated: 2020-07-14T12:46:49Z
file_id: '5492'
file_name: IST-2014-171-v1+1_report.pdf
file_size: 712077
relation: main_file
file_date_updated: 2020-07-14T12:46:49Z
has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '22'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '171'
related_material:
record:
- id: '2217'
relation: later_version
status: public
status: public
title: Model measuring for hybrid systems
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '5418'
abstract:
- lang: eng
text: We consider multi-player graph games with partial-observation and parity objective.
While the decision problem for three-player games with a coalition of the first
and second players against the third player is undecidable, we present a decidability
result for partial-observation games where the first and third player are in a
coalition against the second player, thus where the second player is adversarial
but weaker due to partial-observation. We establish tight complexity bounds in
the case where player 1 is less informed than player 2, namely 2-EXPTIME-completeness
for parity objectives. The symmetric case of player 1 more informed than player
2 is much more complicated, and we show that already in the case where player
1 has perfect observation, memory of size non-elementary is necessary in general
for reachability objectives, and the problem is decidable for safety and reachability
objectives. Our results have tight connections with partial-observation stochastic
games for which we derive new complexity results.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
citation:
ama: Chatterjee K, Doyen L. Games with a Weak Adversary. IST Austria; 2014.
doi:10.15479/AT:IST-2014-176-v1-1
apa: Chatterjee, K., & Doyen, L. (2014). Games with a weak adversary.
IST Austria. https://doi.org/10.15479/AT:IST-2014-176-v1-1
chicago: Chatterjee, Krishnendu, and Laurent Doyen. Games with a Weak Adversary.
IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-176-v1-1.
ieee: K. Chatterjee and L. Doyen, Games with a weak adversary. IST Austria,
2014.
ista: Chatterjee K, Doyen L. 2014. Games with a weak adversary, IST Austria, 18p.
mla: Chatterjee, Krishnendu, and Laurent Doyen. Games with a Weak Adversary.
IST Austria, 2014, doi:10.15479/AT:IST-2014-176-v1-1.
short: K. Chatterjee, L. Doyen, Games with a Weak Adversary, IST Austria, 2014.
date_created: 2018-12-12T11:39:13Z
date_published: 2014-03-22T00:00:00Z
date_updated: 2023-02-23T10:30:58Z
day: '22'
ddc:
- '000'
- '005'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2014-176-v1-1
file:
- access_level: open_access
checksum: 1d6958aa60050e1c3e932c6e5f34c39f
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:07Z
date_updated: 2020-07-14T12:46:49Z
file_id: '5468'
file_name: IST-2014-176-v1+1_icalp_14.pdf
file_size: 328253
relation: main_file
file_date_updated: 2020-07-14T12:46:49Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '18'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '176'
related_material:
record:
- id: '2163'
relation: later_version
status: public
status: public
title: Games with a weak adversary
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '5420'
abstract:
- lang: eng
text: 'We consider concurrent mean-payoff games, a very well-studied class of two-player
(player 1 vs player 2) zero-sum games on finite-state graphs where every transition
is assigned a reward between 0 and 1, and the payoff function is the long-run
average of the rewards. The value is the maximal expected payoff that player 1
can guarantee against all strategies of player 2. We consider the computation
of the set of states with value 1 under finite-memory strategies for player 1,
and our main results for the problem are as follows: (1) we present a polynomial-time
algorithm; (2) we show that whenever there is a finite-memory strategy, there
is a stationary strategy that does not need memory at all; and (3) we present
an optimal bound (which is double exponential) on the patience of stationary strategies
(where patience of a distribution is the inverse of the smallest positive probability
and represents a complexity measure of a stationary strategy).'
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
citation:
ama: Chatterjee K, Ibsen-Jensen R. The Value 1 Problem for Concurrent Mean-Payoff
Games. IST Austria; 2014. doi:10.15479/AT:IST-2014-191-v1-1
apa: Chatterjee, K., & Ibsen-Jensen, R. (2014). The value 1 problem for concurrent
mean-payoff games. IST Austria. https://doi.org/10.15479/AT:IST-2014-191-v1-1
chicago: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. The Value 1 Problem
for Concurrent Mean-Payoff Games. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-191-v1-1.
ieee: K. Chatterjee and R. Ibsen-Jensen, The value 1 problem for concurrent mean-payoff
games. IST Austria, 2014.
ista: Chatterjee K, Ibsen-Jensen R. 2014. The value 1 problem for concurrent mean-payoff
games, IST Austria, 49p.
mla: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. The Value 1 Problem for
Concurrent Mean-Payoff Games. IST Austria, 2014, doi:10.15479/AT:IST-2014-191-v1-1.
short: K. Chatterjee, R. Ibsen-Jensen, The Value 1 Problem for Concurrent Mean-Payoff
Games, IST Austria, 2014.
date_created: 2018-12-12T11:39:14Z
date_published: 2014-04-14T00:00:00Z
date_updated: 2021-01-12T08:02:05Z
day: '14'
ddc:
- '000'
- '005'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2014-191-v1-1
file:
- access_level: open_access
checksum: 49e0fd3e62650346daf7dc04604f7a0a
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:58Z
date_updated: 2020-07-14T12:46:50Z
file_id: '5520'
file_name: IST-2014-191-v1+1_main_full.pdf
file_size: 584368
relation: main_file
file_date_updated: 2020-07-14T12:46:50Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '49'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '191'
status: public
title: The value 1 problem for concurrent mean-payoff games
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '5422'
abstract:
- lang: eng
text: Notes from the Third Plenary for the Research Data Alliance in Dublin, Ireland
on March 26 to 28, 2014 with focus on starting an institutional research data
repository.
author:
- first_name: Jana
full_name: Porsche, Jana
id: 3252EDC2-F248-11E8-B48F-1D18A9856A87
last_name: Porsche
citation:
ama: Porsche J. Notes from Research Data Alliance Plenary Meeting in Dublin,
Ireland. none; 2014.
apa: Porsche, J. (2014). Notes from Research Data Alliance Plenary Meeting in
Dublin, Ireland. none.
chicago: Porsche, Jana. Notes from Research Data Alliance Plenary Meeting in
Dublin, Ireland. none, 2014.
ieee: J. Porsche, Notes from Research Data Alliance Plenary Meeting in Dublin,
Ireland. none, 2014.
ista: Porsche J. 2014. Notes from Research Data Alliance Plenary Meeting in Dublin,
Ireland, none,p.
mla: Porsche, Jana. Notes from Research Data Alliance Plenary Meeting in Dublin,
Ireland. none, 2014.
short: J. Porsche, Notes from Research Data Alliance Plenary Meeting in Dublin,
Ireland, none, 2014.
date_created: 2018-12-12T11:39:14Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2020-07-14T23:04:56Z
ddc:
- '020'
department:
- _id: E-Lib
file:
- access_level: open_access
checksum: 3954896648ce8afa8f7c4425e71cff08
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:40Z
date_updated: 2020-07-14T12:46:50Z
file_id: '5501'
file_name: IST-2014-254-v1+1_Dublin_Day_3.pdf
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relation: main_file
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checksum: 9a0d42b0b832dfe7e4b22fb6816bcbba
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:41Z
date_updated: 2020-07-14T12:46:50Z
file_id: '5502'
file_name: IST-2014-254-v1+2_Dublin_Day_1.pdf
file_size: 221339
relation: main_file
- access_level: open_access
checksum: 498b8d629fb1bd17bff1dc43700a93e6
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:42Z
date_updated: 2020-07-14T12:46:50Z
file_id: '5503'
file_name: IST-2014-254-v1+3_Dublin_Day_2.pdf
file_size: 187778
relation: main_file
file_date_updated: 2020-07-14T12:46:50Z
has_accepted_license: '1'
language:
- iso: eng
oa: 1
oa_version: None
publisher: none
pubrep_id: '254'
status: public
title: Notes from Research Data Alliance Plenary Meeting in Dublin, Ireland
type: report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '5424'
abstract:
- lang: eng
text: We consider partially observable Markov decision processes (POMDPs), that
are a standard framework for robotics applications to model uncertainties present
in the real world, with temporal logic specifications. All temporal logic specifications
in linear-time temporal logic (LTL) can be expressed as parity objectives. We
study the qualitative analysis problem for POMDPs with parity objectives that
asks whether there is a controller (policy) to ensure that the objective holds
with probability 1 (almost-surely). While the qualitative analysis of POMDPs with
parity objectives is undecidable, recent results show that when restricted to
finite-memory policies the problem is EXPTIME-complete. While the problem is intractable
in theory, we present a practical approach to solve the qualitative analysis problem.
We designed several heuristics to deal with the exponential complexity, and have
used our implementation on a number of well-known POMDP examples for robotics
applications. Our results provide the first practical approach to solve the qualitative
analysis of robot motion planning with LTL properties in the presence of uncertainty.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Raghav
full_name: Gupta, Raghav
last_name: Gupta
- first_name: Ayush
full_name: Kanodia, Ayush
last_name: Kanodia
citation:
ama: Chatterjee K, Chmelik M, Gupta R, Kanodia A. Qualitative Analysis of POMDPs
with Temporal Logic Specifications for Robotics Applications. IST Austria;
2014. doi:10.15479/AT:IST-2014-305-v1-1
apa: Chatterjee, K., Chmelik, M., Gupta, R., & Kanodia, A. (2014). Qualitative
analysis of POMDPs with temporal logic specifications for robotics applications.
IST Austria. https://doi.org/10.15479/AT:IST-2014-305-v1-1
chicago: Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia.
Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics
Applications. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-305-v1-1.
ieee: K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, Qualitative analysis
of POMDPs with temporal logic specifications for robotics applications. IST
Austria, 2014.
ista: Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2014. Qualitative analysis of
POMDPs with temporal logic specifications for robotics applications, IST Austria,
12p.
mla: Chatterjee, Krishnendu, et al. Qualitative Analysis of POMDPs with Temporal
Logic Specifications for Robotics Applications. IST Austria, 2014, doi:10.15479/AT:IST-2014-305-v1-1.
short: K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, Qualitative Analysis of
POMDPs with Temporal Logic Specifications for Robotics Applications, IST Austria,
2014.
date_created: 2018-12-12T11:39:15Z
date_published: 2014-09-09T00:00:00Z
date_updated: 2023-02-23T12:25:52Z
day: '09'
ddc:
- '005'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2014-305-v1-1
file:
- access_level: open_access
checksum: 35009d5fad01198341e6c1a3353481b7
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:51Z
date_updated: 2020-07-14T12:46:51Z
file_id: '5512'
file_name: IST-2014-305-v1+1_main.pdf
file_size: 655774
relation: main_file
file_date_updated: 2020-07-14T12:46:51Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '12'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '305'
related_material:
record:
- id: '1732'
relation: later_version
status: public
- id: '5426'
relation: later_version
status: public
status: public
title: Qualitative analysis of POMDPs with temporal logic specifications for robotics
applications
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '5426'
abstract:
- lang: eng
text: We consider partially observable Markov decision processes (POMDPs), that
are a standard framework for robotics applications to model uncertainties present
in the real world, with temporal logic specifications. All temporal logic specifications
in linear-time temporal logic (LTL) can be expressed as parity objectives. We
study the qualitative analysis problem for POMDPs with parity objectives that
asks whether there is a controller (policy) to ensure that the objective holds
with probability 1 (almost-surely). While the qualitative analysis of POMDPs with
parity objectives is undecidable, recent results show that when restricted to
finite-memory policies the problem is EXPTIME-complete. While the problem is intractable
in theory, we present a practical approach to solve the qualitative analysis problem.
We designed several heuristics to deal with the exponential complexity, and have
used our implementation on a number of well-known POMDP examples for robotics
applications. Our results provide the first practical approach to solve the qualitative
analysis of robot motion planning with LTL properties in the presence of uncertainty.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Raghav
full_name: Gupta, Raghav
last_name: Gupta
- first_name: Ayush
full_name: Kanodia, Ayush
last_name: Kanodia
citation:
ama: Chatterjee K, Chmelik M, Gupta R, Kanodia A. Qualitative Analysis of POMDPs
with Temporal Logic Specifications for Robotics Applications. IST Austria;
2014. doi:10.15479/AT:IST-2014-305-v2-1
apa: Chatterjee, K., Chmelik, M., Gupta, R., & Kanodia, A. (2014). Qualitative
analysis of POMDPs with temporal logic specifications for robotics applications.
IST Austria. https://doi.org/10.15479/AT:IST-2014-305-v2-1
chicago: Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia.
Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics
Applications. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-305-v2-1.
ieee: K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, Qualitative analysis
of POMDPs with temporal logic specifications for robotics applications. IST
Austria, 2014.
ista: Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2014. Qualitative analysis of
POMDPs with temporal logic specifications for robotics applications, IST Austria,
10p.
mla: Chatterjee, Krishnendu, et al. Qualitative Analysis of POMDPs with Temporal
Logic Specifications for Robotics Applications. IST Austria, 2014, doi:10.15479/AT:IST-2014-305-v2-1.
short: K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, Qualitative Analysis of
POMDPs with Temporal Logic Specifications for Robotics Applications, IST Austria,
2014.
date_created: 2018-12-12T11:39:16Z
date_published: 2014-09-29T00:00:00Z
date_updated: 2023-02-23T12:25:47Z
day: '29'
ddc:
- '005'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2014-305-v2-1
file:
- access_level: open_access
checksum: 730c0a8e97cf2712a884b2cc423f3919
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:15Z
date_updated: 2020-07-14T12:46:51Z
file_id: '5537'
file_name: IST-2014-305-v2+1_main2.pdf
file_size: 656019
relation: main_file
file_date_updated: 2020-07-14T12:46:51Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '10'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '311'
related_material:
record:
- id: '1732'
relation: later_version
status: public
- id: '5424'
relation: earlier_version
status: public
status: public
title: Qualitative analysis of POMDPs with temporal logic specifications for robotics
applications
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '5423'
abstract:
- lang: eng
text: 'We present a flexible framework for the automated competitive analysis of
on-line scheduling algorithms for firm- deadline real-time tasks based on multi-objective
graphs: Given a taskset and an on-line scheduling algorithm specified as a labeled
transition system, along with some optional safety, liveness, and/or limit-average
constraints for the adversary, we automatically compute the competitive ratio
of the algorithm w.r.t. a clairvoyant scheduler. We demonstrate the flexibility
and power of our approach by comparing the competitive ratio of several on-line
algorithms, including D(over), that have been proposed in the past, for various
tasksets. Our experimental results reveal that none of these algorithms is universally
optimal, in the sense that there are tasksets where other schedulers provide better
performance. Our framework is hence a very useful design tool for selecting optimal
algorithms for a given application. '
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Alexander
full_name: Kössler, Alexander
last_name: Kössler
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Ulrich
full_name: Schmid, Ulrich
last_name: Schmid
citation:
ama: Chatterjee K, Kössler A, Pavlogiannis A, Schmid U. A Framework for Automated
Competitive Analysis of On-Line Scheduling of Firm-Deadline Tasks. IST Austria;
2014. doi:10.15479/AT:IST-2014-300-v1-1
apa: Chatterjee, K., Kössler, A., Pavlogiannis, A., & Schmid, U. (2014). A
framework for automated competitive analysis of on-line scheduling of firm-deadline
tasks. IST Austria. https://doi.org/10.15479/AT:IST-2014-300-v1-1
chicago: Chatterjee, Krishnendu, Alexander Kössler, Andreas Pavlogiannis, and Ulrich
Schmid. A Framework for Automated Competitive Analysis of On-Line Scheduling
of Firm-Deadline Tasks. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-300-v1-1.
ieee: K. Chatterjee, A. Kössler, A. Pavlogiannis, and U. Schmid, A framework
for automated competitive analysis of on-line scheduling of firm-deadline tasks.
IST Austria, 2014.
ista: Chatterjee K, Kössler A, Pavlogiannis A, Schmid U. 2014. A framework for automated
competitive analysis of on-line scheduling of firm-deadline tasks, IST Austria,
14p.
mla: Chatterjee, Krishnendu, et al. A Framework for Automated Competitive Analysis
of On-Line Scheduling of Firm-Deadline Tasks. IST Austria, 2014, doi:10.15479/AT:IST-2014-300-v1-1.
short: K. Chatterjee, A. Kössler, A. Pavlogiannis, U. Schmid, A Framework for Automated
Competitive Analysis of On-Line Scheduling of Firm-Deadline Tasks, IST Austria,
2014.
date_created: 2018-12-12T11:39:15Z
date_published: 2014-07-29T00:00:00Z
date_updated: 2023-02-23T10:11:15Z
day: '29'
ddc:
- '005'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2014-300-v1-1
file:
- access_level: open_access
checksum: 4b8fde4d9ef6653837f6803921d83032
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:53Z
date_updated: 2020-07-14T12:46:50Z
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file_date_updated: 2020-07-14T12:46:50Z
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language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '14'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '300'
related_material:
record:
- id: '1714'
relation: later_version
status: public
status: public
title: A framework for automated competitive analysis of on-line scheduling of firm-deadline
tasks
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '5427'
abstract:
- lang: eng
text: 'We consider graphs with n nodes together with their tree-decomposition that
has b = O ( n ) bags and width t , on the standard RAM computational model with
wordsize W = Θ (log n ) . Our contributions are two-fold: Our first contribution
is an algorithm that given a graph and its tree-decomposition as input, computes
a binary and balanced tree-decomposition of width at most 4 · t + 3 of the graph
in O ( b ) time and space, improving a long-standing (from 1992) bound of O (
n · log n ) time for constant treewidth graphs. Our second contribution is on
reachability queries for low treewidth graphs. We build on our tree-balancing
algorithm and present a data-structure for graph reachability that requires O
( n · t 2 ) preprocessing time, O ( n · t ) space, and O ( d t/ log n e ) time
for pair queries, and O ( n · t · log t/ log n ) time for single-source queries.
For constant t our data-structure uses O ( n ) time for preprocessing, O (1) time
for pair queries, and O ( n/ log n ) time for single-source queries. This is (asymptotically)
optimal and is faster than DFS/BFS when answering more than a constant number
of single-source queries.'
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Optimal Tree-Decomposition
Balancing and Reachability on Low Treewidth Graphs. IST Austria; 2014. doi:10.15479/AT:IST-2014-314-v1-1
apa: Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2014). Optimal
tree-decomposition balancing and reachability on low treewidth graphs. IST
Austria. https://doi.org/10.15479/AT:IST-2014-314-v1-1
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis.
Optimal Tree-Decomposition Balancing and Reachability on Low Treewidth Graphs.
IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-314-v1-1.
ieee: K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, Optimal tree-decomposition
balancing and reachability on low treewidth graphs. IST Austria, 2014.
ista: Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2014. Optimal tree-decomposition
balancing and reachability on low treewidth graphs, IST Austria, 24p.
mla: Chatterjee, Krishnendu, et al. Optimal Tree-Decomposition Balancing and
Reachability on Low Treewidth Graphs. IST Austria, 2014, doi:10.15479/AT:IST-2014-314-v1-1.
short: K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, Optimal Tree-Decomposition
Balancing and Reachability on Low Treewidth Graphs, IST Austria, 2014.
date_created: 2018-12-12T11:39:16Z
date_published: 2014-11-05T00:00:00Z
date_updated: 2021-01-12T08:02:09Z
day: '05'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2014-314-v1-1
file:
- access_level: open_access
checksum: 9d3b90bf4fff74664f182f2d95ef727a
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:10Z
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file_date_updated: 2020-07-14T12:46:52Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '24'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '314'
status: public
title: Optimal tree-decomposition balancing and reachability on low treewidth graphs
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '5425'
abstract:
- lang: eng
text: ' We consider partially observable Markov decision processes (POMDPs) with
a set of target states and every transition is associated with an integer cost.
The optimization objective we study asks to minimize the expected total cost till
the target set is reached, while ensuring that the target set is reached almost-surely
(with probability 1). We show that for integer costs approximating the optimal
cost is undecidable. For positive costs, our results are as follows: (i) we establish
matching lower and upper bounds for the optimal cost and the bound is double exponential;
(ii) we show that the problem of approximating the optimal cost is decidable and
present approximation algorithms developing on the existing algorithms for POMDPs
with finite-horizon objectives. While the worst-case running time of our algorithm
is double exponential, we also present efficient stopping criteria for the algorithm
and show experimentally that it performs well in many examples of interest.'
alternative_title:
- IST Austria Technical Report
author:
- first_name: '1'
full_name: Anonymous, 1
last_name: Anonymous
- first_name: '2'
full_name: Anonymous, 2
last_name: Anonymous
- first_name: '3'
full_name: Anonymous, 3
last_name: Anonymous
- first_name: '4'
full_name: Anonymous, 4
last_name: Anonymous
citation:
ama: Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. Optimal Cost Almost-Sure
Reachability in POMDPs. IST Austria; 2014.
apa: Anonymous, 1, Anonymous, 2, Anonymous, 3, & Anonymous, 4. (2014). Optimal
cost almost-sure reachability in POMDPs. IST Austria.
chicago: Anonymous, 1, 2 Anonymous, 3 Anonymous, and 4 Anonymous. Optimal Cost
Almost-Sure Reachability in POMDPs. IST Austria, 2014.
ieee: 1 Anonymous, 2 Anonymous, 3 Anonymous, and 4 Anonymous, Optimal cost almost-sure
reachability in POMDPs. IST Austria, 2014.
ista: Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. 2014. Optimal cost almost-sure
reachability in POMDPs, IST Austria, 22p.
mla: Anonymous, 1, et al. Optimal Cost Almost-Sure Reachability in POMDPs.
IST Austria, 2014.
short: 1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, Optimal Cost Almost-Sure
Reachability in POMDPs, IST Austria, 2014.
date_created: 2018-12-12T11:39:15Z
date_published: 2014-09-09T00:00:00Z
date_updated: 2023-02-23T10:02:57Z
day: '09'
ddc:
- '000'
file:
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creator: system
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date_updated: 2020-07-14T12:46:51Z
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creator: dernst
date_created: 2019-04-16T14:16:12Z
date_updated: 2020-07-14T12:46:51Z
file_id: '6322'
file_name: IST-2014-307-v1+2_authors.txt
file_size: 117
relation: main_file
file_date_updated: 2020-07-14T12:46:51Z
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language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '22'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '307'
related_material:
record:
- id: '1529'
relation: later_version
status: public
scopus_import: 1
status: public
title: Optimal cost almost-sure reachability in POMDPs
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '5415'
abstract:
- lang: eng
text: 'Recently there has been a significant effort to add quantitative properties
in formal verification and synthesis. While weighted automata over finite and
infinite words provide a natural and flexible framework to express quantitative
properties, perhaps surprisingly, several basic system properties such as average
response time cannot be expressed with weighted automata. In this work, we introduce
nested weighted automata as a new formalism for expressing important quantitative
properties such as average response time. We establish an almost complete decidability
picture for the basic decision problems for nested weighted automata, and illustrate
its applicability in several domains. '
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: Chatterjee K, Henzinger TA, Otop J. Nested Weighted Automata. IST Austria;
2014. doi:10.15479/AT:IST-2014-170-v1-1
apa: Chatterjee, K., Henzinger, T. A., & Otop, J. (2014). Nested weighted
automata. IST Austria. https://doi.org/10.15479/AT:IST-2014-170-v1-1
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. Nested Weighted
Automata. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-170-v1-1.
ieee: K. Chatterjee, T. A. Henzinger, and J. Otop, Nested weighted automata.
IST Austria, 2014.
ista: Chatterjee K, Henzinger TA, Otop J. 2014. Nested weighted automata, IST Austria,
27p.
mla: Chatterjee, Krishnendu, et al. Nested Weighted Automata. IST Austria,
2014, doi:10.15479/AT:IST-2014-170-v1-1.
short: K. Chatterjee, T.A. Henzinger, J. Otop, Nested Weighted Automata, IST Austria,
2014.
date_created: 2018-12-12T11:39:12Z
date_published: 2014-02-19T00:00:00Z
date_updated: 2023-02-23T12:26:19Z
day: '19'
ddc:
- '004'
department:
- _id: KrCh
- _id: ToHe
doi: 10.15479/AT:IST-2014-170-v1-1
file:
- access_level: open_access
checksum: 31f90dcf2cf899c3f8c6427cfcc2b3c7
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:36Z
date_updated: 2020-07-14T12:46:48Z
file_id: '5497'
file_name: IST-2014-170-v1+1_main.pdf
file_size: 573457
relation: main_file
file_date_updated: 2020-07-14T12:46:48Z
has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '27'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '170'
related_material:
record:
- id: '1656'
relation: later_version
status: public
- id: '467'
relation: later_version
status: public
- id: '5436'
relation: later_version
status: public
status: public
title: Nested weighted automata
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '5421'
abstract:
- lang: eng
text: 'Evolution occurs in populations of reproducing individuals. The structure
of the population affects the outcome of the evolutionary process. Evolutionary
graph theory is a powerful approach to study this phenomenon. There are two graphs.
The interaction graph specifies who interacts with whom in the context of evolution.
The replacement graph specifies who competes with whom for reproduction. The vertices
of the two graphs are the same, and each vertex corresponds to an individual.
A key quantity is the fixation probability of a new mutant. It is defined as the
probability that a newly introduced mutant (on a single vertex) generates a lineage
of offspring which eventually takes over the entire population of resident individuals.
The basic computational questions are as follows: (i) the qualitative question
asks whether the fixation probability is positive; and (ii) the quantitative approximation
question asks for an approximation of the fixation probability. Our main results
are: (1) We show that the qualitative question is NP-complete and the quantitative
approximation question is #P-hard in the special case when the interaction and
the replacement graphs coincide and even with the restriction that the resident
individuals do not reproduce (which corresponds to an invading population taking
over an empty structure). (2) We show that in general the qualitative question
is PSPACE-complete and the quantitative approximation question is PSPACE-hard
and can be solved in exponential time.'
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Chatterjee K, Ibsen-Jensen R, Nowak M. The Complexity of Evolution on Graphs.
IST Austria; 2014. doi:10.15479/AT:IST-2014-190-v2-2
apa: Chatterjee, K., Ibsen-Jensen, R., & Nowak, M. (2014). The complexity
of evolution on graphs. IST Austria. https://doi.org/10.15479/AT:IST-2014-190-v2-2
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Martin Nowak. The Complexity
of Evolution on Graphs. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-190-v2-2.
ieee: K. Chatterjee, R. Ibsen-Jensen, and M. Nowak, The complexity of evolution
on graphs. IST Austria, 2014.
ista: Chatterjee K, Ibsen-Jensen R, Nowak M. 2014. The complexity of evolution on
graphs, IST Austria, 27p.
mla: Chatterjee, Krishnendu, et al. The Complexity of Evolution on Graphs.
IST Austria, 2014, doi:10.15479/AT:IST-2014-190-v2-2.
short: K. Chatterjee, R. Ibsen-Jensen, M. Nowak, The Complexity of Evolution on
Graphs, IST Austria, 2014.
date_created: 2018-12-12T11:39:14Z
date_published: 2014-04-18T00:00:00Z
date_updated: 2023-02-23T12:26:33Z
day: '18'
ddc:
- '000'
- '005'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2014-190-v2-2
file:
- access_level: open_access
checksum: 42f3d8b563286eb0d903832bd9a848d3
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:16Z
date_updated: 2020-07-14T12:46:50Z
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file_size: 443529
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checksum: 0c9a2fd822309719634495a35957e34d
content_type: application/pdf
creator: kschuh
date_created: 2019-09-06T07:30:20Z
date_updated: 2020-07-14T12:46:50Z
file_id: '6852'
file_name: IST-2014-190-v1+1_main_full.pdf
file_size: 440911
relation: main_file
file_date_updated: 2020-07-14T12:46:50Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '27'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '190'
related_material:
record:
- id: '5432'
relation: later_version
status: public
- id: '5440'
relation: later_version
status: public
status: public
title: The complexity of evolution on graphs
type: technical_report
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '5813'
abstract:
- lang: eng
text: We consider homogeneous Bose gas in a large cubic box with periodic boundary
conditions, at zero temperature. We analyze its excitation spectrum in a certain
kind of a mean-field infinite-volume limit. We prove that under appropriate conditions
the excitation spectrum has the form predicted by the Bogoliubov approximation.
Our result can be viewed as an extension of the result of Seiringer (Commun. Math.
Phys.306:565–578, 2011) to large volumes.
article_processing_charge: No
author:
- first_name: Jan
full_name: Dereziński, Jan
last_name: Dereziński
- first_name: Marcin M
full_name: Napiórkowski, Marcin M
id: 4197AD04-F248-11E8-B48F-1D18A9856A87
last_name: Napiórkowski
citation:
ama: Dereziński J, Napiórkowski MM. Excitation spectrum of interacting bosons in
the Mean-Field Infinite-Volume limit. Annales Henri Poincaré. 2014;15(12):2409-2439.
doi:10.1007/s00023-013-0302-4
apa: Dereziński, J., & Napiórkowski, M. M. (2014). Excitation spectrum of interacting
bosons in the Mean-Field Infinite-Volume limit. Annales Henri Poincaré.
Springer Nature. https://doi.org/10.1007/s00023-013-0302-4
chicago: Dereziński, Jan, and Marcin M Napiórkowski. “Excitation Spectrum of Interacting
Bosons in the Mean-Field Infinite-Volume Limit.” Annales Henri Poincaré.
Springer Nature, 2014. https://doi.org/10.1007/s00023-013-0302-4.
ieee: J. Dereziński and M. M. Napiórkowski, “Excitation spectrum of interacting
bosons in the Mean-Field Infinite-Volume limit,” Annales Henri Poincaré,
vol. 15, no. 12. Springer Nature, pp. 2409–2439, 2014.
ista: Dereziński J, Napiórkowski MM. 2014. Excitation spectrum of interacting bosons
in the Mean-Field Infinite-Volume limit. Annales Henri Poincaré. 15(12), 2409–2439.
mla: Dereziński, Jan, and Marcin M. Napiórkowski. “Excitation Spectrum of Interacting
Bosons in the Mean-Field Infinite-Volume Limit.” Annales Henri Poincaré,
vol. 15, no. 12, Springer Nature, 2014, pp. 2409–39, doi:10.1007/s00023-013-0302-4.
short: J. Dereziński, M.M. Napiórkowski, Annales Henri Poincaré 15 (2014) 2409–2439.
date_created: 2019-01-10T09:02:58Z
date_published: 2014-01-10T00:00:00Z
date_updated: 2021-11-16T08:13:24Z
day: '10'
ddc:
- '530'
doi: 10.1007/s00023-013-0302-4
extern: '1'
file:
- access_level: open_access
checksum: 1f6c32c5d6ec90cdb0718c7f0103342e
content_type: application/pdf
creator: dernst
date_created: 2019-01-10T09:04:45Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5814'
file_name: 2014_Annales_Derezinski.pdf
file_size: 865230
relation: main_file
file_date_updated: 2020-07-14T12:47:11Z
has_accepted_license: '1'
intvolume: ' 15'
issue: '12'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 2409-2439
publication: Annales Henri Poincaré
publication_identifier:
issn:
- 1424-0637
- 1424-0661
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1007/s00023-014-0390-9
status: public
title: Excitation spectrum of interacting bosons in the Mean-Field Infinite-Volume
limit
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 15
year: '2014'
...
---
_id: '5810'
abstract:
- lang: eng
text: A discrete spherical geodesic path between two voxels s and t lying on a discrete
sphere is a/the 1-connected shortest path from s to t, comprising voxels of the
discrete sphere intersected by the real plane passing through s, t, and the center
of the sphere. We show that the set of sphere voxels intersected by the aforesaid
real plane always contains a 1-connected cycle passing through s and t, and each
voxel in this set lies within an isothetic distance of 32 from the concerned plane.
Hence, to compute the path, the algorithm starts from s, and iteratively computes
each voxel p of the path from the predecessor of p. A novel number-theoretic property
and the 48-symmetry of discrete sphere are used for searching the 1-connected
voxels comprising the path. The algorithm is output-sensitive, having its time
and space complexities both linear in the length of the path. It can be extended
for constructing 1-connected discrete 3D circles of arbitrary orientations, specified
by a few appropriate input parameters. Experimental results and related analysis
demonstrate its efficiency and versatility.
author:
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Partha
full_name: Bhowmick, Partha
last_name: Bhowmick
citation:
ama: Biswas R, Bhowmick P. On Finding Spherical Geodesic Paths and Circles in ℤ3.
2014;8668:396-409. doi:10.1007/978-3-319-09955-2_33
apa: 'Biswas, R., & Bhowmick, P. (2014). On Finding Spherical Geodesic Paths
and Circles in ℤ3. Presented at the DGCI: International Conference on Discrete
Geometry for Computer Imagery, Berlin, Heidelberg: Springer. https://doi.org/10.1007/978-3-319-09955-2_33'
chicago: 'Biswas, Ranita, and Partha Bhowmick. “On Finding Spherical Geodesic Paths
and Circles in ℤ3.” Lecture Notes in Computer Science. Berlin, Heidelberg: Springer,
2014. https://doi.org/10.1007/978-3-319-09955-2_33.'
ieee: R. Biswas and P. Bhowmick, “On Finding Spherical Geodesic Paths and Circles
in ℤ3,” vol. 8668. Springer, Berlin, Heidelberg, pp. 396–409, 2014.
ista: Biswas R, Bhowmick P. 2014. On Finding Spherical Geodesic Paths and Circles
in ℤ3. 8668, 396–409.
mla: Biswas, Ranita, and Partha Bhowmick. On Finding Spherical Geodesic Paths
and Circles in ℤ3. Vol. 8668, Springer, 2014, pp. 396–409, doi:10.1007/978-3-319-09955-2_33.
short: R. Biswas, P. Bhowmick, 8668 (2014) 396–409.
conference:
end_date: 2014-09-12
location: Siena, Italy
name: 'DGCI: International Conference on Discrete Geometry for Computer Imagery'
start_date: 2014-09-10
date_created: 2019-01-08T20:45:32Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2019-01-24T13:22:49Z
doi: 10.1007/978-3-319-09955-2_33
extern: '1'
intvolume: ' 8668'
language:
- iso: eng
oa_version: None
page: 396-409
place: Berlin, Heidelberg
publication_identifier:
isbn:
- '9783642387081'
- '9783642387098'
issn:
- 0302-9743
- 1611-3349
publication_status: published
publisher: Springer
quality_controlled: '1'
series_title: Lecture Notes in Computer Science
status: public
title: On Finding Spherical Geodesic Paths and Circles in ℤ3
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8668
year: '2014'
...
---
_id: '589'
abstract:
- lang: eng
text: We demonstrate a many-atom-cavity system with a high-finesse dual-wavelength
standing wave cavity in which all participating rubidium atoms are nearly identically
coupled to a 780-nm cavity mode. This homogeneous coupling is enforced by a one-dimensional
optical lattice formed by the field of a 1560-nm cavity mode.
author:
- first_name: Jongmin
full_name: Lee, Jongmin
last_name: Lee
- first_name: Geert
full_name: Vrijsen, Geert
last_name: Vrijsen
- first_name: Igor
full_name: Teper, Igor
last_name: Teper
- first_name: Onur
full_name: Onur Hosten
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Mark
full_name: Kasevich, Mark A
last_name: Kasevich
citation:
ama: Lee J, Vrijsen G, Teper I, Hosten O, Kasevich M. Many-atom-cavity QED system
with homogeneous atom-cavity coupling. Optics Letters. 2014;39(13):4005-4008.
doi:10.1364/OL.39.004005
apa: Lee, J., Vrijsen, G., Teper, I., Hosten, O., & Kasevich, M. (2014). Many-atom-cavity
QED system with homogeneous atom-cavity coupling. Optics Letters. OSA.
https://doi.org/10.1364/OL.39.004005
chicago: Lee, Jongmin, Geert Vrijsen, Igor Teper, Onur Hosten, and Mark Kasevich.
“Many-Atom-Cavity QED System with Homogeneous Atom-Cavity Coupling.” Optics
Letters. OSA, 2014. https://doi.org/10.1364/OL.39.004005.
ieee: J. Lee, G. Vrijsen, I. Teper, O. Hosten, and M. Kasevich, “Many-atom-cavity
QED system with homogeneous atom-cavity coupling,” Optics Letters, vol.
39, no. 13. OSA, pp. 4005–4008, 2014.
ista: Lee J, Vrijsen G, Teper I, Hosten O, Kasevich M. 2014. Many-atom-cavity QED
system with homogeneous atom-cavity coupling. Optics Letters. 39(13), 4005–4008.
mla: Lee, Jongmin, et al. “Many-Atom-Cavity QED System with Homogeneous Atom-Cavity
Coupling.” Optics Letters, vol. 39, no. 13, OSA, 2014, pp. 4005–08, doi:10.1364/OL.39.004005.
short: J. Lee, G. Vrijsen, I. Teper, O. Hosten, M. Kasevich, Optics Letters 39 (2014)
4005–4008.
date_created: 2018-12-11T11:47:21Z
date_published: 2014-07-01T00:00:00Z
date_updated: 2021-01-12T08:05:09Z
day: '01'
doi: 10.1364/OL.39.004005
extern: 1
intvolume: ' 39'
issue: '13'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1311.1805
month: '07'
oa: 1
page: 4005 - 4008
publication: Optics Letters
publication_status: published
publisher: OSA
publist_id: '7216'
quality_controlled: 0
status: public
title: Many-atom-cavity QED system with homogeneous atom-cavity coupling
type: journal_article
volume: 39
year: '2014'
...
---
_id: '6126'
abstract:
- lang: eng
text: Aerobic animals constantly monitor and adapt to changes in O2 levels. The
molecular mechanisms involved in sensing O2 are, however, incompletely understood.
Previous studies showed that a hexacoordinated globin called GLB-5 tunes the dynamic
range of O2-sensing neurons in natural C. elegans isolates, but is defective in
the N2 lab reference strain (McGrath et al., 2009; Persson et al., 2009). GLB-5
enables a sharp behavioral switch when O2 changes between 21 and 17%. Here, we
show that GLB-5 also confers rapid behavioral and cellular recovery from exposure
to hypoxia. Hypoxia reconfigures O2-evoked Ca2+ responses in the URX O2 sensors,
and GLB-5 enables rapid recovery of these responses upon re-oxygenation. Forward
genetic screens indicate that GLB-5's effects on O2 sensing require PDL-1, the
C. elegans ortholog of mammalian PrBP/PDE6δ protein. In mammals, PDE6δ regulates
the traffic and activity of prenylated proteins (Zhang et al., 2004; Norton et
al., 2005). PDL-1 promotes localization of GCY-33 and GCY-35, atypical soluble
guanylate cyclases that act as O2 sensors, to the dendritic endings of URX and
BAG neurons, where they colocalize with GLB-5. Both GCY-33 and GCY-35 are predicted
to be prenylated. Dendritic localization is not essential for GCY-35 to function
as an O2 sensor, but disrupting pdl-1 alters the URX neuron's O2 response properties.
Functional GLB-5 can restore dendritic localization of GCY-33 in pdl-1 mutants,
suggesting GCY-33 and GLB-5 are in a complex. Our data suggest GLB-5 and the soluble
guanylate cyclases operate in close proximity to sculpt O2 responses.
author:
- first_name: E.
full_name: Gross, E.
last_name: Gross
- first_name: Z.
full_name: Soltesz, Z.
last_name: Soltesz
- first_name: S.
full_name: Oda, S.
last_name: Oda
- first_name: V.
full_name: Zelmanovich, V.
last_name: Zelmanovich
- first_name: Z.
full_name: Abergel, Z.
last_name: Abergel
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Gross E, Soltesz Z, Oda S, Zelmanovich V, Abergel Z, de Bono M. GLOBIN-5-dependent
O2 responses are regulated by PDL-1/PrBP that targets prenylated soluble guanylate
cyclases to dendritic endings. Journal of Neuroscience. 2014;34(50):16726-16738.
doi:10.1523/jneurosci.5368-13.2014
apa: Gross, E., Soltesz, Z., Oda, S., Zelmanovich, V., Abergel, Z., & de Bono,
M. (2014). GLOBIN-5-dependent O2 responses are regulated by PDL-1/PrBP that targets
prenylated soluble guanylate cyclases to dendritic endings. Journal of Neuroscience.
Society for Neuroscience. https://doi.org/10.1523/jneurosci.5368-13.2014
chicago: Gross, E., Z. Soltesz, S. Oda, V. Zelmanovich, Z. Abergel, and Mario de
Bono. “GLOBIN-5-Dependent O2 Responses Are Regulated by PDL-1/PrBP That Targets
Prenylated Soluble Guanylate Cyclases to Dendritic Endings.” Journal of Neuroscience.
Society for Neuroscience, 2014. https://doi.org/10.1523/jneurosci.5368-13.2014.
ieee: E. Gross, Z. Soltesz, S. Oda, V. Zelmanovich, Z. Abergel, and M. de Bono,
“GLOBIN-5-dependent O2 responses are regulated by PDL-1/PrBP that targets prenylated
soluble guanylate cyclases to dendritic endings,” Journal of Neuroscience,
vol. 34, no. 50. Society for Neuroscience, pp. 16726–16738, 2014.
ista: Gross E, Soltesz Z, Oda S, Zelmanovich V, Abergel Z, de Bono M. 2014. GLOBIN-5-dependent
O2 responses are regulated by PDL-1/PrBP that targets prenylated soluble guanylate
cyclases to dendritic endings. Journal of Neuroscience. 34(50), 16726–16738.
mla: Gross, E., et al. “GLOBIN-5-Dependent O2 Responses Are Regulated by PDL-1/PrBP
That Targets Prenylated Soluble Guanylate Cyclases to Dendritic Endings.” Journal
of Neuroscience, vol. 34, no. 50, Society for Neuroscience, 2014, pp. 16726–38,
doi:10.1523/jneurosci.5368-13.2014.
short: E. Gross, Z. Soltesz, S. Oda, V. Zelmanovich, Z. Abergel, M. de Bono, Journal
of Neuroscience 34 (2014) 16726–16738.
date_created: 2019-03-19T14:52:26Z
date_published: 2014-12-10T00:00:00Z
date_updated: 2021-01-12T08:06:14Z
day: '10'
ddc:
- '570'
doi: 10.1523/jneurosci.5368-13.2014
extern: '1'
external_id:
pmid:
- '25505325'
file:
- access_level: open_access
checksum: a3dd71969f94c43909327cd083283d4b
content_type: application/pdf
creator: kschuh
date_created: 2019-03-19T14:55:58Z
date_updated: 2020-07-14T12:47:20Z
file_id: '6127'
file_name: 2014_SFN_Gross.pdf
file_size: 3263422
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 34'
issue: '50'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 16726-16738
pmid: 1
publication: Journal of Neuroscience
publication_identifier:
issn:
- 0270-6474
- 1529-2401
publication_status: published
publisher: Society for Neuroscience
quality_controlled: '1'
status: public
title: GLOBIN-5-dependent O2 responses are regulated by PDL-1/PrBP that targets prenylated
soluble guanylate cyclases to dendritic endings
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2014'
...
---
_id: '6124'
abstract:
- lang: eng
text: Despite the importance of G-protein coupled receptors (GPCRs) their biogenesis
is poorly understood. Like vertebrates, C. elegans uses a large family of GPCRs
as chemoreceptors. A subset of these receptors, such as ODR-10, requires the odr-4
and odr-8 genes to be appropriately localized to sensory cilia. The odr-4 gene
encodes a conserved tail-anchored transmembrane protein; the molecular identity
of odr-8 is unknown. Here, we show that odr-8 encodes the C. elegans ortholog
of Ufm1-specific protease 2 (UfSP2). UfSPs are cysteine proteases identified biochemically
by their ability to liberate the ubiquitin-like modifier Ufm1 from its pro-form
and protein conjugates. ODR-8/UfSP2 and ODR-4 are expressed in the same set of
twelve chemosensory neurons, and physically interact at the ER membrane. ODR-4
also binds ODR-10, suggesting that an ODR-4/ODR-8 complex promotes GPCR folding,
maturation, or export from the ER. The physical interaction between human ODR4
and UfSP2 suggests that this complex's role in GPCR biogenesis may be evolutionarily
conserved. Unexpectedly, mutant versions of ODR-8/UfSP2 lacking catalytic residues
required for protease activity can rescue all odr-8 mutant phenotypes tested.
Moreover, deleting C. elegans ufm-1 does not alter chemoreceptor traffic to cilia,
either in wild type or in odr-8 mutants. Thus, UfSP2 proteins have protease- and
Ufm1-independent functions in GPCR biogenesis.
article_number: e1004082
author:
- first_name: Changchun
full_name: Chen, Changchun
last_name: Chen
- first_name: Eisuke
full_name: Itakura, Eisuke
last_name: Itakura
- first_name: Katherine P.
full_name: Weber, Katherine P.
last_name: Weber
- first_name: Ramanujan S.
full_name: Hegde, Ramanujan S.
last_name: Hegde
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Chen C, Itakura E, Weber KP, Hegde RS, de Bono M. An ER complex of ODR-4 and
ODR-8/Ufm1 specific protease 2 promotes GPCR maturation by a Ufm1-independent
mechanism. PLoS Genetics. 2014;10(3). doi:10.1371/journal.pgen.1004082
apa: Chen, C., Itakura, E., Weber, K. P., Hegde, R. S., & de Bono, M. (2014).
An ER complex of ODR-4 and ODR-8/Ufm1 specific protease 2 promotes GPCR maturation
by a Ufm1-independent mechanism. PLoS Genetics. Public Library of Science
(PLoS). https://doi.org/10.1371/journal.pgen.1004082
chicago: Chen, Changchun, Eisuke Itakura, Katherine P. Weber, Ramanujan S. Hegde,
and Mario de Bono. “An ER Complex of ODR-4 and ODR-8/Ufm1 Specific Protease 2
Promotes GPCR Maturation by a Ufm1-Independent Mechanism.” PLoS Genetics.
Public Library of Science (PLoS), 2014. https://doi.org/10.1371/journal.pgen.1004082.
ieee: C. Chen, E. Itakura, K. P. Weber, R. S. Hegde, and M. de Bono, “An ER complex
of ODR-4 and ODR-8/Ufm1 specific protease 2 promotes GPCR maturation by a Ufm1-independent
mechanism,” PLoS Genetics, vol. 10, no. 3. Public Library of Science (PLoS),
2014.
ista: Chen C, Itakura E, Weber KP, Hegde RS, de Bono M. 2014. An ER complex of ODR-4
and ODR-8/Ufm1 specific protease 2 promotes GPCR maturation by a Ufm1-independent
mechanism. PLoS Genetics. 10(3), e1004082.
mla: Chen, Changchun, et al. “An ER Complex of ODR-4 and ODR-8/Ufm1 Specific Protease
2 Promotes GPCR Maturation by a Ufm1-Independent Mechanism.” PLoS Genetics,
vol. 10, no. 3, e1004082, Public Library of Science (PLoS), 2014, doi:10.1371/journal.pgen.1004082.
short: C. Chen, E. Itakura, K.P. Weber, R.S. Hegde, M. de Bono, PLoS Genetics 10
(2014).
date_created: 2019-03-19T14:45:56Z
date_published: 2014-03-06T00:00:00Z
date_updated: 2021-01-12T08:06:14Z
day: '06'
ddc:
- '570'
doi: 10.1371/journal.pgen.1004082
extern: '1'
external_id:
pmid:
- '24603482'
file:
- access_level: open_access
checksum: ac19941089a4262bb5bd74434a08b003
content_type: application/pdf
creator: kschuh
date_created: 2019-03-19T14:50:07Z
date_updated: 2020-07-14T12:47:20Z
file_id: '6125'
file_name: 2014_PLOS_Chen.PDF
file_size: 8286819
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Genetics
publication_identifier:
issn:
- 1553-7404
publication_status: published
publisher: Public Library of Science (PLoS)
quality_controlled: '1'
status: public
title: An ER complex of ODR-4 and ODR-8/Ufm1 specific protease 2 promotes GPCR maturation
by a Ufm1-independent mechanism
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2014'
...
---
_id: '6122'
author:
- first_name: Gerit A.
full_name: Linneweber, Gerit A.
last_name: Linneweber
- first_name: Jake
full_name: Jacobson, Jake
last_name: Jacobson
- first_name: Karl Emanuel
full_name: Busch, Karl Emanuel
last_name: Busch
- first_name: Bruno
full_name: Hudry, Bruno
last_name: Hudry
- first_name: Christo P.
full_name: Christov, Christo P.
last_name: Christov
- first_name: Dirk
full_name: Dormann, Dirk
last_name: Dormann
- first_name: Michaela
full_name: Yuan, Michaela
last_name: Yuan
- first_name: Tomoki
full_name: Otani, Tomoki
last_name: Otani
- first_name: Elisabeth
full_name: Knust, Elisabeth
last_name: Knust
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
- first_name: Irene
full_name: Miguel-Aliaga, Irene
last_name: Miguel-Aliaga
citation:
ama: Linneweber GA, Jacobson J, Busch KE, et al. Neuronal control of metabolism
through nutrient-dependent modulation of tracheal branching. Cell. 2014;156(1-2):69-83.
doi:10.1016/j.cell.2013.12.008
apa: Linneweber, G. A., Jacobson, J., Busch, K. E., Hudry, B., Christov, C. P.,
Dormann, D., … Miguel-Aliaga, I. (2014). Neuronal control of metabolism through
nutrient-dependent modulation of tracheal branching. Cell. Elsevier. https://doi.org/10.1016/j.cell.2013.12.008
chicago: Linneweber, Gerit A., Jake Jacobson, Karl Emanuel Busch, Bruno Hudry, Christo P.
Christov, Dirk Dormann, Michaela Yuan, et al. “Neuronal Control of Metabolism
through Nutrient-Dependent Modulation of Tracheal Branching.” Cell. Elsevier,
2014. https://doi.org/10.1016/j.cell.2013.12.008.
ieee: G. A. Linneweber et al., “Neuronal control of metabolism through nutrient-dependent
modulation of tracheal branching,” Cell, vol. 156, no. 1–2. Elsevier, pp.
69–83, 2014.
ista: Linneweber GA, Jacobson J, Busch KE, Hudry B, Christov CP, Dormann D, Yuan
M, Otani T, Knust E, de Bono M, Miguel-Aliaga I. 2014. Neuronal control of metabolism
through nutrient-dependent modulation of tracheal branching. Cell. 156(1–2), 69–83.
mla: Linneweber, Gerit A., et al. “Neuronal Control of Metabolism through Nutrient-Dependent
Modulation of Tracheal Branching.” Cell, vol. 156, no. 1–2, Elsevier, 2014,
pp. 69–83, doi:10.1016/j.cell.2013.12.008.
short: G.A. Linneweber, J. Jacobson, K.E. Busch, B. Hudry, C.P. Christov, D. Dormann,
M. Yuan, T. Otani, E. Knust, M. de Bono, I. Miguel-Aliaga, Cell 156 (2014) 69–83.
date_created: 2019-03-19T14:35:30Z
date_published: 2014-01-16T00:00:00Z
date_updated: 2021-01-12T08:06:13Z
day: '16'
ddc:
- '570'
doi: 10.1016/j.cell.2013.12.008
extern: '1'
external_id:
pmid:
- '24439370'
file:
- access_level: open_access
checksum: ad6ef68f37fb711d9abcd97fc06ad316
content_type: application/pdf
creator: kschuh
date_created: 2019-03-19T14:40:38Z
date_updated: 2020-07-14T12:47:20Z
file_id: '6123'
file_name: 2014_Elsevier_Linneweber.pdf
file_size: 5020084
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 156'
issue: 1-2
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 69-83
pmid: 1
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Neuronal control of metabolism through nutrient-dependent modulation of tracheal
branching
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 156
year: '2014'
...
---
_id: '6319'
abstract:
- lang: fre
text: Nous étudions le comportement asymptotique du nombre de variétés dans une
certaine classe ne satisfaisant pas le principe de Hasse. Cette étude repose sur
des résultats récemmentobtenus par Colliot-Thélène.
author:
- first_name: Régis de la
full_name: Bretèche, Régis de la
last_name: Bretèche
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
citation:
ama: Bretèche R de la, Browning TD. Contre-exemples au principe de Hasse pour certains
tores coflasques. Journal de Théorie des Nombres de Bordeaux. 2014;26(1):25-44.
doi:10.5802/jtnb.857
apa: Bretèche, R. de la, & Browning, T. D. (2014). Contre-exemples au principe
de Hasse pour certains tores coflasques. Journal de Théorie Des Nombres de
Bordeaux. Cellule MathDoc/CEDRAM. https://doi.org/10.5802/jtnb.857
chicago: Bretèche, Régis de la, and Timothy D Browning. “Contre-Exemples Au Principe
de Hasse Pour Certains Tores Coflasques.” Journal de Théorie Des Nombres de
Bordeaux. Cellule MathDoc/CEDRAM, 2014. https://doi.org/10.5802/jtnb.857.
ieee: R. de la Bretèche and T. D. Browning, “Contre-exemples au principe de Hasse
pour certains tores coflasques,” Journal de Théorie des Nombres de Bordeaux,
vol. 26, no. 1. Cellule MathDoc/CEDRAM, pp. 25–44, 2014.
ista: Bretèche R de la, Browning TD. 2014. Contre-exemples au principe de Hasse
pour certains tores coflasques. Journal de Théorie des Nombres de Bordeaux. 26(1),
25–44.
mla: Bretèche, Régis de la, and Timothy D. Browning. “Contre-Exemples Au Principe
de Hasse Pour Certains Tores Coflasques.” Journal de Théorie Des Nombres de
Bordeaux, vol. 26, no. 1, Cellule MathDoc/CEDRAM, 2014, pp. 25–44, doi:10.5802/jtnb.857.
short: R. de la Bretèche, T.D. Browning, Journal de Théorie Des Nombres de Bordeaux
26 (2014) 25–44.
date_created: 2019-04-16T13:40:13Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T08:07:03Z
doi: 10.5802/jtnb.857
extern: '1'
external_id:
arxiv:
- '1210.4236'
intvolume: ' 26'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1210.4236
oa: 1
oa_version: Preprint
page: 25-44
publication: Journal de Théorie des Nombres de Bordeaux
publication_identifier:
issn:
- 1246-7405
- 2118-8572
publication_status: published
publisher: Cellule MathDoc/CEDRAM
quality_controlled: '1'
status: public
title: Contre-exemples au principe de Hasse pour certains tores coflasques
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2014'
...
---
_id: '6740'
abstract:
- lang: eng
text: We describe coding techniques that achieve the capacity of a discrete memoryless
asymmetric channel. To do so, we discuss how recent advances in coding for symmetric
channels yield more efficient solutions also for the asymmetric case. In more
detail, we consider three basic approaches. The first one is Gallager's scheme
that concatenates a linear code with a non-linear mapper, in order to bias the
input distribution. We explicitly show that both polar codes and spatially coupled
codes can be employed in this scenario. Further, we derive a scaling law between
the gap to capacity, the cardinality of channel input and output alphabets, and
the required size of the mapper. The second one is an integrated approach in which
the coding scheme is used both for source coding, in order to create codewords
with the capacity-achieving distribution, and for channel coding, in order to
provide error protection. Such a technique has been recently introduced by Honda
and Yamamoto in the context of polar codes, and we show how to apply it also to
the design of sparse graph codes. The third approach is based on an idea due to
Böcherer and Mathar and separates completely the two tasks of source coding and
channel coding by “chaining” together several codewords. We prove that we can
combine any suitable source code with any suitable channel code in order to provide
optimal schemes for asymmetric channels. In particular, polar codes and spatially
coupled codes fulfill the required conditions.
author:
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Rudiger
full_name: Urbanke, Rudiger
last_name: Urbanke
- first_name: Hamed
full_name: Hassani, Hamed
last_name: Hassani
citation:
ama: 'Mondelli M, Urbanke R, Hassani H. How to achieve the capacity of asymmetric
channels. In: 52nd Annual Allerton Conference on Communication, Control, and
Computing. IEEE; 2014:789-796. doi:10.1109/allerton.2014.7028535'
apa: 'Mondelli, M., Urbanke, R., & Hassani, H. (2014). How to achieve the capacity
of asymmetric channels. In 52nd Annual Allerton Conference on Communication,
Control, and Computing (pp. 789–796). Monticello, IL, United States: IEEE.
https://doi.org/10.1109/allerton.2014.7028535'
chicago: Mondelli, Marco, Rudiger Urbanke, and Hamed Hassani. “How to Achieve the
Capacity of Asymmetric Channels.” In 52nd Annual Allerton Conference on Communication,
Control, and Computing, 789–96. IEEE, 2014. https://doi.org/10.1109/allerton.2014.7028535.
ieee: M. Mondelli, R. Urbanke, and H. Hassani, “How to achieve the capacity of asymmetric
channels,” in 52nd Annual Allerton Conference on Communication, Control, and
Computing, Monticello, IL, United States, 2014, pp. 789–796.
ista: Mondelli M, Urbanke R, Hassani H. 2014. How to achieve the capacity of asymmetric
channels. 52nd Annual Allerton Conference on Communication, Control, and Computing.
Allerton Conference on Communication, Control, and Computing, 789–796.
mla: Mondelli, Marco, et al. “How to Achieve the Capacity of Asymmetric Channels.”
52nd Annual Allerton Conference on Communication, Control, and Computing,
IEEE, 2014, pp. 789–96, doi:10.1109/allerton.2014.7028535.
short: M. Mondelli, R. Urbanke, H. Hassani, in:, 52nd Annual Allerton Conference
on Communication, Control, and Computing, IEEE, 2014, pp. 789–796.
conference:
end_date: 2014-10-03
location: Monticello, IL, United States
name: Allerton Conference on Communication, Control, and Computing
start_date: 2014-09-30
date_created: 2019-07-31T07:24:23Z
date_published: 2014-10-01T00:00:00Z
date_updated: 2023-02-23T12:49:36Z
day: '01'
doi: 10.1109/allerton.2014.7028535
extern: '1'
external_id:
arxiv:
- '1406.7373'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1406.7373
month: '10'
oa: 1
oa_version: Preprint
page: 789-796
publication: 52nd Annual Allerton Conference on Communication, Control, and Computing
publication_identifier:
eisbn:
- 978-1-4799-8009-3
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '6678'
relation: later_version
status: public
status: public
title: How to achieve the capacity of asymmetric channels
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '6739'
abstract:
- lang: eng
text: 'We explore the relationship between polar and RM codes and we describe a
coding scheme which improves upon the performance of the standard polar code at
practical block lengths. Our starting point is the experimental observation that
RM codes have a smaller error probability than polar codes under MAP decoding.
This motivates us to introduce a family of codes that “interpolates” between RM
and polar codes, call this family C inter = {C α : α ∈ [0, 1j}, where C α|α=1
is the original polar code, and C α|α=0 is an RM code. Based on numerical observations,
we remark that the error probability under MAP decoding is an increasing function
of α. MAP decoding has in general exponential complexity, but empirically the
performance of polar codes at finite block lengths is boosted by moving along
the family Cinter even under low-complexity decoding schemes such as, for instance,
belief propagation or successive cancellation list decoder. We demonstrate the
performance gain via numerical simulations for transmission over the erasure channel
as well as the Gaussian channel.'
author:
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Hamed
full_name: Hassani, Hamed
last_name: Hassani
- first_name: Rudiger
full_name: Urbanke, Rudiger
last_name: Urbanke
citation:
ama: 'Mondelli M, Hassani H, Urbanke R. From polar to Reed-Muller codes: A technique
to improve the finite-length performance. IEEE Transactions on Communications.
2014;62(9):3084-3091. doi:10.1109/tcomm.2014.2345069'
apa: 'Mondelli, M., Hassani, H., & Urbanke, R. (2014). From polar to Reed-Muller
codes: A technique to improve the finite-length performance. IEEE Transactions
on Communications. IEEE. https://doi.org/10.1109/tcomm.2014.2345069'
chicago: 'Mondelli, Marco, Hamed Hassani, and Rudiger Urbanke. “From Polar to Reed-Muller
Codes: A Technique to Improve the Finite-Length Performance.” IEEE Transactions
on Communications. IEEE, 2014. https://doi.org/10.1109/tcomm.2014.2345069.'
ieee: 'M. Mondelli, H. Hassani, and R. Urbanke, “From polar to Reed-Muller codes:
A technique to improve the finite-length performance,” IEEE Transactions on
Communications, vol. 62, no. 9. IEEE, pp. 3084–3091, 2014.'
ista: 'Mondelli M, Hassani H, Urbanke R. 2014. From polar to Reed-Muller codes:
A technique to improve the finite-length performance. IEEE Transactions on Communications.
62(9), 3084–3091.'
mla: 'Mondelli, Marco, et al. “From Polar to Reed-Muller Codes: A Technique to Improve
the Finite-Length Performance.” IEEE Transactions on Communications, vol.
62, no. 9, IEEE, 2014, pp. 3084–91, doi:10.1109/tcomm.2014.2345069.'
short: M. Mondelli, H. Hassani, R. Urbanke, IEEE Transactions on Communications
62 (2014) 3084–3091.
date_created: 2019-07-31T07:20:21Z
date_published: 2014-09-01T00:00:00Z
date_updated: 2021-01-12T08:08:46Z
day: '01'
doi: 10.1109/tcomm.2014.2345069
extern: '1'
external_id:
arxiv:
- '1401.3127'
intvolume: ' 62'
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1401.3127
month: '09'
oa: 1
oa_version: Preprint
page: 3084-3091
publication: IEEE Transactions on Communications
publication_identifier:
issn:
- 0090-6778
publication_status: published
publisher: IEEE
quality_controlled: '1'
status: public
title: 'From polar to Reed-Muller codes: A technique to improve the finite-length
performance'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 62
year: '2014'
...
---
_id: '6744'
abstract:
- lang: eng
text: With the aim of extending the coverage and improving the performance of impulse
radio ultra-wideband (UWB) systems, this paper focuses on developing a novel single
differential encoded decode and forward (DF) non-cooperative relaying scheme (NCR).
To favor simple receiver structures, differential noncoherent detection is employed
which enables effective energy capture without any channel estimation. Putting
emphasis on the general case of multi-hop relaying, we illustrate an original
algorithm for the joint power allocation and path selection (JPAPS), minimizing
an approximate expression of the overall bit error rate (BER). In particular,
after deriving a closed-form power allocation strategy, the optimal path selection
is reduced to a shortest path problem on a connected graph, which can be solved
without any topology information with complexity O(N 3 ), N being the number of
available relays of the network. An approximate scheme is also presented, which
reduces the complexity to O(N 2 ) while showing a negligible performance loss,
and for benchmarking purposes, an exhaustive-search based multi-hop DF cooperative
strategy is derived. Simulation results for various network setups corroborate
the effectiveness of the proposed low-complexity JPAPS algorithm, which favorably
compares to existing AF and DF relaying methods.
author:
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Qi
full_name: Zhou, Qi
last_name: Zhou
- first_name: Vincenzo
full_name: Lottici, Vincenzo
last_name: Lottici
- first_name: Xiaoli
full_name: Ma, Xiaoli
last_name: Ma
citation:
ama: Mondelli M, Zhou Q, Lottici V, Ma X. Joint power allocation and path selection
for multi-hop noncoherent decode and forward UWB communications. IEEE Transactions
on Wireless Communications. 2014;13(3):1397-1409. doi:10.1109/twc.2014.020914.130669
apa: Mondelli, M., Zhou, Q., Lottici, V., & Ma, X. (2014). Joint power allocation
and path selection for multi-hop noncoherent decode and forward UWB communications.
IEEE Transactions on Wireless Communications. IEEE. https://doi.org/10.1109/twc.2014.020914.130669
chicago: Mondelli, Marco, Qi Zhou, Vincenzo Lottici, and Xiaoli Ma. “Joint Power
Allocation and Path Selection for Multi-Hop Noncoherent Decode and Forward UWB
Communications.” IEEE Transactions on Wireless Communications. IEEE, 2014.
https://doi.org/10.1109/twc.2014.020914.130669.
ieee: M. Mondelli, Q. Zhou, V. Lottici, and X. Ma, “Joint power allocation and path
selection for multi-hop noncoherent decode and forward UWB communications,” IEEE
Transactions on Wireless Communications, vol. 13, no. 3. IEEE, pp. 1397–1409,
2014.
ista: Mondelli M, Zhou Q, Lottici V, Ma X. 2014. Joint power allocation and path
selection for multi-hop noncoherent decode and forward UWB communications. IEEE
Transactions on Wireless Communications. 13(3), 1397–1409.
mla: Mondelli, Marco, et al. “Joint Power Allocation and Path Selection for Multi-Hop
Noncoherent Decode and Forward UWB Communications.” IEEE Transactions on Wireless
Communications, vol. 13, no. 3, IEEE, 2014, pp. 1397–409, doi:10.1109/twc.2014.020914.130669.
short: M. Mondelli, Q. Zhou, V. Lottici, X. Ma, IEEE Transactions on Wireless Communications
13 (2014) 1397–1409.
date_created: 2019-07-31T09:05:07Z
date_published: 2014-03-20T00:00:00Z
date_updated: 2021-01-12T08:08:48Z
day: '20'
doi: 10.1109/twc.2014.020914.130669
extern: '1'
intvolume: ' 13'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
page: 1397-1409
publication: IEEE Transactions on Wireless Communications
publication_status: published
publisher: IEEE
quality_controlled: '1'
status: public
title: Joint power allocation and path selection for multi-hop noncoherent decode
and forward UWB communications
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2014'
...
---
_id: '10885'
abstract:
- lang: eng
text: "Two-player games on graphs provide the theoretical framework for many important
problems such as reactive synthesis. While the traditional study of two-player
zero-sum games has been extended to multi-player games with several notions of
equilibria, they are decidable only for perfect-information games, whereas several
applications require imperfect-information games.\r\nIn this paper we propose
a new notion of equilibria, called doomsday equilibria, which is a strategy profile
such that all players satisfy their own objective, and if any coalition of players
deviates and violates even one of the players objective, then the objective of
every player is violated.\r\nWe present algorithms and complexity results for
deciding the existence of doomsday equilibria for various classes of ω-regular
objectives, both for imperfect-information games, and for perfect-information
games.We provide optimal complexity bounds for imperfect-information games, and
in most cases for perfect-information games."
acknowledgement: " Supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF
NFN Grant No\r\nS11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft
faculty fellows award."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
- first_name: Emmanuel
full_name: Filiot, Emmanuel
last_name: Filiot
- first_name: Jean-François
full_name: Raskin, Jean-François
last_name: Raskin
citation:
ama: 'Chatterjee K, Doyen L, Filiot E, Raskin J-F. Doomsday equilibria for omega-regular
games. In: VMCAI 2014: Verification, Model Checking, and Abstract Interpretation.
Vol 8318. Springer Nature; 2014:78-97. doi:10.1007/978-3-642-54013-4_5'
apa: 'Chatterjee, K., Doyen, L., Filiot, E., & Raskin, J.-F. (2014). Doomsday
equilibria for omega-regular games. In VMCAI 2014: Verification, Model Checking,
and Abstract Interpretation (Vol. 8318, pp. 78–97). San Diego, CA, United
States: Springer Nature. https://doi.org/10.1007/978-3-642-54013-4_5'
chicago: 'Chatterjee, Krishnendu, Laurent Doyen, Emmanuel Filiot, and Jean-François
Raskin. “Doomsday Equilibria for Omega-Regular Games.” In VMCAI 2014: Verification,
Model Checking, and Abstract Interpretation, 8318:78–97. Springer Nature,
2014. https://doi.org/10.1007/978-3-642-54013-4_5.'
ieee: 'K. Chatterjee, L. Doyen, E. Filiot, and J.-F. Raskin, “Doomsday equilibria
for omega-regular games,” in VMCAI 2014: Verification, Model Checking, and
Abstract Interpretation, San Diego, CA, United States, 2014, vol. 8318, pp.
78–97.'
ista: 'Chatterjee K, Doyen L, Filiot E, Raskin J-F. 2014. Doomsday equilibria for
omega-regular games. VMCAI 2014: Verification, Model Checking, and Abstract Interpretation.
VMCAI: Verifcation, Model Checking, and Abstract Interpretation, LNCS, vol. 8318,
78–97.'
mla: 'Chatterjee, Krishnendu, et al. “Doomsday Equilibria for Omega-Regular Games.”
VMCAI 2014: Verification, Model Checking, and Abstract Interpretation,
vol. 8318, Springer Nature, 2014, pp. 78–97, doi:10.1007/978-3-642-54013-4_5.'
short: 'K. Chatterjee, L. Doyen, E. Filiot, J.-F. Raskin, in:, VMCAI 2014: Verification,
Model Checking, and Abstract Interpretation, Springer Nature, 2014, pp. 78–97.'
conference:
end_date: 2014-01-21
location: San Diego, CA, United States
name: 'VMCAI: Verifcation, Model Checking, and Abstract Interpretation'
start_date: 2014-01-19
date_created: 2022-03-18T13:03:15Z
date_published: 2014-01-30T00:00:00Z
date_updated: 2023-02-23T12:52:24Z
day: '30'
department:
- _id: KrCh
doi: 10.1007/978-3-642-54013-4_5
ec_funded: 1
external_id:
arxiv:
- '1311.3238'
intvolume: ' 8318'
language:
- iso: eng
month: '01'
oa_version: Preprint
page: 78-97
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: 'VMCAI 2014: Verification, Model Checking, and Abstract Interpretation'
publication_identifier:
eisbn:
- '9783642540134'
eissn:
- 1611-3349
isbn:
- '9783642540127'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '681'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Doomsday equilibria for omega-regular games
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8318
year: '2014'
...
---
_id: '6853'
abstract:
- lang: eng
text: This monograph presents a short course in computational geometry and topology.
In the first part the book covers Voronoi diagrams and Delaunay triangulations,
then it presents the theory of alpha complexes which play a crucial role in biology.
The central part of the book is the homology theory and their computation, including
the theory of persistence which is indispensable for applications, e.g. shape
reconstruction. The target audience comprises researchers and practitioners in
mathematics, biology, neuroscience and computer science, but the book may also
be beneficial to graduate students of these fields.
alternative_title:
- SpringerBriefs in Applied Sciences and Technology
article_processing_charge: No
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Edelsbrunner H. A Short Course in Computational Geometry and Topology.
1st ed. Cham: Springer Nature; 2014. doi:10.1007/978-3-319-05957-0'
apa: 'Edelsbrunner, H. (2014). A Short Course in Computational Geometry and Topology
(1st ed.). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-05957-0'
chicago: 'Edelsbrunner, Herbert. A Short Course in Computational Geometry and
Topology. 1st ed. SpringerBriefs in Applied Sciences and Technology. Cham:
Springer Nature, 2014. https://doi.org/10.1007/978-3-319-05957-0.'
ieee: 'H. Edelsbrunner, A Short Course in Computational Geometry and Topology,
1st ed. Cham: Springer Nature, 2014.'
ista: 'Edelsbrunner H. 2014. A Short Course in Computational Geometry and Topology
1st ed., Cham: Springer Nature, IX, 110p.'
mla: Edelsbrunner, Herbert. A Short Course in Computational Geometry and Topology.
1st ed., Springer Nature, 2014, doi:10.1007/978-3-319-05957-0.
short: H. Edelsbrunner, A Short Course in Computational Geometry and Topology, 1st
ed., Springer Nature, Cham, 2014.
date_created: 2019-09-06T09:22:33Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2022-03-04T07:47:54Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/978-3-319-05957-0
edition: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: IX, 110
place: Cham
publication_identifier:
eisbn:
- 9-783-3190-5957-0
eissn:
- 2191-5318
isbn:
- 9-783-3190-5956-3
issn:
- 2191-530X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: available as eBook via catalog IST BookList
relation: other
url: https://koha.app.ist.ac.at/cgi-bin/koha/opac-detail.pl?biblionumber=356106
- description: available via catalog IST BookList
relation: other
url: https://koha.app.ist.ac.at/cgi-bin/koha/opac-detail.pl?biblionumber=373842
scopus_import: '1'
series_title: SpringerBriefs in Applied Sciences and Technology
status: public
title: A Short Course in Computational Geometry and Topology
type: book
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '7038'
article_processing_charge: No
author:
- first_name: Kristóf
full_name: Huszár, Kristóf
id: 33C26278-F248-11E8-B48F-1D18A9856A87
last_name: Huszár
orcid: 0000-0002-5445-5057
- first_name: Michal
full_name: Rolinek, Michal
id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87
last_name: Rolinek
citation:
ama: Huszár K, Rolinek M. Playful Math - An Introduction to Mathematical Games.
IST Austria
apa: Huszár, K., & Rolinek, M. (n.d.). Playful Math - An introduction to
mathematical games. IST Austria.
chicago: Huszár, Kristóf, and Michal Rolinek. Playful Math - An Introduction
to Mathematical Games. IST Austria, n.d.
ieee: K. Huszár and M. Rolinek, Playful Math - An introduction to mathematical
games. IST Austria.
ista: Huszár K, Rolinek M. Playful Math - An introduction to mathematical games,
IST Austria, 5p.
mla: Huszár, Kristóf, and Michal Rolinek. Playful Math - An Introduction to Mathematical
Games. IST Austria.
short: K. Huszár, M. Rolinek, Playful Math - An Introduction to Mathematical Games,
IST Austria, n.d.
date_created: 2019-11-18T15:57:05Z
date_published: 2014-06-30T00:00:00Z
date_updated: 2020-07-14T23:11:45Z
day: '30'
ddc:
- '510'
department:
- _id: VlKo
- _id: UlWa
file:
- access_level: open_access
checksum: 2b94e5e1f4c3fe8ab89b12806276fb09
content_type: application/pdf
creator: dernst
date_created: 2019-11-18T15:57:51Z
date_updated: 2020-07-14T12:47:48Z
file_id: '7039'
file_name: 2014_Playful_Math_Huszar.pdf
file_size: 511233
relation: main_file
file_date_updated: 2020-07-14T12:47:48Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '5'
publication_status: draft
publisher: IST Austria
status: public
title: Playful Math - An introduction to mathematical games
type: working_paper
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '7071'
abstract:
- lang: eng
text: Spin and orbital quantum numbers play a key role in the physics of Mott insulators,
but in most systems they are connected only indirectly—via the Pauli exclusion
principle and the Coulomb interaction. Iridium-based oxides (iridates) introduce
strong spin–orbit coupling directly, such that these numbers become entwined together
and the Mott physics attains a strong orbital character. In the layered honeycomb
iridates this is thought to generate highly spin–anisotropic magnetic interactions,
coupling the spin to a given spatial direction of exchange and leading to strongly
frustrated magnetism. Here we report a new iridate structure that has the same
local connectivity as the layered honeycomb and exhibits striking evidence for
highly spin–anisotropic exchange. The basic structural units of this material
suggest that a new family of three-dimensional structures could exist, the ‘harmonic
honeycomb’ iridates, of which the present compound is the first example.
article_number: '4203'
article_processing_charge: No
article_type: original
author:
- first_name: Kimberly A
full_name: Modic, Kimberly A
id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425
last_name: Modic
orcid: 0000-0001-9760-3147
- first_name: Tess E.
full_name: Smidt, Tess E.
last_name: Smidt
- first_name: Itamar
full_name: Kimchi, Itamar
last_name: Kimchi
- first_name: Nicholas P.
full_name: Breznay, Nicholas P.
last_name: Breznay
- first_name: Alun
full_name: Biffin, Alun
last_name: Biffin
- first_name: Sungkyun
full_name: Choi, Sungkyun
last_name: Choi
- first_name: Roger D.
full_name: Johnson, Roger D.
last_name: Johnson
- first_name: Radu
full_name: Coldea, Radu
last_name: Coldea
- first_name: Pilanda
full_name: Watkins-Curry, Pilanda
last_name: Watkins-Curry
- first_name: Gregory T.
full_name: McCandless, Gregory T.
last_name: McCandless
- first_name: Julia Y.
full_name: Chan, Julia Y.
last_name: Chan
- first_name: Felipe
full_name: Gandara, Felipe
last_name: Gandara
- first_name: Z.
full_name: Islam, Z.
last_name: Islam
- first_name: Ashvin
full_name: Vishwanath, Ashvin
last_name: Vishwanath
- first_name: Arkady
full_name: Shekhter, Arkady
last_name: Shekhter
- first_name: Ross D.
full_name: McDonald, Ross D.
last_name: McDonald
- first_name: James G.
full_name: Analytis, James G.
last_name: Analytis
citation:
ama: Modic KA, Smidt TE, Kimchi I, et al. Realization of a three-dimensional spin–anisotropic
harmonic honeycomb iridate. Nature Communications. 2014;5. doi:10.1038/ncomms5203
apa: Modic, K. A., Smidt, T. E., Kimchi, I., Breznay, N. P., Biffin, A., Choi, S.,
… Analytis, J. G. (2014). Realization of a three-dimensional spin–anisotropic
harmonic honeycomb iridate. Nature Communications. Springer Science and
Business Media LLC. https://doi.org/10.1038/ncomms5203
chicago: Modic, Kimberly A, Tess E. Smidt, Itamar Kimchi, Nicholas P. Breznay, Alun
Biffin, Sungkyun Choi, Roger D. Johnson, et al. “Realization of a Three-Dimensional
Spin–Anisotropic Harmonic Honeycomb Iridate.” Nature Communications. Springer
Science and Business Media LLC, 2014. https://doi.org/10.1038/ncomms5203.
ieee: K. A. Modic et al., “Realization of a three-dimensional spin–anisotropic
harmonic honeycomb iridate,” Nature Communications, vol. 5. Springer Science
and Business Media LLC, 2014.
ista: Modic KA, Smidt TE, Kimchi I, Breznay NP, Biffin A, Choi S, Johnson RD, Coldea
R, Watkins-Curry P, McCandless GT, Chan JY, Gandara F, Islam Z, Vishwanath A,
Shekhter A, McDonald RD, Analytis JG. 2014. Realization of a three-dimensional
spin–anisotropic harmonic honeycomb iridate. Nature Communications. 5, 4203.
mla: Modic, Kimberly A., et al. “Realization of a Three-Dimensional Spin–Anisotropic
Harmonic Honeycomb Iridate.” Nature Communications, vol. 5, 4203, Springer
Science and Business Media LLC, 2014, doi:10.1038/ncomms5203.
short: K.A. Modic, T.E. Smidt, I. Kimchi, N.P. Breznay, A. Biffin, S. Choi, R.D.
Johnson, R. Coldea, P. Watkins-Curry, G.T. McCandless, J.Y. Chan, F. Gandara,
Z. Islam, A. Vishwanath, A. Shekhter, R.D. McDonald, J.G. Analytis, Nature Communications
5 (2014).
date_created: 2019-11-19T13:22:39Z
date_published: 2014-06-27T00:00:00Z
date_updated: 2021-01-12T08:11:42Z
day: '27'
ddc:
- '530'
doi: 10.1038/ncomms5203
extern: '1'
file:
- access_level: open_access
checksum: d290f0bfa93c5169cc6c8086874c5a78
content_type: application/pdf
creator: dernst
date_created: 2019-11-26T12:44:23Z
date_updated: 2020-07-14T12:47:48Z
file_id: '7113'
file_name: 2014_NatureComm_Modic.pdf
file_size: 4832820
relation: main_file
file_date_updated: 2020-07-14T12:47:48Z
has_accepted_license: '1'
intvolume: ' 5'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Science and Business Media LLC
quality_controlled: '1'
status: public
title: Realization of a three-dimensional spin–anisotropic harmonic honeycomb iridate
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2014'
...
---
_id: '7072'
abstract:
- lang: eng
text: We investigate the structural and magnetic properties of two molecule-based
magnets synthesized from the same starting components. Their different structural
motifs promote contrasting exchange pathways and consequently lead to markedly
different magnetic ground states. Through examination of their structural and
magnetic properties we show that [Cu(pyz)(H2O)(gly)2](ClO4)2 may be considered
a quasi-one-dimensional quantum Heisenberg antiferromagnet whereas the related
compound [Cu(pyz)(gly)](ClO4), which is formed from dimers of antiferromagnetically
interacting Cu2+ spins, remains disordered down to at least 0.03 K in zero field
but shows a field-temperature phase diagram reminiscent of that seen in materials
showing a Bose-Einstein condensation of magnons.
article_number: '207201'
article_processing_charge: No
article_type: original
author:
- first_name: T.
full_name: Lancaster, T.
last_name: Lancaster
- first_name: P. A.
full_name: Goddard, P. A.
last_name: Goddard
- first_name: S. J.
full_name: Blundell, S. J.
last_name: Blundell
- first_name: F. R.
full_name: Foronda, F. R.
last_name: Foronda
- first_name: S.
full_name: Ghannadzadeh, S.
last_name: Ghannadzadeh
- first_name: J. S.
full_name: Möller, J. S.
last_name: Möller
- first_name: P. J.
full_name: Baker, P. J.
last_name: Baker
- first_name: F. L.
full_name: Pratt, F. L.
last_name: Pratt
- first_name: C.
full_name: Baines, C.
last_name: Baines
- first_name: L.
full_name: Huang, L.
last_name: Huang
- first_name: J.
full_name: Wosnitza, J.
last_name: Wosnitza
- first_name: R. D.
full_name: McDonald, R. D.
last_name: McDonald
- first_name: Kimberly A
full_name: Modic, Kimberly A
id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425
last_name: Modic
orcid: 0000-0001-9760-3147
- first_name: J.
full_name: Singleton, J.
last_name: Singleton
- first_name: C. V.
full_name: Topping, C. V.
last_name: Topping
- first_name: T. A. W.
full_name: Beale, T. A. W.
last_name: Beale
- first_name: F.
full_name: Xiao, F.
last_name: Xiao
- first_name: J. A.
full_name: Schlueter, J. A.
last_name: Schlueter
- first_name: A. M.
full_name: Barton, A. M.
last_name: Barton
- first_name: R. D.
full_name: Cabrera, R. D.
last_name: Cabrera
- first_name: K. E.
full_name: Carreiro, K. E.
last_name: Carreiro
- first_name: H. E.
full_name: Tran, H. E.
last_name: Tran
- first_name: J. L.
full_name: Manson, J. L.
last_name: Manson
citation:
ama: Lancaster T, Goddard PA, Blundell SJ, et al. Controlling magnetic order and
quantum disorder in molecule-based magnets. Physical Review Letters. 2014;112(20).
doi:10.1103/physrevlett.112.207201
apa: Lancaster, T., Goddard, P. A., Blundell, S. J., Foronda, F. R., Ghannadzadeh,
S., Möller, J. S., … Manson, J. L. (2014). Controlling magnetic order and quantum
disorder in molecule-based magnets. Physical Review Letters. APS. https://doi.org/10.1103/physrevlett.112.207201
chicago: Lancaster, T., P. A. Goddard, S. J. Blundell, F. R. Foronda, S. Ghannadzadeh,
J. S. Möller, P. J. Baker, et al. “Controlling Magnetic Order and Quantum Disorder
in Molecule-Based Magnets.” Physical Review Letters. APS, 2014. https://doi.org/10.1103/physrevlett.112.207201.
ieee: T. Lancaster et al., “Controlling magnetic order and quantum disorder
in molecule-based magnets,” Physical Review Letters, vol. 112, no. 20.
APS, 2014.
ista: Lancaster T, Goddard PA, Blundell SJ, Foronda FR, Ghannadzadeh S, Möller JS,
Baker PJ, Pratt FL, Baines C, Huang L, Wosnitza J, McDonald RD, Modic KA, Singleton
J, Topping CV, Beale TAW, Xiao F, Schlueter JA, Barton AM, Cabrera RD, Carreiro
KE, Tran HE, Manson JL. 2014. Controlling magnetic order and quantum disorder
in molecule-based magnets. Physical Review Letters. 112(20), 207201.
mla: Lancaster, T., et al. “Controlling Magnetic Order and Quantum Disorder in Molecule-Based
Magnets.” Physical Review Letters, vol. 112, no. 20, 207201, APS, 2014,
doi:10.1103/physrevlett.112.207201.
short: T. Lancaster, P.A. Goddard, S.J. Blundell, F.R. Foronda, S. Ghannadzadeh,
J.S. Möller, P.J. Baker, F.L. Pratt, C. Baines, L. Huang, J. Wosnitza, R.D. McDonald,
K.A. Modic, J. Singleton, C.V. Topping, T.A.W. Beale, F. Xiao, J.A. Schlueter,
A.M. Barton, R.D. Cabrera, K.E. Carreiro, H.E. Tran, J.L. Manson, Physical Review
Letters 112 (2014).
date_created: 2019-11-19T13:23:13Z
date_published: 2014-05-19T00:00:00Z
date_updated: 2021-01-12T08:11:42Z
day: '19'
doi: 10.1103/physrevlett.112.207201
extern: '1'
intvolume: ' 112'
issue: '20'
language:
- iso: eng
month: '05'
oa_version: None
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: APS
quality_controlled: '1'
status: public
title: Controlling magnetic order and quantum disorder in molecule-based magnets
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2014'
...
---
_id: '7303'
abstract:
- lang: eng
text: The electrolyte in the non-aqueous (aprotic) lithium air battery has a profound
influence on the reactions that occur at the anode and cathode, and hence its
overall operation on discharge/charge. It must possess a wide range of attributes,
exceeding the requirements of electrolytes for Lithium ion batteries by far. The
most important additional issues are stability at both anode and cathode in the
presence of O2. The known problems with cycling the Li metal/non-aqueous electrolyte
interface are further complicated by O2. New and much less understood are the
reactions at the O2 cathode/electrolyte interface where the highly reversible
formation/decomposition of Li2O2 on discharge/charge is critical for the operation
of the non-aqueous lithium air battery. Many aprotic electrolytes exhibit decomposition
at the cathode during discharge and charge due to the presence of reactive reduced
O2 species affecting potential, capacity and kinetics on discharge and charge,
cyclability and calendar life. Identifying suitable electrolytes is one of the
key challenges for the non-aqueous lithium air battery at the present time. Following
the realisation that cyclability of such cells in the initially used organic carbonate
electrolytes is due to back-to-back irreversible reactions the stability of the
non-aqueous electrolytes became a major focus of research on rechargeable lithium
air batteries. This realisation led to the establishment of a suite of experimental
and computational methods capable of screening the stability of electrolytes.
These allow for greater mechanistic understanding of the reactivity and guide
the way towards designing more stable systems. A range of electrolytes based on
ethers, amides, sulfones, ionic liquids and dimethyl sulfoxide have been investigated.
All are more stable than the organic carbonates, but not all are equally stable.
Even though it was soon realised, by a number of groups, that ethers exhibit side
reactions on discharge and charge, they still remain the choice in many studies.
To date dimethyl sulfoxide and dimethylacetamide were identified as the most stable
electrolytes. In conjunction with the investigation of electrolyte stability the
importance of electrode stability became more prominent. The stability of the
electrolyte cannot be considered in isolation. Its stability depends on the synergy
between electrolyte and electrode. Carbon based electrodes promote electrolyte
decomposition and decompose on their own. Although great progress has been made
in only a few years, future work on aprotic electrolytes for Li-O2 batteries will
need to explore other electrolytes in the quest for yet lower cost, higher safety,
stability and low volatility.
article_processing_charge: No
author:
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Yuhui
full_name: Chen, Yuhui
last_name: Chen
- first_name: Fanny
full_name: Bardé, Fanny
last_name: Bardé
- first_name: Kensuke
full_name: Takechi, Kensuke
last_name: Takechi
- first_name: Fuminori
full_name: Mizuno, Fuminori
last_name: Mizuno
- first_name: Peter G.
full_name: Bruce, Peter G.
last_name: Bruce
citation:
ama: 'Freunberger SA, Chen Y, Bardé F, Takechi K, Mizuno F, Bruce PG. Nonaqueous
Electrolytes. In: Imanishi N, Luntz AC, Bruce P, eds. The Lithium Air Battery:
Fundamentals. New York, NY: Springer Nature; 2014:23-58. doi:10.1007/978-1-4899-8062-5_2'
apa: 'Freunberger, S. A., Chen, Y., Bardé, F., Takechi, K., Mizuno, F., & Bruce,
P. G. (2014). Nonaqueous Electrolytes. In N. Imanishi, A. C. Luntz, & P. Bruce
(Eds.), The Lithium Air Battery: Fundamentals (pp. 23–58). New York, NY:
Springer Nature. https://doi.org/10.1007/978-1-4899-8062-5_2'
chicago: 'Freunberger, Stefan Alexander, Yuhui Chen, Fanny Bardé, Kensuke Takechi,
Fuminori Mizuno, and Peter G. Bruce. “Nonaqueous Electrolytes.” In The Lithium
Air Battery: Fundamentals, edited by Nobuyuki Imanishi, Alan C. Luntz, and
Peter Bruce, 23–58. New York, NY: Springer Nature, 2014. https://doi.org/10.1007/978-1-4899-8062-5_2.'
ieee: 'S. A. Freunberger, Y. Chen, F. Bardé, K. Takechi, F. Mizuno, and P. G. Bruce,
“Nonaqueous Electrolytes,” in The Lithium Air Battery: Fundamentals, N.
Imanishi, A. C. Luntz, and P. Bruce, Eds. New York, NY: Springer Nature, 2014,
pp. 23–58.'
ista: 'Freunberger SA, Chen Y, Bardé F, Takechi K, Mizuno F, Bruce PG. 2014.Nonaqueous
Electrolytes. In: The Lithium Air Battery: Fundamentals. , 23–58.'
mla: 'Freunberger, Stefan Alexander, et al. “Nonaqueous Electrolytes.” The Lithium
Air Battery: Fundamentals, edited by Nobuyuki Imanishi et al., Springer Nature,
2014, pp. 23–58, doi:10.1007/978-1-4899-8062-5_2.'
short: 'S.A. Freunberger, Y. Chen, F. Bardé, K. Takechi, F. Mizuno, P.G. Bruce,
in:, N. Imanishi, A.C. Luntz, P. Bruce (Eds.), The Lithium Air Battery: Fundamentals,
Springer Nature, New York, NY, 2014, pp. 23–58.'
date_created: 2020-01-15T12:17:55Z
date_published: 2014-03-05T00:00:00Z
date_updated: 2021-01-12T08:12:54Z
day: '05'
doi: 10.1007/978-1-4899-8062-5_2
editor:
- first_name: Nobuyuki
full_name: Imanishi, Nobuyuki
last_name: Imanishi
- first_name: Alan C.
full_name: Luntz, Alan C.
last_name: Luntz
- first_name: Peter
full_name: Bruce, Peter
last_name: Bruce
extern: '1'
language:
- iso: eng
month: '03'
oa_version: None
page: 23-58
place: New York, NY
publication: 'The Lithium Air Battery: Fundamentals'
publication_identifier:
eisbn:
- '9781489980625'
isbn:
- '9781489980618'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Nonaqueous Electrolytes
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '7302'
abstract:
- lang: eng
text: Understanding charge carrier transport in Li2O2, the storage material in the
non-aqueous Li-O2 battery, is key to the development of this high-energy battery.
Here, we studied ionic transport properties and Li self-diffusion in nanocrystalline
Li2O2 by conductivity and temperature variable 7Li NMR spectroscopy. Nanostructured
Li2O2, characterized by a mean crystallite size of less than 50 nm as estimated
from X-ray diffraction peak broadening, was prepared by high-energy ball milling
of microcrystalline lithium peroxide with μm sized crystallites. At room temperature
the overall conductivity σ of the microcrystalline reference sample turned out
to be very low (3.4 × 10−13 S cm−1) which is in agreement with results from temperature-variable
7Li NMR line shape measurements. Ball-milling, however, leads to an increase of
σ by approximately two orders of magnitude (1.1 × 10−10 S cm−1); correspondingly,
the activation energy decreases from 0.89 eV to 0.82 eV. The electronic contribution
σeon, however, is in the order of 9 × 10−12 S cm−1 which makes less than 10% of
the total value. Interestingly, 7Li NMR lines of nano-Li2O2 undergo pronounced
heterogeneous motional narrowing which manifests in a two-component line shape
emerging with increasing temperatures. Most likely, the enhancement in σ can be
traced back to the generation of a spin reservoir with highly mobile Li ions;
these are expected to reside in the nearest neighbourhood of defects generated
or near the structurally disordered and defect-rich interfacial regions formed
during mechanical treatment.
article_processing_charge: No
article_type: original
author:
- first_name: A.
full_name: Dunst, A.
last_name: Dunst
- first_name: V.
full_name: Epp, V.
last_name: Epp
- first_name: I.
full_name: Hanzu, I.
last_name: Hanzu
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: M.
full_name: Wilkening, M.
last_name: Wilkening
citation:
ama: Dunst A, Epp V, Hanzu I, Freunberger SA, Wilkening M. Short-range Li diffusion
vs. long-range ionic conduction in nanocrystalline lithium peroxide Li2O2—the
discharge product in lithium-air batteries. Energy & Environmental Science.
2014;7(8):2739-2752. doi:10.1039/c4ee00496e
apa: Dunst, A., Epp, V., Hanzu, I., Freunberger, S. A., & Wilkening, M. (2014).
Short-range Li diffusion vs. long-range ionic conduction in nanocrystalline lithium
peroxide Li2O2—the discharge product in lithium-air batteries. Energy &
Environmental Science. RSC. https://doi.org/10.1039/c4ee00496e
chicago: Dunst, A., V. Epp, I. Hanzu, Stefan Alexander Freunberger, and M. Wilkening.
“Short-Range Li Diffusion vs. Long-Range Ionic Conduction in Nanocrystalline Lithium
Peroxide Li2O2—the Discharge Product in Lithium-Air Batteries.” Energy &
Environmental Science. RSC, 2014. https://doi.org/10.1039/c4ee00496e.
ieee: A. Dunst, V. Epp, I. Hanzu, S. A. Freunberger, and M. Wilkening, “Short-range
Li diffusion vs. long-range ionic conduction in nanocrystalline lithium peroxide
Li2O2—the discharge product in lithium-air batteries,” Energy & Environmental
Science, vol. 7, no. 8. RSC, pp. 2739–2752, 2014.
ista: Dunst A, Epp V, Hanzu I, Freunberger SA, Wilkening M. 2014. Short-range Li
diffusion vs. long-range ionic conduction in nanocrystalline lithium peroxide
Li2O2—the discharge product in lithium-air batteries. Energy & Environmental
Science. 7(8), 2739–2752.
mla: Dunst, A., et al. “Short-Range Li Diffusion vs. Long-Range Ionic Conduction
in Nanocrystalline Lithium Peroxide Li2O2—the Discharge Product in Lithium-Air
Batteries.” Energy & Environmental Science, vol. 7, no. 8, RSC, 2014,
pp. 2739–52, doi:10.1039/c4ee00496e.
short: A. Dunst, V. Epp, I. Hanzu, S.A. Freunberger, M. Wilkening, Energy &
Environmental Science 7 (2014) 2739–2752.
date_created: 2020-01-15T12:17:43Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2021-01-12T08:12:53Z
day: '01'
doi: 10.1039/c4ee00496e
extern: '1'
intvolume: ' 7'
issue: '8'
language:
- iso: eng
month: '08'
oa_version: Published Version
page: 2739-2752
publication: Energy & Environmental Science
publication_identifier:
issn:
- 1754-5692
- 1754-5706
publication_status: published
publisher: RSC
quality_controlled: '1'
status: public
title: Short-range Li diffusion vs. long-range ionic conduction in nanocrystalline
lithium peroxide Li2O2—the discharge product in lithium-air batteries
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2014'
...
---
_id: '7305'
abstract:
- lang: eng
text: When lithium–oxygen batteries discharge, O2 is reduced at the cathode to form
solid Li2O2. Understanding the fundamental mechanism of O2 reduction in aprotic
solvents is therefore essential to realizing their technological potential. Two
different models have been proposed for Li2O2 formation, involving either solution
or electrode surface routes. Here, we describe a single unified mechanism, which,
unlike previous models, can explain O2 reduction across the whole range of solvents
and for which the two previous models are limiting cases. We observe that the
solvent influences O2 reduction through its effect on the solubility of LiO2,
or, more precisely, the free energy of the reaction LiO2* ⇌ Li(sol)+ + O2−(sol) + ion
pairs + higher aggregates (clusters). The unified mechanism shows that low-donor-number
solvents are likely to lead to premature cell death, and that the future direction
of research for lithium–oxygen batteries should focus on the search for new, stable,
high-donor-number electrolytes, because they can support higher capacities and
can better sustain discharge.
article_processing_charge: No
article_type: original
author:
- first_name: Lee
full_name: Johnson, Lee
last_name: Johnson
- first_name: Chunmei
full_name: Li, Chunmei
last_name: Li
- first_name: Zheng
full_name: Liu, Zheng
last_name: Liu
- first_name: Yuhui
full_name: Chen, Yuhui
last_name: Chen
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Praveen C.
full_name: Ashok, Praveen C.
last_name: Ashok
- first_name: Bavishna B.
full_name: Praveen, Bavishna B.
last_name: Praveen
- first_name: Kishan
full_name: Dholakia, Kishan
last_name: Dholakia
- first_name: Jean-Marie
full_name: Tarascon, Jean-Marie
last_name: Tarascon
- first_name: Peter G.
full_name: Bruce, Peter G.
last_name: Bruce
citation:
ama: Johnson L, Li C, Liu Z, et al. The role of LiO2 solubility in O2 reduction
in aprotic solvents and its consequences for Li–O2 batteries. Nature Chemistry.
2014;6(12):1091-1099. doi:10.1038/nchem.2101
apa: Johnson, L., Li, C., Liu, Z., Chen, Y., Freunberger, S. A., Ashok, P. C., …
Bruce, P. G. (2014). The role of LiO2 solubility in O2 reduction in aprotic solvents
and its consequences for Li–O2 batteries. Nature Chemistry. Springer Nature.
https://doi.org/10.1038/nchem.2101
chicago: Johnson, Lee, Chunmei Li, Zheng Liu, Yuhui Chen, Stefan Alexander Freunberger,
Praveen C. Ashok, Bavishna B. Praveen, Kishan Dholakia, Jean-Marie Tarascon, and
Peter G. Bruce. “The Role of LiO2 Solubility in O2 Reduction in Aprotic Solvents
and Its Consequences for Li–O2 Batteries.” Nature Chemistry. Springer Nature,
2014. https://doi.org/10.1038/nchem.2101.
ieee: L. Johnson et al., “The role of LiO2 solubility in O2 reduction in
aprotic solvents and its consequences for Li–O2 batteries,” Nature Chemistry,
vol. 6, no. 12. Springer Nature, pp. 1091–1099, 2014.
ista: Johnson L, Li C, Liu Z, Chen Y, Freunberger SA, Ashok PC, Praveen BB, Dholakia
K, Tarascon J-M, Bruce PG. 2014. The role of LiO2 solubility in O2 reduction in
aprotic solvents and its consequences for Li–O2 batteries. Nature Chemistry. 6(12),
1091–1099.
mla: Johnson, Lee, et al. “The Role of LiO2 Solubility in O2 Reduction in Aprotic
Solvents and Its Consequences for Li–O2 Batteries.” Nature Chemistry, vol.
6, no. 12, Springer Nature, 2014, pp. 1091–99, doi:10.1038/nchem.2101.
short: L. Johnson, C. Li, Z. Liu, Y. Chen, S.A. Freunberger, P.C. Ashok, B.B. Praveen,
K. Dholakia, J.-M. Tarascon, P.G. Bruce, Nature Chemistry 6 (2014) 1091–1099.
date_created: 2020-01-15T12:18:18Z
date_published: 2014-11-10T00:00:00Z
date_updated: 2021-01-12T08:12:55Z
day: '10'
doi: 10.1038/nchem.2101
extern: '1'
intvolume: ' 6'
issue: '12'
language:
- iso: eng
month: '11'
oa_version: None
page: 1091-1099
publication: Nature Chemistry
publication_identifier:
issn:
- 1755-4330
- 1755-4349
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/nchem.2138
status: public
title: The role of LiO2 solubility in O2 reduction in aprotic solvents and its consequences
for Li–O2 batteries
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2014'
...
---
_id: '7304'
abstract:
- lang: eng
text: Lithium-air batteries have received extraordinary attention recently owing
to their theoretical gravimetric energies being considerably higher than those
of Li-ion batteries. There are, however, significant challenges to practical implementation,
including low energy efficiency, cycle life, and power capability. These are due
primarily to the lack of fundamental understanding of oxygen reduction and evolution
reaction kinetics and parasitic reactions between oxygen redox intermediate species
and nominally inactive battery components such as carbon in the oxygen electrode
and electrolytes. In this article, we discuss recent advances in the mechanistic
understanding of oxygen redox reactions in nonaqueous electrolytes and the search
for electrolytes and electrode materials that are chemically stable in the oxygen
electrode. In addition, methods to protect lithium metal against corrosion by
water and dendrite formation in aqueous lithium-air batteries are discussed. Further
materials innovations lie at the heart of research and development efforts that
are needed to enable the development of lithium-oxygen batteries with enhanced
round-trip efficiency and cycle life.
article_processing_charge: No
article_type: original
author:
- first_name: D.G.
full_name: Kwabi, D.G.
last_name: Kwabi
- first_name: N.
full_name: Ortiz-Vitoriano, N.
last_name: Ortiz-Vitoriano
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Y.
full_name: Chen, Y.
last_name: Chen
- first_name: N.
full_name: Imanishi, N.
last_name: Imanishi
- first_name: P.G.
full_name: Bruce, P.G.
last_name: Bruce
- first_name: Y.
full_name: Shao-Horn, Y.
last_name: Shao-Horn
citation:
ama: Kwabi DG, Ortiz-Vitoriano N, Freunberger SA, et al. Materials challenges in
rechargeable lithium-air batteries. MRS Bulletin. 2014;39(5):443-452. doi:10.1557/mrs.2014.87
apa: Kwabi, D. G., Ortiz-Vitoriano, N., Freunberger, S. A., Chen, Y., Imanishi,
N., Bruce, P. G., & Shao-Horn, Y. (2014). Materials challenges in rechargeable
lithium-air batteries. MRS Bulletin. CUP. https://doi.org/10.1557/mrs.2014.87
chicago: Kwabi, D.G., N. Ortiz-Vitoriano, Stefan Alexander Freunberger, Y. Chen,
N. Imanishi, P.G. Bruce, and Y. Shao-Horn. “Materials Challenges in Rechargeable
Lithium-Air Batteries.” MRS Bulletin. CUP, 2014. https://doi.org/10.1557/mrs.2014.87.
ieee: D. G. Kwabi et al., “Materials challenges in rechargeable lithium-air
batteries,” MRS Bulletin, vol. 39, no. 5. CUP, pp. 443–452, 2014.
ista: Kwabi DG, Ortiz-Vitoriano N, Freunberger SA, Chen Y, Imanishi N, Bruce PG,
Shao-Horn Y. 2014. Materials challenges in rechargeable lithium-air batteries.
MRS Bulletin. 39(5), 443–452.
mla: Kwabi, D. G., et al. “Materials Challenges in Rechargeable Lithium-Air Batteries.”
MRS Bulletin, vol. 39, no. 5, CUP, 2014, pp. 443–52, doi:10.1557/mrs.2014.87.
short: D.G. Kwabi, N. Ortiz-Vitoriano, S.A. Freunberger, Y. Chen, N. Imanishi, P.G.
Bruce, Y. Shao-Horn, MRS Bulletin 39 (2014) 443–452.
date_created: 2020-01-15T12:18:05Z
date_published: 2014-05-01T00:00:00Z
date_updated: 2021-01-12T08:12:54Z
day: '01'
doi: 10.1557/mrs.2014.87
extern: '1'
intvolume: ' 39'
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
page: 443-452
publication: MRS Bulletin
publication_identifier:
issn:
- 0883-7694
- 1938-1425
publication_status: published
publisher: CUP
quality_controlled: '1'
status: public
title: Materials challenges in rechargeable lithium-air batteries
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 39
year: '2014'
...
---
_id: '7301'
abstract:
- lang: eng
text: Several problems arise at the O2 (positive) electrode in the Li-air battery,
including solvent/electrode decomposition and electrode passivation by insulating
Li2O2. Progress partially depends on exploring the basic electrochemistry of O2
reduction. Here we describe the effect of complexing-cations on the electrochemical
reduction of O2 in DMSO in the presence and absence of a Li salt. The solubility
of alkaline peroxides in DMSO is enhanced by the complexing-cations, consistent
with their strong interaction with reduced O2. The complexing-cations also increase
the rate of the 1-electron O2 reduction to O2•– by up to six-fold (k° = 2.4 ×10–3
to 1.5 × 10–2 cm s–1) whether or not Li+ ions are present. In the absence of Li+,
the complexing-cations also promote the reduction of O2•– to O22–. In the presence
of Li+ and complexing-cations, and despite the interaction of the reduced O2 with
the latter, SERS confirms that the product is still Li2O2.
article_processing_charge: No
article_type: original
author:
- first_name: Chunmei
full_name: Li, Chunmei
last_name: Li
- first_name: Olivier
full_name: Fontaine, Olivier
last_name: Fontaine
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Lee
full_name: Johnson, Lee
last_name: Johnson
- first_name: Sylvie
full_name: Grugeon, Sylvie
last_name: Grugeon
- first_name: Stéphane
full_name: Laruelle, Stéphane
last_name: Laruelle
- first_name: Peter G.
full_name: Bruce, Peter G.
last_name: Bruce
- first_name: Michel
full_name: Armand, Michel
last_name: Armand
citation:
ama: 'Li C, Fontaine O, Freunberger SA, et al. Aprotic Li–O2 battery: Influence
of complexing agents on oxygen reduction in an aprotic solvent. The Journal
of Physical Chemistry C. 2014;118(7):3393-3401. doi:10.1021/jp4093805'
apa: 'Li, C., Fontaine, O., Freunberger, S. A., Johnson, L., Grugeon, S., Laruelle,
S., … Armand, M. (2014). Aprotic Li–O2 battery: Influence of complexing agents
on oxygen reduction in an aprotic solvent. The Journal of Physical Chemistry
C. ACS. https://doi.org/10.1021/jp4093805'
chicago: 'Li, Chunmei, Olivier Fontaine, Stefan Alexander Freunberger, Lee Johnson,
Sylvie Grugeon, Stéphane Laruelle, Peter G. Bruce, and Michel Armand. “Aprotic
Li–O2 Battery: Influence of Complexing Agents on Oxygen Reduction in an Aprotic
Solvent.” The Journal of Physical Chemistry C. ACS, 2014. https://doi.org/10.1021/jp4093805.'
ieee: 'C. Li et al., “Aprotic Li–O2 battery: Influence of complexing agents
on oxygen reduction in an aprotic solvent,” The Journal of Physical Chemistry
C, vol. 118, no. 7. ACS, pp. 3393–3401, 2014.'
ista: 'Li C, Fontaine O, Freunberger SA, Johnson L, Grugeon S, Laruelle S, Bruce
PG, Armand M. 2014. Aprotic Li–O2 battery: Influence of complexing agents on oxygen
reduction in an aprotic solvent. The Journal of Physical Chemistry C. 118(7),
3393–3401.'
mla: 'Li, Chunmei, et al. “Aprotic Li–O2 Battery: Influence of Complexing Agents
on Oxygen Reduction in an Aprotic Solvent.” The Journal of Physical Chemistry
C, vol. 118, no. 7, ACS, 2014, pp. 3393–401, doi:10.1021/jp4093805.'
short: C. Li, O. Fontaine, S.A. Freunberger, L. Johnson, S. Grugeon, S. Laruelle,
P.G. Bruce, M. Armand, The Journal of Physical Chemistry C 118 (2014) 3393–3401.
date_created: 2020-01-15T12:17:28Z
date_published: 2014-01-29T00:00:00Z
date_updated: 2021-01-12T08:12:53Z
day: '29'
doi: 10.1021/jp4093805
extern: '1'
intvolume: ' 118'
issue: '7'
language:
- iso: eng
month: '01'
oa_version: None
page: 3393-3401
publication: The Journal of Physical Chemistry C
publication_identifier:
issn:
- 1932-7447
- 1932-7455
publication_status: published
publisher: ACS
quality_controlled: '1'
status: public
title: 'Aprotic Li–O2 battery: Influence of complexing agents on oxygen reduction
in an aprotic solvent'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 118
year: '2014'
...
---
_id: '7300'
abstract:
- lang: eng
text: Photoinduced electron transfer (PET), which causes pH-dependent quenching
of fluorescent dyes, is more effectively introduced by phenolic groups than by
amino groups which have been much more commonly used so far. That is demonstrated
by fluorescence measurements involving several classes of fluorophores. Electrochemical
measurements show that PET in several amino-modified dyes is thermodynamically
favorable, even though it was not experimentally found, underlining the importance
of kinetic aspects to the process. Consequently, the attachment of phenolic groups
allows for fast and simple preparation of a wide selection of fluorescent pH-probes
with tailor-made spectral properties, sensitive ranges, and individual advantages,
so that a large number of applications can be realized. Fluorophores carrying
phenolic groups may also be used for sensing analytes other than pH or molecular
switching and signaling.
article_processing_charge: No
article_type: original
author:
- first_name: Daniel
full_name: Aigner, Daniel
last_name: Aigner
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Martin
full_name: Wilkening, Martin
last_name: Wilkening
- first_name: Robert
full_name: Saf, Robert
last_name: Saf
- first_name: Sergey M.
full_name: Borisov, Sergey M.
last_name: Borisov
- first_name: Ingo
full_name: Klimant, Ingo
last_name: Klimant
citation:
ama: Aigner D, Freunberger SA, Wilkening M, Saf R, Borisov SM, Klimant I. Enhancing
photoinduced electron transfer efficiency of fluorescent pH-probes with halogenated
phenols. Analytical Chemistry. 2014;86(18):9293-9300. doi:10.1021/ac502513g
apa: Aigner, D., Freunberger, S. A., Wilkening, M., Saf, R., Borisov, S. M., &
Klimant, I. (2014). Enhancing photoinduced electron transfer efficiency of fluorescent
pH-probes with halogenated phenols. Analytical Chemistry. ACS. https://doi.org/10.1021/ac502513g
chicago: Aigner, Daniel, Stefan Alexander Freunberger, Martin Wilkening, Robert
Saf, Sergey M. Borisov, and Ingo Klimant. “Enhancing Photoinduced Electron Transfer
Efficiency of Fluorescent PH-Probes with Halogenated Phenols.” Analytical Chemistry.
ACS, 2014. https://doi.org/10.1021/ac502513g.
ieee: D. Aigner, S. A. Freunberger, M. Wilkening, R. Saf, S. M. Borisov, and I.
Klimant, “Enhancing photoinduced electron transfer efficiency of fluorescent pH-probes
with halogenated phenols,” Analytical Chemistry, vol. 86, no. 18. ACS,
pp. 9293–9300, 2014.
ista: Aigner D, Freunberger SA, Wilkening M, Saf R, Borisov SM, Klimant I. 2014.
Enhancing photoinduced electron transfer efficiency of fluorescent pH-probes with
halogenated phenols. Analytical Chemistry. 86(18), 9293–9300.
mla: Aigner, Daniel, et al. “Enhancing Photoinduced Electron Transfer Efficiency
of Fluorescent PH-Probes with Halogenated Phenols.” Analytical Chemistry,
vol. 86, no. 18, ACS, 2014, pp. 9293–300, doi:10.1021/ac502513g.
short: D. Aigner, S.A. Freunberger, M. Wilkening, R. Saf, S.M. Borisov, I. Klimant,
Analytical Chemistry 86 (2014) 9293–9300.
date_created: 2020-01-15T12:17:17Z
date_published: 2014-08-14T00:00:00Z
date_updated: 2021-01-12T08:12:53Z
day: '14'
doi: 10.1021/ac502513g
extern: '1'
intvolume: ' 86'
issue: '18'
language:
- iso: eng
month: '08'
oa_version: None
page: 9293-9300
publication: Analytical Chemistry
publication_identifier:
issn:
- 0003-2700
- 1520-6882
publication_status: published
publisher: ACS
quality_controlled: '1'
status: public
title: Enhancing photoinduced electron transfer efficiency of fluorescent pH-probes
with halogenated phenols
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 86
year: '2014'
...
---
_id: '7361'
abstract:
- lang: eng
text: Bistable switches are fundamental regulatory elements of complex systems,
ranging from electronics to living cells. Designed genetic toggle switches have
been constructed from pairs of natural transcriptional repressors wired to inhibit
one another. The complexity of the engineered regulatory circuits can be increased
using orthogonal transcriptional regulators based on designed DNA-binding domains.
However, a mutual repressor-based toggle switch comprising DNA-binding domains
of transcription-activator-like effectors (TALEs) did not support bistability
in mammalian cells. Here, the challenge of engineering a bistable switch based
on monomeric DNA-binding domains is solved via the introduction of a positive
feedback loop composed of activators based on the same TALE domains as their opposing
repressors and competition for the same DNA operator site. This design introduces
nonlinearity and results in epigenetic bistability. This principle could be used
to employ other monomeric DNA-binding domains such as CRISPR for applications
ranging from reprogramming cells to building digital biological memory.
article_number: '5007'
article_processing_charge: No
article_type: original
author:
- first_name: Tina
full_name: Lebar, Tina
last_name: Lebar
- first_name: Urban
full_name: Bezeljak, Urban
id: 2A58201A-F248-11E8-B48F-1D18A9856A87
last_name: Bezeljak
orcid: 0000-0003-1365-5631
- first_name: Anja
full_name: Golob, Anja
last_name: Golob
- first_name: Miha
full_name: Jerala, Miha
last_name: Jerala
- first_name: Lucija
full_name: Kadunc, Lucija
last_name: Kadunc
- first_name: Boštjan
full_name: Pirš, Boštjan
last_name: Pirš
- first_name: Martin
full_name: Stražar, Martin
last_name: Stražar
- first_name: Dušan
full_name: Vučko, Dušan
last_name: Vučko
- first_name: Uroš
full_name: Zupančič, Uroš
last_name: Zupančič
- first_name: Mojca
full_name: Benčina, Mojca
last_name: Benčina
- first_name: Vida
full_name: Forstnerič, Vida
last_name: Forstnerič
- first_name: Rok
full_name: Gaber, Rok
last_name: Gaber
- first_name: Jan
full_name: Lonzarić, Jan
last_name: Lonzarić
- first_name: Andreja
full_name: Majerle, Andreja
last_name: Majerle
- first_name: Alja
full_name: Oblak, Alja
last_name: Oblak
- first_name: Anže
full_name: Smole, Anže
last_name: Smole
- first_name: Roman
full_name: Jerala, Roman
last_name: Jerala
citation:
ama: Lebar T, Bezeljak U, Golob A, et al. A bistable genetic switch based on designable
DNA-binding domains. Nature Communications. 2014;5(1). doi:10.1038/ncomms6007
apa: Lebar, T., Bezeljak, U., Golob, A., Jerala, M., Kadunc, L., Pirš, B., … Jerala,
R. (2014). A bistable genetic switch based on designable DNA-binding domains.
Nature Communications. Springer Nature. https://doi.org/10.1038/ncomms6007
chicago: Lebar, Tina, Urban Bezeljak, Anja Golob, Miha Jerala, Lucija Kadunc, Boštjan
Pirš, Martin Stražar, et al. “A Bistable Genetic Switch Based on Designable DNA-Binding
Domains.” Nature Communications. Springer Nature, 2014. https://doi.org/10.1038/ncomms6007.
ieee: T. Lebar et al., “A bistable genetic switch based on designable DNA-binding
domains,” Nature Communications, vol. 5, no. 1. Springer Nature, 2014.
ista: Lebar T, Bezeljak U, Golob A, Jerala M, Kadunc L, Pirš B, Stražar M, Vučko
D, Zupančič U, Benčina M, Forstnerič V, Gaber R, Lonzarić J, Majerle A, Oblak
A, Smole A, Jerala R. 2014. A bistable genetic switch based on designable DNA-binding
domains. Nature Communications. 5(1), 5007.
mla: Lebar, Tina, et al. “A Bistable Genetic Switch Based on Designable DNA-Binding
Domains.” Nature Communications, vol. 5, no. 1, 5007, Springer Nature,
2014, doi:10.1038/ncomms6007.
short: T. Lebar, U. Bezeljak, A. Golob, M. Jerala, L. Kadunc, B. Pirš, M. Stražar,
D. Vučko, U. Zupančič, M. Benčina, V. Forstnerič, R. Gaber, J. Lonzarić, A. Majerle,
A. Oblak, A. Smole, R. Jerala, Nature Communications 5 (2014).
date_created: 2020-01-25T15:57:17Z
date_published: 2014-09-29T00:00:00Z
date_updated: 2021-01-12T08:13:15Z
day: '29'
doi: 10.1038/ncomms6007
extern: '1'
external_id:
pmid:
- '25264186'
intvolume: ' 5'
issue: '1'
language:
- iso: eng
month: '09'
oa_version: None
pmid: 1
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: A bistable genetic switch based on designable DNA-binding domains
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2014'
...
---
_id: '7455'
abstract:
- lang: eng
text: 'The reaction between NiO and (0001)- and ([1\bar102])-oriented Al2O3 single
crystals has been investigated on model experimental systems by using the ReflEXAFS
technique. Depth-sensitive information is obtained by collecting data above and
below the critical angle for total reflection. A systematic protocol for data
analysis, based on the recently developed CARD code, was implemented, and a detailed
description of the reactive systems was obtained. In particular, for ([1\bar102])-oriented
Al2O3, the reaction with NiO is almost complete after heating for 6 h at 1273 K,
and an almost uniform layer of spinel is found below a mixed (NiO + spinel) layer
at the very upmost part of the sample. In the case of the (0001)-oriented Al2O3,
for the same temperature and heating time, the reaction shows a lower advancement
degree and a residual fraction of at least 30% NiO is detected in the ReflEXAFS
spectra. '
article_processing_charge: No
article_type: original
author:
- first_name: Tommaso
full_name: Costanzo, Tommaso
id: D93824F4-D9BA-11E9-BB12-F207E6697425
last_name: Costanzo
orcid: 0000-0001-9732-3815
- first_name: Federico
full_name: Benzi, Federico
last_name: Benzi
- first_name: Paolo
full_name: Ghigna, Paolo
last_name: Ghigna
- first_name: Sonia
full_name: Pin, Sonia
last_name: Pin
- first_name: Giorgio
full_name: Spinolo, Giorgio
last_name: Spinolo
- first_name: Francesco
full_name: d'Acapito, Francesco
last_name: d'Acapito
citation:
ama: Costanzo T, Benzi F, Ghigna P, Pin S, Spinolo G, d’Acapito F. Studying the
surface reaction between NiO and Al2O3viatotal reflection EXAFS (ReflEXAFS). Journal
of Synchrotron Radiation. 2014;21(2):395-400. doi:10.1107/s1600577513031299
apa: Costanzo, T., Benzi, F., Ghigna, P., Pin, S., Spinolo, G., & d’Acapito,
F. (2014). Studying the surface reaction between NiO and Al2O3viatotal reflection
EXAFS (ReflEXAFS). Journal of Synchrotron Radiation. International Union
of Crystallography. https://doi.org/10.1107/s1600577513031299
chicago: Costanzo, Tommaso, Federico Benzi, Paolo Ghigna, Sonia Pin, Giorgio Spinolo,
and Francesco d’Acapito. “Studying the Surface Reaction between NiO and Al2O3viatotal
Reflection EXAFS (ReflEXAFS).” Journal of Synchrotron Radiation. International
Union of Crystallography, 2014. https://doi.org/10.1107/s1600577513031299.
ieee: T. Costanzo, F. Benzi, P. Ghigna, S. Pin, G. Spinolo, and F. d’Acapito, “Studying
the surface reaction between NiO and Al2O3viatotal reflection EXAFS (ReflEXAFS),”
Journal of Synchrotron Radiation, vol. 21, no. 2. International Union of
Crystallography, pp. 395–400, 2014.
ista: Costanzo T, Benzi F, Ghigna P, Pin S, Spinolo G, d’Acapito F. 2014. Studying
the surface reaction between NiO and Al2O3viatotal reflection EXAFS (ReflEXAFS).
Journal of Synchrotron Radiation. 21(2), 395–400.
mla: Costanzo, Tommaso, et al. “Studying the Surface Reaction between NiO and Al2O3viatotal
Reflection EXAFS (ReflEXAFS).” Journal of Synchrotron Radiation, vol. 21,
no. 2, International Union of Crystallography, 2014, pp. 395–400, doi:10.1107/s1600577513031299.
short: T. Costanzo, F. Benzi, P. Ghigna, S. Pin, G. Spinolo, F. d’Acapito, Journal
of Synchrotron Radiation 21 (2014) 395–400.
date_created: 2020-02-05T14:14:48Z
date_published: 2014-01-10T00:00:00Z
date_updated: 2023-02-23T13:08:22Z
day: '10'
doi: 10.1107/s1600577513031299
extern: '1'
intvolume: ' 21'
issue: '2'
language:
- iso: eng
month: '01'
oa_version: None
page: 395-400
publication: Journal of Synchrotron Radiation
publication_identifier:
issn:
- 1600-5775
publication_status: published
publisher: International Union of Crystallography
quality_controlled: '1'
status: public
title: Studying the surface reaction between NiO and Al2O3viatotal reflection EXAFS
(ReflEXAFS)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2014'
...
---
_id: '7598'
article_processing_charge: No
article_type: original
author:
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: Hong-Wei
full_name: Xue, Hong-Wei
last_name: Xue
citation:
ama: Tan S, Xue H-W. Casein kinase 1 regulates ethylene synthesis by phosphorylating
and promoting the turnover of ACS5. Cell Reports. 2014;9(5):1692-1702.
doi:10.1016/j.celrep.2014.10.047
apa: Tan, S., & Xue, H.-W. (2014). Casein kinase 1 regulates ethylene synthesis
by phosphorylating and promoting the turnover of ACS5. Cell Reports. Elsevier.
https://doi.org/10.1016/j.celrep.2014.10.047
chicago: Tan, Shutang, and Hong-Wei Xue. “Casein Kinase 1 Regulates Ethylene Synthesis
by Phosphorylating and Promoting the Turnover of ACS5.” Cell Reports. Elsevier,
2014. https://doi.org/10.1016/j.celrep.2014.10.047.
ieee: S. Tan and H.-W. Xue, “Casein kinase 1 regulates ethylene synthesis by phosphorylating
and promoting the turnover of ACS5,” Cell Reports, vol. 9, no. 5. Elsevier,
pp. 1692–1702, 2014.
ista: Tan S, Xue H-W. 2014. Casein kinase 1 regulates ethylene synthesis by phosphorylating
and promoting the turnover of ACS5. Cell Reports. 9(5), 1692–1702.
mla: Tan, Shutang, and Hong-Wei Xue. “Casein Kinase 1 Regulates Ethylene Synthesis
by Phosphorylating and Promoting the Turnover of ACS5.” Cell Reports, vol.
9, no. 5, Elsevier, 2014, pp. 1692–702, doi:10.1016/j.celrep.2014.10.047.
short: S. Tan, H.-W. Xue, Cell Reports 9 (2014) 1692–1702.
date_created: 2020-03-21T16:08:18Z
date_published: 2014-12-11T00:00:00Z
date_updated: 2021-01-12T08:14:24Z
day: '11'
ddc:
- '580'
doi: 10.1016/j.celrep.2014.10.047
extern: '1'
file:
- access_level: open_access
checksum: 23c30de4ac98ce9879fc054121517626
content_type: application/pdf
creator: dernst
date_created: 2020-03-23T12:23:40Z
date_updated: 2020-07-14T12:48:01Z
file_id: '7613'
file_name: 2014_CellPress_Tan.pdf
file_size: 2755808
relation: main_file
file_date_updated: 2020-07-14T12:48:01Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '5'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '12'
oa: 1
oa_version: Published Version
page: 1692-1702
publication: Cell Reports
publication_identifier:
issn:
- 2211-1247
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Casein kinase 1 regulates ethylene synthesis by phosphorylating and promoting
the turnover of ACS5
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2014'
...
---
_id: '768'
abstract:
- lang: eng
text: 'Task allocation is a classic distributed problem in which a set of p potentially
faulty processes must cooperate to perform a set of tasks. This paper considers
a new dynamic version of the problem, in which tasks are injected adversarially
during an asynchronous execution. We give the first asynchronous shared-memory
algorithm for dynamic task allocation, and we prove that our solution is optimal
within logarithmic factors. The main algorithmic idea is a randomized concurrent
data structure called a dynamic to-do tree, which allows processes to pick new
tasks to perform at random from the set of available tasks, and to insert tasks
at random empty locations in the data structure. Our analysis shows that these
properties avoid duplicating work unnecessarily. On the other hand, since the
adversary controls the input as well the scheduling, it can induce executions
where lots of processes contend for a few available tasks, which is inefficient.
However, we prove that every algorithm has the same problem: given an arbitrary
input, if OPT is the worst-case complexity of the optimal algorithm on that input,
then the expected work complexity of our algorithm on the same input is O(OPT
log3 m), where m is an upper bound on the number of tasks that are present in
the system at any given time.'
acknowledgement: "Dan Alistarh - This author was supported by the SNF Postdoctoral
Fellows Program, NSF grant CCF-1217921, DoE ASCR grant ER26116/DE-SC0008923, and
by grants from the Oracle and Intel corporations.\r\nJames Aspnes - Supported in
part by NSF grant CCF-0916389.\r\nMichael A. Bender - This research was supported
in part by NSF grants CCF 1114809, CCF 1217708, IIS 1247726, and IIS 1251137.\r\nRati
Gelashvili - This work was supported in part by NSF grants CCF-1217921, CCF-1301926,
DoE ASCR grant ER26116/DE-SC0008923, and by grants from the Oracle and Intel corporations.\r\nSeth
Gilbert - Supported by Singapore AcRF-2 MOE2011-T2-2-042.\r\n"
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: James
full_name: Aspnes, James
last_name: Aspnes
- first_name: Michael
full_name: Bender, Michael
last_name: Bender
- first_name: Rati
full_name: Gelashvili, Rati
last_name: Gelashvili
- first_name: Seth
full_name: Gilbert, Seth
last_name: Gilbert
citation:
ama: 'Alistarh D-A, Aspnes J, Bender M, Gelashvili R, Gilbert S. Dynamic task allocation
in asynchronous shared memory. In: SIAM; 2014:416-435. doi:10.1137/1.9781611973402.31'
apa: 'Alistarh, D.-A., Aspnes, J., Bender, M., Gelashvili, R., & Gilbert, S.
(2014). Dynamic task allocation in asynchronous shared memory (pp. 416–435). Presented
at the SODA: Symposium on Discrete Algorithms, SIAM. https://doi.org/10.1137/1.9781611973402.31'
chicago: Alistarh, Dan-Adrian, James Aspnes, Michael Bender, Rati Gelashvili, and
Seth Gilbert. “Dynamic Task Allocation in Asynchronous Shared Memory,” 416–35.
SIAM, 2014. https://doi.org/10.1137/1.9781611973402.31.
ieee: 'D.-A. Alistarh, J. Aspnes, M. Bender, R. Gelashvili, and S. Gilbert, “Dynamic
task allocation in asynchronous shared memory,” presented at the SODA: Symposium
on Discrete Algorithms, 2014, pp. 416–435.'
ista: 'Alistarh D-A, Aspnes J, Bender M, Gelashvili R, Gilbert S. 2014. Dynamic
task allocation in asynchronous shared memory. SODA: Symposium on Discrete Algorithms,
416–435.'
mla: Alistarh, Dan-Adrian, et al. Dynamic Task Allocation in Asynchronous Shared
Memory. SIAM, 2014, pp. 416–35, doi:10.1137/1.9781611973402.31.
short: D.-A. Alistarh, J. Aspnes, M. Bender, R. Gelashvili, S. Gilbert, in:, SIAM,
2014, pp. 416–435.
conference:
name: 'SODA: Symposium on Discrete Algorithms'
date_created: 2018-12-11T11:48:24Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-02-23T13:13:52Z
day: '01'
doi: 10.1137/1.9781611973402.31
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 416 - 435
publication_status: published
publisher: SIAM
publist_id: '6886'
status: public
title: Dynamic task allocation in asynchronous shared memory
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '769'
abstract:
- lang: eng
text: 'This article presents the first tight bounds on the time complexity of shared-memory
renaming, a fundamental problem in distributed computing in which a set of processes
need to pick distinct identifiers from a small namespace. We first prove an individual
lower bound of ω(k) process steps for deterministic renaming into any namespace
of size subexponential in k, where k is the number of participants. The bound
is tight: it draws an exponential separation between deterministic and randomized
solutions, and implies new tight bounds for deterministic concurrent fetch-and-increment
counters, queues, and stacks. The proof is based on a new reduction from renaming
to another fundamental problem in distributed computing: mutual exclusion. We
complement this individual bound with a global lower bound of ω(klog(k/c)) on
the total step complexity of renaming into a namespace of size ck, for any c =
1. This result applies to randomized algorithms against a strong adversary, and
helps derive new global lower bounds for randomized approximate counter implementations,
that are tight within logarithmic factors. On the algorithmic side, we give a
protocol that transforms any sorting network into a randomized strong adaptive
renaming algorithm, with expected cost equal to the depth of the sorting network.
This gives a tight adaptive renaming algorithm with expected step complexity O(log
k), where k is the contention in the current execution. This algorithm is the
first to achieve sublinear time, and it is time-optimal as per our randomized
lower bound. Finally, we use this renaming protocol to build monotone-consistent
counters with logarithmic step complexity and linearizable fetch-and-increment
registers with polylogarithmic cost.'
acknowledgement: "The work of J. Aspnes was supported in part by NSF grant CCF-0916389.
The work of S. Gilbert was\r\nsupported by Singapore AcRF-2 MOE 2011-T2-2-042.\r\nK.
Censor-Hillel is a Shalon Fellow. Part of this work was performed while K. Censor-Hillel
was a postdoc at\r\nMIT, supported by the Simons Postdoctoral Fellowship."
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: James
full_name: Aspnes, James
last_name: Aspnes
- first_name: Keren
full_name: Censor Hillel, Keren
last_name: Censor Hillel
- first_name: Seth
full_name: Gilbert, Seth
last_name: Gilbert
- first_name: Rachid
full_name: Guerraoui, Rachid
last_name: Guerraoui
citation:
ama: Alistarh D-A, Aspnes J, Censor Hillel K, Gilbert S, Guerraoui R. Tight bounds
for asynchronous renaming. Journal of the ACM. 2014;61(3). doi:10.1145/2597630
apa: Alistarh, D.-A., Aspnes, J., Censor Hillel, K., Gilbert, S., & Guerraoui,
R. (2014). Tight bounds for asynchronous renaming. Journal of the ACM.
ACM. https://doi.org/10.1145/2597630
chicago: Alistarh, Dan-Adrian, James Aspnes, Keren Censor Hillel, Seth Gilbert,
and Rachid Guerraoui. “Tight Bounds for Asynchronous Renaming.” Journal of
the ACM. ACM, 2014. https://doi.org/10.1145/2597630.
ieee: D.-A. Alistarh, J. Aspnes, K. Censor Hillel, S. Gilbert, and R. Guerraoui,
“Tight bounds for asynchronous renaming,” Journal of the ACM, vol. 61,
no. 3. ACM, 2014.
ista: Alistarh D-A, Aspnes J, Censor Hillel K, Gilbert S, Guerraoui R. 2014. Tight
bounds for asynchronous renaming. Journal of the ACM. 61(3).
mla: Alistarh, Dan-Adrian, et al. “Tight Bounds for Asynchronous Renaming.” Journal
of the ACM, vol. 61, no. 3, ACM, 2014, doi:10.1145/2597630.
short: D.-A. Alistarh, J. Aspnes, K. Censor Hillel, S. Gilbert, R. Guerraoui, Journal
of the ACM 61 (2014).
date_created: 2018-12-11T11:48:24Z
date_published: 2014-05-01T00:00:00Z
date_updated: 2023-02-23T13:14:09Z
day: '01'
doi: 10.1145/2597630
extern: '1'
intvolume: ' 61'
issue: '3'
language:
- iso: eng
month: '05'
oa_version: None
publication: Journal of the ACM
publication_status: published
publisher: ACM
publist_id: '6887'
status: public
title: Tight bounds for asynchronous renaming
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 61
year: '2014'
...
---
_id: '770'
abstract:
- lang: eng
text: 'Dynamic memory reclamation is arguably the biggest open problem in concurrent
data structure design: All known solutions induce high overhead, or must be customized
to the specific data structure by the programmer, or both. This paper presents
StackTrack, the first concurrent memory reclamation scheme that can be applied
automatically by a compiler, while maintaining efficiency. StackTrack eliminates
most of the expensive bookkeeping required for memory reclamation by leveraging
the power of hardware transactional memory (HTM) in a new way: it tracks thread
variables dynamically, and in an atomic fashion. This effectively makes all memory
references visible without having threads pay the overhead of writing out this
information. Our empirical results show that this new approach matches or outperforms
prior, non-automated, techniques.'
acknowledgement: "Dan Alistarh - Part of this work was performed while the
\ author was a Postdoctoral\r\nAssociate a MIT CSAIL, supported in part by NSF
grant CCF-1217921,\r\nDoE ASCR grant ER26116/DE-SC0008923, and by grants from the
Oracle\r\nand Intel corporations.\r\nPatrick Eugester - Supported in part by DARPA
grant N11AP20014 and NSF grant CNS-\r\n1117065.\r\nMaurice Herlihy - Supported by
NSF grant 1301924.\r\nNir Shavit - Supported in part by NSF grants CCF-1217921 and
CCF-1301926, DoE\r\nASCR grant ER26116/DE-SC0008923, and by grants from the Oracle
and\r\nIntel corporations."
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Patrick
full_name: Eugster, Patrick
last_name: Eugster
- first_name: Maurice
full_name: Herlihy, Maurice
last_name: Herlihy
- first_name: Alexander
full_name: Matveev, Alexander
last_name: Matveev
- first_name: Nir
full_name: Shavit, Nir
last_name: Shavit
citation:
ama: 'Alistarh D-A, Eugster P, Herlihy M, Matveev A, Shavit N. StackTrack: An automated
transactional approach to concurrent memory reclamation. In: ACM; 2014. doi:10.1145/2592798.2592808'
apa: 'Alistarh, D.-A., Eugster, P., Herlihy, M., Matveev, A., & Shavit, N. (2014).
StackTrack: An automated transactional approach to concurrent memory reclamation.
Presented at the EuroSys: European Conference on Computer Systems, ACM. https://doi.org/10.1145/2592798.2592808'
chicago: 'Alistarh, Dan-Adrian, Patrick Eugster, Maurice Herlihy, Alexander Matveev,
and Nir Shavit. “StackTrack: An Automated Transactional Approach to Concurrent
Memory Reclamation.” ACM, 2014. https://doi.org/10.1145/2592798.2592808.'
ieee: 'D.-A. Alistarh, P. Eugster, M. Herlihy, A. Matveev, and N. Shavit, “StackTrack:
An automated transactional approach to concurrent memory reclamation,” presented
at the EuroSys: European Conference on Computer Systems, 2014.'
ista: 'Alistarh D-A, Eugster P, Herlihy M, Matveev A, Shavit N. 2014. StackTrack:
An automated transactional approach to concurrent memory reclamation. EuroSys:
European Conference on Computer Systems.'
mla: 'Alistarh, Dan-Adrian, et al. StackTrack: An Automated Transactional Approach
to Concurrent Memory Reclamation. ACM, 2014, doi:10.1145/2592798.2592808.'
short: D.-A. Alistarh, P. Eugster, M. Herlihy, A. Matveev, N. Shavit, in:, ACM,
2014.
conference:
name: 'EuroSys: European Conference on Computer Systems'
date_created: 2018-12-11T11:48:24Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-02-23T13:14:25Z
day: '01'
doi: 10.1145/2592798.2592808
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
publication_status: published
publisher: ACM
publist_id: '6888'
status: public
title: 'StackTrack: An automated transactional approach to concurrent memory reclamation'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '771'
abstract:
- lang: eng
text: 'We consider the following natural problem: n failure-prone servers, communicating
synchronously through message passing, must assign themselves one-to-one to n
distinct items. Existing literature suggests two possible approaches to this problem.
First, model it as an instance of tight renaming in synchronous message-passing
systems; for deterministic solutions, a tight bound of ©(logn) communication rounds
is known. Second, model the scenario as an instance of randomized load-balancing,
for which elegant sub-logarithmic solutions exist. However, careful examination
reveals that known load-balancing schemes do not apply to our scenario, because
they either do not tolerate faults or do not ensure one-to-one allocation. It
is thus natural to ask if sublogarithmic solutions exist for this apparently simple
but intriguing problem. In this paper, we combine the two approaches to provide
a new randomized solution for tight renaming, which terminates in O (log log n)
communication rounds with high probability, against a strong adaptive adversary.
Our solution, called Balls-into-Leaves, combines the deterministic approach with
a new randomized scheme to obtain perfectly balanced allocations. The algorithm
arranges the items as leaves of a tree, and participants repeatedly perform random
choices among the leaves. The algorithm exchanges information in each round to
split the participants into progressively smaller groups whose random choices
do not conflict. We then extend the algorithm to terminate early in O(log log)
rounds w.h.p., where is the actual number of failures. These results imply an
exponential separation between deterministic and randomized algorithms for the
tight renaming problem in message-passing systems.'
acknowledgement: "Dan Alistarh was partially supported by the SNF Post-\r\ndoctoral
Fellows Program, NSF grant CCF-1217921, DoE\r\nASCR grant ER26116/DE-SC0008923,
and by grants from\r\nthe Oracle and Intel corporations.\r\nOksana Denysyuk and
Lu ́ıs Rodrigues were partially supported by Funda ̧c ̃ao para a Ciˆencia e Tecnologia
(FCT) via\r\nthe project PEPITA (PTDC/EEI-SCR/2776/2012) and via\r\nthe INESC-ID
multi-annual funding through the PIDDAC\r\nProgram fund grant, under project PEst-OE/EEI/LA0021/\r\n2013.\r\nNir
Shavit was supported in part by NSF grants CCF-1217921 and CCF-1301926, DoE ASCR
grant ER26116/DE-SC0008923, and by grants from the Oracle and Intel corporations."
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Oksana
full_name: Denysyuk, Oksana
last_name: Denysyuk
- first_name: Luís
full_name: Rodrígues, Luís
last_name: Rodrígues
- first_name: Nir
full_name: Shavit, Nir
last_name: Shavit
citation:
ama: 'Alistarh D-A, Denysyuk O, Rodrígues L, Shavit N. Balls-into-Leaves: Sub-logarithmic
renaming in synchronous message-passing systems. In: ACM; 2014:232-241. doi:10.1145/2611462.2611499'
apa: 'Alistarh, D.-A., Denysyuk, O., Rodrígues, L., & Shavit, N. (2014). Balls-into-Leaves:
Sub-logarithmic renaming in synchronous message-passing systems (pp. 232–241).
Presented at the PODC: Principles of Distributed Computing, ACM. https://doi.org/10.1145/2611462.2611499'
chicago: 'Alistarh, Dan-Adrian, Oksana Denysyuk, Luís Rodrígues, and Nir Shavit.
“Balls-into-Leaves: Sub-Logarithmic Renaming in Synchronous Message-Passing Systems,”
232–41. ACM, 2014. https://doi.org/10.1145/2611462.2611499.'
ieee: 'D.-A. Alistarh, O. Denysyuk, L. Rodrígues, and N. Shavit, “Balls-into-Leaves:
Sub-logarithmic renaming in synchronous message-passing systems,” presented at
the PODC: Principles of Distributed Computing, 2014, pp. 232–241.'
ista: 'Alistarh D-A, Denysyuk O, Rodrígues L, Shavit N. 2014. Balls-into-Leaves:
Sub-logarithmic renaming in synchronous message-passing systems. PODC: Principles
of Distributed Computing, 232–241.'
mla: 'Alistarh, Dan-Adrian, et al. Balls-into-Leaves: Sub-Logarithmic Renaming
in Synchronous Message-Passing Systems. ACM, 2014, pp. 232–41, doi:10.1145/2611462.2611499.'
short: D.-A. Alistarh, O. Denysyuk, L. Rodrígues, N. Shavit, in:, ACM, 2014, pp.
232–241.
conference:
name: 'PODC: Principles of Distributed Computing'
date_created: 2018-12-11T11:48:25Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-02-23T13:14:49Z
day: '01'
doi: 10.1145/2611462.2611499
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 232 - 241
publication_status: published
publisher: ACM
publist_id: '6884'
status: public
title: 'Balls-into-Leaves: Sub-logarithmic renaming in synchronous message-passing
systems'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '772'
abstract:
- lang: eng
text: Lock-free concurrent algorithms guarantee that some concurrent operation will
always make progress in a finite number of steps. Yet programmers prefer to treat
concurrent code as if it were wait-free, guaranteeing that all operations always
make progress. Unfortunately, designing wait-free algorithms is generally a very
complex task, and the resulting algorithms are not always efficient. While obtaining
efficient wait-free algorithms has been a long-time goal for the theory community,
most non-blocking commercial code is only lock-free. This paper suggests a simple
solution to this problem. We show that, for a large class of lock-free algorithms,
under scheduling conditions which approximate those found in commercial hardware
architectures, lock-free algorithms behave as if they are wait-free. In other
words, programmers can keep on designing simple lock-free algorithms instead of
complex wait-free ones, and in practice, they will get wait-free progress. Our
main contribution is a new way of analyzing a general class of lock-free algorithms
under a stochastic scheduler. Our analysis relates the individual performance
of processes with the global performance of the system using Markov chain lifting
between a complex per-process chain and a simpler system progress chain. We show
that lock-free algorithms are not only wait-free with probability 1, but that
in fact a general subset of lock-free algorithms can be closely bounded in terms
of the average number of steps required until an operation completes. To the best
of our knowledge, this is the first attempt to analyze progress conditions, typically
stated in relation to a worst case adversary, in a stochastic model capturing
their expected asymptotic behavior.
acknowledgement: "Dan Alistarh - Part of this work was performed while the author
was a Postdoctoral Associate at MIT CSAIL, where he was supported by SNF\r\nPostdoctoral
Fellows Program, NSF grant CCF-1217921, DoE\r\nASCR grant ER26116/DE-SC0008923,
and by grants from the Oracle and Intel corporations.\r\nKeron Censor-Hillel - Shalon
Fellow\r\nNir Shavit - This work was supported in part by NSF grants CCF-1217921
and\r\nCCF-1301926, DoE ASCR grant ER26116/DE-SC0008923, and\r\nby grants from the
Oracle and Intel corporations."
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Keren
full_name: Censor Hillel, Keren
last_name: Censor Hillel
- first_name: Nir
full_name: Shavit, Nir
last_name: Shavit
citation:
ama: 'Alistarh D-A, Censor Hillel K, Shavit N. Are lock-free concurrent algorithms
practically wait-free? In: ACM; 2014:714-723. doi:10.1145/2591796.2591836'
apa: 'Alistarh, D.-A., Censor Hillel, K., & Shavit, N. (2014). Are lock-free
concurrent algorithms practically wait-free? (pp. 714–723). Presented at the STOC:
Symposium on Theory of Computing, ACM. https://doi.org/10.1145/2591796.2591836'
chicago: Alistarh, Dan-Adrian, Keren Censor Hillel, and Nir Shavit. “Are Lock-Free
Concurrent Algorithms Practically Wait-Free?,” 714–23. ACM, 2014. https://doi.org/10.1145/2591796.2591836.
ieee: 'D.-A. Alistarh, K. Censor Hillel, and N. Shavit, “Are lock-free concurrent
algorithms practically wait-free?,” presented at the STOC: Symposium on Theory
of Computing, 2014, pp. 714–723.'
ista: 'Alistarh D-A, Censor Hillel K, Shavit N. 2014. Are lock-free concurrent algorithms
practically wait-free? STOC: Symposium on Theory of Computing, 714–723.'
mla: Alistarh, Dan-Adrian, et al. Are Lock-Free Concurrent Algorithms Practically
Wait-Free? ACM, 2014, pp. 714–23, doi:10.1145/2591796.2591836.
short: D.-A. Alistarh, K. Censor Hillel, N. Shavit, in:, ACM, 2014, pp. 714–723.
conference:
name: 'STOC: Symposium on Theory of Computing'
date_created: 2018-12-11T11:48:25Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-02-23T13:15:13Z
day: '01'
doi: 10.1145/2591796.2591836
extern: '1'
external_id:
arxiv:
- '1311.3200'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1311.3200
month: '01'
oa: 1
oa_version: Preprint
page: 714 - 723
publication_status: published
publisher: ACM
publist_id: '6885'
status: public
title: Are lock-free concurrent algorithms practically wait-free?
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '773'
abstract:
- lang: eng
text: "We describe a new randomized consensus protocol with expected message complexity
O(n2log2n) when fewer than n/2 processes may fail by crashing. This is an almost-linear
improvement over the best previously known protocol, and within logarithmic factors
of a known Ω(n2) message lower bound. The protocol further ensures that no process
sends more than O(n log3n) messages in expectation, which is again within logarithmic
factors of optimal.We also present a generalization of the algorithm to an arbitrary
number of failures t, which uses expected O(nt + t2log2t) total messages. Our
protocol uses messages of size O(log n), and can therefore scale to large networks.\r\n\r\nWe
consider the problem of consensus in the challenging classic model. In this model,
the adversary is adaptive; it can choose which processors crash at any point during
the course of the algorithm. Further, communication is via asynchronous message
passing: there is no known upper bound on the time to send a message from one
processor to another, and all messages and coin flips are seen by the adversary.\r\n\r\nOur
approach is to build a message-efficient, resilient mechanism for aggregating
individual processor votes, implementing the message-passing equivalent of a weak
shared coin. Roughly, in our protocol, a processor first announces its votes to
small groups, then propagates them to increasingly larger groups as it generates
more and more votes. To bound the number of messages that an individual process
might have to send or receive, the protocol progressively increases the weight
of generated votes. The main technical challenge is bounding the impact of votes
that are still “in flight” (generated, but not fully propagated) on the final
outcome of the shared coin, especially since such votes might have different weights.
We achieve this by leveraging the structure of the algorithm, and a technical
argument based on martingale concentration bounds. Overall, we show that it is
possible to build an efficient message-passing implementation of a shared coin,
and in the process (almost-optimally) solve the classic consensus problem in the
asynchronous message-passing model."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: James
full_name: Aspnes, James
last_name: Aspnes
- first_name: Valerie
full_name: King, Valerie
last_name: King
- first_name: Jared
full_name: Saia, Jared
last_name: Saia
citation:
ama: 'Alistarh D-A, Aspnes J, King V, Saia J. Communication-efficient randomized
consensus. In: Kuhn F, ed. Vol 8784. Springer; 2014:61-75. doi:10.1007/978-3-662-45174-8_5'
apa: 'Alistarh, D.-A., Aspnes, J., King, V., & Saia, J. (2014). Communication-efficient
randomized consensus. In F. Kuhn (Ed.) (Vol. 8784, pp. 61–75). Presented at the
DISC: Distributed Computing, Austin, USA: Springer. https://doi.org/10.1007/978-3-662-45174-8_5'
chicago: Alistarh, Dan-Adrian, James Aspnes, Valerie King, and Jared Saia. “Communication-Efficient
Randomized Consensus.” edited by Fabian Kuhn, 8784:61–75. Springer, 2014. https://doi.org/10.1007/978-3-662-45174-8_5.
ieee: 'D.-A. Alistarh, J. Aspnes, V. King, and J. Saia, “Communication-efficient
randomized consensus,” presented at the DISC: Distributed Computing, Austin, USA,
2014, vol. 8784, pp. 61–75.'
ista: 'Alistarh D-A, Aspnes J, King V, Saia J. 2014. Communication-efficient randomized
consensus. DISC: Distributed Computing, LNCS, vol. 8784, 61–75.'
mla: Alistarh, Dan-Adrian, et al. Communication-Efficient Randomized Consensus.
Edited by Fabian Kuhn, vol. 8784, Springer, 2014, pp. 61–75, doi:10.1007/978-3-662-45174-8_5.
short: D.-A. Alistarh, J. Aspnes, V. King, J. Saia, in:, F. Kuhn (Ed.), Springer,
2014, pp. 61–75.
conference:
end_date: 2014-10-15
location: Austin, USA
name: 'DISC: Distributed Computing'
start_date: 2014-10-12
date_created: 2018-12-11T11:48:25Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-02-23T13:15:36Z
day: '01'
doi: 10.1007/978-3-662-45174-8_5
editor:
- first_name: Fabian
full_name: Kuhn, Fabian
last_name: Kuhn
extern: '1'
intvolume: ' 8784'
language:
- iso: eng
month: '01'
oa_version: None
page: 61 - 75
publication_status: published
publisher: Springer
publist_id: '6881'
status: public
title: Communication-efficient randomized consensus
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8784
year: '2014'
...
---
_id: '774'
abstract:
- lang: eng
text: Lock-free concurrent algorithms guarantee that some concurrent operation will
always make progress in a finite number of steps. Yet programmers would prefer
to treat concurrent code as if it were wait-free, guaranteeing that all operations
always make progress. Unfortunately, designing wait-free algorithms is in general
a complex undertaking, and the resulting algorithms are not always efficient,
so most non-blocking commercial code is only lock-free, and the design of efficient
wait-free algorithms has been left to the academic community. In [2], we suggest
a solution to this problem. We show that, for a large class of lock-free algorithms,
under scheduling conditions which approximate those found in commercial hardware
architectures, lock-free algorithms behave as if they are wait-free. In other
words, programmers can keep on designing simple lock-free algorithms instead of
complex wait-free ones, and in practice, they will get wait-free progress. Our
main contribution is a new way of analyzing a general class of lock-free algorithms
under a stochastic scheduler. Our analysis relates the individual performance
of processes with the global performance of the system using Markov chain lifting
between a complex per-process chain and a simpler system progress chain. We show
that lock-free algorithms are not only wait-free with probability 1, but that
in fact a broad subset of lock-free algorithms can be closely bounded in terms
of the average number of steps required until an operation completes.
acknowledgement: "Dan Alistarh - Part of this work was performed while the
\ author was a\r\nPostdoctoral Associate at MIT CSAIL, where he was supported
\ by SNF Postdoctoral Fellows Program, NSF grant\r\nCCF-1217921, DoE ASCR
grant ER26116/DE-SC0008923,\r\nand by grants from the Oracle and Intel corporations.\r\nKeren
Censor-Hille - Shalon Fellow\r\nNir Shavit - This work was supported in part
\ by NSF grants CCF-1217921 and CCF-1301926, DoE ASCR grant ER26116/DE-\r\nSC0008923,
and by grants from the Oracle and Intel corporations."
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Keren
full_name: Censor Hille, Keren
last_name: Censor Hille
- first_name: Nir
full_name: Shavit, Nir
last_name: Shavit
citation:
ama: 'Alistarh D-A, Censor Hille K, Shavit N. Brief announcement: Are lock-free
concurrent algorithms practically wait-free? In: ACM; 2014:50-52. doi:10.1145/2611462.2611502'
apa: 'Alistarh, D.-A., Censor Hille, K., & Shavit, N. (2014). Brief announcement:
Are lock-free concurrent algorithms practically wait-free? (pp. 50–52). Presented
at the PODC: Principles of Distributed Computing, ACM. https://doi.org/10.1145/2611462.2611502'
chicago: 'Alistarh, Dan-Adrian, Keren Censor Hille, and Nir Shavit. “Brief Announcement:
Are Lock-Free Concurrent Algorithms Practically Wait-Free?,” 50–52. ACM, 2014.
https://doi.org/10.1145/2611462.2611502.'
ieee: 'D.-A. Alistarh, K. Censor Hille, and N. Shavit, “Brief announcement: Are
lock-free concurrent algorithms practically wait-free?,” presented at the PODC:
Principles of Distributed Computing, 2014, pp. 50–52.'
ista: 'Alistarh D-A, Censor Hille K, Shavit N. 2014. Brief announcement: Are lock-free
concurrent algorithms practically wait-free? PODC: Principles of Distributed Computing,
50–52.'
mla: 'Alistarh, Dan-Adrian, et al. Brief Announcement: Are Lock-Free Concurrent
Algorithms Practically Wait-Free? ACM, 2014, pp. 50–52, doi:10.1145/2611462.2611502.'
short: D.-A. Alistarh, K. Censor Hille, N. Shavit, in:, ACM, 2014, pp. 50–52.
conference:
name: 'PODC: Principles of Distributed Computing'
date_created: 2018-12-11T11:48:26Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-02-23T13:15:54Z
day: '01'
doi: 10.1145/2611462.2611502
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 50 - 52
publication_status: published
publisher: ACM
publist_id: '6882'
status: public
title: 'Brief announcement: Are lock-free concurrent algorithms practically wait-free?'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '775'
abstract:
- lang: eng
text: 'The long-lived renaming problem appears in shared-memory systems where a
set of threads need to register and deregister frequently from the computation,
while concurrent operations scan the set of currently registered threads. Instances
of this problem show up in concurrent implementations of transactional memory,
flat combining, thread barriers, and memory reclamation schemes for lock-free
data structures. In this paper, we analyze a randomized solution for long-lived
renaming. The algorithmic technique we consider, called the Level Array, has previously
been used for hashing and one-shot (single-use) renaming. Our main contribution
is to prove that, in long-lived executions, where processes may register and deregister
polynomially many times, the technique guarantees constant steps on average and
O (log log n) steps with high probability for registering, unit cost for deregistering,
and O (n) steps for collect queries, where n is an upper bound on the number of
processes that may be active at any point in time. We also show that the algorithm
has the surprising property that it is self-healing: under reasonable assumptions
on the schedule, operations running while the data structure is in a degraded
state implicitly help the data structure re-balance itself. This subtle mechanism
obviates the need for expensive periodic rebuilding procedures. Our benchmarks
validate this approach, showing that, for typical use parameters, the average
number of steps a process takes to register is less than two and the worst-case
number of steps is bounded by six, even in executions with billions of operations.
We contrast this with other randomized implementations, whose worst-case behavior
we show to be unreliable, and with deterministic implementations, whose cost is
linear in n.'
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Justin
full_name: Kopinsky, Justin
last_name: Kopinsky
- first_name: Alexander
full_name: Matveev, Alexander
last_name: Matveev
- first_name: Nir
full_name: Shavit, Nir
last_name: Shavit
citation:
ama: 'Alistarh D-A, Kopinsky J, Matveev A, Shavit N. The levelarray: A fast, practical
long-lived renaming algorithm. In: IEEE; 2014:348-357. doi:10.1109/ICDCS.2014.43'
apa: 'Alistarh, D.-A., Kopinsky, J., Matveev, A., & Shavit, N. (2014). The levelarray:
A fast, practical long-lived renaming algorithm (pp. 348–357). Presented at the
ICDCS: International Conference on Distributed Computing Systems, IEEE. https://doi.org/10.1109/ICDCS.2014.43'
chicago: 'Alistarh, Dan-Adrian, Justin Kopinsky, Alexander Matveev, and Nir Shavit.
“The Levelarray: A Fast, Practical Long-Lived Renaming Algorithm,” 348–57. IEEE,
2014. https://doi.org/10.1109/ICDCS.2014.43.'
ieee: 'D.-A. Alistarh, J. Kopinsky, A. Matveev, and N. Shavit, “The levelarray:
A fast, practical long-lived renaming algorithm,” presented at the ICDCS: International
Conference on Distributed Computing Systems, 2014, pp. 348–357.'
ista: 'Alistarh D-A, Kopinsky J, Matveev A, Shavit N. 2014. The levelarray: A fast,
practical long-lived renaming algorithm. ICDCS: International Conference on Distributed
Computing Systems, 348–357.'
mla: 'Alistarh, Dan-Adrian, et al. The Levelarray: A Fast, Practical Long-Lived
Renaming Algorithm. IEEE, 2014, pp. 348–57, doi:10.1109/ICDCS.2014.43.'
short: D.-A. Alistarh, J. Kopinsky, A. Matveev, N. Shavit, in:, IEEE, 2014, pp.
348–357.
conference:
name: 'ICDCS: International Conference on Distributed Computing Systems'
date_created: 2018-12-11T11:48:26Z
date_published: 2014-08-29T00:00:00Z
date_updated: 2023-02-23T13:16:18Z
day: '29'
doi: 10.1109/ICDCS.2014.43
extern: '1'
external_id:
arxiv:
- '1405.5461'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1405.5461
month: '08'
oa: 1
oa_version: Preprint
page: 348 - 357
publication_status: published
publisher: IEEE
publist_id: '6883'
status: public
title: 'The levelarray: A fast, practical long-lived renaming algorithm'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '7743'
abstract:
- lang: eng
text: Experimental studies have demonstrated that environmental variation can create
genotype‐environment interactions (GEIs) in the traits involved in sexual selection.
Understanding the genetic architecture of phenotype across environments will require
statistical tests that can describe both changes in genetic variance and covariance
across environments. This chapter outlines the theoretical framework for the processes
of sexual selection in the wild, identifying key parameters in wild systems, and
highlighting the potential effects of the environment. It describes the proposed
approaches for the estimation of these key parameters in a quantitative genetic
framework within naturally occurring pedigreed populations. The chapter provides
a worked example for a range of analysis methods. It aims to provide an overview
of the analytical methods that can be used to model GEIs for traits involved in
sexual selection in naturally occurring pedigreed populations.
article_processing_charge: No
author:
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Anna
full_name: Qvarnström, Anna
last_name: Qvarnström
citation:
ama: 'Robinson MR, Qvarnström A. Influence of the environment on the genetic architecture
of traits involved in sexual selection within wild populations. In: Hunt J, Hosken
D, eds. Genotype-by-Environment Interactions and Sexual Selection. Chichester,
UK: Wiley; 2014:137-168. doi:10.1002/9781118912591.ch6'
apa: 'Robinson, M. R., & Qvarnström, A. (2014). Influence of the environment
on the genetic architecture of traits involved in sexual selection within wild
populations. In J. Hunt & D. Hosken (Eds.), Genotype-by-Environment Interactions
and Sexual Selection (pp. 137–168). Chichester, UK: Wiley. https://doi.org/10.1002/9781118912591.ch6'
chicago: 'Robinson, Matthew Richard, and Anna Qvarnström. “Influence of the Environment
on the Genetic Architecture of Traits Involved in Sexual Selection within Wild
Populations.” In Genotype-by-Environment Interactions and Sexual Selection,
edited by John Hunt and David Hosken, 137–68. Chichester, UK: Wiley, 2014. https://doi.org/10.1002/9781118912591.ch6.'
ieee: 'M. R. Robinson and A. Qvarnström, “Influence of the environment on the genetic
architecture of traits involved in sexual selection within wild populations,”
in Genotype-by-Environment Interactions and Sexual Selection, J. Hunt and
D. Hosken, Eds. Chichester, UK: Wiley, 2014, pp. 137–168.'
ista: 'Robinson MR, Qvarnström A. 2014.Influence of the environment on the genetic
architecture of traits involved in sexual selection within wild populations. In:
Genotype-by-Environment Interactions and Sexual Selection. , 137–168.'
mla: Robinson, Matthew Richard, and Anna Qvarnström. “Influence of the Environment
on the Genetic Architecture of Traits Involved in Sexual Selection within Wild
Populations.” Genotype-by-Environment Interactions and Sexual Selection,
edited by John Hunt and David Hosken, Wiley, 2014, pp. 137–68, doi:10.1002/9781118912591.ch6.
short: M.R. Robinson, A. Qvarnström, in:, J. Hunt, D. Hosken (Eds.), Genotype-by-Environment
Interactions and Sexual Selection, Wiley, Chichester, UK, 2014, pp. 137–168.
date_created: 2020-04-30T10:58:39Z
date_published: 2014-08-29T00:00:00Z
date_updated: 2021-01-12T08:15:13Z
day: '29'
doi: 10.1002/9781118912591.ch6
editor:
- first_name: John
full_name: Hunt, John
last_name: Hunt
- first_name: David
full_name: Hosken, David
last_name: Hosken
extern: '1'
language:
- iso: eng
month: '08'
oa_version: None
page: 137-168
place: Chichester, UK
publication: Genotype-by-Environment Interactions and Sexual Selection
publication_identifier:
eisbn:
- '9781118912591'
isbn:
- '9780470671795'
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Influence of the environment on the genetic architecture of traits involved
in sexual selection within wild populations
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '7744'
article_processing_charge: No
article_type: original
author:
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Naomi R.
full_name: Wray, Naomi R.
last_name: Wray
- first_name: Peter M.
full_name: Visscher, Peter M.
last_name: Visscher
citation:
ama: Robinson MR, Wray NR, Visscher PM. Explaining additional genetic variation
in complex traits. Trends in Genetics. 2014;30(4):124-132. doi:10.1016/j.tig.2014.02.003
apa: Robinson, M. R., Wray, N. R., & Visscher, P. M. (2014). Explaining additional
genetic variation in complex traits. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2014.02.003
chicago: Robinson, Matthew Richard, Naomi R. Wray, and Peter M. Visscher. “Explaining
Additional Genetic Variation in Complex Traits.” Trends in Genetics. Elsevier,
2014. https://doi.org/10.1016/j.tig.2014.02.003.
ieee: M. R. Robinson, N. R. Wray, and P. M. Visscher, “Explaining additional genetic
variation in complex traits,” Trends in Genetics, vol. 30, no. 4. Elsevier,
pp. 124–132, 2014.
ista: Robinson MR, Wray NR, Visscher PM. 2014. Explaining additional genetic variation
in complex traits. Trends in Genetics. 30(4), 124–132.
mla: Robinson, Matthew Richard, et al. “Explaining Additional Genetic Variation
in Complex Traits.” Trends in Genetics, vol. 30, no. 4, Elsevier, 2014,
pp. 124–32, doi:10.1016/j.tig.2014.02.003.
short: M.R. Robinson, N.R. Wray, P.M. Visscher, Trends in Genetics 30 (2014) 124–132.
date_created: 2020-04-30T10:58:58Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2021-01-12T08:15:14Z
day: '01'
doi: 10.1016/j.tig.2014.02.003
extern: '1'
intvolume: ' 30'
issue: '4'
language:
- iso: eng
month: '04'
oa_version: None
page: 124-132
publication: Trends in Genetics
publication_identifier:
issn:
- 0168-9525
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Explaining additional genetic variation in complex traits
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2014'
...
---
_id: '7768'
abstract:
- lang: eng
text: We investigate the vibrational modes of quasi-two-dimensional disordered colloidal
packings of hard colloidal spheres with short-range attractions as a function
of packing fraction. Certain properties of the vibrational density of states (vDOS)
are shown to correlate with the density and structure of the samples (i.e., in
sparsely versus densely packed samples). Specifically, a crossover from dense
glassy to sparse gel-like states is suggested by an excess of phonon modes at
low frequency and by a variation in the slope of the vDOS with frequency at low
frequency. This change in phonon mode distribution is demonstrated to arise largely
from localized vibrations that involve individual and/or small clusters of particles
with few local bonds. Conventional order parameters and void statistics did not
exhibit obvious gel-glass signatures as a function of volume fraction. These mode
behaviors and accompanying structural insights offer a potentially new set of
indicators for identification of glass-gel transitions and for assignment of gel-like
versus glass-like character to a disordered solid material.
article_number: '062305'
article_processing_charge: No
article_type: original
author:
- first_name: Matthew A.
full_name: Lohr, Matthew A.
last_name: Lohr
- first_name: Tim
full_name: Still, Tim
last_name: Still
- first_name: Raman
full_name: Ganti, Raman
last_name: Ganti
- first_name: Matthew D.
full_name: Gratale, Matthew D.
last_name: Gratale
- first_name: Zoey S.
full_name: Davidson, Zoey S.
last_name: Davidson
- first_name: Kevin B.
full_name: Aptowicz, Kevin B.
last_name: Aptowicz
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Daniel M.
full_name: Sussman, Daniel M.
last_name: Sussman
- first_name: A. G.
full_name: Yodh, A. G.
last_name: Yodh
citation:
ama: Lohr MA, Still T, Ganti R, et al. Vibrational and structural signatures of
the crossover between dense glassy and sparse gel-like attractive colloidal packings.
Physical Review E. 2014;90(6). doi:10.1103/physreve.90.062305
apa: Lohr, M. A., Still, T., Ganti, R., Gratale, M. D., Davidson, Z. S., Aptowicz,
K. B., … Yodh, A. G. (2014). Vibrational and structural signatures of the crossover
between dense glassy and sparse gel-like attractive colloidal packings. Physical
Review E. American Physical Society. https://doi.org/10.1103/physreve.90.062305
chicago: Lohr, Matthew A., Tim Still, Raman Ganti, Matthew D. Gratale, Zoey S. Davidson,
Kevin B. Aptowicz, Carl Peter Goodrich, Daniel M. Sussman, and A. G. Yodh. “Vibrational
and Structural Signatures of the Crossover between Dense Glassy and Sparse Gel-like
Attractive Colloidal Packings.” Physical Review E. American Physical Society,
2014. https://doi.org/10.1103/physreve.90.062305.
ieee: M. A. Lohr et al., “Vibrational and structural signatures of the crossover
between dense glassy and sparse gel-like attractive colloidal packings,” Physical
Review E, vol. 90, no. 6. American Physical Society, 2014.
ista: Lohr MA, Still T, Ganti R, Gratale MD, Davidson ZS, Aptowicz KB, Goodrich
CP, Sussman DM, Yodh AG. 2014. Vibrational and structural signatures of the crossover
between dense glassy and sparse gel-like attractive colloidal packings. Physical
Review E. 90(6), 062305.
mla: Lohr, Matthew A., et al. “Vibrational and Structural Signatures of the Crossover
between Dense Glassy and Sparse Gel-like Attractive Colloidal Packings.” Physical
Review E, vol. 90, no. 6, 062305, American Physical Society, 2014, doi:10.1103/physreve.90.062305.
short: M.A. Lohr, T. Still, R. Ganti, M.D. Gratale, Z.S. Davidson, K.B. Aptowicz,
C.P. Goodrich, D.M. Sussman, A.G. Yodh, Physical Review E 90 (2014).
date_created: 2020-04-30T11:41:54Z
date_published: 2014-12-05T00:00:00Z
date_updated: 2021-01-12T08:15:24Z
day: '05'
doi: 10.1103/physreve.90.062305
extern: '1'
intvolume: ' 90'
issue: '6'
language:
- iso: eng
month: '12'
oa_version: None
publication: Physical Review E
publication_identifier:
issn:
- 1539-3755
- 1550-2376
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Vibrational and structural signatures of the crossover between dense glassy
and sparse gel-like attractive colloidal packings
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 90
year: '2014'
...
---
_id: '7771'
abstract:
- lang: eng
text: 'In their Letter, Schreck, Bertrand, O''Hern and Shattuck [Phys. Rev. Lett.
107, 078301 (2011)] study nonlinearities in jammed particulate systems that arise
when contacts are altered. They conclude that there is "no harmonic regime in
the large system limit for all compressions" and "at jamming onset for any system
size." Their argument rests on the claim that for finite-range repulsive potentials,
of the form used in studies of jamming, the breaking or forming of a single contact
is sufficient to destroy the linear regime. We dispute these conclusions and argue
that linear response is both justified and essential for understanding the nature
of the jammed solid. '
article_number: '049801 '
article_processing_charge: No
article_type: letter_note
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: Sidney R.
full_name: Nagel, Sidney R.
last_name: Nagel
citation:
ama: Goodrich CP, Liu AJ, Nagel SR. Comment on “Repulsive contact interactions make
jammed particulate systems inherently nonharmonic.” Physical Review Letters.
2014;112(4). doi:10.1103/physrevlett.112.049801
apa: Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2014). Comment on “Repulsive
contact interactions make jammed particulate systems inherently nonharmonic.”
Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.112.049801
chicago: Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “Comment on ‘Repulsive
Contact Interactions Make Jammed Particulate Systems Inherently Nonharmonic.’”
Physical Review Letters. American Physical Society, 2014. https://doi.org/10.1103/physrevlett.112.049801.
ieee: C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Comment on ‘Repulsive contact
interactions make jammed particulate systems inherently nonharmonic,’” Physical
Review Letters, vol. 112, no. 4. American Physical Society, 2014.
ista: Goodrich CP, Liu AJ, Nagel SR. 2014. Comment on “Repulsive contact interactions
make jammed particulate systems inherently nonharmonic”. Physical Review Letters.
112(4), 049801.
mla: Goodrich, Carl Peter, et al. “Comment on ‘Repulsive Contact Interactions Make
Jammed Particulate Systems Inherently Nonharmonic.’” Physical Review Letters,
vol. 112, no. 4, 049801, American Physical Society, 2014, doi:10.1103/physrevlett.112.049801.
short: C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review Letters 112 (2014).
date_created: 2020-04-30T11:42:39Z
date_published: 2014-04-20T00:00:00Z
date_updated: 2021-01-12T08:15:26Z
day: '20'
doi: 10.1103/physrevlett.112.049801
extern: '1'
external_id:
arxiv:
- '1306.1285'
intvolume: ' 112'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1306.1285
month: '04'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_identifier:
issn:
- 0031-9007
- 1079-7114
publication_status: published
publisher: American Physical Society
status: public
title: Comment on “Repulsive contact interactions make jammed particulate systems
inherently nonharmonic”
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2014'
...
---
_id: '7772'
abstract:
- lang: eng
text: Particle tracking and displacement covariance matrix techniques are employed
to investigate the phonon dispersion relations of two-dimensional colloidal glasses
composed of soft, thermoresponsive microgel particles whose temperature-sensitive
size permits in situ variation of particle packing fraction. Bulk, B, and shear,
G, moduli of the colloidal glasses are extracted from the dispersion relations
as a function of packing fraction, and variation of the ratio G/B with packing
fraction is found to agree quantitatively with predictions for jammed packings
of frictional soft particles. In addition, G and B individually agree with numerical
predictions for frictional particles. This remarkable level of agreement enabled
us to extract an energy scale for the interparticle interaction from the individual
elastic constants and to derive an approximate estimate for the interparticle
friction coefficient.
article_number: '012301'
article_processing_charge: No
article_type: original
author:
- first_name: Tim
full_name: Still, Tim
last_name: Still
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Ke
full_name: Chen, Ke
last_name: Chen
- first_name: Peter J.
full_name: Yunker, Peter J.
last_name: Yunker
- first_name: Samuel
full_name: Schoenholz, Samuel
last_name: Schoenholz
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: A. G.
full_name: Yodh, A. G.
last_name: Yodh
citation:
ama: Still T, Goodrich CP, Chen K, et al. Phonon dispersion and elastic moduli of
two-dimensional disordered colloidal packings of soft particles with frictional
interactions. Physical Review E. 2014;89(1). doi:10.1103/physreve.89.012301
apa: Still, T., Goodrich, C. P., Chen, K., Yunker, P. J., Schoenholz, S., Liu, A.
J., & Yodh, A. G. (2014). Phonon dispersion and elastic moduli of two-dimensional
disordered colloidal packings of soft particles with frictional interactions.
Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.89.012301
chicago: Still, Tim, Carl Peter Goodrich, Ke Chen, Peter J. Yunker, Samuel Schoenholz,
Andrea J. Liu, and A. G. Yodh. “Phonon Dispersion and Elastic Moduli of Two-Dimensional
Disordered Colloidal Packings of Soft Particles with Frictional Interactions.”
Physical Review E. American Physical Society, 2014. https://doi.org/10.1103/physreve.89.012301.
ieee: T. Still et al., “Phonon dispersion and elastic moduli of two-dimensional
disordered colloidal packings of soft particles with frictional interactions,”
Physical Review E, vol. 89, no. 1. American Physical Society, 2014.
ista: Still T, Goodrich CP, Chen K, Yunker PJ, Schoenholz S, Liu AJ, Yodh AG. 2014.
Phonon dispersion and elastic moduli of two-dimensional disordered colloidal packings
of soft particles with frictional interactions. Physical Review E. 89(1), 012301.
mla: Still, Tim, et al. “Phonon Dispersion and Elastic Moduli of Two-Dimensional
Disordered Colloidal Packings of Soft Particles with Frictional Interactions.”
Physical Review E, vol. 89, no. 1, 012301, American Physical Society, 2014,
doi:10.1103/physreve.89.012301.
short: T. Still, C.P. Goodrich, K. Chen, P.J. Yunker, S. Schoenholz, A.J. Liu, A.G.
Yodh, Physical Review E 89 (2014).
date_created: 2020-04-30T11:43:02Z
date_published: 2014-01-03T00:00:00Z
date_updated: 2021-01-12T08:15:26Z
day: '03'
doi: 10.1103/physreve.89.012301
extern: '1'
intvolume: ' 89'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
publication: Physical Review E
publication_identifier:
issn:
- 1539-3755
- 1550-2376
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Phonon dispersion and elastic moduli of two-dimensional disordered colloidal
packings of soft particles with frictional interactions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 89
year: '2014'
...
---
_id: '7773'
abstract:
- lang: eng
text: 'For more than a century, physicists have described real solids in terms of
perturbations about perfect crystalline order1. Such an approach takes us only
so far: a glass, another ubiquitous form of rigid matter, cannot be described
in any meaningful sense as a defected crystal2. Is there an opposite extreme to
a crystal—a solid with complete disorder—that forms an alternative starting point
for understanding real materials? Here, we argue that the solid comprising particles
with finite-ranged interactions at the jamming transition3,4,5 constitutes such
a limit. It has been shown that the physics associated with this transition can
be extended to interactions that are long ranged6. We demonstrate that jamming
physics is not restricted to amorphous systems, but dominates the behaviour of
solids with surprisingly high order. Just as the free-electron and tight-binding
models represent two idealized cases from which to understand electronic structure1,
we identify two extreme limits of mechanical behaviour. Thus, the physics of jamming
can be set side by side with the physics of crystals to provide an organizing
structure for understanding the mechanical properties of solids over the entire
spectrum of disorder.'
article_processing_charge: No
article_type: original
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: Sidney R.
full_name: Nagel, Sidney R.
last_name: Nagel
citation:
ama: Goodrich CP, Liu AJ, Nagel SR. Solids between the mechanical extremes of order
and disorder. Nature Physics. 2014;10(8):578-581. doi:10.1038/nphys3006
apa: Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2014). Solids between the
mechanical extremes of order and disorder. Nature Physics. Springer Nature.
https://doi.org/10.1038/nphys3006
chicago: Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “Solids between
the Mechanical Extremes of Order and Disorder.” Nature Physics. Springer
Nature, 2014. https://doi.org/10.1038/nphys3006.
ieee: C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Solids between the mechanical
extremes of order and disorder,” Nature Physics, vol. 10, no. 8. Springer
Nature, pp. 578–581, 2014.
ista: Goodrich CP, Liu AJ, Nagel SR. 2014. Solids between the mechanical extremes
of order and disorder. Nature Physics. 10(8), 578–581.
mla: Goodrich, Carl Peter, et al. “Solids between the Mechanical Extremes of Order
and Disorder.” Nature Physics, vol. 10, no. 8, Springer Nature, 2014, pp.
578–81, doi:10.1038/nphys3006.
short: C.P. Goodrich, A.J. Liu, S.R. Nagel, Nature Physics 10 (2014) 578–581.
date_created: 2020-04-30T11:43:29Z
date_published: 2014-07-06T00:00:00Z
date_updated: 2021-01-12T08:15:26Z
day: '06'
doi: 10.1038/nphys3006
extern: '1'
intvolume: ' 10'
issue: '8'
language:
- iso: eng
month: '07'
oa_version: None
page: 578-581
publication: Nature Physics
publication_identifier:
issn:
- 1745-2473
- 1745-2481
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Solids between the mechanical extremes of order and disorder
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2014'
...
---
_id: '7769'
abstract:
- lang: eng
text: 'Athermal packings of soft repulsive spheres exhibit a sharp jamming transition
in the thermodynamic limit. Upon further compression, various structural and mechanical
properties display clean power-law behavior over many decades in pressure. As
with any phase transition, the rounding of such behavior in finite systems close
to the transition plays an important role in understanding the nature of the transition
itself. The situation for jamming is surprisingly rich: the assumption that jammed
packings are isotropic is only strictly true in the large-size limit, and finite-size
has a profound effect on the very meaning of jamming. Here, we provide a comprehensive
numerical study of finite-size effects in sphere packings above the jamming transition,
focusing on stability as well as the scaling of the contact number and the elastic
response.'
article_number: '022138'
article_processing_charge: No
article_type: original
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Simon
full_name: Dagois-Bohy, Simon
last_name: Dagois-Bohy
- first_name: Brian P.
full_name: Tighe, Brian P.
last_name: Tighe
- first_name: Martin
full_name: van Hecke, Martin
last_name: van Hecke
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: Sidney R.
full_name: Nagel, Sidney R.
last_name: Nagel
citation:
ama: 'Goodrich CP, Dagois-Bohy S, Tighe BP, van Hecke M, Liu AJ, Nagel SR. Jamming
in finite systems: Stability, anisotropy, fluctuations, and scaling. Physical
Review E. 2014;90(2). doi:10.1103/physreve.90.022138'
apa: 'Goodrich, C. P., Dagois-Bohy, S., Tighe, B. P., van Hecke, M., Liu, A. J.,
& Nagel, S. R. (2014). Jamming in finite systems: Stability, anisotropy, fluctuations,
and scaling. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.90.022138'
chicago: 'Goodrich, Carl Peter, Simon Dagois-Bohy, Brian P. Tighe, Martin van Hecke,
Andrea J. Liu, and Sidney R. Nagel. “Jamming in Finite Systems: Stability, Anisotropy,
Fluctuations, and Scaling.” Physical Review E. American Physical Society,
2014. https://doi.org/10.1103/physreve.90.022138.'
ieee: 'C. P. Goodrich, S. Dagois-Bohy, B. P. Tighe, M. van Hecke, A. J. Liu, and
S. R. Nagel, “Jamming in finite systems: Stability, anisotropy, fluctuations,
and scaling,” Physical Review E, vol. 90, no. 2. American Physical Society,
2014.'
ista: 'Goodrich CP, Dagois-Bohy S, Tighe BP, van Hecke M, Liu AJ, Nagel SR. 2014.
Jamming in finite systems: Stability, anisotropy, fluctuations, and scaling. Physical
Review E. 90(2), 022138.'
mla: 'Goodrich, Carl Peter, et al. “Jamming in Finite Systems: Stability, Anisotropy,
Fluctuations, and Scaling.” Physical Review E, vol. 90, no. 2, 022138,
American Physical Society, 2014, doi:10.1103/physreve.90.022138.'
short: C.P. Goodrich, S. Dagois-Bohy, B.P. Tighe, M. van Hecke, A.J. Liu, S.R. Nagel,
Physical Review E 90 (2014).
date_created: 2020-04-30T11:42:09Z
date_published: 2014-08-27T00:00:00Z
date_updated: 2021-01-12T08:15:24Z
day: '27'
doi: 10.1103/physreve.90.022138
extern: '1'
intvolume: ' 90'
issue: '2'
language:
- iso: eng
month: '08'
oa_version: None
publication: Physical Review E
publication_identifier:
issn:
- 1539-3755
- 1550-2376
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: 'Jamming in finite systems: Stability, anisotropy, fluctuations, and scaling'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 90
year: '2014'
...
---
_id: '7770'
abstract:
- lang: eng
text: Packings of frictionless athermal particles that interact only when they overlap
experience a jamming transition as a function of packing density. Such packings
provide the foundation for the theory of jamming. This theory rests on the observation
that, despite the multitude of disordered configurations, the mechanical response
to linear order depends only on the distance to the transition. We investigate
the validity and utility of such measurements that invoke the harmonic approximation
and show that, despite particles coming in and out of contact, there is a well-defined
linear regime in the thermodynamic limit.
article_number: '022201'
article_processing_charge: No
article_type: original
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: Sidney R.
full_name: Nagel, Sidney R.
last_name: Nagel
citation:
ama: Goodrich CP, Liu AJ, Nagel SR. Contact nonlinearities and linear response in
jammed particulate packings. Physical Review E. 2014;90(2). doi:10.1103/physreve.90.022201
apa: Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2014). Contact nonlinearities
and linear response in jammed particulate packings. Physical Review E.
American Physical Society. https://doi.org/10.1103/physreve.90.022201
chicago: Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “Contact Nonlinearities
and Linear Response in Jammed Particulate Packings.” Physical Review E.
American Physical Society, 2014. https://doi.org/10.1103/physreve.90.022201.
ieee: C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Contact nonlinearities and linear
response in jammed particulate packings,” Physical Review E, vol. 90, no.
2. American Physical Society, 2014.
ista: Goodrich CP, Liu AJ, Nagel SR. 2014. Contact nonlinearities and linear response
in jammed particulate packings. Physical Review E. 90(2), 022201.
mla: Goodrich, Carl Peter, et al. “Contact Nonlinearities and Linear Response in
Jammed Particulate Packings.” Physical Review E, vol. 90, no. 2, 022201,
American Physical Society, 2014, doi:10.1103/physreve.90.022201.
short: C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review E 90 (2014).
date_created: 2020-04-30T11:42:24Z
date_published: 2014-08-04T00:00:00Z
date_updated: 2021-01-12T08:15:25Z
day: '04'
doi: 10.1103/physreve.90.022201
extern: '1'
intvolume: ' 90'
issue: '2'
language:
- iso: eng
month: '08'
oa_version: None
publication: Physical Review E
publication_identifier:
issn:
- 1539-3755
- 1550-2376
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Contact nonlinearities and linear response in jammed particulate packings
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 90
year: '2014'
...
---
_id: '8021'
abstract:
- lang: eng
text: 'Most excitatory inputs in the mammalian brain are made on dendritic spines,
rather than on dendritic shafts. Spines compartmentalize calcium, and this biochemical
isolation can underlie input-specific synaptic plasticity, providing a raison
d''etre for spines. However, recent results indicate that the spine can experience
a membrane potential different from that in the parent dendrite, as though the
spine neck electrically isolated the spine. Here we use two-photon calcium imaging
of mouse neocortical pyramidal neurons to analyze the correlation between the
morphologies of spines activated under minimal synaptic stimulation and the excitatory
postsynaptic potentials they generate. We find that excitatory postsynaptic potential
amplitudes are inversely correlated with spine neck lengths. Furthermore, a spike
timing-dependent plasticity protocol, in which two-photon glutamate uncaging over
a spine is paired with postsynaptic spikes, produces rapid shrinkage of the spine
neck and concomitant increases in the amplitude of the evoked spine potentials.
Using numerical simulations, we explore the parameter regimes for the spine neck
resistance and synaptic conductance changes necessary to explain our observations.
Our data, directly correlating synaptic and morphological plasticity, imply that
long-necked spines have small or negligible somatic voltage contributions, but
that, upon synaptic stimulation paired with postsynaptic activity, they can shorten
their necks and increase synaptic efficacy, thus changing the input/output gain
of pyramidal neurons. '
article_processing_charge: No
article_type: original
author:
- first_name: R.
full_name: Araya, R.
last_name: Araya
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: R.
full_name: Yuste, R.
last_name: Yuste
citation:
ama: Araya R, Vogels TP, Yuste R. Activity-dependent dendritic spine neck changes
are correlated with synaptic strength. Proceedings of the National Academy
of Sciences. 2014;111(28):E2895-E2904. doi:10.1073/pnas.1321869111
apa: Araya, R., Vogels, T. P., & Yuste, R. (2014). Activity-dependent dendritic
spine neck changes are correlated with synaptic strength. Proceedings of the
National Academy of Sciences. Proceedings of the National Academy of Sciences.
https://doi.org/10.1073/pnas.1321869111
chicago: Araya, R., Tim P Vogels, and R. Yuste. “Activity-Dependent Dendritic Spine
Neck Changes Are Correlated with Synaptic Strength.” Proceedings of the National
Academy of Sciences. Proceedings of the National Academy of Sciences, 2014.
https://doi.org/10.1073/pnas.1321869111.
ieee: R. Araya, T. P. Vogels, and R. Yuste, “Activity-dependent dendritic spine
neck changes are correlated with synaptic strength,” Proceedings of the National
Academy of Sciences, vol. 111, no. 28. Proceedings of the National Academy
of Sciences, pp. E2895–E2904, 2014.
ista: Araya R, Vogels TP, Yuste R. 2014. Activity-dependent dendritic spine neck
changes are correlated with synaptic strength. Proceedings of the National Academy
of Sciences. 111(28), E2895–E2904.
mla: Araya, R., et al. “Activity-Dependent Dendritic Spine Neck Changes Are Correlated
with Synaptic Strength.” Proceedings of the National Academy of Sciences,
vol. 111, no. 28, Proceedings of the National Academy of Sciences, 2014, pp. E2895–904,
doi:10.1073/pnas.1321869111.
short: R. Araya, T.P. Vogels, R. Yuste, Proceedings of the National Academy of Sciences
111 (2014) E2895–E2904.
date_created: 2020-06-25T13:06:24Z
date_published: 2014-07-15T00:00:00Z
date_updated: 2021-01-12T08:16:34Z
day: '15'
doi: 10.1073/pnas.1321869111
extern: '1'
external_id:
pmid:
- '24982196'
intvolume: ' 111'
issue: '28'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4104910/
month: '07'
oa: 1
oa_version: Published Version
page: E2895-E2904
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
status: public
title: Activity-dependent dendritic spine neck changes are correlated with synaptic
strength
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 111
year: '2014'
...
---
_id: '8023'
abstract:
- lang: eng
text: Uniform random sparse network architectures are ubiquitous in computational
neuroscience, but the implicit hypothesis that they are a good representation
of real neuronal networks has been met with skepticism. Here we used two experimental
data sets, a study of triplet connectivity statistics and a data set measuring
neuronal responses to channelrhodopsin stimuli, to evaluate the fidelity of thousands
of model networks. Network architectures comprised three neuron types (excitatory,
fast spiking, and nonfast spiking inhibitory) and were created from a set of rules
that govern the statistics of the resulting connection types. In a high-dimensional
parameter scan, we varied the degree distributions (i.e., how many cells each
neuron connects with) and the synaptic weight correlations of synapses from or
onto the same neuron. These variations converted initially uniform random and
homogeneously connected networks, in which every neuron sent and received equal
numbers of synapses with equal synaptic strength distributions, to highly heterogeneous
networks in which the number of synapses per neuron, as well as average synaptic
strength of synapses from or to a neuron were variable. By evaluating the impact
of each variable on the network structure and dynamics, and their similarity to
the experimental data, we could falsify the uniform random sparse connectivity
hypothesis for 7 of 36 connectivity parameters, but we also confirmed the hypothesis
in 8 cases. Twenty-one parameters had no substantial impact on the results of
the test protocols we used.
article_processing_charge: No
article_type: original
author:
- first_name: Christian
full_name: Tomm, Christian
last_name: Tomm
- first_name: Michael
full_name: Avermann, Michael
last_name: Avermann
- first_name: Carl
full_name: Petersen, Carl
last_name: Petersen
- first_name: Wulfram
full_name: Gerstner, Wulfram
last_name: Gerstner
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: Tomm C, Avermann M, Petersen C, Gerstner W, Vogels TP. Connection-type-specific
biases make uniform random network models consistent with cortical recordings.
Journal of Neurophysiology. 2014;112(8):1801-1814. doi:10.1152/jn.00629.2013
apa: Tomm, C., Avermann, M., Petersen, C., Gerstner, W., & Vogels, T. P. (2014).
Connection-type-specific biases make uniform random network models consistent
with cortical recordings. Journal of Neurophysiology. American Physiological
Society. https://doi.org/10.1152/jn.00629.2013
chicago: Tomm, Christian, Michael Avermann, Carl Petersen, Wulfram Gerstner, and
Tim P Vogels. “Connection-Type-Specific Biases Make Uniform Random Network Models
Consistent with Cortical Recordings.” Journal of Neurophysiology. American
Physiological Society, 2014. https://doi.org/10.1152/jn.00629.2013.
ieee: C. Tomm, M. Avermann, C. Petersen, W. Gerstner, and T. P. Vogels, “Connection-type-specific
biases make uniform random network models consistent with cortical recordings,”
Journal of Neurophysiology, vol. 112, no. 8. American Physiological Society,
pp. 1801–1814, 2014.
ista: Tomm C, Avermann M, Petersen C, Gerstner W, Vogels TP. 2014. Connection-type-specific
biases make uniform random network models consistent with cortical recordings.
Journal of Neurophysiology. 112(8), 1801–1814.
mla: Tomm, Christian, et al. “Connection-Type-Specific Biases Make Uniform Random
Network Models Consistent with Cortical Recordings.” Journal of Neurophysiology,
vol. 112, no. 8, American Physiological Society, 2014, pp. 1801–14, doi:10.1152/jn.00629.2013.
short: C. Tomm, M. Avermann, C. Petersen, W. Gerstner, T.P. Vogels, Journal of Neurophysiology
112 (2014) 1801–1814.
date_created: 2020-06-25T13:08:30Z
date_published: 2014-10-15T00:00:00Z
date_updated: 2021-01-12T08:16:35Z
day: '15'
ddc:
- '570'
doi: 10.1152/jn.00629.2013
extern: '1'
external_id:
pmid:
- '24944218'
file:
- access_level: open_access
checksum: 7c06a086da6f924342650de6dc555c3f
content_type: application/pdf
creator: cziletti
date_created: 2020-07-16T10:12:13Z
date_updated: 2020-07-16T10:12:13Z
file_id: '8122'
file_name: 2014_JNeurophysiol_Tomm.pdf
file_size: 1632295
relation: main_file
success: 1
file_date_updated: 2020-07-16T10:12:13Z
has_accepted_license: '1'
intvolume: ' 112'
issue: '8'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '10'
oa: 1
oa_version: Published Version
page: 1801-1814
pmid: 1
publication: Journal of Neurophysiology
publication_identifier:
eissn:
- 1522-1598
issn:
- 0022-3077
publication_status: published
publisher: American Physiological Society
quality_controlled: '1'
status: public
title: Connection-type-specific biases make uniform random network models consistent
with cortical recordings
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 112
year: '2014'
...
---
_id: '8022'
abstract:
- lang: eng
text: Populations of neurons in motor cortex engage in complex transient dynamics
of large amplitude during the execution of limb movements. Traditional network
models with stochastically assigned synapses cannot reproduce this behavior. Here
we introduce a class of cortical architectures with strong and random excitatory
recurrence that is stabilized by intricate, fine-tuned inhibition, optimized from
a control theory perspective. Such networks transiently amplify specific activity
states and can be used to reliably execute multidimensional movement patterns.
Similar to the experimental observations, these transients must be preceded by
a steady-state initialization phase from which the network relaxes back into the
background state by way of complex internal dynamics. In our networks, excitation
and inhibition are as tightly balanced as recently reported in experiments across
several brain areas, suggesting inhibitory control of complex excitatory recurrence
as a generic organizational principle in cortex.
article_processing_charge: No
article_type: original
author:
- first_name: Guillaume
full_name: Hennequin, Guillaume
last_name: Hennequin
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: Wulfram
full_name: Gerstner, Wulfram
last_name: Gerstner
citation:
ama: Hennequin G, Vogels TP, Gerstner W. Optimal control of transient dynamics in
balanced networks supports generation of complex movements. Neuron. 2014;82(6):1394-1406.
doi:10.1016/j.neuron.2014.04.045
apa: Hennequin, G., Vogels, T. P., & Gerstner, W. (2014). Optimal control of
transient dynamics in balanced networks supports generation of complex movements.
Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.04.045
chicago: Hennequin, Guillaume, Tim P Vogels, and Wulfram Gerstner. “Optimal Control
of Transient Dynamics in Balanced Networks Supports Generation of Complex Movements.”
Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2014.04.045.
ieee: G. Hennequin, T. P. Vogels, and W. Gerstner, “Optimal control of transient
dynamics in balanced networks supports generation of complex movements,” Neuron,
vol. 82, no. 6. Elsevier, pp. 1394–1406, 2014.
ista: Hennequin G, Vogels TP, Gerstner W. 2014. Optimal control of transient dynamics
in balanced networks supports generation of complex movements. Neuron. 82(6),
1394–1406.
mla: Hennequin, Guillaume, et al. “Optimal Control of Transient Dynamics in Balanced
Networks Supports Generation of Complex Movements.” Neuron, vol. 82, no.
6, Elsevier, 2014, pp. 1394–406, doi:10.1016/j.neuron.2014.04.045.
short: G. Hennequin, T.P. Vogels, W. Gerstner, Neuron 82 (2014) 1394–1406.
date_created: 2020-06-25T13:07:37Z
date_published: 2014-06-18T00:00:00Z
date_updated: 2021-01-12T08:16:35Z
day: '18'
doi: 10.1016/j.neuron.2014.04.045
extern: '1'
external_id:
pmid:
- '24945778'
intvolume: ' 82'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6364799/
month: '06'
oa: 1
oa_version: Submitted Version
page: 1394-1406
pmid: 1
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Optimal control of transient dynamics in balanced networks supports generation
of complex movements
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 82
year: '2014'
...
---
_id: '809'
abstract:
- lang: eng
text: The assembly of HIV-1 is mediated by oligomerization of the major structural
polyprotein, Gag, into a hexameric protein lattice at the plasma membrane of the
infected cell. This leads to budding and release of progeny immature virus particles.
Subsequent proteolytic cleavage of Gag triggers rearrangement of the particles
to form mature infectious virions. Obtaining a structural model of the assembled
lattice of Gag within immature virus particles is necessary to understand the
interactions that mediate assembly of HIV-1 particles in the infected cell, and
to describe the substrate that is subsequently cleaved by the viral protease.
An 8-Å resolution structure of an immature virus-like tubular array assembled
from a Gag-derived protein of the related retrovirus Mason-Pfizer monkey virus
(M-PMV) has previously been reported, and a model for the arrangement of the HIV-1
capsid (CA) domains has been generated based on homology to this structure. Here
we have assembled tubular arrays of a HIV-1 Gag-derived protein with an immature-like
arrangement of the C-terminal CA domains and have solved their structure by using
hybrid cryo-EM and tomography analysis. The structure reveals the arrangement
of the C-terminal domain of CA within an immature-like HIV-1 Gag lattice, and
provides, to our knowledge, the first high-resolution view of the region immediately
downstream of CA, which is essential for assembly, and is significantly different
from the respective region in M-PMV. Our results reveal a hollow column of density
for this region in HIV-1 that is compatible with the presence of a six-helix bundle
at this position.
acknowledgement: 'The authors thank Leonardo Trabuco for help with running MDFF, Maria
Anders for preparing amprenavir-inhibited virus, Marie-Christine Vaney for help
with X-ray data processing and structure refinement, Ahmed Haouz and Patrick Weber
(robotized crystallization facility Proteopole, Institut Pasteur) for help in crystal
screening, and the European Molecular Biology Laboratory (EMBL) Information Technology
Services Unit and Frank Thommen for technical support. This study was supported
by Deutsche Forschungsgemeinschaft Grants BR 3635/2-1 (to J.A.G.B.) and KR 906/7-1
(to H.-G.K.) and a Federation of European Biochemical Societies long-term fellowship
(to T.A.M.B.). The laboratory of J.A.G.B. acknowledges financial support from EMBL
and the Chica und Heinz Schaller Stiftung. '
author:
- first_name: Tanmay
full_name: Bharata, Tanmay A
last_name: Bharata
- first_name: Luis
full_name: Menendez, Luis R
last_name: Menendez
- first_name: Wim
full_name: Hagena, Wim J
last_name: Hagena
- first_name: Vanda
full_name: Luxd, Vanda
last_name: Luxd
- first_name: Sebastien
full_name: Igonete, Sebastien
last_name: Igonete
- first_name: Martin
full_name: Schorba, Martin
last_name: Schorba
- first_name: Florian
full_name: Florian Schur
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Hans
full_name: Kraüsslich, Hans Georg
last_name: Kraüsslich
- first_name: John
full_name: Briggsa, John A
last_name: Briggsa
citation:
ama: Bharata T, Menendez L, Hagena W, et al. Cryo electron microscopy of tubular
arrays of HIV-1 Gag resolves structures essential for immature virus assembly.
PNAS. 2014;111(22):8233-8238. doi:10.1073/pnas.1401455111
apa: Bharata, T., Menendez, L., Hagena, W., Luxd, V., Igonete, S., Schorba, M.,
… Briggsa, J. (2014). Cryo electron microscopy of tubular arrays of HIV-1 Gag
resolves structures essential for immature virus assembly. PNAS. National
Academy of Sciences. https://doi.org/10.1073/pnas.1401455111
chicago: Bharata, Tanmay, Luis Menendez, Wim Hagena, Vanda Luxd, Sebastien Igonete,
Martin Schorba, Florian KM Schur, Hans Kraüsslich, and John Briggsa. “Cryo Electron
Microscopy of Tubular Arrays of HIV-1 Gag Resolves Structures Essential for Immature
Virus Assembly.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1401455111.
ieee: T. Bharata et al., “Cryo electron microscopy of tubular arrays of HIV-1
Gag resolves structures essential for immature virus assembly,” PNAS, vol.
111, no. 22. National Academy of Sciences, pp. 8233–8238, 2014.
ista: Bharata T, Menendez L, Hagena W, Luxd V, Igonete S, Schorba M, Schur FK, Kraüsslich
H, Briggsa J. 2014. Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves
structures essential for immature virus assembly. PNAS. 111(22), 8233–8238.
mla: Bharata, Tanmay, et al. “Cryo Electron Microscopy of Tubular Arrays of HIV-1
Gag Resolves Structures Essential for Immature Virus Assembly.” PNAS, vol.
111, no. 22, National Academy of Sciences, 2014, pp. 8233–38, doi:10.1073/pnas.1401455111.
short: T. Bharata, L. Menendez, W. Hagena, V. Luxd, S. Igonete, M. Schorba, F.K.
Schur, H. Kraüsslich, J. Briggsa, PNAS 111 (2014) 8233–8238.
date_created: 2018-12-11T11:48:37Z
date_published: 2014-06-03T00:00:00Z
date_updated: 2021-01-12T08:16:50Z
day: '03'
doi: 10.1073/pnas.1401455111
extern: 1
intvolume: ' 111'
issue: '22'
month: '06'
page: 8233 - 8238
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6838'
quality_controlled: 0
status: public
title: Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves structures
essential for immature virus assembly
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
volume: 111
year: '2014'
...
---
_id: '8244'
abstract:
- lang: eng
text: Passive immunotherapy with monoclonal antibodies represents a cornerstone
of human anticancer therapies, but has not been established in veterinary medicine
yet. As the tumor-associated antigen EGFR (ErbB-1) is highly conserved between
humans and dogs, and considering the effectiveness of the anti-EGFR antibody cetuximab
in human clinical oncology, we present here a “caninized” version of this antibody,
can225IgG, for comparative oncology studies. Variable region genes of 225, the
murine precursor of cetuximab, were fused with canine constant heavy gamma and
kappa chain genes, respectively, and transfected into Chinese hamster ovary (CHO)
DUKX-B11 cells. Of note, 480 clones were screened and the best clones were selected
according to productivity and highest specificity in EGFR-coated ELISA. Upon purification
with Protein G, the recombinant cetuximab-like canine IgG was tested for integrity,
correct assembly, and functionality. Specific binding to the surface of EGFR-overexpressing
cells was assessed by flow cytometry and immunofluorescence; moreover, binding
to canine mammary tissue was demonstrated by immunohistochemistry. In cell viability
and proliferation assays, incubation with can225IgG led to significant tumor cell
growth inhibition. Moreover, this antibody mediated significant tumor cell killing
via phagocytosis in vitro. We thus present here, for the first time, the generation
of a canine IgG antibody and its hypothetical structure. On the basis of its cetuximab-like
binding site, on the one hand, and the expression of a 91% homologous EGFR molecule
in canine cancer, on the other hand, this antibody may be a promising research
compound to establish passive immunotherapy in dog patients with cancer.
article_processing_charge: No
article_type: original
author:
- first_name: J.
full_name: Singer, J.
last_name: Singer
- first_name: Judit
full_name: Fazekas, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas
orcid: 0000-0002-8777-3502
- first_name: W.
full_name: Wang, W.
last_name: Wang
- first_name: M.
full_name: Weichselbaumer, M.
last_name: Weichselbaumer
- first_name: M.
full_name: Matz, M.
last_name: Matz
- first_name: A.
full_name: Mader, A.
last_name: Mader
- first_name: W.
full_name: Steinfellner, W.
last_name: Steinfellner
- first_name: S.
full_name: Meitz, S.
last_name: Meitz
- first_name: D.
full_name: Mechtcheriakova, D.
last_name: Mechtcheriakova
- first_name: Y.
full_name: Sobanov, Y.
last_name: Sobanov
- first_name: M.
full_name: Willmann, M.
last_name: Willmann
- first_name: T.
full_name: Stockner, T.
last_name: Stockner
- first_name: E.
full_name: Spillner, E.
last_name: Spillner
- first_name: R.
full_name: Kunert, R.
last_name: Kunert
- first_name: E.
full_name: Jensen-Jarolim, E.
last_name: Jensen-Jarolim
citation:
ama: Singer J, Singer J, Wang W, et al. Generation of a canine anti-EGFR (ErbB-1)
antibody for passive immunotherapy in dog cancer patients. Molecular Cancer
Therapeutics. 2014;13(7):1777-1790. doi:10.1158/1535-7163.mct-13-0288
apa: Singer, J., Singer, J., Wang, W., Weichselbaumer, M., Matz, M., Mader, A.,
… Jensen-Jarolim, E. (2014). Generation of a canine anti-EGFR (ErbB-1) antibody
for passive immunotherapy in dog cancer patients. Molecular Cancer Therapeutics.
American Association for Cancer Research. https://doi.org/10.1158/1535-7163.mct-13-0288
chicago: Singer, J., Judit Singer, W. Wang, M. Weichselbaumer, M. Matz, A. Mader,
W. Steinfellner, et al. “Generation of a Canine Anti-EGFR (ErbB-1) Antibody for
Passive Immunotherapy in Dog Cancer Patients.” Molecular Cancer Therapeutics.
American Association for Cancer Research, 2014. https://doi.org/10.1158/1535-7163.mct-13-0288.
ieee: J. Singer et al., “Generation of a canine anti-EGFR (ErbB-1) antibody
for passive immunotherapy in dog cancer patients,” Molecular Cancer Therapeutics,
vol. 13, no. 7. American Association for Cancer Research, pp. 1777–1790, 2014.
ista: Singer J, Singer J, Wang W, Weichselbaumer M, Matz M, Mader A, Steinfellner
W, Meitz S, Mechtcheriakova D, Sobanov Y, Willmann M, Stockner T, Spillner E,
Kunert R, Jensen-Jarolim E. 2014. Generation of a canine anti-EGFR (ErbB-1) antibody
for passive immunotherapy in dog cancer patients. Molecular Cancer Therapeutics.
13(7), 1777–1790.
mla: Singer, J., et al. “Generation of a Canine Anti-EGFR (ErbB-1) Antibody for
Passive Immunotherapy in Dog Cancer Patients.” Molecular Cancer Therapeutics,
vol. 13, no. 7, American Association for Cancer Research, 2014, pp. 1777–90, doi:10.1158/1535-7163.mct-13-0288.
short: J. Singer, J. Singer, W. Wang, M. Weichselbaumer, M. Matz, A. Mader, W. Steinfellner,
S. Meitz, D. Mechtcheriakova, Y. Sobanov, M. Willmann, T. Stockner, E. Spillner,
R. Kunert, E. Jensen-Jarolim, Molecular Cancer Therapeutics 13 (2014) 1777–1790.
date_created: 2020-08-10T11:54:29Z
date_published: 2014-07-01T00:00:00Z
date_updated: 2021-01-12T08:17:42Z
day: '01'
doi: 10.1158/1535-7163.mct-13-0288
extern: '1'
intvolume: ' 13'
issue: '7'
language:
- iso: eng
month: '07'
oa_version: None
page: 1777-1790
publication: Molecular Cancer Therapeutics
publication_identifier:
issn:
- 1535-7163
- 1538-8514
publication_status: published
publisher: American Association for Cancer Research
quality_controlled: '1'
status: public
title: Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy
in dog cancer patients
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2014'
...
---
_id: '8459'
abstract:
- lang: eng
text: Nuclear magnetic resonance (NMR) is a powerful tool for observing the motion
of biomolecules at the atomic level. One technique, the analysis of relaxation
dispersion phenomenon, is highly suited for studying the kinetics and thermodynamics
of biological processes. Built on top of the relax computational environment for
NMR dynamics is a new dispersion analysis designed to be comprehensive, accurate
and easy-to-use. The software supports more models, both numeric and analytic,
than current solutions. An automated protocol, available for scripting and driving
the graphical user interface (GUI), is designed to simplify the analysis of dispersion
data for NMR spectroscopists. Decreases in optimization time are granted by parallelization
for running on computer clusters and by skipping an initial grid search by using
parameters from one solution as the starting point for another —using analytic
model results for the numeric models, taking advantage of model nesting, and using
averaged non-clustered results for the clustered analysis.
article_processing_charge: No
article_type: original
author:
- first_name: Sébastien
full_name: Morin, Sébastien
last_name: Morin
- first_name: Troels E
full_name: Linnet, Troels E
last_name: Linnet
- first_name: Mathilde
full_name: Lescanne, Mathilde
last_name: Lescanne
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Gary S
full_name: Thompson, Gary S
last_name: Thompson
- first_name: Martin
full_name: Tollinger, Martin
last_name: Tollinger
- first_name: Kaare
full_name: Teilum, Kaare
last_name: Teilum
- first_name: Stéphane
full_name: Gagné, Stéphane
last_name: Gagné
- first_name: Dominique
full_name: Marion, Dominique
last_name: Marion
- first_name: Christian
full_name: Griesinger, Christian
last_name: Griesinger
- first_name: Martin
full_name: Blackledge, Martin
last_name: Blackledge
- first_name: Edward J
full_name: d’Auvergne, Edward J
last_name: d’Auvergne
citation:
ama: 'Morin S, Linnet TE, Lescanne M, et al. Relax: The analysis of biomolecular
kinetics and thermodynamics using NMR relaxation dispersion data. Bioinformatics.
2014;30(15):2219-2220. doi:10.1093/bioinformatics/btu166'
apa: 'Morin, S., Linnet, T. E., Lescanne, M., Schanda, P., Thompson, G. S., Tollinger,
M., … d’Auvergne, E. J. (2014). Relax: The analysis of biomolecular kinetics and
thermodynamics using NMR relaxation dispersion data. Bioinformatics. Oxford
University Press. https://doi.org/10.1093/bioinformatics/btu166'
chicago: 'Morin, Sébastien, Troels E Linnet, Mathilde Lescanne, Paul Schanda, Gary
S Thompson, Martin Tollinger, Kaare Teilum, et al. “Relax: The Analysis of Biomolecular
Kinetics and Thermodynamics Using NMR Relaxation Dispersion Data.” Bioinformatics.
Oxford University Press, 2014. https://doi.org/10.1093/bioinformatics/btu166.'
ieee: 'S. Morin et al., “Relax: The analysis of biomolecular kinetics and
thermodynamics using NMR relaxation dispersion data,” Bioinformatics, vol.
30, no. 15. Oxford University Press, pp. 2219–2220, 2014.'
ista: 'Morin S, Linnet TE, Lescanne M, Schanda P, Thompson GS, Tollinger M, Teilum
K, Gagné S, Marion D, Griesinger C, Blackledge M, d’Auvergne EJ. 2014. Relax:
The analysis of biomolecular kinetics and thermodynamics using NMR relaxation
dispersion data. Bioinformatics. 30(15), 2219–2220.'
mla: 'Morin, Sébastien, et al. “Relax: The Analysis of Biomolecular Kinetics and
Thermodynamics Using NMR Relaxation Dispersion Data.” Bioinformatics, vol.
30, no. 15, Oxford University Press, 2014, pp. 2219–20, doi:10.1093/bioinformatics/btu166.'
short: S. Morin, T.E. Linnet, M. Lescanne, P. Schanda, G.S. Thompson, M. Tollinger,
K. Teilum, S. Gagné, D. Marion, C. Griesinger, M. Blackledge, E.J. d’Auvergne,
Bioinformatics 30 (2014) 2219–2220.
date_created: 2020-09-18T10:08:07Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2021-01-12T08:19:25Z
day: '01'
doi: 10.1093/bioinformatics/btu166
extern: '1'
intvolume: ' 30'
issue: '15'
keyword:
- Statistics and Probability
- Computational Theory and Mathematics
- Biochemistry
- Molecular Biology
- Computational Mathematics
- Computer Science Applications
language:
- iso: eng
month: '08'
oa_version: None
page: 2219-2220
publication: Bioinformatics
publication_identifier:
issn:
- 1367-4803
- 1460-2059
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1093/bioinformatics/btz397
status: public
title: 'Relax: The analysis of biomolecular kinetics and thermodynamics using NMR
relaxation dispersion data'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2014'
...
---
_id: '8458'
abstract:
- lang: eng
text: The maintenance of bacterial cell shape and integrity is largely attributed
to peptidoglycan, a highly cross-linked biopolymer. The transpeptidases that perform
this cross-linking are important targets for antibiotics. Despite this biomedical
importance, to date no structure of a protein in complex with an intact bacterial
peptidoglycan has been resolved, primarily due to the large size and flexibility
of peptidoglycan sacculi. Here we use solid-state NMR spectroscopy to derive for
the first time an atomic model of an l,d-transpeptidase from Bacillus subtilis
bound to its natural substrate, the intact B. subtilis peptidoglycan. Importantly,
the model obtained from protein chemical shift perturbation data shows that both
domains—the catalytic domain as well as the proposed peptidoglycan recognition
domain—are important for the interaction and reveals a novel binding motif that
involves residues outside of the classical enzymatic pocket. Experiments on mutants
and truncated protein constructs independently confirm the binding site and the
implication of both domains. Through measurements of dipolar-coupling derived
order parameters of bond motion we show that protein binding reduces the flexibility
of peptidoglycan. This first report of an atomic model of a protein–peptidoglycan
complex paves the way for the design of new antibiotic drugs targeting l,d-transpeptidases.
The strategy developed here can be extended to the study of a large variety of
enzymes involved in peptidoglycan morphogenesis.
article_processing_charge: No
article_type: original
author:
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Sébastien
full_name: Triboulet, Sébastien
last_name: Triboulet
- first_name: Cédric
full_name: Laguri, Cédric
last_name: Laguri
- first_name: Catherine M.
full_name: Bougault, Catherine M.
last_name: Bougault
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Morgane
full_name: Callon, Morgane
last_name: Callon
- first_name: Michel
full_name: Arthur, Michel
last_name: Arthur
- first_name: Jean-Pierre
full_name: Simorre, Jean-Pierre
last_name: Simorre
citation:
ama: Schanda P, Triboulet S, Laguri C, et al. Atomic model of a cell-wall cross-linking
enzyme in complex with an intact bacterial peptidoglycan. Journal of the American
Chemical Society. 2014;136(51):17852-17860. doi:10.1021/ja5105987
apa: Schanda, P., Triboulet, S., Laguri, C., Bougault, C. M., Ayala, I., Callon,
M., … Simorre, J.-P. (2014). Atomic model of a cell-wall cross-linking enzyme
in complex with an intact bacterial peptidoglycan. Journal of the American
Chemical Society. American Chemical Society. https://doi.org/10.1021/ja5105987
chicago: Schanda, Paul, Sébastien Triboulet, Cédric Laguri, Catherine M. Bougault,
Isabel Ayala, Morgane Callon, Michel Arthur, and Jean-Pierre Simorre. “Atomic
Model of a Cell-Wall Cross-Linking Enzyme in Complex with an Intact Bacterial
Peptidoglycan.” Journal of the American Chemical Society. American Chemical
Society, 2014. https://doi.org/10.1021/ja5105987.
ieee: P. Schanda et al., “Atomic model of a cell-wall cross-linking enzyme
in complex with an intact bacterial peptidoglycan,” Journal of the American
Chemical Society, vol. 136, no. 51. American Chemical Society, pp. 17852–17860,
2014.
ista: Schanda P, Triboulet S, Laguri C, Bougault CM, Ayala I, Callon M, Arthur M,
Simorre J-P. 2014. Atomic model of a cell-wall cross-linking enzyme in complex
with an intact bacterial peptidoglycan. Journal of the American Chemical Society.
136(51), 17852–17860.
mla: Schanda, Paul, et al. “Atomic Model of a Cell-Wall Cross-Linking Enzyme in
Complex with an Intact Bacterial Peptidoglycan.” Journal of the American Chemical
Society, vol. 136, no. 51, American Chemical Society, 2014, pp. 17852–60,
doi:10.1021/ja5105987.
short: P. Schanda, S. Triboulet, C. Laguri, C.M. Bougault, I. Ayala, M. Callon,
M. Arthur, J.-P. Simorre, Journal of the American Chemical Society 136 (2014)
17852–17860.
date_created: 2020-09-18T10:07:52Z
date_published: 2014-11-27T00:00:00Z
date_updated: 2021-01-12T08:19:24Z
day: '27'
doi: 10.1021/ja5105987
extern: '1'
intvolume: ' 136'
issue: '51'
language:
- iso: eng
month: '11'
oa_version: None
page: 17852-17860
publication: Journal of the American Chemical Society
publication_identifier:
issn:
- 0002-7863
- 1520-5126
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: Atomic model of a cell-wall cross-linking enzyme in complex with an intact
bacterial peptidoglycan
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 136
year: '2014'
...
---
_id: '8460'
abstract:
- lang: eng
text: The function of proteins depends on their ability to sample a variety of states
differing in structure and free energy. Deciphering how the various thermally
accessible conformations are connected, and understanding their structures and
relative energies is crucial in rationalizing protein function. Many biomolecular
reactions take place within microseconds to milliseconds, and this timescale is
therefore of central functional importance. Here we show that R1ρ relaxation dispersion
experiments in magic‐angle‐spinning solid‐state NMR spectroscopy make it possible
to investigate the thermodynamics and kinetics of such exchange process, and gain
insight into structural features of short‐lived states.
article_processing_charge: No
article_type: original
author:
- first_name: Peixiang
full_name: Ma, Peixiang
last_name: Ma
- first_name: Jens D.
full_name: Haller, Jens D.
last_name: Haller
- first_name: Jérémy
full_name: Zajakala, Jérémy
last_name: Zajakala
- first_name: Pavel
full_name: Macek, Pavel
last_name: Macek
- first_name: Astrid C.
full_name: Sivertsen, Astrid C.
last_name: Sivertsen
- first_name: Dieter
full_name: Willbold, Dieter
last_name: Willbold
- first_name: Jérôme
full_name: Boisbouvier, Jérôme
last_name: Boisbouvier
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Ma P, Haller JD, Zajakala J, et al. Probing transient conformational states
of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy. Angewandte
Chemie International Edition. 2014;53(17):4312-4317. doi:10.1002/anie.201311275
apa: Ma, P., Haller, J. D., Zajakala, J., Macek, P., Sivertsen, A. C., Willbold,
D., … Schanda, P. (2014). Probing transient conformational states of proteins
by solid-state R1ρ relaxation-dispersion NMR spectroscopy. Angewandte Chemie
International Edition. Wiley. https://doi.org/10.1002/anie.201311275
chicago: Ma, Peixiang, Jens D. Haller, Jérémy Zajakala, Pavel Macek, Astrid C. Sivertsen,
Dieter Willbold, Jérôme Boisbouvier, and Paul Schanda. “Probing Transient Conformational
States of Proteins by Solid-State R1ρ Relaxation-Dispersion NMR Spectroscopy.”
Angewandte Chemie International Edition. Wiley, 2014. https://doi.org/10.1002/anie.201311275.
ieee: P. Ma et al., “Probing transient conformational states of proteins
by solid-state R1ρ relaxation-dispersion NMR spectroscopy,” Angewandte Chemie
International Edition, vol. 53, no. 17. Wiley, pp. 4312–4317, 2014.
ista: Ma P, Haller JD, Zajakala J, Macek P, Sivertsen AC, Willbold D, Boisbouvier
J, Schanda P. 2014. Probing transient conformational states of proteins by solid-state
R1ρ relaxation-dispersion NMR spectroscopy. Angewandte Chemie International Edition.
53(17), 4312–4317.
mla: Ma, Peixiang, et al. “Probing Transient Conformational States of Proteins by
Solid-State R1ρ Relaxation-Dispersion NMR Spectroscopy.” Angewandte Chemie
International Edition, vol. 53, no. 17, Wiley, 2014, pp. 4312–17, doi:10.1002/anie.201311275.
short: P. Ma, J.D. Haller, J. Zajakala, P. Macek, A.C. Sivertsen, D. Willbold, J.
Boisbouvier, P. Schanda, Angewandte Chemie International Edition 53 (2014) 4312–4317.
date_created: 2020-09-18T10:08:53Z
date_published: 2014-03-18T00:00:00Z
date_updated: 2021-01-12T08:19:25Z
day: '18'
doi: 10.1002/anie.201311275
extern: '1'
intvolume: ' 53'
issue: '17'
language:
- iso: eng
month: '03'
oa_version: None
page: 4312-4317
publication: Angewandte Chemie International Edition
publication_identifier:
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion
NMR spectroscopy
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 53
year: '2014'
...
---
_id: '8501'
abstract:
- lang: eng
text: In this paper, we study small perturbations of a class of non-convex integrable
Hamiltonians with two degrees of freedom, and we prove a result of diffusion for
an open and dense set of perturbations, with an optimal time of diffusion which
grows linearly with respect to the inverse of the size of the perturbation.
article_processing_charge: No
article_type: original
author:
- first_name: Abed
full_name: Bounemoura, Abed
last_name: Bounemoura
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
citation:
ama: Bounemoura A, Kaloshin V. Generic fast diffusion for a class of non-convex
Hamiltonians with two degrees of freedom. Moscow Mathematical Journal.
2014;14(2):181-203. doi:10.17323/1609-4514-2014-14-2-181-203
apa: Bounemoura, A., & Kaloshin, V. (2014). Generic fast diffusion for a class
of non-convex Hamiltonians with two degrees of freedom. Moscow Mathematical
Journal. Independent University of Moscow. https://doi.org/10.17323/1609-4514-2014-14-2-181-203
chicago: Bounemoura, Abed, and Vadim Kaloshin. “Generic Fast Diffusion for a Class
of Non-Convex Hamiltonians with Two Degrees of Freedom.” Moscow Mathematical
Journal. Independent University of Moscow, 2014. https://doi.org/10.17323/1609-4514-2014-14-2-181-203.
ieee: A. Bounemoura and V. Kaloshin, “Generic fast diffusion for a class of non-convex
Hamiltonians with two degrees of freedom,” Moscow Mathematical Journal,
vol. 14, no. 2. Independent University of Moscow, pp. 181–203, 2014.
ista: Bounemoura A, Kaloshin V. 2014. Generic fast diffusion for a class of non-convex
Hamiltonians with two degrees of freedom. Moscow Mathematical Journal. 14(2),
181–203.
mla: Bounemoura, Abed, and Vadim Kaloshin. “Generic Fast Diffusion for a Class of
Non-Convex Hamiltonians with Two Degrees of Freedom.” Moscow Mathematical Journal,
vol. 14, no. 2, Independent University of Moscow, 2014, pp. 181–203, doi:10.17323/1609-4514-2014-14-2-181-203.
short: A. Bounemoura, V. Kaloshin, Moscow Mathematical Journal 14 (2014) 181–203.
date_created: 2020-09-18T10:47:09Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2021-01-12T08:19:43Z
day: '01'
doi: 10.17323/1609-4514-2014-14-2-181-203
extern: '1'
external_id:
arxiv:
- '1304.3050'
intvolume: ' 14'
issue: '2'
keyword:
- General Mathematics
language:
- iso: eng
month: '04'
oa_version: Preprint
page: 181-203
publication: Moscow Mathematical Journal
publication_identifier:
issn:
- 1609-3321
- 1609-4514
publication_status: published
publisher: Independent University of Moscow
quality_controlled: '1'
status: public
title: Generic fast diffusion for a class of non-convex Hamiltonians with two degrees
of freedom
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2014'
...
---
_id: '8500'
abstract:
- lang: eng
text: The main model studied in this paper is a lattice of pendula with a nearest‐neighbor
coupling. If the coupling is weak, then the system is near‐integrable and KAM
tori fill most of the phase space. For all KAM trajectories the energy of each
pendulum stays within a narrow band for all time. Still, we show that for an arbitrarily
weak coupling of a certain localized type, the neighboring pendula can exchange
energy. In fact, the energy can be transferred between the pendula in any prescribed
way.
article_processing_charge: No
article_type: original
author:
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Mark
full_name: Levi, Mark
last_name: Levi
- first_name: Maria
full_name: Saprykina, Maria
last_name: Saprykina
citation:
ama: Kaloshin V, Levi M, Saprykina M. Arnol′d diffusion in a pendulum lattice. Communications
on Pure and Applied Mathematics. 2014;67(5):748-775. doi:10.1002/cpa.21509
apa: Kaloshin, V., Levi, M., & Saprykina, M. (2014). Arnol′d diffusion in a
pendulum lattice. Communications on Pure and Applied Mathematics. Wiley.
https://doi.org/10.1002/cpa.21509
chicago: Kaloshin, Vadim, Mark Levi, and Maria Saprykina. “Arnol′d Diffusion in
a Pendulum Lattice.” Communications on Pure and Applied Mathematics. Wiley,
2014. https://doi.org/10.1002/cpa.21509.
ieee: V. Kaloshin, M. Levi, and M. Saprykina, “Arnol′d diffusion in a pendulum lattice,”
Communications on Pure and Applied Mathematics, vol. 67, no. 5. Wiley,
pp. 748–775, 2014.
ista: Kaloshin V, Levi M, Saprykina M. 2014. Arnol′d diffusion in a pendulum lattice.
Communications on Pure and Applied Mathematics. 67(5), 748–775.
mla: Kaloshin, Vadim, et al. “Arnol′d Diffusion in a Pendulum Lattice.” Communications
on Pure and Applied Mathematics, vol. 67, no. 5, Wiley, 2014, pp. 748–75,
doi:10.1002/cpa.21509.
short: V. Kaloshin, M. Levi, M. Saprykina, Communications on Pure and Applied Mathematics
67 (2014) 748–775.
date_created: 2020-09-18T10:47:01Z
date_published: 2014-05-01T00:00:00Z
date_updated: 2022-08-25T13:58:13Z
day: '01'
doi: 10.1002/cpa.21509
extern: '1'
intvolume: ' 67'
issue: '5'
keyword:
- Applied Mathematics
- General Mathematics
language:
- iso: eng
month: '05'
oa_version: None
page: 748-775
publication: Communications on Pure and Applied Mathematics
publication_identifier:
issn:
- 0010-3640
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Arnol′d diffusion in a pendulum lattice
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 67
year: '2014'
...
---
_id: '852'
abstract:
- lang: eng
text: 'Rapid divergence of gene copies after duplication is thought to determine
the fate of the copies and evolution of novel protein functions. However, data
on howlong the gene copies continue to experience an elevated rate of evolution
remain scarce. Standard theory of gene duplications based on some level of genetic
redundancy of gene copies predicts that the period of accelerated evolutionmust
end relatively quickly. Using a maximum-likelihood approach we estimate preduplication,
initial postduplication, and recent postduplication rates of evolution that occurred
in themammalian lineage.Wefind that both gene copies experience a similar in magnitude
acceleration in their rate of evolution. The copy located in the original genomic
position typically returns to the preduplication rates of evolution in a short
period of time. The burst of faster evolution of the copy that is located in a
new genomic position typically lasts longer. Furthermore, the fast-evolving copies
on average continue to evolve faster than the preduplication rates far longer
than predicted by standard theory of gene duplications.We hypothesize that the
prolonged elevated rates of evolution are determined by functional properties
that were acquired during, or soon after, the gene duplication event. '
author:
- first_name: Oriol
full_name: Rosello, Oriol P
last_name: Rosello
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Rosello O, Kondrashov F. Long-Term asymmetrical acceleration of protein evolution
after gene duplication. Genome Biology and Evolution. 2014;6(8):1949-1955.
doi:10.1093/gbe/evu159
apa: Rosello, O., & Kondrashov, F. (2014). Long-Term asymmetrical acceleration
of protein evolution after gene duplication. Genome Biology and Evolution.
Oxford University Press. https://doi.org/10.1093/gbe/evu159
chicago: Rosello, Oriol, and Fyodor Kondrashov. “Long-Term Asymmetrical Acceleration
of Protein Evolution after Gene Duplication.” Genome Biology and Evolution.
Oxford University Press, 2014. https://doi.org/10.1093/gbe/evu159.
ieee: O. Rosello and F. Kondrashov, “Long-Term asymmetrical acceleration of protein
evolution after gene duplication,” Genome Biology and Evolution, vol. 6,
no. 8. Oxford University Press, pp. 1949–1955, 2014.
ista: Rosello O, Kondrashov F. 2014. Long-Term asymmetrical acceleration of protein
evolution after gene duplication. Genome Biology and Evolution. 6(8), 1949–1955.
mla: Rosello, Oriol, and Fyodor Kondrashov. “Long-Term Asymmetrical Acceleration
of Protein Evolution after Gene Duplication.” Genome Biology and Evolution,
vol. 6, no. 8, Oxford University Press, 2014, pp. 1949–55, doi:10.1093/gbe/evu159.
short: O. Rosello, F. Kondrashov, Genome Biology and Evolution 6 (2014) 1949–1955.
date_created: 2018-12-11T11:48:51Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2021-01-12T08:19:51Z
day: '01'
doi: 10.1093/gbe/evu159
extern: 1
intvolume: ' 6'
issue: '8'
month: '08'
page: 1949 - 1955
publication: Genome Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '6797'
quality_controlled: 0
status: public
title: Long-Term asymmetrical acceleration of protein evolution after gene duplication
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 6
year: '2014'
...
---
_id: '856'
abstract:
- lang: eng
text: The emergence of new genes throughout evolution requires rewiring and extension
of regulatory networks. However, the molecular details of how the transcriptional
regulation of new gene copies evolves remain largely unexplored. Here we show
how duplication of a transcription factor gene allowed the emergence of two independent
regulatory circuits. Interestingly, the ancestral transcription factor was promiscuous
and could bind different motifs in its target promoters. After duplication, one
paralogue evolved increased binding specificity so that it only binds one type
of motif, whereas the other copy evolved a decreased activity so that it only
activates promoters that contain multiple binding sites. Interestingly, only a
few mutations in both the DNA-binding domains and in the promoter binding sites
were required to gradually disentangle the two networks. These results reveal
how duplication of a promiscuous transcription factor followed by concerted cis
and trans mutations allows expansion of a regulatory network.
acknowledgement: 'K.P. acknowledges financial support from TRIPLE I and a Belspo mobility
grant from the Belgian Federal Science Policy Office co-funded by the Marie Curie
Actions from the European Commission. Research in the lab of K.J.V. is supported
by ERC Starting Grant 241426, HFSP programme grant RGP0050/2013, VIB, EMBO YIP programme,
KU Leuven Programme Financing, FWO, and IWT. A.V. acknowledges RIKEN for the FPR
grant. The work of F.A.K. was supported by a grant of the HHMI International Early
Career Scientist Programme (grant #55007424), the Spanish Ministry of Economy and
Competitiveness (grant #BFU2012-31329) as part of the EMBO YIP programme, two grants
from the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia
Severo Ochoa 2013–2017 (grant #Sev-2012-0208)’ and (grant #BES-2013-064004) funded
by the European Regional Development Fund (ERDF), the European Union and the European
Research Council (grant #335980_EinME). K.V. is supported by an FWO postdoctoral
fellowship. Funders had no role in study design, data collection and analysis, decision
to publish or preparation of the manuscript.'
author:
- first_name: Ksenia
full_name: Pougach, Ksenia S
last_name: Pougach
- first_name: Arnout
full_name: Voet, Arnout R
last_name: Voet
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Karin
full_name: Voordeckers, Karin
last_name: Voordeckers
- first_name: Joaquin
full_name: Christiaens, Joaquin F
last_name: Christiaens
- first_name: Bianka
full_name: Baying, Bianka
last_name: Baying
- first_name: Vladimı́R
full_name: Bénès, Vladimı́r
last_name: Bénès
- first_name: Ryo
full_name: Sakai, Ryo
last_name: Sakai
- first_name: Jan
full_name: Aerts, Jan A
last_name: Aerts
- first_name: Bo
full_name: Zhu, Bo
last_name: Zhu
- first_name: Patrick
full_name: Van Dijck, Patrick
last_name: Van Dijck
- first_name: Kevin
full_name: Verstrepen, Kevin J
last_name: Verstrepen
citation:
ama: Pougach K, Voet A, Kondrashov F, et al. Duplication of a promiscuous transcription
factor drives the emergence of a new regulatory network. Nature Communications.
2014;5. doi:10.1038/ncomms5868
apa: Pougach, K., Voet, A., Kondrashov, F., Voordeckers, K., Christiaens, J., Baying,
B., … Verstrepen, K. (2014). Duplication of a promiscuous transcription factor
drives the emergence of a new regulatory network. Nature Communications.
Nature Publishing Group. https://doi.org/10.1038/ncomms5868
chicago: Pougach, Ksenia, Arnout Voet, Fyodor Kondrashov, Karin Voordeckers, Joaquin
Christiaens, Bianka Baying, Vladimı́R Bénès, et al. “Duplication of a Promiscuous
Transcription Factor Drives the Emergence of a New Regulatory Network.” Nature
Communications. Nature Publishing Group, 2014. https://doi.org/10.1038/ncomms5868.
ieee: K. Pougach et al., “Duplication of a promiscuous transcription factor
drives the emergence of a new regulatory network,” Nature Communications,
vol. 5. Nature Publishing Group, 2014.
ista: Pougach K, Voet A, Kondrashov F, Voordeckers K, Christiaens J, Baying B, Bénès
V, Sakai R, Aerts J, Zhu B, Van Dijck P, Verstrepen K. 2014. Duplication of a
promiscuous transcription factor drives the emergence of a new regulatory network.
Nature Communications. 5.
mla: Pougach, Ksenia, et al. “Duplication of a Promiscuous Transcription Factor
Drives the Emergence of a New Regulatory Network.” Nature Communications,
vol. 5, Nature Publishing Group, 2014, doi:10.1038/ncomms5868.
short: K. Pougach, A. Voet, F. Kondrashov, K. Voordeckers, J. Christiaens, B. Baying,
V. Bénès, R. Sakai, J. Aerts, B. Zhu, P. Van Dijck, K. Verstrepen, Nature Communications
5 (2014).
date_created: 2018-12-11T11:48:52Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T08:20:01Z
day: '01'
doi: 10.1038/ncomms5868
extern: 1
intvolume: ' 5'
month: '01'
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '6790'
quality_controlled: 0
status: public
title: Duplication of a promiscuous transcription factor drives the emergence of a
new regulatory network
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 5
year: '2014'
...
---
_id: '863'
abstract:
- lang: eng
text: The origins of neural systems remain unresolved. In contrast to other basal
metazoans, ctenophores (comb jellies) have both complex nervous and mesoderm-derived
muscular systems. These holoplanktonic predators also have sophisticated ciliated
locomotion, behaviour and distinct development. Here we present the draft genome
of Pleurobrachia bachei, Pacific sea gooseberry, together with ten other ctenophore
transcriptomes, and show that they are remarkably distinct from other animal genomes
in their content of neurogenic, immune and developmental genes. Our integrative
analyses place Ctenophora as the earliest lineage within Metazoa. This hypothesis
is supported by comparative analysis of multiple gene families, including the
apparent absence of HOX genes, canonical microRNA machinery, and reduced immune
complement in ctenophores. Although two distinct nervous systems are well recognized
in ctenophores, many bilaterian neuron-specific genes and genes of 'classical'
neurotransmitter pathways either are absent or, if present, are not expressed
in neurons. Our metabolomic and physiological data are consistent with the hypothesis
that ctenophore neural systems, and possibly muscle specification, evolved independently
from those in other animals.
acknowledgement: We thank Friday Harbor Laboratories for facilities during animal
collection and Marine Genomics apprenticeships (L.L.M., B.J.S.); E. Dabe, G. Winters,
J. Netherton, N. Churches and C. Bostwick for help with animal, tissue, in situ,
RNA and DNA assays; and X.-X. Tan, F. Lu and T. Tyazelova for sequencing. We thank
F. Nivens for videos and P. L. Williams for database support. This work was supported
by NSF (NSF-0744649 and NSF CNS-0821622 to L.L.M.; NSF CHE-1111705 to J.V.S.), NIH
(1R01GM097502, R01MH097062, R21RR025699 and 5R21DA030118 to L.L.M.; P30 DA018310
to J.V.S.; R01 AG029360 and 1S10RR027052 to E.I.R.), NASA NNX13AJ31G (to K.M.H.,
L.L.M. and K.M.K.), NSERC 458115 and 211598 (J.P.R.), University of Florida Opportunity
Funds/McKnight Brain Research and Florida Biodiversity Institute (L.L.M.), Rostock
Inc./A.V. Chikunov (E.I.R.), grant from Russian Federation Government 14.B25.31.0033
(Resolution No.220) (E.I.R.). F.A.K., I.S.P. and R.D. were supported by HHMI (55007424),
EMBO and MINECO (BFU2012-31329 and Sev-2012-0208). Contributions of AU Marine Biology
Program 117 and Molette laboratory 22.
author:
- first_name: Leonid
full_name: Moroz, Leonid L
last_name: Moroz
- first_name: Kevin
full_name: Kocot, Kevin M
last_name: Kocot
- first_name: Mathew
full_name: Citarella, Mathew R
last_name: Citarella
- first_name: Sohn
full_name: Dosung, Sohn
last_name: Dosung
- first_name: Tigran
full_name: Norekian, Tigran P
last_name: Norekian
- first_name: Inna
full_name: Povolotskaya, Inna
last_name: Povolotskaya
- first_name: Anastasia
full_name: Grigorenko, Anastasia P
last_name: Grigorenko
- first_name: Christopher
full_name: Dailey, Christopher A
last_name: Dailey
- first_name: Eugene
full_name: Berezikov, Eugene
last_name: Berezikov
- first_name: Katherine
full_name: Buckley, Katherine M
last_name: Buckley
- first_name: Andrey
full_name: Ptitsyn, Andrey A
last_name: Ptitsyn
- first_name: Denis
full_name: Reshetov, Denis A
last_name: Reshetov
- first_name: Krishanu
full_name: Mukherjee, Krishanu
last_name: Mukherjee
- first_name: Tatiana
full_name: Moroz, Tatiana P
last_name: Moroz
- first_name: Yelena
full_name: Bobkova, Yelena V
last_name: Bobkova
- first_name: Fahong
full_name: Yu, Fahong
last_name: Yu
- first_name: Vladimir
full_name: Kapitonov, Vladimir V
last_name: Kapitonov
- first_name: Jerzy
full_name: Jurka, Jerzy W
last_name: Jurka
- first_name: Yuriy
full_name: Bobkov, Yuriy V
last_name: Bobkov
- first_name: Joshua
full_name: Swore, Joshua J
last_name: Swore
- first_name: David
full_name: Girardo, David O
last_name: Girardo
- first_name: Alexander
full_name: Fodor, Alexander
last_name: Fodor
- first_name: Fedor
full_name: Gusev, Fedor E
last_name: Gusev
- first_name: Rachel
full_name: Sanford, Rachel S
last_name: Sanford
- first_name: Rebecca
full_name: Bruders, Rebecca
last_name: Bruders
- first_name: Ellen
full_name: Kittler, Ellen L
last_name: Kittler
- first_name: Claudia
full_name: Mills, Claudia E
last_name: Mills
- first_name: Jonathan
full_name: Rast, Jonathan P
last_name: Rast
- first_name: Romain
full_name: Derelle, Romain
last_name: Derelle
- first_name: Victor
full_name: Solovyev, Victor
last_name: Solovyev
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Billie
full_name: Swalla, Billie J
last_name: Swalla
- first_name: Jonathan
full_name: Sweedler, Jonathan V
last_name: Sweedler
- first_name: Evgeny
full_name: Rogaev, Evgeny I
last_name: Rogaev
- first_name: Kenneth
full_name: Halanych, Kenneth M
last_name: Halanych
- first_name: Andrea
full_name: Kohn, Andrea B
last_name: Kohn
citation:
ama: Moroz L, Kocot K, Citarella M, et al. The ctenophore genome and the evolutionary
origins of neural systems. Nature. 2014;510(7503):109-114. doi:10.1038/nature13400
apa: Moroz, L., Kocot, K., Citarella, M., Dosung, S., Norekian, T., Povolotskaya,
I., … Kohn, A. (2014). The ctenophore genome and the evolutionary origins of neural
systems. Nature. Nature Publishing Group. https://doi.org/10.1038/nature13400
chicago: Moroz, Leonid, Kevin Kocot, Mathew Citarella, Sohn Dosung, Tigran Norekian,
Inna Povolotskaya, Anastasia Grigorenko, et al. “The Ctenophore Genome and the
Evolutionary Origins of Neural Systems.” Nature. Nature Publishing Group,
2014. https://doi.org/10.1038/nature13400.
ieee: L. Moroz et al., “The ctenophore genome and the evolutionary origins
of neural systems,” Nature, vol. 510, no. 7503. Nature Publishing Group,
pp. 109–114, 2014.
ista: Moroz L, Kocot K, Citarella M, Dosung S, Norekian T, Povolotskaya I, Grigorenko
A, Dailey C, Berezikov E, Buckley K, Ptitsyn A, Reshetov D, Mukherjee K, Moroz
T, Bobkova Y, Yu F, Kapitonov V, Jurka J, Bobkov Y, Swore J, Girardo D, Fodor
A, Gusev F, Sanford R, Bruders R, Kittler E, Mills C, Rast J, Derelle R, Solovyev
V, Kondrashov F, Swalla B, Sweedler J, Rogaev E, Halanych K, Kohn A. 2014. The
ctenophore genome and the evolutionary origins of neural systems. Nature. 510(7503),
109–114.
mla: Moroz, Leonid, et al. “The Ctenophore Genome and the Evolutionary Origins of
Neural Systems.” Nature, vol. 510, no. 7503, Nature Publishing Group, 2014,
pp. 109–14, doi:10.1038/nature13400.
short: L. Moroz, K. Kocot, M. Citarella, S. Dosung, T. Norekian, I. Povolotskaya,
A. Grigorenko, C. Dailey, E. Berezikov, K. Buckley, A. Ptitsyn, D. Reshetov, K.
Mukherjee, T. Moroz, Y. Bobkova, F. Yu, V. Kapitonov, J. Jurka, Y. Bobkov, J.
Swore, D. Girardo, A. Fodor, F. Gusev, R. Sanford, R. Bruders, E. Kittler, C.
Mills, J. Rast, R. Derelle, V. Solovyev, F. Kondrashov, B. Swalla, J. Sweedler,
E. Rogaev, K. Halanych, A. Kohn, Nature 510 (2014) 109–114.
date_created: 2018-12-11T11:48:54Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T08:20:21Z
day: '01'
doi: 10.1038/nature13400
extern: 1
intvolume: ' 510'
issue: '7503'
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '01'
page: 109 - 114
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6785'
quality_controlled: 0
status: public
title: The ctenophore genome and the evolutionary origins of neural systems
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
volume: 510
year: '2014'
...
---
_id: '865'
abstract:
- lang: eng
text: Research on existing drugs often discovers novel mechanisms of their action
and leads to the expansion of their therapeutic scope and subsequent remarketing.
The Wnt signaling pathway is of the immediate therapeutic relevance, as it plays
critical roles in cancer development and progression. However, drugs which disrupt
this pathway are unavailable despite the high demand. Here we report an attempt
to identify antagonists of the Wnt-FZD interaction among the library of the FDA-approved
drugs. We performed an in silico screening which brought up several potential
antagonists of the ligand-receptor interaction. 14 of these substances were tested
using the TopFlash luciferase reporter assay and four of them identified as active
and specific inhibitors of the Wnt3a-induced signaling. However, further analysis
through GTP-binding and β-catenin stabilization assays showed that the compounds
do not target the Wnt-FZD pair, but inhibit the signaling at downstream levels.
We further describe the previously unknown inhibitory activity of an anti-leprosy
drug clofazimine in the Wnt pathway and provide data demonstrating its efficiency
in suppressing growth of Wnt-dependent triple-negative breast cancer cells. These
data provide a basis for further investigations of the efficiency of clofazimine
in treatment of Wnt-dependent cancers.
author:
- first_name: Alexey
full_name: Koval, Alexey V
last_name: Koval
- first_name: Peter
full_name: Vlasov, Peter K
last_name: Vlasov
- first_name: Polina
full_name: Shichkova, Polina
last_name: Shichkova
- first_name: S
full_name: Khunderyakova, S
last_name: Khunderyakova
- first_name: Yury
full_name: Markov, Yury
last_name: Markov
- first_name: J
full_name: Panchenko, J
last_name: Panchenko
- first_name: A
full_name: Volodina, A
last_name: Volodina
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Vladimir
full_name: Katanaev, Vladimir L
last_name: Katanaev
citation:
ama: Koval A, Vlasov P, Shichkova P, et al. Anti leprosy drug clofazimine inhibits
growth of triple-negative breast cancer cells via inhibition of canonical Wnt
signaling. Biochemical Pharmacology. 2014;87(4):571-578. doi:10.1016/j.bcp.2013.12.007
apa: Koval, A., Vlasov, P., Shichkova, P., Khunderyakova, S., Markov, Y., Panchenko,
J., … Katanaev, V. (2014). Anti leprosy drug clofazimine inhibits growth of triple-negative
breast cancer cells via inhibition of canonical Wnt signaling. Biochemical
Pharmacology. Elsevier. https://doi.org/10.1016/j.bcp.2013.12.007
chicago: Koval, Alexey, Peter Vlasov, Polina Shichkova, S Khunderyakova, Yury Markov,
J Panchenko, A Volodina, Fyodor Kondrashov, and Vladimir Katanaev. “Anti Leprosy
Drug Clofazimine Inhibits Growth of Triple-Negative Breast Cancer Cells via Inhibition
of Canonical Wnt Signaling.” Biochemical Pharmacology. Elsevier, 2014.
https://doi.org/10.1016/j.bcp.2013.12.007.
ieee: A. Koval et al., “Anti leprosy drug clofazimine inhibits growth of
triple-negative breast cancer cells via inhibition of canonical Wnt signaling,”
Biochemical Pharmacology, vol. 87, no. 4. Elsevier, pp. 571–578, 2014.
ista: Koval A, Vlasov P, Shichkova P, Khunderyakova S, Markov Y, Panchenko J, Volodina
A, Kondrashov F, Katanaev V. 2014. Anti leprosy drug clofazimine inhibits growth
of triple-negative breast cancer cells via inhibition of canonical Wnt signaling.
Biochemical Pharmacology. 87(4), 571–578.
mla: Koval, Alexey, et al. “Anti Leprosy Drug Clofazimine Inhibits Growth of Triple-Negative
Breast Cancer Cells via Inhibition of Canonical Wnt Signaling.” Biochemical
Pharmacology, vol. 87, no. 4, Elsevier, 2014, pp. 571–78, doi:10.1016/j.bcp.2013.12.007.
short: A. Koval, P. Vlasov, P. Shichkova, S. Khunderyakova, Y. Markov, J. Panchenko,
A. Volodina, F. Kondrashov, V. Katanaev, Biochemical Pharmacology 87 (2014) 571–578.
date_created: 2018-12-11T11:48:55Z
date_published: 2014-02-15T00:00:00Z
date_updated: 2021-01-12T08:20:24Z
day: '15'
doi: 10.1016/j.bcp.2013.12.007
extern: 1
intvolume: ' 87'
issue: '4'
month: '02'
page: 571 - 578
publication: Biochemical Pharmacology
publication_status: published
publisher: Elsevier
publist_id: '6782'
quality_controlled: 0
status: public
title: Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer
cells via inhibition of canonical Wnt signaling
type: journal_article
volume: 87
year: '2014'
...
---
_id: '925'
abstract:
- lang: eng
text: The morphological stability of biological tubes is crucial for the efficient
circulation of fluids and gases. Failure of this stability causes irregularly
shaped tubes found in multiple pathological conditions. Here, we report that Drosophila
mutants of the ESCRT III component Shrub/Vps32 exhibit a strikingly elongated
sinusoidal tube phenotype. This is caused by excessive apical membrane synthesis
accompanied by the ectopic accumulation and overactivation of Crumbs in swollen
endosomes. Furthermore, we demonstrate that the apical extracellular matrix (aECM)
of the tracheal tube is a viscoelastic material coupled with the apical membrane.
We present a simple mechanical model in which aECM elasticity, apical membrane
growth, and their interaction are three vital parameters determining the stability
of biological tubes. Our findings demonstrate a mechanical role for the extracellular
matrix and suggest that the interaction of the apical membrane and an elastic
aECM determines the final morphology of biological tubes independent of cell shape.
acknowledgement: We thank F. Gao, R.E. Ward, S. Luschnig, T. Okajima, M. Affolter,
D. Bilder, E. Knust, T. Tanaka, A. Nakamura, C. Samakovlis, K. Saigo, M. Furuse,
the Bloomington Stock Center, Drosophila Genetic Resource Center in Kyoto, Japan,
and the Developmental Studies Hybridoma Bank for generously providing antibodies
and fly stocks; H. Wada for UAS-3×TagRFP fly and dye injection; Y.H. Zhang for plasmid
and protocol for CBP preparation; and J. Prost and J.F. Joanny for their support
for the project and discussion. We also thank T. Shibata, Y. Morishita, T. Kondo,
and G. Sheng for critically reading the manuscript. This work was supported by a
Grant-in-Aid for Scientific Research on Innovative Areas from MEXT Japan to S.H.
and the RIKEN Foreign Postdoctoral Researcher Program to B.D.
article_processing_charge: No
author:
- first_name: Bo
full_name: Dong, Bo
last_name: Dong
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Shigeo
full_name: Hayashi, Shigeo
last_name: Hayashi
citation:
ama: Dong B, Hannezo EB, Hayashi S. Balance between apical membrane growth and luminal
matrix resistance determines epithelial tubule shape. Cell Reports. 2014;7(4):941-950.
doi:10.1016/j.celrep.2014.03.066
apa: Dong, B., Hannezo, E. B., & Hayashi, S. (2014). Balance between apical
membrane growth and luminal matrix resistance determines epithelial tubule shape.
Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2014.03.066
chicago: Dong, Bo, Edouard B Hannezo, and Shigeo Hayashi. “Balance between Apical
Membrane Growth and Luminal Matrix Resistance Determines Epithelial Tubule Shape.”
Cell Reports. Cell Press, 2014. https://doi.org/10.1016/j.celrep.2014.03.066.
ieee: B. Dong, E. B. Hannezo, and S. Hayashi, “Balance between apical membrane growth
and luminal matrix resistance determines epithelial tubule shape,” Cell Reports,
vol. 7, no. 4. Cell Press, pp. 941–950, 2014.
ista: Dong B, Hannezo EB, Hayashi S. 2014. Balance between apical membrane growth
and luminal matrix resistance determines epithelial tubule shape. Cell Reports.
7(4), 941–950.
mla: Dong, Bo, et al. “Balance between Apical Membrane Growth and Luminal Matrix
Resistance Determines Epithelial Tubule Shape.” Cell Reports, vol. 7, no.
4, Cell Press, 2014, pp. 941–50, doi:10.1016/j.celrep.2014.03.066.
short: B. Dong, E.B. Hannezo, S. Hayashi, Cell Reports 7 (2014) 941–950.
date_created: 2018-12-11T11:49:14Z
date_published: 2014-05-22T00:00:00Z
date_updated: 2021-01-12T08:21:57Z
day: '22'
doi: 10.1016/j.celrep.2014.03.066
extern: '1'
intvolume: ' 7'
issue: '4'
language:
- iso: eng
month: '05'
oa_version: None
page: 941 - 950
publication: Cell Reports
publication_status: published
publisher: Cell Press
publist_id: '6515'
status: public
title: Balance between apical membrane growth and luminal matrix resistance determines
epithelial tubule shape
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2014'
...
---
_id: '927'
abstract:
- lang: eng
text: Morphogenesis during embryo development requires the coordination of mechanical
forces to generate the macroscopic shapes of organs. We propose a minimal theoretical
model, based on cell adhesion and actomyosin contractility, which describes the
various shapes of epithelial cells and the bending and buckling of epithelial
sheets, as well as the relative stability of cellular tubes and spheres. We show
that, to understand these processes, a full 3D description of the cells is needed,
but that simple scaling laws can still be derived. The morphologies observed in
vivo can be understood as stable points of mechanical equations and the transitions
between them are either continuous or discontinuous. We then focus on epithelial
sheet bending, a ubiquitous morphogenetic process. We calculate the curvature
of an epithelium as a function of actin belt tension as well as of cell-cell and
and cell-substrate tension. The model allows for a comparison of the relative
stabilities of spherical or cylindrical cellular structures (acini or tubes).
Finally, we propose a unique type of buckling instability of epithelia, driven
by a flattening of individual cell shapes, and discuss experimental tests to verify
our predictions.
article_processing_charge: No
author:
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Jacques
full_name: Prost, Jacques
last_name: Prost
- first_name: Jean
full_name: Joanny, Jean
last_name: Joanny
citation:
ama: Hannezo EB, Prost J, Joanny J. Theory of epithelial sheet morphology in three
dimensions. PNAS. 2014;111(1):27-32. doi:10.1073/pnas.1312076111
apa: Hannezo, E. B., Prost, J., & Joanny, J. (2014). Theory of epithelial sheet
morphology in three dimensions. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1312076111
chicago: Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Theory of Epithelial
Sheet Morphology in Three Dimensions.” PNAS. National Academy of Sciences,
2014. https://doi.org/10.1073/pnas.1312076111.
ieee: E. B. Hannezo, J. Prost, and J. Joanny, “Theory of epithelial sheet morphology
in three dimensions,” PNAS, vol. 111, no. 1. National Academy of Sciences,
pp. 27–32, 2014.
ista: Hannezo EB, Prost J, Joanny J. 2014. Theory of epithelial sheet morphology
in three dimensions. PNAS. 111(1), 27–32.
mla: Hannezo, Edouard B., et al. “Theory of Epithelial Sheet Morphology in Three
Dimensions.” PNAS, vol. 111, no. 1, National Academy of Sciences, 2014,
pp. 27–32, doi:10.1073/pnas.1312076111.
short: E.B. Hannezo, J. Prost, J. Joanny, PNAS 111 (2014) 27–32.
date_created: 2018-12-11T11:49:14Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T08:21:58Z
day: '01'
doi: 10.1073/pnas.1312076111
extern: '1'
intvolume: ' 111'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 27 - 32
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6517'
status: public
title: Theory of epithelial sheet morphology in three dimensions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 111
year: '2014'
...
---
_id: '9519'
abstract:
- lang: eng
text: Transposons are selfish genetic sequences that can increase their copy number
and inflict substantial damage on their hosts. To combat these genomic parasites,
plants have evolved multiple pathways to identify and silence transposons by methylating
their DNA. Plants have also evolved mechanisms to limit the collateral damage
from the antitransposon machinery. In this review, we examine recent developments
that have elucidated many of the molecular workings of these pathways. We also
highlight the evidence that the methylation and demethylation pathways interact,
indicating that plants have a highly sophisticated, integrated system of transposon
defense that has an important role in the regulation of gene expression.
article_processing_charge: No
article_type: review
author:
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Kim MY, Zilberman D. DNA methylation as a system of plant genomic immunity.
Trends in Plant Science. 2014;19(5):320-326. doi:10.1016/j.tplants.2014.01.014
apa: Kim, M. Y., & Zilberman, D. (2014). DNA methylation as a system of plant
genomic immunity. Trends in Plant Science. Elsevier. https://doi.org/10.1016/j.tplants.2014.01.014
chicago: Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant
Genomic Immunity.” Trends in Plant Science. Elsevier, 2014. https://doi.org/10.1016/j.tplants.2014.01.014.
ieee: M. Y. Kim and D. Zilberman, “DNA methylation as a system of plant genomic
immunity,” Trends in Plant Science, vol. 19, no. 5. Elsevier, pp. 320–326,
2014.
ista: Kim MY, Zilberman D. 2014. DNA methylation as a system of plant genomic immunity.
Trends in Plant Science. 19(5), 320–326.
mla: Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant
Genomic Immunity.” Trends in Plant Science, vol. 19, no. 5, Elsevier, 2014,
pp. 320–26, doi:10.1016/j.tplants.2014.01.014.
short: M.Y. Kim, D. Zilberman, Trends in Plant Science 19 (2014) 320–326.
date_created: 2021-06-07T14:38:09Z
date_published: 2014-05-04T00:00:00Z
date_updated: 2021-12-14T08:24:48Z
day: '04'
department:
- _id: DaZi
doi: 10.1016/j.tplants.2014.01.014
extern: '1'
external_id:
pmid:
- '24618094 '
intvolume: ' 19'
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
page: 320-326
pmid: 1
publication: Trends in Plant Science
publication_identifier:
eissn:
- 1878-4372
issn:
- 1360-1385
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA methylation as a system of plant genomic immunity
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 19
year: '2014'
...
---
_id: '96'
abstract:
- lang: eng
text: Multielectron spin qubits are demonstrated, and performance examined by comparing
coherent exchange oscillations in coupled single-electron and multielectron quantum
dots, measured in the same device. Fast (>1 GHz) exchange oscillations with
a quality factor Q∼15 are found for the multielectron case, compared to Q∼2 for
the single-electron case, the latter consistent with experiments in the literature.
A model of dephasing that includes voltage and hyperfine noise is developed that
is in good agreement with both single- and multielectron data, though in both
cases additional exchange-independent dephasing is needed to obtain quantitative
agreement across a broad parameter range.
acknowledgement: The research is supported by the Intelligence Advanced Research Projects
Activity (IARPA), through the Army Research Office Grant No. W911NF-12-1-0354, the
DARPA QuEST Program, the Department of Energy, Office of Science, and the Danish
National Research Foundation.
article_number: '026801'
author:
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: Ferdinand
full_name: Kuemmeth, Ferdinand
last_name: Kuemmeth
- first_name: Micah
full_name: Hanson, Micah
last_name: Hanson
- first_name: Arthur
full_name: Gossard, Arthur
last_name: Gossard
- first_name: Charles
full_name: Marcus, Charles
last_name: Marcus
citation:
ama: Higginbotham AP, Kuemmeth F, Hanson M, Gossard A, Marcus C. Coherent operations
and screening in multielectron spin qubits. APS Physics, Physical Review Letters.
2014;112(2). doi:10.1103/PhysRevLett.112.026801
apa: Higginbotham, A. P., Kuemmeth, F., Hanson, M., Gossard, A., & Marcus, C.
(2014). Coherent operations and screening in multielectron spin qubits. APS
Physics, Physical Review Letters. American Physiological Society. https://doi.org/10.1103/PhysRevLett.112.026801
chicago: Higginbotham, Andrew P, Ferdinand Kuemmeth, Micah Hanson, Arthur Gossard,
and Charles Marcus. “Coherent Operations and Screening in Multielectron Spin Qubits.”
APS Physics, Physical Review Letters. American Physiological Society, 2014.
https://doi.org/10.1103/PhysRevLett.112.026801.
ieee: A. P. Higginbotham, F. Kuemmeth, M. Hanson, A. Gossard, and C. Marcus, “Coherent
operations and screening in multielectron spin qubits,” APS Physics, Physical
Review Letters, vol. 112, no. 2. American Physiological Society, 2014.
ista: Higginbotham AP, Kuemmeth F, Hanson M, Gossard A, Marcus C. 2014. Coherent
operations and screening in multielectron spin qubits. APS Physics, Physical Review
Letters. 112(2), 026801.
mla: Higginbotham, Andrew P., et al. “Coherent Operations and Screening in Multielectron
Spin Qubits.” APS Physics, Physical Review Letters, vol. 112, no. 2, 026801,
American Physiological Society, 2014, doi:10.1103/PhysRevLett.112.026801.
short: A.P. Higginbotham, F. Kuemmeth, M. Hanson, A. Gossard, C. Marcus, APS Physics,
Physical Review Letters 112 (2014).
date_created: 2018-12-11T11:44:36Z
date_published: 2014-01-14T00:00:00Z
date_updated: 2021-01-12T08:22:14Z
day: '14'
doi: 10.1103/PhysRevLett.112.026801
extern: '1'
external_id:
arxiv:
- '1306.2720'
intvolume: ' 112'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1306.2720
month: '01'
oa: 1
oa_version: Preprint
publication: APS Physics, Physical Review Letters
publication_status: published
publisher: American Physiological Society
publist_id: '7958'
quality_controlled: '1'
status: public
title: Coherent operations and screening in multielectron spin qubits
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2014'
...
---
_id: '9594'
abstract:
- lang: eng
text: Let d≥3 be a fixed integer. We give an asympotic formula for the expected
number of spanning trees in a uniformly random d-regular graph with n vertices.
(The asymptotics are as n→∞, restricted to even n if d is odd.) We also obtain
the asymptotic distribution of the number of spanning trees in a uniformly random
cubic graph, and conjecture that the corresponding result holds for arbitrary
(fixed) d. Numerical evidence is presented which supports our conjecture.
article_number: P1.45
article_processing_charge: No
article_type: original
author:
- first_name: Catherine
full_name: Greenhill, Catherine
last_name: Greenhill
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: David
full_name: Wind, David
last_name: Wind
citation:
ama: Greenhill C, Kwan MA, Wind D. On the number of spanning trees in random regular
graphs. The Electronic Journal of Combinatorics. 2014;21(1). doi:10.37236/3752
apa: Greenhill, C., Kwan, M. A., & Wind, D. (2014). On the number of spanning
trees in random regular graphs. The Electronic Journal of Combinatorics.
The Electronic Journal of Combinatorics. https://doi.org/10.37236/3752
chicago: Greenhill, Catherine, Matthew Alan Kwan, and David Wind. “On the Number
of Spanning Trees in Random Regular Graphs.” The Electronic Journal of Combinatorics.
The Electronic Journal of Combinatorics, 2014. https://doi.org/10.37236/3752.
ieee: C. Greenhill, M. A. Kwan, and D. Wind, “On the number of spanning trees in
random regular graphs,” The Electronic Journal of Combinatorics, vol. 21,
no. 1. The Electronic Journal of Combinatorics, 2014.
ista: Greenhill C, Kwan MA, Wind D. 2014. On the number of spanning trees in random
regular graphs. The Electronic Journal of Combinatorics. 21(1), P1.45.
mla: Greenhill, Catherine, et al. “On the Number of Spanning Trees in Random Regular
Graphs.” The Electronic Journal of Combinatorics, vol. 21, no. 1, P1.45,
The Electronic Journal of Combinatorics, 2014, doi:10.37236/3752.
short: C. Greenhill, M.A. Kwan, D. Wind, The Electronic Journal of Combinatorics
21 (2014).
date_created: 2021-06-23T06:29:35Z
date_published: 2014-02-28T00:00:00Z
date_updated: 2023-02-23T14:02:12Z
day: '28'
doi: 10.37236/3752
extern: '1'
external_id:
arxiv:
- '1309.6710'
intvolume: ' 21'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.37236/3752
month: '02'
oa: 1
oa_version: Published Version
publication: The Electronic Journal of Combinatorics
publication_identifier:
eissn:
- 1077-8926
publication_status: published
publisher: The Electronic Journal of Combinatorics
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the number of spanning trees in random regular graphs
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 21
year: '2014'
...
---
_id: '9655'
abstract:
- lang: eng
text: Correlative microscopy incorporates the specificity of fluorescent protein
labeling into high-resolution electron micrographs. Several approaches exist for
correlative microscopy, most of which have used the green fluorescent protein
(GFP) as the label for light microscopy. Here we use chemical tagging and synthetic
fluorophores instead, in order to achieve protein-specific labeling, and to perform
multicolor imaging. We show that synthetic fluorophores preserve their post-embedding
fluorescence in the presence of uranyl acetate. Post-embedding fluorescence is
of such quality that the specimen can be prepared with identical protocols for
scanning electron microscopy (SEM) and transmission electron microscopy (TEM);
this is particularly valuable when singular or otherwise difficult samples are
examined. We show that synthetic fluorophores give bright, well-resolved signals
in super-resolution light microscopy, enabling us to superimpose light microscopic
images with a precision of up to 25 nm in the x–y plane on electron micrographs.
To exemplify the preservation quality of our new method we visualize the molecular
arrangement of cadherins in adherens junctions of mouse epithelial cells.
article_processing_charge: No
article_type: original
author:
- first_name: Mario
full_name: Perkovic, Mario
last_name: Perkovic
- first_name: Michael
full_name: Kunz, Michael
last_name: Kunz
- first_name: Ulrike
full_name: Endesfelder, Ulrike
last_name: Endesfelder
- first_name: Stefanie
full_name: Bunse, Stefanie
last_name: Bunse
- first_name: Christoph
full_name: Wigge, Christoph
last_name: Wigge
- first_name: Zhou
full_name: Yu, Zhou
last_name: Yu
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
- first_name: Margot P.
full_name: Scheffer, Margot P.
last_name: Scheffer
- first_name: Anja
full_name: Seybert, Anja
last_name: Seybert
- first_name: Sebastian
full_name: Malkusch, Sebastian
last_name: Malkusch
- first_name: Erin M.
full_name: Schuman, Erin M.
last_name: Schuman
- first_name: Mike
full_name: Heilemann, Mike
last_name: Heilemann
- first_name: Achilleas S.
full_name: Frangakis, Achilleas S.
last_name: Frangakis
citation:
ama: Perkovic M, Kunz M, Endesfelder U, et al. Correlative light- and electron microscopy
with chemical tags. Journal of Structural Biology. 2014;186(2):205-213.
doi:10.1016/j.jsb.2014.03.018
apa: Perkovic, M., Kunz, M., Endesfelder, U., Bunse, S., Wigge, C., Yu, Z., … Frangakis,
A. S. (2014). Correlative light- and electron microscopy with chemical tags. Journal
of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2014.03.018
chicago: Perkovic, Mario, Michael Kunz, Ulrike Endesfelder, Stefanie Bunse, Christoph
Wigge, Zhou Yu, Victor-Valentin Hodirnau, et al. “Correlative Light- and Electron
Microscopy with Chemical Tags.” Journal of Structural Biology. Elsevier,
2014. https://doi.org/10.1016/j.jsb.2014.03.018.
ieee: M. Perkovic et al., “Correlative light- and electron microscopy with
chemical tags,” Journal of Structural Biology, vol. 186, no. 2. Elsevier,
pp. 205–213, 2014.
ista: Perkovic M, Kunz M, Endesfelder U, Bunse S, Wigge C, Yu Z, Hodirnau V-V, Scheffer
MP, Seybert A, Malkusch S, Schuman EM, Heilemann M, Frangakis AS. 2014. Correlative
light- and electron microscopy with chemical tags. Journal of Structural Biology.
186(2), 205–213.
mla: Perkovic, Mario, et al. “Correlative Light- and Electron Microscopy with Chemical
Tags.” Journal of Structural Biology, vol. 186, no. 2, Elsevier, 2014,
pp. 205–13, doi:10.1016/j.jsb.2014.03.018.
short: M. Perkovic, M. Kunz, U. Endesfelder, S. Bunse, C. Wigge, Z. Yu, V.-V. Hodirnau,
M.P. Scheffer, A. Seybert, S. Malkusch, E.M. Schuman, M. Heilemann, A.S. Frangakis,
Journal of Structural Biology 186 (2014) 205–213.
date_created: 2021-07-14T09:05:42Z
date_published: 2014-05-01T00:00:00Z
date_updated: 2021-07-22T08:26:32Z
day: '01'
ddc:
- '570'
doi: 10.1016/j.jsb.2014.03.018
extern: '1'
external_id:
pmid:
- '24698954'
file:
- access_level: open_access
checksum: a322991b43cdc5935c99db88d285aa3a
content_type: application/pdf
creator: asandaue
date_created: 2021-07-22T08:06:34Z
date_updated: 2021-07-22T08:06:34Z
file_id: '9701'
file_name: 2014_JournalOfStructuralBiology_Perkovic.pdf
file_size: 3454628
relation: main_file
success: 1
file_date_updated: 2021-07-22T08:06:34Z
has_accepted_license: '1'
intvolume: ' 186'
issue: '2'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/3.0/
month: '05'
oa: 1
oa_version: Published Version
page: 205-213
pmid: 1
publication: Journal of Structural Biology
publication_identifier:
issn:
- 1047-8477
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Correlative light- and electron microscopy with chemical tags
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND
3.0)
short: CC BY-NC-ND (3.0)
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 186
year: '2014'
...
---
_id: '9686'
abstract:
- lang: eng
text: It is well known that ultrasonic vibration can soften metals, and this phenomenon
has been widely exploited in industrial applications concerning metal forming
and bonding. Recent experiments show that the simultaneous application of oscillatory
stresses from audible to ultrasonic frequency ranges can lead to not only softening
but also significant dislocation annihilation and subgrain formation in metal
samples from the nano- to macro-size range. These findings indicate that the existing
understanding of ultrasound softening – that the vibrations either impose additional
stress waves to augment the quasi-static applied load, or cause heating of the
metal, whereas the metal’s intrinsic deformation resistance or mechanism remains
unaltered – is far from complete. To understand the softening and the associated
enhanced subgrain formation and dislocation annihilation, a new simulator based
on the dynamics of dislocation-density functions is employed. This new simulator
considers the flux, production and annihilation, as well as the Taylor and elastic
interactions between dislocation densities. Softening during vibrations as well
as enhanced cell formation is predicted. The simulations reveal the main mechanism
for subcell formation under oscillatory loadings to be the enhanced elimination
of statistically stored dislocations (SSDs) by the oscillatory stress, leaving
behind geometrically necessary dislocations with low Schmid factors which then
form the subgrain walls. The oscillatory stress helps the depletion of the SSDs,
because the chance for them to meet up and annihilate is increased with reversals
of dislocation motions. This is the first simulation effort to successfully predict
the cell formation phenomenon under vibratory loadings.
article_processing_charge: No
article_type: original
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: H.S.
full_name: Leung, H.S.
last_name: Leung
- first_name: A.H.W.
full_name: Ngan, A.H.W.
last_name: Ngan
citation:
ama: Cheng B, Leung HS, Ngan AHW. Strength of metals under vibrations – dislocation-density-function
dynamics simulations. Philosophical Magazine. 2014;95(16-18):1845-1865.
doi:10.1080/14786435.2014.897008
apa: Cheng, B., Leung, H. S., & Ngan, A. H. W. (2014). Strength of metals under
vibrations – dislocation-density-function dynamics simulations. Philosophical
Magazine. Taylor & Francis. https://doi.org/10.1080/14786435.2014.897008
chicago: Cheng, Bingqing, H.S. Leung, and A.H.W. Ngan. “Strength of Metals under
Vibrations – Dislocation-Density-Function Dynamics Simulations.” Philosophical
Magazine. Taylor & Francis, 2014. https://doi.org/10.1080/14786435.2014.897008.
ieee: B. Cheng, H. S. Leung, and A. H. W. Ngan, “Strength of metals under vibrations
– dislocation-density-function dynamics simulations,” Philosophical Magazine,
vol. 95, no. 16–18. Taylor & Francis, pp. 1845–1865, 2014.
ista: Cheng B, Leung HS, Ngan AHW. 2014. Strength of metals under vibrations – dislocation-density-function
dynamics simulations. Philosophical Magazine. 95(16–18), 1845–1865.
mla: Cheng, Bingqing, et al. “Strength of Metals under Vibrations – Dislocation-Density-Function
Dynamics Simulations.” Philosophical Magazine, vol. 95, no. 16–18, Taylor
& Francis, 2014, pp. 1845–65, doi:10.1080/14786435.2014.897008.
short: B. Cheng, H.S. Leung, A.H.W. Ngan, Philosophical Magazine 95 (2014) 1845–1865.
date_created: 2021-07-19T09:27:15Z
date_published: 2014-06-23T00:00:00Z
date_updated: 2023-02-23T14:04:59Z
day: '23'
doi: 10.1080/14786435.2014.897008
extern: '1'
intvolume: ' 95'
issue: 16-18
language:
- iso: eng
month: '06'
oa_version: None
page: 1845-1865
publication: Philosophical Magazine
publication_identifier:
eissn:
- 1478-6443
issn:
- 1478-6435
publication_status: published
publisher: Taylor & Francis
quality_controlled: '1'
scopus_import: '1'
status: public
title: Strength of metals under vibrations – dislocation-density-function dynamics
simulations
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 95
year: '2014'
...
---
_id: '2083'
abstract:
- lang: eng
text: Understanding the effects of sex and migration on adaptation to novel environments
remains a key problem in evolutionary biology. Using a single-cell alga Chlamydomonas
reinhardtii, we investigated how sex and migration affected rates of evolutionary
rescue in a sink environment, and subsequent changes in fitness following evolutionary
rescue. We show that sex and migration affect both the rate of evolutionary rescue
and subsequent adaptation. However, their combined effects change as the populations
adapt to a sink habitat. Both sex and migration independently increased rates
of evolutionary rescue, but the effect of sex on subsequent fitness improvements,
following initial rescue, changed with migration, as sex was beneficial in the
absence of migration but constraining adaptation when combined with migration.
These results suggest that sex and migration are beneficial during the initial
stages of adaptation, but can become detrimental as the population adapts to its
environment.
acknowledgement: The authors are grateful to the Leverhulme Trust (F/00 215/AW) for
funding this work.
article_processing_charge: No
article_type: original
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Andrew
full_name: Morgan, Andrew
last_name: Morgan
- first_name: Paul
full_name: Neve, Paul
last_name: Neve
- first_name: Nick
full_name: Colegrave, Nick
last_name: Colegrave
citation:
ama: Lagator M, Morgan A, Neve P, Colegrave N. Role of sex and migration in adaptation
to sink environments. Evolution. 2014;68(8):2296-2305. doi:10.1111/evo.12440
apa: Lagator, M., Morgan, A., Neve, P., & Colegrave, N. (2014). Role of sex
and migration in adaptation to sink environments. Evolution. Wiley. https://doi.org/10.1111/evo.12440
chicago: Lagator, Mato, Andrew Morgan, Paul Neve, and Nick Colegrave. “Role of Sex
and Migration in Adaptation to Sink Environments.” Evolution. Wiley, 2014.
https://doi.org/10.1111/evo.12440.
ieee: M. Lagator, A. Morgan, P. Neve, and N. Colegrave, “Role of sex and migration
in adaptation to sink environments,” Evolution, vol. 68, no. 8. Wiley,
pp. 2296–2305, 2014.
ista: Lagator M, Morgan A, Neve P, Colegrave N. 2014. Role of sex and migration
in adaptation to sink environments. Evolution. 68(8), 2296–2305.
mla: Lagator, Mato, et al. “Role of Sex and Migration in Adaptation to Sink Environments.”
Evolution, vol. 68, no. 8, Wiley, 2014, pp. 2296–305, doi:10.1111/evo.12440.
short: M. Lagator, A. Morgan, P. Neve, N. Colegrave, Evolution 68 (2014) 2296–2305.
date_created: 2018-12-11T11:55:36Z
date_published: 2014-04-25T00:00:00Z
date_updated: 2023-02-23T14:06:51Z
day: '25'
ddc:
- '570'
department:
- _id: CaGu
doi: 10.1111/evo.12440
file:
- access_level: open_access
checksum: 8d459b07e4a11bb5fde92d969184fe48
content_type: application/pdf
creator: dernst
date_created: 2020-05-14T16:40:31Z
date_updated: 2020-07-14T12:45:28Z
file_id: '7845'
file_name: 2014_Evolution_Lagator.pdf
file_size: 467254
relation: main_file
file_date_updated: 2020-07-14T12:45:28Z
has_accepted_license: '1'
intvolume: ' 68'
issue: '8'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 2296 - 2305
publication: Evolution
publication_status: published
publisher: Wiley
publist_id: '4954'
quality_controlled: '1'
related_material:
record:
- id: '9747'
relation: research_data
status: public
scopus_import: 1
status: public
title: Role of sex and migration in adaptation to sink environments
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 68
year: '2014'
...
---
_id: '9747'
abstract:
- lang: eng
text: Understanding the effects of sex and migration on adaptation to novel environments
remains a key problem in evolutionary biology. Using a single-cell alga Chlamydomonas
reinhardtii, we investigated how sex and migration affected rates of evolutionary
rescue in a sink environment, and subsequent changes in fitness following evolutionary
rescue. We show that sex and migration affect both the rate of evolutionary rescue
and subsequent adaptation. However, their combined effects change as the populations
adapt to a sink habitat. Both sex and migration independently increased rates
of evolutionary rescue, but the effect of sex on subsequent fitness improvements,
following initial rescue, changed with migration, as sex was beneficial in the
absence of migration but constraining adaptation when combined with migration.
These results suggest that sex and migration are beneficial during the initial
stages of adaptation, but can become detrimental as the population adapts to its
environment.
article_processing_charge: No
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Andrew
full_name: Morgan, Andrew
last_name: Morgan
- first_name: Paul
full_name: Neve, Paul
last_name: Neve
- first_name: Nick
full_name: Colegrave, Nick
last_name: Colegrave
citation:
ama: 'Lagator M, Morgan A, Neve P, Colegrave N. Data from: Role of sex and migration
in adaptation to sink environments. 2014. doi:10.5061/dryad.s42n1'
apa: 'Lagator, M., Morgan, A., Neve, P., & Colegrave, N. (2014). Data from:
Role of sex and migration in adaptation to sink environments. Dryad. https://doi.org/10.5061/dryad.s42n1'
chicago: 'Lagator, Mato, Andrew Morgan, Paul Neve, and Nick Colegrave. “Data from:
Role of Sex and Migration in Adaptation to Sink Environments.” Dryad, 2014. https://doi.org/10.5061/dryad.s42n1.'
ieee: 'M. Lagator, A. Morgan, P. Neve, and N. Colegrave, “Data from: Role of sex
and migration in adaptation to sink environments.” Dryad, 2014.'
ista: 'Lagator M, Morgan A, Neve P, Colegrave N. 2014. Data from: Role of sex and
migration in adaptation to sink environments, Dryad, 10.5061/dryad.s42n1.'
mla: 'Lagator, Mato, et al. Data from: Role of Sex and Migration in Adaptation
to Sink Environments. Dryad, 2014, doi:10.5061/dryad.s42n1.'
short: M. Lagator, A. Morgan, P. Neve, N. Colegrave, (2014).
date_created: 2021-07-28T15:32:55Z
date_published: 2014-04-17T00:00:00Z
date_updated: 2023-02-23T10:27:31Z
day: '17'
department:
- _id: CaGu
doi: 10.5061/dryad.s42n1
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.s42n1
month: '04'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2083'
relation: used_in_publication
status: public
status: public
title: 'Data from: Role of sex and migration in adaptation to sink environments'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '977'
abstract:
- lang: eng
text: We propose a method for detecting many-body localization (MBL) in disordered
spin systems. The method involves pulsed coherent spin manipulations that probe
the dephasing of a given spin due to its entanglement with a set of distant spins.
It allows one to distinguish the MBL phase from a noninteracting localized phase
and a delocalized phase. In particular, we show that for a properly chosen pulse
sequence the MBL phase exhibits a characteristic power-law decay reflecting its
slow growth of entanglement. We find that this power-law decay is robust with
respect to thermal and disorder averaging, provide numerical simulations supporting
our results, and discuss possible experimental realizations in solid-state and
cold-atom systems.
acknowledgement: |-
We thank E. Altman, Y. Bahri, I. Bloch, T. Giamarchi, D. Huse, V. Oganesyan, A. Pal, D. Pekker, and G. Refael for insightful discussions. The authors acknowledge support from the Harvard Quantum Optics Center, Harvard-MIT CUA, the DARPA OLE program, AFOSR Quantum Simulation MURI, ARO-MURI on Atomtronics, the ARO-MURI Quism program, the Austrian Science Fund (FWF) Project No. J 3361-N20, NSERC grant, and Sloan Research Fellowship. Simulations presented in this article were performed on computational resources supported by the High Performance Computing Center (PICSciE) at Princeton University and the Research Computing Center at Harvard University. Research at Perimeter Institute was supported by the Government of Canada and by the Province of Ontario.
M. S., M. K., and S. G. contributed equally to this work.
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Michael
full_name: Knap, Michael J
last_name: Knap
- first_name: Sarang
full_name: Gopalakrishnan, Sarang
last_name: Gopalakrishnan
- first_name: Zlatko
full_name: Papić, Zlatko
last_name: Papić
- first_name: Norman
full_name: Yao, Norman Y
last_name: Yao
- first_name: Chris
full_name: Laumann, Chris R
last_name: Laumann
- first_name: Dmitry
full_name: Abanin, Dmitry A
last_name: Abanin
- first_name: Mikhail
full_name: Lukin, Mikhail D
last_name: Lukin
- first_name: Eugene
full_name: Demler, Eugene A
last_name: Demler
citation:
ama: Serbyn M, Knap M, Gopalakrishnan S, et al. Interferometric probes of many-body
localization. Physical Review Letters. 2014;113(14). doi:10.1103/PhysRevLett.113.147204
apa: Serbyn, M., Knap, M., Gopalakrishnan, S., Papić, Z., Yao, N., Laumann, C.,
… Demler, E. (2014). Interferometric probes of many-body localization. Physical
Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.113.147204
chicago: Serbyn, Maksym, Michael Knap, Sarang Gopalakrishnan, Zlatko Papić, Norman
Yao, Chris Laumann, Dmitry Abanin, Mikhail Lukin, and Eugene Demler. “Interferometric
Probes of Many-Body Localization.” Physical Review Letters. American Physical
Society, 2014. https://doi.org/10.1103/PhysRevLett.113.147204.
ieee: M. Serbyn et al., “Interferometric probes of many-body localization,”
Physical Review Letters, vol. 113, no. 14. American Physical Society, 2014.
ista: Serbyn M, Knap M, Gopalakrishnan S, Papić Z, Yao N, Laumann C, Abanin D, Lukin
M, Demler E. 2014. Interferometric probes of many-body localization. Physical
Review Letters. 113(14).
mla: Serbyn, Maksym, et al. “Interferometric Probes of Many-Body Localization.”
Physical Review Letters, vol. 113, no. 14, American Physical Society, 2014,
doi:10.1103/PhysRevLett.113.147204.
short: M. Serbyn, M. Knap, S. Gopalakrishnan, Z. Papić, N. Yao, C. Laumann, D. Abanin,
M. Lukin, E. Demler, Physical Review Letters 113 (2014).
date_created: 2018-12-11T11:49:30Z
date_published: 2014-10-03T00:00:00Z
date_updated: 2021-01-12T08:22:22Z
day: '03'
doi: 10.1103/PhysRevLett.113.147204
extern: 1
intvolume: ' 113'
issue: '14'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1403.0693
month: '10'
oa: 1
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '6421'
quality_controlled: 0
status: public
title: Interferometric probes of many-body localization
type: journal_article
volume: 113
year: '2014'
...
---
_id: '980'
abstract:
- lang: eng
text: Many-body localized (MBL) systems are characterized by the absence of transport
and thermalization and, therefore, cannot be described by conventional statistical
mechanics. In this paper, using analytic arguments and numerical simulations,
we study the behavior of local observables in an isolated MBL system following
a quantum quench. For the case of a global quench, we find that the local observables
reach stationary, highly nonthermal values at long times as a result of slow dephasing
characteristic of the MBL phase. These stationary values retain the local memory
of the initial state due to the existence of local integrals of motion in the
MBL phase. The temporal fluctuations around stationary values exhibit universal
power-law decay in time, with an exponent set by the localization length and the
diagonal entropy of the initial state. Such a power-law decay holds for any local
observable and is related to the logarithmic in time growth of entanglement in
the MBL phase. This behavior distinguishes the MBL phase from both the Anderson
insulator (where no stationary state is reached) and from the ergodic phase (where
relaxation is expected to be exponential). For the case of a local quench, we
also find a power-law approach of local observables to their stationary values
when the system is prepared in a mixed state. Quench protocols considered in this
paper can be naturally implemented in systems of ultracold atoms in disordered
optical lattices, and the behavior of local observables provides a direct experimental
signature of many-body localization.
acknowledgement: Research at Perimeter Institute is supported by the Government of
Canada through Industry Canada and by the Province of Ontario through the Ministry
of Economic Development & Innovation. We acknowledge support by NSERC Discovery
Grant (D.A.).
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Zlatko
full_name: Papić, Zlatko
last_name: Papić
- first_name: Dmitry
full_name: Abanin, Dmitry A
last_name: Abanin
citation:
ama: Serbyn M, Papić Z, Abanin D. Quantum quenches in the many-body localized phase.
Physical Review B - Condensed Matter and Materials Physics. 2014;90(17).
doi:10.1103/PhysRevB.90.174302
apa: Serbyn, M., Papić, Z., & Abanin, D. (2014). Quantum quenches in the many-body
localized phase. Physical Review B - Condensed Matter and Materials Physics.
American Physical Society. https://doi.org/10.1103/PhysRevB.90.174302
chicago: Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Quantum Quenches in the
Many-Body Localized Phase.” Physical Review B - Condensed Matter and Materials
Physics. American Physical Society, 2014. https://doi.org/10.1103/PhysRevB.90.174302.
ieee: M. Serbyn, Z. Papić, and D. Abanin, “Quantum quenches in the many-body localized
phase,” Physical Review B - Condensed Matter and Materials Physics, vol.
90, no. 17. American Physical Society, 2014.
ista: Serbyn M, Papić Z, Abanin D. 2014. Quantum quenches in the many-body localized
phase. Physical Review B - Condensed Matter and Materials Physics. 90(17).
mla: Serbyn, Maksym, et al. “Quantum Quenches in the Many-Body Localized Phase.”
Physical Review B - Condensed Matter and Materials Physics, vol. 90, no.
17, American Physical Society, 2014, doi:10.1103/PhysRevB.90.174302.
short: M. Serbyn, Z. Papić, D. Abanin, Physical Review B - Condensed Matter and
Materials Physics 90 (2014).
date_created: 2018-12-11T11:49:31Z
date_published: 2014-11-06T00:00:00Z
date_updated: 2021-01-12T08:22:24Z
day: '06'
doi: 10.1103/PhysRevB.90.174302
extern: 1
intvolume: ' 90'
issue: '17'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1408.4105
month: '11'
oa: 1
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
publist_id: '6420'
quality_controlled: 0
status: public
title: Quantum quenches in the many-body localized phase
type: journal_article
volume: 90
year: '2014'
...
---
_id: '98'
abstract:
- lang: eng
text: Relaxation and dephasing of hole spins are measured in a gate-defined Ge/Si
nanowire double quantum dot using a fast pulsed-gate method and dispersive readout.
An inhomogeneous dephasing time T2* ∼ 0.18 μs exceeds corresponding measurements
in III-V semiconductors by more than an order of magnitude, as expected for predominately
nuclear-spin-free materials. Dephasing is observed to be exponential in time,
indicating the presence of a broadband noise source, rather than Gaussian, previously
seen in systems with nuclear-spin-dominated dephasing.
acknowledgement: Funding from the Department of Energy, Office of Science & SCGF,
the EC FP7-ICT project SiSPIN no. 323841, and the Danish National Research Foundation
is acknowledged.
author:
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: Thorvald
full_name: Larsen, Thorvald
last_name: Larsen
- first_name: Jun
full_name: Yao, Jun
last_name: Yao
- first_name: Hao
full_name: Yan, Hao
last_name: Yan
- first_name: Charles
full_name: Lieber, Charles
last_name: Lieber
- first_name: Charles
full_name: Marcus, Charles
last_name: Marcus
- first_name: Ferdinand
full_name: Kuemmeth, Ferdinand
last_name: Kuemmeth
citation:
ama: Higginbotham AP, Larsen T, Yao J, et al. Hole spin coherence in a Ge/Si heterostructure
nanowire. Nano Letters. 2014;14(6):3582-3586. doi:10.1021/nl501242b
apa: Higginbotham, A. P., Larsen, T., Yao, J., Yan, H., Lieber, C., Marcus, C.,
& Kuemmeth, F. (2014). Hole spin coherence in a Ge/Si heterostructure nanowire.
Nano Letters. American Chemical Society. https://doi.org/10.1021/nl501242b
chicago: Higginbotham, Andrew P, Thorvald Larsen, Jun Yao, Hao Yan, Charles Lieber,
Charles Marcus, and Ferdinand Kuemmeth. “Hole Spin Coherence in a Ge/Si Heterostructure
Nanowire.” Nano Letters. American Chemical Society, 2014. https://doi.org/10.1021/nl501242b.
ieee: A. P. Higginbotham et al., “Hole spin coherence in a Ge/Si heterostructure
nanowire,” Nano Letters, vol. 14, no. 6. American Chemical Society, pp.
3582–3586, 2014.
ista: Higginbotham AP, Larsen T, Yao J, Yan H, Lieber C, Marcus C, Kuemmeth F. 2014.
Hole spin coherence in a Ge/Si heterostructure nanowire. Nano Letters. 14(6),
3582–3586.
mla: Higginbotham, Andrew P., et al. “Hole Spin Coherence in a Ge/Si Heterostructure
Nanowire.” Nano Letters, vol. 14, no. 6, American Chemical Society, 2014,
pp. 3582–86, doi:10.1021/nl501242b.
short: A.P. Higginbotham, T. Larsen, J. Yao, H. Yan, C. Lieber, C. Marcus, F. Kuemmeth,
Nano Letters 14 (2014) 3582–3586.
date_created: 2018-12-11T11:44:37Z
date_published: 2014-05-05T00:00:00Z
date_updated: 2021-01-12T08:22:24Z
day: '05'
doi: 10.1021/nl501242b
extern: '1'
external_id:
arxiv:
- '1403.2093'
intvolume: ' 14'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1403.2093
month: '05'
oa: 1
oa_version: Preprint
page: 3582 - 3586
publication: Nano Letters
publication_status: published
publisher: American Chemical Society
publist_id: '7956'
quality_controlled: '1'
status: public
title: Hole spin coherence in a Ge/Si heterostructure nanowire
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2014'
...
---
_id: '2086'
abstract:
- lang: eng
text: Pathogens may gain a fitness advantage through manipulation of the behaviour
of their hosts. Likewise, host behavioural changes can be a defence mechanism,
counteracting the impact of pathogens on host fitness. We apply harmonic radar
technology to characterize the impact of an emerging pathogen - Nosema ceranae
(Microsporidia) - on honeybee (Apis mellifera) flight and orientation performance
in the field. Honeybees are the most important commercial pollinators. Emerging
diseases have been proposed to play a prominent role in colony decline, partly
through sub-lethal behavioural manipulation of their hosts. We found that homing
success was significantly reduced in diseased (65.8%) versus healthy foragers
(92.5%). Although lost bees had significantly reduced continuous flight times
and prolonged resting times, other flight characteristics and navigational abilities
showed no significant difference between infected and non-infected bees. Our results
suggest that infected bees express normal flight characteristics but are constrained
in their homing ability, potentially compromising the colony by reducing its resource
inputs, but also counteracting the intra-colony spread of infection. We provide
the first high-resolution analysis of sub-lethal effects of an emerging disease
on insect flight behaviour. The potential causes and the implications for both
host and parasite are discussed.
acknowledgement: This study was funded jointly by a grant from BBSRC, Defra, NERC,
the Scottish Government and the Wellcome Trust, under the Insect Pollinators Initiative
(grant numbers BB/I00097/1 and BB/I000100/1). Rothamsted Research is a national
institute of bioscience strategically funded by the UK Biotechnology and Biological
Sciences Research Council (BBSRC).
article_number: e103989
author:
- first_name: Stephan
full_name: Wolf, Stephan
last_name: Wolf
- first_name: Dino
full_name: Mcmahon, Dino
last_name: Mcmahon
- first_name: Ka
full_name: Lim, Ka
last_name: Lim
- first_name: Christopher
full_name: Pull, Christopher
id: 3C7F4840-F248-11E8-B48F-1D18A9856A87
last_name: Pull
orcid: 0000-0003-1122-3982
- first_name: Suzanne
full_name: Clark, Suzanne
last_name: Clark
- first_name: Robert
full_name: Paxton, Robert
last_name: Paxton
- first_name: Juliet
full_name: Osborne, Juliet
last_name: Osborne
citation:
ama: 'Wolf S, Mcmahon D, Lim K, et al. So near and yet so far: Harmonic radar reveals
reduced homing ability of Nosema infected honeybees. PLoS One. 2014;9(8).
doi:10.1371/journal.pone.0103989'
apa: 'Wolf, S., Mcmahon, D., Lim, K., Pull, C., Clark, S., Paxton, R., & Osborne,
J. (2014). So near and yet so far: Harmonic radar reveals reduced homing ability
of Nosema infected honeybees. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0103989'
chicago: 'Wolf, Stephan, Dino Mcmahon, Ka Lim, Christopher Pull, Suzanne Clark,
Robert Paxton, and Juliet Osborne. “So near and yet so Far: Harmonic Radar Reveals
Reduced Homing Ability of Nosema Infected Honeybees.” PLoS One. Public
Library of Science, 2014. https://doi.org/10.1371/journal.pone.0103989.'
ieee: 'S. Wolf et al., “So near and yet so far: Harmonic radar reveals reduced
homing ability of Nosema infected honeybees,” PLoS One, vol. 9, no. 8.
Public Library of Science, 2014.'
ista: 'Wolf S, Mcmahon D, Lim K, Pull C, Clark S, Paxton R, Osborne J. 2014. So
near and yet so far: Harmonic radar reveals reduced homing ability of Nosema infected
honeybees. PLoS One. 9(8), e103989.'
mla: 'Wolf, Stephan, et al. “So near and yet so Far: Harmonic Radar Reveals Reduced
Homing Ability of Nosema Infected Honeybees.” PLoS One, vol. 9, no. 8,
e103989, Public Library of Science, 2014, doi:10.1371/journal.pone.0103989.'
short: S. Wolf, D. Mcmahon, K. Lim, C. Pull, S. Clark, R. Paxton, J. Osborne, PLoS
One 9 (2014).
date_created: 2018-12-11T11:55:37Z
date_published: 2014-08-06T00:00:00Z
date_updated: 2023-02-23T14:11:56Z
day: '06'
ddc:
- '570'
department:
- _id: SyCr
doi: 10.1371/journal.pone.0103989
file:
- access_level: open_access
checksum: 2fc62c6739eada4bddf026afbae669db
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:55Z
date_updated: 2020-07-14T12:45:28Z
file_id: '5042'
file_name: IST-2016-437-v1+1_journal.pone.0103989.pdf
file_size: 1013386
relation: main_file
file_date_updated: 2020-07-14T12:45:28Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '4949'
pubrep_id: '437'
quality_controlled: '1'
related_material:
record:
- id: '9888'
relation: research_data
status: public
scopus_import: 1
status: public
title: 'So near and yet so far: Harmonic radar reveals reduced homing ability of Nosema
infected honeybees'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2014'
...