---
_id: '1940'
abstract:
- lang: eng
text: We typically think of cells as responding to external signals independently
by regulating their gene expression levels, yet they often locally exchange information
and coordinate. Can such spatial coupling be of benefit for conveying signals
subject to gene regulatory noise? Here we extend our information-theoretic framework
for gene regulation to spatially extended systems. As an example, we consider
a lattice of nuclei responding to a concentration field of a transcriptional regulator
(the "input") by expressing a single diffusible target gene. When input
concentrations are low, diffusive coupling markedly improves information transmission;
optimal gene activation functions also systematically change. A qualitatively
new regulatory strategy emerges where individual cells respond to the input in
a nearly step-like fashion that is subsequently averaged out by strong diffusion.
While motivated by early patterning events in the Drosophila embryo, our framework
is generically applicable to spatially coupled stochastic gene expression models.
article_number: '062710'
author:
- first_name: Thomas R
full_name: Sokolowski, Thomas R
id: 3E999752-F248-11E8-B48F-1D18A9856A87
last_name: Sokolowski
orcid: 0000-0002-1287-3779
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Sokolowski TR, Tkačik G. Optimizing information flow in small genetic networks.
IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft Matter
Physics. 2015;91(6). doi:10.1103/PhysRevE.91.062710
apa: Sokolowski, T. R., & Tkačik, G. (2015). Optimizing information flow in
small genetic networks. IV. Spatial coupling. Physical Review E Statistical
Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.91.062710
chicago: Sokolowski, Thomas R, and Gašper Tkačik. “Optimizing Information Flow in
Small Genetic Networks. IV. Spatial Coupling.” Physical Review E Statistical
Nonlinear and Soft Matter Physics. American Institute of Physics, 2015. https://doi.org/10.1103/PhysRevE.91.062710.
ieee: T. R. Sokolowski and G. Tkačik, “Optimizing information flow in small genetic
networks. IV. Spatial coupling,” Physical Review E Statistical Nonlinear and
Soft Matter Physics, vol. 91, no. 6. American Institute of Physics, 2015.
ista: Sokolowski TR, Tkačik G. 2015. Optimizing information flow in small genetic
networks. IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft
Matter Physics. 91(6), 062710.
mla: Sokolowski, Thomas R., and Gašper Tkačik. “Optimizing Information Flow in Small
Genetic Networks. IV. Spatial Coupling.” Physical Review E Statistical Nonlinear
and Soft Matter Physics, vol. 91, no. 6, 062710, American Institute of Physics,
2015, doi:10.1103/PhysRevE.91.062710.
short: T.R. Sokolowski, G. Tkačik, Physical Review E Statistical Nonlinear and Soft
Matter Physics 91 (2015).
date_created: 2018-12-11T11:54:49Z
date_published: 2015-06-15T00:00:00Z
date_updated: 2021-01-12T06:54:13Z
day: '15'
department:
- _id: GaTk
doi: 10.1103/PhysRevE.91.062710
intvolume: ' 91'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1501.04015
month: '06'
oa: 1
oa_version: Preprint
publication: Physical Review E Statistical Nonlinear and Soft Matter Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '5145'
quality_controlled: '1'
scopus_import: 1
status: public
title: Optimizing information flow in small genetic networks. IV. Spatial coupling
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 91
year: '2015'
...
---
_id: '1938'
abstract:
- lang: eng
text: 'We numerically investigate the distribution of extrema of ''chaotic'' Laplacian
eigenfunctions on two-dimensional manifolds. Our contribution is two-fold: (a)
we count extrema on grid graphs with a small number of randomly added edges and
show the behavior to coincide with the 1957 prediction of Longuet-Higgins for
the continuous case and (b) we compute the regularity of their spatial distribution
using discrepancy, which is a classical measure from the theory of Monte Carlo
integration. The first part suggests that grid graphs with randomly added edges
should behave like two-dimensional surfaces with ergodic geodesic flow; in the
second part we show that the extrema are more regularly distributed in space than
the grid Z2.'
acknowledgement: "F.P. was supported by the Graduate School of IST Austria. S.S. was
partially supported by CRC1060 of the DFG\r\nThe authors thank Olga Symonova and
Michael Kerber for sharing their implementation of the persistence algorithm. "
author:
- first_name: Florian
full_name: Pausinger, Florian
id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87
last_name: Pausinger
orcid: 0000-0002-8379-3768
- first_name: Stefan
full_name: Steinerberger, Stefan
last_name: Steinerberger
citation:
ama: Pausinger F, Steinerberger S. On the distribution of local extrema in quantum
chaos. Physics Letters, Section A. 2015;379(6):535-541. doi:10.1016/j.physleta.2014.12.010
apa: Pausinger, F., & Steinerberger, S. (2015). On the distribution of local
extrema in quantum chaos. Physics Letters, Section A. Elsevier. https://doi.org/10.1016/j.physleta.2014.12.010
chicago: Pausinger, Florian, and Stefan Steinerberger. “On the Distribution of Local
Extrema in Quantum Chaos.” Physics Letters, Section A. Elsevier, 2015.
https://doi.org/10.1016/j.physleta.2014.12.010.
ieee: F. Pausinger and S. Steinerberger, “On the distribution of local extrema in
quantum chaos,” Physics Letters, Section A, vol. 379, no. 6. Elsevier,
pp. 535–541, 2015.
ista: Pausinger F, Steinerberger S. 2015. On the distribution of local extrema in
quantum chaos. Physics Letters, Section A. 379(6), 535–541.
mla: Pausinger, Florian, and Stefan Steinerberger. “On the Distribution of Local
Extrema in Quantum Chaos.” Physics Letters, Section A, vol. 379, no. 6,
Elsevier, 2015, pp. 535–41, doi:10.1016/j.physleta.2014.12.010.
short: F. Pausinger, S. Steinerberger, Physics Letters, Section A 379 (2015) 535–541.
date_created: 2018-12-11T11:54:49Z
date_published: 2015-03-06T00:00:00Z
date_updated: 2021-01-12T06:54:12Z
day: '06'
department:
- _id: HeEd
doi: 10.1016/j.physleta.2014.12.010
intvolume: ' 379'
issue: '6'
language:
- iso: eng
month: '03'
oa_version: None
page: 535 - 541
publication: Physics Letters, Section A
publication_status: published
publisher: Elsevier
publist_id: '5152'
quality_controlled: '1'
scopus_import: 1
status: public
title: On the distribution of local extrema in quantum chaos
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 379
year: '2015'
...
---
_id: '1944'
acknowledgement: This work was supported by the European Research Council (project
ERC-2011-StG-20101109-PSDP); the Agency for Innovation by Science and Technology
(IWT) (predoctoral fellowship to H.R.); and the People Programme (Marie Curie Actions)
of the European Union
author:
- first_name: Hana
full_name: Rakusová, Hana
last_name: Rakusová
- first_name: Matyas
full_name: Fendrych, Matyas
id: 43905548-F248-11E8-B48F-1D18A9856A87
last_name: Fendrych
orcid: 0000-0002-9767-8699
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Rakusová H, Fendrych M, Friml J. Intracellular trafficking and PIN-mediated
cell polarity during tropic responses in plants. Current Opinion in Plant Biology.
2015;23(2):116-123. doi:10.1016/j.pbi.2014.12.002
apa: Rakusová, H., Fendrych, M., & Friml, J. (2015). Intracellular trafficking
and PIN-mediated cell polarity during tropic responses in plants. Current Opinion
in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2014.12.002
chicago: Rakusová, Hana, Matyas Fendrych, and Jiří Friml. “Intracellular Trafficking
and PIN-Mediated Cell Polarity during Tropic Responses in Plants.” Current
Opinion in Plant Biology. Elsevier, 2015. https://doi.org/10.1016/j.pbi.2014.12.002.
ieee: H. Rakusová, M. Fendrych, and J. Friml, “Intracellular trafficking and PIN-mediated
cell polarity during tropic responses in plants,” Current Opinion in Plant
Biology, vol. 23, no. 2. Elsevier, pp. 116–123, 2015.
ista: Rakusová H, Fendrych M, Friml J. 2015. Intracellular trafficking and PIN-mediated
cell polarity during tropic responses in plants. Current Opinion in Plant Biology.
23(2), 116–123.
mla: Rakusová, Hana, et al. “Intracellular Trafficking and PIN-Mediated Cell Polarity
during Tropic Responses in Plants.” Current Opinion in Plant Biology, vol.
23, no. 2, Elsevier, 2015, pp. 116–23, doi:10.1016/j.pbi.2014.12.002.
short: H. Rakusová, M. Fendrych, J. Friml, Current Opinion in Plant Biology 23 (2015)
116–123.
date_created: 2018-12-11T11:54:51Z
date_published: 2015-02-01T00:00:00Z
date_updated: 2021-01-12T06:54:15Z
day: '01'
department:
- _id: JiFr
doi: 10.1016/j.pbi.2014.12.002
ec_funded: 1
intvolume: ' 23'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 116 - 123
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Current Opinion in Plant Biology
publication_status: published
publisher: Elsevier
publist_id: '5140'
quality_controlled: '1'
scopus_import: 1
status: public
title: Intracellular trafficking and PIN-mediated cell polarity during tropic responses
in plants
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2015'
...
---
_id: '1992'
abstract:
- lang: eng
text: "We present a method and a tool for generating succinct representations of
sets of concurrent traces. We focus on trace sets that contain all correct or
all incorrect permutations of events from a given trace. We represent trace sets
as HB-Formulas that are Boolean combinations of happens-before constraints between
events. To generate a representation of incorrect interleavings, our method iteratively
explores interleavings that violate the specification and gathers generalizations
of the discovered interleavings into an HB-Formula; its complement yields a representation
of correct interleavings.\r\n\r\nWe claim that our trace set representations can
drive diverse verification, fault localization, repair, and synthesis techniques
for concurrent programs. We demonstrate this by using our tool in three case studies
involving synchronization synthesis, bug summarization, and abstraction refinement
based verification. In each case study, our initial experimental results have
been promising.\r\n\r\nIn the first case study, we present an algorithm for inferring
missing synchronization from an HB-Formula representing correct interleavings
of a given trace. The algorithm applies rules to rewrite specific patterns in
the HB-Formula into locks, barriers, and wait-notify constructs. In the second
case study, we use an HB-Formula representing incorrect interleavings for bug
summarization. While the HB-Formula itself is a concise counterexample summary,
we present additional inference rules to help identify specific concurrency bugs
such as data races, define-use order violations, and two-stage access bugs. In
the final case study, we present a novel predicate learning procedure that uses
HB-Formulas representing abstract counterexamples to accelerate counterexample-guided
abstraction refinement (CEGAR). In each iteration of the CEGAR loop, the procedure
refines the abstraction to eliminate multiple spurious abstract counterexamples
drawn from the HB-Formula."
author:
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- 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: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
- first_name: Roopsha
full_name: Samanta, Roopsha
id: 3D2AAC08-F248-11E8-B48F-1D18A9856A87
last_name: Samanta
- first_name: Thorsten
full_name: Tarrach, Thorsten
id: 3D6E8F2C-F248-11E8-B48F-1D18A9856A87
last_name: Tarrach
orcid: 0000-0003-4409-8487
citation:
ama: 'Gupta A, Henzinger TA, Radhakrishna A, Samanta R, Tarrach T. Succinct representation
of concurrent trace sets. In: ACM; 2015:433-444. doi:10.1145/2676726.2677008'
apa: 'Gupta, A., Henzinger, T. A., Radhakrishna, A., Samanta, R., & Tarrach,
T. (2015). Succinct representation of concurrent trace sets (pp. 433–444). Presented
at the POPL: Principles of Programming Languages, Mumbai, India: ACM. https://doi.org/10.1145/2676726.2677008'
chicago: Gupta, Ashutosh, Thomas A Henzinger, Arjun Radhakrishna, Roopsha Samanta,
and Thorsten Tarrach. “Succinct Representation of Concurrent Trace Sets,” 433–44.
ACM, 2015. https://doi.org/10.1145/2676726.2677008.
ieee: 'A. Gupta, T. A. Henzinger, A. Radhakrishna, R. Samanta, and T. Tarrach, “Succinct
representation of concurrent trace sets,” presented at the POPL: Principles of
Programming Languages, Mumbai, India, 2015, pp. 433–444.'
ista: 'Gupta A, Henzinger TA, Radhakrishna A, Samanta R, Tarrach T. 2015. Succinct
representation of concurrent trace sets. POPL: Principles of Programming Languages,
433–444.'
mla: Gupta, Ashutosh, et al. Succinct Representation of Concurrent Trace Sets.
ACM, 2015, pp. 433–44, doi:10.1145/2676726.2677008.
short: A. Gupta, T.A. Henzinger, A. Radhakrishna, R. Samanta, T. Tarrach, in:, ACM,
2015, pp. 433–444.
conference:
end_date: 2015-01-17
location: Mumbai, India
name: 'POPL: Principles of Programming Languages'
start_date: 2015-01-15
date_created: 2018-12-11T11:55:05Z
date_published: 2015-01-15T00:00:00Z
date_updated: 2021-01-12T06:54:33Z
day: '15'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1145/2676726.2677008
file:
- access_level: open_access
checksum: f0d4395b600f410a191256ac0b73af32
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:56Z
date_updated: 2020-07-14T12:45:22Z
file_id: '5314'
file_name: IST-2015-317-v1+1_author_version.pdf
file_size: 399462
relation: main_file
file_date_updated: 2020-07-14T12:45:22Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 433 - 444
publication_identifier:
isbn:
- 978-1-4503-3300-9
publication_status: published
publisher: ACM
publist_id: '5091'
pubrep_id: '317'
quality_controlled: '1'
scopus_import: 1
status: public
title: Succinct representation of concurrent trace sets
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1997'
abstract:
- lang: eng
text: We prove that the three-state toric homogeneous Markov chain model has Markov
degree two. In algebraic terminology this means, that a certain class of toric
ideals is generated by quadratic binomials. This was conjectured by Haws, Martin
del Campo, Takemura and Yoshida, who proved that they are generated by degree
six binomials.
author:
- first_name: Patrik
full_name: Noren, Patrik
id: 46870C74-F248-11E8-B48F-1D18A9856A87
last_name: Noren
citation:
ama: Noren P. The three-state toric homogeneous Markov chain model has Markov degree
two. Journal of Symbolic Computation. 2015;68/Part 2(May-June):285-296.
doi:10.1016/j.jsc.2014.09.014
apa: Noren, P. (2015). The three-state toric homogeneous Markov chain model has
Markov degree two. Journal of Symbolic Computation. Elsevier. https://doi.org/10.1016/j.jsc.2014.09.014
chicago: Noren, Patrik. “The Three-State Toric Homogeneous Markov Chain Model Has
Markov Degree Two.” Journal of Symbolic Computation. Elsevier, 2015. https://doi.org/10.1016/j.jsc.2014.09.014.
ieee: P. Noren, “The three-state toric homogeneous Markov chain model has Markov
degree two,” Journal of Symbolic Computation, vol. 68/Part 2, no. May-June.
Elsevier, pp. 285–296, 2015.
ista: Noren P. 2015. The three-state toric homogeneous Markov chain model has Markov
degree two. Journal of Symbolic Computation. 68/Part 2(May-June), 285–296.
mla: Noren, Patrik. “The Three-State Toric Homogeneous Markov Chain Model Has Markov
Degree Two.” Journal of Symbolic Computation, vol. 68/Part 2, no. May-June,
Elsevier, 2015, pp. 285–96, doi:10.1016/j.jsc.2014.09.014.
short: P. Noren, Journal of Symbolic Computation 68/Part 2 (2015) 285–296.
date_created: 2018-12-11T11:55:07Z
date_published: 2015-05-01T00:00:00Z
date_updated: 2021-01-12T06:54:35Z
day: '01'
department:
- _id: CaUh
doi: 10.1016/j.jsc.2014.09.014
issue: May-June
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1207.0077
month: '05'
oa: 1
oa_version: Preprint
page: 285 - 296
publication: Journal of Symbolic Computation
publication_status: published
publisher: Elsevier
publist_id: '5082'
quality_controlled: '1'
scopus_import: 1
status: public
title: The three-state toric homogeneous Markov chain model has Markov degree two
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 68/Part 2
year: '2015'
...
---
_id: '2008'
abstract:
- lang: eng
text: The paper describes a generalized iterative proportional fitting procedure
that can be used for maximum likelihood estimation in a special class of the general
log-linear model. The models in this class, called relational, apply to multivariate
discrete sample spaces that do not necessarily have a Cartesian product structure
and may not contain an overall effect. When applied to the cell probabilities,
the models without the overall effect are curved exponential families and the
values of the sufficient statistics are reproduced by the MLE only up to a constant
of proportionality. The paper shows that Iterative Proportional Fitting, Generalized
Iterative Scaling, and Improved Iterative Scaling fail to work for such models.
The algorithm proposed here is based on iterated Bregman projections. As a by-product,
estimates of the multiplicative parameters are also obtained. An implementation
of the algorithm is available as an R-package.
acknowledgement: Part of the material presented here was contained in the PhD thesis
of the first author to which the second author and Thomas Richardson were advisers.
The authors wish to thank him for several comments and suggestions. We also thank
the reviewers and the Associate Editor for helpful comments. The proof of Proposition 1
uses the idea of Olga Klimova, to whom the authors are also indebted. The second
author was supported in part by Grant K-106154 from the Hungarian National Scientific
Research Fund (OTKA).
author:
- first_name: Anna
full_name: Klimova, Anna
id: 31934120-F248-11E8-B48F-1D18A9856A87
last_name: Klimova
- first_name: Tamás
full_name: Rudas, Tamás
last_name: Rudas
citation:
ama: Klimova A, Rudas T. Iterative scaling in curved exponential families. Scandinavian
Journal of Statistics. 2015;42(3):832-847. doi:10.1111/sjos.12139
apa: Klimova, A., & Rudas, T. (2015). Iterative scaling in curved exponential
families. Scandinavian Journal of Statistics. Wiley. https://doi.org/10.1111/sjos.12139
chicago: Klimova, Anna, and Tamás Rudas. “Iterative Scaling in Curved Exponential
Families.” Scandinavian Journal of Statistics. Wiley, 2015. https://doi.org/10.1111/sjos.12139.
ieee: A. Klimova and T. Rudas, “Iterative scaling in curved exponential families,”
Scandinavian Journal of Statistics, vol. 42, no. 3. Wiley, pp. 832–847,
2015.
ista: Klimova A, Rudas T. 2015. Iterative scaling in curved exponential families.
Scandinavian Journal of Statistics. 42(3), 832–847.
mla: Klimova, Anna, and Tamás Rudas. “Iterative Scaling in Curved Exponential Families.”
Scandinavian Journal of Statistics, vol. 42, no. 3, Wiley, 2015, pp. 832–47,
doi:10.1111/sjos.12139.
short: A. Klimova, T. Rudas, Scandinavian Journal of Statistics 42 (2015) 832–847.
date_created: 2018-12-11T11:55:11Z
date_published: 2015-09-01T00:00:00Z
date_updated: 2021-01-12T06:54:41Z
day: '01'
department:
- _id: CaUh
doi: 10.1111/sjos.12139
intvolume: ' 42'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1307.3282
month: '09'
oa: 1
oa_version: Preprint
page: 832 - 847
publication: Scandinavian Journal of Statistics
publication_status: published
publisher: Wiley
publist_id: '5068'
quality_controlled: '1'
scopus_import: 1
status: public
title: Iterative scaling in curved exponential families
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2015'
...
---
_id: '2006'
abstract:
- lang: eng
text: 'The monotone secant conjecture posits a rich class of polynomial systems,
all of whose solutions are real. These systems come from the Schubert calculus
on flag manifolds, and the monotone secant conjecture is a compelling generalization
of the Shapiro conjecture for Grassmannians (Theorem of Mukhin, Tarasov, and Varchenko).
We present some theoretical evidence for this conjecture, as well as computational
evidence obtained by 1.9 teraHertz-years of computing, and we discuss some of
the phenomena we observed in our data. '
article_processing_charge: No
author:
- first_name: Nicolas
full_name: Hein, Nicolas
last_name: Hein
- first_name: Christopher
full_name: Hillar, Christopher
last_name: Hillar
- first_name: Abraham
full_name: Martin Del Campo Sanchez, Abraham
id: 4CF47F6A-F248-11E8-B48F-1D18A9856A87
last_name: Martin Del Campo Sanchez
- first_name: Frank
full_name: Sottile, Frank
last_name: Sottile
- first_name: Zach
full_name: Teitler, Zach
last_name: Teitler
citation:
ama: Hein N, Hillar C, Martin del Campo Sanchez A, Sottile F, Teitler Z. The monotone
secant conjecture in the real Schubert calculus. Experimental Mathematics.
2015;24(3):261-269. doi:10.1080/10586458.2014.980044
apa: Hein, N., Hillar, C., Martin del Campo Sanchez, A., Sottile, F., & Teitler,
Z. (2015). The monotone secant conjecture in the real Schubert calculus. Experimental
Mathematics. Taylor & Francis. https://doi.org/10.1080/10586458.2014.980044
chicago: Hein, Nicolas, Christopher Hillar, Abraham Martin del Campo Sanchez, Frank
Sottile, and Zach Teitler. “The Monotone Secant Conjecture in the Real Schubert
Calculus.” Experimental Mathematics. Taylor & Francis, 2015. https://doi.org/10.1080/10586458.2014.980044.
ieee: N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, and Z. Teitler,
“The monotone secant conjecture in the real Schubert calculus,” Experimental
Mathematics, vol. 24, no. 3. Taylor & Francis, pp. 261–269, 2015.
ista: Hein N, Hillar C, Martin del Campo Sanchez A, Sottile F, Teitler Z. 2015.
The monotone secant conjecture in the real Schubert calculus. Experimental Mathematics.
24(3), 261–269.
mla: Hein, Nicolas, et al. “The Monotone Secant Conjecture in the Real Schubert
Calculus.” Experimental Mathematics, vol. 24, no. 3, Taylor & Francis,
2015, pp. 261–69, doi:10.1080/10586458.2014.980044.
short: N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, Z. Teitler,
Experimental Mathematics 24 (2015) 261–269.
date_created: 2018-12-11T11:55:10Z
date_published: 2015-06-23T00:00:00Z
date_updated: 2021-01-12T06:54:40Z
day: '23'
department:
- _id: CaUh
doi: 10.1080/10586458.2014.980044
intvolume: ' 24'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1109.3436
month: '06'
oa: 1
oa_version: Preprint
page: 261 - 269
publication: Experimental Mathematics
publication_status: published
publisher: Taylor & Francis
publist_id: '5070'
quality_controlled: '1'
scopus_import: 1
status: public
title: The monotone secant conjecture in the real Schubert calculus
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2015'
...
---
_id: '2014'
abstract:
- lang: eng
text: The concepts of faithfulness and strong-faithfulness are important for statistical
learning of graphical models. Graphs are not sufficient for describing the association
structure of a discrete distribution. Hypergraphs representing hierarchical log-linear
models are considered instead, and the concept of parametric (strong-) faithfulness
with respect to a hypergraph is introduced. Strong-faithfulness ensures the existence
of uniformly consistent parameter estimators and enables building uniformly consistent
procedures for a hypergraph search. The strength of association in a discrete
distribution can be quantified with various measures, leading to different concepts
of strong-faithfulness. Lower and upper bounds for the proportions of distributions
that do not satisfy strong-faithfulness are computed for different parameterizations
and measures of association.
author:
- first_name: Anna
full_name: Klimova, Anna
id: 31934120-F248-11E8-B48F-1D18A9856A87
last_name: Klimova
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
- first_name: Tamás
full_name: Rudas, Tamás
last_name: Rudas
citation:
ama: Klimova A, Uhler C, Rudas T. Faithfulness and learning hypergraphs from discrete
distributions. Computational Statistics & Data Analysis. 2015;87(7):57-72.
doi:10.1016/j.csda.2015.01.017
apa: Klimova, A., Uhler, C., & Rudas, T. (2015). Faithfulness and learning hypergraphs
from discrete distributions. Computational Statistics & Data Analysis.
Elsevier. https://doi.org/10.1016/j.csda.2015.01.017
chicago: Klimova, Anna, Caroline Uhler, and Tamás Rudas. “Faithfulness and Learning
Hypergraphs from Discrete Distributions.” Computational Statistics & Data
Analysis. Elsevier, 2015. https://doi.org/10.1016/j.csda.2015.01.017.
ieee: A. Klimova, C. Uhler, and T. Rudas, “Faithfulness and learning hypergraphs
from discrete distributions,” Computational Statistics & Data Analysis,
vol. 87, no. 7. Elsevier, pp. 57–72, 2015.
ista: Klimova A, Uhler C, Rudas T. 2015. Faithfulness and learning hypergraphs from
discrete distributions. Computational Statistics & Data Analysis. 87(7), 57–72.
mla: Klimova, Anna, et al. “Faithfulness and Learning Hypergraphs from Discrete
Distributions.” Computational Statistics & Data Analysis, vol. 87,
no. 7, Elsevier, 2015, pp. 57–72, doi:10.1016/j.csda.2015.01.017.
short: A. Klimova, C. Uhler, T. Rudas, Computational Statistics & Data Analysis
87 (2015) 57–72.
date_created: 2018-12-11T11:55:13Z
date_published: 2015-07-01T00:00:00Z
date_updated: 2021-01-12T06:54:43Z
day: '01'
department:
- _id: CaUh
doi: 10.1016/j.csda.2015.01.017
intvolume: ' 87'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1404.6617
month: '07'
oa: 1
oa_version: Preprint
page: 57 - 72
publication: Computational Statistics & Data Analysis
publication_status: published
publisher: Elsevier
publist_id: '5062'
quality_controlled: '1'
scopus_import: 1
status: public
title: Faithfulness and learning hypergraphs from discrete distributions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 87
year: '2015'
...
---
_id: '2025'
abstract:
- lang: eng
text: Small GTP-binding proteins of the Ras superfamily play diverse roles in intracellular
trafficking. Among them, the Rab, Arf, and Rho families function in successive
steps of vesicle transport, in forming vesicles from donor membranes, directing
vesicle trafficking toward target membranes and docking vesicles onto target membranes.
These proteins act as molecular switches that are controlled by a cycle of GTP
binding and hydrolysis regulated by guanine nucleotide exchange factors (GEFs)
and GTPase-activating proteins (GAPs). In this study we explored the role of GAPs
in the regulation of the endocytic pathway using fluorescently labeled yeast mating
pheromone α-factor. Among 25 non-essential GAP mutants, we found that deletion
of the GLO3 gene, encoding Arf-GAP protein, caused defective internalization of
fluorescently labeled α-factor. Quantitative analysis revealed that glo3Δ cells
show defective α-factor binding to the cell surface. Interestingly, Ste2p, the
α-factor receptor, was mis-localized from the plasma membrane to the vacuole in
glo3Δ cells. Domain deletion mutants of Glo3p revealed that a GAP-independent
function, as well as the GAP activity, of Glo3p is important for both α-factor
binding and Ste2p localization at the cell surface. Additionally, we found that
deletion of the GLO3 gene affects the size and number of Arf1p-residing Golgi
compartments and causes a defect in transport from the TGN to the plasma membrane.
Furthermore, we demonstrated that glo3Δ cells were defective in the late endosome-to-TGN
transport pathway, but not in the early endosome-to-TGN transport pathway. These
findings suggest novel roles for Arf-GAP Glo3p in endocytic recycling of cell
surface proteins.
author:
- first_name: Daiki
full_name: Kawada, Daiki
last_name: Kawada
- first_name: Hiromu
full_name: Kobayashi, Hiromu
last_name: Kobayashi
- first_name: Tsuyoshi
full_name: Tomita, Tsuyoshi
last_name: Tomita
- first_name: Eisuke
full_name: Nakata, Eisuke
last_name: Nakata
- first_name: Makoto
full_name: Nagano, Makoto
last_name: Nagano
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Junko
full_name: Toshima, Junko
last_name: Toshima
- first_name: Jiro
full_name: Toshimaa, Jiro
last_name: Toshimaa
citation:
ama: Kawada D, Kobayashi H, Tomita T, et al. The yeast Arf-GAP Glo3p is required
for the endocytic recycling of cell surface proteins. Biochimica et Biophysica
Acta - Molecular Cell Research. 2015;1853(1):144-156. doi:10.1016/j.bbamcr.2014.10.009
apa: Kawada, D., Kobayashi, H., Tomita, T., Nakata, E., Nagano, M., Siekhaus, D.
E., … Toshimaa, J. (2015). The yeast Arf-GAP Glo3p is required for the endocytic
recycling of cell surface proteins. Biochimica et Biophysica Acta - Molecular
Cell Research. Elsevier. https://doi.org/10.1016/j.bbamcr.2014.10.009
chicago: Kawada, Daiki, Hiromu Kobayashi, Tsuyoshi Tomita, Eisuke Nakata, Makoto
Nagano, Daria E Siekhaus, Junko Toshima, and Jiro Toshimaa. “The Yeast Arf-GAP
Glo3p Is Required for the Endocytic Recycling of Cell Surface Proteins.” Biochimica
et Biophysica Acta - Molecular Cell Research. Elsevier, 2015. https://doi.org/10.1016/j.bbamcr.2014.10.009.
ieee: D. Kawada et al., “The yeast Arf-GAP Glo3p is required for the endocytic
recycling of cell surface proteins,” Biochimica et Biophysica Acta - Molecular
Cell Research, vol. 1853, no. 1. Elsevier, pp. 144–156, 2015.
ista: Kawada D, Kobayashi H, Tomita T, Nakata E, Nagano M, Siekhaus DE, Toshima
J, Toshimaa J. 2015. The yeast Arf-GAP Glo3p is required for the endocytic recycling
of cell surface proteins. Biochimica et Biophysica Acta - Molecular Cell Research.
1853(1), 144–156.
mla: Kawada, Daiki, et al. “The Yeast Arf-GAP Glo3p Is Required for the Endocytic
Recycling of Cell Surface Proteins.” Biochimica et Biophysica Acta - Molecular
Cell Research, vol. 1853, no. 1, Elsevier, 2015, pp. 144–56, doi:10.1016/j.bbamcr.2014.10.009.
short: D. Kawada, H. Kobayashi, T. Tomita, E. Nakata, M. Nagano, D.E. Siekhaus,
J. Toshima, J. Toshimaa, Biochimica et Biophysica Acta - Molecular Cell Research
1853 (2015) 144–156.
date_created: 2018-12-11T11:55:17Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:54:48Z
day: '01'
ddc:
- '570'
department:
- _id: DaSi
doi: 10.1016/j.bbamcr.2014.10.009
file:
- access_level: open_access
checksum: 5bb328edebb6a91337cadd7d63f961b7
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:18Z
date_updated: 2020-07-14T12:45:25Z
file_id: '4936'
file_name: IST-2016-615-v1+1_BBAMCR.pdf
file_size: 926685
relation: main_file
file_date_updated: 2020-07-14T12:45:25Z
has_accepted_license: '1'
intvolume: ' 1853'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 144 - 156
publication: Biochimica et Biophysica Acta - Molecular Cell Research
publication_status: published
publisher: Elsevier
publist_id: '5047'
pubrep_id: '615'
quality_controlled: '1'
scopus_import: 1
status: public
title: The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface
proteins
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: 1853
year: '2015'
...
---
_id: '2030'
abstract:
- lang: eng
text: A hybrid-parallel direct-numerical-simulation method with application to turbulent
Taylor-Couette flow is presented. The Navier-Stokes equations are discretized
in cylindrical coordinates with the spectral Fourier-Galerkin method in the axial
and azimuthal directions, and high-order finite differences in the radial direction.
Time is advanced by a second-order, semi-implicit projection scheme, which requires
the solution of five Helmholtz/Poisson equations, avoids staggered grids and renders
very small slip velocities. Nonlinear terms are evaluated with the pseudospectral
method. The code is parallelized using a hybrid MPI-OpenMP strategy, which, compared
with a flat MPI parallelization, is simpler to implement, allows to reduce inter-node
communications and MPI overhead that become relevant at high processor-core counts,
and helps to contain the memory footprint. A strong scaling study shows that the
hybrid code maintains scalability up to more than 20,000 processor cores and thus
allows to perform simulations at higher resolutions than previously feasible.
In particular, it opens up the possibility to simulate turbulent Taylor-Couette
flows at Reynolds numbers up to O(105). This enables to probe hydrodynamic turbulence
in Keplerian flows in experimentally relevant regimes.
author:
- first_name: Liang
full_name: Shi, Liang
id: 374A3F1A-F248-11E8-B48F-1D18A9856A87
last_name: Shi
- first_name: Markus
full_name: Rampp, Markus
last_name: Rampp
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Marc
full_name: Avila, Marc
last_name: Avila
citation:
ama: Shi L, Rampp M, Hof B, Avila M. A hybrid MPI-OpenMP parallel implementation
for pseudospectral simulations with application to Taylor-Couette flow. Computers
and Fluids. 2015;106(1):1-11. doi:10.1016/j.compfluid.2014.09.021
apa: Shi, L., Rampp, M., Hof, B., & Avila, M. (2015). A hybrid MPI-OpenMP parallel
implementation for pseudospectral simulations with application to Taylor-Couette
flow. Computers and Fluids. Elsevier. https://doi.org/10.1016/j.compfluid.2014.09.021
chicago: Shi, Liang, Markus Rampp, Björn Hof, and Marc Avila. “A Hybrid MPI-OpenMP
Parallel Implementation for Pseudospectral Simulations with Application to Taylor-Couette
Flow.” Computers and Fluids. Elsevier, 2015. https://doi.org/10.1016/j.compfluid.2014.09.021.
ieee: L. Shi, M. Rampp, B. Hof, and M. Avila, “A hybrid MPI-OpenMP parallel implementation
for pseudospectral simulations with application to Taylor-Couette flow,” Computers
and Fluids, vol. 106, no. 1. Elsevier, pp. 1–11, 2015.
ista: Shi L, Rampp M, Hof B, Avila M. 2015. A hybrid MPI-OpenMP parallel implementation
for pseudospectral simulations with application to Taylor-Couette flow. Computers
and Fluids. 106(1), 1–11.
mla: Shi, Liang, et al. “A Hybrid MPI-OpenMP Parallel Implementation for Pseudospectral
Simulations with Application to Taylor-Couette Flow.” Computers and Fluids,
vol. 106, no. 1, Elsevier, 2015, pp. 1–11, doi:10.1016/j.compfluid.2014.09.021.
short: L. Shi, M. Rampp, B. Hof, M. Avila, Computers and Fluids 106 (2015) 1–11.
date_created: 2018-12-11T11:55:18Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:54:51Z
day: '01'
department:
- _id: BjHo
doi: 10.1016/j.compfluid.2014.09.021
intvolume: ' 106'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1311.2481
month: '01'
oa: 1
oa_version: Preprint
page: 1 - 11
publication: Computers and Fluids
publication_status: published
publisher: Elsevier
publist_id: '5042'
quality_controlled: '1'
scopus_import: 1
status: public
title: A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations
with application to Taylor-Couette flow
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 106
year: '2015'
...
---
_id: '2035'
abstract:
- lang: eng
text: "Considering a continuous self-map and the induced endomorphism on homology,
we study the eigenvalues and eigenspaces of the latter. Taking a filtration of
representations, we define the persistence of the eigenspaces, effectively introducing
a hierarchical organization of the map. The algorithm that computes this information
for a finite sample is proved to be stable, and to give the correct answer for
a sufficiently dense sample. Results computed with an implementation of the algorithm
provide evidence of its practical utility.\r\n"
acknowledgement: This research is partially supported by the Toposys project FP7-ICT-318493-STREP,
by ESF under the ACAT Research Network Programme, by the Russian Government under
mega project 11.G34.31.0053, and by the Polish National Science Center under Grant
No. N201 419639.
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Grzegorz
full_name: Jablonski, Grzegorz
id: 4483EF78-F248-11E8-B48F-1D18A9856A87
last_name: Jablonski
orcid: 0000-0002-3536-9866
- first_name: Marian
full_name: Mrozek, Marian
last_name: Mrozek
citation:
ama: Edelsbrunner H, Jablonski G, Mrozek M. The persistent homology of a self-map.
Foundations of Computational Mathematics. 2015;15(5):1213-1244. doi:10.1007/s10208-014-9223-y
apa: Edelsbrunner, H., Jablonski, G., & Mrozek, M. (2015). The persistent homology
of a self-map. Foundations of Computational Mathematics. Springer. https://doi.org/10.1007/s10208-014-9223-y
chicago: Edelsbrunner, Herbert, Grzegorz Jablonski, and Marian Mrozek. “The Persistent
Homology of a Self-Map.” Foundations of Computational Mathematics. Springer,
2015. https://doi.org/10.1007/s10208-014-9223-y.
ieee: H. Edelsbrunner, G. Jablonski, and M. Mrozek, “The persistent homology of
a self-map,” Foundations of Computational Mathematics, vol. 15, no. 5.
Springer, pp. 1213–1244, 2015.
ista: Edelsbrunner H, Jablonski G, Mrozek M. 2015. The persistent homology of a
self-map. Foundations of Computational Mathematics. 15(5), 1213–1244.
mla: Edelsbrunner, Herbert, et al. “The Persistent Homology of a Self-Map.” Foundations
of Computational Mathematics, vol. 15, no. 5, Springer, 2015, pp. 1213–44,
doi:10.1007/s10208-014-9223-y.
short: H. Edelsbrunner, G. Jablonski, M. Mrozek, Foundations of Computational Mathematics
15 (2015) 1213–1244.
date_created: 2018-12-11T11:55:20Z
date_published: 2015-10-01T00:00:00Z
date_updated: 2021-01-12T06:54:53Z
day: '01'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1007/s10208-014-9223-y
ec_funded: 1
file:
- access_level: open_access
checksum: 3566f3a8b0c1bc550e62914a88c584ff
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:10Z
date_updated: 2020-07-14T12:45:26Z
file_id: '4670'
file_name: IST-2016-486-v1+1_s10208-014-9223-y.pdf
file_size: 1317546
relation: main_file
file_date_updated: 2020-07-14T12:45:26Z
has_accepted_license: '1'
intvolume: ' 15'
issue: '5'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 1213 - 1244
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: Foundations of Computational Mathematics
publication_status: published
publisher: Springer
publist_id: '5022'
pubrep_id: '486'
quality_controlled: '1'
scopus_import: 1
status: public
title: The persistent homology of a self-map
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: 15
year: '2015'
...
---
_id: '2034'
abstract:
- lang: eng
text: Opacity is a generic security property, that has been defined on (non-probabilistic)
transition systems and later on Markov chains with labels. For a secret predicate,
given as a subset of runs, and a function describing the view of an external observer,
the value of interest for opacity is a measure of the set of runs disclosing the
secret. We extend this definition to the richer framework of Markov decision processes,
where non-deterministicchoice is combined with probabilistic transitions, and
we study related decidability problems with partial or complete observation hypotheses
for the schedulers. We prove that all questions are decidable with complete observation
and ω-regular secrets. With partial observation, we prove that all quantitative
questions are undecidable but the question whether a system is almost surely non-opaquebecomes
decidable for a restricted class of ω-regular secrets, as well as for all ω-regular
secrets under finite-memory schedulers.
author:
- first_name: Béatrice
full_name: Bérard, Béatrice
last_name: Bérard
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Nathalie
full_name: Sznajder, Nathalie
last_name: Sznajder
citation:
ama: Bérard B, Chatterjee K, Sznajder N. Probabilistic opacity for Markov decision
processes. Information Processing Letters. 2015;115(1):52-59. doi:10.1016/j.ipl.2014.09.001
apa: Bérard, B., Chatterjee, K., & Sznajder, N. (2015). Probabilistic opacity
for Markov decision processes. Information Processing Letters. Elsevier.
https://doi.org/10.1016/j.ipl.2014.09.001
chicago: Bérard, Béatrice, Krishnendu Chatterjee, and Nathalie Sznajder. “Probabilistic
Opacity for Markov Decision Processes.” Information Processing Letters.
Elsevier, 2015. https://doi.org/10.1016/j.ipl.2014.09.001.
ieee: B. Bérard, K. Chatterjee, and N. Sznajder, “Probabilistic opacity for Markov
decision processes,” Information Processing Letters, vol. 115, no. 1.
Elsevier, pp. 52–59, 2015.
ista: Bérard B, Chatterjee K, Sznajder N. 2015. Probabilistic opacity for Markov
decision processes. Information Processing Letters. 115(1), 52–59.
mla: Bérard, Béatrice, et al. “Probabilistic Opacity for Markov Decision Processes.”
Information Processing Letters, vol. 115, no. 1, Elsevier, 2015, pp. 52–59,
doi:10.1016/j.ipl.2014.09.001.
short: B. Bérard, K. Chatterjee, N. Sznajder, Information Processing Letters 115
(2015) 52–59.
date_created: 2018-12-11T11:55:20Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:54:52Z
day: '01'
department:
- _id: KrCh
doi: 10.1016/j.ipl.2014.09.001
ec_funded: 1
intvolume: ' 115'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1407.4225
month: '01'
oa: 1
oa_version: Preprint
page: 52 - 59
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: ' Information Processing Letters'
publication_status: published
publisher: Elsevier
publist_id: '5025'
quality_controlled: '1'
scopus_import: 1
status: public
title: Probabilistic opacity for Markov decision processes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 115
year: '2015'
...
---
_id: '2085'
abstract:
- lang: eng
text: 'We study the spectrum of a large system of N identical bosons interacting
via a two-body potential with strength 1/N. In this mean-field regime, Bogoliubov''s
theory predicts that the spectrum of the N-particle Hamiltonian can be approximated
by that of an effective quadratic Hamiltonian acting on Fock space, which describes
the fluctuations around a condensed state. Recently, Bogoliubov''s theory has
been justified rigorously in the case that the low-energy eigenvectors of the
N-particle Hamiltonian display complete condensation in the unique minimizer of
the corresponding Hartree functional. In this paper, we shall justify Bogoliubov''s
theory for the high-energy part of the spectrum of the N-particle Hamiltonian
corresponding to (non-linear) excited states of the Hartree functional. Moreover,
we shall extend the existing results on the excitation spectrum to the case of
non-uniqueness and/or degeneracy of the Hartree minimizer. In particular, the
latter covers the case of rotating Bose gases, when the rotation speed is large
enough to break the symmetry and to produce multiple quantized vortices in the
Hartree minimizer. '
author:
- first_name: Phan
full_name: Nam, Phan
id: 404092F4-F248-11E8-B48F-1D18A9856A87
last_name: Nam
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Nam P, Seiringer R. Collective excitations of Bose gases in the mean-field
regime. Archive for Rational Mechanics and Analysis. 2015;215(2):381-417.
doi:10.1007/s00205-014-0781-6
apa: Nam, P., & Seiringer, R. (2015). Collective excitations of Bose gases in
the mean-field regime. Archive for Rational Mechanics and Analysis. Springer.
https://doi.org/10.1007/s00205-014-0781-6
chicago: Nam, Phan, and Robert Seiringer. “Collective Excitations of Bose Gases
in the Mean-Field Regime.” Archive for Rational Mechanics and Analysis.
Springer, 2015. https://doi.org/10.1007/s00205-014-0781-6.
ieee: P. Nam and R. Seiringer, “Collective excitations of Bose gases in the mean-field
regime,” Archive for Rational Mechanics and Analysis, vol. 215, no. 2.
Springer, pp. 381–417, 2015.
ista: Nam P, Seiringer R. 2015. Collective excitations of Bose gases in the mean-field
regime. Archive for Rational Mechanics and Analysis. 215(2), 381–417.
mla: Nam, Phan, and Robert Seiringer. “Collective Excitations of Bose Gases in the
Mean-Field Regime.” Archive for Rational Mechanics and Analysis, vol. 215,
no. 2, Springer, 2015, pp. 381–417, doi:10.1007/s00205-014-0781-6.
short: P. Nam, R. Seiringer, Archive for Rational Mechanics and Analysis 215 (2015)
381–417.
date_created: 2018-12-11T11:55:37Z
date_published: 2015-02-01T00:00:00Z
date_updated: 2021-01-12T06:55:13Z
day: '01'
department:
- _id: RoSe
doi: 10.1007/s00205-014-0781-6
intvolume: ' 215'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1402.1153
month: '02'
oa: 1
oa_version: Preprint
page: 381 - 417
publication: Archive for Rational Mechanics and Analysis
publication_status: published
publisher: Springer
publist_id: '4951'
quality_controlled: '1'
scopus_import: 1
status: public
title: Collective excitations of Bose gases in the mean-field regime
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 215
year: '2015'
...
---
_id: '2166'
abstract:
- lang: eng
text: 'We consider the spectral statistics of large random band matrices on mesoscopic
energy scales. We show that the correlation function of the local eigenvalue density
exhibits a universal power law behaviour that differs from the Wigner-Dyson- Mehta
statistics. This law had been predicted in the physics literature by Altshuler
and Shklovskii in (Zh Eksp Teor Fiz (Sov Phys JETP) 91(64):220(127), 1986); it
describes the correlations of the eigenvalue density in general metallic sampleswith
weak disorder. Our result rigorously establishes the Altshuler-Shklovskii formulas
for band matrices. In two dimensions, where the leading term vanishes owing to
an algebraic cancellation, we identify the first non-vanishing term and show that
it differs substantially from the prediction of Kravtsov and Lerner in (Phys Rev
Lett 74:2563-2566, 1995). The proof is given in the current paper and its companion
(Ann. H. Poincaré. arXiv:1309.5107, 2014). '
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Antti
full_name: Knowles, Antti
last_name: Knowles
citation:
ama: 'Erdös L, Knowles A. The Altshuler-Shklovskii formulas for random band matrices
I: the unimodular case. Communications in Mathematical Physics. 2015;333(3):1365-1416.
doi:10.1007/s00220-014-2119-5'
apa: 'Erdös, L., & Knowles, A. (2015). The Altshuler-Shklovskii formulas for
random band matrices I: the unimodular case. Communications in Mathematical
Physics. Springer. https://doi.org/10.1007/s00220-014-2119-5'
chicago: 'Erdös, László, and Antti Knowles. “The Altshuler-Shklovskii Formulas for
Random Band Matrices I: The Unimodular Case.” Communications in Mathematical
Physics. Springer, 2015. https://doi.org/10.1007/s00220-014-2119-5.'
ieee: 'L. Erdös and A. Knowles, “The Altshuler-Shklovskii formulas for random band
matrices I: the unimodular case,” Communications in Mathematical Physics,
vol. 333, no. 3. Springer, pp. 1365–1416, 2015.'
ista: 'Erdös L, Knowles A. 2015. The Altshuler-Shklovskii formulas for random band
matrices I: the unimodular case. Communications in Mathematical Physics. 333(3),
1365–1416.'
mla: 'Erdös, László, and Antti Knowles. “The Altshuler-Shklovskii Formulas for Random
Band Matrices I: The Unimodular Case.” Communications in Mathematical Physics,
vol. 333, no. 3, Springer, 2015, pp. 1365–416, doi:10.1007/s00220-014-2119-5.'
short: L. Erdös, A. Knowles, Communications in Mathematical Physics 333 (2015) 1365–1416.
date_created: 2018-12-11T11:56:05Z
date_published: 2015-02-01T00:00:00Z
date_updated: 2021-01-12T06:55:43Z
day: '01'
department:
- _id: LaEr
doi: 10.1007/s00220-014-2119-5
intvolume: ' 333'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1309.5106
month: '02'
oa: 1
oa_version: Preprint
page: 1365 - 1416
publication: Communications in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '4818'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'The Altshuler-Shklovskii formulas for random band matrices I: the unimodular
case'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 333
year: '2015'
...
---
_id: '1832'
abstract:
- lang: eng
text: 'Linearizability of concurrent data structures is usually proved by monolithic
simulation arguments relying on the identification of the so-called linearization
points. Regrettably, such proofs, whether manual or automatic, are often complicated
and scale poorly to advanced non-blocking concurrency patterns, such as helping
and optimistic updates. In response, we propose a more modular way of checking
linearizability of concurrent queue algorithms that does not involve identifying
linearization points. We reduce the task of proving linearizability with respect
to the queue specification to establishing four basic properties, each of which
can be proved independently by simpler arguments. As a demonstration of our approach,
we verify the Herlihy and Wing queue, an algorithm that is challenging to verify
by a simulation proof. '
article_number: '20'
article_processing_charge: No
article_type: original
author:
- first_name: Soham
full_name: Chakraborty, Soham
last_name: Chakraborty
- 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: Ali
full_name: Sezgin, Ali
last_name: Sezgin
- first_name: Viktor
full_name: Vafeiadis, Viktor
last_name: Vafeiadis
citation:
ama: Chakraborty S, Henzinger TA, Sezgin A, Vafeiadis V. Aspect-oriented linearizability
proofs. Logical Methods in Computer Science. 2015;11(1). doi:10.2168/LMCS-11(1:20)2015
apa: Chakraborty, S., Henzinger, T. A., Sezgin, A., & Vafeiadis, V. (2015).
Aspect-oriented linearizability proofs. Logical Methods in Computer Science.
International Federation of Computational Logic. https://doi.org/10.2168/LMCS-11(1:20)2015
chicago: Chakraborty, Soham, Thomas A Henzinger, Ali Sezgin, and Viktor Vafeiadis.
“Aspect-Oriented Linearizability Proofs.” Logical Methods in Computer Science.
International Federation of Computational Logic, 2015. https://doi.org/10.2168/LMCS-11(1:20)2015.
ieee: S. Chakraborty, T. A. Henzinger, A. Sezgin, and V. Vafeiadis, “Aspect-oriented
linearizability proofs,” Logical Methods in Computer Science, vol. 11,
no. 1. International Federation of Computational Logic, 2015.
ista: Chakraborty S, Henzinger TA, Sezgin A, Vafeiadis V. 2015. Aspect-oriented
linearizability proofs. Logical Methods in Computer Science. 11(1), 20.
mla: Chakraborty, Soham, et al. “Aspect-Oriented Linearizability Proofs.” Logical
Methods in Computer Science, vol. 11, no. 1, 20, International Federation
of Computational Logic, 2015, doi:10.2168/LMCS-11(1:20)2015.
short: S. Chakraborty, T.A. Henzinger, A. Sezgin, V. Vafeiadis, Logical Methods
in Computer Science 11 (2015).
date_created: 2018-12-11T11:54:15Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2023-02-23T10:38:13Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.2168/LMCS-11(1:20)2015
ec_funded: 1
file:
- access_level: open_access
checksum: 7370e164d0a731f442424a92669efc34
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:27Z
date_updated: 2020-07-14T12:45:17Z
file_id: '4881'
file_name: IST-2015-390-v1+1_1502.07639.pdf
file_size: 380203
relation: main_file
file_date_updated: 2020-07-14T12:45:17Z
has_accepted_license: '1'
intvolume: ' 11'
issue: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nd/4.0/
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication: Logical Methods in Computer Science
publication_status: published
publisher: International Federation of Computational Logic
publist_id: '5271'
pubrep_id: '390'
quality_controlled: '1'
related_material:
record:
- id: '2328'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Aspect-oriented linearizability proofs
tmp:
image: /image/cc_by_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
short: CC BY-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2015'
...
---
_id: '2271'
abstract:
- lang: eng
text: "A class of valued constraint satisfaction problems (VCSPs) is characterised
by a valued constraint language, a fixed set of cost functions on a finite domain.
Finite-valued constraint languages contain functions that take on rational costs
and general-valued constraint languages contain functions that take on rational
or infinite costs. An instance of the problem is specified by a sum of functions
from the language with the goal to minimise the sum. This framework includes and
generalises well-studied constraint satisfaction problems (CSPs) and maximum constraint
satisfaction problems (Max-CSPs).\r\nOur main result is a precise algebraic characterisation
of valued constraint languages whose instances can be solved exactly by the basic
linear programming relaxation (BLP). For a general-valued constraint language
Γ, BLP is a decision procedure for Γ if and only if Γ admits a symmetric fractional
polymorphism of every arity. For a finite-valued constraint language Γ, BLP is
a decision procedure if and only if Γ admits a symmetric fractional polymorphism
of some arity, or equivalently, if Γ admits a symmetric fractional polymorphism
of arity 2.\r\nUsing these results, we obtain tractability of several novel and
previously widely-open classes of VCSPs, including problems over valued constraint
languages that are: (1) submodular on arbitrary lattices; (2) bisubmodular (also
known as k-submodular) on arbitrary finite domains; (3) weakly (and hence strongly)
tree-submodular on arbitrary trees. "
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Johan
full_name: Thapper, Johan
last_name: Thapper
- first_name: Stanislav
full_name: Živný, Stanislav
last_name: Živný
citation:
ama: Kolmogorov V, Thapper J, Živný S. The power of linear programming for general-valued
CSPs. SIAM Journal on Computing. 2015;44(1):1-36. doi:10.1137/130945648
apa: Kolmogorov, V., Thapper, J., & Živný, S. (2015). The power of linear programming
for general-valued CSPs. SIAM Journal on Computing. SIAM. https://doi.org/10.1137/130945648
chicago: Kolmogorov, Vladimir, Johan Thapper, and Stanislav Živný. “The Power of
Linear Programming for General-Valued CSPs.” SIAM Journal on Computing.
SIAM, 2015. https://doi.org/10.1137/130945648.
ieee: V. Kolmogorov, J. Thapper, and S. Živný, “The power of linear programming
for general-valued CSPs,” SIAM Journal on Computing, vol. 44, no. 1. SIAM,
pp. 1–36, 2015.
ista: Kolmogorov V, Thapper J, Živný S. 2015. The power of linear programming for
general-valued CSPs. SIAM Journal on Computing. 44(1), 1–36.
mla: Kolmogorov, Vladimir, et al. “The Power of Linear Programming for General-Valued
CSPs.” SIAM Journal on Computing, vol. 44, no. 1, SIAM, 2015, pp. 1–36,
doi:10.1137/130945648.
short: V. Kolmogorov, J. Thapper, S. Živný, SIAM Journal on Computing 44 (2015)
1–36.
date_created: 2018-12-11T11:56:41Z
date_published: 2015-02-01T00:00:00Z
date_updated: 2023-02-23T10:46:30Z
day: '01'
department:
- _id: VlKo
doi: 10.1137/130945648
external_id:
arxiv:
- '1311.4219'
intvolume: ' 44'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1311.4219
month: '02'
oa: 1
oa_version: Preprint
page: 1 - 36
publication: SIAM Journal on Computing
publication_status: published
publisher: SIAM
publist_id: '4673'
quality_controlled: '1'
related_material:
record:
- id: '2518'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: The power of linear programming for general-valued CSPs
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 44
year: '2015'
...
---
_id: '257'
abstract:
- lang: eng
text: For suitable pairs of diagonal quadratic forms in eight variables we use the
circle method to investigate the density of simultaneous integer solutions and
relate this to the problem of estimating linear correlations among sums of two
squares.
acknowledgement: While working on this paper the first author was supported by ERC
grant 306457 and the second author was supported by SwarnaJayanti Fellowship 2011–12,
DST, Government of India.
author:
- first_name: Timothy D
full_name: Timothy Browning
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Ritabrata
full_name: Munshi, Ritabrata
last_name: Munshi
citation:
ama: Browning TD, Munshi R. Pairs of diagonal quadratic forms and linear correlations
among sums of two squares. Forum Mathematicum. 2015;27(4):2025-2050. doi:10.1515/forum-2013-6024
apa: Browning, T. D., & Munshi, R. (2015). Pairs of diagonal quadratic forms
and linear correlations among sums of two squares. Forum Mathematicum.
Walter de Gruyter GmbH. https://doi.org/10.1515/forum-2013-6024
chicago: Browning, Timothy D, and Ritabrata Munshi. “Pairs of Diagonal Quadratic
Forms and Linear Correlations among Sums of Two Squares.” Forum Mathematicum.
Walter de Gruyter GmbH, 2015. https://doi.org/10.1515/forum-2013-6024.
ieee: T. D. Browning and R. Munshi, “Pairs of diagonal quadratic forms and linear
correlations among sums of two squares,” Forum Mathematicum, vol. 27, no.
4. Walter de Gruyter GmbH, pp. 2025–2050, 2015.
ista: Browning TD, Munshi R. 2015. Pairs of diagonal quadratic forms and linear
correlations among sums of two squares. Forum Mathematicum. 27(4), 2025–2050.
mla: Browning, Timothy D., and Ritabrata Munshi. “Pairs of Diagonal Quadratic Forms
and Linear Correlations among Sums of Two Squares.” Forum Mathematicum,
vol. 27, no. 4, Walter de Gruyter GmbH, 2015, pp. 2025–50, doi:10.1515/forum-2013-6024.
short: T.D. Browning, R. Munshi, Forum Mathematicum 27 (2015) 2025–2050.
date_created: 2018-12-11T11:45:28Z
date_published: 2015-07-10T00:00:00Z
date_updated: 2021-01-12T06:58:18Z
day: '10'
doi: 10.1515/forum-2013-6024
extern: 1
intvolume: ' 27'
issue: '4'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1302.2434
month: '07'
oa: 1
page: 2025 - 2050
publication: Forum Mathematicum
publication_status: published
publisher: Walter de Gruyter GmbH
publist_id: '7645'
quality_controlled: 0
status: public
title: Pairs of diagonal quadratic forms and linear correlations among sums of two
squares
type: journal_article
volume: 27
year: '2015'
...
---
_id: '258'
abstract:
- lang: eng
text: Given a number field k and a projective algebraic variety X defined over k,
the question of whether X contains a k-rational point is both very natural and
very difficult. In the event that the set X(k) of k-rational points is not empty,
one can also ask how the points of X(k) are distributed. Are they dense in X under
the Zariski topology? Are they dense in the set.
author:
- 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: 'Browning TD. A survey of applications of the circle method to rational points.
In: Arithmetic and Geometry. Cambridge University Press; 2015:89-113. doi:10.1017/CBO9781316106877.009'
apa: Browning, T. D. (2015). A survey of applications of the circle method to rational
points. In Arithmetic and Geometry (pp. 89–113). Cambridge University Press.
https://doi.org/10.1017/CBO9781316106877.009
chicago: Browning, Timothy D. “A Survey of Applications of the Circle Method to
Rational Points.” In Arithmetic and Geometry, 89–113. Cambridge University
Press, 2015. https://doi.org/10.1017/CBO9781316106877.009.
ieee: T. D. Browning, “A survey of applications of the circle method to rational
points,” in Arithmetic and Geometry, Cambridge University Press, 2015,
pp. 89–113.
ista: 'Browning TD. 2015.A survey of applications of the circle method to rational
points. In: Arithmetic and Geometry. , 89–113.'
mla: Browning, Timothy D. “A Survey of Applications of the Circle Method to Rational
Points.” Arithmetic and Geometry, Cambridge University Press, 2015, pp.
89–113, doi:10.1017/CBO9781316106877.009.
short: T.D. Browning, in:, Arithmetic and Geometry, Cambridge University Press,
2015, pp. 89–113.
date_created: 2018-12-11T11:45:28Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2021-01-12T06:58:22Z
day: '01'
doi: 10.1017/CBO9781316106877.009
extern: '1'
language:
- iso: eng
month: '08'
oa_version: None
page: 89 - 113
publication: Arithmetic and Geometry
publication_status: published
publisher: Cambridge University Press
publist_id: '7644'
quality_controlled: '1'
status: public
title: A survey of applications of the circle method to rational points
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '259'
abstract:
- lang: eng
text: 'The Hasse principle and weak approximation is established for non-singular
cubic hypersurfaces X over the function field '
acknowledgement: "EP/J018260/1\tEngineering and Physical Sciences Research Council
EPSRC"
author:
- first_name: Timothy D
full_name: Timothy Browning
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Pankaj
full_name: Vishe, Pankaj
last_name: Vishe
citation:
ama: Browning TD, Vishe P. Rational points on cubic hypersurfaces over F_q(t) .
Geometric and Functional Analysis. 2015;25(3):671-732. doi:10.1007/s00039-015-0328-5
apa: Browning, T. D., & Vishe, P. (2015). Rational points on cubic hypersurfaces
over F_q(t) . Geometric and Functional Analysis. Birkhäuser. https://doi.org/10.1007/s00039-015-0328-5
chicago: Browning, Timothy D, and Pankaj Vishe. “Rational Points on Cubic Hypersurfaces
over F_q(T) .” Geometric and Functional Analysis. Birkhäuser, 2015. https://doi.org/10.1007/s00039-015-0328-5.
ieee: T. D. Browning and P. Vishe, “Rational points on cubic hypersurfaces over
F_q(t) ,” Geometric and Functional Analysis, vol. 25, no. 3. Birkhäuser,
pp. 671–732, 2015.
ista: Browning TD, Vishe P. 2015. Rational points on cubic hypersurfaces over F_q(t)
. Geometric and Functional Analysis. 25(3), 671–732.
mla: Browning, Timothy D., and Pankaj Vishe. “Rational Points on Cubic Hypersurfaces
over F_q(T) .” Geometric and Functional Analysis, vol. 25, no. 3, Birkhäuser,
2015, pp. 671–732, doi:10.1007/s00039-015-0328-5.
short: T.D. Browning, P. Vishe, Geometric and Functional Analysis 25 (2015) 671–732.
date_created: 2018-12-11T11:45:29Z
date_published: 2015-06-11T00:00:00Z
date_updated: 2021-01-12T06:58:25Z
day: '11'
doi: 10.1007/s00039-015-0328-5
extern: 1
intvolume: ' 25'
issue: '3'
month: '06'
page: 671 - 732
publication: Geometric and Functional Analysis
publication_status: published
publisher: Birkhäuser
publist_id: '7643'
quality_controlled: 0
status: public
title: 'Rational points on cubic hypersurfaces over F_q(t) '
type: journal_article
volume: 25
year: '2015'
...
---
_id: '1598'
abstract:
- lang: eng
text: 'We consider Markov decision processes (MDPs) with specifications given as
Büchi (liveness) objectives, and examine the problem of computing the set of almost-sure
winning vertices such that the objective can be ensured with probability 1 from
these vertices. We study for the first time the average-case complexity of the
classical algorithm for computing the set of almost-sure winning vertices for
MDPs with Büchi objectives. Our contributions are as follows: First, we show that
for MDPs with constant out-degree the expected number of iterations is at most
logarithmic and the average-case running time is linear (as compared to the worst-case
linear number of iterations and quadratic time complexity). Second, for the average-case
analysis over all MDPs we show that the expected number of iterations is constant
and the average-case running time is linear (again as compared to the worst-case
linear number of iterations and quadratic time complexity). Finally we also show
that when all MDPs are equally likely, the probability that the classical algorithm
requires more than a constant number of iterations is exponentially small.'
acknowledgement: "The research was supported by FWF Grant No. P 23499-N23, FWF NFN
Grant No. S11407-N23 (RiSE), ERC Start Grant (279307: Graph Games), and the Microsoft
Faculty Fellows Award. Nisarg Shah is also supported by NSF Grant CCF-1215883.\r\n"
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: Manas
full_name: Joglekar, Manas
last_name: Joglekar
- first_name: Nisarg
full_name: Shah, Nisarg
last_name: Shah
citation:
ama: Chatterjee K, Joglekar M, Shah N. Average case analysis of the classical algorithm
for Markov decision processes with Büchi objectives. Theoretical Computer Science.
2015;573(3):71-89. doi:10.1016/j.tcs.2015.01.050
apa: Chatterjee, K., Joglekar, M., & Shah, N. (2015). Average case analysis
of the classical algorithm for Markov decision processes with Büchi objectives.
Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2015.01.050
chicago: Chatterjee, Krishnendu, Manas Joglekar, and Nisarg Shah. “Average Case
Analysis of the Classical Algorithm for Markov Decision Processes with Büchi Objectives.”
Theoretical Computer Science. Elsevier, 2015. https://doi.org/10.1016/j.tcs.2015.01.050.
ieee: K. Chatterjee, M. Joglekar, and N. Shah, “Average case analysis of the classical
algorithm for Markov decision processes with Büchi objectives,” Theoretical
Computer Science, vol. 573, no. 3. Elsevier, pp. 71–89, 2015.
ista: Chatterjee K, Joglekar M, Shah N. 2015. Average case analysis of the classical
algorithm for Markov decision processes with Büchi objectives. Theoretical Computer
Science. 573(3), 71–89.
mla: Chatterjee, Krishnendu, et al. “Average Case Analysis of the Classical Algorithm
for Markov Decision Processes with Büchi Objectives.” Theoretical Computer
Science, vol. 573, no. 3, Elsevier, 2015, pp. 71–89, doi:10.1016/j.tcs.2015.01.050.
short: K. Chatterjee, M. Joglekar, N. Shah, Theoretical Computer Science 573 (2015)
71–89.
date_created: 2018-12-11T11:52:56Z
date_published: 2015-03-30T00:00:00Z
date_updated: 2023-02-23T10:55:03Z
day: '30'
department:
- _id: KrCh
doi: 10.1016/j.tcs.2015.01.050
ec_funded: 1
external_id:
arxiv:
- '1202.4175'
intvolume: ' 573'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1202.4175
month: '03'
oa: 1
oa_version: Preprint
page: 71 - 89
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: Theoretical Computer Science
publication_status: published
publisher: Elsevier
publist_id: '5571'
quality_controlled: '1'
related_material:
record:
- id: '2715'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Average case analysis of the classical algorithm for Markov decision processes
with Büchi objectives
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 573
year: '2015'
...
---
_id: '1805'
abstract:
- lang: eng
text: 'We consider the problem of deciding whether the persistent homology group
of a simplicial pair (K,L) can be realized as the homology H∗(X) of some complex
X with L ⊂ X ⊂ K. We show that this problem is NP-complete even if K is embedded
in double-struck R3. As a consequence, we show that it is NP-hard to simplify
level and sublevel sets of scalar functions on double-struck S3 within a given
tolerance constraint. This problem has relevance to the visualization of medical
images by isosurfaces. We also show an implication to the theory of well groups
of scalar functions: not every well group can be realized by some level set, and
deciding whether a well group can be realized is NP-hard.'
author:
- first_name: Dominique
full_name: Attali, Dominique
last_name: Attali
- first_name: Ulrich
full_name: Bauer, Ulrich
id: 2ADD483A-F248-11E8-B48F-1D18A9856A87
last_name: Bauer
orcid: 0000-0002-9683-0724
- first_name: Olivier
full_name: Devillers, Olivier
last_name: Devillers
- first_name: Marc
full_name: Glisse, Marc
last_name: Glisse
- first_name: André
full_name: Lieutier, André
last_name: Lieutier
citation:
ama: 'Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. Homological reconstruction
and simplification in R3. Computational Geometry: Theory and Applications.
2015;48(8):606-621. doi:10.1016/j.comgeo.2014.08.010'
apa: 'Attali, D., Bauer, U., Devillers, O., Glisse, M., & Lieutier, A. (2015).
Homological reconstruction and simplification in R3. Computational Geometry:
Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2014.08.010'
chicago: 'Attali, Dominique, Ulrich Bauer, Olivier Devillers, Marc Glisse, and André
Lieutier. “Homological Reconstruction and Simplification in R3.” Computational
Geometry: Theory and Applications. Elsevier, 2015. https://doi.org/10.1016/j.comgeo.2014.08.010.'
ieee: 'D. Attali, U. Bauer, O. Devillers, M. Glisse, and A. Lieutier, “Homological
reconstruction and simplification in R3,” Computational Geometry: Theory and
Applications, vol. 48, no. 8. Elsevier, pp. 606–621, 2015.'
ista: 'Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. 2015. Homological reconstruction
and simplification in R3. Computational Geometry: Theory and Applications. 48(8),
606–621.'
mla: 'Attali, Dominique, et al. “Homological Reconstruction and Simplification in
R3.” Computational Geometry: Theory and Applications, vol. 48, no. 8, Elsevier,
2015, pp. 606–21, doi:10.1016/j.comgeo.2014.08.010.'
short: 'D. Attali, U. Bauer, O. Devillers, M. Glisse, A. Lieutier, Computational
Geometry: Theory and Applications 48 (2015) 606–621.'
date_created: 2018-12-11T11:54:06Z
date_published: 2015-06-03T00:00:00Z
date_updated: 2023-02-23T10:59:19Z
day: '03'
department:
- _id: HeEd
doi: 10.1016/j.comgeo.2014.08.010
ec_funded: 1
intvolume: ' 48'
issue: '8'
language:
- iso: eng
month: '06'
oa_version: None
page: 606 - 621
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: 'Computational Geometry: Theory and Applications'
publication_status: published
publisher: Elsevier
publist_id: '5305'
quality_controlled: '1'
related_material:
record:
- id: '2812'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Homological reconstruction and simplification in R3
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 48
year: '2015'
...
---
_id: '333'
abstract:
- lang: eng
text: 'We present a hybrid intercalation battery based on a sodium/magnesium (Na/Mg)
dual salt electrolyte, metallic magnesium anode, and a cathode based on FeS2 nanocrystals
(NCs). Compared to lithium or sodium, metallic magnesium anode is safer due to
dendrite-free electroplating and offers extremely high volumetric (3833 mAh cm-3)
and gravimetric capacities (2205 mAh g-1). Na-ion cathodes, FeS2 NCs in the present
study, may serve as attractive alternatives to Mg-ion cathodes due to the higher
voltage of operation and fast, highly reversible insertion of Na-ions. In this
proof-of-concept study, electrochemical cycling of the Na/Mg hybrid battery was
characterized by high rate capability, high Coulombic efficiency of 99.8%, and
high energy density. In particular, with an average discharge voltage of ∼1.1
V and a cathodic capacity of 189 mAh g-1 at a current of 200 mA g-1, the presented
Mg/FeS2 hybrid battery delivers energy densities of up to 210 Wh kg-1, comparable
to commercial Li-ion batteries and approximately twice as high as state-of-the-art
Mg-ion batteries based on Mo6S8 cathodes. Further significant gains in the energy
density are expected from the development of Na/Mg electrolytes with a broader
electrochemical stability window. Fully based on Earth-abundant elements, hybrid
Na-Mg batteries are highly promising for large-scale stationary energy storage. '
article_processing_charge: No
article_type: original
author:
- first_name: Marc
full_name: Walter, Marc
last_name: Walter
- first_name: Kostiantyn
full_name: Kravchyk, Kostiantyn
last_name: Kravchyk
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Maksym
full_name: Kovalenko, Maksym
last_name: Kovalenko
citation:
ama: Walter M, Kravchyk K, Ibáñez M, Kovalenko M. Efficient and inexpensive sodium
magnesium hybrid battery. Chemistry of Materials. 2015;27(21):7452-7458.
doi:10.1021/acs.chemmater.5b03531
apa: Walter, M., Kravchyk, K., Ibáñez, M., & Kovalenko, M. (2015). Efficient
and inexpensive sodium magnesium hybrid battery. Chemistry of Materials.
ACS. https://doi.org/10.1021/acs.chemmater.5b03531
chicago: Walter, Marc, Kostiantyn Kravchyk, Maria Ibáñez, and Maksym Kovalenko.
“Efficient and Inexpensive Sodium Magnesium Hybrid Battery.” Chemistry of Materials.
ACS, 2015. https://doi.org/10.1021/acs.chemmater.5b03531.
ieee: M. Walter, K. Kravchyk, M. Ibáñez, and M. Kovalenko, “Efficient and inexpensive
sodium magnesium hybrid battery,” Chemistry of Materials, vol. 27, no.
21. ACS, pp. 7452–7458, 2015.
ista: Walter M, Kravchyk K, Ibáñez M, Kovalenko M. 2015. Efficient and inexpensive
sodium magnesium hybrid battery. Chemistry of Materials. 27(21), 7452–7458.
mla: Walter, Marc, et al. “Efficient and Inexpensive Sodium Magnesium Hybrid Battery.”
Chemistry of Materials, vol. 27, no. 21, ACS, 2015, pp. 7452–58, doi:10.1021/acs.chemmater.5b03531.
short: M. Walter, K. Kravchyk, M. Ibáñez, M. Kovalenko, Chemistry of Materials 27
(2015) 7452–7458.
date_created: 2018-12-11T11:45:52Z
date_published: 2015-10-16T00:00:00Z
date_updated: 2021-01-12T07:42:42Z
day: '16'
doi: 10.1021/acs.chemmater.5b03531
extern: '1'
intvolume: ' 27'
issue: '21'
language:
- iso: eng
month: '10'
oa_version: None
page: 7452 - 7458
publication: Chemistry of Materials
publication_status: published
publisher: ACS
publist_id: '7507'
quality_controlled: '1'
status: public
title: Efficient and inexpensive sodium magnesium hybrid battery
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 27
year: '2015'
...
---
_id: '354'
abstract:
- lang: eng
text: 'A simple and effective method to introduce precise amounts of doping in nanomaterials
produced from the bottom-up assembly of colloidal nanoparticles (NPs) is described.
The procedure takes advantage of a ligand displacement step to incorporate controlled
concentrations of halide ions while removing carboxylic acids from the NP surface.
Upon consolidation of the NPs into dense pellets, halide ions diffuse within the
crystal structure, doping the anion sublattice and achieving n-type electrical
doping. Through the characterization of the thermoelectric properties of nanocrystalline
PbS, we demonstrate this strategy to be effective to control charge transport
properties on thermoelectric nanomaterials assembled from NP building blocks.
This approach is subsequently extended to PbTexSe1-x@PbS core-shell NPs, where
a significant enhancement of the thermoelectric figure of merit is achieved. '
acknowledgement: At IREC, work was supported by European Regional Development Funds
and the Framework 7 program under project UNION (FP7-NMP 310250). M.I. and S.O.
thank AGAUR for their Beatriu i Pinós postdoctoral grant and the PhD grant, respectively.
At Northwestern, work was supported by the Revolutionary Materials for Solid State
Energy Conversion, an Energy Frontier Research Center funded by the U.S. Department
of Energy, Office of Science, and Office of Basic Energy Sciences under Award Number
DE-SC0001054.
article_processing_charge: No
article_type: original
author:
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Rachel
full_name: Korkosz, Rachel
last_name: Korkosz
- first_name: Zhishan
full_name: Luo, Zhishan
last_name: Luo
- first_name: Pau
full_name: Riba, Pau
last_name: Riba
- first_name: Doris
full_name: Cadavid, Doris
last_name: Cadavid
- first_name: Silvia
full_name: Ortega, Silvia
last_name: Ortega
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
- first_name: Mercouri
full_name: Kanatzidis, Mercouri
last_name: Kanatzidis
citation:
ama: Ibáñez M, Korkosz R, Luo Z, et al. Electron doping in bottom up engineered
thermoelectric nanomaterials through HCl mediated ligand displacement. Journal
of the American Chemical Society. 2015;137(12):4046-4049. doi:10.1021/jacs.5b00091
apa: Ibáñez, M., Korkosz, R., Luo, Z., Riba, P., Cadavid, D., Ortega, S., … Kanatzidis,
M. (2015). Electron doping in bottom up engineered thermoelectric nanomaterials
through HCl mediated ligand displacement. Journal of the American Chemical
Society. American Chemical Society. https://doi.org/10.1021/jacs.5b00091
chicago: Ibáñez, Maria, Rachel Korkosz, Zhishan Luo, Pau Riba, Doris Cadavid, Silvia
Ortega, Andreu Cabot, and Mercouri Kanatzidis. “Electron Doping in Bottom up Engineered
Thermoelectric Nanomaterials through HCl Mediated Ligand Displacement.” Journal
of the American Chemical Society. American Chemical Society, 2015. https://doi.org/10.1021/jacs.5b00091.
ieee: M. Ibáñez et al., “Electron doping in bottom up engineered thermoelectric
nanomaterials through HCl mediated ligand displacement,” Journal of the American
Chemical Society, vol. 137, no. 12. American Chemical Society, pp. 4046–4049,
2015.
ista: Ibáñez M, Korkosz R, Luo Z, Riba P, Cadavid D, Ortega S, Cabot A, Kanatzidis
M. 2015. Electron doping in bottom up engineered thermoelectric nanomaterials
through HCl mediated ligand displacement. Journal of the American Chemical Society.
137(12), 4046–4049.
mla: Ibáñez, Maria, et al. “Electron Doping in Bottom up Engineered Thermoelectric
Nanomaterials through HCl Mediated Ligand Displacement.” Journal of the American
Chemical Society, vol. 137, no. 12, American Chemical Society, 2015, pp. 4046–49,
doi:10.1021/jacs.5b00091.
short: M. Ibáñez, R. Korkosz, Z. Luo, P. Riba, D. Cadavid, S. Ortega, A. Cabot,
M. Kanatzidis, Journal of the American Chemical Society 137 (2015) 4046–4049.
date_created: 2018-12-11T11:45:59Z
date_published: 2015-03-11T00:00:00Z
date_updated: 2021-01-12T07:44:10Z
day: '11'
doi: 10.1021/jacs.5b00091
extern: '1'
intvolume: ' 137'
issue: '12'
language:
- iso: eng
month: '03'
oa_version: None
page: 4046 - 4049
publication: Journal of the American Chemical Society
publication_status: published
publisher: American Chemical Society
publist_id: '7470'
quality_controlled: '1'
status: public
title: Electron doping in bottom up engineered thermoelectric nanomaterials through
HCl mediated ligand displacement
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 137
year: '2015'
...
---
_id: '360'
abstract:
- lang: eng
text: 'A cation exchange-based route was used to produce Cu2ZnSnS4 (CZTS)-Ag2S nanoparticles
with controlled composition. We report a detailed study of the formation of such
CZTS-Ag2S nanoheterostructures and of their photocatalytic properties. When compared
to pure CZTS, the use of nanoscale p-n heterostructures as light absorbers for
photocatalytic water splitting provides superior photocurrents. We associate this
experimental fact to a higher separation efficiency of the photogenerated electron-hole
pairs. We believe this and other type-II nanoheterostructures will open the door
to the use of CZTS, with excellent light absorption properties and made of abundant
and environmental friendly elements, to the field of photocatalysis. '
article_processing_charge: No
author:
- first_name: Xuelian
full_name: Yu, Xuelian
last_name: Yu
- first_name: Jingjing
full_name: Liu, Jingjing
last_name: Liu
- first_name: Aziz
full_name: Genç, Aziz
last_name: Genç
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Zhishan
full_name: Luo, Zhishan
last_name: Luo
- first_name: Alexey
full_name: Shavel, Alexey
last_name: Shavel
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Guangjin
full_name: Zhang, Guangjin
last_name: Zhang
- first_name: Yihe
full_name: Zhang, Yihe
last_name: Zhang
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: Yu X, Liu J, Genç A, et al. Cu2ZnSnS4-Ag2S nanoscale p-n heterostructures as
sensitizers for photoelectrochemical water splitting. Langmuir. 2015;31(38):10555-10561.
doi:10.1021/acs.langmuir.5b02490
apa: Yu, X., Liu, J., Genç, A., Ibáñez, M., Luo, Z., Shavel, A., … Cabot, A. (2015).
Cu2ZnSnS4-Ag2S nanoscale p-n heterostructures as sensitizers for photoelectrochemical
water splitting. Langmuir. American Chemical Society. https://doi.org/10.1021/acs.langmuir.5b02490
chicago: Yu, Xuelian, Jingjing Liu, Aziz Genç, Maria Ibáñez, Zhishan Luo, Alexey
Shavel, Jordi Arbiol, Guangjin Zhang, Yihe Zhang, and Andreu Cabot. “Cu2ZnSnS4-Ag2S
Nanoscale p-n Heterostructures as Sensitizers for Photoelectrochemical Water Splitting.”
Langmuir. American Chemical Society, 2015. https://doi.org/10.1021/acs.langmuir.5b02490.
ieee: X. Yu et al., “Cu2ZnSnS4-Ag2S nanoscale p-n heterostructures as sensitizers
for photoelectrochemical water splitting,” Langmuir, vol. 31, no. 38. American
Chemical Society, pp. 10555–10561, 2015.
ista: Yu X, Liu J, Genç A, Ibáñez M, Luo Z, Shavel A, Arbiol J, Zhang G, Zhang Y,
Cabot A. 2015. Cu2ZnSnS4-Ag2S nanoscale p-n heterostructures as sensitizers for
photoelectrochemical water splitting. Langmuir. 31(38), 10555–10561.
mla: Yu, Xuelian, et al. “Cu2ZnSnS4-Ag2S Nanoscale p-n Heterostructures as Sensitizers
for Photoelectrochemical Water Splitting.” Langmuir, vol. 31, no. 38, American
Chemical Society, 2015, pp. 10555–61, doi:10.1021/acs.langmuir.5b02490.
short: X. Yu, J. Liu, A. Genç, M. Ibáñez, Z. Luo, A. Shavel, J. Arbiol, G. Zhang,
Y. Zhang, A. Cabot, Langmuir 31 (2015) 10555–10561.
date_created: 2018-12-11T11:46:01Z
date_published: 2015-09-29T00:00:00Z
date_updated: 2021-01-12T07:44:34Z
day: '29'
doi: 10.1021/acs.langmuir.5b02490
extern: '1'
intvolume: ' 31'
issue: '38'
language:
- iso: eng
month: '09'
oa_version: None
page: 10555 - 10561
publication: Langmuir
publication_status: published
publisher: American Chemical Society
publist_id: '7467'
status: public
title: Cu2ZnSnS4-Ag2S nanoscale p-n heterostructures as sensitizers for photoelectrochemical
water splitting
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2015'
...
---
_id: '362'
abstract:
- lang: eng
text: 'Monodisperse Pd2Sn nanorods with tuned size and aspect ratio were prepared
by co-reduction of metal salts in the presence of trioctylphosphine, amine, and
chloride ions. Asymmetric Pd2Sn nanostructures were achieved by the selective
desorption of a surfactant mediated by chlorine ions. A preliminary evaluation
of the geometry influence on catalytic properties evidenced Pd2Sn nanorods to
have improved catalytic performance. In view of these results, Pd2Sn nanorods
were also evaluated for water denitration. '
article_processing_charge: No
author:
- first_name: Zhishan
full_name: Lu, Zhishan
last_name: Lu
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Ana
full_name: Antolín, Ana
last_name: Antolín
- first_name: Aziz
full_name: Genç, Aziz
last_name: Genç
- first_name: Alexey
full_name: Shavel, Alexey
last_name: Shavel
- first_name: Sandra
full_name: Contreras, Sandra
last_name: Contreras
- first_name: Francesc
full_name: Medina, Francesc
last_name: Medina
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: Lu Z, Ibáñez M, Antolín A, et al. Size and aspect ratio control of Pd inf 2
inf Sn nanorods and their water denitration properties. Langmuir. 2015;31(13):3952-3957.
doi:10.1021/la504906q
apa: Lu, Z., Ibáñez, M., Antolín, A., Genç, A., Shavel, A., Contreras, S., … Cabot,
A. (2015). Size and aspect ratio control of Pd inf 2 inf Sn nanorods and their
water denitration properties. Langmuir. American Chemical Society. https://doi.org/10.1021/la504906q
chicago: Lu, Zhishan, Maria Ibáñez, Ana Antolín, Aziz Genç, Alexey Shavel, Sandra
Contreras, Francesc Medina, Jordi Arbiol, and Andreu Cabot. “Size and Aspect Ratio
Control of Pd Inf 2 Inf Sn Nanorods and Their Water Denitration Properties.” Langmuir.
American Chemical Society, 2015. https://doi.org/10.1021/la504906q.
ieee: Z. Lu et al., “Size and aspect ratio control of Pd inf 2 inf Sn nanorods
and their water denitration properties,” Langmuir, vol. 31, no. 13. American
Chemical Society, pp. 3952–3957, 2015.
ista: Lu Z, Ibáñez M, Antolín A, Genç A, Shavel A, Contreras S, Medina F, Arbiol
J, Cabot A. 2015. Size and aspect ratio control of Pd inf 2 inf Sn nanorods and
their water denitration properties. Langmuir. 31(13), 3952–3957.
mla: Lu, Zhishan, et al. “Size and Aspect Ratio Control of Pd Inf 2 Inf Sn Nanorods
and Their Water Denitration Properties.” Langmuir, vol. 31, no. 13, American
Chemical Society, 2015, pp. 3952–57, doi:10.1021/la504906q.
short: Z. Lu, M. Ibáñez, A. Antolín, A. Genç, A. Shavel, S. Contreras, F. Medina,
J. Arbiol, A. Cabot, Langmuir 31 (2015) 3952–3957.
date_created: 2018-12-11T11:46:02Z
date_published: 2015-04-07T00:00:00Z
date_updated: 2021-01-12T07:44:42Z
day: '07'
doi: 10.1021/la504906q
extern: '1'
intvolume: ' 31'
issue: '13'
language:
- iso: eng
month: '04'
oa_version: None
page: 3952 - 3957
publication: Langmuir
publication_status: published
publisher: American Chemical Society
publist_id: '7469'
status: public
title: Size and aspect ratio control of Pd inf 2 inf Sn nanorods and their water denitration
properties
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2015'
...
---
_id: '1731'
abstract:
- lang: eng
text: 'We consider two-player zero-sum games on graphs. These games can be classified
on the basis of the information of the players and on the mode of interaction
between them. On the basis of information the classification is as follows: (a)
partial-observation (both players have partial view of the game); (b) one-sided
complete-observation (one player has complete observation); and (c) complete-observation
(both players have complete view of the game). On the basis of mode of interaction
we have the following classification: (a) concurrent (both players interact simultaneously);
and (b) turn-based (both players interact in turn). The two sources of randomness
in these games are randomness in transition function and randomness in strategies.
In general, randomized strategies are more powerful than deterministic strategies,
and randomness in transitions gives more general classes of games. In this work
we present a complete characterization for the classes of games where randomness
is not helpful in: (a) the transition function probabilistic transition can be
simulated by deterministic transition); and (b) strategies (pure strategies are
as powerful as randomized strategies). As consequence of our characterization
we obtain new undecidability results for these games. '
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: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: Chatterjee K, Doyen L, Gimbert H, Henzinger TA. Randomness for free. Information
and Computation. 2015;245(12):3-16. doi:10.1016/j.ic.2015.06.003
apa: Chatterjee, K., Doyen, L., Gimbert, H., & Henzinger, T. A. (2015). Randomness
for free. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2015.06.003
chicago: Chatterjee, Krishnendu, Laurent Doyen, Hugo Gimbert, and Thomas A Henzinger.
“Randomness for Free.” Information and Computation. Elsevier, 2015. https://doi.org/10.1016/j.ic.2015.06.003.
ieee: K. Chatterjee, L. Doyen, H. Gimbert, and T. A. Henzinger, “Randomness for
free,” Information and Computation, vol. 245, no. 12. Elsevier, pp. 3–16,
2015.
ista: Chatterjee K, Doyen L, Gimbert H, Henzinger TA. 2015. Randomness for free.
Information and Computation. 245(12), 3–16.
mla: Chatterjee, Krishnendu, et al. “Randomness for Free.” Information and Computation,
vol. 245, no. 12, Elsevier, 2015, pp. 3–16, doi:10.1016/j.ic.2015.06.003.
short: K. Chatterjee, L. Doyen, H. Gimbert, T.A. Henzinger, Information and Computation
245 (2015) 3–16.
date_created: 2018-12-11T11:53:42Z
date_published: 2015-12-01T00:00:00Z
date_updated: 2023-02-23T11:45:42Z
day: '01'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1016/j.ic.2015.06.003
ec_funded: 1
intvolume: ' 245'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1006.0673
month: '12'
oa: 1
oa_version: Preprint
page: 3 - 16
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
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25EFB36C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '215543'
name: COMponent-Based Embedded Systems design Techniques
- _id: 25F1337C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '214373'
name: Design for Embedded Systems
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: Information and Computation
publication_status: published
publisher: Elsevier
publist_id: '5395'
quality_controlled: '1'
related_material:
record:
- id: '3856'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Randomness for free
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 245
year: '2015'
...
---
_id: '334'
abstract:
- lang: eng
text: A cation exchange-based route was used to produce Cu2ZnSnS4 (CZTS)-Ag2S nanoparticles
with controlled composition. We report a detailed study of the formation of such
CZTS-Ag2S nanoheterostructures and of their photocatalytic properties. When compared
to pure CZTS, the use of nanoscale p-n heterostructures as light absorbers for
photocatalytic water splitting provides superior photocurrents. We associate this
experimental fact to a higher separation efficiency of the photogenerated electron-hole
pairs. We believe this and other type-II nanoheterostructures will open the door
to the use of CZTS, with excellent light absorption properties and made of abundant
and environmental friendly elements, to the field of photocatalysis.
acknowledgement: This work was supported by the European Regional Development Funds,
the Framework 7 program under project SCALENANO (FP7-NMP-ENERGY-2011-284486), the
Spanish MINECO under Contract ENE2013-46624-C4-3-R and Fundamental Research Funds
for the Central Universities (2652015086). Authors acknowledge the funding from
Generalitat de Catalunya 2014 SGR 1638.
article_processing_charge: No
article_type: original
author:
- first_name: Xuelian
full_name: Yu, Xuelian
last_name: Yu
- first_name: Jingjing
full_name: Liu, Jingjing
last_name: Liu
- first_name: Aziz
full_name: Genç, Aziz
last_name: Genç
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Zhishan
full_name: Luo, Zhishan
last_name: Luo
- first_name: Alexey
full_name: Shavel, Alexey
last_name: Shavel
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Guangjin
full_name: Zhang, Guangjin
last_name: Zhang
- first_name: Yihe
full_name: Zhang, Yihe
last_name: Zhang
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: Yu X, Liu J, Genç A, et al. Cu2ZnSnS4–Ag2S Nanoscale p–n heterostructures as
sensitizers for photoelectrochemical water splitting. Langmuir. 2015;31(38):10555-10561.
doi:10.1021/acs.langmuir.5b02490
apa: Yu, X., Liu, J., Genç, A., Ibáñez, M., Luo, Z., Shavel, A., … Cabot, A. (2015).
Cu2ZnSnS4–Ag2S Nanoscale p–n heterostructures as sensitizers for photoelectrochemical
water splitting. Langmuir. American Chemical Society. https://doi.org/10.1021/acs.langmuir.5b02490
chicago: Yu, Xuelian, Jingjing Liu, Aziz Genç, Maria Ibáñez, Zhishan Luo, Alexey
Shavel, Jordi Arbiol, Guangjin Zhang, Yihe Zhang, and Andreu Cabot. “Cu2ZnSnS4–Ag2S
Nanoscale p–n Heterostructures as Sensitizers for Photoelectrochemical Water Splitting.”
Langmuir. American Chemical Society, 2015. https://doi.org/10.1021/acs.langmuir.5b02490.
ieee: X. Yu et al., “Cu2ZnSnS4–Ag2S Nanoscale p–n heterostructures as sensitizers
for photoelectrochemical water splitting,” Langmuir, vol. 31, no. 38. American
Chemical Society, pp. 10555–10561, 2015.
ista: Yu X, Liu J, Genç A, Ibáñez M, Luo Z, Shavel A, Arbiol J, Zhang G, Zhang Y,
Cabot A. 2015. Cu2ZnSnS4–Ag2S Nanoscale p–n heterostructures as sensitizers for
photoelectrochemical water splitting. Langmuir. 31(38), 10555–10561.
mla: Yu, Xuelian, et al. “Cu2ZnSnS4–Ag2S Nanoscale p–n Heterostructures as Sensitizers
for Photoelectrochemical Water Splitting.” Langmuir, vol. 31, no. 38, American
Chemical Society, 2015, pp. 10555–61, doi:10.1021/acs.langmuir.5b02490.
short: X. Yu, J. Liu, A. Genç, M. Ibáñez, Z. Luo, A. Shavel, J. Arbiol, G. Zhang,
Y. Zhang, A. Cabot, Langmuir 31 (2015) 10555–10561.
date_created: 2018-12-11T11:45:52Z
date_published: 2015-09-07T00:00:00Z
date_updated: 2021-01-12T07:42:46Z
day: '07'
doi: 10.1021/acs.langmuir.5b02490
extern: '1'
intvolume: ' 31'
issue: '38'
language:
- iso: eng
month: '09'
oa_version: None
page: 10555 - 10561
publication: Langmuir
publication_status: published
publisher: American Chemical Society
publist_id: '7508'
quality_controlled: '1'
status: public
title: Cu2ZnSnS4–Ag2S Nanoscale p–n heterostructures as sensitizers for photoelectrochemical
water splitting
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2015'
...
---
_id: '361'
abstract:
- lang: eng
text: We report the synthesis and photocatalytic and magnetic characterization of
colloidal nanoheterostructures formed by combining a Pt-based magnetic metal alloy
(PtCo, PtNi) with Cu2ZnSnS4 (CZTS). While CZTS is one of the main candidate materials
for solar energy conversion, the introduction of a Pt-based alloy on its surface
strongly influences its chemical and electronic properties, ultimately determining
its functionality. In this regard, up to a 15-fold increase of the photocatalytic
hydrogen evolution activity was obtained with CZTS–PtCo when compared with CZTS.
Furthermore, two times higher hydrogen evolution rates were obtained for CZTS–PtCo
when compared with CZTS–Pt, in spite of the lower precious metal loading of the
former. Besides, the magnetic properties of the PtCo nanoparticles attached to
the CZTS nanocrystals were retained in the heterostructures, which could facilitate
catalyst purification and recovery for its posterior recycling and/or reutilization.
acknowledgement: This work was supported by the National Natural Science Foundation
of China (Grant 21401212), Fundamental Research Funds for the Central Universities
(2652015086), the Framework 7 program under project SCALENANO (FP7-NMP-ENERGY-2011-284486),
and the MICINN project ENE2013-46624-C4-3-R. Authors acknowledge the funding from
Generalitat de Catalunya 2014 SGR 1638.
article_processing_charge: No
author:
- first_name: Xuelian
full_name: Yu, Xuelian
last_name: Yu
- first_name: Xiaoqiang
full_name: An, Xiaoqiang
last_name: An
- first_name: Aziz
full_name: Genç, Aziz
last_name: Genç
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Yihe
full_name: Zhang, Yihe
last_name: Zhang
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: Yu X, An X, Genç A, et al. Cu2ZnSnS4–PtM (M = Co, Ni) nanoheterostructures
for photocatalytic hydrogen evolution. Journal of Physical Chemistry C.
2015;119(38):21882-21888. doi:10.1021/acs.jpcc.5b06199
apa: Yu, X., An, X., Genç, A., Ibáñez, M., Arbiol, J., Zhang, Y., & Cabot, A.
(2015). Cu2ZnSnS4–PtM (M = Co, Ni) nanoheterostructures for photocatalytic hydrogen
evolution. Journal of Physical Chemistry C. American Chemical Society.
https://doi.org/10.1021/acs.jpcc.5b06199
chicago: Yu, Xuelian, Xiaoqiang An, Aziz Genç, Maria Ibáñez, Jordi Arbiol, Yihe
Zhang, and Andreu Cabot. “Cu2ZnSnS4–PtM (M = Co, Ni) Nanoheterostructures for
Photocatalytic Hydrogen Evolution.” Journal of Physical Chemistry C. American
Chemical Society, 2015. https://doi.org/10.1021/acs.jpcc.5b06199.
ieee: X. Yu et al., “Cu2ZnSnS4–PtM (M = Co, Ni) nanoheterostructures for
photocatalytic hydrogen evolution,” Journal of Physical Chemistry C, vol.
119, no. 38. American Chemical Society, pp. 21882–21888, 2015.
ista: Yu X, An X, Genç A, Ibáñez M, Arbiol J, Zhang Y, Cabot A. 2015. Cu2ZnSnS4–PtM
(M = Co, Ni) nanoheterostructures for photocatalytic hydrogen evolution. Journal
of Physical Chemistry C. 119(38), 21882–21888.
mla: Yu, Xuelian, et al. “Cu2ZnSnS4–PtM (M = Co, Ni) Nanoheterostructures for Photocatalytic
Hydrogen Evolution.” Journal of Physical Chemistry C, vol. 119, no. 38,
American Chemical Society, 2015, pp. 21882–88, doi:10.1021/acs.jpcc.5b06199.
short: X. Yu, X. An, A. Genç, M. Ibáñez, J. Arbiol, Y. Zhang, A. Cabot, Journal
of Physical Chemistry C 119 (2015) 21882–21888.
date_created: 2018-12-11T11:46:01Z
date_published: 2015-08-26T00:00:00Z
date_updated: 2021-01-12T07:44:38Z
day: '26'
doi: 10.1021/acs.jpcc.5b06199
extern: '1'
intvolume: ' 119'
issue: '38'
language:
- iso: eng
month: '08'
oa_version: None
page: 21882 - 21888
publication: Journal of Physical Chemistry C
publication_status: published
publisher: American Chemical Society
publist_id: '7468'
status: public
title: Cu2ZnSnS4–PtM (M = Co, Ni) nanoheterostructures for photocatalytic hydrogen
evolution
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 119
year: '2015'
...
---
_id: '1856'
abstract:
- lang: eng
text: 'The traditional synthesis question given a specification asks for the automatic
construction of a system that satisfies the specification, whereas often there
exists a preference order among the different systems that satisfy the given specification.
Under a probabilistic assumption about the possible inputs, such a preference
order is naturally expressed by a weighted automaton, which assigns to each word
a value, such that a system is preferred if it generates a higher expected value.
We solve the following optimal synthesis problem: given an omega-regular specification,
a Markov chain that describes the distribution of inputs, and a weighted automaton
that measures how well a system satisfies the given specification under the input
assumption, synthesize a system that optimizes the measured value. For safety
specifications and quantitative measures that are defined by mean-payoff automata,
the optimal synthesis problem reduces to finding a strategy in a Markov decision
process (MDP) that is optimal for a long-run average reward objective, which can
be achieved in polynomial time. For general omega-regular specifications along
with mean-payoff automata, the solution rests on a new, polynomial-time algorithm
for computing optimal strategies in MDPs with mean-payoff parity objectives. Our
algorithm constructs optimal strategies that consist of two memoryless strategies
and a counter. The counter is in general not bounded. To obtain a finite-state
system, we show how to construct an ε-optimal strategy with a bounded counter,
for all ε > 0. Furthermore, we show how to decide in polynomial time if it
is possible to construct an optimal finite-state system (i.e., a system without
a counter) for a given specification. We have implemented our approach and the
underlying algorithms in a tool that takes qualitative and quantitative specifications
and automatically constructs a system that satisfies the qualitative specification
and optimizes the quantitative specification, if such a system exists. We present
some experimental results showing optimal systems that were automatically generated
in this way.'
article_number: '9'
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: Barbara
full_name: Jobstmann, Barbara
last_name: Jobstmann
- first_name: Rohit
full_name: Singh, Rohit
last_name: Singh
citation:
ama: Chatterjee K, Henzinger TA, Jobstmann B, Singh R. Measuring and synthesizing
systems in probabilistic environments. Journal of the ACM. 2015;62(1).
doi:10.1145/2699430
apa: Chatterjee, K., Henzinger, T. A., Jobstmann, B., & Singh, R. (2015). Measuring
and synthesizing systems in probabilistic environments. Journal of the ACM.
ACM. https://doi.org/10.1145/2699430
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Barbara Jobstmann, and Rohit
Singh. “Measuring and Synthesizing Systems in Probabilistic Environments.” Journal
of the ACM. ACM, 2015. https://doi.org/10.1145/2699430.
ieee: K. Chatterjee, T. A. Henzinger, B. Jobstmann, and R. Singh, “Measuring and
synthesizing systems in probabilistic environments,” Journal of the ACM,
vol. 62, no. 1. ACM, 2015.
ista: Chatterjee K, Henzinger TA, Jobstmann B, Singh R. 2015. Measuring and synthesizing
systems in probabilistic environments. Journal of the ACM. 62(1), 9.
mla: Chatterjee, Krishnendu, et al. “Measuring and Synthesizing Systems in Probabilistic
Environments.” Journal of the ACM, vol. 62, no. 1, 9, ACM, 2015, doi:10.1145/2699430.
short: K. Chatterjee, T.A. Henzinger, B. Jobstmann, R. Singh, Journal of the ACM
62 (2015).
date_created: 2018-12-11T11:54:23Z
date_published: 2015-02-01T00:00:00Z
date_updated: 2023-02-23T11:46:04Z
day: '01'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1145/2699430
ec_funded: 1
intvolume: ' 62'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1004.0739
month: '02'
oa: 1
oa_version: Preprint
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
- _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: Journal of the ACM
publication_status: published
publisher: ACM
publist_id: '5244'
quality_controlled: '1'
related_material:
record:
- id: '3864'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Measuring and synthesizing systems in probabilistic environments
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 62
year: '2015'
...
---
_id: '388'
abstract:
- lang: eng
text: We use ultrafast optical spectroscopy to observe binding of charged single-particle
excitations (SE) in the magnetically frustrated Mott insulator Na2IrO3. Above
the antiferromagnetic ordering temperature (TN) the system response is due to
both Hubbard excitons (HE) and their constituent unpaired SE. The SE response
becomes strongly suppressed immediately below TN. We argue that this increase
in binding energy is due to a unique interplay between the frustrated Kitaev and
the weak Heisenberg-type ordering term in the Hamiltonian, mediating an effective
interaction between the spin-singlet SE. This interaction grows with distance
causing the SE to become trapped in the HE, similar to quark confinement inside
hadrons. This binding of charged particles, induced by magnetic ordering, is a
result of a confinement-deconfinement transition of spin excitations. This observation
provides evidence for spin liquid type behavior which is expected in Na2IrO3.
article_processing_charge: No
article_type: original
author:
- first_name: Zhanybek
full_name: Alpichshev, Zhanybek
id: 45E67A2A-F248-11E8-B48F-1D18A9856A87
last_name: Alpichshev
orcid: 0000-0002-7183-5203
- first_name: Fahad
full_name: Mahmood, Fahad
last_name: Mahmood
- first_name: Gang
full_name: Cao, Gang
last_name: Cao
- first_name: Nuh
full_name: Gedik, Nuh
last_name: Gedik
citation:
ama: Alpichshev Z, Mahmood F, Cao G, Gedik N. Confinement deconfinement transition
as an indication of spin liquid type behavior in Na2IrO3. Physical Review Letters.
2015;114(1). doi:10.1103/PhysRevLett.114.017203
apa: Alpichshev, Z., Mahmood, F., Cao, G., & Gedik, N. (2015). Confinement deconfinement
transition as an indication of spin liquid type behavior in Na2IrO3. Physical
Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.114.017203
chicago: Alpichshev, Zhanybek, Fahad Mahmood, Gang Cao, and Nuh Gedik. “Confinement
Deconfinement Transition as an Indication of Spin Liquid Type Behavior in Na2IrO3.”
Physical Review Letters. American Physical Society, 2015. https://doi.org/10.1103/PhysRevLett.114.017203.
ieee: Z. Alpichshev, F. Mahmood, G. Cao, and N. Gedik, “Confinement deconfinement
transition as an indication of spin liquid type behavior in Na2IrO3,” Physical
Review Letters, vol. 114, no. 1. American Physical Society, 2015.
ista: Alpichshev Z, Mahmood F, Cao G, Gedik N. 2015. Confinement deconfinement transition
as an indication of spin liquid type behavior in Na2IrO3. Physical Review Letters.
114(1).
mla: Alpichshev, Zhanybek, et al. “Confinement Deconfinement Transition as an Indication
of Spin Liquid Type Behavior in Na2IrO3.” Physical Review Letters, vol.
114, no. 1, American Physical Society, 2015, doi:10.1103/PhysRevLett.114.017203.
short: Z. Alpichshev, F. Mahmood, G. Cao, N. Gedik, Physical Review Letters 114
(2015).
date_created: 2018-12-11T11:46:11Z
date_published: 2015-07-07T00:00:00Z
date_updated: 2021-01-12T07:52:54Z
day: '07'
doi: 10.1103/PhysRevLett.114.017203
extern: '1'
intvolume: ' 114'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://dspace.mit.edu/handle/1721.1/92979
month: '07'
oa: 1
oa_version: Published Version
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '7441'
quality_controlled: '1'
status: public
title: Confinement deconfinement transition as an indication of spin liquid type behavior
in Na2IrO3
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 114
year: '2015'
...
---
_id: '1661'
abstract:
- lang: eng
text: The computation of the winning set for one-pair Streett objectives and for
k-pair Streett objectives in (standard) graphs as well as in game graphs are central
problems in computer-aided verification, with application to the verification
of closed systems with strong fairness conditions, the verification of open systems,
checking interface compatibility, well-formed ness of specifications, and the
synthesis of reactive systems. We give faster algorithms for the computation of
the winning set for (1) one-pair Streett objectives (aka parity-3 problem) in
game graphs and (2) for k-pair Streett objectives in graphs. For both problems
this represents the first improvement in asymptotic running time in 15 years.
acknowledgement: 'K. C. is supported by the Austrian Science Fund (FWF): P23499-N23
and S11407-N23 (RiSE), an ERC Start Grant (279307: Graph Games), and a Microsoft
Faculty Fellows Award. M. H. is supported by the Austrian Science Fund (FWF): P23499-N23
and the Vienna Science and Technology Fund (WWTF) grant ICT10-002. V. L. is supported
by the Vienna Science and Technology Fund (WWTF) grant ICT10-002. The research leading
to these results has received funding from the European Research Council under the
European Union’s Seventh Framework Programme (FP/2007-2013) / ERC Grant Agreement
no. 340506.'
article_number: '7174888'
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: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Veronika
full_name: Loitzenbauer, Veronika
last_name: Loitzenbauer
citation:
ama: 'Chatterjee K, Henzinger MH, Loitzenbauer V. Improved algorithms for one-pair
and k-pair Streett objectives. In: Proceedings - Symposium on Logic in Computer
Science. Vol 2015-July. IEEE; 2015. doi:10.1109/LICS.2015.34'
apa: 'Chatterjee, K., Henzinger, M. H., & Loitzenbauer, V. (2015). Improved
algorithms for one-pair and k-pair Streett objectives. In Proceedings - Symposium
on Logic in Computer Science (Vol. 2015–July). Kyoto, Japan: IEEE. https://doi.org/10.1109/LICS.2015.34'
chicago: Chatterjee, Krishnendu, Monika H Henzinger, and Veronika Loitzenbauer.
“Improved Algorithms for One-Pair and k-Pair Streett Objectives.” In Proceedings
- Symposium on Logic in Computer Science, Vol. 2015–July. IEEE, 2015. https://doi.org/10.1109/LICS.2015.34.
ieee: K. Chatterjee, M. H. Henzinger, and V. Loitzenbauer, “Improved algorithms
for one-pair and k-pair Streett objectives,” in Proceedings - Symposium on
Logic in Computer Science, Kyoto, Japan, 2015, vol. 2015–July.
ista: 'Chatterjee K, Henzinger MH, Loitzenbauer V. 2015. Improved algorithms for
one-pair and k-pair Streett objectives. Proceedings - Symposium on Logic in Computer
Science. LICS: Logic in Computer Science vol. 2015–July, 7174888.'
mla: Chatterjee, Krishnendu, et al. “Improved Algorithms for One-Pair and k-Pair
Streett Objectives.” Proceedings - Symposium on Logic in Computer Science,
vol. 2015–July, 7174888, IEEE, 2015, doi:10.1109/LICS.2015.34.
short: K. Chatterjee, M.H. Henzinger, V. Loitzenbauer, in:, Proceedings - Symposium
on Logic in Computer Science, IEEE, 2015.
conference:
end_date: 2015-07-10
location: Kyoto, Japan
name: 'LICS: Logic in Computer Science'
start_date: 2015-07-06
date_created: 2018-12-11T11:53:19Z
date_published: 2015-07-01T00:00:00Z
date_updated: 2023-02-23T12:20:05Z
day: '01'
department:
- _id: KrCh
doi: 10.1109/LICS.2015.34
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprints.cs.univie.ac.at/4368/
month: '07'
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: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Proceedings - Symposium on Logic in Computer Science
publication_status: published
publisher: IEEE
publist_id: '5489'
quality_controlled: '1'
related_material:
record:
- id: '464'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Improved algorithms for one-pair and k-pair Streett objectives
type: conference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 2015-July
year: '2015'
...
---
_id: '473'
abstract:
- lang: eng
text: We prove that nonlinear Gibbs measures can be obtained from the corresponding
many-body, grand-canonical, quantum Gibbs states, in a mean-field limit where
the temperature T diverges and the interaction strength behaves as 1/T. We proceed
by characterizing the interacting Gibbs state as minimizing a functional counting
the free-energy relatively to the non-interacting case. We then perform an infinite-dimensional
analogue of phase-space semiclassical analysis, using fine properties of the quantum
relative entropy, the link between quantum de Finetti measures and upper/lower
symbols in a coherent state basis, as well as Berezin-Lieb type inequalities.
Our results cover the measure built on the defocusing nonlinear Schrödinger functional
on a finite interval, as well as smoother interactions in dimensions d 2.
author:
- first_name: Mathieu
full_name: Lewin, Mathieu
last_name: Lewin
- first_name: Nam
full_name: Phan Thanh, Nam
id: 404092F4-F248-11E8-B48F-1D18A9856A87
last_name: Phan Thanh
- first_name: Nicolas
full_name: Rougerie, Nicolas
last_name: Rougerie
citation:
ama: Lewin M, Nam P, Rougerie N. Derivation of nonlinear gibbs measures from many-body
quantum mechanics. Journal de l’Ecole Polytechnique - Mathematiques. 2015;2:65-115.
doi:10.5802/jep.18
apa: Lewin, M., Nam, P., & Rougerie, N. (2015). Derivation of nonlinear gibbs
measures from many-body quantum mechanics. Journal de l’Ecole Polytechnique
- Mathematiques. Ecole Polytechnique. https://doi.org/10.5802/jep.18
chicago: Lewin, Mathieu, Phan Nam, and Nicolas Rougerie. “Derivation of Nonlinear
Gibbs Measures from Many-Body Quantum Mechanics.” Journal de l’Ecole Polytechnique
- Mathematiques. Ecole Polytechnique, 2015. https://doi.org/10.5802/jep.18.
ieee: M. Lewin, P. Nam, and N. Rougerie, “Derivation of nonlinear gibbs measures
from many-body quantum mechanics,” Journal de l’Ecole Polytechnique - Mathematiques,
vol. 2. Ecole Polytechnique, pp. 65–115, 2015.
ista: Lewin M, Nam P, Rougerie N. 2015. Derivation of nonlinear gibbs measures from
many-body quantum mechanics. Journal de l’Ecole Polytechnique - Mathematiques.
2, 65–115.
mla: Lewin, Mathieu, et al. “Derivation of Nonlinear Gibbs Measures from Many-Body
Quantum Mechanics.” Journal de l’Ecole Polytechnique - Mathematiques, vol.
2, Ecole Polytechnique, 2015, pp. 65–115, doi:10.5802/jep.18.
short: M. Lewin, P. Nam, N. Rougerie, Journal de l’Ecole Polytechnique - Mathematiques
2 (2015) 65–115.
date_created: 2018-12-11T11:46:40Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T08:00:52Z
day: '01'
ddc:
- '539'
department:
- _id: RoSe
doi: 10.5802/jep.18
ec_funded: 1
file:
- access_level: open_access
checksum: a40eb4016717ddc9927154798a4c164a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:53Z
date_updated: 2020-07-14T12:46:35Z
file_id: '4974'
file_name: IST-2018-951-v1+1_2015_Thanh-Nam_Derivation_of.pdf
file_size: 1084254
relation: main_file
file_date_updated: 2020-07-14T12:46:35Z
has_accepted_license: '1'
intvolume: ' 2'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 65 - 115
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Journal de l'Ecole Polytechnique - Mathematiques
publication_status: published
publisher: Ecole Polytechnique
publist_id: '7344'
pubrep_id: '951'
quality_controlled: '1'
scopus_import: 1
status: public
title: Derivation of nonlinear gibbs measures from many-body quantum mechanics
tmp:
image: /image/cc_by_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
short: CC BY-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2015'
...
---
_id: '477'
abstract:
- lang: eng
text: Dendritic cells are potent antigen-presenting cells endowed with the unique
ability to initiate adaptive immune responses upon inflammation. Inflammatory
processes are often associated with an increased production of serotonin, which
operates by activating specific receptors. However, the functional role of serotonin
receptors in regulation of dendritic cell functions is poorly understood. Here,
we demonstrate that expression of serotonin receptor 5-HT7 (5-HT7TR) as well as
its downstream effector Cdc42 is upregulated in dendritic cells upon maturation.
Although dendritic cell maturation was independent of 5-HT7TR, receptor stimulation
affected dendritic cell morphology through Cdc42-mediated signaling. In addition,
basal activity of 5-HT7TR was required for the proper expression of the chemokine
receptor CCR7, which is a key factor that controls dendritic cell migration. Consistent
with this, we observed that 5-HT7TR enhances chemotactic motility of dendritic
cells in vitro by modulating their directionality and migration velocity. Accordingly,
migration of dendritic cells in murine colon explants was abolished after pharmacological
receptor inhibition. Our results indicate that there is a crucial role for 5-HT7TR-Cdc42-mediated
signaling in the regulation of dendritic cell morphology and motility, suggesting
that 5-HT7TR could be a new target for treatment of a variety of inflammatory
and immune disorders.
author:
- first_name: Katrin
full_name: Holst, Katrin
last_name: Holst
- first_name: Daria
full_name: Guseva, Daria
last_name: Guseva
- first_name: Susann
full_name: Schindler, Susann
last_name: Schindler
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Armin
full_name: Braun, Armin
last_name: Braun
- first_name: Himpriya
full_name: Chopra, Himpriya
last_name: Chopra
- first_name: Oliver
full_name: Pabst, Oliver
last_name: Pabst
- first_name: Evgeni
full_name: Ponimaskin, Evgeni
last_name: Ponimaskin
citation:
ama: Holst K, Guseva D, Schindler S, et al. The serotonin receptor 5-HT7R regulates
the morphology and migratory properties of dendritic cells. Journal of Cell
Science. 2015;128(15):2866-2880. doi:10.1242/jcs.167999
apa: Holst, K., Guseva, D., Schindler, S., Sixt, M. K., Braun, A., Chopra, H., …
Ponimaskin, E. (2015). The serotonin receptor 5-HT7R regulates the morphology
and migratory properties of dendritic cells. Journal of Cell Science. Company
of Biologists. https://doi.org/10.1242/jcs.167999
chicago: Holst, Katrin, Daria Guseva, Susann Schindler, Michael K Sixt, Armin Braun,
Himpriya Chopra, Oliver Pabst, and Evgeni Ponimaskin. “The Serotonin Receptor
5-HT7R Regulates the Morphology and Migratory Properties of Dendritic Cells.”
Journal of Cell Science. Company of Biologists, 2015. https://doi.org/10.1242/jcs.167999.
ieee: K. Holst et al., “The serotonin receptor 5-HT7R regulates the morphology
and migratory properties of dendritic cells,” Journal of Cell Science,
vol. 128, no. 15. Company of Biologists, pp. 2866–2880, 2015.
ista: Holst K, Guseva D, Schindler S, Sixt MK, Braun A, Chopra H, Pabst O, Ponimaskin
E. 2015. The serotonin receptor 5-HT7R regulates the morphology and migratory
properties of dendritic cells. Journal of Cell Science. 128(15), 2866–2880.
mla: Holst, Katrin, et al. “The Serotonin Receptor 5-HT7R Regulates the Morphology
and Migratory Properties of Dendritic Cells.” Journal of Cell Science,
vol. 128, no. 15, Company of Biologists, 2015, pp. 2866–80, doi:10.1242/jcs.167999.
short: K. Holst, D. Guseva, S. Schindler, M.K. Sixt, A. Braun, H. Chopra, O. Pabst,
E. Ponimaskin, Journal of Cell Science 128 (2015) 2866–2880.
date_created: 2018-12-11T11:46:41Z
date_published: 2015-06-15T00:00:00Z
date_updated: 2021-01-12T08:00:54Z
day: '15'
department:
- _id: MiSi
doi: 10.1242/jcs.167999
intvolume: ' 128'
issue: '15'
language:
- iso: eng
month: '06'
oa_version: None
page: 2866 - 2880
publication: Journal of Cell Science
publication_status: published
publisher: Company of Biologists
publist_id: '7343'
quality_controlled: '1'
scopus_import: 1
status: public
title: The serotonin receptor 5-HT7R regulates the morphology and migratory properties
of dendritic cells
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 128
year: '2015'
...
---
_id: '523'
abstract:
- lang: eng
text: We consider two-player games played on weighted directed graphs with mean-payoff
and total-payoff objectives, two classical quantitative objectives. While for
single-dimensional games the complexity and memory bounds for both objectives
coincide, we show that in contrast to multi-dimensional mean-payoff games that
are known to be coNP-complete, multi-dimensional total-payoff games are undecidable.
We introduce conservative approximations of these objectives, where the payoff
is considered over a local finite window sliding along a play, instead of the
whole play. For single dimension, we show that (i) if the window size is polynomial,
deciding the winner takes polynomial time, and (ii) the existence of a bounded
window can be decided in NP ∩ coNP, and is at least as hard as solving mean-payoff
games. For multiple dimensions, we show that (i) the problem with fixed window
size is EXPTIME-complete, and (ii) there is no primitive-recursive algorithm to
decide the existence of a bounded window.
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: Mickael
full_name: Randour, Mickael
last_name: Randour
- first_name: Jean
full_name: Raskin, Jean
last_name: Raskin
citation:
ama: Chatterjee K, Doyen L, Randour M, Raskin J. Looking at mean-payoff and total-payoff
through windows. Information and Computation. 2015;242(6):25-52. doi:10.1016/j.ic.2015.03.010
apa: Chatterjee, K., Doyen, L., Randour, M., & Raskin, J. (2015). Looking at
mean-payoff and total-payoff through windows. Information and Computation.
Elsevier. https://doi.org/10.1016/j.ic.2015.03.010
chicago: Chatterjee, Krishnendu, Laurent Doyen, Mickael Randour, and Jean Raskin.
“Looking at Mean-Payoff and Total-Payoff through Windows.” Information and
Computation. Elsevier, 2015. https://doi.org/10.1016/j.ic.2015.03.010.
ieee: K. Chatterjee, L. Doyen, M. Randour, and J. Raskin, “Looking at mean-payoff
and total-payoff through windows,” Information and Computation, vol. 242,
no. 6. Elsevier, pp. 25–52, 2015.
ista: Chatterjee K, Doyen L, Randour M, Raskin J. 2015. Looking at mean-payoff and
total-payoff through windows. Information and Computation. 242(6), 25–52.
mla: Chatterjee, Krishnendu, et al. “Looking at Mean-Payoff and Total-Payoff through
Windows.” Information and Computation, vol. 242, no. 6, Elsevier, 2015,
pp. 25–52, doi:10.1016/j.ic.2015.03.010.
short: K. Chatterjee, L. Doyen, M. Randour, J. Raskin, Information and Computation
242 (2015) 25–52.
date_created: 2018-12-11T11:46:57Z
date_published: 2015-03-24T00:00:00Z
date_updated: 2023-02-23T10:36:02Z
day: '24'
department:
- _id: KrCh
doi: 10.1016/j.ic.2015.03.010
ec_funded: 1
intvolume: ' 242'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1302.4248
month: '03'
oa: 1
oa_version: Preprint
page: 25 - 52
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: Information and Computation
publication_status: published
publisher: Elsevier
publist_id: '7296'
quality_controlled: '1'
related_material:
record:
- id: '2279'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Looking at mean-payoff and total-payoff through windows
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 242
year: '2015'
...
---
_id: '532'
abstract:
- lang: eng
text: Ethylene is a gaseous phytohormone that plays vital roles in plant growth
and development. Previous studies uncovered EIN2 as an essential signal transducer
linking ethylene perception on ER to transcriptional regulation in the nucleus
through a “cleave and shuttle” model. In this study, we report another mechanism
of EIN2-mediated ethylene signaling, whereby EIN2 imposes the translational repression
of EBF1 and EBF2 mRNA. We find that the EBF1/2 3′ UTRs mediate EIN2-directed translational
repression and identify multiple poly-uridylates (PolyU) motifs as functional
cis elements of 3′ UTRs. Furthermore, we demonstrate that ethylene induces EIN2
to associate with 3′ UTRs and target EBF1/2 mRNA to cytoplasmic processing-body
(P-body) through interacting with multiple P-body factors, including EIN5 and
PABs. Our study illustrates translational regulation as a key step in ethylene
signaling and presents mRNA 3′ UTR functioning as a “signal transducer” to sense
and relay cellular signaling in plants.
author:
- first_name: Wenyang
full_name: Li, Wenyang
last_name: Li
- first_name: Mengdi
full_name: Ma, Mengdi
last_name: Ma
- first_name: Ying
full_name: Feng, Ying
last_name: Feng
- first_name: Hongjiang
full_name: Li, Hongjiang
id: 33CA54A6-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0001-5039-9660
- first_name: Yichuan
full_name: Wang, Yichuan
last_name: Wang
- first_name: Yutong
full_name: Ma, Yutong
last_name: Ma
- first_name: Mingzhe
full_name: Li, Mingzhe
last_name: Li
- first_name: Fengying
full_name: An, Fengying
last_name: An
- first_name: Hongwei
full_name: Guo, Hongwei
last_name: Guo
citation:
ama: Li W, Ma M, Feng Y, et al. EIN2-directed translational regulation of ethylene
signaling in arabidopsis. Cell. 2015;163(3):670-683. doi:10.1016/j.cell.2015.09.037
apa: Li, W., Ma, M., Feng, Y., Li, H., Wang, Y., Ma, Y., … Guo, H. (2015). EIN2-directed
translational regulation of ethylene signaling in arabidopsis. Cell. Cell
Press. https://doi.org/10.1016/j.cell.2015.09.037
chicago: Li, Wenyang, Mengdi Ma, Ying Feng, Hongjiang Li, Yichuan Wang, Yutong Ma,
Mingzhe Li, Fengying An, and Hongwei Guo. “EIN2-Directed Translational Regulation
of Ethylene Signaling in Arabidopsis.” Cell. Cell Press, 2015. https://doi.org/10.1016/j.cell.2015.09.037.
ieee: W. Li et al., “EIN2-directed translational regulation of ethylene signaling
in arabidopsis,” Cell, vol. 163, no. 3. Cell Press, pp. 670–683, 2015.
ista: Li W, Ma M, Feng Y, Li H, Wang Y, Ma Y, Li M, An F, Guo H. 2015. EIN2-directed
translational regulation of ethylene signaling in arabidopsis. Cell. 163(3), 670–683.
mla: Li, Wenyang, et al. “EIN2-Directed Translational Regulation of Ethylene Signaling
in Arabidopsis.” Cell, vol. 163, no. 3, Cell Press, 2015, pp. 670–83, doi:10.1016/j.cell.2015.09.037.
short: W. Li, M. Ma, Y. Feng, H. Li, Y. Wang, Y. Ma, M. Li, F. An, H. Guo, Cell
163 (2015) 670–683.
date_created: 2018-12-11T11:47:00Z
date_published: 2015-10-22T00:00:00Z
date_updated: 2021-01-12T08:01:27Z
day: '22'
department:
- _id: JiFr
doi: 10.1016/j.cell.2015.09.037
intvolume: ' 163'
issue: '3'
language:
- iso: eng
month: '10'
oa_version: None
page: 670 - 683
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '7285'
quality_controlled: '1'
scopus_import: 1
status: public
title: EIN2-directed translational regulation of ethylene signaling in arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 163
year: '2015'
...
---
_id: '524'
abstract:
- lang: eng
text: 'We consider concurrent games played by two players on a finite-state graph,
where in every round the players simultaneously choose a move, and the current
state along with the joint moves determine the successor state. We study the most
fundamental objective for concurrent games, namely, mean-payoff or limit-average
objective, where a reward is associated to each transition, and the goal of player
1 is to maximize the long-run average of the rewards, and the objective of player
2 is strictly the opposite (i.e., the games are zero-sum). The path constraint
for player 1 could be qualitative, i.e., the mean-payoff is the maximal reward,
or arbitrarily close to it; or quantitative, i.e., a given threshold between the
minimal and maximal reward. We consider the computation of the almost-sure (resp.
positive) winning sets, where player 1 can ensure that the path constraint is
satisfied with probability 1 (resp. positive probability). Almost-sure winning
with qualitative constraint exactly corresponds to the question of whether there
exists a strategy to ensure that the payoff is the maximal reward of the game.
Our main results for qualitative path constraints are as follows: (1) we establish
qualitative determinacy results that show that for every state either player 1
has a strategy to ensure almost-sure (resp. positive) winning against all player-2
strategies, or player 2 has a spoiling strategy to falsify almost-sure (resp.
positive) winning against all player-1 strategies; (2) we present optimal strategy
complexity results that precisely characterize the classes of strategies required
for almost-sure and positive winning for both players; and (3) we present quadratic
time algorithms to compute the almost-sure and the positive winning sets, matching
the best known bound of the algorithms for much simpler problems (such as reachability
objectives). For quantitative constraints we show that a polynomial time solution
for the almost-sure or the positive winning set would imply a solution to a long-standing
open problem (of solving the value problem of turn-based deterministic mean-payoff
games) that is not known to be solvable in polynomial time.'
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. Qualitative analysis of concurrent mean payoff
games. Information and Computation. 2015;242(6):2-24. doi:10.1016/j.ic.2015.03.009
apa: Chatterjee, K., & Ibsen-Jensen, R. (2015). Qualitative analysis of concurrent
mean payoff games. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2015.03.009
chicago: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “Qualitative Analysis
of Concurrent Mean Payoff Games.” Information and Computation. Elsevier,
2015. https://doi.org/10.1016/j.ic.2015.03.009.
ieee: K. Chatterjee and R. Ibsen-Jensen, “Qualitative analysis of concurrent mean
payoff games,” Information and Computation, vol. 242, no. 6. Elsevier,
pp. 2–24, 2015.
ista: Chatterjee K, Ibsen-Jensen R. 2015. Qualitative analysis of concurrent mean
payoff games. Information and Computation. 242(6), 2–24.
mla: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “Qualitative Analysis of Concurrent
Mean Payoff Games.” Information and Computation, vol. 242, no. 6, Elsevier,
2015, pp. 2–24, doi:10.1016/j.ic.2015.03.009.
short: K. Chatterjee, R. Ibsen-Jensen, Information and Computation 242 (2015) 2–24.
date_created: 2018-12-11T11:46:57Z
date_published: 2015-10-11T00:00:00Z
date_updated: 2023-02-23T12:24:45Z
day: '11'
department:
- _id: KrCh
doi: 10.1016/j.ic.2015.03.009
external_id:
arxiv:
- '1409.5306'
intvolume: ' 242'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1409.5306
month: '10'
oa: 1
oa_version: Preprint
page: 2 - 24
publication: Information and Computation
publication_status: published
publisher: Elsevier
publist_id: '7295'
quality_controlled: '1'
related_material:
record:
- id: '5403'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Qualitative analysis of concurrent mean payoff games
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 242
year: '2015'
...
---
_id: '1481'
abstract:
- lang: eng
text: 'Simple board games, like Tic-Tac-Toe and CONNECT-4, play an important role
not only in the development of mathematical and logical skills, but also in the
emotional and social development. In this paper, we address the problem of generating
targeted starting positions for such games. This can facilitate new approaches
for bringing novice players to mastery, and also leads to discovery of interesting
game variants. We present an approach that generates starting states of varying
hardness levels for player 1 in a two-player board game, given rules of the board
game, the desired number of steps required for player 1 to win, and the expertise
levels of the two players. Our approach leverages symbolic methods and iterative
simulation to efficiently search the extremely large state space. We present experimental
results that include discovery of states of varying hardness levels for several
simple grid-based board games. The presence of such states for standard game variants
like 4×4 Tic-Tac-Toe opens up new games to be played that have never been played
as the default start state is heavily biased. '
acknowledgement: "A Technical Report of this paper is available at: \r\nhttps://repository.ist.ac.at/id/eprint/146.\r\n"
article_processing_charge: No
author:
- first_name: Umair
full_name: Ahmed, Umair
last_name: Ahmed
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Sumit
full_name: Gulwani, Sumit
last_name: Gulwani
citation:
ama: 'Ahmed U, Chatterjee K, Gulwani S. Automatic generation of alternative starting
positions for simple traditional board games. In: Proceedings of the Twenty-Ninth
AAAI Conference on Artificial Intelligence. Vol 2. AAAI Press; 2015:745-752.'
apa: 'Ahmed, U., Chatterjee, K., & Gulwani, S. (2015). Automatic generation
of alternative starting positions for simple traditional board games. In Proceedings
of the Twenty-Ninth AAAI Conference on Artificial Intelligence (Vol. 2, pp.
745–752). Austin, TX, USA: AAAI Press.'
chicago: Ahmed, Umair, Krishnendu Chatterjee, and Sumit Gulwani. “Automatic Generation
of Alternative Starting Positions for Simple Traditional Board Games.” In Proceedings
of the Twenty-Ninth AAAI Conference on Artificial Intelligence, 2:745–52.
AAAI Press, 2015.
ieee: U. Ahmed, K. Chatterjee, and S. Gulwani, “Automatic generation of alternative
starting positions for simple traditional board games,” in Proceedings of the
Twenty-Ninth AAAI Conference on Artificial Intelligence, Austin, TX, USA,
2015, vol. 2, pp. 745–752.
ista: 'Ahmed U, Chatterjee K, Gulwani S. 2015. Automatic generation of alternative
starting positions for simple traditional board games. Proceedings of the Twenty-Ninth
AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence
vol. 2, 745–752.'
mla: Ahmed, Umair, et al. “Automatic Generation of Alternative Starting Positions
for Simple Traditional Board Games.” Proceedings of the Twenty-Ninth AAAI Conference
on Artificial Intelligence, vol. 2, AAAI Press, 2015, pp. 745–52.
short: U. Ahmed, K. Chatterjee, S. Gulwani, in:, Proceedings of the Twenty-Ninth
AAAI Conference on Artificial Intelligence, AAAI Press, 2015, pp. 745–752.
conference:
end_date: 2015-01-30
location: Austin, TX, USA
name: 'AAAI: Conference on Artificial Intelligence'
start_date: 2015-01-25
date_created: 2018-12-11T11:52:16Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2023-02-23T12:25:07Z
day: '01'
department:
- _id: KrCh
ec_funded: 1
intvolume: ' 2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.aaai.org/ocs/index.php/AAAI/AAAI15/paper/download/9523/9300
month: '01'
oa: 1
oa_version: None
page: 745 - 752
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _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: Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence
publication_status: published
publisher: AAAI Press
publist_id: '5713'
quality_controlled: '1'
related_material:
record:
- id: '5410'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Automatic generation of alternative starting positions for simple traditional
board games
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2015'
...
---
_id: '1732'
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.
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. In: IEEE; 2015:325-330.
doi:10.1109/ICRA.2015.7139019'
apa: 'Chatterjee, K., Chmelik, M., Gupta, R., & Kanodia, A. (2015). Qualitative
analysis of POMDPs with temporal logic specifications for robotics applications
(pp. 325–330). Presented at the ICRA: International Conference on Robotics and
Automation, Seattle, WA, United States: IEEE. https://doi.org/10.1109/ICRA.2015.7139019'
chicago: Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia.
“Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics
Applications,” 325–30. IEEE, 2015. https://doi.org/10.1109/ICRA.2015.7139019.
ieee: 'K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, “Qualitative analysis
of POMDPs with temporal logic specifications for robotics applications,” presented
at the ICRA: International Conference on Robotics and Automation, Seattle, WA,
United States, 2015, pp. 325–330.'
ista: 'Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2015. Qualitative analysis of
POMDPs with temporal logic specifications for robotics applications. ICRA: International
Conference on Robotics and Automation, 325–330.'
mla: Chatterjee, Krishnendu, et al. Qualitative Analysis of POMDPs with Temporal
Logic Specifications for Robotics Applications. IEEE, 2015, pp. 325–30, doi:10.1109/ICRA.2015.7139019.
short: K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, in:, IEEE, 2015, pp. 325–330.
conference:
end_date: 2015-05-30
location: Seattle, WA, United States
name: 'ICRA: International Conference on Robotics and Automation'
start_date: 2015-05-26
date_created: 2018-12-11T11:53:43Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2023-02-23T12:25:52Z
day: '01'
department:
- _id: KrCh
doi: 10.1109/ICRA.2015.7139019
ec_funded: 1
external_id:
arxiv:
- '1409.3360'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1409.3360
month: '01'
oa: 1
oa_version: Preprint
page: 325 - 330
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'
publication_status: published
publisher: IEEE
publist_id: '5394'
quality_controlled: '1'
related_material:
record:
- id: '5424'
relation: earlier_version
status: public
- id: '5426'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Qualitative analysis of POMDPs with temporal logic specifications for robotics
applications
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '5431'
abstract:
- lang: eng
text: "We consider finite-state concurrent stochastic games, played by k>=2 players
for an infinite number of rounds, where in every round, each player simultaneously
and independently of the other players chooses an action, whereafter the successor
state is determined by a probability distribution given by the current state and
the chosen actions. We consider reachability objectives that given a target set
of states require that some state in the target set is visited, and the dual safety
objectives that given a target set require that only states in the target set
are visited. We are interested in the complexity of stationary strategies measured
by their patience, which is defined as the inverse of the smallest non-zero probability
employed.\r\n\r\n Our main results are as follows: We show that in two-player
zero-sum concurrent stochastic games (with reachability objective for one player
and the complementary safety objective for the other player): (i) the optimal
bound on the patience of optimal and epsilon-optimal strategies, for both players
is doubly exponential; and (ii) even in games with a single non-absorbing state
exponential (in the number of actions) patience is necessary. In general we study
the class of non-zero-sum games admitting epsilon-Nash equilibria. We show that
if there is at least one player with reachability objective, then doubly-exponential
patience is needed in general for epsilon-Nash equilibrium strategies, whereas
in contrast if all players have safety objectives, then the optimal bound on patience
for epsilon-Nash equilibrium strategies is only exponential."
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: Kristoffer
full_name: Hansen, Kristoffer
last_name: Hansen
citation:
ama: Chatterjee K, Ibsen-Jensen R, Hansen K. The Patience of Concurrent Stochastic
Games with Safety and Reachability Objectives. IST Austria; 2015. doi:10.15479/AT:IST-2015-322-v1-1
apa: Chatterjee, K., Ibsen-Jensen, R., & Hansen, K. (2015). The patience
of concurrent stochastic games with safety and reachability objectives. IST
Austria. https://doi.org/10.15479/AT:IST-2015-322-v1-1
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Kristoffer Hansen. The
Patience of Concurrent Stochastic Games with Safety and Reachability Objectives.
IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-322-v1-1.
ieee: K. Chatterjee, R. Ibsen-Jensen, and K. Hansen, The patience of concurrent
stochastic games with safety and reachability objectives. IST Austria, 2015.
ista: Chatterjee K, Ibsen-Jensen R, Hansen K. 2015. The patience of concurrent stochastic
games with safety and reachability objectives, IST Austria, 25p.
mla: Chatterjee, Krishnendu, et al. The Patience of Concurrent Stochastic Games
with Safety and Reachability Objectives. IST Austria, 2015, doi:10.15479/AT:IST-2015-322-v1-1.
short: K. Chatterjee, R. Ibsen-Jensen, K. Hansen, The Patience of Concurrent Stochastic
Games with Safety and Reachability Objectives, IST Austria, 2015.
date_created: 2018-12-12T11:39:17Z
date_published: 2015-02-19T00:00:00Z
date_updated: 2021-01-12T08:02:13Z
day: '19'
ddc:
- '005'
- '519'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2015-322-v1-1
file:
- access_level: open_access
checksum: bfb858262c30445b8e472c40069178a2
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:31Z
date_updated: 2020-07-14T12:46:53Z
file_id: '5491'
file_name: IST-2015-322-v1+1_safetygames.pdf
file_size: 661015
relation: main_file
file_date_updated: 2020-07-14T12:46:53Z
has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '25'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '322'
status: public
title: The patience of concurrent stochastic games with safety and reachability objectives
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '5434'
abstract:
- lang: eng
text: DEC-POMDPs extend POMDPs to a multi-agent setting, where several agents operate
in an uncertain environment independently to achieve a joint objective. DEC-POMDPs
have been studied with finite-horizon and infinite-horizon discounted-sum objectives,
and there exist solvers both for exact and approximate solutions. In this work
we consider Goal-DEC-POMDPs, where given a set of target states, the objective
is to ensure that the target set is reached with minimal cost. We consider the
indefinite-horizon (infinite-horizon with either discounted-sum, or undiscounted-sum,
where absorbing goal states have zero-cost) problem. We present a new method to
solve the problem that extends methods for finite-horizon DEC- POMDPs and the
RTDP-Bel approach for POMDPs. We present experimental results on several examples,
and show our approach presents promising results.
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
citation:
ama: Anonymous 1, Anonymous 2. Optimal Cost Indefinite-Horizon Reachability in
Goal DEC-POMDPs. IST Austria; 2015.
apa: Anonymous, 1, & Anonymous, 2. (2015). Optimal cost indefinite-horizon
reachability in goal DEC-POMDPs. IST Austria.
chicago: Anonymous, 1, and 2 Anonymous. Optimal Cost Indefinite-Horizon Reachability
in Goal DEC-POMDPs. IST Austria, 2015.
ieee: 1 Anonymous and 2 Anonymous, Optimal cost indefinite-horizon reachability
in goal DEC-POMDPs. IST Austria, 2015.
ista: Anonymous 1, Anonymous 2. 2015. Optimal cost indefinite-horizon reachability
in goal DEC-POMDPs, IST Austria, 16p.
mla: Anonymous, 1, and 2 Anonymous. Optimal Cost Indefinite-Horizon Reachability
in Goal DEC-POMDPs. IST Austria, 2015.
short: 1 Anonymous, 2 Anonymous, Optimal Cost Indefinite-Horizon Reachability in
Goal DEC-POMDPs, IST Austria, 2015.
date_created: 2018-12-12T11:39:18Z
date_published: 2015-02-19T00:00:00Z
date_updated: 2020-07-14T23:04:59Z
day: '19'
ddc:
- '000'
file:
- access_level: open_access
checksum: 8542fd0b10aed7811cd41077b8ccb632
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:14Z
date_updated: 2020-07-14T12:46:53Z
file_id: '5475'
file_name: IST-2015-326-v1+1_main.pdf
file_size: 378162
relation: main_file
- access_level: closed
checksum: 84c31c537bdaf7a91909f18d25d640ab
content_type: text/plain
creator: dernst
date_created: 2019-04-16T13:00:33Z
date_updated: 2020-07-14T12:46:53Z
file_id: '6317'
file_name: IST-2015-326-v1+2_authors.txt
file_size: 64
relation: main_file
file_date_updated: 2020-07-14T12:46:53Z
has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '16'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '326'
status: public
title: Optimal cost indefinite-horizon reachability in goal DEC-POMDPs
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1657'
abstract:
- lang: eng
text: 'We consider Markov decision processes (MDPs) with multiple limit-average
(or mean-payoff) objectives. There exist two different views: (i) ~the expectation
semantics, where the goal is to optimize the expected mean-payoff objective, and
(ii) ~the satisfaction semantics, where the goal is to maximize the probability
of runs such that the mean-payoff value stays above a given vector. We consider
optimization with respect to both objectives at once, thus unifying the existing
semantics. Precisely, the goal is to optimize the expectation while ensuring the
satisfaction constraint. Our problem captures the notion of optimization with
respect to strategies that are risk-averse (i.e., Ensure certain probabilistic
guarantee). Our main results are as follows: First, we present algorithms for
the decision problems, which are always polynomial in the size of the MDP. We
also show that an approximation of the Pareto curve can be computed in time polynomial
in the size of the MDP, and the approximation factor, but exponential in the number
of dimensions. Second, we present a complete characterization of the strategy
complexity (in terms of memory bounds and randomization) required to solve our
problem. '
acknowledgement: "A Technical Report of this paper is available at: https://repository.ist.ac.at/327\r\n"
alternative_title:
- LICS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Zuzana
full_name: Komárková, Zuzana
last_name: Komárková
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
citation:
ama: Chatterjee K, Komárková Z, Kretinsky J. Unifying two views on multiple mean-payoff
objectives in Markov decision processes. 2015:244-256. doi:10.1109/LICS.2015.32
apa: 'Chatterjee, K., Komárková, Z., & Kretinsky, J. (2015). Unifying two views
on multiple mean-payoff objectives in Markov decision processes. Presented at
the LICS: Logic in Computer Science, Kyoto, Japan: IEEE. https://doi.org/10.1109/LICS.2015.32'
chicago: Chatterjee, Krishnendu, Zuzana Komárková, and Jan Kretinsky. “Unifying
Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes.” LICS.
IEEE, 2015. https://doi.org/10.1109/LICS.2015.32.
ieee: K. Chatterjee, Z. Komárková, and J. Kretinsky, “Unifying two views on multiple
mean-payoff objectives in Markov decision processes.” IEEE, pp. 244–256, 2015.
ista: Chatterjee K, Komárková Z, Kretinsky J. 2015. Unifying two views on multiple
mean-payoff objectives in Markov decision processes. , 244–256.
mla: Chatterjee, Krishnendu, et al. Unifying Two Views on Multiple Mean-Payoff
Objectives in Markov Decision Processes. IEEE, 2015, pp. 244–56, doi:10.1109/LICS.2015.32.
short: K. Chatterjee, Z. Komárková, J. Kretinsky, (2015) 244–256.
conference:
end_date: 2015-07-10
location: Kyoto, Japan
name: 'LICS: Logic in Computer Science'
start_date: 2015-07-06
date_created: 2018-12-11T11:53:18Z
date_published: 2015-07-01T00:00:00Z
date_updated: 2023-02-23T12:26:16Z
day: '01'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1109/LICS.2015.32
ec_funded: 1
language:
- iso: eng
month: '07'
oa_version: None
page: 244 - 256
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _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: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: IEEE
publist_id: '5493'
quality_controlled: '1'
related_material:
record:
- id: '466'
relation: later_version
status: public
- id: '5429'
relation: earlier_version
status: public
- id: '5435'
relation: earlier_version
status: public
scopus_import: 1
series_title: LICS
status: public
title: Unifying two views on multiple mean-payoff objectives in Markov decision processes
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1656'
abstract:
- lang: eng
text: Recently there has been a significant effort to handle 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, some basic system properties such as average
response time cannot be expressed using weighted automata, nor in any other know
decidable formalism. In this work, we introduce nested weighted automata as a
natural extension of weighted automata which makes it possible to express important
quantitative properties such as average response time. In nested weighted automata,
a master automaton spins off and collects results from weighted slave automata,
each of which computes a quantity along a finite portion of an infinite word.
Nested weighted automata can be viewed as the quantitative analogue of monitor
automata, which are used in run-time verification. We establish an almost complete
decidability picture for the basic decision problems about nested weighted automata,
and illustrate their applicability in several domains. In particular, nested weighted
automata can be used to decide average response time properties.
acknowledgement: "This research was funded in part by the European Research Council
(ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF)
projects S11402-N23 (RiSE), Z211-N23 (Wittgenstein Award), FWF Grant No P23499-
N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games),
and Microsoft faculty fellows award.\r\nA Technical Report of the paper is available
at: \r\nhttps://repository.ist.ac.at/331/\r\n"
article_number: '7174926'
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. In: Proceedings
- Symposium on Logic in Computer Science. Vol 2015-July. IEEE; 2015. doi:10.1109/LICS.2015.72'
apa: 'Chatterjee, K., Henzinger, T. A., & Otop, J. (2015). Nested weighted automata.
In Proceedings - Symposium on Logic in Computer Science (Vol. 2015–July).
Kyoto, Japan: IEEE. https://doi.org/10.1109/LICS.2015.72'
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Nested Weighted
Automata.” In Proceedings - Symposium on Logic in Computer Science, Vol.
2015–July. IEEE, 2015. https://doi.org/10.1109/LICS.2015.72.
ieee: K. Chatterjee, T. A. Henzinger, and J. Otop, “Nested weighted automata,” in
Proceedings - Symposium on Logic in Computer Science, Kyoto, Japan, 2015,
vol. 2015–July.
ista: 'Chatterjee K, Henzinger TA, Otop J. 2015. Nested weighted automata. Proceedings
- Symposium on Logic in Computer Science. LICS: Logic in Computer Science vol.
2015–July, 7174926.'
mla: Chatterjee, Krishnendu, et al. “Nested Weighted Automata.” Proceedings -
Symposium on Logic in Computer Science, vol. 2015–July, 7174926, IEEE, 2015,
doi:10.1109/LICS.2015.72.
short: K. Chatterjee, T.A. Henzinger, J. Otop, in:, Proceedings - Symposium on Logic
in Computer Science, IEEE, 2015.
conference:
end_date: 2015-07-10
location: Kyoto, Japan
name: 'LICS: Logic in Computer Science'
start_date: 2015-07-06
date_created: 2018-12-11T11:53:17Z
date_published: 2015-07-31T00:00:00Z
date_updated: 2023-02-23T12:26:19Z
day: '31'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1109/LICS.2015.72
ec_funded: 1
external_id:
arxiv:
- '1606.03598'
language:
- iso: eng
month: '07'
oa_version: None
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
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _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: Proceedings - Symposium on Logic in Computer Science
publication_status: published
publisher: IEEE
publist_id: '5494'
quality_controlled: '1'
related_material:
record:
- id: '467'
relation: later_version
status: public
- id: '5415'
relation: earlier_version
status: public
- id: '5436'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Nested weighted automata
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2015-July
year: '2015'
...
---
_id: '5429'
abstract:
- lang: eng
text: "We consider Markov decision processes (MDPs) with multiple limit-average
(or mean-payoff) objectives. \r\nThere have been two different views: (i) the
expectation semantics, where the goal is to optimize the expected mean-payoff
objective, and (ii) the satisfaction semantics, where the goal is to maximize
the probability of runs such that the mean-payoff value stays above a given vector.
\ \r\nWe consider the problem where the goal is to optimize the expectation under
the constraint that the satisfaction semantics is ensured, and thus consider a
generalization that unifies the existing semantics.\r\nOur problem captures the
notion of optimization with respect to strategies that are risk-averse (i.e.,
ensures certain probabilistic guarantee).\r\nOur main results are algorithms for
the decision problem which are always polynomial in the size of the MDP. We also
show that an approximation of the Pareto-curve can be computed in time polynomial
in the size of the MDP, and the approximation factor, but exponential in the number
of dimensions.\r\nFinally, we present a complete characterization of the strategy
complexity (in terms of memory bounds and randomization) required to solve our
problem."
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: Zuzana
full_name: Komarkova, Zuzana
last_name: Komarkova
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
citation:
ama: Chatterjee K, Komarkova Z, Kretinsky J. Unifying Two Views on Multiple Mean-Payoff
Objectives in Markov Decision Processes. IST Austria; 2015. doi:10.15479/AT:IST-2015-318-v1-1
apa: Chatterjee, K., Komarkova, Z., & Kretinsky, J. (2015). Unifying two
views on multiple mean-payoff objectives in Markov decision processes. IST
Austria. https://doi.org/10.15479/AT:IST-2015-318-v1-1
chicago: Chatterjee, Krishnendu, Zuzana Komarkova, and Jan Kretinsky. Unifying
Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes.
IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-318-v1-1.
ieee: K. Chatterjee, Z. Komarkova, and J. Kretinsky, Unifying two views on multiple
mean-payoff objectives in Markov decision processes. IST Austria, 2015.
ista: Chatterjee K, Komarkova Z, Kretinsky J. 2015. Unifying two views on multiple
mean-payoff objectives in Markov decision processes, IST Austria, 41p.
mla: Chatterjee, Krishnendu, et al. Unifying Two Views on Multiple Mean-Payoff
Objectives in Markov Decision Processes. IST Austria, 2015, doi:10.15479/AT:IST-2015-318-v1-1.
short: K. Chatterjee, Z. Komarkova, J. Kretinsky, Unifying Two Views on Multiple
Mean-Payoff Objectives in Markov Decision Processes, IST Austria, 2015.
date_created: 2018-12-12T11:39:17Z
date_published: 2015-01-12T00:00:00Z
date_updated: 2023-02-23T12:26:16Z
day: '12'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2015-318-v1-1
file:
- access_level: open_access
checksum: e4869a584567c506349abda9c8ec7db3
content_type: application/pdf
creator: system
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date_updated: 2020-07-14T12:46:52Z
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language:
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month: '01'
oa: 1
oa_version: Published Version
page: '41'
publication_identifier:
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- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '318'
related_material:
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relation: later_version
status: public
- id: '5435'
relation: later_version
status: public
status: public
title: Unifying two views on multiple mean-payoff objectives in Markov decision processes
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '5435'
abstract:
- lang: eng
text: "We consider Markov decision processes (MDPs) with multiple limit-average
(or mean-payoff) objectives. \r\nThere have been two different views: (i) the
expectation semantics, where the goal is to optimize the expected mean-payoff
objective, and (ii) the satisfaction semantics, where the goal is to maximize
the probability of runs such that the mean-payoff value stays above a given vector.
\ \r\nWe consider the problem where the goal is to optimize the expectation under
the constraint that the satisfaction semantics is ensured, and thus consider a
generalization that unifies the existing semantics. Our problem captures the notion
of optimization with respect to strategies that are risk-averse (i.e., ensures
certain probabilistic guarantee).\r\nOur main results are algorithms for the decision
problem which are always polynomial in the size of the MDP.\r\nWe also show that
an approximation of the Pareto-curve can be computed in time polynomial in the
size of the MDP, and the approximation factor, but exponential in the number of
dimensions. Finally, we present a complete characterization of the strategy complexity
(in terms of memory bounds and randomization) required to solve our problem."
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: Zuzana
full_name: Komarkova, Zuzana
last_name: Komarkova
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
citation:
ama: Chatterjee K, Komarkova Z, Kretinsky J. Unifying Two Views on Multiple Mean-Payoff
Objectives in Markov Decision Processes. IST Austria; 2015. doi:10.15479/AT:IST-2015-318-v2-1
apa: Chatterjee, K., Komarkova, Z., & Kretinsky, J. (2015). Unifying two
views on multiple mean-payoff objectives in Markov decision processes. IST
Austria. https://doi.org/10.15479/AT:IST-2015-318-v2-1
chicago: Chatterjee, Krishnendu, Zuzana Komarkova, and Jan Kretinsky. Unifying
Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes.
IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-318-v2-1.
ieee: K. Chatterjee, Z. Komarkova, and J. Kretinsky, Unifying two views on multiple
mean-payoff objectives in Markov decision processes. IST Austria, 2015.
ista: Chatterjee K, Komarkova Z, Kretinsky J. 2015. Unifying two views on multiple
mean-payoff objectives in Markov decision processes, IST Austria, 51p.
mla: Chatterjee, Krishnendu, et al. Unifying Two Views on Multiple Mean-Payoff
Objectives in Markov Decision Processes. IST Austria, 2015, doi:10.15479/AT:IST-2015-318-v2-1.
short: K. Chatterjee, Z. Komarkova, J. Kretinsky, Unifying Two Views on Multiple
Mean-Payoff Objectives in Markov Decision Processes, IST Austria, 2015.
date_created: 2018-12-12T11:39:19Z
date_published: 2015-02-23T00:00:00Z
date_updated: 2023-02-23T12:26:00Z
day: '23'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2015-318-v2-1
file:
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checksum: 75284adec80baabdfe71ff9ebbc27445
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:03Z
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has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '51'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '327'
related_material:
record:
- id: '1657'
relation: later_version
status: public
- id: '466'
relation: later_version
status: public
- id: '5429'
relation: earlier_version
status: public
status: public
title: Unifying two views on multiple mean-payoff objectives in Markov decision processes
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '5436'
abstract:
- lang: eng
text: "Recently there has been a significant effort to handle 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, some basic system properties such as average
response time cannot be expressed using weighted automata, nor in any other know
decidable formalism. In this work, we introduce nested weighted automata as a
natural extension of weighted automata which makes it possible to express important
quantitative properties such as average response time.\r\nIn nested weighted automata,
a master automaton spins off and collects results from weighted slave automata,
each of which computes a quantity along a finite portion of an infinite word.
Nested weighted automata can be viewed as the quantitative analogue of monitor
automata, which are used in run-time verification. We establish an almost complete
decidability picture for the basic decision problems about nested weighted automata,
and illustrate their applicability in several domains. In particular, nested weighted
automata can be used to decide average response time properties."
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;
2015. doi:10.15479/AT:IST-2015-170-v2-2
apa: Chatterjee, K., Henzinger, T. A., & Otop, J. (2015). Nested weighted
automata. IST Austria. https://doi.org/10.15479/AT:IST-2015-170-v2-2
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. Nested Weighted
Automata. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-170-v2-2.
ieee: K. Chatterjee, T. A. Henzinger, and J. Otop, Nested weighted automata.
IST Austria, 2015.
ista: Chatterjee K, Henzinger TA, Otop J. 2015. Nested weighted automata, IST Austria,
29p.
mla: Chatterjee, Krishnendu, et al. Nested Weighted Automata. IST Austria,
2015, doi:10.15479/AT:IST-2015-170-v2-2.
short: K. Chatterjee, T.A. Henzinger, J. Otop, Nested Weighted Automata, IST Austria,
2015.
date_created: 2018-12-12T11:39:19Z
date_published: 2015-04-24T00:00:00Z
date_updated: 2023-02-23T12:25:21Z
day: '24'
ddc:
- '000'
department:
- _id: KrCh
- _id: ToHe
doi: 10.15479/AT:IST-2015-170-v2-2
file:
- access_level: open_access
checksum: 3c402f47d3669c28d04d1af405a08e3f
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:19Z
date_updated: 2020-07-14T12:46:54Z
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file_name: IST-2015-170-v2+2_report.pdf
file_size: 569991
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file_date_updated: 2020-07-14T12:46:54Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '29'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '331'
related_material:
record:
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relation: later_version
status: public
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relation: later_version
status: public
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relation: earlier_version
status: public
status: public
title: Nested weighted automata
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1659'
abstract:
- lang: eng
text: 'The target discounted-sum problem is the following: Given a rational discount
factor 0 < λ < 1 and three rational values a, b, and t, does there exist
a finite or an infinite sequence w ε(a, b)∗ or w ε(a, b)w, such that Σ|w| i=0
w(i)λi equals t? The problem turns out to relate to many fields of mathematics
and computer science, and its decidability question is surprisingly hard to solve.
We solve the finite version of the problem, and show the hardness of the infinite
version, linking it to various areas and open problems in mathematics and computer
science: β-expansions, discounted-sum automata, piecewise affine maps, and generalizations
of the Cantor set. We provide some partial results to the infinite version, among
which are solutions to its restriction to eventually-periodic sequences and to
the cases that λ λ 1/2 or λ = 1/n, for every n ε N. We use our results for solving
some open problems on discounted-sum automata, among which are the exact-value
problem for nondeterministic automata over finite words and the universality and
inclusion problems for functional automata.'
acknowledgement: 'A technical report of the article is available at: https://research-explorer.app.ist.ac.at/record/5439'
article_processing_charge: No
author:
- first_name: Udi
full_name: Boker, Udi
id: 31E297B6-F248-11E8-B48F-1D18A9856A87
last_name: Boker
- 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: 'Boker U, Henzinger TA, Otop J. The target discounted-sum problem. In: LICS.
Logic in Computer Science. IEEE; 2015:750-761. doi:10.1109/LICS.2015.74'
apa: 'Boker, U., Henzinger, T. A., & Otop, J. (2015). The target discounted-sum
problem. In LICS (pp. 750–761). Kyoto, Japan: IEEE. https://doi.org/10.1109/LICS.2015.74'
chicago: Boker, Udi, Thomas A Henzinger, and Jan Otop. “The Target Discounted-Sum
Problem.” In LICS, 750–61. Logic in Computer Science. IEEE, 2015. https://doi.org/10.1109/LICS.2015.74.
ieee: U. Boker, T. A. Henzinger, and J. Otop, “The target discounted-sum problem,”
in LICS, Kyoto, Japan, 2015, pp. 750–761.
ista: 'Boker U, Henzinger TA, Otop J. 2015. The target discounted-sum problem. LICS.
LICS: Logic in Computer ScienceLogic in Computer Science, 750–761.'
mla: Boker, Udi, et al. “The Target Discounted-Sum Problem.” LICS, IEEE,
2015, pp. 750–61, doi:10.1109/LICS.2015.74.
short: U. Boker, T.A. Henzinger, J. Otop, in:, LICS, IEEE, 2015, pp. 750–761.
conference:
end_date: 2015-07-10
location: Kyoto, Japan
name: 'LICS: Logic in Computer Science'
start_date: 2015-007-06
date_created: 2018-12-11T11:53:19Z
date_published: 2015-07-01T00:00:00Z
date_updated: 2023-02-23T12:26:27Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1109/LICS.2015.74
ec_funded: 1
file:
- access_level: open_access
checksum: 6abebca9c1a620e9e103a8f9222befac
content_type: application/pdf
creator: dernst
date_created: 2020-05-15T08:53:29Z
date_updated: 2020-07-14T12:45:10Z
file_id: '7852'
file_name: 2015_LICS_Boker.pdf
file_size: 340215
relation: main_file
file_date_updated: 2020-07-14T12:45:10Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 750 - 761
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
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: LICS
publication_identifier:
eisbn:
- '978-1-4799-8875-4 '
issn:
- '1043-6871 '
publication_status: published
publisher: IEEE
publist_id: '5491'
quality_controlled: '1'
related_material:
record:
- id: '5439'
relation: earlier_version
status: public
scopus_import: 1
series_title: Logic in Computer Science
status: public
title: The target discounted-sum problem
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1610'
abstract:
- lang: eng
text: The edit distance between two words w1, w2 is the minimal number of word operations
(letter insertions, deletions, and substitutions) necessary to transform w1 to
w2. The edit distance generalizes to languages L1,L2, where the edit distance
is the minimal number k such that for every word from L1 there exists a word in
L2 with edit distance at most k. We study the edit distance computation problem
between pushdown automata and their subclasses. The problem of computing edit
distance to pushdown automata is undecidable, and in practice, the interesting
question is to compute the edit distance from a pushdown automaton (the implementation,
a standard model for programs with recursion) to a regular language (the specification).
In this work, we present a complete picture of decidability and complexity for
deciding whether, for a given threshold k, the edit distance from a pushdown automaton
to a finite automaton is at most k.
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: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- 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: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: 'Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. Edit distance for pushdown
automata. In: 42nd International Colloquium. Vol 9135. Springer Nature;
2015:121-133. doi:10.1007/978-3-662-47666-6_10'
apa: 'Chatterjee, K., Henzinger, T. A., Ibsen-Jensen, R., & Otop, J. (2015).
Edit distance for pushdown automata. In 42nd International Colloquium (Vol.
9135, pp. 121–133). Kyoto, Japan: Springer Nature. https://doi.org/10.1007/978-3-662-47666-6_10'
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Jan
Otop. “Edit Distance for Pushdown Automata.” In 42nd International Colloquium,
9135:121–33. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-47666-6_10.
ieee: K. Chatterjee, T. A. Henzinger, R. Ibsen-Jensen, and J. Otop, “Edit distance
for pushdown automata,” in 42nd International Colloquium, Kyoto, Japan,
2015, vol. 9135, no. Part II, pp. 121–133.
ista: 'Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. 2015. Edit distance for
pushdown automata. 42nd International Colloquium. ICALP: Automata, Languages and
Programming, LNCS, vol. 9135, 121–133.'
mla: Chatterjee, Krishnendu, et al. “Edit Distance for Pushdown Automata.” 42nd
International Colloquium, vol. 9135, no. Part II, Springer Nature, 2015, pp.
121–33, doi:10.1007/978-3-662-47666-6_10.
short: K. Chatterjee, T.A. Henzinger, R. Ibsen-Jensen, J. Otop, in:, 42nd International
Colloquium, Springer Nature, 2015, pp. 121–133.
conference:
end_date: 2015-07-10
location: Kyoto, Japan
name: 'ICALP: Automata, Languages and Programming'
start_date: 2015-07-06
date_created: 2018-12-11T11:53:01Z
date_published: 2015-07-01T00:00:00Z
date_updated: 2023-02-23T12:26:24Z
day: '01'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/978-3-662-47666-6_10
ec_funded: 1
external_id:
arxiv:
- '1504.08259'
intvolume: ' 9135'
issue: Part II
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1504.08259
month: '07'
oa: 1
oa_version: None
page: 121 - 133
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _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
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: 42nd International Colloquium
publication_identifier:
isbn:
- 978-3-662-47665-9
publication_status: published
publisher: Springer Nature
publist_id: '5556'
pubrep_id: '321'
quality_controlled: '1'
related_material:
record:
- id: '465'
relation: later_version
status: public
- id: '5438'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Edit distance for pushdown automata
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9135
year: '2015'
...
---
_id: '5437'
abstract:
- lang: eng
text: "We consider the core algorithmic problems related to verification of systems
with respect to three classical quantitative properties, namely, the mean-payoff
property, the ratio property, and the minimum initial credit for energy property.
\r\nThe algorithmic problem given a graph and a quantitative property asks to
compute the optimal value (the infimum value over all traces) from every node
of the graph. We consider graphs with constant treewidth, and it is well-known
that the control-flow graphs of most programs have constant treewidth. Let $n$
denote the number of nodes of a graph, $m$ the number of edges (for constant treewidth
graphs $m=O(n)$) and $W$ the largest absolute value of the weights.\r\nOur main
theoretical results are as follows.\r\nFirst, for constant treewidth graphs we
present an algorithm that approximates the mean-payoff value within a multiplicative
factor of $\\epsilon$ in time $O(n \\cdot \\log (n/\\epsilon))$ and linear space,
as compared to the classical algorithms that require quadratic time. Second, for
the ratio property we present an algorithm that for constant treewidth graphs
works in time $O(n \\cdot \\log (|a\\cdot b|))=O(n\\cdot\\log (n\\cdot W))$, when
the output is $\\frac{a}{b}$, as compared to the previously best known algorithm
with running time $O(n^2 \\cdot \\log (n\\cdot W))$. Third, for the minimum initial
credit problem we show that (i)~for general graphs the problem can be solved in
$O(n^2\\cdot m)$ time and the associated decision problem can be solved in $O(n\\cdot
m)$ time, improving the previous known $O(n^3\\cdot m\\cdot \\log (n\\cdot W))$
and $O(n^2 \\cdot m)$ bounds, respectively; and (ii)~for constant treewidth graphs
we present an algorithm that requires $O(n\\cdot \\log n)$ time, improving the
previous known $O(n^4 \\cdot \\log (n \\cdot W))$ bound.\r\nWe have implemented
some of our algorithms and show that they present a significant speedup on standard
benchmarks. "
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. Faster Algorithms for Quantitative
Verification in Constant Treewidth Graphs. IST Austria; 2015. doi:10.15479/AT:IST-2015-330-v2-1
apa: Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2015). Faster
algorithms for quantitative verification in constant treewidth graphs. IST
Austria. https://doi.org/10.15479/AT:IST-2015-330-v2-1
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis.
Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs.
IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-330-v2-1.
ieee: K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, Faster algorithms
for quantitative verification in constant treewidth graphs. IST Austria, 2015.
ista: Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2015. Faster algorithms for
quantitative verification in constant treewidth graphs, IST Austria, 27p.
mla: Chatterjee, Krishnendu, et al. Faster Algorithms for Quantitative Verification
in Constant Treewidth Graphs. IST Austria, 2015, doi:10.15479/AT:IST-2015-330-v2-1.
short: K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, Faster Algorithms for Quantitative
Verification in Constant Treewidth Graphs, IST Austria, 2015.
date_created: 2018-12-12T11:39:19Z
date_published: 2015-04-27T00:00:00Z
date_updated: 2023-02-23T12:26:05Z
day: '27'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2015-330-v2-1
file:
- access_level: open_access
checksum: f5917c20f84018b362d385c000a2e123
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:12Z
date_updated: 2020-07-14T12:46:54Z
file_id: '5473'
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file_date_updated: 2020-07-14T12:46:54Z
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: '333'
related_material:
record:
- id: '1607'
relation: later_version
status: public
- id: '5430'
relation: earlier_version
status: public
status: public
title: Faster algorithms for quantitative verification in constant treewidth graphs
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '5430'
abstract:
- lang: eng
text: We consider the core algorithmic problems related to verification of systems
with respect to three classical quantitative properties, namely, the mean- payoff
property, the ratio property, and the minimum initial credit for energy property.
The algorithmic problem given a graph and a quantitative property asks to compute
the optimal value (the infimum value over all traces) from every node of the graph.
We consider graphs with constant treewidth, and it is well-known that the control-flow
graphs of most programs have constant treewidth. Let n denote the number of nodes
of a graph, m the number of edges (for constant treewidth graphs m = O ( n ) )
and W the largest absolute value of the weights. Our main theoretical results
are as follows. First, for constant treewidth graphs we present an algorithm that
approximates the mean-payoff value within a mul- tiplicative factor of ∊ in time
O ( n · log( n/∊ )) and linear space, as compared to the classical algorithms
that require quadratic time. Second, for the ratio property we present an algorithm
that for constant treewidth graphs works in time O ( n · log( | a · b · n | ))
= O ( n · log( n · W )) , when the output is a b , as compared to the previously
best known algorithm with running time O ( n 2 · log( n · W )) . Third, for the
minimum initial credit problem we show that (i) for general graphs the problem
can be solved in O ( n 2 · m ) time and the associated decision problem can be
solved in O ( n · m ) time, improving the previous known O ( n 3 · m · log( n
· W )) and O ( n 2 · m ) bounds, respectively; and (ii) for constant treewidth
graphs we present an algorithm that requires O ( n · log n ) time, improving the
previous known O ( n 4 · log( n · W )) bound. We have implemented some of our
algorithms and show that they present a significant speedup on standard benchmarks.
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. Faster Algorithms for Quantitative
Verification in Constant Treewidth Graphs. IST Austria; 2015. doi:10.15479/AT:IST-2015-319-v1-1
apa: Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2015). Faster
algorithms for quantitative verification in constant treewidth graphs. IST
Austria. https://doi.org/10.15479/AT:IST-2015-319-v1-1
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis.
Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs.
IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-319-v1-1.
ieee: K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, Faster algorithms
for quantitative verification in constant treewidth graphs. IST Austria, 2015.
ista: Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2015. Faster algorithms for
quantitative verification in constant treewidth graphs, IST Austria, 31p.
mla: Chatterjee, Krishnendu, et al. Faster Algorithms for Quantitative Verification
in Constant Treewidth Graphs. IST Austria, 2015, doi:10.15479/AT:IST-2015-319-v1-1.
short: K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, Faster Algorithms for Quantitative
Verification in Constant Treewidth Graphs, IST Austria, 2015.
date_created: 2018-12-12T11:39:17Z
date_published: 2015-02-10T00:00:00Z
date_updated: 2023-02-23T12:26:22Z
day: '10'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2015-319-v1-1
file:
- access_level: open_access
checksum: 62c6ea01e342553dcafb88a070fb1ad5
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:21Z
date_updated: 2020-07-14T12:46:52Z
file_id: '5482'
file_name: IST-2015-319-v1+1_long.pdf
file_size: 1089651
relation: main_file
file_date_updated: 2020-07-14T12:46:52Z
has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '31'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '319'
related_material:
record:
- id: '1607'
relation: later_version
status: public
- id: '5437'
relation: later_version
status: public
status: public
title: Faster algorithms for quantitative verification in constant treewidth graphs
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '5439'
abstract:
- lang: eng
text: 'The target discounted-sum problem is the following: Given a rational discount
factor 0 < λ < 1 and three rational values a, b, and t, does there exist a finite
or an infinite sequence w ε(a, b)∗ or w ε(a, b)w, such that Σ|w| i=0 w(i)λi equals
t? The problem turns out to relate to many fields of mathematics and computer
science, and its decidability question is surprisingly hard to solve. We solve
the finite version of the problem, and show the hardness of the infinite version,
linking it to various areas and open problems in mathematics and computer science:
β-expansions, discounted-sum automata, piecewise affine maps, and generalizations
of the Cantor set. We provide some partial results to the infinite version, among
which are solutions to its restriction to eventually-periodic sequences and to
the cases that λ λ 1/2 or λ = 1/n, for every n ε N. We use our results for solving
some open problems on discounted-sum automata, among which are the exact-value
problem for nondeterministic automata over finite words and the universality and
inclusion problems for functional automata. '
alternative_title:
- IST Austria Technical Report
author:
- first_name: Udi
full_name: Boker, Udi
id: 31E297B6-F248-11E8-B48F-1D18A9856A87
last_name: Boker
- 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: Boker U, Henzinger TA, Otop J. The Target Discounted-Sum Problem. IST
Austria; 2015. doi:10.15479/AT:IST-2015-335-v1-1
apa: Boker, U., Henzinger, T. A., & Otop, J. (2015). The target discounted-sum
problem. IST Austria. https://doi.org/10.15479/AT:IST-2015-335-v1-1
chicago: Boker, Udi, Thomas A Henzinger, and Jan Otop. The Target Discounted-Sum
Problem. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-335-v1-1.
ieee: U. Boker, T. A. Henzinger, and J. Otop, The target discounted-sum problem.
IST Austria, 2015.
ista: Boker U, Henzinger TA, Otop J. 2015. The target discounted-sum problem, IST
Austria, 20p.
mla: Boker, Udi, et al. The Target Discounted-Sum Problem. IST Austria, 2015,
doi:10.15479/AT:IST-2015-335-v1-1.
short: U. Boker, T.A. Henzinger, J. Otop, The Target Discounted-Sum Problem, IST
Austria, 2015.
date_created: 2018-12-12T11:39:20Z
date_published: 2015-05-18T00:00:00Z
date_updated: 2023-02-23T10:08:48Z
day: '18'
ddc:
- '004'
- '512'
- '513'
department:
- _id: ToHe
doi: 10.15479/AT:IST-2015-335-v1-1
file:
- access_level: open_access
checksum: 40405907aa012acece1bc26cf0be554d
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:55Z
date_updated: 2020-07-14T12:46:55Z
file_id: '5517'
file_name: IST-2015-335-v1+1_report.pdf
file_size: 589619
relation: main_file
file_date_updated: 2020-07-14T12:46:55Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '20'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '335'
related_material:
record:
- id: '1659'
relation: later_version
status: public
status: public
title: The target discounted-sum problem
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '5438'
abstract:
- lang: eng
text: "The edit distance between two words w1, w2 is the minimal number of word
operations (letter insertions, deletions, and substitutions) necessary to transform
w1 to w2. The edit distance generalizes to languages L1, L2, where the edit distance
is the minimal number k such that for every word from L1 there exists a word in
L2 with edit distance at most k. We study the edit distance computation problem
between pushdown automata and their subclasses.\r\nThe problem of computing edit
distance to a pushdown automaton is undecidable, and in practice, the interesting
question is to compute the edit distance from a pushdown automaton (the implementation,
a standard model for programs with recursion) to a regular language (the specification).
In this work, we present a complete picture of decidability and complexity for
deciding whether, for a given threshold k, the edit distance from a pushdown automaton
to a finite automaton is at most k. "
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: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. Edit Distance for Pushdown
Automata. IST Austria; 2015. doi:10.15479/AT:IST-2015-334-v1-1
apa: Chatterjee, K., Henzinger, T. A., Ibsen-Jensen, R., & Otop, J. (2015).
Edit distance for pushdown automata. IST Austria. https://doi.org/10.15479/AT:IST-2015-334-v1-1
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Jan
Otop. Edit Distance for Pushdown Automata. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-334-v1-1.
ieee: K. Chatterjee, T. A. Henzinger, R. Ibsen-Jensen, and J. Otop, Edit distance
for pushdown automata. IST Austria, 2015.
ista: Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. 2015. Edit distance for
pushdown automata, IST Austria, 15p.
mla: Chatterjee, Krishnendu, et al. Edit Distance for Pushdown Automata.
IST Austria, 2015, doi:10.15479/AT:IST-2015-334-v1-1.
short: K. Chatterjee, T.A. Henzinger, R. Ibsen-Jensen, J. Otop, Edit Distance for
Pushdown Automata, IST Austria, 2015.
date_created: 2018-12-12T11:39:20Z
date_published: 2015-05-05T00:00:00Z
date_updated: 2023-02-23T12:20:08Z
day: '05'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2015-334-v1-1
file:
- access_level: open_access
checksum: 8a5f2d77560e552af87eb1982437a43b
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:56Z
date_updated: 2020-07-14T12:46:55Z
file_id: '5518'
file_name: IST-2015-334-v1+1_report.pdf
file_size: 422573
relation: main_file
file_date_updated: 2020-07-14T12:46:55Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '15'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '334'
related_material:
record:
- id: '1610'
relation: later_version
status: public
- id: '465'
relation: later_version
status: public
status: public
title: Edit distance for pushdown automata
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '5440'
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 for payoff 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 of the population. The fitness (or the reproductive rate) is a non-negative
number, and depends on the payoff. 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 as follows: First, we consider
a special case of the general problem, where the residents do not reproduce. We
show that the qualitative question is NP-complete, and the quantitative approximation
question is #P-complete, and the hardness results hold even in the special case
where the interaction and the replacement graphs coincide. Second, we show that
in general both the qualitative and the quantitative approximation questions are
PSPACE-complete. The PSPACE-hardness result for quantitative approximation holds
even when the fitness is always positive.'
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 Evolutionary Games
on Graphs. IST Austria; 2015. doi:10.15479/AT:IST-2015-323-v2-2
apa: Chatterjee, K., Ibsen-Jensen, R., & Nowak, M. (2015). The complexity
of evolutionary games on graphs. IST Austria. https://doi.org/10.15479/AT:IST-2015-323-v2-2
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Martin Nowak. The Complexity
of Evolutionary Games on Graphs. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-323-v2-2.
ieee: K. Chatterjee, R. Ibsen-Jensen, and M. Nowak, The complexity of evolutionary
games on graphs. IST Austria, 2015.
ista: Chatterjee K, Ibsen-Jensen R, Nowak M. 2015. The complexity of evolutionary
games on graphs, IST Austria, 18p.
mla: Chatterjee, Krishnendu, et al. The Complexity of Evolutionary Games on Graphs.
IST Austria, 2015, doi:10.15479/AT:IST-2015-323-v2-2.
short: K. Chatterjee, R. Ibsen-Jensen, M. Nowak, The Complexity of Evolutionary
Games on Graphs, IST Austria, 2015.
date_created: 2018-12-12T11:39:21Z
date_published: 2015-06-16T00:00:00Z
date_updated: 2023-02-23T12:26:10Z
day: '16'
ddc:
- '005'
- '576'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2015-323-v2-2
file:
- access_level: open_access
checksum: 66aace7d367032af97c15e35c9be9636
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:23Z
date_updated: 2020-07-14T12:46:56Z
file_id: '5484'
file_name: IST-2015-323-v2+2_main.pdf
file_size: 466161
relation: main_file
file_date_updated: 2020-07-14T12:46:56Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '18'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '338'
related_material:
record:
- id: '5421'
relation: earlier_version
status: public
- id: '5432'
relation: earlier_version
status: public
status: public
title: The complexity of evolutionary games on graphs
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '5432'
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. \r\nThe vertices
of the two graphs are the same, and each vertex corresponds to an individual of
the population. 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. \r\nOur main results are:\r\n(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).\r\n(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.\r\n"
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 Evolutionary Games
on Graphs. IST Austria; 2015. doi:10.15479/AT:IST-2015-323-v1-1
apa: Chatterjee, K., Ibsen-Jensen, R., & Nowak, M. (2015). The complexity
of evolutionary games on graphs. IST Austria. https://doi.org/10.15479/AT:IST-2015-323-v1-1
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Martin Nowak. The Complexity
of Evolutionary Games on Graphs. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-323-v1-1.
ieee: K. Chatterjee, R. Ibsen-Jensen, and M. Nowak, The complexity of evolutionary
games on graphs. IST Austria, 2015.
ista: Chatterjee K, Ibsen-Jensen R, Nowak M. 2015. The complexity of evolutionary
games on graphs, IST Austria, 29p.
mla: Chatterjee, Krishnendu, et al. The Complexity of Evolutionary Games on Graphs.
IST Austria, 2015, doi:10.15479/AT:IST-2015-323-v1-1.
short: K. Chatterjee, R. Ibsen-Jensen, M. Nowak, The Complexity of Evolutionary
Games on Graphs, IST Austria, 2015.
date_created: 2018-12-12T11:39:18Z
date_published: 2015-02-19T00:00:00Z
date_updated: 2023-02-23T12:26:33Z
day: '19'
ddc:
- '005'
- '576'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2015-323-v1-1
file:
- access_level: open_access
checksum: 546c1b291d545e7b24aaaf4199dac671
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:57Z
date_updated: 2020-07-14T12:46:53Z
file_id: '5519'
file_name: IST-2015-323-v1+1_main.pdf
file_size: 576347
relation: main_file
file_date_updated: 2020-07-14T12:46:53Z
has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '29'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '323'
related_material:
record:
- id: '5421'
relation: earlier_version
status: public
- id: '5440'
relation: later_version
status: public
status: public
title: The complexity of evolutionary games on graphs
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '5444'
abstract:
- lang: eng
text: A comprehensive understanding of the clonal evolution of cancer is critical
for understanding neoplasia. Genome-wide sequencing data enables evolutionary
studies at unprecedented depth. However, classical phylogenetic methods often
struggle with noisy sequencing data of impure DNA samples and fail to detect subclones
that have different evolutionary trajectories. We have developed a tool, called
Treeomics, that allows us to reconstruct the phylogeny of a cancer with commonly
available sequencing technologies. Using Bayesian inference and Integer Linear
Programming, robust phylogenies consistent with the biological processes underlying
cancer evolution were obtained for pancreatic, ovarian, and prostate cancers.
Furthermore, Treeomics correctly identified sequencing artifacts such as those
resulting from low statistical power; nearly 7% of variants were misclassified
by conventional statistical methods. These artifacts can skew phylogenies by creating
illusory tumor heterogeneity among distinct samples. Importantly, we show that
the evolutionary trees generated with Treeomics are mathematically optimal.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Johannes
full_name: Reiter, Johannes
id: 4A918E98-F248-11E8-B48F-1D18A9856A87
last_name: Reiter
orcid: 0000-0002-0170-7353
- first_name: Alvin
full_name: Makohon-Moore, Alvin
last_name: Makohon-Moore
- first_name: Jeffrey
full_name: Gerold, Jeffrey
last_name: Gerold
- first_name: Ivana
full_name: Bozic, Ivana
last_name: Bozic
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Christine
full_name: Iacobuzio-Donahue, Christine
last_name: Iacobuzio-Donahue
- first_name: Bert
full_name: Vogelstein, Bert
last_name: Vogelstein
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Reiter J, Makohon-Moore A, Gerold J, et al. Reconstructing Robust Phylogenies
of Metastatic Cancers. IST Austria; 2015. doi:10.15479/AT:IST-2015-399-v1-1
apa: Reiter, J., Makohon-Moore, A., Gerold, J., Bozic, I., Chatterjee, K., Iacobuzio-Donahue,
C., … Nowak, M. (2015). Reconstructing robust phylogenies of metastatic cancers.
IST Austria. https://doi.org/10.15479/AT:IST-2015-399-v1-1
chicago: Reiter, Johannes, Alvin Makohon-Moore, Jeffrey Gerold, Ivana Bozic, Krishnendu
Chatterjee, Christine Iacobuzio-Donahue, Bert Vogelstein, and Martin Nowak. Reconstructing
Robust Phylogenies of Metastatic Cancers. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-399-v1-1.
ieee: J. Reiter et al., Reconstructing robust phylogenies of metastatic
cancers. IST Austria, 2015.
ista: Reiter J, Makohon-Moore A, Gerold J, Bozic I, Chatterjee K, Iacobuzio-Donahue
C, Vogelstein B, Nowak M. 2015. Reconstructing robust phylogenies of metastatic
cancers, IST Austria, 25p.
mla: Reiter, Johannes, et al. Reconstructing Robust Phylogenies of Metastatic
Cancers. IST Austria, 2015, doi:10.15479/AT:IST-2015-399-v1-1.
short: J. Reiter, A. Makohon-Moore, J. Gerold, I. Bozic, K. Chatterjee, C. Iacobuzio-Donahue,
B. Vogelstein, M. Nowak, Reconstructing Robust Phylogenies of Metastatic Cancers,
IST Austria, 2015.
date_created: 2018-12-12T11:39:22Z
date_published: 2015-12-30T00:00:00Z
date_updated: 2020-07-14T23:05:07Z
day: '30'
ddc:
- '000'
- '576'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2015-399-v1-1
file:
- access_level: open_access
checksum: c47d33bdda06181753c0af36f16e7b5d
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:24Z
date_updated: 2020-07-14T12:46:58Z
file_id: '5485'
file_name: IST-2015-399-v1+1_treeomics.pdf
file_size: 3533200
relation: main_file
file_date_updated: 2020-07-14T12:46:58Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '25'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '399'
status: public
title: Reconstructing robust phylogenies of metastatic cancers
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '5443'
abstract:
- lang: eng
text: POMDPs are standard models for probabilistic planning problems, where an agent
interacts with an uncertain environment. We study the problem of almost-sure reachability,
where given a set of target states, the question is to decide whether there is
a policy to ensure that the target set is reached with probability 1 (almost-surely).
While in general the problem is EXPTIME-complete, in many practical cases policies
with a small amount of memory suffice. Moreover, the existing solution to the
problem is explicit, which first requires to construct explicitly an exponential
reduction to a belief-support MDP. In this work, we first study the existence
of observation-stationary strategies, which is NP-complete, and then small-memory
strategies. We present a symbolic algorithm by an efficient encoding to SAT and
using a SAT solver for the problem. We report experimental results demonstrating
the scalability of our symbolic (SAT-based) approach.
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: Jessica
full_name: Davies, Jessica
id: 378E0060-F248-11E8-B48F-1D18A9856A87
last_name: Davies
citation:
ama: Chatterjee K, Chmelik M, Davies J. A Symbolic SAT-Based Algorithm for Almost-Sure
Reachability with Small Strategies in POMDPs. IST Austria; 2015. doi:10.15479/AT:IST-2015-325-v2-1
apa: Chatterjee, K., Chmelik, M., & Davies, J. (2015). A symbolic SAT-based
algorithm for almost-sure reachability with small strategies in POMDPs. IST
Austria. https://doi.org/10.15479/AT:IST-2015-325-v2-1
chicago: Chatterjee, Krishnendu, Martin Chmelik, and Jessica Davies. A Symbolic
SAT-Based Algorithm for Almost-Sure Reachability with Small Strategies in POMDPs.
IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-325-v2-1.
ieee: K. Chatterjee, M. Chmelik, and J. Davies, A symbolic SAT-based algorithm
for almost-sure reachability with small strategies in POMDPs. IST Austria,
2015.
ista: Chatterjee K, Chmelik M, Davies J. 2015. A symbolic SAT-based algorithm for
almost-sure reachability with small strategies in POMDPs, IST Austria, 23p.
mla: Chatterjee, Krishnendu, et al. A Symbolic SAT-Based Algorithm for Almost-Sure
Reachability with Small Strategies in POMDPs. IST Austria, 2015, doi:10.15479/AT:IST-2015-325-v2-1.
short: K. Chatterjee, M. Chmelik, J. Davies, A Symbolic SAT-Based Algorithm for
Almost-Sure Reachability with Small Strategies in POMDPs, IST Austria, 2015.
date_created: 2018-12-12T11:39:22Z
date_published: 2015-11-06T00:00:00Z
date_updated: 2023-02-21T16:24:05Z
day: '06'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2015-325-v2-1
file:
- access_level: open_access
checksum: f0fa31ad8161ed655137e94012123ef9
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:05Z
date_updated: 2020-07-14T12:46:57Z
file_id: '5466'
file_name: IST-2015-325-v2+1_main.pdf
file_size: 412379
relation: main_file
file_date_updated: 2020-07-14T12:46:57Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '23'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '362'
related_material:
record:
- id: '1166'
relation: later_version
status: public
status: public
title: A symbolic SAT-based algorithm for almost-sure reachability with small strategies
in POMDPs
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '5804'
abstract:
- lang: eng
text: We present here the first integer-based algorithm for constructing a well-defined
lattice sphere specified by integer radius and integer center. The algorithm evolves
from a unique correspondence between the lattice points comprising the sphere
and the distribution of sum of three square numbers in integer intervals. We characterize
these intervals to derive a useful set of recurrences, which, in turn, aids in
efficient computation. Each point of the lattice sphere is determined by resorting
to only a few primitive operations in the integer domain. The symmetry of its
quadraginta octants provides an added advantage by confining the computation to
its prima quadraginta octant. Detailed theoretical analysis and experimental results
have been furnished to demonstrate its simplicity and elegance.
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. From prima quadraginta octant to lattice sphere through
primitive integer operations. Theoretical Computer Science. 2015;624(4):56-72.
doi:10.1016/j.tcs.2015.11.018
apa: Biswas, R., & Bhowmick, P. (2015). From prima quadraginta octant to lattice
sphere through primitive integer operations. Theoretical Computer Science.
Elsevier. https://doi.org/10.1016/j.tcs.2015.11.018
chicago: Biswas, Ranita, and Partha Bhowmick. “From Prima Quadraginta Octant to
Lattice Sphere through Primitive Integer Operations.” Theoretical Computer
Science. Elsevier, 2015. https://doi.org/10.1016/j.tcs.2015.11.018.
ieee: R. Biswas and P. Bhowmick, “From prima quadraginta octant to lattice sphere
through primitive integer operations,” Theoretical Computer Science, vol.
624, no. 4. Elsevier, pp. 56–72, 2015.
ista: Biswas R, Bhowmick P. 2015. From prima quadraginta octant to lattice sphere
through primitive integer operations. Theoretical Computer Science. 624(4), 56–72.
mla: Biswas, Ranita, and Partha Bhowmick. “From Prima Quadraginta Octant to Lattice
Sphere through Primitive Integer Operations.” Theoretical Computer Science,
vol. 624, no. 4, Elsevier, 2015, pp. 56–72, doi:10.1016/j.tcs.2015.11.018.
short: R. Biswas, P. Bhowmick, Theoretical Computer Science 624 (2015) 56–72.
date_created: 2019-01-08T20:44:06Z
date_published: 2015-04-18T00:00:00Z
date_updated: 2021-01-12T08:03:36Z
day: '18'
doi: 10.1016/j.tcs.2015.11.018
extern: '1'
intvolume: ' 624'
issue: '4'
language:
- iso: eng
month: '04'
oa_version: None
page: 56-72
publication: Theoretical Computer Science
publication_identifier:
issn:
- 0304-3975
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: From prima quadraginta octant to lattice sphere through primitive integer operations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 624
year: '2015'
...
---
_id: '5807'
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 different topological classes of spherical geodesic
paths and circles inZ3. Theoretical Computer Science. 2015;605(11):146-163.
doi:10.1016/j.tcs.2015.09.003
apa: Biswas, R., & Bhowmick, P. (2015). On different topological classes of
spherical geodesic paths and circles inZ3. Theoretical Computer Science.
Elsevier. https://doi.org/10.1016/j.tcs.2015.09.003
chicago: Biswas, Ranita, and Partha Bhowmick. “On Different Topological Classes
of Spherical Geodesic Paths and Circles InZ3.” Theoretical Computer Science.
Elsevier, 2015. https://doi.org/10.1016/j.tcs.2015.09.003.
ieee: R. Biswas and P. Bhowmick, “On different topological classes of spherical
geodesic paths and circles inZ3,” Theoretical Computer Science, vol. 605,
no. 11. Elsevier, pp. 146–163, 2015.
ista: Biswas R, Bhowmick P. 2015. On different topological classes of spherical
geodesic paths and circles inZ3. Theoretical Computer Science. 605(11), 146–163.
mla: Biswas, Ranita, and Partha Bhowmick. “On Different Topological Classes of Spherical
Geodesic Paths and Circles InZ3.” Theoretical Computer Science, vol. 605,
no. 11, Elsevier, 2015, pp. 146–63, doi:10.1016/j.tcs.2015.09.003.
short: R. Biswas, P. Bhowmick, Theoretical Computer Science 605 (2015) 146–163.
date_created: 2019-01-08T20:44:52Z
date_published: 2015-11-09T00:00:00Z
date_updated: 2021-01-12T08:03:37Z
day: '09'
doi: 10.1016/j.tcs.2015.09.003
extern: '1'
intvolume: ' 605'
issue: '11'
language:
- iso: eng
month: '11'
oa_version: None
page: 146-163
publication: Theoretical Computer Science
publication_identifier:
issn:
- 0304-3975
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: On different topological classes of spherical geodesic paths and circles inZ3
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 605
year: '2015'
...
---
_id: '5808'
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. Layer the sphere. The Visual Computer. 2015;31(6-8):787-797.
doi:10.1007/s00371-015-1101-3
apa: Biswas, R., & Bhowmick, P. (2015). Layer the sphere. The Visual Computer.
Springer Nature. https://doi.org/10.1007/s00371-015-1101-3
chicago: Biswas, Ranita, and Partha Bhowmick. “Layer the Sphere.” The Visual
Computer. Springer Nature, 2015. https://doi.org/10.1007/s00371-015-1101-3.
ieee: R. Biswas and P. Bhowmick, “Layer the sphere,” The Visual Computer,
vol. 31, no. 6–8. Springer Nature, pp. 787–797, 2015.
ista: Biswas R, Bhowmick P. 2015. Layer the sphere. The Visual Computer. 31(6–8),
787–797.
mla: Biswas, Ranita, and Partha Bhowmick. “Layer the Sphere.” The Visual Computer,
vol. 31, no. 6–8, Springer Nature, 2015, pp. 787–97, doi:10.1007/s00371-015-1101-3.
short: R. Biswas, P. Bhowmick, The Visual Computer 31 (2015) 787–797.
date_created: 2019-01-08T20:45:05Z
date_published: 2015-05-08T00:00:00Z
date_updated: 2021-01-12T08:03:37Z
day: '08'
doi: 10.1007/s00371-015-1101-3
extern: '1'
intvolume: ' 31'
issue: 6-8
language:
- iso: eng
month: '05'
oa_version: None
page: 787-797
publication: The Visual Computer
publication_identifier:
issn:
- 0178-2789
- 1432-2315
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Layer the sphere
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2015'
...
---
_id: '594'
abstract:
- lang: eng
text: Transcription of eukaryotic protein-coding genes commences with the assembly
of a conserved initiation complex, which consists of RNA polymerase II (Pol II)
and the general transcription factors, at promoter DNA. After two decades of research,
the structural basis of transcription initiation is emerging. Crystal structures
of many components of the initiation complex have been resolved, and structural
information on Pol II complexes with general transcription factors has recently
been obtained. Although mechanistic details await elucidation, available data
outline how Pol II cooperates with the general transcription factors to bind to
and open promoter DNA, and how Pol II directs RNA synthesis and escapes from the
promoter.
article_processing_charge: No
author:
- first_name: Sarah
full_name: Sainsbury, Sarah
last_name: Sainsbury
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
- first_name: Patrick
full_name: Cramer, Patrick
last_name: Cramer
citation:
ama: Sainsbury S, Bernecky C, Cramer P. Structural basis of transcription initiation
by RNA polymerase II. Nature Reviews Molecular Cell Biology. 2015;16(3):129-143.
doi:10.1038/nrm3952
apa: Sainsbury, S., Bernecky, C., & Cramer, P. (2015). Structural basis of transcription
initiation by RNA polymerase II. Nature Reviews Molecular Cell Biology.
Nature Publishing Group. https://doi.org/10.1038/nrm3952
chicago: Sainsbury, Sarah, Carrie Bernecky, and Patrick Cramer. “Structural Basis
of Transcription Initiation by RNA Polymerase II.” Nature Reviews Molecular
Cell Biology. Nature Publishing Group, 2015. https://doi.org/10.1038/nrm3952.
ieee: S. Sainsbury, C. Bernecky, and P. Cramer, “Structural basis of transcription
initiation by RNA polymerase II,” Nature Reviews Molecular Cell Biology,
vol. 16, no. 3. Nature Publishing Group, pp. 129–143, 2015.
ista: Sainsbury S, Bernecky C, Cramer P. 2015. Structural basis of transcription
initiation by RNA polymerase II. Nature Reviews Molecular Cell Biology. 16(3),
129–143.
mla: Sainsbury, Sarah, et al. “Structural Basis of Transcription Initiation by RNA
Polymerase II.” Nature Reviews Molecular Cell Biology, vol. 16, no. 3,
Nature Publishing Group, 2015, pp. 129–43, doi:10.1038/nrm3952.
short: S. Sainsbury, C. Bernecky, P. Cramer, Nature Reviews Molecular Cell Biology
16 (2015) 129–143.
date_created: 2018-12-11T11:47:23Z
date_published: 2015-03-26T00:00:00Z
date_updated: 2021-01-12T08:05:16Z
day: '26'
doi: 10.1038/nrm3952
extern: '1'
intvolume: ' 16'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
page: 129 - 143
publication: Nature Reviews Molecular Cell Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '7206'
status: public
title: Structural basis of transcription initiation by RNA polymerase II
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2015'
...
---
_id: '1511'
abstract:
- lang: eng
text: 'The fact that the complete graph K_5 does not embed in the plane has been
generalized in two independent directions. On the one hand, the solution of the
classical Heawood problem for graphs on surfaces established that the complete
graph K_n embeds in a closed surface M if and only if (n-3)(n-4) is at most 6b_1(M),
where b_1(M) is the first Z_2-Betti number of M. On the other hand, Van Kampen
and Flores proved that the k-skeleton of the n-dimensional simplex (the higher-dimensional
analogue of K_{n+1}) embeds in R^{2k} if and only if n is less or equal to 2k+2.
Two decades ago, Kuhnel conjectured that the k-skeleton of the n-simplex embeds
in a compact, (k-1)-connected 2k-manifold with kth Z_2-Betti number b_k only if
the following generalized Heawood inequality holds: binom{n-k-1}{k+1} is at most
binom{2k+1}{k+1} b_k. This is a common generalization of the case of graphs on
surfaces as well as the Van Kampen--Flores theorem. In the spirit of Kuhnel''s
conjecture, we prove that if the k-skeleton of the n-simplex embeds in a 2k-manifold
with kth Z_2-Betti number b_k, then n is at most 2b_k binom{2k+2}{k} + 2k + 5.
This bound is weaker than the generalized Heawood inequality, but does not require
the assumption that M is (k-1)-connected. Our proof uses a result of Volovikov
about maps that satisfy a certain homological triviality condition.'
acknowledgement: "The work by Z. P. was partially supported by the Charles University
Grant SVV-2014-260103. The\r\nwork by Z. P. and M. T. was partially supported by
the project CE-ITI (GACR P202/12/G061) of\r\nthe Czech Science Foundation and by
the ERC Advanced Grant No. 267165. Part of the research\r\nwork of M. T. was conducted
at IST Austria, supported by an IST Fellowship. The work by U.W.\r\nwas partially
supported by the Swiss National Science Foundation (grants SNSF-200020-138230 and\r\nSNSF-PP00P2-138948)."
alternative_title:
- LIPIcs
author:
- first_name: Xavier
full_name: Goaoc, Xavier
last_name: Goaoc
- first_name: Isaac
full_name: Mabillard, Isaac
id: 32BF9DAA-F248-11E8-B48F-1D18A9856A87
last_name: Mabillard
- first_name: Pavel
full_name: Paták, Pavel
last_name: Paták
- first_name: Zuzana
full_name: Patakova, Zuzana
id: 48B57058-F248-11E8-B48F-1D18A9856A87
last_name: Patakova
orcid: 0000-0002-3975-1683
- first_name: Martin
full_name: Tancer, Martin
id: 38AC689C-F248-11E8-B48F-1D18A9856A87
last_name: Tancer
orcid: 0000-0002-1191-6714
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: 'Goaoc X, Mabillard I, Paták P, Patakova Z, Tancer M, Wagner U. On generalized
Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability
result. In: Vol 34. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:476-490.
doi:10.4230/LIPIcs.SOCG.2015.476'
apa: 'Goaoc, X., Mabillard, I., Paták, P., Patakova, Z., Tancer, M., & Wagner,
U. (2015). On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type
nonembeddability result (Vol. 34, pp. 476–490). Presented at the SoCG: Symposium
on Computational Geometry, Eindhoven, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPIcs.SOCG.2015.476'
chicago: 'Goaoc, Xavier, Isaac Mabillard, Pavel Paták, Zuzana Patakova, Martin Tancer,
and Uli Wagner. “On Generalized Heawood Inequalities for Manifolds: A Van Kampen–Flores-Type
Nonembeddability Result,” 34:476–90. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2015. https://doi.org/10.4230/LIPIcs.SOCG.2015.476.'
ieee: 'X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, and U. Wagner,
“On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability
result,” presented at the SoCG: Symposium on Computational Geometry, Eindhoven,
Netherlands, 2015, vol. 34, pp. 476–490.'
ista: 'Goaoc X, Mabillard I, Paták P, Patakova Z, Tancer M, Wagner U. 2015. On generalized
Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability
result. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 34, 476–490.'
mla: 'Goaoc, Xavier, et al. On Generalized Heawood Inequalities for Manifolds:
A Van Kampen–Flores-Type Nonembeddability Result. Vol. 34, Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2015, pp. 476–90, doi:10.4230/LIPIcs.SOCG.2015.476.'
short: X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:,
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 476–490.
conference:
end_date: 2015-06-25
location: Eindhoven, Netherlands
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2015-06-22
date_created: 2018-12-11T11:52:27Z
date_published: 2015-06-11T00:00:00Z
date_updated: 2023-02-23T12:38:00Z
day: '11'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.4230/LIPIcs.SOCG.2015.476
ec_funded: 1
file:
- access_level: open_access
checksum: 0945811875351796324189312ca29e9e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:18Z
date_updated: 2020-07-14T12:44:59Z
file_id: '4871'
file_name: IST-2016-502-v1+1_42.pdf
file_size: 636735
relation: main_file
file_date_updated: 2020-07-14T12:44:59Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 476 - 490
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '5666'
pubrep_id: '502'
quality_controlled: '1'
related_material:
record:
- id: '610'
relation: later_version
status: public
scopus_import: 1
status: public
title: 'On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type
nonembeddability result'
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: '34 '
year: '2015'
...
---
_id: '6118'
abstract:
- lang: eng
text: 'Carbon dioxide (CO2) gradients are ubiquitous and provide animals with information
about their environment, such as the potential presence of prey or predators.
The nematode Caenorhabditis elegans avoids elevated CO2, and previous work identified
three neuron pairs called “BAG,” “AFD,” and “ASE” that respond to CO2 stimuli.
Using in vivo Ca2+ imaging and behavioral analysis, we show that C. elegans can
detect CO2 independently of these sensory pathways. Many of the C. elegans sensory
neurons we examined, including the AWC olfactory neurons, the ASJ and ASK gustatory
neurons, and the ASH and ADL nociceptors, respond to a rise in CO2 with a rise
in Ca2+. In contrast, glial sheath cells harboring the sensory endings of C. elegans’
major chemosensory neurons exhibit strong and sustained decreases in Ca2+ in response
to high CO2. Some of these CO2 responses appear to be cell intrinsic. Worms therefore
may couple detection of CO2 to that of other cues at the earliest stages of sensory
processing. We show that C. elegans persistently suppresses oviposition at high
CO2. Hermaphrodite-specific neurons (HSNs), the executive neurons driving egg-laying,
are tonically inhibited when CO2 is elevated. CO2 modulates the egg-laying system
partly through the AWC olfactory neurons: High CO2 tonically activates AWC by
a cGMP-dependent mechanism, and AWC output inhibits the HSNs. Our work shows that
CO2 is a more complex sensory cue for C. elegans than previously thought, both
in terms of behavior and neural circuitry.'
author:
- first_name: Lorenz A.
full_name: Fenk, Lorenz A.
last_name: Fenk
- 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: Fenk LA, de Bono M. Environmental CO2 inhibits Caenorhabditis elegans egg-laying
by modulating olfactory neurons and evokes widespread changes in neural activity.
Proceedings of the National Academy of Sciences. 2015;112(27):E3525-E3534.
doi:10.1073/pnas.1423808112
apa: Fenk, L. A., & de Bono, M. (2015). Environmental CO2 inhibits Caenorhabditis
elegans egg-laying by modulating olfactory neurons and evokes widespread changes
in neural activity. Proceedings of the National Academy of Sciences. National
Academy of Sciences. https://doi.org/10.1073/pnas.1423808112
chicago: Fenk, Lorenz A., and Mario de Bono. “Environmental CO2 Inhibits Caenorhabditis
Elegans Egg-Laying by Modulating Olfactory Neurons and Evokes Widespread Changes
in Neural Activity.” Proceedings of the National Academy of Sciences. National
Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1423808112.
ieee: L. A. Fenk and M. de Bono, “Environmental CO2 inhibits Caenorhabditis elegans
egg-laying by modulating olfactory neurons and evokes widespread changes in neural
activity,” Proceedings of the National Academy of Sciences, vol. 112, no.
27. National Academy of Sciences, pp. E3525–E3534, 2015.
ista: Fenk LA, de Bono M. 2015. Environmental CO2 inhibits Caenorhabditis elegans
egg-laying by modulating olfactory neurons and evokes widespread changes in neural
activity. Proceedings of the National Academy of Sciences. 112(27), E3525–E3534.
mla: Fenk, Lorenz A., and Mario de Bono. “Environmental CO2 Inhibits Caenorhabditis
Elegans Egg-Laying by Modulating Olfactory Neurons and Evokes Widespread Changes
in Neural Activity.” Proceedings of the National Academy of Sciences, vol.
112, no. 27, National Academy of Sciences, 2015, pp. E3525–34, doi:10.1073/pnas.1423808112.
short: L.A. Fenk, M. de Bono, Proceedings of the National Academy of Sciences 112
(2015) E3525–E3534.
date_created: 2019-03-19T14:15:50Z
date_published: 2015-07-07T00:00:00Z
date_updated: 2021-01-12T08:06:12Z
day: '07'
ddc:
- '570'
doi: 10.1073/pnas.1423808112
extern: '1'
external_id:
pmid:
- '26100886'
file:
- access_level: open_access
checksum: 3d2da5af8d72467e382a565abc2e003d
content_type: application/pdf
creator: kschuh
date_created: 2019-03-19T14:21:07Z
date_updated: 2020-07-14T12:47:20Z
file_id: '6119'
file_name: 2015_PNAS_Fenk.pdf
file_size: 2822681
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 112'
issue: '27'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: E3525-E3534
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
status: public
title: Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating
olfactory neurons and evokes widespread changes in neural activity
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '6120'
abstract:
- lang: eng
text: Brains organize behavior and physiology to optimize the response to threats
or opportunities. We dissect how 21% O2, an indicator of surface exposure, reprograms
C. elegans' global state, inducing sustained locomotory arousal and altering expression
of neuropeptides, metabolic enzymes, and other non-neural genes. The URX O2-sensing
neurons drive arousal at 21% O2 by tonically activating the RMG interneurons.
Stimulating RMG is sufficient to switch behavioral state. Ablating the ASH, ADL,
or ASK sensory neurons connected to RMG by gap junctions does not disrupt arousal.
However, disrupting cation currents in these neurons curtails RMG neurosecretion
and arousal. RMG signals high O2 by peptidergic secretion. Neuropeptide reporters
reveal neural circuit state, as neurosecretion stimulates neuropeptide expression.
Neural imaging in unrestrained animals shows that URX and RMG encode O2 concentration
rather than behavior, while the activity of downstream interneurons such as AVB
and AIY reflect both O2 levels and the behavior being executed.
article_number: e04241
author:
- first_name: Patrick
full_name: Laurent, Patrick
last_name: Laurent
- first_name: Zoltan
full_name: Soltesz, Zoltan
last_name: Soltesz
- first_name: Geoffrey M
full_name: Nelson, Geoffrey M
last_name: Nelson
- first_name: Changchun
full_name: Chen, Changchun
last_name: Chen
- first_name: Fausto
full_name: Arellano-Carbajal, Fausto
last_name: Arellano-Carbajal
- first_name: Emmanuel
full_name: Levy, Emmanuel
last_name: Levy
- 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: Laurent P, Soltesz Z, Nelson GM, et al. Decoding a neural circuit controlling
global animal state in C. elegans. eLife. 2015;4. doi:10.7554/elife.04241
apa: Laurent, P., Soltesz, Z., Nelson, G. M., Chen, C., Arellano-Carbajal, F., Levy,
E., & de Bono, M. (2015). Decoding a neural circuit controlling global animal
state in C. elegans. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.04241
chicago: Laurent, Patrick, Zoltan Soltesz, Geoffrey M Nelson, Changchun Chen, Fausto
Arellano-Carbajal, Emmanuel Levy, and Mario de Bono. “Decoding a Neural Circuit
Controlling Global Animal State in C. Elegans.” ELife. eLife Sciences Publications,
2015. https://doi.org/10.7554/elife.04241.
ieee: P. Laurent et al., “Decoding a neural circuit controlling global animal
state in C. elegans,” eLife, vol. 4. eLife Sciences Publications, 2015.
ista: Laurent P, Soltesz Z, Nelson GM, Chen C, Arellano-Carbajal F, Levy E, de Bono
M. 2015. Decoding a neural circuit controlling global animal state in C. elegans.
eLife. 4, e04241.
mla: Laurent, Patrick, et al. “Decoding a Neural Circuit Controlling Global Animal
State in C. Elegans.” ELife, vol. 4, e04241, eLife Sciences Publications,
2015, doi:10.7554/elife.04241.
short: P. Laurent, Z. Soltesz, G.M. Nelson, C. Chen, F. Arellano-Carbajal, E. Levy,
M. de Bono, ELife 4 (2015).
date_created: 2019-03-19T14:23:51Z
date_published: 2015-03-11T00:00:00Z
date_updated: 2021-01-12T08:06:13Z
day: '11'
ddc:
- '570'
doi: 10.7554/elife.04241
extern: '1'
external_id:
pmid:
- '25760081'
file:
- access_level: open_access
checksum: cf641b7a363aecd0a101755d23dee7e0
content_type: application/pdf
creator: kschuh
date_created: 2019-03-19T14:29:43Z
date_updated: 2020-07-14T12:47:20Z
file_id: '6121'
file_name: 2015_elife_Laurent.pdf
file_size: 6723528
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 4'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
status: public
title: Decoding a neural circuit controlling global animal state in C. elegans
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: 4
year: '2015'
...
---
_id: '1637'
abstract:
- lang: eng
text: An instance of the Valued Constraint Satisfaction Problem (VCSP) is given
by a finite set of variables, a finite domain of labels, and a sum of functions,
each function depending on a subset of the variables. Each function can take finite
values specifying costs of assignments of labels to its variables or the infinite
value, which indicates an infeasible assignment. The goal is to find an assignment
of labels to the variables that minimizes the sum. We study, assuming that P ≠
NP, how the complexity of this very general problem depends on the set of functions
allowed in the instances, the so-called constraint language. The case when all
allowed functions take values in {0, ∞} corresponds to ordinary CSPs, where one
deals only with the feasibility issue and there is no optimization. This case
is the subject of the Algebraic CSP Dichotomy Conjecture predicting for which
constraint languages CSPs are tractable (i.e. solvable in polynomial time) and
for which NP-hard. The case when all allowed functions take only finite values
corresponds to finite-valued CSP, where the feasibility aspect is trivial and
one deals only with the optimization issue. The complexity of finite-valued CSPs
was fully classified by Thapper and Zivny. An algebraic necessary condition for
tractability of a general-valued CSP with a fixed constraint language was recently
given by Kozik and Ochremiak. As our main result, we prove that if a constraint
language satisfies this algebraic necessary condition, and the feasibility CSP
(i.e. the problem of deciding whether a given instance has a feasible solution)
corresponding to the VCSP with this language is tractable, then the VCSP is tractable.
The algorithm is a simple combination of the assumed algorithm for the feasibility
CSP and the standard LP relaxation. As a corollary, we obtain that a dichotomy
for ordinary CSPs would imply a dichotomy for general-valued CSPs.
alternative_title:
- 56th Annual Symposium on Foundations of Computer Science
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Andrei
full_name: Krokhin, Andrei
last_name: Krokhin
- first_name: Michal
full_name: Rolinek, Michal
id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87
last_name: Rolinek
citation:
ama: 'Kolmogorov V, Krokhin A, Rolinek M. The complexity of general-valued CSPs.
In: IEEE; 2015:1246-1258. doi:10.1109/FOCS.2015.80'
apa: 'Kolmogorov, V., Krokhin, A., & Rolinek, M. (2015). The complexity of general-valued
CSPs (pp. 1246–1258). Presented at the FOCS: Foundations of Computer Science,
Berkeley, CA, United States: IEEE. https://doi.org/10.1109/FOCS.2015.80'
chicago: Kolmogorov, Vladimir, Andrei Krokhin, and Michal Rolinek. “The Complexity
of General-Valued CSPs,” 1246–58. IEEE, 2015. https://doi.org/10.1109/FOCS.2015.80.
ieee: 'V. Kolmogorov, A. Krokhin, and M. Rolinek, “The complexity of general-valued
CSPs,” presented at the FOCS: Foundations of Computer Science, Berkeley, CA, United
States, 2015, pp. 1246–1258.'
ista: 'Kolmogorov V, Krokhin A, Rolinek M. 2015. The complexity of general-valued
CSPs. FOCS: Foundations of Computer Science, 56th Annual Symposium on Foundations
of Computer Science, , 1246–1258.'
mla: Kolmogorov, Vladimir, et al. The Complexity of General-Valued CSPs.
IEEE, 2015, pp. 1246–58, doi:10.1109/FOCS.2015.80.
short: V. Kolmogorov, A. Krokhin, M. Rolinek, in:, IEEE, 2015, pp. 1246–1258.
conference:
end_date: 2015-10-20
location: Berkeley, CA, United States
name: 'FOCS: Foundations of Computer Science'
start_date: 2015-10-18
date_created: 2018-12-11T11:53:10Z
date_published: 2015-12-01T00:00:00Z
date_updated: 2023-02-23T12:44:26Z
day: '01'
department:
- _id: VlKo
doi: 10.1109/FOCS.2015.80
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1502.07327
month: '12'
oa: 1
oa_version: Preprint
page: 1246 - 1258
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication_status: published
publisher: IEEE
publist_id: '5518'
quality_controlled: '1'
related_material:
record:
- id: '644'
relation: other
status: public
scopus_import: 1
status: public
title: The complexity of general-valued CSPs
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '6507'
abstract:
- lang: eng
text: The osteoclast-associated receptor (OSCAR) is a collagen-binding immune receptor
with important roles in dendritic cell maturation and activation of inflammatory
monocytes as well as in osteoclastogenesis. The crystal structure of the OSCAR
ectodomain is presented, both free and in complex with a consensus triple-helical
peptide (THP). The structures revealed a collagen-binding site in each immunoglobulin-like
domain (D1 and D2). The THP binds near a predicted collagen-binding groove in
D1, but a more extensive interaction with D2 is facilitated by the unusually wide
D1-D2 interdomain angle in OSCAR. Direct binding assays, combined with site-directed
mutagenesis, confirm that the primary collagen-binding site in OSCAR resides in
D2, in marked contrast to the related collagen receptors, glycoprotein VI (GPVI)
and leukocyte-associated immunoglobulin-like receptor-1 (LAIR-1). Monomeric OSCAR
D1D2 binds to the consensus THP with a KD of 28 µM measured in solution, but shows
a higher affinity (KD 1.5 μM) when binding to a solid-phase THP, most likely due
to an avidity effect. These data suggest a 2-stage model for the interaction of
OSCAR with a collagen fibril, with transient, low-affinity interactions initiated
by the membrane-distal D1, followed by firm adhesion to the primary binding site
in D2.
author:
- first_name: Long
full_name: Zhou, Long
id: 3E751364-F248-11E8-B48F-1D18A9856A87
last_name: Zhou
orcid: 0000-0002-1864-8951
- first_name: J. M.
full_name: Hinerman, J. M.
last_name: Hinerman
- first_name: M.
full_name: Blaszczyk, M.
last_name: Blaszczyk
- first_name: J. L. C.
full_name: Miller, J. L. C.
last_name: Miller
- first_name: D. G.
full_name: Conrady, D. G.
last_name: Conrady
- first_name: A. D.
full_name: Barrow, A. D.
last_name: Barrow
- first_name: D. Y.
full_name: Chirgadze, D. Y.
last_name: Chirgadze
- first_name: D.
full_name: Bihan, D.
last_name: Bihan
- first_name: R. W.
full_name: Farndale, R. W.
last_name: Farndale
- first_name: A. B.
full_name: Herr, A. B.
last_name: Herr
citation:
ama: Zhou L, Hinerman JM, Blaszczyk M, et al. Structural basis for collagen recognition
by the immune receptor OSCAR. Blood. 2015;127(5):529-537. doi:10.1182/blood-2015-08-667055
apa: Zhou, L., Hinerman, J. M., Blaszczyk, M., Miller, J. L. C., Conrady, D. G.,
Barrow, A. D., … Herr, A. B. (2015). Structural basis for collagen recognition
by the immune receptor OSCAR. Blood. American Society of Hematology. https://doi.org/10.1182/blood-2015-08-667055
chicago: Zhou, Long, J. M. Hinerman, M. Blaszczyk, J. L. C. Miller, D. G. Conrady,
A. D. Barrow, D. Y. Chirgadze, D. Bihan, R. W. Farndale, and A. B. Herr. “Structural
Basis for Collagen Recognition by the Immune Receptor OSCAR.” Blood. American
Society of Hematology, 2015. https://doi.org/10.1182/blood-2015-08-667055.
ieee: L. Zhou et al., “Structural basis for collagen recognition by the immune
receptor OSCAR,” Blood, vol. 127, no. 5. American Society of Hematology,
pp. 529–537, 2015.
ista: Zhou L, Hinerman JM, Blaszczyk M, Miller JLC, Conrady DG, Barrow AD, Chirgadze
DY, Bihan D, Farndale RW, Herr AB. 2015. Structural basis for collagen recognition
by the immune receptor OSCAR. Blood. 127(5), 529–537.
mla: Zhou, Long, et al. “Structural Basis for Collagen Recognition by the Immune
Receptor OSCAR.” Blood, vol. 127, no. 5, American Society of Hematology,
2015, pp. 529–37, doi:10.1182/blood-2015-08-667055.
short: L. Zhou, J.M. Hinerman, M. Blaszczyk, J.L.C. Miller, D.G. Conrady, A.D. Barrow,
D.Y. Chirgadze, D. Bihan, R.W. Farndale, A.B. Herr, Blood 127 (2015) 529–537.
date_created: 2019-05-31T09:38:50Z
date_published: 2015-11-02T00:00:00Z
date_updated: 2021-01-12T08:07:47Z
day: '02'
doi: 10.1182/blood-2015-08-667055
extern: '1'
external_id:
pmid:
- '26552697'
intvolume: ' 127'
issue: '5'
language:
- iso: eng
month: '11'
oa_version: None
page: 529-537
pmid: 1
publication: Blood
publication_identifier:
issn:
- 0006-4971
- 1528-0020
publication_status: published
publisher: American Society of Hematology
quality_controlled: '1'
status: public
title: Structural basis for collagen recognition by the immune receptor OSCAR
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 127
year: '2015'
...
---
_id: '6737'
abstract:
- lang: eng
text: This paper presents polar coding schemes for the two-user discrete memoryless
broadcast channel (DM-BC) which achieve Marton's region with both common and private
messages. This is the best achievable rate region known to date, and it is tight
for all classes of two-user DM-BCs whose capacity regions are known. To accomplish
this task, we first construct polar codes for both the superposition as well as
binning strategy. By combining these two schemes, we obtain Marton's region with
private messages only. Finally, we show how to handle the case of common information.
The proposed coding schemes possess the usual advantages of polar codes, i.e.,
they have low encoding and decoding complexity and a superpolynomial decay rate
of the error probability. We follow the lead of Goela, Abbe, and Gastpar, who
recently introduced polar codes emulating the superposition and binning schemes.
To align the polar indices, for both schemes, their solution involves some degradedness
constraints that are assumed to hold between the auxiliary random variables and
channel outputs. To remove these constraints, we consider the transmission of
k blocks and employ a chaining construction that guarantees the proper alignment
of the polarized indices. The techniques described in this paper are quite general,
and they can be adopted to many other multiterminal scenarios whenever there polar
indices need to be aligned.
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: Igal
full_name: Sason, Igal
last_name: Sason
- first_name: Rudiger
full_name: Urbanke, Rudiger
last_name: Urbanke
citation:
ama: Mondelli M, Hassani H, Sason I, Urbanke R. Achieving Marton’s region for broadcast
channels using polar codes. IEEE Transactions on Information Theory. 2015;61(2):783-800.
doi:10.1109/tit.2014.2368555
apa: Mondelli, M., Hassani, H., Sason, I., & Urbanke, R. (2015). Achieving Marton’s
region for broadcast channels using polar codes. IEEE Transactions on Information
Theory. IEEE. https://doi.org/10.1109/tit.2014.2368555
chicago: Mondelli, Marco, Hamed Hassani, Igal Sason, and Rudiger Urbanke. “Achieving
Marton’s Region for Broadcast Channels Using Polar Codes.” IEEE Transactions
on Information Theory. IEEE, 2015. https://doi.org/10.1109/tit.2014.2368555.
ieee: M. Mondelli, H. Hassani, I. Sason, and R. Urbanke, “Achieving Marton’s region
for broadcast channels using polar codes,” IEEE Transactions on Information
Theory, vol. 61, no. 2. IEEE, pp. 783–800, 2015.
ista: Mondelli M, Hassani H, Sason I, Urbanke R. 2015. Achieving Marton’s region
for broadcast channels using polar codes. IEEE Transactions on Information Theory.
61(2), 783–800.
mla: Mondelli, Marco, et al. “Achieving Marton’s Region for Broadcast Channels Using
Polar Codes.” IEEE Transactions on Information Theory, vol. 61, no. 2,
IEEE, 2015, pp. 783–800, doi:10.1109/tit.2014.2368555.
short: M. Mondelli, H. Hassani, I. Sason, R. Urbanke, IEEE Transactions on Information
Theory 61 (2015) 783–800.
date_created: 2019-07-31T07:03:38Z
date_published: 2015-02-01T00:00:00Z
date_updated: 2021-01-12T08:08:46Z
day: '01'
doi: 10.1109/tit.2014.2368555
extern: '1'
external_id:
arxiv:
- '1401.6060'
intvolume: ' 61'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1401.6060
month: '02'
oa: 1
oa_version: Preprint
page: 783-800
publication: IEEE Transactions on Information Theory
publication_status: published
publisher: IEEE
quality_controlled: '1'
status: public
title: Achieving Marton’s region for broadcast channels using polar codes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 61
year: '2015'
...
---
_id: '6736'
abstract:
- lang: eng
text: Motivated by the significant performance gains which polar codes experience
under successive cancellation list decoding, their scaling exponent is studied
as a function of the list size. In particular, the error probability is fixed,
and the tradeoff between the block length and back-off from capacity is analyzed.
A lower bound is provided on the error probability under MAP decoding with list
size L for any binary-input memoryless output-symmetric channel and for any class
of linear codes such that their minimum distance is unbounded as the block length
grows large. Then, it is shown that under MAP decoding, although the introduction
of a list can significantly improve the involved constants, the scaling exponent
itself, i.e., the speed at which capacity is approached, stays unaffected for
any finite list size. In particular, this result applies to polar codes, since
their minimum distance tends to infinity as the block length increases. A similar
result is proved for genie-aided successive cancellation decoding when transmission
takes place over the binary erasure channel, namely, the scaling exponent remains
constant for any fixed number of helps from the genie. Note that since genie-aided
successive cancellation decoding might be strictly worse than successive cancellation
list decoding, the problem of establishing the scaling exponent of the latter
remains open.
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. Scaling exponent of list decoders with applications
to polar codes. IEEE Transactions on Information Theory. 2015;61(9):4838-4851.
doi:10.1109/tit.2015.2453315
apa: Mondelli, M., Hassani, H., & Urbanke, R. (2015). Scaling exponent of list
decoders with applications to polar codes. IEEE Transactions on Information
Theory. IEEE. https://doi.org/10.1109/tit.2015.2453315
chicago: Mondelli, Marco, Hamed Hassani, and Rudiger Urbanke. “Scaling Exponent
of List Decoders with Applications to Polar Codes.” IEEE Transactions on Information
Theory. IEEE, 2015. https://doi.org/10.1109/tit.2015.2453315.
ieee: M. Mondelli, H. Hassani, and R. Urbanke, “Scaling exponent of list decoders
with applications to polar codes,” IEEE Transactions on Information Theory,
vol. 61, no. 9. IEEE, pp. 4838–4851, 2015.
ista: Mondelli M, Hassani H, Urbanke R. 2015. Scaling exponent of list decoders
with applications to polar codes. IEEE Transactions on Information Theory. 61(9),
4838–4851.
mla: Mondelli, Marco, et al. “Scaling Exponent of List Decoders with Applications
to Polar Codes.” IEEE Transactions on Information Theory, vol. 61, no.
9, IEEE, 2015, pp. 4838–51, doi:10.1109/tit.2015.2453315.
short: M. Mondelli, H. Hassani, R. Urbanke, IEEE Transactions on Information Theory
61 (2015) 4838–4851.
date_created: 2019-07-31T06:50:34Z
date_published: 2015-09-01T00:00:00Z
date_updated: 2021-01-12T08:08:45Z
day: '01'
doi: 10.1109/tit.2015.2453315
extern: '1'
external_id:
arxiv:
- '1304.5220'
intvolume: ' 61'
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1304.5220
month: '09'
oa: 1
oa_version: Preprint
page: 4838-4851
publication: IEEE Transactions on Information Theory
publication_status: published
publisher: IEEE
quality_controlled: '1'
status: public
title: Scaling exponent of list decoders with applications to polar codes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 61
year: '2015'
...
---
_id: '7070'
abstract:
- lang: eng
text: 'Torque magnetization measurements on YBa2Cu3Oy (YBCO) at doping y=6.67 (p=0.12),
in dc fields (B) up to 33 T and temperatures down to 4.5 K, show that weak diamagnetism
persists above the extrapolated irreversibility field Hirr(T=0)≈24 T. The differential
susceptibility dM/dB, however, is more rapidly suppressed for B≳16 T than expected
from the properties of the low field superconducting state, and saturates at a
low value for fields B≳24 T. In addition, torque measurements on a p=0.11 YBCO
crystal in pulsed field up to 65 T and temperatures down to 8 K show similar behavior,
with no additional features at higher fields. We offer two candidate scenarios
to explain these observations: (a) superconductivity survives but is heavily suppressed
at high field by competition with charge-density-wave (CDW) order; (b) static
superconductivity disappears near 24 T and is followed by a region of fluctuating
superconductivity, which causes dM/dB to saturate at high field. The diamagnetic
signal observed above 50 T for the p=0.11 crystal at 40 K and below may be caused
by changes in the normal state susceptibility rather than bulk or fluctuating
superconductivity. There will be orbital (Landau) diamagnetism from electron pockets
and possibly a reduction in spin susceptibility caused by the stronger three-dimensional
ordered CDW.'
article_number: '180509'
article_processing_charge: No
article_type: original
author:
- first_name: Jing Fei
full_name: Yu, Jing Fei
last_name: Yu
- first_name: B. J.
full_name: Ramshaw, B. J.
last_name: Ramshaw
- first_name: I.
full_name: Kokanović, I.
last_name: Kokanović
- 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: N.
full_name: Harrison, N.
last_name: Harrison
- first_name: James
full_name: Day, James
last_name: Day
- first_name: Ruixing
full_name: Liang, Ruixing
last_name: Liang
- first_name: W. N.
full_name: Hardy, W. N.
last_name: Hardy
- first_name: D. A.
full_name: Bonn, D. A.
last_name: Bonn
- first_name: A.
full_name: McCollam, A.
last_name: McCollam
- first_name: S. R.
full_name: Julian, S. R.
last_name: Julian
- first_name: J. R.
full_name: Cooper, J. R.
last_name: Cooper
citation:
ama: Yu JF, Ramshaw BJ, Kokanović I, et al. Magnetization of underdoped YBa2Cu3Oy
above the irreversibility field. Physical Review B. 2015;92(18). doi:10.1103/physrevb.92.180509
apa: Yu, J. F., Ramshaw, B. J., Kokanović, I., Modic, K. A., Harrison, N., Day,
J., … Cooper, J. R. (2015). Magnetization of underdoped YBa2Cu3Oy above the irreversibility
field. Physical Review B. APS. https://doi.org/10.1103/physrevb.92.180509
chicago: Yu, Jing Fei, B. J. Ramshaw, I. Kokanović, Kimberly A Modic, N. Harrison,
James Day, Ruixing Liang, et al. “Magnetization of Underdoped YBa2Cu3Oy above
the Irreversibility Field.” Physical Review B. APS, 2015. https://doi.org/10.1103/physrevb.92.180509.
ieee: J. F. Yu et al., “Magnetization of underdoped YBa2Cu3Oy above the irreversibility
field,” Physical Review B, vol. 92, no. 18. APS, 2015.
ista: Yu JF, Ramshaw BJ, Kokanović I, Modic KA, Harrison N, Day J, Liang R, Hardy
WN, Bonn DA, McCollam A, Julian SR, Cooper JR. 2015. Magnetization of underdoped
YBa2Cu3Oy above the irreversibility field. Physical Review B. 92(18), 180509.
mla: Yu, Jing Fei, et al. “Magnetization of Underdoped YBa2Cu3Oy above the Irreversibility
Field.” Physical Review B, vol. 92, no. 18, 180509, APS, 2015, doi:10.1103/physrevb.92.180509.
short: J.F. Yu, B.J. Ramshaw, I. Kokanović, K.A. Modic, N. Harrison, J. Day, R.
Liang, W.N. Hardy, D.A. Bonn, A. McCollam, S.R. Julian, J.R. Cooper, Physical
Review B 92 (2015).
date_created: 2019-11-19T13:22:06Z
date_published: 2015-11-23T00:00:00Z
date_updated: 2021-01-12T08:11:42Z
day: '23'
doi: 10.1103/physrevb.92.180509
extern: '1'
intvolume: ' 92'
issue: '18'
language:
- iso: eng
month: '11'
oa_version: None
publication: Physical Review B
publication_identifier:
issn:
- 1098-0121
- 1550-235X
publication_status: published
publisher: APS
quality_controlled: '1'
status: public
title: Magnetization of underdoped YBa2Cu3Oy above the irreversibility field
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 92
year: '2015'
...
---
_id: '7456'
abstract:
- lang: eng
text: The rational design of monodisperse ferroelectric nanocrystals with controlled
size and shape and their organization into hierarchical structures has been a
critical step for understanding the polar ordering in nanoscale ferroelectrics,
as well as the design of nanocrystal-based functional materials which harness
the properties of individual nanoparticles and the collective interactions between
them. We report here on the synthesis and self-assembly of aggregate-free, single-crystalline
titanium-based perovskite nanoparticles with controlled morphology and surface
composition by using a simple, easily scalable and highly versatile colloidal
route. Single-crystalline, non-aggregated BaTiO3 colloidal nanocrystals, used
as a model system, have been prepared under solvothermal conditions at temperatures
as low as 180 °C. The shape of the nanocrystals was tuned from spheroidal to cubic
upon changing the polarity of the solvent, whereas their size was varied from
16 to 30 nm for spheres and 5 to 78 nm for cubes by changing the concentration
of the precursors and the reaction time, respectively. The hydrophobic, oleic
acid-passivated nanoparticles exhibit very good solubility in non-polar solvents
and can be rendered dispersible in polar solvents by a simple process involving
the oxidative cleavage of the double bond upon treating the nanopowders with the
Lemieux–von Rudloff reagent. Lattice dynamic analysis indicated that regardless
of their size, BaTiO3 nanocrystals present local disorder within the perovskite
unit cell, associated with the existence of polar ordering. We also demonstrate
for the first time that, in addition to being used for fabricating large area,
crack-free, highly uniform films, BaTiO3 nanocubes can serve as building blocks
for the design of 2D and 3D mesoscale structures, such as superlattices and superparticles.
Interestingly, the type of superlattice structure (simple cubic or face centered
cubic) appears to be determined by the type of solvent in which the nanocrystals
were dispersed. This approach provides an excellent platform for the synthesis
of other titanium-based perovskite colloidal nanocrystals with controlled chemical
composition, surface structure and morphology and for their assembly into complex
architectures, therefore opening the door for the design of novel mesoscale functional
materials/nanocomposites with potential applications in energy conversion, data
storage and the biomedical field.
article_processing_charge: No
article_type: original
author:
- first_name: Daniela
full_name: Caruntu, Daniela
last_name: Caruntu
- first_name: Taha
full_name: Rostamzadeh, Taha
last_name: Rostamzadeh
- first_name: Tommaso
full_name: Costanzo, Tommaso
id: D93824F4-D9BA-11E9-BB12-F207E6697425
last_name: Costanzo
orcid: 0000-0001-9732-3815
- first_name: Saman
full_name: Salemizadeh Parizi, Saman
last_name: Salemizadeh Parizi
- first_name: Gabriel
full_name: Caruntu, Gabriel
last_name: Caruntu
citation:
ama: Caruntu D, Rostamzadeh T, Costanzo T, Salemizadeh Parizi S, Caruntu G. Solvothermal
synthesis and controlled self-assembly of monodisperse titanium-based perovskite
colloidal nanocrystals. Nanoscale. 2015;7(30):12955-12969. doi:10.1039/c5nr00737b
apa: Caruntu, D., Rostamzadeh, T., Costanzo, T., Salemizadeh Parizi, S., & Caruntu,
G. (2015). Solvothermal synthesis and controlled self-assembly of monodisperse
titanium-based perovskite colloidal nanocrystals. Nanoscale. RSC. https://doi.org/10.1039/c5nr00737b
chicago: Caruntu, Daniela, Taha Rostamzadeh, Tommaso Costanzo, Saman Salemizadeh
Parizi, and Gabriel Caruntu. “Solvothermal Synthesis and Controlled Self-Assembly
of Monodisperse Titanium-Based Perovskite Colloidal Nanocrystals.” Nanoscale.
RSC, 2015. https://doi.org/10.1039/c5nr00737b.
ieee: D. Caruntu, T. Rostamzadeh, T. Costanzo, S. Salemizadeh Parizi, and G. Caruntu,
“Solvothermal synthesis and controlled self-assembly of monodisperse titanium-based
perovskite colloidal nanocrystals,” Nanoscale, vol. 7, no. 30. RSC, pp.
12955–12969, 2015.
ista: Caruntu D, Rostamzadeh T, Costanzo T, Salemizadeh Parizi S, Caruntu G. 2015.
Solvothermal synthesis and controlled self-assembly of monodisperse titanium-based
perovskite colloidal nanocrystals. Nanoscale. 7(30), 12955–12969.
mla: Caruntu, Daniela, et al. “Solvothermal Synthesis and Controlled Self-Assembly
of Monodisperse Titanium-Based Perovskite Colloidal Nanocrystals.” Nanoscale,
vol. 7, no. 30, RSC, 2015, pp. 12955–69, doi:10.1039/c5nr00737b.
short: D. Caruntu, T. Rostamzadeh, T. Costanzo, S. Salemizadeh Parizi, G. Caruntu,
Nanoscale 7 (2015) 12955–12969.
date_created: 2020-02-05T14:16:37Z
date_published: 2015-08-14T00:00:00Z
date_updated: 2023-02-23T13:08:24Z
day: '14'
doi: 10.1039/c5nr00737b
extern: '1'
external_id:
pmid:
- '26168304'
intvolume: ' 7'
issue: '30'
language:
- iso: eng
month: '08'
oa_version: None
page: 12955-12969
pmid: 1
publication: Nanoscale
publication_identifier:
issn:
- 2040-3364
- 2040-3372
publication_status: published
publisher: RSC
quality_controlled: '1'
status: public
title: Solvothermal synthesis and controlled self-assembly of monodisperse titanium-based
perovskite colloidal nanocrystals
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2015'
...
---
_id: '7457'
abstract:
- lang: eng
text: A new organic–inorganic ferroelectric hybrid capacitor designed by uniformly
incorporating surface modified monodisperse 15 nm ferroelectric BaTiO3 nanocubes
into non-polar polymer blends of poly(methyl methacrylate) (PMMA) polymer and
acrylonitrile-butadiene-styrene (ABS) terpolymer is described. The investigation
of spatial distribution of nanofillers via a non-distractive thermal pulse method
illustrates that the surface functionalization of nanocubes plays a key role in
the uniform distribution of charge polarization within the polymer matrix. The
discharged energy density of the nanocomposite with 30 vol% BaTiO3 nanocubes is
∼44 × 10−3 J cm−3, which is almost six times higher than that of the neat polymer.
The facile processing, along with the superior mechanical and electrical properties
of the BaTiO3/PMMA–ABS nanocomposites make them suitable for implementation into
capacitive electrical energy storage devices.
article_processing_charge: No
article_type: original
author:
- first_name: Saman Salemizadeh
full_name: Parizi, Saman Salemizadeh
last_name: Parizi
- first_name: Gavin
full_name: Conley, Gavin
last_name: Conley
- first_name: Tommaso
full_name: Costanzo, Tommaso
id: D93824F4-D9BA-11E9-BB12-F207E6697425
last_name: Costanzo
orcid: 0000-0001-9732-3815
- first_name: Bob
full_name: Howell, Bob
last_name: Howell
- first_name: Axel
full_name: Mellinger, Axel
last_name: Mellinger
- first_name: Gabriel
full_name: Caruntu, Gabriel
last_name: Caruntu
citation:
ama: Parizi SS, Conley G, Costanzo T, Howell B, Mellinger A, Caruntu G. Fabrication
of barium titanate/acrylonitrile-butadiene styrene/poly(methyl methacrylate) nanocomposite
films for hybrid ferroelectric capacitors. RSC Advances. 2015;5(93):76356-76362.
doi:10.1039/c5ra11347d
apa: Parizi, S. S., Conley, G., Costanzo, T., Howell, B., Mellinger, A., & Caruntu,
G. (2015). Fabrication of barium titanate/acrylonitrile-butadiene styrene/poly(methyl
methacrylate) nanocomposite films for hybrid ferroelectric capacitors. RSC
Advances. RSC. https://doi.org/10.1039/c5ra11347d
chicago: Parizi, Saman Salemizadeh, Gavin Conley, Tommaso Costanzo, Bob Howell,
Axel Mellinger, and Gabriel Caruntu. “Fabrication of Barium Titanate/Acrylonitrile-Butadiene
Styrene/Poly(Methyl Methacrylate) Nanocomposite Films for Hybrid Ferroelectric
Capacitors.” RSC Advances. RSC, 2015. https://doi.org/10.1039/c5ra11347d.
ieee: S. S. Parizi, G. Conley, T. Costanzo, B. Howell, A. Mellinger, and G. Caruntu,
“Fabrication of barium titanate/acrylonitrile-butadiene styrene/poly(methyl methacrylate)
nanocomposite films for hybrid ferroelectric capacitors,” RSC Advances,
vol. 5, no. 93. RSC, pp. 76356–76362, 2015.
ista: Parizi SS, Conley G, Costanzo T, Howell B, Mellinger A, Caruntu G. 2015. Fabrication
of barium titanate/acrylonitrile-butadiene styrene/poly(methyl methacrylate) nanocomposite
films for hybrid ferroelectric capacitors. RSC Advances. 5(93), 76356–76362.
mla: Parizi, Saman Salemizadeh, et al. “Fabrication of Barium Titanate/Acrylonitrile-Butadiene
Styrene/Poly(Methyl Methacrylate) Nanocomposite Films for Hybrid Ferroelectric
Capacitors.” RSC Advances, vol. 5, no. 93, RSC, 2015, pp. 76356–62, doi:10.1039/c5ra11347d.
short: S.S. Parizi, G. Conley, T. Costanzo, B. Howell, A. Mellinger, G. Caruntu,
RSC Advances 5 (2015) 76356–76362.
date_created: 2020-02-05T14:17:26Z
date_published: 2015-09-01T00:00:00Z
date_updated: 2023-02-23T13:08:26Z
day: '01'
doi: 10.1039/c5ra11347d
extern: '1'
intvolume: ' 5'
issue: '93'
language:
- iso: eng
month: '09'
oa_version: Submitted Version
page: 76356-76362
publication: RSC Advances
publication_identifier:
issn:
- 2046-2069
publication_status: published
publisher: RSC
quality_controlled: '1'
status: public
title: Fabrication of barium titanate/acrylonitrile-butadiene styrene/poly(methyl
methacrylate) nanocomposite films for hybrid ferroelectric capacitors
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2015'
...
---
_id: '7742'
abstract:
- lang: eng
text: Across-nation differences in the mean values for complex traits are common1,2,3,4,5,6,7,8,
but the reasons for these differences are unknown. Here we find that many independent
loci contribute to population genetic differences in height and body mass index
(BMI) in 9,416 individuals across 14 European countries. Using discovery data
on over 250,000 individuals and unbiased effect size estimates from 17,500 sibling
pairs, we estimate that 24% (95% credible interval (CI) = 9%, 41%) and 8% (95%
CI = 4%, 16%) of the captured additive genetic variance for height and BMI, respectively,
reflect population genetic differences. Population genetic divergence differed
significantly from that in a null model (height, P < 3.94 × 10−8; BMI, P < 5.95
× 10−4), and we find an among-population genetic correlation for tall and slender
individuals (r = −0.80, 95% CI = −0.95, −0.60), consistent with correlated selection
for both phenotypes. Observed differences in height among populations reflected
the predicted genetic means (r = 0.51; P < 0.001), but environmental differences
across Europe masked genetic differentiation for BMI (P < 0.58).
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: Gibran
full_name: Hemani, Gibran
last_name: Hemani
- first_name: Carolina
full_name: Medina-Gomez, Carolina
last_name: Medina-Gomez
- first_name: Massimo
full_name: Mezzavilla, Massimo
last_name: Mezzavilla
- first_name: Tonu
full_name: Esko, Tonu
last_name: Esko
- first_name: Konstantin
full_name: Shakhbazov, Konstantin
last_name: Shakhbazov
- first_name: Joseph E
full_name: Powell, Joseph E
last_name: Powell
- first_name: Anna
full_name: Vinkhuyzen, Anna
last_name: Vinkhuyzen
- first_name: Sonja I
full_name: Berndt, Sonja I
last_name: Berndt
- first_name: Stefan
full_name: Gustafsson, Stefan
last_name: Gustafsson
- first_name: Anne E
full_name: Justice, Anne E
last_name: Justice
- first_name: Bratati
full_name: Kahali, Bratati
last_name: Kahali
- first_name: Adam E
full_name: Locke, Adam E
last_name: Locke
- first_name: Tune H
full_name: Pers, Tune H
last_name: Pers
- first_name: Sailaja
full_name: Vedantam, Sailaja
last_name: Vedantam
- first_name: Andrew R
full_name: Wood, Andrew R
last_name: Wood
- first_name: Wouter
full_name: van Rheenen, Wouter
last_name: van Rheenen
- first_name: Ole A
full_name: Andreassen, Ole A
last_name: Andreassen
- first_name: Paolo
full_name: Gasparini, Paolo
last_name: Gasparini
- first_name: Andres
full_name: Metspalu, Andres
last_name: Metspalu
- first_name: Leonard H van den
full_name: Berg, Leonard H van den
last_name: Berg
- first_name: Jan H
full_name: Veldink, Jan H
last_name: Veldink
- first_name: Fernando
full_name: Rivadeneira, Fernando
last_name: Rivadeneira
- first_name: Thomas M
full_name: Werge, Thomas M
last_name: Werge
- first_name: Goncalo R
full_name: Abecasis, Goncalo R
last_name: Abecasis
- first_name: Dorret I
full_name: Boomsma, Dorret I
last_name: Boomsma
- first_name: Daniel I
full_name: Chasman, Daniel I
last_name: Chasman
- first_name: Eco J C
full_name: de Geus, Eco J C
last_name: de Geus
- first_name: Timothy M
full_name: Frayling, Timothy M
last_name: Frayling
- first_name: Joel N
full_name: Hirschhorn, Joel N
last_name: Hirschhorn
- first_name: Jouke Jan
full_name: Hottenga, Jouke Jan
last_name: Hottenga
- first_name: Erik
full_name: Ingelsson, Erik
last_name: Ingelsson
- first_name: Ruth J F
full_name: Loos, Ruth J F
last_name: Loos
- first_name: Patrik K E
full_name: Magnusson, Patrik K E
last_name: Magnusson
- first_name: Nicholas G
full_name: Martin, Nicholas G
last_name: Martin
- first_name: Grant W
full_name: Montgomery, Grant W
last_name: Montgomery
- first_name: Kari E
full_name: North, Kari E
last_name: North
- first_name: Nancy L
full_name: Pedersen, Nancy L
last_name: Pedersen
- first_name: Timothy D
full_name: Spector, Timothy D
last_name: Spector
- first_name: Elizabeth K
full_name: Speliotes, Elizabeth K
last_name: Speliotes
- first_name: Michael E
full_name: Goddard, Michael E
last_name: Goddard
- first_name: Jian
full_name: Yang, Jian
last_name: Yang
- first_name: Peter M
full_name: Visscher, Peter M
last_name: Visscher
citation:
ama: Robinson MR, Hemani G, Medina-Gomez C, et al. Population genetic differentiation
of height and body mass index across Europe. Nature Genetics. 2015;47(11):1357-1362.
doi:10.1038/ng.3401
apa: Robinson, M. R., Hemani, G., Medina-Gomez, C., Mezzavilla, M., Esko, T., Shakhbazov,
K., … Visscher, P. M. (2015). Population genetic differentiation of height and
body mass index across Europe. Nature Genetics. Springer Nature. https://doi.org/10.1038/ng.3401
chicago: Robinson, Matthew Richard, Gibran Hemani, Carolina Medina-Gomez, Massimo
Mezzavilla, Tonu Esko, Konstantin Shakhbazov, Joseph E Powell, et al. “Population
Genetic Differentiation of Height and Body Mass Index across Europe.” Nature
Genetics. Springer Nature, 2015. https://doi.org/10.1038/ng.3401.
ieee: M. R. Robinson et al., “Population genetic differentiation of height
and body mass index across Europe,” Nature Genetics, vol. 47, no. 11. Springer
Nature, pp. 1357–1362, 2015.
ista: Robinson MR, Hemani G, Medina-Gomez C, Mezzavilla M, Esko T, Shakhbazov K,
Powell JE, Vinkhuyzen A, Berndt SI, Gustafsson S, Justice AE, Kahali B, Locke
AE, Pers TH, Vedantam S, Wood AR, van Rheenen W, Andreassen OA, Gasparini P, Metspalu
A, Berg LH van den, Veldink JH, Rivadeneira F, Werge TM, Abecasis GR, Boomsma
DI, Chasman DI, de Geus EJC, Frayling TM, Hirschhorn JN, Hottenga JJ, Ingelsson
E, Loos RJF, Magnusson PKE, Martin NG, Montgomery GW, North KE, Pedersen NL, Spector
TD, Speliotes EK, Goddard ME, Yang J, Visscher PM. 2015. Population genetic differentiation
of height and body mass index across Europe. Nature Genetics. 47(11), 1357–1362.
mla: Robinson, Matthew Richard, et al. “Population Genetic Differentiation of Height
and Body Mass Index across Europe.” Nature Genetics, vol. 47, no. 11, Springer
Nature, 2015, pp. 1357–62, doi:10.1038/ng.3401.
short: M.R. Robinson, G. Hemani, C. Medina-Gomez, M. Mezzavilla, T. Esko, K. Shakhbazov,
J.E. Powell, A. Vinkhuyzen, S.I. Berndt, S. Gustafsson, A.E. Justice, B. Kahali,
A.E. Locke, T.H. Pers, S. Vedantam, A.R. Wood, W. van Rheenen, O.A. Andreassen,
P. Gasparini, A. Metspalu, L.H. van den Berg, J.H. Veldink, F. Rivadeneira, T.M.
Werge, G.R. Abecasis, D.I. Boomsma, D.I. Chasman, E.J.C. de Geus, T.M. Frayling,
J.N. Hirschhorn, J.J. Hottenga, E. Ingelsson, R.J.F. Loos, P.K.E. Magnusson, N.G.
Martin, G.W. Montgomery, K.E. North, N.L. Pedersen, T.D. Spector, E.K. Speliotes,
M.E. Goddard, J. Yang, P.M. Visscher, Nature Genetics 47 (2015) 1357–1362.
date_created: 2020-04-30T10:58:23Z
date_published: 2015-09-14T00:00:00Z
date_updated: 2021-01-12T08:15:13Z
day: '14'
doi: 10.1038/ng.3401
extern: '1'
intvolume: ' 47'
issue: '11'
language:
- iso: eng
month: '09'
oa_version: None
page: 1357-1362
publication: Nature Genetics
publication_identifier:
issn:
- 1061-4036
- 1546-1718
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Population genetic differentiation of height and body mass index across Europe
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 47
year: '2015'
...
---
_id: '7741'
abstract:
- lang: eng
text: Phenotypes expressed in a social context are not only a function of the individual,
but can also be shaped by the phenotypes of social partners. These social effects
may play a major role in the evolution of cooperative breeding if social partners
differ in the quality of care they provide and if individual carers adjust their
effort in relation to that of other carers. When applying social effects models
to wild study systems, it is also important to explore sources of individual plasticity
that could masquerade as social effects. We studied offspring provisioning rates
of parents and helpers in a wild population of long-tailed tits Aegithalos caudatus
using a quantitative genetic framework to identify these social effects and partition
them into genetic, permanent environment and current environment components. Controlling
for other effects, individuals were consistent in their provisioning effort at
a given nest, but adjusted their effort based on who was in their social group,
indicating the presence of social effects. However, these social effects differed
between years and social contexts, indicating a current environment effect, rather
than indicating a genetic or permanent environment effect. While this study reveals
the importance of examining environmental and genetic sources of social effects,
the framework we present is entirely general, enabling a greater understanding
of potentially important social effects within any ecological population.
article_number: '20150689'
article_processing_charge: No
article_type: original
author:
- first_name: Mark James
full_name: Adams, Mark James
last_name: Adams
- 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: Maria-Elena
full_name: Mannarelli, Maria-Elena
last_name: Mannarelli
- first_name: Ben J.
full_name: Hatchwell, Ben J.
last_name: Hatchwell
citation:
ama: 'Adams MJ, Robinson MR, Mannarelli M-E, Hatchwell BJ. Social genetic and social
environment effects on parental and helper care in a cooperatively breeding bird.
Proceedings of the Royal Society B: Biological Sciences. 2015;282(1810).
doi:10.1098/rspb.2015.0689'
apa: 'Adams, M. J., Robinson, M. R., Mannarelli, M.-E., & Hatchwell, B. J. (2015).
Social genetic and social environment effects on parental and helper care in a
cooperatively breeding bird. Proceedings of the Royal Society B: Biological
Sciences. The Royal Society. https://doi.org/10.1098/rspb.2015.0689'
chicago: 'Adams, Mark James, Matthew Richard Robinson, Maria-Elena Mannarelli, and
Ben J. Hatchwell. “Social Genetic and Social Environment Effects on Parental and
Helper Care in a Cooperatively Breeding Bird.” Proceedings of the Royal Society
B: Biological Sciences. The Royal Society, 2015. https://doi.org/10.1098/rspb.2015.0689.'
ieee: 'M. J. Adams, M. R. Robinson, M.-E. Mannarelli, and B. J. Hatchwell, “Social
genetic and social environment effects on parental and helper care in a cooperatively
breeding bird,” Proceedings of the Royal Society B: Biological Sciences,
vol. 282, no. 1810. The Royal Society, 2015.'
ista: 'Adams MJ, Robinson MR, Mannarelli M-E, Hatchwell BJ. 2015. Social genetic
and social environment effects on parental and helper care in a cooperatively
breeding bird. Proceedings of the Royal Society B: Biological Sciences. 282(1810),
20150689.'
mla: 'Adams, Mark James, et al. “Social Genetic and Social Environment Effects on
Parental and Helper Care in a Cooperatively Breeding Bird.” Proceedings of
the Royal Society B: Biological Sciences, vol. 282, no. 1810, 20150689, The
Royal Society, 2015, doi:10.1098/rspb.2015.0689.'
short: 'M.J. Adams, M.R. Robinson, M.-E. Mannarelli, B.J. Hatchwell, Proceedings
of the Royal Society B: Biological Sciences 282 (2015).'
date_created: 2020-04-30T10:58:07Z
date_published: 2015-07-07T00:00:00Z
date_updated: 2021-01-12T08:15:12Z
day: '07'
doi: 10.1098/rspb.2015.0689
extern: '1'
external_id:
pmid:
- '26063846'
intvolume: ' 282'
issue: '1810'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1098/rspb.2015.0689
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: 'Proceedings of the Royal Society B: Biological Sciences'
publication_identifier:
issn:
- 0962-8452
- 1471-2954
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
status: public
title: Social genetic and social environment effects on parental and helper care in
a cooperatively breeding bird
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 282
year: '2015'
...
---
_id: '7739'
abstract:
- lang: eng
text: Currently, there is much debate on the genetic architecture of quantitative
traits in wild populations. Is trait variation influenced by many genes of small
effect or by a few genes of major effect? Where is additive genetic variation
located in the genome? Do the same loci cause similar phenotypic variation in
different populations? Great tits (Parus major) have been studied extensively
in long‐term studies across Europe and consequently are considered an ecological
‘model organism’. Recently, genomic resources have been developed for the great
tit, including a custom SNP chip and genetic linkage map. In this study, we used
a suite of approaches to investigate the genetic architecture of eight quantitative
traits in two long‐term study populations of great tits—one in the Netherlands
and the other in the United Kingdom. Overall, we found little evidence for the
presence of genes of large effects in either population. Instead, traits appeared
to be influenced by many genes of small effect, with conservative estimates of
the number of contributing loci ranging from 31 to 310. Despite concordance between
population‐specific heritabilities, we found no evidence for the presence of loci
having similar effects in both populations. While population‐specific genetic
architectures are possible, an undetected shared architecture cannot be rejected
because of limited power to map loci of small and moderate effects. This study
is one of few examples of genetic architecture analysis in replicated wild populations
and highlights some of the challenges and limitations researchers will face when
attempting similar molecular quantitative genetic studies in free‐living populations.
article_processing_charge: No
article_type: original
author:
- first_name: Anna W.
full_name: Santure, Anna W.
last_name: Santure
- first_name: Jocelyn
full_name: Poissant, Jocelyn
last_name: Poissant
- first_name: Isabelle
full_name: De Cauwer, Isabelle
last_name: De Cauwer
- first_name: Kees
full_name: van Oers, Kees
last_name: van Oers
- 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: John L.
full_name: Quinn, John L.
last_name: Quinn
- first_name: Martien A. M.
full_name: Groenen, Martien A. M.
last_name: Groenen
- first_name: Marcel E.
full_name: Visser, Marcel E.
last_name: Visser
- first_name: Ben C.
full_name: Sheldon, Ben C.
last_name: Sheldon
- first_name: Jon
full_name: Slate, Jon
last_name: Slate
citation:
ama: Santure AW, Poissant J, De Cauwer I, et al. Replicated analysis of the genetic
architecture of quantitative traits in two wild great tit populations. Molecular
Ecology. 2015;24:6148-6162. doi:10.1111/mec.13452
apa: Santure, A. W., Poissant, J., De Cauwer, I., van Oers, K., Robinson, M. R.,
Quinn, J. L., … Slate, J. (2015). Replicated analysis of the genetic architecture
of quantitative traits in two wild great tit populations. Molecular Ecology.
Wiley. https://doi.org/10.1111/mec.13452
chicago: Santure, Anna W., Jocelyn Poissant, Isabelle De Cauwer, Kees van Oers,
Matthew Richard Robinson, John L. Quinn, Martien A. M. Groenen, Marcel E. Visser,
Ben C. Sheldon, and Jon Slate. “Replicated Analysis of the Genetic Architecture
of Quantitative Traits in Two Wild Great Tit Populations.” Molecular Ecology.
Wiley, 2015. https://doi.org/10.1111/mec.13452.
ieee: A. W. Santure et al., “Replicated analysis of the genetic architecture
of quantitative traits in two wild great tit populations,” Molecular Ecology,
vol. 24. Wiley, pp. 6148–6162, 2015.
ista: Santure AW, Poissant J, De Cauwer I, van Oers K, Robinson MR, Quinn JL, Groenen
MAM, Visser ME, Sheldon BC, Slate J. 2015. Replicated analysis of the genetic
architecture of quantitative traits in two wild great tit populations. Molecular
Ecology. 24, 6148–6162.
mla: Santure, Anna W., et al. “Replicated Analysis of the Genetic Architecture of
Quantitative Traits in Two Wild Great Tit Populations.” Molecular Ecology,
vol. 24, Wiley, 2015, pp. 6148–62, doi:10.1111/mec.13452.
short: A.W. Santure, J. Poissant, I. De Cauwer, K. van Oers, M.R. Robinson, J.L.
Quinn, M.A.M. Groenen, M.E. Visser, B.C. Sheldon, J. Slate, Molecular Ecology
24 (2015) 6148–6162.
date_created: 2020-04-30T10:51:01Z
date_published: 2015-12-10T00:00:00Z
date_updated: 2021-01-12T08:15:12Z
day: '10'
doi: 10.1111/mec.13452
extern: '1'
intvolume: ' 24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/mec.13452
month: '12'
oa: 1
oa_version: Published Version
page: 6148-6162
publication: Molecular Ecology
publication_identifier:
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Replicated analysis of the genetic architecture of quantitative traits in two
wild great tit populations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2015'
...
---
_id: '776'
abstract:
- lang: eng
text: High-performance concurrent priority queues are essential for applications
such as task scheduling and discrete event simulation. Unfortunately, even the
best performing implementations do not scale past a number of threads in the single
digits. This is because of the sequential bottleneck in accessing the elements
at the head of the queue in order to perform a DeleteMin operation. In this paper,
we present the SprayList, a scalable priority queue with relaxed ordering semantics.
Starting from a non-blocking SkipList, the main innovation behind our design is
that the DeleteMin operations avoid a sequential bottleneck by "spraying"
themselves onto the head of the SkipList list in a coordinated fashion. The spraying
is implemented using a carefully designed random walk, so that DeleteMin returns
an element among the first O(plog3p) in the list, with high probability, where
p is the number of threads. We prove that the running time of a DeleteMin operation
is O(log3p), with high probability, independent of the size of the list. Our experiments
show that the relaxed semantics allow the data structure to scale for high thread
counts, comparable to a classic unordered SkipList. Furthermore, we observe that,
for reasonably parallel workloads, the scalability benefits of relaxation considerably
outweigh the additional work due to out-of-order execution.
acknowledgement: "Support is gratefully acknowledged from the National Science Foundation
under grants CCF-1217921, CCF-1301926, and IIS-1447786, the Department of Energy
under grant ER26116/DE-SC0008923, and the Oracle\r\nand 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: Justin
full_name: Kopinsky, Justin
last_name: Kopinsky
- first_name: Jerry
full_name: Li, Jerry
last_name: Li
- first_name: Nir
full_name: Shavit, Nir
last_name: Shavit
citation:
ama: 'Alistarh D-A, Kopinsky J, Li J, Shavit N. The SprayList: A scalable relaxed
priority queue. In: Vol 2015-January. ACM; 2015:11-20. doi:10.1145/2688500.2688523'
apa: 'Alistarh, D.-A., Kopinsky, J., Li, J., & Shavit, N. (2015). The SprayList:
A scalable relaxed priority queue (Vol. 2015–January, pp. 11–20). Presented at
the PPoPP: Principles and Practice of Parallel Pogramming, ACM. https://doi.org/10.1145/2688500.2688523'
chicago: 'Alistarh, Dan-Adrian, Justin Kopinsky, Jerry Li, and Nir Shavit. “The
SprayList: A Scalable Relaxed Priority Queue,” 2015–January:11–20. ACM, 2015.
https://doi.org/10.1145/2688500.2688523.'
ieee: 'D.-A. Alistarh, J. Kopinsky, J. Li, and N. Shavit, “The SprayList: A scalable
relaxed priority queue,” presented at the PPoPP: Principles and Practice of Parallel
Pogramming, 2015, vol. 2015–January, pp. 11–20.'
ista: 'Alistarh D-A, Kopinsky J, Li J, Shavit N. 2015. The SprayList: A scalable
relaxed priority queue. PPoPP: Principles and Practice of Parallel Pogramming
vol. 2015–January, 11–20.'
mla: 'Alistarh, Dan-Adrian, et al. The SprayList: A Scalable Relaxed Priority
Queue. Vol. 2015–January, ACM, 2015, pp. 11–20, doi:10.1145/2688500.2688523.'
short: D.-A. Alistarh, J. Kopinsky, J. Li, N. Shavit, in:, ACM, 2015, pp. 11–20.
conference:
name: 'PPoPP: Principles and Practice of Parallel Pogramming'
date_created: 2018-12-11T11:48:26Z
date_published: 2015-01-24T00:00:00Z
date_updated: 2023-02-23T13:16:43Z
day: '24'
doi: 10.1145/2688500.2688523
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 11 - 20
publication_status: published
publisher: ACM
publist_id: '6878'
status: public
title: 'The SprayList: A scalable relaxed priority queue'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2015-January
year: '2015'
...
---
_id: '7765'
abstract:
- lang: eng
text: 'We introduce a principle unique to disordered solids wherein the contribution
of any bond to one global perturbation is uncorrelated with its contribution to
another. Coupled with sufficient variability in the contributions of different
bonds, this “independent bond-level response” paves the way for the design of
real materials with unusual and exquisitely tuned properties. To illustrate this,
we choose two global perturbations: compression and shear. By applying a bond
removal procedure that is both simple and experimentally relevant to remove a
very small fraction of bonds, we can drive disordered spring networks to both
the incompressible and completely auxetic limits of mechanical behavior.'
article_number: '225501'
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. The principle of independent bond-level response:
Tuning by pruning to exploit disorder for global behavior. Physical Review
Letters. 2015;114(22). doi:10.1103/physrevlett.114.225501'
apa: 'Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2015). The principle of independent
bond-level response: Tuning by pruning to exploit disorder for global behavior.
Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.114.225501'
chicago: 'Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “The Principle
of Independent Bond-Level Response: Tuning by Pruning to Exploit Disorder for
Global Behavior.” Physical Review Letters. American Physical Society, 2015.
https://doi.org/10.1103/physrevlett.114.225501.'
ieee: 'C. P. Goodrich, A. J. Liu, and S. R. Nagel, “The principle of independent
bond-level response: Tuning by pruning to exploit disorder for global behavior,”
Physical Review Letters, vol. 114, no. 22. American Physical Society, 2015.'
ista: 'Goodrich CP, Liu AJ, Nagel SR. 2015. The principle of independent bond-level
response: Tuning by pruning to exploit disorder for global behavior. Physical
Review Letters. 114(22), 225501.'
mla: 'Goodrich, Carl Peter, et al. “The Principle of Independent Bond-Level Response:
Tuning by Pruning to Exploit Disorder for Global Behavior.” Physical Review
Letters, vol. 114, no. 22, 225501, American Physical Society, 2015, doi:10.1103/physrevlett.114.225501.'
short: C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review Letters 114 (2015).
date_created: 2020-04-30T11:41:08Z
date_published: 2015-06-04T00:00:00Z
date_updated: 2021-01-12T08:15:23Z
day: '04'
doi: 10.1103/physrevlett.114.225501
extern: '1'
intvolume: ' 114'
issue: '22'
language:
- iso: eng
month: '06'
oa_version: None
publication: Physical Review Letters
publication_identifier:
issn:
- 0031-9007
- 1079-7114
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: 'The principle of independent bond-level response: Tuning by pruning to exploit
disorder for global behavior'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 114
year: '2015'
...
---
_id: '7767'
abstract:
- lang: eng
text: We present a model of soft active particles that leads to a rich array of
collective behavior found also in dense biological swarms of bacteria and other
unicellular organisms. Our model uses only local interactions, such as Vicsek-type
nearest-neighbor alignment, short-range repulsion, and a local boundary term.
Changing the relative strength of these interactions leads to migrating swarms,
rotating swarms, and jammed swarms, as well as swarms that exhibit run-and-tumble
motion, alternating between migration and either rotating or jammed states. Interestingly,
although a migrating swarm moves slower than an individual particle, the diffusion
constant can be up to three orders of magnitude larger, suggesting that collective
motion can be highly advantageous, for example, when searching for food.
article_number: '032706'
article_processing_charge: No
article_type: original
author:
- first_name: Ruben
full_name: van Drongelen, Ruben
last_name: van Drongelen
- first_name: Anshuman
full_name: Pal, Anshuman
last_name: Pal
- 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: Timon
full_name: Idema, Timon
last_name: Idema
citation:
ama: van Drongelen R, Pal A, Goodrich CP, Idema T. Collective dynamics of soft active
particles. Physical Review E. 2015;91(3). doi:10.1103/physreve.91.032706
apa: van Drongelen, R., Pal, A., Goodrich, C. P., & Idema, T. (2015). Collective
dynamics of soft active particles. Physical Review E. American Physical
Society. https://doi.org/10.1103/physreve.91.032706
chicago: Drongelen, Ruben van, Anshuman Pal, Carl Peter Goodrich, and Timon Idema.
“Collective Dynamics of Soft Active Particles.” Physical Review E. American
Physical Society, 2015. https://doi.org/10.1103/physreve.91.032706.
ieee: R. van Drongelen, A. Pal, C. P. Goodrich, and T. Idema, “Collective dynamics
of soft active particles,” Physical Review E, vol. 91, no. 3. American
Physical Society, 2015.
ista: van Drongelen R, Pal A, Goodrich CP, Idema T. 2015. Collective dynamics of
soft active particles. Physical Review E. 91(3), 032706.
mla: van Drongelen, Ruben, et al. “Collective Dynamics of Soft Active Particles.”
Physical Review E, vol. 91, no. 3, 032706, American Physical Society, 2015,
doi:10.1103/physreve.91.032706.
short: R. van Drongelen, A. Pal, C.P. Goodrich, T. Idema, Physical Review E 91 (2015).
date_created: 2020-04-30T11:41:38Z
date_published: 2015-03-01T00:00:00Z
date_updated: 2021-01-12T08:15:24Z
day: '01'
doi: 10.1103/physreve.91.032706
extern: '1'
intvolume: ' 91'
issue: '3'
language:
- iso: eng
month: '03'
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: Collective dynamics of soft active particles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 91
year: '2015'
...
---
_id: '7766'
abstract:
- lang: eng
text: We study the vibrational properties near a free surface of disordered spring
networks derived from jammed sphere packings. In bulk systems, without surfaces,
it is well understood that such systems have a plateau in the density of vibrational
modes extending down to a frequency scale ω*. This frequency is controlled by
ΔZ = 〈Z〉 − 2d, the difference between the average coordination of the spheres
and twice the spatial dimension, d, of the system, which vanishes at the jamming
transition. In the presence of a free surface we find that there is a density
of disordered vibrational modes associated with the surface that extends far below
ω*. The total number of these low-frequency surface modes is controlled by ΔZ,
and the profile of their decay into the bulk has two characteristic length scales,
which diverge as ΔZ−1/2 and ΔZ−1 as the jamming transition is approached.
article_processing_charge: No
article_type: original
author:
- first_name: Daniel M.
full_name: Sussman, Daniel M.
last_name: Sussman
- 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: Sussman DM, Goodrich CP, Liu AJ, Nagel SR. Disordered surface vibrations in
jammed sphere packings. Soft Matter. 2015;11(14):2745-2751. doi:10.1039/c4sm02905d
apa: Sussman, D. M., Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2015). Disordered
surface vibrations in jammed sphere packings. Soft Matter. Royal Society
of Chemistry. https://doi.org/10.1039/c4sm02905d
chicago: Sussman, Daniel M., Carl Peter Goodrich, Andrea J. Liu, and Sidney R. Nagel.
“Disordered Surface Vibrations in Jammed Sphere Packings.” Soft Matter.
Royal Society of Chemistry, 2015. https://doi.org/10.1039/c4sm02905d.
ieee: D. M. Sussman, C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Disordered surface
vibrations in jammed sphere packings,” Soft Matter, vol. 11, no. 14. Royal
Society of Chemistry, pp. 2745–2751, 2015.
ista: Sussman DM, Goodrich CP, Liu AJ, Nagel SR. 2015. Disordered surface vibrations
in jammed sphere packings. Soft Matter. 11(14), 2745–2751.
mla: Sussman, Daniel M., et al. “Disordered Surface Vibrations in Jammed Sphere
Packings.” Soft Matter, vol. 11, no. 14, Royal Society of Chemistry, 2015,
pp. 2745–51, doi:10.1039/c4sm02905d.
short: D.M. Sussman, C.P. Goodrich, A.J. Liu, S.R. Nagel, Soft Matter 11 (2015)
2745–2751.
date_created: 2020-04-30T11:41:23Z
date_published: 2015-02-15T00:00:00Z
date_updated: 2021-01-12T08:15:23Z
day: '15'
doi: 10.1039/c4sm02905d
extern: '1'
intvolume: ' 11'
issue: '14'
language:
- iso: eng
month: '02'
oa_version: None
page: 2745-2751
publication: Soft Matter
publication_identifier:
issn:
- 1744-683X
- 1744-6848
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
status: public
title: Disordered surface vibrations in jammed sphere packings
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2015'
...
---
_id: '777'
abstract:
- lang: eng
text: 'In many applications, the data is of rich structure that can be represented
by a hypergraph, where the data items are represented by vertices and the associations
among items are represented by hyperedges. Equivalently, we are given an input
bipartite graph with two types of vertices: items, and associations (which we
refer to as topics). We consider the problem of partitioning the set of items
into a given number of components such that the maximum number of topics covered
by a component is minimized. This is a clustering problem with various applications,
e.g. partitioning of a set of information objects such as documents, images, and
videos, and load balancing in the context of modern computation platforms.Inthis
paper, we focus on the streaming computation model for this problem, in which
items arrive online one at a time and each item must be assigned irrevocably to
a component at its arrival time. Motivated by scalability requirements, we focus
on the class of streaming computation algorithms with memory limited to be at
most linear in the number of components. We show that a greedy assignment strategy
is able to recover a hidden co-clustering of items under a natural set of recovery
conditions. We also report results of an extensive empirical evaluation, which
demonstrate that this greedy strategy yields superior performance when compared
with alternative approaches.'
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: Jennifer
full_name: Iglesias, Jennifer
last_name: Iglesias
- first_name: Milan
full_name: Vojnović, Milan
last_name: Vojnović
citation:
ama: 'Alistarh D-A, Iglesias J, Vojnović M. Streaming min-max hypergraph partitioning.
In: Vol 2015-January. Neural Information Processing Systems; 2015:1900-1908.'
apa: 'Alistarh, D.-A., Iglesias, J., & Vojnović, M. (2015). Streaming min-max
hypergraph partitioning (Vol. 2015–January, pp. 1900–1908). Presented at the NIPS:
Neural Information Processing Systems, Neural Information Processing Systems.'
chicago: Alistarh, Dan-Adrian, Jennifer Iglesias, and Milan Vojnović. “Streaming
Min-Max Hypergraph Partitioning,” 2015–January:1900–1908. Neural Information Processing
Systems, 2015.
ieee: 'D.-A. Alistarh, J. Iglesias, and M. Vojnović, “Streaming min-max hypergraph
partitioning,” presented at the NIPS: Neural Information Processing Systems, 2015,
vol. 2015–January, pp. 1900–1908.'
ista: 'Alistarh D-A, Iglesias J, Vojnović M. 2015. Streaming min-max hypergraph
partitioning. NIPS: Neural Information Processing Systems vol. 2015–January, 1900–1908.'
mla: Alistarh, Dan-Adrian, et al. Streaming Min-Max Hypergraph Partitioning.
Vol. 2015–January, Neural Information Processing Systems, 2015, pp. 1900–08.
short: D.-A. Alistarh, J. Iglesias, M. Vojnović, in:, Neural Information Processing
Systems, 2015, pp. 1900–1908.
conference:
name: 'NIPS: Neural Information Processing Systems'
date_created: 2018-12-11T11:48:27Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2023-02-23T13:17:09Z
day: '01'
extern: '1'
language:
- iso: eng
main_file_link:
- url: http://papers.nips.cc/paper/5897-streaming-min-max-hypergraph-partitioning
month: '01'
oa_version: None
page: 1900 - 1908
publication_status: published
publisher: Neural Information Processing Systems
publist_id: '6879'
status: public
title: Streaming min-max hypergraph partitioning
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2015-January
year: '2015'
...
---
_id: '778'
abstract:
- lang: eng
text: Several Hybrid Transactional Memory (HyTM) schemes have recently been proposed
to complement the fast, but best-effort nature of Hardware Transactional Memory
(HTM) with a slow, reliable software backup. However, the costs of providing concurrency
between hardware and software transactions in HyTM are still not well understood.
In this paper, we propose a general model for HyTM implementations, which captures
the ability of hardware transactions to buffer memory accesses. The model allows
us to formally quantify and analyze the amount of overhead (instrumentation) caused
by the potential presence of software transactions.We prove that (1) it is impossible
to build a strictly serializable HyTM implementation that has both uninstrumented
reads and writes, even for very weak progress guarantees, and (2) the instrumentation
cost incurred by a hardware transaction in any progressive opaque HyTM is linear
in the size of the transaction’s data set.We further describe two implementations
which exhibit optimal instrumentation costs for two different progress conditions.
In sum, this paper proposes the first formal HyTM model and captures for the first
time the trade-off between the degree of hardware-software TM concurrency and
the amount of instrumentation overhead.
acknowledgement: P. Kuznetsov-The author is supported by the Agence Nationale de la
Recherche, ANR-14-CE35-0010-01, project DISCMAT. N. Shavit-Support is gratfeully
acknowledgedfrom the National Science Foundation under grants CCF-1217921, CCF-1201926,
and IIS-1447786, the Department of Energy under grant ER26116/DE-SC0008923, and
the Oracle and Intel corporations.
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: Justin
full_name: Kopinsky, Justin
last_name: Kopinsky
- first_name: Petr
full_name: Kuznetsov, Petr
last_name: Kuznetsov
- first_name: Srivatsan
full_name: Ravi, Srivatsan
last_name: Ravi
- first_name: Nir
full_name: Shavit, Nir
last_name: Shavit
citation:
ama: 'Alistarh D-A, Kopinsky J, Kuznetsov P, Ravi S, Shavit N. Inherent limitations
of hybrid transactional memory. In: Vol 9363. Springer; 2015:185-199. doi:10.1007/978-3-662-48653-5_13'
apa: 'Alistarh, D.-A., Kopinsky, J., Kuznetsov, P., Ravi, S., & Shavit, N. (2015).
Inherent limitations of hybrid transactional memory (Vol. 9363, pp. 185–199).
Presented at the DISC: Distributed Computing, Springer. https://doi.org/10.1007/978-3-662-48653-5_13'
chicago: Alistarh, Dan-Adrian, Justin Kopinsky, Petr Kuznetsov, Srivatsan Ravi,
and Nir Shavit. “Inherent Limitations of Hybrid Transactional Memory,” 9363:185–99.
Springer, 2015. https://doi.org/10.1007/978-3-662-48653-5_13.
ieee: 'D.-A. Alistarh, J. Kopinsky, P. Kuznetsov, S. Ravi, and N. Shavit, “Inherent
limitations of hybrid transactional memory,” presented at the DISC: Distributed
Computing, 2015, vol. 9363, pp. 185–199.'
ista: 'Alistarh D-A, Kopinsky J, Kuznetsov P, Ravi S, Shavit N. 2015. Inherent limitations
of hybrid transactional memory. DISC: Distributed Computing, LNCS, vol. 9363,
185–199.'
mla: Alistarh, Dan-Adrian, et al. Inherent Limitations of Hybrid Transactional
Memory. Vol. 9363, Springer, 2015, pp. 185–99, doi:10.1007/978-3-662-48653-5_13.
short: D.-A. Alistarh, J. Kopinsky, P. Kuznetsov, S. Ravi, N. Shavit, in:, Springer,
2015, pp. 185–199.
conference:
name: 'DISC: Distributed Computing'
date_created: 2018-12-11T11:48:27Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2023-02-23T13:17:35Z
day: '01'
doi: 10.1007/978-3-662-48653-5_13
extern: '1'
external_id:
arxiv:
- '1405.5689'
intvolume: ' 9363'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1405.5689
month: '01'
oa: 1
oa_version: None
page: 185 - 199
publication_status: published
publisher: Springer
publist_id: '6880'
quality_controlled: '1'
status: public
title: Inherent limitations of hybrid transactional memory
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9363
year: '2015'
...
---
_id: '7779'
abstract:
- lang: eng
text: "The fact that a disordered material is not constrained in its properties
in\r\nthe same way as a crystal presents significant and yet largely untapped\r\npotential
for novel material design. However, unlike their crystalline\r\ncounterparts,
disordered solids are not well understood. One of the primary\r\nobstacles is
the lack of a theoretical framework for thinking about disorder\r\nand its relation
to mechanical properties. To this end, we study an idealized\r\nsystem of frictionless
athermal soft spheres that, when compressed, undergoes a\r\njamming phase transition
with diverging length scales and clean power-law\r\nsignatures. This critical
point is the cornerstone of a much larger \"jamming\r\nscenario\" that has the
potential to provide the essential theoretical\r\nfoundation necessary for a unified
understanding of the mechanics of disordered\r\nsolids. We begin by showing that
jammed sphere packings have a valid linear\r\nregime despite the presence of \"contact
nonlinearities.\" We then investigate\r\nthe critical nature of the transition,
focusing on diverging length scales and\r\nfinite-size effects. Next, we argue
that jamming plays the same role for\r\ndisordered solids as the perfect crystal
plays for crystalline solids. Not only\r\ncan it be considered an idealized starting
point for understanding disordered\r\nmaterials, but it can even influence systems
that have a relatively high amount\r\nof crystalline order. The behavior of solids
can thus be thought of as existing\r\non a spectrum, with the perfect crystal
and the jamming transition at opposing\r\nends. Finally, we introduce a new principle
wherein the contribution of an\r\nindividual bond to one global property is independent
of its contribution to\r\nanother. This principle allows the different global
responses of a disordered\r\nsystem to be manipulated independently and provides
a great deal of flexibility\r\nin designing materials with unique, textured and
tunable properties."
article_processing_charge: No
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
citation:
ama: 'Goodrich CP. Unearthing the anticrystal: Criticality in the linear response
of disordered solids. arXiv:151008820. 2015.'
apa: 'Goodrich, C. P. (2015). Unearthing the anticrystal: Criticality in the linear
response of disordered solids. arXiv:1510.08820.'
chicago: 'Goodrich, Carl Peter. “Unearthing the Anticrystal: Criticality in the
Linear Response of Disordered Solids.” ArXiv:1510.08820, 2015.'
ieee: 'C. P. Goodrich, “Unearthing the anticrystal: Criticality in the linear response
of disordered solids,” arXiv:1510.08820. 2015.'
ista: 'Goodrich CP. 2015. Unearthing the anticrystal: Criticality in the linear
response of disordered solids. arXiv:1510.08820, .'
mla: 'Goodrich, Carl Peter. “Unearthing the Anticrystal: Criticality in the Linear
Response of Disordered Solids.” ArXiv:1510.08820, 2015.'
short: C.P. Goodrich, ArXiv:1510.08820 (2015).
date_created: 2020-04-30T12:16:18Z
date_published: 2015-10-29T00:00:00Z
date_updated: 2021-01-12T08:15:28Z
day: '29'
extern: '1'
external_id:
arxiv:
- '1510.08820'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1510.08820
month: '10'
oa: 1
oa_version: Preprint
page: '242'
publication: arXiv:1510.08820
publication_status: published
status: public
title: 'Unearthing the anticrystal: Criticality in the linear response of disordered
solids'
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '779'
abstract:
- lang: eng
text: 'The concurrent memory reclamation problem is that of devising a way for a
deallocating thread to verify that no other concurrent threads hold references
to a memory block being deallocated. To date, in the absence of automatic garbage
collection, there is no satisfactory solution to this problem; existing tracking
methods like hazard pointers, reference counters, or epoch-based techniques like
RCU, are either prohibitively expensive or require significant programming expertise,
to the extent that implementing them efficiently can be worthy of a publication.
None of the existing techniques are automatic or even semi-automated. In this
paper, we take a new approach to concurrent memory reclamation: instead of manually
tracking access to memory locations as done in techniques like hazard pointers,
or restricting shared accesses to specific epoch boundaries as in RCU, our algorithm,
called ThreadScan, leverages operating system signaling to automatically detect
which memory locations are being accessed by concurrent threads. Initial empirical
evidence shows that ThreadScan scales surprisingly well and requires negligible
programming effort beyond the standard use of Malloc and Free.'
acknowledgement: Support is gratefully acknowledged from the National Science Foundation
under grants CCF-1217921, CCF-1301926, and IIS-1447786, the Department of Energy
under grant ER26116/DE-SC0008923, and the Oracle corporation. In particular, we
would like to thank Dave Dice, Alex Kogan, and Mark Moir from the Oracle Scalable
Synchronization Research Group for very useful feedback on earlier drafts of this
paper.
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: Alexander
full_name: Matveev, Alexander
last_name: Matveev
- first_name: William
full_name: Leiserson, William
last_name: Leiserson
- first_name: Nir
full_name: Shavit, Nir
last_name: Shavit
citation:
ama: 'Alistarh D-A, Matveev A, Leiserson W, Shavit N. ThreadScan: Automatic and
scalable memory reclamation. In: Vol 2015-June. ACM; 2015:123-132. doi:10.1145/2755573.2755600'
apa: 'Alistarh, D.-A., Matveev, A., Leiserson, W., & Shavit, N. (2015). ThreadScan:
Automatic and scalable memory reclamation (Vol. 2015–June, pp. 123–132). Presented
at the SPAA: Symposium on Parallelism in Algorithms and Architectures, ACM. https://doi.org/10.1145/2755573.2755600'
chicago: 'Alistarh, Dan-Adrian, Alexander Matveev, William Leiserson, and Nir Shavit.
“ThreadScan: Automatic and Scalable Memory Reclamation,” 2015–June:123–32. ACM,
2015. https://doi.org/10.1145/2755573.2755600.'
ieee: 'D.-A. Alistarh, A. Matveev, W. Leiserson, and N. Shavit, “ThreadScan: Automatic
and scalable memory reclamation,” presented at the SPAA: Symposium on Parallelism
in Algorithms and Architectures, 2015, vol. 2015–June, pp. 123–132.'
ista: 'Alistarh D-A, Matveev A, Leiserson W, Shavit N. 2015. ThreadScan: Automatic
and scalable memory reclamation. SPAA: Symposium on Parallelism in Algorithms
and Architectures vol. 2015–June, 123–132.'
mla: 'Alistarh, Dan-Adrian, et al. ThreadScan: Automatic and Scalable Memory
Reclamation. Vol. 2015–June, ACM, 2015, pp. 123–32, doi:10.1145/2755573.2755600.'
short: D.-A. Alistarh, A. Matveev, W. Leiserson, N. Shavit, in:, ACM, 2015, pp.
123–132.
conference:
name: 'SPAA: Symposium on Parallelism in Algorithms and Architectures'
date_created: 2018-12-11T11:48:27Z
date_published: 2015-06-13T00:00:00Z
date_updated: 2023-02-23T12:35:42Z
day: '13'
doi: 10.1145/2755573.2755600
extern: '1'
language:
- iso: eng
month: '06'
oa_version: None
page: 123 - 132
publication_status: published
publisher: ACM
publist_id: '6876'
related_material:
record:
- id: '6001'
relation: later_version
status: public
status: public
title: 'ThreadScan: Automatic and scalable memory reclamation'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2015-June
year: '2015'
...
---
_id: '780'
abstract:
- lang: eng
text: 'Population protocols are networks of finite-state agents, interacting randomly,
and updating their states using simple rules. Despite their extreme simplicity,
these systems have been shown to cooperatively perform complex computational tasks,
such as simulating register machines to compute standard arithmetic functions.
The election of a unique leader agent is a key requirement in such computational
constructions. Yet, the fastest currently known population protocol for electing
a leader only has linear convergence time, and it has recently been shown that
no population protocol using a constant number of states per node may overcome
this linear bound. In this paper, we give the first population protocol for leader
election with polylogarithmic convergence time, using polylogarithmic memory states
per node. The protocol structure is quite simple: each node has an associated
value, and is either a leader (still in contention) or a minion (following some
leader). A leader keeps incrementing its value and “defeats” other leaders in
one-to-one interactions, and will drop from contention and become a minion if
it meets a leader with higher value. Importantly, a leader also drops out if it
meets a minion with higher absolute value. While these rules are quite simple,
the proof that this algorithm achieves polylogarithmic convergence time is non-trivial.
In particular, the argument combines careful use of concentration inequalities
with anti-concentration bounds, showing that the leaders’ values become spread
apart as the execution progresses, which in turn implies that straggling leaders
get quickly eliminated. We complement our analysis with empirical results, showing
that our protocol converges extremely fast, even for large network sizes.'
acknowledgement: Support is gratefully acknowledged from the National Science Foundation
under grants CCF-1217921, CCF-1301926, and IIS-1447786, the Department of Energy
under grant ER26116/DE-SC0008923, and the Oracle and Intel corporations.”
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: Rati
full_name: Gelashvili, Rati
last_name: Gelashvili
citation:
ama: 'Alistarh D-A, Gelashvili R. Polylogarithmic-time leader election in population
protocols. In: Vol 9135. Springer; 2015:479-491. doi:10.1007/978-3-662-47666-6_38'
apa: 'Alistarh, D.-A., & Gelashvili, R. (2015). Polylogarithmic-time leader
election in population protocols (Vol. 9135, pp. 479–491). Presented at the ICALP:
International Colloquium on Automota, Languages and Programming, Springer. https://doi.org/10.1007/978-3-662-47666-6_38'
chicago: Alistarh, Dan-Adrian, and Rati Gelashvili. “Polylogarithmic-Time Leader
Election in Population Protocols,” 9135:479–91. Springer, 2015. https://doi.org/10.1007/978-3-662-47666-6_38.
ieee: 'D.-A. Alistarh and R. Gelashvili, “Polylogarithmic-time leader election in
population protocols,” presented at the ICALP: International Colloquium on Automota,
Languages and Programming, 2015, vol. 9135, pp. 479–491.'
ista: 'Alistarh D-A, Gelashvili R. 2015. Polylogarithmic-time leader election in
population protocols. ICALP: International Colloquium on Automota, Languages and
Programming vol. 9135, 479–491.'
mla: Alistarh, Dan-Adrian, and Rati Gelashvili. Polylogarithmic-Time Leader Election
in Population Protocols. Vol. 9135, Springer, 2015, pp. 479–91, doi:10.1007/978-3-662-47666-6_38.
short: D.-A. Alistarh, R. Gelashvili, in:, Springer, 2015, pp. 479–491.
conference:
name: 'ICALP: International Colloquium on Automota, Languages and Programming'
date_created: 2018-12-11T11:48:28Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2023-02-23T13:18:11Z
day: '01'
doi: 10.1007/978-3-662-47666-6_38
extern: '1'
external_id:
arxiv:
- '1502.05745'
intvolume: ' 9135'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1502.05745
month: '01'
oa: 1
oa_version: Preprint
page: 479 - 491
publication_status: published
publisher: Springer
publist_id: '6877'
status: public
title: Polylogarithmic-time leader election in population protocols
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9135
year: '2015'
...
---
_id: '781'
abstract:
- lang: eng
text: 'Population protocols, roughly defined as systems consisting of large numbers
of simple identical agents, interacting at random and updating their state following
simple rules, are an important research topic at the intersection of distributed
computing and biology. One of the fundamental tasks that a population protocol
may solve is majority: each node starts in one of two states; the goal is for
all nodes to reach a correct consensus on which of the two states was initially
the majority. Despite considerable research effort, known protocols for this problem
are either exact but slow (taking linear parallel time to converge), or fast but
approximate (with non-zero probability of error). In this paper, we show that
this trade-off between preciasion and speed is not inherent. We present a new
protocol called Average and Conquer (AVC) that solves majority ex-actly in expected
parallel convergence time O(log n/(sε) + log n log s), where n is the number of
nodes, εn is the initial node advantage of the majority state, and s = Ω(log n
log log n) is the number of states the protocol employs. This shows that the majority
problem can be solved exactly in time poly-logarithmic in n, provided that the
memory per node is s = Ω(1/ε + lognlog1/ε). On the negative side, we establish
a lower bound of Ω(1/ε) on the expected paraallel convergence time for the case
of four memory states per node, and a lower bound of Ω(logn) parallel time for
protocols using any number of memory states per node.per node, and a lower bound
of (log n) parallel time for protocols using any number of memory states per node.'
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: Rati
full_name: Gelashvili, Rati
last_name: Gelashvili
- first_name: Milan
full_name: Vojnović, Milan
last_name: Vojnović
citation:
ama: 'Alistarh D-A, Gelashvili R, Vojnović M. Fast and exact majority in population
protocols. In: Vol 2015-July. ACM; 2015:47-56. doi:10.1145/2767386.2767429'
apa: 'Alistarh, D.-A., Gelashvili, R., & Vojnović, M. (2015). Fast and exact
majority in population protocols (Vol. 2015–July, pp. 47–56). Presented at the
PODC: Principles of Distributed Computing, ACM. https://doi.org/10.1145/2767386.2767429'
chicago: Alistarh, Dan-Adrian, Rati Gelashvili, and Milan Vojnović. “Fast and Exact
Majority in Population Protocols,” 2015–July:47–56. ACM, 2015. https://doi.org/10.1145/2767386.2767429.
ieee: 'D.-A. Alistarh, R. Gelashvili, and M. Vojnović, “Fast and exact majority
in population protocols,” presented at the PODC: Principles of Distributed Computing,
2015, vol. 2015–July, pp. 47–56.'
ista: 'Alistarh D-A, Gelashvili R, Vojnović M. 2015. Fast and exact majority in
population protocols. PODC: Principles of Distributed Computing vol. 2015–July,
47–56.'
mla: Alistarh, Dan-Adrian, et al. Fast and Exact Majority in Population Protocols.
Vol. 2015–July, ACM, 2015, pp. 47–56, doi:10.1145/2767386.2767429.
short: D.-A. Alistarh, R. Gelashvili, M. Vojnović, in:, ACM, 2015, pp. 47–56.
conference:
name: 'PODC: Principles of Distributed Computing'
date_created: 2018-12-11T11:48:28Z
date_published: 2015-07-21T00:00:00Z
date_updated: 2023-02-23T13:18:35Z
day: '21'
doi: 10.1145/2767386.2767429
extern: '1'
language:
- iso: eng
month: '07'
oa_version: None
page: 47 - 56
publication_status: published
publisher: ACM
publist_id: '6873'
status: public
title: Fast and exact majority in population protocols
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2015-July
year: '2015'
...
---
_id: '782'
abstract:
- lang: eng
text: 'In this work, we consider the following random process, mo- Tivated by the
analysis of lock-free concurrent algorithms under high memory contention. In each
round, a new scheduling step is allocated to one of n threads, according to a
distribution p = (p1; p2; : : : ; pn), where thread i is scheduled with probability
pi. When some thread first reaches a set threshold of executed steps, it registers
a win, completing its current operation, and resets its step count to 1. At the
same time, threads whose step count was close to the threshold also get reset
because of the win, but to 0 steps, being penalized for almost winning. We are
interested in two questions: how often does some thread complete an operation
(system latency), and how often does a specific thread complete an operation (individual
latency)? We provide asymptotically tight bounds for the system and individual
latency of this general concurrency pattern, for arbitrary scheduling distributions
p. Surprisingly, a sim- ple characterization exists: in expectation, the system
will complete a new operation every Θ(1/p 2) steps, while thread i will complete
a new operation every Θ(1/2=p i ) steps. The proof is interesting in its own right,
as it requires a careful analysis of how the higher norms of the vector p inuence
the thread step counts and latencies in this random process. Our result offers
a simple connection between the scheduling distribution and the average performance
of concurrent algorithms, which has several applications.'
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: Thomas
full_name: Sauerwald, Thomas
last_name: Sauerwald
- first_name: Milan
full_name: Vojnović, Milan
last_name: Vojnović
citation:
ama: 'Alistarh D-A, Sauerwald T, Vojnović M. Lock-Free algorithms under stochastic
schedulers. In: Vol 2015-July. ACM; 2015:251-260. doi:10.1145/2767386.2767430'
apa: 'Alistarh, D.-A., Sauerwald, T., & Vojnović, M. (2015). Lock-Free algorithms
under stochastic schedulers (Vol. 2015–July, pp. 251–260). Presented at the PODC:
Principles of Distributed Computing, ACM. https://doi.org/10.1145/2767386.2767430'
chicago: Alistarh, Dan-Adrian, Thomas Sauerwald, and Milan Vojnović. “Lock-Free
Algorithms under Stochastic Schedulers,” 2015–July:251–60. ACM, 2015. https://doi.org/10.1145/2767386.2767430.
ieee: 'D.-A. Alistarh, T. Sauerwald, and M. Vojnović, “Lock-Free algorithms under
stochastic schedulers,” presented at the PODC: Principles of Distributed Computing,
2015, vol. 2015–July, pp. 251–260.'
ista: 'Alistarh D-A, Sauerwald T, Vojnović M. 2015. Lock-Free algorithms under stochastic
schedulers. PODC: Principles of Distributed Computing vol. 2015–July, 251–260.'
mla: Alistarh, Dan-Adrian, et al. Lock-Free Algorithms under Stochastic Schedulers.
Vol. 2015–July, ACM, 2015, pp. 251–60, doi:10.1145/2767386.2767430.
short: D.-A. Alistarh, T. Sauerwald, M. Vojnović, in:, ACM, 2015, pp. 251–260.
conference:
name: 'PODC: Principles of Distributed Computing'
date_created: 2018-12-11T11:48:28Z
date_published: 2015-07-21T00:00:00Z
date_updated: 2023-02-23T13:18:50Z
day: '21'
doi: 10.1145/2767386.2767430
extern: '1'
language:
- iso: eng
month: '07'
oa_version: None
page: 251 - 260
publication_status: published
publisher: ACM
publist_id: '6874'
status: public
title: Lock-Free algorithms under stochastic schedulers
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2015-July
year: '2015'
...
---
_id: '783'
abstract:
- lang: eng
text: 'The problem of electing a leader from among n contenders is one of the fundamental
questions in distributed computing. In its simplest formulation, the task is as
follows: given n processors, all participants must eventually return a win or
lose indication, such that a single contender may win. Despite a considerable
amount of work on leader election, the following question is still open: can we
elect a leader in an asynchronous fault-prone system faster than just running
a Θ(log n)-time tournament, against a strong adaptive adversary? In this paper,
we answer this question in the affirmative, improving on a decades-old upper bound.
We introduce two new algorithmic ideas to reduce the time complexity of electing
a leader to O(log∗ n), using O(n2) point-to-point messages. A non-trivial application
of our algorithm is a new upper bound for the tight renaming problem, assigning
n items to the n participants in expected O(log2 n) time and O(n2) messages. We
complement our results with lower bound of Ω(n2) messages for solving these two
problems, closing the question of their message complexity.'
acknowledgement: "Support is gratefully acknowledged from the National Science Foundation
under grants CCF-1217921, CCF-1301926,\r\nand IIS-1447786, the Department of
\ Energy under grant\r\nER26116/DE-SC0008923, and the Oracle and Intel corporations.\r\nThe
authors would like to thank Prof. Nir Shavit for ad-\r\nvice and encouragement
during this work, and the anonymous reviewers for their very useful suggestions."
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: Rati
full_name: Gelashvili, Rati
last_name: Gelashvili
- first_name: Adrian
full_name: Vladu, Adrian
last_name: Vladu
citation:
ama: 'Alistarh D-A, Gelashvili R, Vladu A. How to elect a leader faster than a tournament.
In: Vol 2015-July. ACM; 2015:365-374. doi:10.1145/2767386.2767420'
apa: 'Alistarh, D.-A., Gelashvili, R., & Vladu, A. (2015). How to elect a leader
faster than a tournament (Vol. 2015–July, pp. 365–374). Presented at the PODC:
Principles of Distributed Computing, ACM. https://doi.org/10.1145/2767386.2767420'
chicago: Alistarh, Dan-Adrian, Rati Gelashvili, and Adrian Vladu. “How to Elect
a Leader Faster than a Tournament,” 2015–July:365–74. ACM, 2015. https://doi.org/10.1145/2767386.2767420.
ieee: 'D.-A. Alistarh, R. Gelashvili, and A. Vladu, “How to elect a leader faster
than a tournament,” presented at the PODC: Principles of Distributed Computing,
2015, vol. 2015–July, pp. 365–374.'
ista: 'Alistarh D-A, Gelashvili R, Vladu A. 2015. How to elect a leader faster than
a tournament. PODC: Principles of Distributed Computing vol. 2015–July, 365–374.'
mla: Alistarh, Dan-Adrian, et al. How to Elect a Leader Faster than a Tournament.
Vol. 2015–July, ACM, 2015, pp. 365–74, doi:10.1145/2767386.2767420.
short: D.-A. Alistarh, R. Gelashvili, A. Vladu, in:, ACM, 2015, pp. 365–374.
conference:
name: 'PODC: Principles of Distributed Computing'
date_created: 2018-12-11T11:48:28Z
date_published: 2015-07-21T00:00:00Z
date_updated: 2023-02-23T13:18:55Z
day: '21'
doi: 10.1145/2767386.2767420
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1411.1001
month: '07'
oa: 1
oa_version: None
page: 365 - 374
publication_status: published
publisher: ACM
publist_id: '6875'
status: public
title: How to elect a leader faster than a tournament
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2015-July
year: '2015'
...
---
_id: '784'
abstract:
- lang: eng
text: We demonstrate an optical switch design that can scale up to a thousand ports
with high per-port bandwidth (25 Gbps+) and low switching latency (40 ns). Our
design uses a broadcast and select architecture, based on a passive star coupler
and fast tunable transceivers. In addition we employ time division multiplexing
to achieve very low switching latency. Our demo shows the feasibility of the switch
data plane using a small testbed, comprising two transmitters and a receiver,
connected through a star coupler.
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: Hitesh
full_name: Ballani, Hitesh
last_name: Ballani
- first_name: Paolo
full_name: Costa, Paolo
last_name: Costa
- first_name: Adam
full_name: Funnell, Adam
last_name: Funnell
- first_name: Joshua
full_name: Benjamin, Joshua
last_name: Benjamin
- first_name: Philip
full_name: Watts, Philip
last_name: Watts
- first_name: Benn
full_name: Thomsen, Benn
last_name: Thomsen
citation:
ama: 'Alistarh D-A, Ballani H, Costa P, et al. A high-radix, low-latency optical
switch for data centers. In: ACM; 2015:367-368. doi:10.1145/2785956.2790035'
apa: 'Alistarh, D.-A., Ballani, H., Costa, P., Funnell, A., Benjamin, J., Watts,
P., & Thomsen, B. (2015). A high-radix, low-latency optical switch for data
centers (pp. 367–368). Presented at the SIGCOMM: Special Interest Group on Data
Communication, London, United Kindgdom: ACM. https://doi.org/10.1145/2785956.2790035'
chicago: Alistarh, Dan-Adrian, Hitesh Ballani, Paolo Costa, Adam Funnell, Joshua
Benjamin, Philip Watts, and Benn Thomsen. “A High-Radix, Low-Latency Optical Switch
for Data Centers,” 367–68. ACM, 2015. https://doi.org/10.1145/2785956.2790035.
ieee: 'D.-A. Alistarh et al., “A high-radix, low-latency optical switch for
data centers,” presented at the SIGCOMM: Special Interest Group on Data Communication,
London, United Kindgdom, 2015, pp. 367–368.'
ista: 'Alistarh D-A, Ballani H, Costa P, Funnell A, Benjamin J, Watts P, Thomsen
B. 2015. A high-radix, low-latency optical switch for data centers. SIGCOMM: Special
Interest Group on Data Communication, 367–368.'
mla: Alistarh, Dan-Adrian, et al. A High-Radix, Low-Latency Optical Switch for
Data Centers. ACM, 2015, pp. 367–68, doi:10.1145/2785956.2790035.
short: D.-A. Alistarh, H. Ballani, P. Costa, A. Funnell, J. Benjamin, P. Watts,
B. Thomsen, in:, ACM, 2015, pp. 367–368.
conference:
end_date: 2015-08-21
location: London, United Kindgdom
name: 'SIGCOMM: Special Interest Group on Data Communication'
start_date: 2015-08-17
date_created: 2018-12-11T11:48:29Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2023-02-23T13:18:57Z
day: '01'
doi: 10.1145/2785956.2790035
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 367 - 368
publication_identifier:
isbn:
- 978-1-4503-3542-3
publication_status: published
publisher: ACM
publist_id: '6872'
quality_controlled: '1'
status: public
title: A high-radix, low-latency optical switch for data centers
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '802'
abstract:
- lang: eng
text: Glycoinositolphosphoceramides (GIPCs) are complex sphingolipids present at
the plasma membrane of various eukaryotes with the important exception of mammals.
In fungi, these glycosphingolipids commonly contain an alpha-mannose residue (Man)
linked at position 2 of the inositol. However, several pathogenic fungi additionally
synthesize zwitterionic GIPCs carrying an alpha-glucosamine residue (GlcN) at
this position. In the human pathogen Aspergillus fumigatus, the GlcNalpha1,2IPC
core (where IPC is inositolphosphoceramide) is elongated to Manalpha1,3Manalpha1,6GlcNalpha1,2IPC,
which is the most abundant GIPC synthesized by this fungus. In this study, we
identified an A. fumigatus N-acetylglucosaminyltransferase, named GntA, and demonstrate
its involvement in the initiation of zwitterionic GIPC biosynthesis. Targeted
deletion of the gene encoding GntA in A. fumigatus resulted in complete absence
of zwitterionic GIPC; a phenotype that could be reverted by episomal expression
of GntA in the mutant. The N-acetylhexosaminyltransferase activity of GntA was
substantiated by production of N-acetylhexosamine-IPC in the yeast Saccharomyces
cerevisiae upon GntA expression. Using an in vitro assay, GntA was furthermore
shown to use UDP-N-acetylglucosamine as donor substrate to generate a glycolipid
product resistant to saponification and to digestion by phosphatidylinositol-phospholipase
C as expected for GlcNAcalpha1,2IPC. Finally, as the enzymes involved in mannosylation
of IPC, GntA was localized to the Golgi apparatus, the site of IPC synthesis.
author:
- first_name: Jakob
full_name: Engel, Jakob
last_name: Engel
- first_name: Philipp S
full_name: Schmalhorst, Philipp S
id: 309D50DA-F248-11E8-B48F-1D18A9856A87
last_name: Schmalhorst
orcid: 0000-0002-5795-0133
- first_name: Anke
full_name: Kruger, Anke
last_name: Kruger
- first_name: Christina
full_name: Muller, Christina
last_name: Muller
- first_name: Falk
full_name: Buettner, Falk
last_name: Buettner
- first_name: Françoise
full_name: Routier, Françoise
last_name: Routier
citation:
ama: Engel J, Schmalhorst PS, Kruger A, Muller C, Buettner F, Routier F. Characterization
of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic
glycoinositolphosphoceramide biosynthesis. Glycobiology. 2015;25(12):1423-1430.
doi:10.1093/glycob/cwv059
apa: Engel, J., Schmalhorst, P. S., Kruger, A., Muller, C., Buettner, F., &
Routier, F. (2015). Characterization of an N-acetylglucosaminyltransferase involved
in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis.
Glycobiology. Oxford University Press. https://doi.org/10.1093/glycob/cwv059
chicago: Engel, Jakob, Philipp S Schmalhorst, Anke Kruger, Christina Muller, Falk
Buettner, and Françoise Routier. “Characterization of an N-Acetylglucosaminyltransferase
Involved in Aspergillus Fumigatus Zwitterionic Glycoinositolphosphoceramide Biosynthesis.”
Glycobiology. Oxford University Press, 2015. https://doi.org/10.1093/glycob/cwv059.
ieee: J. Engel, P. S. Schmalhorst, A. Kruger, C. Muller, F. Buettner, and F. Routier,
“Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus
fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis,” Glycobiology,
vol. 25, no. 12. Oxford University Press, pp. 1423–1430, 2015.
ista: Engel J, Schmalhorst PS, Kruger A, Muller C, Buettner F, Routier F. 2015.
Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus
fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis. Glycobiology.
25(12), 1423–1430.
mla: Engel, Jakob, et al. “Characterization of an N-Acetylglucosaminyltransferase
Involved in Aspergillus Fumigatus Zwitterionic Glycoinositolphosphoceramide Biosynthesis.”
Glycobiology, vol. 25, no. 12, Oxford University Press, 2015, pp. 1423–30,
doi:10.1093/glycob/cwv059.
short: J. Engel, P.S. Schmalhorst, A. Kruger, C. Muller, F. Buettner, F. Routier,
Glycobiology 25 (2015) 1423–1430.
date_created: 2018-12-11T11:48:35Z
date_published: 2015-12-01T00:00:00Z
date_updated: 2021-01-12T08:16:33Z
day: '01'
department:
- _id: CaHe
doi: 10.1093/glycob/cwv059
external_id:
pmid:
- '26306635'
intvolume: ' 25'
issue: '12'
language:
- iso: eng
month: '12'
oa_version: None
page: 1423 - 1430
pmid: 1
publication: Glycobiology
publication_status: published
publisher: Oxford University Press
publist_id: '6851'
quality_controlled: '1'
scopus_import: 1
status: public
title: Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus
fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2015'
...
---
_id: '815'
abstract:
- lang: eng
text: "The polyprotein Gag is the primary structural component of retroviruses.
Gag consists of independently folded domains connected by flexible linkers. Interactions
between the conserved capsid (CA) domains of Gag mediate formation of hexameric
protein lattices that drive assembly of immature virus particles. Proteolytic
cleavage of Gag by the viral protease (PR) is required for maturation of retroviruses
from an immature form into an infectious form. Within the assembled Gag lattices
of HIV-1 and Mason- Pfizer monkey virus (M-PMV), the C-terminal domain of CA adopts
similar quaternary arrangements, while the N-terminal domain of CA is packed in
very different manners. Here, we have used cryo-electron tomography and subtomogram
averaging to study in vitro-assembled, immature virus-like Rous sarcoma virus
(RSV) Gag particles and have determined the structure of CA and the surrounding
regions to a resolution of ~8 Å. We found that the C-terminal domain of RSV CA
is arranged similarly to HIV-1 and M-PMV, whereas the N-terminal domain of CA
adopts a novel arrangement in which the upstream p10 domain folds back into the
CA lattice. In this position the cleavage site between CA and p10 appears to be
inaccessible to PR. Below CA, an extended density is consistent with the presence
of a six-helix bundle formed by the spacer-peptide region. We have also assessed
the affect of lattice assembly on proteolytic processing by exogenous PR. The
cleavage between p10 and CA is indeed inhibited in the assembled lattice, a finding
consistent with structural regulation of proteolytic maturation.\r\n"
author:
- first_name: Florian
full_name: Schur, Florian
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Robert
full_name: Dick, Robert
last_name: Dick
- first_name: Wim
full_name: Hagen, Wim
last_name: Hagen
- first_name: Volker
full_name: Vogt, Volker
last_name: Vogt
- first_name: John
full_name: Briggs, John
last_name: Briggs
citation:
ama: Schur FK, Dick R, Hagen W, Vogt V, Briggs J. The structure of immature virus
like Rous sarcoma virus gag particles reveals a structural role for the p10 domain
in assembly. Journal of Virology. 2015;89(20):10294-10302. doi:10.1128/JVI.01502-15
apa: Schur, F. K., Dick, R., Hagen, W., Vogt, V., & Briggs, J. (2015). The structure
of immature virus like Rous sarcoma virus gag particles reveals a structural role
for the p10 domain in assembly. Journal of Virology. ASM. https://doi.org/10.1128/JVI.01502-15
chicago: Schur, Florian KM, Robert Dick, Wim Hagen, Volker Vogt, and John Briggs.
“The Structure of Immature Virus like Rous Sarcoma Virus Gag Particles Reveals
a Structural Role for the P10 Domain in Assembly.” Journal of Virology.
ASM, 2015. https://doi.org/10.1128/JVI.01502-15.
ieee: F. K. Schur, R. Dick, W. Hagen, V. Vogt, and J. Briggs, “The structure of
immature virus like Rous sarcoma virus gag particles reveals a structural role
for the p10 domain in assembly,” Journal of Virology, vol. 89, no. 20.
ASM, pp. 10294–10302, 2015.
ista: Schur FK, Dick R, Hagen W, Vogt V, Briggs J. 2015. The structure of immature
virus like Rous sarcoma virus gag particles reveals a structural role for the
p10 domain in assembly. Journal of Virology. 89(20), 10294–10302.
mla: Schur, Florian KM, et al. “The Structure of Immature Virus like Rous Sarcoma
Virus Gag Particles Reveals a Structural Role for the P10 Domain in Assembly.”
Journal of Virology, vol. 89, no. 20, ASM, 2015, pp. 10294–302, doi:10.1128/JVI.01502-15.
short: F.K. Schur, R. Dick, W. Hagen, V. Vogt, J. Briggs, Journal of Virology 89
(2015) 10294–10302.
date_created: 2018-12-11T11:48:39Z
date_published: 2015-09-22T00:00:00Z
date_updated: 2021-01-12T08:17:09Z
day: '22'
doi: 10.1128/JVI.01502-15
extern: '1'
external_id:
pmid:
- '26223638'
intvolume: ' 89'
issue: '20'
language:
- iso: eng
month: '09'
oa_version: None
page: 10294 - 10302
pmid: 1
publication: Journal of Virology
publication_status: published
publisher: ASM
publist_id: '6837'
quality_controlled: '1'
status: public
title: The structure of immature virus like Rous sarcoma virus gag particles reveals
a structural role for the p10 domain in assembly
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 89
year: '2015'
...
---
_id: '814'
abstract:
- lang: eng
text: Human immunodeficiency virus type 1 (HIV-1) assembly proceeds in two stages.
First, the 55 kilodalton viral Gag polyprotein assembles into a hexameric protein
lattice at the plasma membrane of the infected cell, inducing budding and release
of an immature particle. Second, Gag is cleaved by the viral protease, leading
to internal rearrangement of the virus into the mature, infectious form. Immature
and mature HIV-1 particles are heterogeneous in size and morphology, preventing
high-resolution analysis of their protein arrangement in situ by conventional
structural biology methods. Here we apply cryo-electron tomography and sub-tomogram
averaging methods to resolve the structure of the capsid lattice within intact
immature HIV-1 particles at subnanometre resolution, allowing unambiguous positioning
of all α-helices. The resulting model reveals tertiary and quaternary structural
interactions that mediate HIV-1 assembly. Strikingly, these interactions differ
from those predicted by the current model based on in vitro-assembled arrays of
Gag-derived proteins from Mason-Pfizer monkey virus. To validate this difference,
we solve the structure of the capsid lattice within intact immature Mason-Pfizer
monkey virus particles. Comparison with the immature HIV-1 structure reveals that
retroviral capsid proteins, while having conserved tertiary structures, adopt
different quaternary arrangements during virus assembly. The approach demonstrated
here should be applicable to determine structures of other proteins at subnanometre
resolution within heterogeneous environments.
acknowledgement: This study was supported by Deutsche Forschungsgemeinschaft grants
BR 3635/2-1 to J.A.G.B., KR 906/7-1 to H.-G.K. and by Grant Agency of the Czech
Republic 14-15326S to M.R. The Briggs laboratory acknowledges financial support
from the European Molecular Biology Laboratory and from the Chica und Heinz Schaller
Stiftung. We thank B. Glass, M. Anders and S. Mattei for preparation of samples,
and R. Hadravova, K. H. Bui, F. Thommen, M. Schorb, S. Dodonova, S. Glatt, P. Ulbrich
and T. Bharat for technical support and/or discussion. This study was technically
supported by the European Molecular Biology Laboratory IT services unit.
author:
- first_name: Florian
full_name: Florian Schur
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Wim
full_name: Hagen, Wim J
last_name: Hagen
- first_name: Michaela
full_name: Rumlová, Michaela
last_name: Rumlová
- first_name: Tomáš
full_name: Ruml, Tomáš
last_name: Ruml
- first_name: B
full_name: Müller B
last_name: Müller
- first_name: Hans
full_name: Kraüsslich, Hans Georg
last_name: Kraüsslich
- first_name: John
full_name: Briggs, John A
last_name: Briggs
citation:
ama: Schur FK, Hagen W, Rumlová M, et al. Structure of the immature HIV-1 capsid
in intact virus particles at 8.8 Å resolution. Nature. 2015;517(7535):505-508.
doi:10.1038/nature13838
apa: Schur, F. K., Hagen, W., Rumlová, M., Ruml, T., Müller, B., Kraüsslich, H.,
& Briggs, J. (2015). Structure of the immature HIV-1 capsid in intact virus
particles at 8.8 Å resolution. Nature. Nature Publishing Group. https://doi.org/10.1038/nature13838
chicago: Schur, Florian KM, Wim Hagen, Michaela Rumlová, Tomáš Ruml, B Müller, Hans
Kraüsslich, and John Briggs. “Structure of the Immature HIV-1 Capsid in Intact
Virus Particles at 8.8 Å Resolution.” Nature. Nature Publishing Group,
2015. https://doi.org/10.1038/nature13838.
ieee: F. K. Schur et al., “Structure of the immature HIV-1 capsid in intact
virus particles at 8.8 Å resolution,” Nature, vol. 517, no. 7535. Nature
Publishing Group, pp. 505–508, 2015.
ista: Schur FK, Hagen W, Rumlová M, Ruml T, Müller B, Kraüsslich H, Briggs J. 2015.
Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution.
Nature. 517(7535), 505–508.
mla: Schur, Florian KM, et al. “Structure of the Immature HIV-1 Capsid in Intact
Virus Particles at 8.8 Å Resolution.” Nature, vol. 517, no. 7535, Nature
Publishing Group, 2015, pp. 505–08, doi:10.1038/nature13838.
short: F.K. Schur, W. Hagen, M. Rumlová, T. Ruml, B. Müller, H. Kraüsslich, J. Briggs,
Nature 517 (2015) 505–508.
date_created: 2018-12-11T11:48:39Z
date_published: 2015-01-22T00:00:00Z
date_updated: 2021-01-12T08:17:08Z
day: '22'
doi: 10.1038/nature13838
extern: 1
intvolume: ' 517'
issue: '7535'
month: '01'
page: 505 - 508
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6836'
quality_controlled: 0
status: public
title: Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution
type: journal_article
volume: 517
year: '2015'
...
---
_id: '8242'
article_number: AB101
article_processing_charge: No
article_type: original
author:
- first_name: Lukas
full_name: Einhorn, Lukas
last_name: Einhorn
- first_name: Judit
full_name: Fazekas, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas
orcid: 0000-0002-8777-3502
- first_name: Martina
full_name: Muhr, Martina
last_name: Muhr
- first_name: Alexandra
full_name: Schoos, Alexandra
last_name: Schoos
- first_name: Kumiko
full_name: Oida, Kumiko
last_name: Oida
- first_name: Josef
full_name: Singer, Josef
last_name: Singer
- first_name: Lucia
full_name: Panakova, Lucia
last_name: Panakova
- first_name: Krisztina
full_name: Manzano-Szalai, Krisztina
last_name: Manzano-Szalai
- first_name: Erika
full_name: Jensen-Jarolim, Erika
last_name: Jensen-Jarolim
citation:
ama: Einhorn L, Singer J, Muhr M, et al. Generation of recombinant FcεRIα of dog,
cat and horse for component-resolved allergy diagnosis in veterinary patients.
Journal of Allergy and Clinical Immunology. 2015;135(2). doi:10.1016/j.jaci.2014.12.1263
apa: Einhorn, L., Singer, J., Muhr, M., Schoos, A., Oida, K., Singer, J., … Jensen-Jarolim,
E. (2015). Generation of recombinant FcεRIα of dog, cat and horse for component-resolved
allergy diagnosis in veterinary patients. Journal of Allergy and Clinical Immunology.
Elsevier. https://doi.org/10.1016/j.jaci.2014.12.1263
chicago: Einhorn, Lukas, Judit Singer, Martina Muhr, Alexandra Schoos, Kumiko Oida,
Josef Singer, Lucia Panakova, Krisztina Manzano-Szalai, and Erika Jensen-Jarolim.
“Generation of Recombinant FcεRIα of Dog, Cat and Horse for Component-Resolved
Allergy Diagnosis in Veterinary Patients.” Journal of Allergy and Clinical
Immunology. Elsevier, 2015. https://doi.org/10.1016/j.jaci.2014.12.1263.
ieee: L. Einhorn et al., “Generation of recombinant FcεRIα of dog, cat and
horse for component-resolved allergy diagnosis in veterinary patients,” Journal
of Allergy and Clinical Immunology, vol. 135, no. 2. Elsevier, 2015.
ista: Einhorn L, Singer J, Muhr M, Schoos A, Oida K, Singer J, Panakova L, Manzano-Szalai
K, Jensen-Jarolim E. 2015. Generation of recombinant FcεRIα of dog, cat and horse
for component-resolved allergy diagnosis in veterinary patients. Journal of Allergy
and Clinical Immunology. 135(2), AB101.
mla: Einhorn, Lukas, et al. “Generation of Recombinant FcεRIα of Dog, Cat and Horse
for Component-Resolved Allergy Diagnosis in Veterinary Patients.” Journal of
Allergy and Clinical Immunology, vol. 135, no. 2, AB101, Elsevier, 2015, doi:10.1016/j.jaci.2014.12.1263.
short: L. Einhorn, J. Singer, M. Muhr, A. Schoos, K. Oida, J. Singer, L. Panakova,
K. Manzano-Szalai, E. Jensen-Jarolim, Journal of Allergy and Clinical Immunology
135 (2015).
date_created: 2020-08-10T11:54:09Z
date_published: 2015-02-01T00:00:00Z
date_updated: 2021-01-12T08:17:42Z
day: '01'
doi: 10.1016/j.jaci.2014.12.1263
extern: '1'
intvolume: ' 135'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
publication: Journal of Allergy and Clinical Immunology
publication_identifier:
issn:
- 0091-6749
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Generation of recombinant FcεRIα of dog, cat and horse for component-resolved
allergy diagnosis in veterinary patients
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 135
year: '2015'
...
---
_id: '832'
abstract:
- lang: eng
text: Plants maintain capacity to form new organs such as leaves, flowers, lateral
shoots and roots throughout their postembryonic lifetime. Lateral roots (LRs)
originate from a few pericycle cells that acquire attributes of founder cells
(FCs), undergo series of anticlinal divisions, and give rise to a few short initial
cells. After initiation, coordinated cell division and differentiation occur,
giving rise to lateral root primordia (LRP). Primordia continue to grow, emerge
through the cortex and epidermal layers of the primary root, and finally a new
apical meristem is established taking over the responsibility for growth of mature
lateral roots [for detailed description of the individual stages of lateral root
organogenesis see Malamy and Benfey (1997)]. To examine this highly dynamic developmental
process and to investigate a role of various hormonal, genetic and environmental
factors in the regulation of lateral root organogenesis, the real time imaging
based analyses represent extremely powerful tools (Laskowski et al., 2008; De
Smet et al., 2012; Marhavy et al., 2013 and 2014). Herein, we describe a protocol
for real time lateral root primordia (LRP) analysis, which enables the monitoring
of an onset of the specific gene expression and subcellular protein localization
during primordia organogenesis, as well as the evaluation of the impact of genetic
and environmental perturbations on LRP organogenesis.
acknowledgement: "European Research Council with a Starting Independent Research grant:
ERC-2007-Stg-207362-HCPO, Czech Science Foundation: GA13-39982S\nWe thank Matyas
Fendrych for critical reading and comments. The protocol was developed based on
previously published work of De Rybel et al. (2010) and Laskowski et al. (2008). "
author:
- first_name: Peter
full_name: Peter Marhavy
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavy
orcid: 0000-0001-5227-5741
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Marhavý P, Benková E. Real time analysis of lateral root organogenesis in arabidopsis.
Bio-protocol. 2015;5(8). doi:10.21769/BioProtoc.1446
apa: Marhavý, P., & Benková, E. (2015). Real time analysis of lateral root organogenesis
in arabidopsis. Bio-Protocol. Bio-protocol LLC. https://doi.org/10.21769/BioProtoc.1446
chicago: Marhavý, Peter, and Eva Benková. “Real Time Analysis of Lateral Root Organogenesis
in Arabidopsis.” Bio-Protocol. Bio-protocol LLC, 2015. https://doi.org/10.21769/BioProtoc.1446.
ieee: P. Marhavý and E. Benková, “Real time analysis of lateral root organogenesis
in arabidopsis,” Bio-protocol, vol. 5, no. 8. Bio-protocol LLC, 2015.
ista: Marhavý P, Benková E. 2015. Real time analysis of lateral root organogenesis
in arabidopsis. Bio-protocol. 5(8).
mla: Marhavý, Peter, and Eva Benková. “Real Time Analysis of Lateral Root Organogenesis
in Arabidopsis.” Bio-Protocol, vol. 5, no. 8, Bio-protocol LLC, 2015, doi:10.21769/BioProtoc.1446.
short: P. Marhavý, E. Benková, Bio-Protocol 5 (2015).
date_created: 2018-12-11T11:48:44Z
date_published: 2015-04-20T00:00:00Z
date_updated: 2021-01-12T08:18:07Z
day: '20'
doi: 10.21769/BioProtoc.1446
extern: 1
intvolume: ' 5'
issue: '8'
month: '04'
publication: Bio-protocol
publication_status: published
publisher: Bio-protocol LLC
publist_id: '6816'
quality_controlled: 0
status: public
title: Real time analysis of lateral root organogenesis in arabidopsis
type: journal_article
volume: 5
year: '2015'
...
---
_id: '8456'
abstract:
- lang: eng
text: The large majority of three-dimensional structures of biological macromolecules
have been determined by X-ray diffraction of crystalline samples. High-resolution
structure determination crucially depends on the homogeneity of the protein crystal.
Overall ‘rocking’ motion of molecules in the crystal is expected to influence
diffraction quality, and such motion may therefore affect the process of solving
crystal structures. Yet, so far overall molecular motion has not directly been
observed in protein crystals, and the timescale of such dynamics remains unclear.
Here we use solid-state NMR, X-ray diffraction methods and μs-long molecular dynamics
simulations to directly characterize the rigid-body motion of a protein in different
crystal forms. For ubiquitin crystals investigated in this study we determine
the range of possible correlation times of rocking motion, 0.1–100 μs. The amplitude
of rocking varies from one crystal form to another and is correlated with the
resolution obtainable in X-ray diffraction experiments.
article_number: '8361'
article_processing_charge: No
article_type: original
author:
- first_name: Peixiang
full_name: Ma, Peixiang
last_name: Ma
- first_name: Yi
full_name: Xue, Yi
last_name: Xue
- first_name: Nicolas
full_name: Coquelle, Nicolas
last_name: Coquelle
- first_name: Jens D.
full_name: Haller, Jens D.
last_name: Haller
- first_name: Tairan
full_name: Yuwen, Tairan
last_name: Yuwen
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Oleg
full_name: Mikhailovskii, Oleg
last_name: Mikhailovskii
- first_name: Dieter
full_name: Willbold, Dieter
last_name: Willbold
- first_name: Jacques-Philippe
full_name: Colletier, Jacques-Philippe
last_name: Colletier
- first_name: Nikolai R.
full_name: Skrynnikov, Nikolai R.
last_name: Skrynnikov
- 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, Xue Y, Coquelle N, et al. Observing the overall rocking motion of a protein
in a crystal. Nature Communications. 2015;6. doi:10.1038/ncomms9361
apa: Ma, P., Xue, Y., Coquelle, N., Haller, J. D., Yuwen, T., Ayala, I., … Schanda,
P. (2015). Observing the overall rocking motion of a protein in a crystal. Nature
Communications. Springer Nature. https://doi.org/10.1038/ncomms9361
chicago: Ma, Peixiang, Yi Xue, Nicolas Coquelle, Jens D. Haller, Tairan Yuwen, Isabel
Ayala, Oleg Mikhailovskii, et al. “Observing the Overall Rocking Motion of a Protein
in a Crystal.” Nature Communications. Springer Nature, 2015. https://doi.org/10.1038/ncomms9361.
ieee: P. Ma et al., “Observing the overall rocking motion of a protein in
a crystal,” Nature Communications, vol. 6. Springer Nature, 2015.
ista: Ma P, Xue Y, Coquelle N, Haller JD, Yuwen T, Ayala I, Mikhailovskii O, Willbold
D, Colletier J-P, Skrynnikov NR, Schanda P. 2015. Observing the overall rocking
motion of a protein in a crystal. Nature Communications. 6, 8361.
mla: Ma, Peixiang, et al. “Observing the Overall Rocking Motion of a Protein in
a Crystal.” Nature Communications, vol. 6, 8361, Springer Nature, 2015,
doi:10.1038/ncomms9361.
short: P. Ma, Y. Xue, N. Coquelle, J.D. Haller, T. Yuwen, I. Ayala, O. Mikhailovskii,
D. Willbold, J.-P. Colletier, N.R. Skrynnikov, P. Schanda, Nature Communications
6 (2015).
date_created: 2020-09-18T10:07:36Z
date_published: 2015-10-05T00:00:00Z
date_updated: 2021-01-12T08:19:24Z
day: '05'
doi: 10.1038/ncomms9361
extern: '1'
intvolume: ' 6'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Physics and Astronomy
- General Chemistry
language:
- iso: eng
month: '10'
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Observing the overall rocking motion of a protein in a crystal
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2015'
...
---
_id: '8457'
abstract:
- lang: eng
text: We review recent advances in methodologies to study microseconds‐to‐milliseconds
exchange processes in biological molecules using magic‐angle spinning solid‐state
nuclear magnetic resonance (MAS ssNMR) spectroscopy. The particularities of MAS
ssNMR, as compared to solution‐state NMR, are elucidated using numerical simulations
and experimental data. These simulations reveal the potential of MAS NMR to provide
detailed insight into short‐lived conformations of biological molecules. Recent
studies of conformational exchange dynamics in microcrystalline ubiquitin are
discussed.
article_processing_charge: No
article_type: original
author:
- first_name: Peixiang
full_name: Ma, Peixiang
last_name: Ma
- 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, Schanda P. Conformational exchange processes in biological systems:
Detection by solid-state NMR. eMagRes. 2015;4(3):699-708. doi:10.1002/9780470034590.emrstm1418'
apa: 'Ma, P., & Schanda, P. (2015). Conformational exchange processes in biological
systems: Detection by solid-state NMR. EMagRes. Wiley. https://doi.org/10.1002/9780470034590.emrstm1418'
chicago: 'Ma, Peixiang, and Paul Schanda. “Conformational Exchange Processes in
Biological Systems: Detection by Solid-State NMR.” EMagRes. Wiley, 2015.
https://doi.org/10.1002/9780470034590.emrstm1418.'
ieee: 'P. Ma and P. Schanda, “Conformational exchange processes in biological systems:
Detection by solid-state NMR,” eMagRes, vol. 4, no. 3. Wiley, pp. 699–708,
2015.'
ista: 'Ma P, Schanda P. 2015. Conformational exchange processes in biological systems:
Detection by solid-state NMR. eMagRes. 4(3), 699–708.'
mla: 'Ma, Peixiang, and Paul Schanda. “Conformational Exchange Processes in Biological
Systems: Detection by Solid-State NMR.” EMagRes, vol. 4, no. 3, Wiley,
2015, pp. 699–708, doi:10.1002/9780470034590.emrstm1418.'
short: P. Ma, P. Schanda, EMagRes 4 (2015) 699–708.
date_created: 2020-09-18T10:07:45Z
date_published: 2015-09-10T00:00:00Z
date_updated: 2021-01-12T08:19:24Z
day: '10'
doi: 10.1002/9780470034590.emrstm1418
extern: '1'
intvolume: ' 4'
issue: '3'
language:
- iso: eng
month: '09'
oa_version: None
page: 699-708
publication: eMagRes
publication_identifier:
isbn:
- '9780470034590'
- '9780470058213'
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: 'Conformational exchange processes in biological systems: Detection by solid-state
NMR'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2015'
...
---
_id: '848'
abstract:
- lang: eng
text: The nature of factors governing the tempo and mode of protein evolution is
a fundamental issue in evolutionary biology. Specifically, whether or not interactions
between different sites, or epistasis, are important in directing the course of
evolution became one of the central questions. Several recent reports have scrutinized
patterns of long-term protein evolution claiming them to be compatible only with
an epistatic fitness landscape. However, these claims have not yet been substantiated
with a formal model of protein evolution. Here, we formulate a simple covarion-like
model of protein evolution focusing on the rate at which the fitness impact of
amino acids at a site changes with time. We then apply the model to the data on
convergent and divergent protein evolution to test whether or not the incorporation
of epistatic interactions is necessary to explain the data. We find that convergent
evolution cannot be explained without the incorporation of epistasis and the rate
at which an amino acid state switches from being acceptable at a site to being
deleterious is faster than the rate of amino acid substitution. Specifically,
for proteins that have persisted in modern prokaryotic organisms since the last
universal common ancestor for one amino acid substitution approximately ten amino
acid states switch from being accessible to being deleterious, or vice versa.
Thus, molecular evolution can only be perceived in the context of rapid turnover
of which amino acids are available for evolution.
author:
- first_name: Dinara
full_name: Usmanova, Dinara
last_name: Usmanova
- first_name: Luca
full_name: Ferretti, Luca
last_name: Ferretti
- first_name: Inna
full_name: Povolotskaya, Inna
last_name: Povolotskaya
- first_name: Peter
full_name: Vlasov, Peter
last_name: Vlasov
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Usmanova D, Ferretti L, Povolotskaya I, Vlasov P, Kondrashov F. A model of
substitution trajectories in sequence space and long-term protein evolution. Molecular
Biology and Evolution. 2015;32(2):542-554. doi:10.1093/molbev/msu318
apa: Usmanova, D., Ferretti, L., Povolotskaya, I., Vlasov, P., & Kondrashov,
F. (2015). A model of substitution trajectories in sequence space and long-term
protein evolution. Molecular Biology and Evolution. Oxford University Press.
https://doi.org/10.1093/molbev/msu318
chicago: Usmanova, Dinara, Luca Ferretti, Inna Povolotskaya, Peter Vlasov, and Fyodor
Kondrashov. “A Model of Substitution Trajectories in Sequence Space and Long-Term
Protein Evolution.” Molecular Biology and Evolution. Oxford University
Press, 2015. https://doi.org/10.1093/molbev/msu318.
ieee: D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, and F. Kondrashov, “A
model of substitution trajectories in sequence space and long-term protein evolution,”
Molecular Biology and Evolution, vol. 32, no. 2. Oxford University Press,
pp. 542–554, 2015.
ista: Usmanova D, Ferretti L, Povolotskaya I, Vlasov P, Kondrashov F. 2015. A model
of substitution trajectories in sequence space and long-term protein evolution.
Molecular Biology and Evolution. 32(2), 542–554.
mla: Usmanova, Dinara, et al. “A Model of Substitution Trajectories in Sequence
Space and Long-Term Protein Evolution.” Molecular Biology and Evolution,
vol. 32, no. 2, Oxford University Press, 2015, pp. 542–54, doi:10.1093/molbev/msu318.
short: D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, F. Kondrashov, Molecular
Biology and Evolution 32 (2015) 542–554.
date_created: 2018-12-11T11:48:49Z
date_published: 2015-02-01T00:00:00Z
date_updated: 2021-01-12T08:19:33Z
day: '01'
doi: 10.1093/molbev/msu318
extern: '1'
intvolume: ' 32'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 542 - 554
publication: Molecular Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '6804'
quality_controlled: '1'
status: public
title: A model of substitution trajectories in sequence space and long-term protein
evolution
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2015'
...
---
_id: '8498'
abstract:
- lang: eng
text: "In the present note we announce a proof of a strong form of Arnold diffusion
for smooth convex Hamiltonian systems. Let ${\\mathbb T}^2$ be a 2-dimensional
torus and B2 be the unit ball around the origin in ${\\mathbb R}^2$ . Fix ρ >
0. Our main result says that for a 'generic' time-periodic perturbation of an
integrable system of two degrees of freedom $H_0(p)+\\varepsilon H_1(\\theta,p,t),\\quad
\\ \\theta\\in {\\mathbb T}^2,\\ p\\in B^2,\\ t\\in {\\mathbb T}={\\mathbb R}/{\\mathbb
Z}$ , with a strictly convex H0, there exists a ρ-dense orbit (θε, pε, t)(t) in
${\\mathbb T}^2 \\times B^2 \\times {\\mathbb T}$ , namely, a ρ-neighborhood of
the orbit contains ${\\mathbb T}^2 \\times B^2 \\times {\\mathbb T}$ .\r\n\r\nOur
proof is a combination of geometric and variational methods. The fundamental elements
of the construction are the usage of crumpled normally hyperbolic invariant cylinders
from [9], flower and simple normally hyperbolic invariant manifolds from [36]
as well as their kissing property at a strong double resonance. This allows us
to build a 'connected' net of three-dimensional normally hyperbolic invariant
manifolds. To construct diffusing orbits along this net we employ a version of
the Mather variational method [41] equipped with weak KAM theory [28], proposed
by Bernard in [7]."
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: K
full_name: Zhang, K
last_name: Zhang
citation:
ama: Kaloshin V, Zhang K. Arnold diffusion for smooth convex systems of two and
a half degrees of freedom. Nonlinearity. 2015;28(8):2699-2720. doi:10.1088/0951-7715/28/8/2699
apa: Kaloshin, V., & Zhang, K. (2015). Arnold diffusion for smooth convex systems
of two and a half degrees of freedom. Nonlinearity. IOP Publishing. https://doi.org/10.1088/0951-7715/28/8/2699
chicago: Kaloshin, Vadim, and K Zhang. “Arnold Diffusion for Smooth Convex Systems
of Two and a Half Degrees of Freedom.” Nonlinearity. IOP Publishing, 2015.
https://doi.org/10.1088/0951-7715/28/8/2699.
ieee: V. Kaloshin and K. Zhang, “Arnold diffusion for smooth convex systems of two
and a half degrees of freedom,” Nonlinearity, vol. 28, no. 8. IOP Publishing,
pp. 2699–2720, 2015.
ista: Kaloshin V, Zhang K. 2015. Arnold diffusion for smooth convex systems of two
and a half degrees of freedom. Nonlinearity. 28(8), 2699–2720.
mla: Kaloshin, Vadim, and K. Zhang. “Arnold Diffusion for Smooth Convex Systems
of Two and a Half Degrees of Freedom.” Nonlinearity, vol. 28, no. 8, IOP
Publishing, 2015, pp. 2699–720, doi:10.1088/0951-7715/28/8/2699.
short: V. Kaloshin, K. Zhang, Nonlinearity 28 (2015) 2699–2720.
date_created: 2020-09-18T10:46:43Z
date_published: 2015-06-30T00:00:00Z
date_updated: 2021-01-12T08:19:41Z
day: '30'
doi: 10.1088/0951-7715/28/8/2699
extern: '1'
intvolume: ' 28'
issue: '8'
keyword:
- Mathematical Physics
- General Physics and Astronomy
- Applied Mathematics
- Statistical and Nonlinear Physics
language:
- iso: eng
month: '06'
oa_version: None
page: 2699-2720
publication: Nonlinearity
publication_identifier:
issn:
- 0951-7715
- 1361-6544
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
status: public
title: Arnold diffusion for smooth convex systems of two and a half degrees of freedom
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 28
year: '2015'
...
---
_id: '8499'
abstract:
- lang: eng
text: "We consider the cubic defocusing nonlinear Schrödinger equation in the two
dimensional torus. Fix s>1. Recently Colliander, Keel, Staffilani, Tao and Takaoka
proved the existence of solutions with s-Sobolev norm growing in time.\r\n\r\nWe
establish the existence of solutions with polynomial time estimates. More exactly,
there is c>0 such that for any K≫1 we find a solution u and a time T such that
∥u(T)∥Hs≥K∥u(0)∥Hs. Moreover, the time T satisfies the polynomial bound 0Journal of the European Mathematical Society. 2015;17(1):71-149.
doi:10.4171/jems/499
apa: Guardia, M., & Kaloshin, V. (2015). Growth of Sobolev norms in the cubic
defocusing nonlinear Schrödinger equation. Journal of the European Mathematical
Society. European Mathematical Society Publishing House. https://doi.org/10.4171/jems/499
chicago: Guardia, Marcel, and Vadim Kaloshin. “Growth of Sobolev Norms in the Cubic
Defocusing Nonlinear Schrödinger Equation.” Journal of the European Mathematical
Society. European Mathematical Society Publishing House, 2015. https://doi.org/10.4171/jems/499.
ieee: M. Guardia and V. Kaloshin, “Growth of Sobolev norms in the cubic defocusing
nonlinear Schrödinger equation,” Journal of the European Mathematical Society,
vol. 17, no. 1. European Mathematical Society Publishing House, pp. 71–149, 2015.
ista: Guardia M, Kaloshin V. 2015. Growth of Sobolev norms in the cubic defocusing
nonlinear Schrödinger equation. Journal of the European Mathematical Society.
17(1), 71–149.
mla: Guardia, Marcel, and Vadim Kaloshin. “Growth of Sobolev Norms in the Cubic
Defocusing Nonlinear Schrödinger Equation.” Journal of the European Mathematical
Society, vol. 17, no. 1, European Mathematical Society Publishing House, 2015,
pp. 71–149, doi:10.4171/jems/499.
short: M. Guardia, V. Kaloshin, Journal of the European Mathematical Society 17
(2015) 71–149.
date_created: 2020-09-18T10:46:50Z
date_published: 2015-02-05T00:00:00Z
date_updated: 2021-01-12T08:19:41Z
day: '05'
doi: 10.4171/jems/499
extern: '1'
intvolume: ' 17'
issue: '1'
language:
- iso: eng
month: '02'
oa_version: None
page: 71-149
publication: Journal of the European Mathematical Society
publication_identifier:
issn:
- 1435-9855
publication_status: published
publisher: European Mathematical Society Publishing House
quality_controlled: '1'
status: public
title: Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2015'
...
---
_id: '9057'
abstract:
- lang: eng
text: Motility is a basic feature of living microorganisms, and how it works is
often determined by environmental cues. Recent efforts have focused on developing
artificial systems that can mimic microorganisms, in particular their self-propulsion.
We report on the design and characterization of synthetic self-propelled particles
that migrate upstream, known as positive rheotaxis. This phenomenon results from
a purely physical mechanism involving the interplay between the polarity of the
particles and their alignment by a viscous torque. We show quantitative agreement
between experimental data and a simple model of an overdamped Brownian pendulum.
The model notably predicts the existence of a stagnation point in a diverging
flow. We take advantage of this property to demonstrate that our active particles
can sense and predictably organize in an imposed flow. Our colloidal system represents
an important step toward the realization of biomimetic microsystems with the ability
to sense and respond to environmental changes.
article_number: e1400214
article_processing_charge: No
article_type: original
author:
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
- first_name: Stefano
full_name: Sacanna, Stefano
last_name: Sacanna
- first_name: Anaïs
full_name: Abramian, Anaïs
last_name: Abramian
- first_name: Jérémie
full_name: Barral, Jérémie
last_name: Barral
- first_name: Kasey
full_name: Hanson, Kasey
last_name: Hanson
- first_name: Alexander Y.
full_name: Grosberg, Alexander Y.
last_name: Grosberg
- first_name: David J.
full_name: Pine, David J.
last_name: Pine
- first_name: Paul M.
full_name: Chaikin, Paul M.
last_name: Chaikin
citation:
ama: Palacci JA, Sacanna S, Abramian A, et al. Artificial rheotaxis. Science
Advances. 2015;1(4). doi:10.1126/sciadv.1400214
apa: Palacci, J. A., Sacanna, S., Abramian, A., Barral, J., Hanson, K., Grosberg,
A. Y., … Chaikin, P. M. (2015). Artificial rheotaxis. Science Advances.
American Association for the Advancement of Science . https://doi.org/10.1126/sciadv.1400214
chicago: Palacci, Jérémie A, Stefano Sacanna, Anaïs Abramian, Jérémie Barral, Kasey
Hanson, Alexander Y. Grosberg, David J. Pine, and Paul M. Chaikin. “Artificial
Rheotaxis.” Science Advances. American Association for the Advancement
of Science , 2015. https://doi.org/10.1126/sciadv.1400214.
ieee: J. A. Palacci et al., “Artificial rheotaxis,” Science Advances,
vol. 1, no. 4. American Association for the Advancement of Science , 2015.
ista: Palacci JA, Sacanna S, Abramian A, Barral J, Hanson K, Grosberg AY, Pine DJ,
Chaikin PM. 2015. Artificial rheotaxis. Science Advances. 1(4), e1400214.
mla: Palacci, Jérémie A., et al. “Artificial Rheotaxis.” Science Advances,
vol. 1, no. 4, e1400214, American Association for the Advancement of Science ,
2015, doi:10.1126/sciadv.1400214.
short: J.A. Palacci, S. Sacanna, A. Abramian, J. Barral, K. Hanson, A.Y. Grosberg,
D.J. Pine, P.M. Chaikin, Science Advances 1 (2015).
date_created: 2021-02-02T13:15:02Z
date_published: 2015-05-01T00:00:00Z
date_updated: 2023-02-23T13:47:52Z
day: '01'
ddc:
- '530'
doi: 10.1126/sciadv.1400214
extern: '1'
external_id:
arxiv:
- '1505.05111'
pmid:
- '26601175'
file:
- access_level: open_access
checksum: b97d62433581875c1b85210c5f6ae370
content_type: application/pdf
creator: cziletti
date_created: 2021-02-02T13:22:19Z
date_updated: 2021-02-02T13:22:19Z
file_id: '9058'
file_name: 2015_ScienceAdvances_Palacci.pdf
file_size: 2416780
relation: main_file
success: 1
file_date_updated: 2021-02-02T13:22:19Z
has_accepted_license: '1'
intvolume: ' 1'
issue: '4'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Science Advances
publication_identifier:
issn:
- 2375-2548
publication_status: published
publisher: 'American Association for the Advancement of Science '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Artificial rheotaxis
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 1
year: '2015'
...
---
_id: '906'
abstract:
- lang: eng
text: The origin and evolution of novel biochemical functions remains one of the
key questions in molecular evolution. We study recently emerged methacrylate reductase
function that is thought to have emerged in the last century and reported in Geobacter
sulfurreducens strain AM-1. We report the sequence and study the evolution of
the operon coding for the flavin-containing methacrylate reductase (Mrd) and tetraheme
cytochrome (Mcc) in the genome of G. sulfurreducens AM-1. Different types of signal
peptides in functionally interlinked proteins Mrd and Mcc suggest a possible complex
mechanism of biogenesis for chromoproteids of the methacrylate redox system. The
homologs of the Mrd and Mcc sequence found in δ-Proteobacteria and Deferribacteres
are also organized into an operon and their phylogenetic distribution suggested
that these two genes tend to be horizontally transferred together. Specifically,
the mrd and mcc genes from G. sulfurreducens AM-1 are not monophyletic with any
of the homologs found in other Geobacter genomes. The acquisition of methacrylate
reductase function by G. sulfurreducens AM-1 appears linked to a horizontal gene
transfer event. However, the new function of the products of mrd and mcc may have
evolved either prior or subsequent to their acquisition by G. sulfurreducens AM-1.
acknowledgement: 'Funding: The work has been supported by a grant of the HHMI International
Early Career Scientist Program (55007424), the Spanish Ministry of Economy and Competitiveness
(EUI-EURYIP-2011-4320) as part of the EMBO YIP program, two grants from the Spanish
Ministry of Economy and Competitiveness, "Centro de Excelencia Severo Ochoa 2013–2017
(Sev-2012-0208)" and (BFU2012-31329), the European Union and the European Research
Council under grant agreement 335980_EinME. The funders had no role in study design,
data collection and analysis, decision to publish, or preparation of the manuscript.Our
author Dr., Prof. Akimenko Vasilii K. (1942–2013) passed away during work on the
article. Prof. Akimenko was a leading biochemist in IBPM RAS and active researcher
until last days. A number of his work remains unfinished. We mourn premature care
of Prof. Akimenko Vasilii. We thank Heinz Himmelbauer and the CRG Genomic Unit for
the sequencing.'
author:
- first_name: Oksana
full_name: Arkhipova, Oksana V
last_name: Arkhipova
- first_name: Margarita
full_name: Meer, Margarita V
last_name: Meer
- first_name: Galina
full_name: Mikoulinskaia, Galina V
last_name: Mikoulinskaia
- first_name: Marina
full_name: Zakharova, Marina V
last_name: Zakharova
- first_name: Alexander
full_name: Galushko, Alexander S
last_name: Galushko
- first_name: Vasilii
full_name: Akimenko, Vasilii K
last_name: Akimenko
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Arkhipova O, Meer M, Mikoulinskaia G, et al. Recent origin of the methacrylate
redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer.
PLoS One. 2015;10(5). doi:10.1371/journal.pone.0125888
apa: Arkhipova, O., Meer, M., Mikoulinskaia, G., Zakharova, M., Galushko, A., Akimenko,
V., & Kondrashov, F. (2015). Recent origin of the methacrylate redox system
in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One.
Public Library of Science. https://doi.org/10.1371/journal.pone.0125888
chicago: Arkhipova, Oksana, Margarita Meer, Galina Mikoulinskaia, Marina Zakharova,
Alexander Galushko, Vasilii Akimenko, and Fyodor Kondrashov. “Recent Origin of
the Methacrylate Redox System in Geobacter Sulfurreducens AM-1 through Horizontal
Gene Transfer.” PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0125888.
ieee: O. Arkhipova et al., “Recent origin of the methacrylate redox system
in Geobacter sulfurreducens AM-1 through horizontal gene transfer,” PLoS One,
vol. 10, no. 5. Public Library of Science, 2015.
ista: Arkhipova O, Meer M, Mikoulinskaia G, Zakharova M, Galushko A, Akimenko V,
Kondrashov F. 2015. Recent origin of the methacrylate redox system in Geobacter
sulfurreducens AM-1 through horizontal gene transfer. PLoS One. 10(5).
mla: Arkhipova, Oksana, et al. “Recent Origin of the Methacrylate Redox System in
Geobacter Sulfurreducens AM-1 through Horizontal Gene Transfer.” PLoS One,
vol. 10, no. 5, Public Library of Science, 2015, doi:10.1371/journal.pone.0125888.
short: O. Arkhipova, M. Meer, G. Mikoulinskaia, M. Zakharova, A. Galushko, V. Akimenko,
F. Kondrashov, PLoS One 10 (2015).
date_created: 2018-12-11T11:49:08Z
date_published: 2015-05-11T00:00:00Z
date_updated: 2021-01-12T08:21:48Z
day: '11'
doi: 10.1371/journal.pone.0125888
extern: 1
intvolume: ' 10'
issue: '5'
month: '05'
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '6742'
quality_controlled: 0
status: public
title: Recent origin of the methacrylate redox system in Geobacter sulfurreducens
AM-1 through horizontal gene transfer
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: 10
year: '2015'
...
---
_id: '9141'
abstract:
- lang: eng
text: The breaking of internal tides is believed to provide a large part of the
power needed to mix the abyssal ocean and sustain the meridional overturning circulation.
Both the fraction of internal tide energy that is dissipated locally and the resulting
vertical mixing distribution are crucial for the ocean state, but remain poorly
quantified. Here we present a first worldwide estimate of mixing due to internal
tides generated at small‐scale abyssal hills. Our estimate is based on linear
wave theory, a nonlinear parameterization for wave breaking and uses quasi‐global
small‐scale abyssal hill bathymetry, stratification, and tidal data. We show that
a large fraction of abyssal‐hill generated internal tide energy is locally dissipated
over mid‐ocean ridges in the Southern Hemisphere. Significant dissipation occurs
above ridge crests, and, upon rescaling by the local stratification, follows a
monotonic exponential decay with height off the bottom, with a nonuniform decay
scale. We however show that a substantial part of the dissipation occurs over
the smoother flanks of mid‐ocean ridges, and exhibits a middepth maximum due to
the interplay of wave amplitude with stratification. We link the three‐dimensional
map of dissipation to abyssal hills characteristics, ocean stratification, and
tidal forcing, and discuss its potential implementation in time‐evolving parameterizations
for global climate models. Current tidal parameterizations only account for waves
generated at large‐scale satellite‐resolved bathymetry. Our results suggest that
the presence of small‐scale, mostly unresolved abyssal hills could significantly
enhance the spatial inhomogeneity of tidal mixing, particularly above mid‐ocean
ridges in the Southern Hemisphere.
article_processing_charge: No
article_type: original
author:
- first_name: Adrien
full_name: Lefauve, Adrien
last_name: Lefauve
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
- first_name: Angélique
full_name: Melet, Angélique
last_name: Melet
citation:
ama: 'Lefauve A, Muller CJ, Melet A. A three-dimensional map of tidal dissipation
over abyssal hills. Journal of Geophysical Research: Oceans. 2015;120(7):4760-4777.
doi:10.1002/2014jc010598'
apa: 'Lefauve, A., Muller, C. J., & Melet, A. (2015). A three-dimensional map
of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans.
American Geophysical Union. https://doi.org/10.1002/2014jc010598'
chicago: 'Lefauve, Adrien, Caroline J Muller, and Angélique Melet. “A Three-Dimensional
Map of Tidal Dissipation over Abyssal Hills.” Journal of Geophysical Research:
Oceans. American Geophysical Union, 2015. https://doi.org/10.1002/2014jc010598.'
ieee: 'A. Lefauve, C. J. Muller, and A. Melet, “A three-dimensional map of tidal
dissipation over abyssal hills,” Journal of Geophysical Research: Oceans,
vol. 120, no. 7. American Geophysical Union, pp. 4760–4777, 2015.'
ista: 'Lefauve A, Muller CJ, Melet A. 2015. A three-dimensional map of tidal dissipation
over abyssal hills. Journal of Geophysical Research: Oceans. 120(7), 4760–4777.'
mla: 'Lefauve, Adrien, et al. “A Three-Dimensional Map of Tidal Dissipation over
Abyssal Hills.” Journal of Geophysical Research: Oceans, vol. 120, no.
7, American Geophysical Union, 2015, pp. 4760–77, doi:10.1002/2014jc010598.'
short: 'A. Lefauve, C.J. Muller, A. Melet, Journal of Geophysical Research: Oceans
120 (2015) 4760–4777.'
date_created: 2021-02-15T14:21:49Z
date_published: 2015-06-08T00:00:00Z
date_updated: 2022-01-24T13:45:41Z
day: '08'
doi: 10.1002/2014jc010598
extern: '1'
intvolume: ' 120'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/2014JC010598
month: '06'
oa: 1
oa_version: Published Version
page: 4760-4777
publication: 'Journal of Geophysical Research: Oceans'
publication_identifier:
issn:
- 2169-9275
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
status: public
title: A three-dimensional map of tidal dissipation over abyssal hills
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 120
year: '2015'
...
---
_id: '928'
abstract:
- lang: eng
text: The actomyosin cytoskeleton is a primary force-generating mechanism in morphogenesis,
thus a robust spatial control of cytoskeletal positioning is essential. In this
report, we demonstrate that actomyosin contractility and planar cell polarity
(PCP) interact in post-mitotic Ciona notochord cells to self-assemble and reposition
actomyosin rings, which play an essential role for cell elongation. Intriguingly,
rings always form at the cells′ anterior edge before migrating towards the center
as contractility increases, reflecting a novel dynamical property of the cortex.
Our drug and genetic manipulations uncover a tug-of-war between contractility,
which localizes cortical flows toward the equator and PCP, which tries to reposition
them. We develop a simple model of the physical forces underlying this tug-of-war,
which quantitatively reproduces our results. We thus propose a quantitative framework
for dissecting the relative contribution of contractility and PCP to the self-assembly
and repositioning of cytoskeletal structures, which should be applicable to other
morphogenetic events.
article_number: e09206
author:
- first_name: Ivonne
full_name: Sehring, Ivonne
last_name: Sehring
- first_name: Pierre
full_name: Recho, Pierre
last_name: Recho
- first_name: Elsa
full_name: Denker, Elsa
last_name: Denker
- first_name: Matthew
full_name: Kourakis, Matthew
last_name: Kourakis
- first_name: Birthe
full_name: Mathiesen, Birthe
last_name: Mathiesen
- 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: Bo
full_name: Dong, Bo
last_name: Dong
- first_name: Di
full_name: Jiang, Di
last_name: Jiang
citation:
ama: Sehring I, Recho P, Denker E, et al. Assembly and positioning of actomyosin
rings by contractility and planar cell polarity. eLife. 2015;4. doi:10.7554/eLife.09206
apa: Sehring, I., Recho, P., Denker, E., Kourakis, M., Mathiesen, B., Hannezo, E.
B., … Jiang, D. (2015). Assembly and positioning of actomyosin rings by contractility
and planar cell polarity. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.09206
chicago: Sehring, Ivonne, Pierre Recho, Elsa Denker, Matthew Kourakis, Birthe Mathiesen,
Edouard B Hannezo, Bo Dong, and Di Jiang. “Assembly and Positioning of Actomyosin
Rings by Contractility and Planar Cell Polarity.” ELife. eLife Sciences
Publications, 2015. https://doi.org/10.7554/eLife.09206.
ieee: I. Sehring et al., “Assembly and positioning of actomyosin rings by
contractility and planar cell polarity,” eLife, vol. 4. eLife Sciences
Publications, 2015.
ista: Sehring I, Recho P, Denker E, Kourakis M, Mathiesen B, Hannezo EB, Dong B,
Jiang D. 2015. Assembly and positioning of actomyosin rings by contractility and
planar cell polarity. eLife. 4, e09206.
mla: Sehring, Ivonne, et al. “Assembly and Positioning of Actomyosin Rings by Contractility
and Planar Cell Polarity.” ELife, vol. 4, e09206, eLife Sciences Publications,
2015, doi:10.7554/eLife.09206.
short: I. Sehring, P. Recho, E. Denker, M. Kourakis, B. Mathiesen, E.B. Hannezo,
B. Dong, D. Jiang, ELife 4 (2015).
date_created: 2018-12-11T11:49:15Z
date_published: 2015-10-21T00:00:00Z
date_updated: 2021-01-12T08:21:58Z
day: '21'
ddc:
- '539'
- '570'
doi: 10.7554/eLife.09206
extern: '1'
file:
- access_level: open_access
checksum: 1e4024b3161adcae4a53a0b3dc8a946e
content_type: application/pdf
creator: dernst
date_created: 2018-12-20T15:50:56Z
date_updated: 2020-07-14T12:48:15Z
file_id: '5769'
file_name: 2015_eLife_Sehring.pdf
file_size: 7202224
relation: main_file
file_date_updated: 2020-07-14T12:48:15Z
has_accepted_license: '1'
intvolume: ' 4'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
publist_id: '6512'
quality_controlled: '1'
status: public
title: Assembly and positioning of actomyosin rings by contractility and planar cell
polarity
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: '2015'
...
---
_id: '9575'
abstract:
- lang: eng
text: We give several results showing that different discrete structures typically
gain certain spanning substructures (in particular, Hamilton cycles) after a modest
random perturbation. First, we prove that adding linearly many random edges to
a dense k-uniform hypergraph ensures the (asymptotically almost sure) existence
of a perfect matching or a loose Hamilton cycle. The proof involves an interesting
application of Szemerédi's Regularity Lemma, which might be independently useful.
We next prove that digraphs with certain strong expansion properties are pancyclic,
and use this to show that adding a linear number of random edges typically makes
a dense digraph pancyclic. Finally, we prove that perturbing a certain (minimum-degree-dependent)
number of random edges in a tournament typically ensures the existence of multiple
edge-disjoint Hamilton cycles. All our results are tight.
article_processing_charge: No
article_type: original
author:
- first_name: Michael
full_name: Krivelevich, Michael
last_name: Krivelevich
- 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: Benny
full_name: Sudakov, Benny
last_name: Sudakov
citation:
ama: Krivelevich M, Kwan MA, Sudakov B. Cycles and matchings in randomly perturbed
digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. 2015;49:181-187.
doi:10.1016/j.endm.2015.06.027
apa: Krivelevich, M., Kwan, M. A., & Sudakov, B. (2015). Cycles and matchings
in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete
Mathematics. Elsevier. https://doi.org/10.1016/j.endm.2015.06.027
chicago: Krivelevich, Michael, Matthew Alan Kwan, and Benny Sudakov. “Cycles and
Matchings in Randomly Perturbed Digraphs and Hypergraphs.” Electronic Notes
in Discrete Mathematics. Elsevier, 2015. https://doi.org/10.1016/j.endm.2015.06.027.
ieee: M. Krivelevich, M. A. Kwan, and B. Sudakov, “Cycles and matchings in randomly
perturbed digraphs and hypergraphs,” Electronic Notes in Discrete Mathematics,
vol. 49. Elsevier, pp. 181–187, 2015.
ista: Krivelevich M, Kwan MA, Sudakov B. 2015. Cycles and matchings in randomly
perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics.
49, 181–187.
mla: Krivelevich, Michael, et al. “Cycles and Matchings in Randomly Perturbed Digraphs
and Hypergraphs.” Electronic Notes in Discrete Mathematics, vol. 49, Elsevier,
2015, pp. 181–87, doi:10.1016/j.endm.2015.06.027.
short: M. Krivelevich, M.A. Kwan, B. Sudakov, Electronic Notes in Discrete Mathematics
49 (2015) 181–187.
date_created: 2021-06-21T06:40:34Z
date_published: 2015-11-01T00:00:00Z
date_updated: 2023-02-23T14:01:28Z
day: '01'
doi: 10.1016/j.endm.2015.06.027
extern: '1'
external_id:
arxiv:
- '1501.04816'
intvolume: ' 49'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1501.04816
month: '11'
oa: 1
oa_version: Preprint
page: 181-187
publication: Electronic Notes in Discrete Mathematics
publication_identifier:
issn:
- 1571-0653
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cycles and matchings in randomly perturbed digraphs and hypergraphs
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 49
year: '2015'
...