---
_id: '12987'
abstract:
- lang: eng
text: Chromosomal inversion polymorphisms, segments of chromosomes that are flipped
in orientation and occur in reversed order in some individuals, have long been
recognized to play an important role in local adaptation. They can reduce recombination
in heterozygous individuals and thus help to maintain sets of locally adapted
alleles. In a wide range of organisms, populations adapted to different habitats
differ in frequency of inversion arrangements. However, getting a full understanding
of the importance of inversions for adaptation requires confirmation of their
influence on traits under divergent selection. Here, we studied a marine snail,
Littorina saxatilis, that has evolved ecotypes adapted to wave exposure or crab
predation. These two types occur in close proximity on different parts of the
shore. Gene flow between them exists in contact zones. However, they exhibit strong
phenotypic divergence in several traits under habitat-specific selection, including
size, shape and behaviour. We used crosses between these ecotypes to identify
genomic regions that explain variation in these traits by using QTL analysis and
variance partitioning across linkage groups. We could show that previously detected
inversion regions contribute to adaptive divergence. Some inversions influenced
multiple traits suggesting that they contain sets of locally adaptive alleles.
Our study also identified regions without known inversions that are important
for phenotypic divergence. Thus, we provide a more complete overview of the importance
of inversions in relation to the remaining genome.
article_processing_charge: No
author:
- first_name: Eva
full_name: Koch, Eva
last_name: Koch
- first_name: Hernán E.
full_name: Morales, Hernán E.
last_name: Morales
- first_name: Jenny
full_name: Larsson, Jenny
last_name: Larsson
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Alan R.
full_name: Lemmon, Alan R.
last_name: Lemmon
- first_name: E. Moriarty
full_name: Lemmon, E. Moriarty
last_name: Lemmon
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: 'Koch E, Morales HE, Larsson J, et al. Data from: Genetic variation for adaptive
traits is associated with polymorphic inversions in Littorina saxatilis. 2021.
doi:10.5061/DRYAD.ZGMSBCCB4'
apa: 'Koch, E., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon,
A. R., … Butlin, R. K. (2021). Data from: Genetic variation for adaptive traits
is associated with polymorphic inversions in Littorina saxatilis. Dryad. https://doi.org/10.5061/DRYAD.ZGMSBCCB4'
chicago: 'Koch, Eva, Hernán E. Morales, Jenny Larsson, Anja M Westram, Rui Faria,
Alan R. Lemmon, E. Moriarty Lemmon, Kerstin Johannesson, and Roger K. Butlin.
“Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic
Inversions in Littorina Saxatilis.” Dryad, 2021. https://doi.org/10.5061/DRYAD.ZGMSBCCB4.'
ieee: 'E. Koch et al., “Data from: Genetic variation for adaptive traits
is associated with polymorphic inversions in Littorina saxatilis.” Dryad, 2021.'
ista: 'Koch E, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM,
Johannesson K, Butlin RK. 2021. Data from: Genetic variation for adaptive traits
is associated with polymorphic inversions in Littorina saxatilis, Dryad, 10.5061/DRYAD.ZGMSBCCB4.'
mla: 'Koch, Eva, et al. Data from: Genetic Variation for Adaptive Traits Is Associated
with Polymorphic Inversions in Littorina Saxatilis. Dryad, 2021, doi:10.5061/DRYAD.ZGMSBCCB4.'
short: E. Koch, H.E. Morales, J. Larsson, A.M. Westram, R. Faria, A.R. Lemmon, E.M.
Lemmon, K. Johannesson, R.K. Butlin, (2021).
date_created: 2023-05-16T12:34:09Z
date_published: 2021-04-10T00:00:00Z
date_updated: 2023-08-08T13:34:07Z
day: '10'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.5061/DRYAD.ZGMSBCCB4
has_accepted_license: '1'
license: https://creativecommons.org/publicdomain/zero/1.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.zgmsbccb4
month: '04'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '9394'
relation: used_in_publication
status: public
status: public
title: 'Data from: Genetic variation for adaptive traits is associated with polymorphic
inversions in Littorina saxatilis'
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '9408'
abstract:
- lang: eng
text: We present a computational design system that assists users to model, optimize,
and fabricate quad-robots with soft skins. Our system addresses the challenging
task of predicting their physical behavior by fully integrating the multibody
dynamics of the mechanical skeleton and the elastic behavior of the soft skin.
The developed motion control strategy uses an alternating optimization scheme
to avoid expensive full space time-optimization, interleaving space-time optimization
for the skeleton, and frame-by-frame optimization for the full dynamics. The output
are motor torques to drive the robot to achieve a user prescribed motion trajectory.
We also provide a collection of convenient engineering tools and empirical manufacturing
guidance to support the fabrication of the designed quad-robot. We validate the
feasibility of designs generated with our system through physics simulations and
with a physically-fabricated prototype.
acknowledgement: The authors would like to thank anonymous reviewers for their constructive
comments. Weiwei Xu is partially supported by Zhejiang Lab. Yin Yang is partially
spported by NSF under Grant Nos. CHS 1845024 and 1717972. Weiwei Xu and Hujun Bao
are supported by Fundamental Research Funds for the Central Universities. This project
has received funding from the European Research Council (ERC) under the European
Unions Horizon 2020 research and innovation programme (Grant agreement No 715767).
article_number: 2881-2895
article_processing_charge: No
author:
- first_name: Xudong
full_name: Feng, Xudong
last_name: Feng
- first_name: Jiafeng
full_name: Liu, Jiafeng
last_name: Liu
- first_name: Huamin
full_name: Wang, Huamin
last_name: Wang
- first_name: Yin
full_name: Yang, Yin
last_name: Yang
- first_name: Hujun
full_name: Bao, Hujun
last_name: Bao
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Weiwei
full_name: Xu, Weiwei
last_name: Xu
citation:
ama: Feng X, Liu J, Wang H, et al. Computational design of skinned Quad-Robots.
IEEE Transactions on Visualization and Computer Graphics. 2021;27(6). doi:10.1109/TVCG.2019.2957218
apa: Feng, X., Liu, J., Wang, H., Yang, Y., Bao, H., Bickel, B., & Xu, W. (2021).
Computational design of skinned Quad-Robots. IEEE Transactions on Visualization
and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2019.2957218
chicago: Feng, Xudong, Jiafeng Liu, Huamin Wang, Yin Yang, Hujun Bao, Bernd Bickel,
and Weiwei Xu. “Computational Design of Skinned Quad-Robots.” IEEE Transactions
on Visualization and Computer Graphics. IEEE, 2021. https://doi.org/10.1109/TVCG.2019.2957218.
ieee: X. Feng et al., “Computational design of skinned Quad-Robots,” IEEE
Transactions on Visualization and Computer Graphics, vol. 27, no. 6. IEEE,
2021.
ista: Feng X, Liu J, Wang H, Yang Y, Bao H, Bickel B, Xu W. 2021. Computational
design of skinned Quad-Robots. IEEE Transactions on Visualization and Computer
Graphics. 27(6), 2881–2895.
mla: Feng, Xudong, et al. “Computational Design of Skinned Quad-Robots.” IEEE
Transactions on Visualization and Computer Graphics, vol. 27, no. 6, 2881–2895,
IEEE, 2021, doi:10.1109/TVCG.2019.2957218.
short: X. Feng, J. Liu, H. Wang, Y. Yang, H. Bao, B. Bickel, W. Xu, IEEE Transactions
on Visualization and Computer Graphics 27 (2021).
date_created: 2021-05-23T22:01:42Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2023-08-08T13:45:46Z
day: '01'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1109/TVCG.2019.2957218
ec_funded: 1
external_id:
isi:
- '000649620700009'
pmid:
- '31804937'
file:
- access_level: open_access
checksum: a78e6ac94e33ade4ffaea66943d5f7dc
content_type: application/pdf
creator: kschuh
date_created: 2021-05-25T15:08:49Z
date_updated: 2021-05-25T15:08:49Z
file_id: '9427'
file_name: 2021_TVCG_Feng.pdf
file_size: 6183002
relation: main_file
success: 1
file_date_updated: 2021-05-25T15:08:49Z
has_accepted_license: '1'
intvolume: ' 27'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: IEEE Transactions on Visualization and Computer Graphics
publication_identifier:
eissn:
- '10772626'
issn:
- '19410506'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Computational design of skinned Quad-Robots
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 27
year: '2021'
...
---
_id: '9410'
abstract:
- lang: eng
text: Antibiotic concentrations vary dramatically in the body and the environment.
Hence, understanding the dynamics of resistance evolution along antibiotic concentration
gradients is critical for predicting and slowing the emergence and spread of resistance.
While it has been shown that increasing the concentration of an antibiotic slows
resistance evolution, how adaptation to one antibiotic concentration correlates
with fitness at other points along the gradient has not received much attention.
Here, we selected populations of Escherichia coli at several points along a concentration
gradient for three different antibiotics, asking how rapidly resistance evolved
and whether populations became specialized to the antibiotic concentration they
were selected on. Populations selected at higher concentrations evolved resistance
more slowly but exhibited equal or higher fitness across the whole gradient. Populations
selected at lower concentrations evolved resistance rapidly, but overall fitness
in the presence of antibiotics was lower. However, these populations readily adapted
to higher concentrations upon subsequent selection. Our results indicate that
resistance management strategies must account not only for the rates of resistance
evolution but also for the fitness of evolved strains.
acknowledgement: We would like to thank Martin Ackermann, Camilo Barbosa, Nick Barton,
Jonathan Bollback, Sebastian Bonhoeffer, Nick Colegrave, Calin Guet, Alex Hall,
Sally Otto, Tiago Paixao, Srdjan Sarikas, Hinrich Schulenburg, Marjon de Vos and
Michael Whitlock for insightful support.
article_number: '20200913'
article_processing_charge: No
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Hildegard
full_name: Uecker, Hildegard
id: 2DB8F68A-F248-11E8-B48F-1D18A9856A87
last_name: Uecker
orcid: 0000-0001-9435-2813
- first_name: Paul
full_name: Neve, Paul
last_name: Neve
citation:
ama: Lagator M, Uecker H, Neve P. Adaptation at different points along antibiotic
concentration gradients. Biology letters. 2021;17(5). doi:10.1098/rsbl.2020.0913
apa: Lagator, M., Uecker, H., & Neve, P. (2021). Adaptation at different points
along antibiotic concentration gradients. Biology Letters. Royal Society
of London. https://doi.org/10.1098/rsbl.2020.0913
chicago: Lagator, Mato, Hildegard Uecker, and Paul Neve. “Adaptation at Different
Points along Antibiotic Concentration Gradients.” Biology Letters. Royal
Society of London, 2021. https://doi.org/10.1098/rsbl.2020.0913.
ieee: M. Lagator, H. Uecker, and P. Neve, “Adaptation at different points along
antibiotic concentration gradients,” Biology letters, vol. 17, no. 5. Royal
Society of London, 2021.
ista: Lagator M, Uecker H, Neve P. 2021. Adaptation at different points along antibiotic
concentration gradients. Biology letters. 17(5), 20200913.
mla: Lagator, Mato, et al. “Adaptation at Different Points along Antibiotic Concentration
Gradients.” Biology Letters, vol. 17, no. 5, 20200913, Royal Society of
London, 2021, doi:10.1098/rsbl.2020.0913.
short: M. Lagator, H. Uecker, P. Neve, Biology Letters 17 (2021).
date_created: 2021-05-23T22:01:43Z
date_published: 2021-05-12T00:00:00Z
date_updated: 2023-08-08T13:44:35Z
day: '12'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1098/rsbl.2020.0913
ec_funded: 1
external_id:
isi:
- '000651501400001'
pmid:
- ' 33975485'
file:
- access_level: open_access
checksum: 9c13c1f5af7609c97c741f11d293188a
content_type: application/pdf
creator: kschuh
date_created: 2021-05-25T14:09:03Z
date_updated: 2021-05-25T14:09:03Z
file_id: '9425'
file_name: 2021_BiologyLetters_Lagator.pdf
file_size: 726759
relation: main_file
success: 1
file_date_updated: 2021-05-25T14:09:03Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Biology letters
publication_identifier:
eissn:
- 1744957X
publication_status: published
publisher: Royal Society of London
quality_controlled: '1'
scopus_import: '1'
status: public
title: Adaptation at different points along antibiotic concentration gradients
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 17
year: '2021'
...
---
_id: '9412'
abstract:
- lang: eng
text: We extend our recent result [22] on the central limit theorem for the linear
eigenvalue statistics of non-Hermitian matrices X with independent, identically
distributed complex entries to the real symmetry class. We find that the expectation
and variance substantially differ from their complex counterparts, reflecting
(i) the special spectral symmetry of real matrices onto the real axis; and (ii)
the fact that real i.i.d. matrices have many real eigenvalues. Our result generalizes
the previously known special cases where either the test function is analytic
[49] or the first four moments of the matrix elements match the real Gaussian
[59, 44]. The key element of the proof is the analysis of several weakly dependent
Dyson Brownian motions (DBMs). The conceptual novelty of the real case compared
with [22] is that the correlation structure of the stochastic differentials in
each individual DBM is non-trivial, potentially even jeopardising its well-posedness.
article_number: '24'
article_processing_charge: No
author:
- first_name: Giorgio
full_name: Cipolloni, Giorgio
id: 42198EFA-F248-11E8-B48F-1D18A9856A87
last_name: Cipolloni
orcid: 0000-0002-4901-7992
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Dominik J
full_name: Schröder, Dominik J
id: 408ED176-F248-11E8-B48F-1D18A9856A87
last_name: Schröder
orcid: 0000-0002-2904-1856
citation:
ama: Cipolloni G, Erdös L, Schröder DJ. Fluctuation around the circular law for
random matrices with real entries. Electronic Journal of Probability. 2021;26.
doi:10.1214/21-EJP591
apa: Cipolloni, G., Erdös, L., & Schröder, D. J. (2021). Fluctuation around
the circular law for random matrices with real entries. Electronic Journal
of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/21-EJP591
chicago: Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Fluctuation
around the Circular Law for Random Matrices with Real Entries.” Electronic
Journal of Probability. Institute of Mathematical Statistics, 2021. https://doi.org/10.1214/21-EJP591.
ieee: G. Cipolloni, L. Erdös, and D. J. Schröder, “Fluctuation around the circular
law for random matrices with real entries,” Electronic Journal of Probability,
vol. 26. Institute of Mathematical Statistics, 2021.
ista: Cipolloni G, Erdös L, Schröder DJ. 2021. Fluctuation around the circular law
for random matrices with real entries. Electronic Journal of Probability. 26,
24.
mla: Cipolloni, Giorgio, et al. “Fluctuation around the Circular Law for Random
Matrices with Real Entries.” Electronic Journal of Probability, vol. 26,
24, Institute of Mathematical Statistics, 2021, doi:10.1214/21-EJP591.
short: G. Cipolloni, L. Erdös, D.J. Schröder, Electronic Journal of Probability
26 (2021).
date_created: 2021-05-23T22:01:44Z
date_published: 2021-03-23T00:00:00Z
date_updated: 2023-08-08T13:39:19Z
day: '23'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1214/21-EJP591
ec_funded: 1
external_id:
arxiv:
- '2002.02438'
isi:
- '000641855600001'
file:
- access_level: open_access
checksum: 864ab003ad4cffea783f65aa8c2ba69f
content_type: application/pdf
creator: kschuh
date_created: 2021-05-25T13:24:19Z
date_updated: 2021-05-25T13:24:19Z
file_id: '9423'
file_name: 2021_EJP_Cipolloni.pdf
file_size: 865148
relation: main_file
success: 1
file_date_updated: 2021-05-25T13:24:19Z
has_accepted_license: '1'
intvolume: ' 26'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Electronic Journal of Probability
publication_identifier:
eissn:
- '10836489'
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fluctuation around the circular law for random matrices with real entries
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 26
year: '2021'
...
---
_id: '9407'
abstract:
- lang: eng
text: 'High impact epidemics constitute one of the largest threats humanity is facing
in the 21st century. In the absence of pharmaceutical interventions, physical
distancing together with testing, contact tracing and quarantining are crucial
in slowing down epidemic dynamics. Yet, here we show that if testing capacities
are limited, containment may fail dramatically because such combined countermeasures
drastically change the rules of the epidemic transition: Instead of continuous,
the response to countermeasures becomes discontinuous. Rather than following the
conventional exponential growth, the outbreak that is initially strongly suppressed
eventually accelerates and scales faster than exponential during an explosive
growth period. As a consequence, containment measures either suffice to stop the
outbreak at low total case numbers or fail catastrophically if marginally too
weak, thus implying large uncertainties in reliably estimating overall epidemic
dynamics, both during initial phases and during second wave scenarios.'
acknowledgement: The authors thank Malte Schröder for valuable discussions and creating
the scale-free network topologies. B.H. thanks Mukund Vasudevan for helpful discussion.
The research by M.T. was supported by the Deutsche Forschungsgemeinschaft (DFG,
German Research Foundation) under Germany´s Excellence Strategy–EXC-2068–390729961–Cluster
of Excellence Physics of Life of TU Dresden.
article_number: '2586'
article_processing_charge: No
article_type: original
author:
- first_name: Davide
full_name: Scarselli, Davide
id: 40315C30-F248-11E8-B48F-1D18A9856A87
last_name: Scarselli
orcid: 0000-0001-5227-4271
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
- first_name: Marc
full_name: Timme, Marc
last_name: Timme
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Scarselli D, Budanur NB, Timme M, Hof B. Discontinuous epidemic transition
due to limited testing. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-22725-9
apa: Scarselli, D., Budanur, N. B., Timme, M., & Hof, B. (2021). Discontinuous
epidemic transition due to limited testing. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-021-22725-9
chicago: Scarselli, Davide, Nazmi B Budanur, Marc Timme, and Björn Hof. “Discontinuous
Epidemic Transition Due to Limited Testing.” Nature Communications. Springer
Nature, 2021. https://doi.org/10.1038/s41467-021-22725-9.
ieee: D. Scarselli, N. B. Budanur, M. Timme, and B. Hof, “Discontinuous epidemic
transition due to limited testing,” Nature Communications, vol. 12, no.
1. Springer Nature, 2021.
ista: Scarselli D, Budanur NB, Timme M, Hof B. 2021. Discontinuous epidemic transition
due to limited testing. Nature Communications. 12(1), 2586.
mla: Scarselli, Davide, et al. “Discontinuous Epidemic Transition Due to Limited
Testing.” Nature Communications, vol. 12, no. 1, 2586, Springer Nature,
2021, doi:10.1038/s41467-021-22725-9.
short: D. Scarselli, N.B. Budanur, M. Timme, B. Hof, Nature Communications 12 (2021).
date_created: 2021-05-23T22:01:42Z
date_published: 2021-05-10T00:00:00Z
date_updated: 2023-08-08T13:45:13Z
day: '10'
ddc:
- '570'
department:
- _id: BjHo
doi: 10.1038/s41467-021-22725-9
external_id:
isi:
- '000687305500044'
file:
- access_level: open_access
checksum: fe26c1b8a7da1ae07a6c03f80ff06ea1
content_type: application/pdf
creator: kschuh
date_created: 2021-05-25T14:18:40Z
date_updated: 2021-05-25T14:18:40Z
file_id: '9426'
file_name: 2021_NatureCommunications_Scarselli.pdf
file_size: 1176573
relation: main_file
success: 1
file_date_updated: 2021-05-25T14:18:40Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
eissn:
- '20411723'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/smashing-the-covid-curve/
scopus_import: '1'
status: public
title: Discontinuous epidemic transition due to limited testing
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '9411'
abstract:
- lang: eng
text: The dynamics of a triangular magnetocapillary swimmer is studied using the
lattice Boltzmann method. We extend on our previous work, which deals with the
self-assembly and a specific type of the swimmer motion characterized by the swimmer’s
maximum velocity centred around the particle’s inverse viscous time. Here, we
identify additional regimes of motion. First, modifying the ratio of surface tension
and magnetic forces allows to study the swimmer propagation in the regime of significantly
lower frequencies mainly defined by the strength of the magnetocapillary potential.
Second, introducing a constant magnetic contribution in each of the particles
in addition to their magnetic moment induced by external fields leads to another
regime characterized by strong in-plane swimmer reorientations that resemble experimental
observations.
acknowledgement: This work was financially supported by the DFG Priority Programme
SPP 1726 “Microswimmers–From Single Particle Motion to Collective Behaviour” (HA
4382/5-1). We further acknowledge the Jülich Supercomputing Centre (JSC) and the
High Performance Computing Centre Stuttgart (HLRS) for the allocation of computing
time.
article_number: '59'
article_processing_charge: No
author:
- first_name: Alexander
full_name: Sukhov, Alexander
last_name: Sukhov
- first_name: Maxime
full_name: Hubert, Maxime
last_name: Hubert
- first_name: Galien M
full_name: Grosjean, Galien M
id: 0C5FDA4A-9CF6-11E9-8939-FF05E6697425
last_name: Grosjean
orcid: 0000-0001-5154-417X
- first_name: Oleg
full_name: Trosman, Oleg
last_name: Trosman
- first_name: Sebastian
full_name: Ziegler, Sebastian
last_name: Ziegler
- first_name: Ylona
full_name: Collard, Ylona
last_name: Collard
- first_name: Nicolas
full_name: Vandewalle, Nicolas
last_name: Vandewalle
- first_name: Ana Sunčana
full_name: Smith, Ana Sunčana
last_name: Smith
- first_name: Jens
full_name: Harting, Jens
last_name: Harting
citation:
ama: Sukhov A, Hubert M, Grosjean GM, et al. Regimes of motion of magnetocapillary
swimmers. European Physical Journal E. 2021;44(4). doi:10.1140/epje/s10189-021-00065-2
apa: Sukhov, A., Hubert, M., Grosjean, G. M., Trosman, O., Ziegler, S., Collard,
Y., … Harting, J. (2021). Regimes of motion of magnetocapillary swimmers. European
Physical Journal E. Springer. https://doi.org/10.1140/epje/s10189-021-00065-2
chicago: Sukhov, Alexander, Maxime Hubert, Galien M Grosjean, Oleg Trosman, Sebastian
Ziegler, Ylona Collard, Nicolas Vandewalle, Ana Sunčana Smith, and Jens Harting.
“Regimes of Motion of Magnetocapillary Swimmers.” European Physical Journal
E. Springer, 2021. https://doi.org/10.1140/epje/s10189-021-00065-2.
ieee: A. Sukhov et al., “Regimes of motion of magnetocapillary swimmers,”
European Physical Journal E, vol. 44, no. 4. Springer, 2021.
ista: Sukhov A, Hubert M, Grosjean GM, Trosman O, Ziegler S, Collard Y, Vandewalle
N, Smith AS, Harting J. 2021. Regimes of motion of magnetocapillary swimmers.
European Physical Journal E. 44(4), 59.
mla: Sukhov, Alexander, et al. “Regimes of Motion of Magnetocapillary Swimmers.”
European Physical Journal E, vol. 44, no. 4, 59, Springer, 2021, doi:10.1140/epje/s10189-021-00065-2.
short: A. Sukhov, M. Hubert, G.M. Grosjean, O. Trosman, S. Ziegler, Y. Collard,
N. Vandewalle, A.S. Smith, J. Harting, European Physical Journal E 44 (2021).
date_created: 2021-05-23T22:01:44Z
date_published: 2021-04-24T00:00:00Z
date_updated: 2023-08-08T13:36:28Z
day: '24'
ddc:
- '530'
department:
- _id: ScWa
doi: 10.1140/epje/s10189-021-00065-2
external_id:
isi:
- '000643251300001'
file:
- access_level: open_access
checksum: 0ef342d011afbe3c5cb058fda9a3f395
content_type: application/pdf
creator: kschuh
date_created: 2021-05-25T11:32:14Z
date_updated: 2021-05-25T11:32:14Z
file_id: '9422'
file_name: 2021_EPJE_Sukhov.pdf
file_size: 2507870
relation: main_file
success: 1
file_date_updated: 2021-05-25T11:32:14Z
has_accepted_license: '1'
intvolume: ' 44'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: European Physical Journal E
publication_identifier:
eissn:
- 1292895X
issn:
- '12928941'
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: Regimes of motion of magnetocapillary swimmers
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 44
year: '2021'
...
---
_id: '9414'
abstract:
- lang: eng
text: Microtubule plus-end depolymerization rate is a potentially important target
of physiological regulation, but it has been challenging to measure, so its role
in spatial organization is poorly understood. Here we apply a method for tracking
plus ends based on time difference imaging to measure depolymerization rates in
large interphase asters growing in Xenopus egg extract. We observed strong spatial
regulation of depolymerization rates, which were higher in the aster interior
compared with the periphery, and much less regulation of polymerization or catastrophe
rates. We interpret these data in terms of a limiting component model, where aster
growth results in lower levels of soluble tubulin and microtubule-associated proteins
(MAPs) in the interior cytosol compared with that at the periphery. The steady-state
polymer fraction of tubulin was ∼30%, so tubulin is not strongly depleted in the
aster interior. We propose that the limiting component for microtubule assembly
is a MAP that inhibits depolymerization, and that egg asters are tuned to low
microtubule density.
acknowledgement: The authors thank the members of Mitchison, Brugués, and Jay Gatlin
groups (University of Wyoming) for discussions. We thank Heino Andreas (MPI-CBG)
for frog maintenance. We thank Nikon for microscopy support at Marine Biological
Laboratory (MBL). K.I. was supported by fellowships from the Honjo International
Scholarship Foundation and Center of Systems Biology Dresden. F.D. was supported
by the DIGGS-BB fellowship provided by the German Research Foundation (DFG). P.C.
is supported by a Boehringer Ingelheim Fonds PhD fellowship. J.F.P. was supported
by a fellowship from the Fannie and John Hertz Foundation. M.L.’s research is supported
by European Research Council (ERC) Grant no. ERC-2015-StG-679239. J.B.’s research
is supported by the Human Frontiers Science Program (CDA00074/2014). T.J.M.’s research
is supported by National Institutes of Health Grant no. R35GM131753.
article_processing_charge: No
article_type: original
author:
- first_name: Keisuke
full_name: Ishihara, Keisuke
last_name: Ishihara
- first_name: Franziska
full_name: Decker, Franziska
last_name: Decker
- first_name: Paulo R
full_name: Dos Santos Caldas, Paulo R
id: 38FCDB4C-F248-11E8-B48F-1D18A9856A87
last_name: Dos Santos Caldas
orcid: 0000-0001-6730-4461
- first_name: James F.
full_name: Pelletier, James F.
last_name: Pelletier
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Jan
full_name: Brugués, Jan
last_name: Brugués
- first_name: Timothy J.
full_name: Mitchison, Timothy J.
last_name: Mitchison
citation:
ama: Ishihara K, Decker F, Dos Santos Caldas PR, et al. Spatial variation of microtubule
depolymerization in large asters. Molecular Biology of the Cell. 2021;32(9):869-879.
doi:10.1091/MBC.E20-11-0723
apa: Ishihara, K., Decker, F., Dos Santos Caldas, P. R., Pelletier, J. F., Loose,
M., Brugués, J., & Mitchison, T. J. (2021). Spatial variation of microtubule
depolymerization in large asters. Molecular Biology of the Cell. American
Society for Cell Biology. https://doi.org/10.1091/MBC.E20-11-0723
chicago: Ishihara, Keisuke, Franziska Decker, Paulo R Dos Santos Caldas, James F.
Pelletier, Martin Loose, Jan Brugués, and Timothy J. Mitchison. “Spatial Variation
of Microtubule Depolymerization in Large Asters.” Molecular Biology of the
Cell. American Society for Cell Biology, 2021. https://doi.org/10.1091/MBC.E20-11-0723.
ieee: K. Ishihara et al., “Spatial variation of microtubule depolymerization
in large asters,” Molecular Biology of the Cell, vol. 32, no. 9. American
Society for Cell Biology, pp. 869–879, 2021.
ista: Ishihara K, Decker F, Dos Santos Caldas PR, Pelletier JF, Loose M, Brugués
J, Mitchison TJ. 2021. Spatial variation of microtubule depolymerization in large
asters. Molecular Biology of the Cell. 32(9), 869–879.
mla: Ishihara, Keisuke, et al. “Spatial Variation of Microtubule Depolymerization
in Large Asters.” Molecular Biology of the Cell, vol. 32, no. 9, American
Society for Cell Biology, 2021, pp. 869–79, doi:10.1091/MBC.E20-11-0723.
short: K. Ishihara, F. Decker, P.R. Dos Santos Caldas, J.F. Pelletier, M. Loose,
J. Brugués, T.J. Mitchison, Molecular Biology of the Cell 32 (2021) 869–879.
date_created: 2021-05-23T22:01:45Z
date_published: 2021-04-19T00:00:00Z
date_updated: 2023-08-08T13:36:02Z
day: '19'
department:
- _id: MaLo
doi: 10.1091/MBC.E20-11-0723
ec_funded: 1
external_id:
isi:
- '000641574700005'
intvolume: ' 32'
isi: 1
issue: '9'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/3.0/
main_file_link:
- open_access: '1'
url: https://www.molbiolcell.org/doi/10.1091/mbc.E20-11-0723
month: '04'
oa: 1
oa_version: Published Version
page: 869-879
project:
- _id: 2595697A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '679239'
name: Self-Organization of the Bacterial Cell
- _id: 260D98C8-B435-11E9-9278-68D0E5697425
name: Reconstitution of Bacterial Cell Division Using Purified Components
publication: Molecular Biology of the Cell
publication_identifier:
eissn:
- 1939-4586
issn:
- 1059-1524
publication_status: published
publisher: American Society for Cell Biology
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spatial variation of microtubule depolymerization in large asters
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/3.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA
3.0)
short: CC BY-NC-SA (3.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 32
year: '2021'
...
---
_id: '9356'
abstract:
- lang: eng
text: 'In runtime verification, a monitor watches a trace of a system and, if possible,
decides after observing each finite prefix whether or not the unknown infinite
trace satisfies a given specification. We generalize the theory of runtime verification
to monitors that attempt to estimate numerical values of quantitative trace properties
(instead of attempting to conclude boolean values of trace specifications), such
as maximal or average response time along a trace. Quantitative monitors are approximate:
with every finite prefix, they can improve their estimate of the infinite trace''s
unknown property value. Consequently, quantitative monitors can be compared with
regard to a precision-cost trade-off: better approximations of the property value
require more monitor resources, such as states (in the case of finite-state monitors)
or registers, and additional resources yield better approximations. We introduce
a formal framework for quantitative and approximate monitoring, show how it conservatively
generalizes the classical boolean setting for monitoring, and give several precision-cost
trade-offs for monitors. For example, we prove that there are quantitative properties
for which every additional register improves monitoring precision.'
acknowledgement: We thank the anonymous reviewers for their helpful comments. This
research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23
(Wittgenstein Award).
article_number: '9470547'
article_processing_charge: No
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Naci E
full_name: Sarac, Naci E
id: 8C6B42F8-C8E6-11E9-A03A-F2DCE5697425
last_name: Sarac
citation:
ama: 'Henzinger TA, Sarac NE. Quantitative and approximate monitoring. In: Proceedings
of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. Institute
of Electrical and Electronics Engineers; 2021. doi:10.1109/LICS52264.2021.9470547'
apa: 'Henzinger, T. A., & Sarac, N. E. (2021). Quantitative and approximate
monitoring. In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in
Computer Science. Online: Institute of Electrical and Electronics Engineers.
https://doi.org/10.1109/LICS52264.2021.9470547'
chicago: Henzinger, Thomas A, and Naci E Sarac. “Quantitative and Approximate Monitoring.”
In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science.
Institute of Electrical and Electronics Engineers, 2021. https://doi.org/10.1109/LICS52264.2021.9470547.
ieee: T. A. Henzinger and N. E. Sarac, “Quantitative and approximate monitoring,”
in Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science,
Online, 2021.
ista: 'Henzinger TA, Sarac NE. 2021. Quantitative and approximate monitoring. Proceedings
of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Symposium
on Logic in Computer Science, 9470547.'
mla: Henzinger, Thomas A., and Naci E. Sarac. “Quantitative and Approximate Monitoring.”
Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science,
9470547, Institute of Electrical and Electronics Engineers, 2021, doi:10.1109/LICS52264.2021.9470547.
short: T.A. Henzinger, N.E. Sarac, in:, Proceedings of the 36th Annual ACM/IEEE
Symposium on Logic in Computer Science, Institute of Electrical and Electronics
Engineers, 2021.
conference:
end_date: 2021-07-02
location: Online
name: 'LICS: Symposium on Logic in Computer Science'
start_date: 2021-06-29
date_created: 2021-04-30T17:30:47Z
date_published: 2021-06-29T00:00:00Z
date_updated: 2023-08-08T13:52:56Z
day: '29'
ddc:
- '000'
department:
- _id: GradSch
- _id: ToHe
doi: 10.1109/LICS52264.2021.9470547
external_id:
arxiv:
- '2105.08353'
isi:
- '000947350400021'
file:
- access_level: open_access
checksum: 6e4cba3f72775f479c5b1b75d1a4a0c4
content_type: application/pdf
creator: esarac
date_created: 2021-06-16T08:23:54Z
date_updated: 2021-06-16T08:23:54Z
file_id: '9557'
file_name: qam.pdf
file_size: 641990
relation: main_file
success: 1
file_date_updated: 2021-06-16T08:23:54Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer
Science
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantitative and approximate monitoring
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '9439'
abstract:
- lang: eng
text: The ability to adapt to changes in stimulus statistics is a hallmark of sensory
systems. Here, we developed a theoretical framework that can account for the dynamics
of adaptation from an information processing perspective. We use this framework
to optimize and analyze adaptive sensory codes, and we show that codes optimized
for stationary environments can suffer from prolonged periods of poor performance
when the environment changes. To mitigate the adversarial effects of these environmental
changes, sensory systems must navigate tradeoffs between the ability to accurately
encode incoming stimuli and the ability to rapidly detect and adapt to changes
in the distribution of these stimuli. We derive families of codes that balance
these objectives, and we demonstrate their close match to experimentally observed
neural dynamics during mean and variance adaptation. Our results provide a unifying
perspective on adaptation across a range of sensory systems, environments, and
sensory tasks.
acknowledgement: We thank D. Kastner and T. Münch for generously providing figures
from their work. We also thank V. Jayaraman, M. Noorman, T. Ma, and K. Krishnamurthy
for useful discussions and feedback on the manuscript. W.F.M. was funded by the
European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie
Grant Agreement No. 754411. A.M.H. was supported by the Howard Hughes Medical Institute.
article_processing_charge: No
article_type: original
author:
- first_name: Wiktor F
full_name: Mlynarski, Wiktor F
id: 358A453A-F248-11E8-B48F-1D18A9856A87
last_name: Mlynarski
- first_name: Ann M.
full_name: Hermundstad, Ann M.
last_name: Hermundstad
citation:
ama: Mlynarski WF, Hermundstad AM. Efficient and adaptive sensory codes. Nature
Neuroscience. 2021;24:998-1009. doi:10.1038/s41593-021-00846-0
apa: Mlynarski, W. F., & Hermundstad, A. M. (2021). Efficient and adaptive sensory
codes. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-021-00846-0
chicago: Mlynarski, Wiktor F, and Ann M. Hermundstad. “Efficient and Adaptive Sensory
Codes.” Nature Neuroscience. Springer Nature, 2021. https://doi.org/10.1038/s41593-021-00846-0.
ieee: W. F. Mlynarski and A. M. Hermundstad, “Efficient and adaptive sensory codes,”
Nature Neuroscience, vol. 24. Springer Nature, pp. 998–1009, 2021.
ista: Mlynarski WF, Hermundstad AM. 2021. Efficient and adaptive sensory codes.
Nature Neuroscience. 24, 998–1009.
mla: Mlynarski, Wiktor F., and Ann M. Hermundstad. “Efficient and Adaptive Sensory
Codes.” Nature Neuroscience, vol. 24, Springer Nature, 2021, pp. 998–1009,
doi:10.1038/s41593-021-00846-0.
short: W.F. Mlynarski, A.M. Hermundstad, Nature Neuroscience 24 (2021) 998–1009.
date_created: 2021-05-30T22:01:24Z
date_published: 2021-05-20T00:00:00Z
date_updated: 2023-08-08T13:51:14Z
day: '20'
department:
- _id: GaTk
doi: 10.1038/s41593-021-00846-0
ec_funded: 1
external_id:
isi:
- '000652577300003'
intvolume: ' 24'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'https://doi.org/10.1101/669200 '
month: '05'
oa: 1
oa_version: Preprint
page: 998-1009
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Nature Neuroscience
publication_identifier:
eissn:
- 1546-1726
issn:
- 1097-6256
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Efficient and adaptive sensory codes
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 24
year: '2021'
...
---
_id: '9443'
abstract:
- lang: eng
text: Endoplasmic reticulum–plasma membrane contact sites (ER–PM CS) play fundamental
roles in all eukaryotic cells. Arabidopsis thaliana mutants lacking the ER–PM
protein tether synaptotagmin1 (SYT1) exhibit decreased PM integrity under multiple
abiotic stresses, such as freezing, high salt, osmotic stress, and mechanical
damage. Here, we show that, together with SYT1, the stress-induced SYT3 is an
ER–PM tether that also functions in maintaining PM integrity. The ER–PM CS localization
of SYT1 and SYT3 is dependent on PM phosphatidylinositol-4-phosphate and is regulated
by abiotic stress. Lipidomic analysis revealed that cold stress increased the
accumulation of diacylglycerol at the PM in a syt1/3 double mutant relative to
wild-type while the levels of most glycerolipid species remain unchanged. In addition,
the SYT1-green fluorescent protein fusion preferentially binds diacylglycerol
in vivo with little affinity for polar glycerolipids. Our work uncovers a SYT-dependent
mechanism of stress adaptation counteracting the detrimental accumulation of diacylglycerol
at the PM produced during episodes of abiotic stress.
acknowledgement: "We would also like to thank Lothar Willmitzer for the lipidomic
analysis at the Max Planck Institute of Molecular Plant Physiology (Potsdam, Germany).
We thank Manuela Vega from SCI for her technical assistance in image analysis. We
thank John R. Pearson and the Bionand Nanoimaging Unit, F. David Navas Fernández
and the SCAI Imaging Facility and The Plant Cell Biology facility at the Shanghai
Center for Plant Stress Biology for assistance with confocal microscopy. The FaFAH1
clone was a gift from Iraida Amaya Saavedra (IFAPA-Centro de Churriana, Málaga,
Spain). The AHA3 antibody against the H+-ATPase was a gift from Ramón Serrano Salom
(Instituto de Biología Molecular y Celular de Plantas, Valencia, Spain). The MAP-mTU2-SAC1
construct was provided by Yvon Jaillais (Laboratoire Reproduction et Développement
des Plantes, Univ Lyon, France). The pGWB5 from the pGWB vector series, was provided
by Tsuyoshi Nakagawa (Department of Molecular and Functional Genomics, Shimane University).
We thank Plan Propio from the University of Málaga for financial support.\r\nFunding"
article_processing_charge: No
article_type: original
author:
- first_name: N
full_name: Ruiz-Lopez, N
last_name: Ruiz-Lopez
- first_name: J
full_name: Pérez-Sancho, J
last_name: Pérez-Sancho
- first_name: A
full_name: Esteban Del Valle, A
last_name: Esteban Del Valle
- first_name: RP
full_name: Haslam, RP
last_name: Haslam
- first_name: S
full_name: Vanneste, S
last_name: Vanneste
- first_name: R
full_name: Catalá, R
last_name: Catalá
- first_name: C
full_name: Perea-Resa, C
last_name: Perea-Resa
- first_name: D
full_name: Van Damme, D
last_name: Van Damme
- first_name: S
full_name: García-Hernández, S
last_name: García-Hernández
- first_name: A
full_name: Albert, A
last_name: Albert
- first_name: J
full_name: Vallarino, J
last_name: Vallarino
- first_name: J
full_name: Lin, J
last_name: Lin
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: AP
full_name: Macho, AP
last_name: Macho
- first_name: J
full_name: Salinas, J
last_name: Salinas
- first_name: A
full_name: Rosado, A
last_name: Rosado
- first_name: JA
full_name: Napier, JA
last_name: Napier
- first_name: V
full_name: Amorim-Silva, V
last_name: Amorim-Silva
- first_name: MA
full_name: Botella, MA
last_name: Botella
citation:
ama: Ruiz-Lopez N, Pérez-Sancho J, Esteban Del Valle A, et al. Synaptotagmins at
the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol
homeostasis during abiotic stress. Plant Cell. 2021;33(7):2431-2453. doi:10.1093/plcell/koab122
apa: Ruiz-Lopez, N., Pérez-Sancho, J., Esteban Del Valle, A., Haslam, R., Vanneste,
S., Catalá, R., … Botella, M. (2021). Synaptotagmins at the endoplasmic reticulum-plasma
membrane contact sites maintain diacylglycerol homeostasis during abiotic stress.
Plant Cell. American Society of Plant Biologists. https://doi.org/10.1093/plcell/koab122
chicago: Ruiz-Lopez, N, J Pérez-Sancho, A Esteban Del Valle, RP Haslam, S Vanneste,
R Catalá, C Perea-Resa, et al. “Synaptotagmins at the Endoplasmic Reticulum-Plasma
Membrane Contact Sites Maintain Diacylglycerol Homeostasis during Abiotic Stress.”
Plant Cell. American Society of Plant Biologists, 2021. https://doi.org/10.1093/plcell/koab122.
ieee: N. Ruiz-Lopez et al., “Synaptotagmins at the endoplasmic reticulum-plasma
membrane contact sites maintain diacylglycerol homeostasis during abiotic stress,”
Plant Cell, vol. 33, no. 7. American Society of Plant Biologists, pp. 2431–2453,
2021.
ista: Ruiz-Lopez N, Pérez-Sancho J, Esteban Del Valle A, Haslam R, Vanneste S, Catalá
R, Perea-Resa C, Van Damme D, García-Hernández S, Albert A, Vallarino J, Lin J,
Friml J, Macho A, Salinas J, Rosado A, Napier J, Amorim-Silva V, Botella M. 2021.
Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain
diacylglycerol homeostasis during abiotic stress. Plant Cell. 33(7), 2431–2453.
mla: Ruiz-Lopez, N., et al. “Synaptotagmins at the Endoplasmic Reticulum-Plasma
Membrane Contact Sites Maintain Diacylglycerol Homeostasis during Abiotic Stress.”
Plant Cell, vol. 33, no. 7, American Society of Plant Biologists, 2021,
pp. 2431–53, doi:10.1093/plcell/koab122.
short: N. Ruiz-Lopez, J. Pérez-Sancho, A. Esteban Del Valle, R. Haslam, S. Vanneste,
R. Catalá, C. Perea-Resa, D. Van Damme, S. García-Hernández, A. Albert, J. Vallarino,
J. Lin, J. Friml, A. Macho, J. Salinas, A. Rosado, J. Napier, V. Amorim-Silva,
M. Botella, Plant Cell 33 (2021) 2431–2453.
date_created: 2021-06-02T13:13:58Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2023-08-08T13:54:32Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1093/plcell/koab122
ec_funded: 1
external_id:
isi:
- '000703938100026'
pmid:
- '33944955'
file:
- access_level: open_access
checksum: 22d596678d00310d793611864a6d0fcd
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-14T13:36:38Z
date_updated: 2021-10-14T13:36:38Z
file_id: '10141'
file_name: 2021_PlantCell_RuizLopez.pdf
file_size: 2952028
relation: main_file
success: 1
file_date_updated: 2021-10-14T13:36:38Z
has_accepted_license: '1'
intvolume: ' 33'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 2431-2453
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Plant Cell
publication_identifier:
eissn:
- 1532-298x
issn:
- 1040-4651
publication_status: published
publisher: American Society of Plant Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain
diacylglycerol homeostasis during abiotic stress
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 33
year: '2021'
...
---
_id: '9431'
abstract:
- lang: eng
text: Inositol hexakisphosphate (IP6) is an assembly cofactor for HIV-1. We report
here that IP6 is also used for assembly of Rous sarcoma virus (RSV), a retrovirus
from a different genus. IP6 is ~100-fold more potent at promoting RSV mature capsid
protein (CA) assembly than observed for HIV-1 and removal of IP6 in cells reduces
infectivity by 100-fold. Here, visualized by cryo-electron tomography and subtomogram
averaging, mature capsid-like particles show an IP6-like density in the CA hexamer,
coordinated by rings of six lysines and six arginines. Phosphate and IP6 have
opposing effects on CA in vitro assembly, inducing formation of T = 1 icosahedrons
and tubes, respectively, implying that phosphate promotes pentamer and IP6 hexamer
formation. Subtomogram averaging and classification optimized for analysis of
pleomorphic retrovirus particles reveal that the heterogeneity of mature RSV CA
polyhedrons results from an unexpected, intrinsic CA hexamer flexibility. In contrast,
the CA pentamer forms rigid units organizing the local architecture. These different
features of hexamers and pentamers determine the structural mechanism to form
CA polyhedrons of variable shape in mature RSV particles.
acknowledged_ssus:
- _id: ScienComp
- _id: LifeSc
- _id: EM-Fac
acknowledgement: This work was funded by the National Institute of Allergy and Infectious
Diseases under awards R01AI147890 to R.A.D., R01AI150454 to V.M.V, R35GM136258 in
support of J-P.R.F, and the Austrian Science Fund (FWF) grant P31445 to F.K.M.S.
Access to high-resolution cryo-ET data acquisition at EMBL Heidelberg was supported
by iNEXT (grant no. 653706), funded by the Horizon 2020 program of the European
Union (PID 4246). We thank Wim Hagen and Felix Weis at EMBL Heidelberg for support
in cryo-ET data acquisition. This work made use of the Cornell Center for Materials
Research Shared Facilities, which are supported through the NSF MRSEC program (DMR-179875).
This research was also supported by the Scientific Service Units (SSUs) of IST Austria
through resources provided by Scientific Computing (SciComp), the Life Science Facility
(LSF), and the Electron Microscopy Facility (EMF).
article_number: '3226'
article_processing_charge: No
article_type: original
author:
- first_name: Martin
full_name: Obr, Martin
id: 4741CA5A-F248-11E8-B48F-1D18A9856A87
last_name: Obr
- first_name: Clifton L.
full_name: Ricana, Clifton L.
last_name: Ricana
- first_name: Nadia
full_name: Nikulin, Nadia
last_name: Nikulin
- first_name: Jon-Philip R.
full_name: Feathers, Jon-Philip R.
last_name: Feathers
- first_name: Marco
full_name: Klanschnig, Marco
last_name: Klanschnig
- first_name: Andreas
full_name: Thader, Andreas
id: 3A18A7B8-F248-11E8-B48F-1D18A9856A87
last_name: Thader
- first_name: Marc C.
full_name: Johnson, Marc C.
last_name: Johnson
- first_name: Volker M.
full_name: Vogt, Volker M.
last_name: Vogt
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Robert A.
full_name: Dick, Robert A.
last_name: Dick
citation:
ama: Obr M, Ricana CL, Nikulin N, et al. Structure of the mature Rous sarcoma virus
lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature
Communications. 2021;12(1). doi:10.1038/s41467-021-23506-0
apa: Obr, M., Ricana, C. L., Nikulin, N., Feathers, J.-P. R., Klanschnig, M., Thader,
A., … Dick, R. A. (2021). Structure of the mature Rous sarcoma virus lattice reveals
a role for IP6 in the formation of the capsid hexamer. Nature Communications.
Nature Research. https://doi.org/10.1038/s41467-021-23506-0
chicago: Obr, Martin, Clifton L. Ricana, Nadia Nikulin, Jon-Philip R. Feathers,
Marco Klanschnig, Andreas Thader, Marc C. Johnson, Volker M. Vogt, Florian KM
Schur, and Robert A. Dick. “Structure of the Mature Rous Sarcoma Virus Lattice
Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” Nature Communications.
Nature Research, 2021. https://doi.org/10.1038/s41467-021-23506-0.
ieee: M. Obr et al., “Structure of the mature Rous sarcoma virus lattice
reveals a role for IP6 in the formation of the capsid hexamer,” Nature Communications,
vol. 12, no. 1. Nature Research, 2021.
ista: Obr M, Ricana CL, Nikulin N, Feathers J-PR, Klanschnig M, Thader A, Johnson
MC, Vogt VM, Schur FK, Dick RA. 2021. Structure of the mature Rous sarcoma virus
lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature
Communications. 12(1), 3226.
mla: Obr, Martin, et al. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals
a Role for IP6 in the Formation of the Capsid Hexamer.” Nature Communications,
vol. 12, no. 1, 3226, Nature Research, 2021, doi:10.1038/s41467-021-23506-0.
short: M. Obr, C.L. Ricana, N. Nikulin, J.-P.R. Feathers, M. Klanschnig, A. Thader,
M.C. Johnson, V.M. Vogt, F.K. Schur, R.A. Dick, Nature Communications 12 (2021).
date_created: 2021-05-28T14:25:50Z
date_published: 2021-05-28T00:00:00Z
date_updated: 2023-08-08T13:53:53Z
day: '28'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.1038/s41467-021-23506-0
external_id:
isi:
- '000659145000011'
file:
- access_level: open_access
checksum: 53ccc53d09a9111143839dbe7784e663
content_type: application/pdf
creator: kschuh
date_created: 2021-06-09T15:21:14Z
date_updated: 2021-06-09T15:21:14Z
file_id: '9538'
file_name: 2021_NatureCommunications_Obr.pdf
file_size: 6166295
relation: main_file
success: 1
file_date_updated: 2021-06-09T15:21:14Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Physics and Astronomy
- General Chemistry
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 26736D6A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31445
name: Structural conservation and diversity in retroviral capsid
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Nature Research
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/how-retroviruses-become-infectious/
scopus_import: '1'
status: public
title: Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in
the formation of the capsid hexamer
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '9467'
abstract:
- lang: eng
text: "Turbulence in the flow of fluid through a pipe can be suppressed by buoyancy
forces. As the suppression of turbulence leads to severe heat transfer deterioration,
this is an important and undesirable phenomenon in both heating and cooling applications.
Vertical flow is often considered, as the axial buoyancy force can help drive
the flow. With heating measured by the buoyancy parameter \U0001D436, our direct
numerical simulations show that shear-driven turbulence may either be completely
laminarised or it transitions to a relatively quiescent convection-driven state.
Buoyancy forces cause a flattening of the base flow profile, which in isothermal
pipe flow has recently been linked to complete suppression of turbulence (Kühnen
et al., Nat. Phys., vol. 14, 2018, pp. 386–390), and the flattened laminar base
profile has enhanced nonlinear stability (Marensi et al., J. Fluid Mech., vol.
863, 2019, pp. 50–875). In agreement with these findings, the nonlinear lower-branch
travelling-wave solution analysed here, which is believed to mediate transition
to turbulence in isothermal pipe flow, is shown to be suppressed by buoyancy.
A linear instability of the laminar base flow is responsible for the appearance
of the relatively quiescent convection driven state for \U0001D436≳4 across the
range of Reynolds numbers considered. In the suppression of turbulence, however,
i.e. in the transition from turbulence, we find clearer association with the analysis
of He et al. (J. Fluid Mech., vol. 809, 2016, pp. 31–71) than with the above dynamical
systems approach, which describes better the transition to turbulence. The laminarisation
criterion He et al. propose, based on an apparent Reynolds number of the flow
as measured by its driving pressure gradient, is found to capture the critical
\U0001D436=\U0001D436\U0001D450\U0001D45F(\U0001D445\U0001D452) above which the
flow will be laminarised or switch to the convection-driven type. Our analysis
suggests that it is the weakened rolls, rather than the streaks, which appear
to be critical for laminarisation."
acknowledgement: The anonymous referees are kindly acknowledged for their useful suggestions
andcomments.
article_number: A17
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Elena
full_name: Marensi, Elena
id: 0BE7553A-1004-11EA-B805-18983DDC885E
last_name: Marensi
- first_name: Shuisheng
full_name: He, Shuisheng
last_name: He
- first_name: Ashley P.
full_name: Willis, Ashley P.
last_name: Willis
citation:
ama: Marensi E, He S, Willis AP. Suppression of turbulence and travelling waves
in a vertical heated pipe. Journal of Fluid Mechanics. 2021;919. doi:10.1017/jfm.2021.371
apa: Marensi, E., He, S., & Willis, A. P. (2021). Suppression of turbulence
and travelling waves in a vertical heated pipe. Journal of Fluid Mechanics.
Cambridge University Press. https://doi.org/10.1017/jfm.2021.371
chicago: Marensi, Elena, Shuisheng He, and Ashley P. Willis. “Suppression of Turbulence
and Travelling Waves in a Vertical Heated Pipe.” Journal of Fluid Mechanics.
Cambridge University Press, 2021. https://doi.org/10.1017/jfm.2021.371.
ieee: E. Marensi, S. He, and A. P. Willis, “Suppression of turbulence and travelling
waves in a vertical heated pipe,” Journal of Fluid Mechanics, vol. 919.
Cambridge University Press, 2021.
ista: Marensi E, He S, Willis AP. 2021. Suppression of turbulence and travelling
waves in a vertical heated pipe. Journal of Fluid Mechanics. 919, A17.
mla: Marensi, Elena, et al. “Suppression of Turbulence and Travelling Waves in a
Vertical Heated Pipe.” Journal of Fluid Mechanics, vol. 919, A17, Cambridge
University Press, 2021, doi:10.1017/jfm.2021.371.
short: E. Marensi, S. He, A.P. Willis, Journal of Fluid Mechanics 919 (2021).
date_created: 2021-06-06T22:01:30Z
date_published: 2021-07-25T00:00:00Z
date_updated: 2023-08-08T13:58:41Z
day: '25'
ddc:
- '530'
department:
- _id: BjHo
doi: 10.1017/jfm.2021.371
external_id:
arxiv:
- '2008.13486'
isi:
- '000653785000001'
file:
- access_level: open_access
checksum: 867ad077e45c181c2c5ec1311ba27c41
content_type: application/pdf
creator: kschuh
date_created: 2021-08-03T09:53:28Z
date_updated: 2021-08-03T09:53:28Z
file_id: '9766'
file_name: 2021_JournalFluidMechanics_Marensi.pdf
file_size: 4087358
relation: main_file
success: 1
file_date_updated: 2021-08-03T09:53:28Z
has_accepted_license: '1'
intvolume: ' 919'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Journal of Fluid Mechanics
publication_identifier:
eissn:
- '14697645'
issn:
- '00221120'
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Suppression of turbulence and travelling waves in a vertical heated pipe
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 919
year: '2021'
...
---
_id: '9470'
abstract:
- lang: eng
text: A key step in understanding the genetic basis of different evolutionary outcomes
(e.g., adaptation) is to determine the roles played by different mutation types
(e.g., SNPs, translocations and inversions). To do this we must simultaneously
consider different mutation types in an evolutionary framework. Here, we propose
a research framework that directly utilizes the most important characteristics
of mutations, their population genetic effects, to determine their relative evolutionary
significance in a given scenario. We review known population genetic effects of
different mutation types and show how these may be connected to different evolutionary
outcomes. We provide examples of how to implement this framework and pinpoint
areas where more data, theory and synthesis are needed. Linking experimental and
theoretical approaches to examine different mutation types simultaneously is a
critical step towards understanding their evolutionary significance.
acknowledgement: We thank the editor, two helpful reviewers, Roger Butlin, Kerstin
Johannesson, Valentina Peona, Rike Stelkens, Julie Blommaert, Nick Barton, and João
Alpedrinha for helpful comments that improved the manuscript. The authors acknowledge
funding from the Swedish Research Council Formas (2017-01597 to AS), the Swedish
Research Council Vetenskapsrådet (2016-05139 to AS, 2019-04452 to TS) and from the
European Research Council (ERC) under the European Union’s Horizon 2020 research
and innovation programme (grant agreement no. 757451 to TS). ELB was funded by a
Carl Tryggers grant awarded to Tanja Slotte. Anja M. Westram was funded by the European
Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie
grant agreement No 797747. Inês Fragata was funded by a Junior Researcher contract
from FCT (CEECIND/02616/2018).
article_processing_charge: No
author:
- first_name: Emma L.
full_name: Berdan, Emma L.
last_name: Berdan
- first_name: Alexandre
full_name: Blanckaert, Alexandre
last_name: Blanckaert
- first_name: Tanja
full_name: Slotte, Tanja
last_name: Slotte
- first_name: Alexander
full_name: Suh, Alexander
last_name: Suh
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Inês
full_name: Fragata, Inês
last_name: Fragata
citation:
ama: 'Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. Unboxing
mutations: Connecting mutation types with evolutionary consequences. Molecular
Ecology. 2021;30(12):2710-2723. doi:10.1111/mec.15936'
apa: 'Berdan, E. L., Blanckaert, A., Slotte, T., Suh, A., Westram, A. M., &
Fragata, I. (2021). Unboxing mutations: Connecting mutation types with evolutionary
consequences. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.15936'
chicago: 'Berdan, Emma L., Alexandre Blanckaert, Tanja Slotte, Alexander Suh, Anja
M Westram, and Inês Fragata. “Unboxing Mutations: Connecting Mutation Types with
Evolutionary Consequences.” Molecular Ecology. Wiley, 2021. https://doi.org/10.1111/mec.15936.'
ieee: 'E. L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A. M. Westram, and I. Fragata,
“Unboxing mutations: Connecting mutation types with evolutionary consequences,”
Molecular Ecology, vol. 30, no. 12. Wiley, pp. 2710–2723, 2021.'
ista: 'Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. 2021. Unboxing
mutations: Connecting mutation types with evolutionary consequences. Molecular
Ecology. 30(12), 2710–2723.'
mla: 'Berdan, Emma L., et al. “Unboxing Mutations: Connecting Mutation Types with
Evolutionary Consequences.” Molecular Ecology, vol. 30, no. 12, Wiley,
2021, pp. 2710–23, doi:10.1111/mec.15936.'
short: E.L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A.M. Westram, I. Fragata,
Molecular Ecology 30 (2021) 2710–2723.
date_created: 2021-06-06T22:01:31Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2023-08-08T13:59:18Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/mec.15936
ec_funded: 1
external_id:
isi:
- '000652056400001'
file:
- access_level: open_access
checksum: e6f4731365bde2614b333040a08265d8
content_type: application/pdf
creator: kschuh
date_created: 2021-06-11T15:34:53Z
date_updated: 2021-06-11T15:34:53Z
file_id: '9545'
file_name: 2021_MolecularEcology_Berdan.pdf
file_size: 1031978
relation: main_file
success: 1
file_date_updated: 2021-06-11T15:34:53Z
has_accepted_license: '1'
intvolume: ' 30'
isi: 1
issue: '12'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 2710-2723
project:
- _id: 265B41B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '797747'
name: Theoretical and empirical approaches to understanding Parallel Adaptation
publication: Molecular Ecology
publication_identifier:
eissn:
- 1365294X
issn:
- '09621083'
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Unboxing mutations: Connecting mutation types with evolutionary consequences'
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 30
year: '2021'
...
---
_id: '9468'
abstract:
- lang: eng
text: "Motivated by the successful application of geometry to proving the Harary--Hill
conjecture for “pseudolinear” drawings of $K_n$, we introduce “pseudospherical”
drawings of graphs. A spherical drawing of a graph $G$ is a drawing in the unit
sphere $\\mathbb{S}^2$ in which the vertices of $G$ are represented as points---no
three on a great circle---and the edges of $G$ are shortest-arcs in $\\mathbb{S}^2$
connecting pairs of vertices. Such a drawing has three properties: (1) every edge
$e$ is contained in a simple closed curve $\\gamma_e$ such that the only vertices
in $\\gamma_e$ are the ends of $e$; (2) if $e\\ne f$, then $\\gamma_e\\cap\\gamma_f$
has precisely two crossings; and (3) if $e\\ne f$, then $e$ intersects $\\gamma_f$
at most once, in either a crossing or an end of $e$. We use properties (1)--(3)
to define a pseudospherical drawing of $G$. Our main result is that for the complete
graph, properties (1)--(3) are equivalent to the same three properties but with
“precisely two crossings” in (2) replaced by “at most two crossings.” The proof
requires a result in the geometric transversal theory of arrangements of pseudocircles.
This is proved using the surprising result that the absence of special arcs (coherent
spirals) in an arrangement of simple closed curves characterizes the fact that
any two curves in the arrangement have at most two crossings. Our studies provide
the necessary ideas for exhibiting a drawing of $K_{10}$ that has no extension
to an arrangement of pseudocircles and a drawing of $K_9$ that does extend to
an arrangement of pseudocircles, but no such extension has all pairs of pseudocircles
crossing twice.\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: Alan M
full_name: Arroyo Guevara, Alan M
id: 3207FDC6-F248-11E8-B48F-1D18A9856A87
last_name: Arroyo Guevara
orcid: 0000-0003-2401-8670
- first_name: R. Bruce
full_name: Richter, R. Bruce
last_name: Richter
- first_name: Matthew
full_name: Sunohara, Matthew
last_name: Sunohara
citation:
ama: Arroyo Guevara AM, Richter RB, Sunohara M. Extending drawings of complete graphs
into arrangements of pseudocircles. SIAM Journal on Discrete Mathematics.
2021;35(2):1050-1076. doi:10.1137/20M1313234
apa: Arroyo Guevara, A. M., Richter, R. B., & Sunohara, M. (2021). Extending
drawings of complete graphs into arrangements of pseudocircles. SIAM Journal
on Discrete Mathematics. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/20M1313234
chicago: Arroyo Guevara, Alan M, R. Bruce Richter, and Matthew Sunohara. “Extending
Drawings of Complete Graphs into Arrangements of Pseudocircles.” SIAM Journal
on Discrete Mathematics. Society for Industrial and Applied Mathematics, 2021.
https://doi.org/10.1137/20M1313234.
ieee: A. M. Arroyo Guevara, R. B. Richter, and M. Sunohara, “Extending drawings
of complete graphs into arrangements of pseudocircles,” SIAM Journal on Discrete
Mathematics, vol. 35, no. 2. Society for Industrial and Applied Mathematics,
pp. 1050–1076, 2021.
ista: Arroyo Guevara AM, Richter RB, Sunohara M. 2021. Extending drawings of complete
graphs into arrangements of pseudocircles. SIAM Journal on Discrete Mathematics.
35(2), 1050–1076.
mla: Arroyo Guevara, Alan M., et al. “Extending Drawings of Complete Graphs into
Arrangements of Pseudocircles.” SIAM Journal on Discrete Mathematics, vol.
35, no. 2, Society for Industrial and Applied Mathematics, 2021, pp. 1050–76,
doi:10.1137/20M1313234.
short: A.M. Arroyo Guevara, R.B. Richter, M. Sunohara, SIAM Journal on Discrete
Mathematics 35 (2021) 1050–1076.
date_created: 2021-06-06T22:01:30Z
date_published: 2021-05-20T00:00:00Z
date_updated: 2023-08-08T13:58:12Z
day: '20'
department:
- _id: UlWa
doi: 10.1137/20M1313234
ec_funded: 1
external_id:
arxiv:
- '2001.06053'
isi:
- '000674142200022'
intvolume: ' 35'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2001.06053
month: '05'
oa: 1
oa_version: Preprint
page: 1050-1076
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: SIAM Journal on Discrete Mathematics
publication_identifier:
issn:
- '08954801'
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Extending drawings of complete graphs into arrangements of pseudocircles
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 35
year: '2021'
...
---
_id: '9462'
abstract:
- lang: eng
text: We consider a system of N trapped bosons with repulsive interactions in a
combined semiclassical mean-field limit at positive temperature. We show that
the free energy is well approximated by the minimum of the Hartree free energy
functional – a natural extension of the Hartree energy functional to positive
temperatures. The Hartree free energy functional converges in the same limit to
a semiclassical free energy functional, and we show that the system displays Bose–Einstein
condensation if and only if it occurs in the semiclassical free energy functional.
This allows us to show that for weak coupling the critical temperature decreases
due to the repulsive interactions.
acknowledgement: Funding from the European Union's Horizon 2020 research and innovation
programme under the ERC grant agreement No 694227 (R.S.) and under the Marie Sklodowska-Curie
grant agreement No 836146 (A.D.) is gratefully acknowledged. A.D. acknowledges support
of the Swiss National Science Foundation through the Ambizione grant PZ00P2 185851.
article_number: '109096'
article_processing_charge: No
article_type: original
author:
- first_name: Andreas
full_name: Deuchert, Andreas
last_name: Deuchert
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Deuchert A, Seiringer R. Semiclassical approximation and critical temperature
shift for weakly interacting trapped bosons. Journal of Functional Analysis.
2021;281(6). doi:10.1016/j.jfa.2021.109096
apa: Deuchert, A., & Seiringer, R. (2021). Semiclassical approximation and critical
temperature shift for weakly interacting trapped bosons. Journal of Functional
Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2021.109096
chicago: Deuchert, Andreas, and Robert Seiringer. “Semiclassical Approximation and
Critical Temperature Shift for Weakly Interacting Trapped Bosons.” Journal
of Functional Analysis. Elsevier, 2021. https://doi.org/10.1016/j.jfa.2021.109096.
ieee: A. Deuchert and R. Seiringer, “Semiclassical approximation and critical temperature
shift for weakly interacting trapped bosons,” Journal of Functional Analysis,
vol. 281, no. 6. Elsevier, 2021.
ista: Deuchert A, Seiringer R. 2021. Semiclassical approximation and critical temperature
shift for weakly interacting trapped bosons. Journal of Functional Analysis. 281(6),
109096.
mla: Deuchert, Andreas, and Robert Seiringer. “Semiclassical Approximation and Critical
Temperature Shift for Weakly Interacting Trapped Bosons.” Journal of Functional
Analysis, vol. 281, no. 6, 109096, Elsevier, 2021, doi:10.1016/j.jfa.2021.109096.
short: A. Deuchert, R. Seiringer, Journal of Functional Analysis 281 (2021).
date_created: 2021-06-06T22:01:28Z
date_published: 2021-09-15T00:00:00Z
date_updated: 2023-08-08T13:56:27Z
day: '15'
department:
- _id: RoSe
doi: 10.1016/j.jfa.2021.109096
ec_funded: 1
external_id:
arxiv:
- '2009.00992'
isi:
- '000656508600008'
intvolume: ' 281'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2009.00992
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Journal of Functional Analysis
publication_identifier:
eissn:
- 1096-0783
issn:
- 0022-1236
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Semiclassical approximation and critical temperature shift for weakly interacting
trapped bosons
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 281
year: '2021'
...
---
_id: '9469'
abstract:
- lang: eng
text: In this paper, we consider reflected three-operator splitting methods for
monotone inclusion problems in real Hilbert spaces. To do this, we first obtain
weak convergence analysis and nonasymptotic O(1/n) convergence rate of the reflected
Krasnosel'skiĭ-Mann iteration for finding a fixed point of nonexpansive mapping
in real Hilbert spaces under some seemingly easy to implement conditions on the
iterative parameters. We then apply our results to three-operator splitting for
the monotone inclusion problem and consequently obtain the corresponding convergence
analysis. Furthermore, we derive reflected primal-dual algorithms for highly structured
monotone inclusion problems. Some numerical implementations are drawn from splitting
methods to support the theoretical analysis.
acknowledgement: The authors are grateful to the anonymous referees and the handling
Editor for their insightful comments which have improved the earlier version of
the manuscript greatly. The second author is grateful to the University of Hafr
Al Batin. The last author has received funding from the European Research Council
(ERC) under the European Union's Seventh Framework Program (FP7-2007-2013) (Grant
agreement No. 616160).
article_processing_charge: No
article_type: original
author:
- first_name: Olaniyi S.
full_name: Iyiola, Olaniyi S.
last_name: Iyiola
- first_name: Cyril D.
full_name: Enyi, Cyril D.
last_name: Enyi
- first_name: Yekini
full_name: Shehu, Yekini
id: 3FC7CB58-F248-11E8-B48F-1D18A9856A87
last_name: Shehu
orcid: 0000-0001-9224-7139
citation:
ama: Iyiola OS, Enyi CD, Shehu Y. Reflected three-operator splitting method for
monotone inclusion problem. Optimization Methods and Software. 2021. doi:10.1080/10556788.2021.1924715
apa: Iyiola, O. S., Enyi, C. D., & Shehu, Y. (2021). Reflected three-operator
splitting method for monotone inclusion problem. Optimization Methods and Software.
Taylor and Francis. https://doi.org/10.1080/10556788.2021.1924715
chicago: Iyiola, Olaniyi S., Cyril D. Enyi, and Yekini Shehu. “Reflected Three-Operator
Splitting Method for Monotone Inclusion Problem.” Optimization Methods and
Software. Taylor and Francis, 2021. https://doi.org/10.1080/10556788.2021.1924715.
ieee: O. S. Iyiola, C. D. Enyi, and Y. Shehu, “Reflected three-operator splitting
method for monotone inclusion problem,” Optimization Methods and Software.
Taylor and Francis, 2021.
ista: Iyiola OS, Enyi CD, Shehu Y. 2021. Reflected three-operator splitting method
for monotone inclusion problem. Optimization Methods and Software.
mla: Iyiola, Olaniyi S., et al. “Reflected Three-Operator Splitting Method for Monotone
Inclusion Problem.” Optimization Methods and Software, Taylor and Francis,
2021, doi:10.1080/10556788.2021.1924715.
short: O.S. Iyiola, C.D. Enyi, Y. Shehu, Optimization Methods and Software (2021).
date_created: 2021-06-06T22:01:30Z
date_published: 2021-05-12T00:00:00Z
date_updated: 2023-08-08T13:57:43Z
day: '12'
department:
- _id: VlKo
doi: 10.1080/10556788.2021.1924715
ec_funded: 1
external_id:
isi:
- '000650507600001'
isi: 1
language:
- iso: eng
month: '05'
oa_version: None
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: Optimization Methods and Software
publication_identifier:
eissn:
- 1029-4937
issn:
- 1055-6788
publication_status: published
publisher: Taylor and Francis
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reflected three-operator splitting method for monotone inclusion problem
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '9540'
abstract:
- lang: eng
text: The hexameric AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis
and initiates cytoplasmic maturation of the large ribosomal subunit by releasing
the shuttling maturation factor Rlp24. Drg1 monomers contain two AAA-domains (D1
and D2) that act in a concerted manner. Rlp24 release is inhibited by the drug
diazaborine which blocks ATP hydrolysis in D2. The mode of inhibition was unknown.
Here we show the first cryo-EM structure of Drg1 revealing the inhibitory mechanism.
Diazaborine forms a covalent bond to the 2′-OH of the nucleotide in D2, explaining
its specificity for this site. As a consequence, the D2 domain is locked in a
rigid, inactive state, stalling the whole Drg1 hexamer. Resistance mechanisms
identified include abolished drug binding and altered positioning of the nucleotide.
Our results suggest nucleotide-modifying compounds as potential novel inhibitors
for AAA-ATPases.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: We are deeply grateful to the late Gregor Högenauer who built the
foundation for this study with his visionary work on the inhibitor diazaborine and
its bacterial target. We thank Rolf Breinbauer for insightful discussions on boron
chemistry. We thank Anton Meinhart and Tim Clausen for the valuable discussion of
the manuscript. We are indebted to Thomas Köcher for the MS measurement of the diazaborine-ATPγS
adduct. We thank the team of the VBCF for support during early phases of this work
and the IST Austria Electron Microscopy Facility for providing equipment. The lab
of D.H. is supported by Boehringer Ingelheim. The work was funded by FWF projects
P32536 and P32977 (to H.B.).
article_number: '3483'
article_processing_charge: No
article_type: original
author:
- first_name: Michael
full_name: Prattes, Michael
last_name: Prattes
- first_name: Irina
full_name: Grishkovskaya, Irina
last_name: Grishkovskaya
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
- first_name: Ingrid
full_name: Rössler, Ingrid
last_name: Rössler
- first_name: Isabella
full_name: Klein, Isabella
last_name: Klein
- first_name: Christina
full_name: Hetzmannseder, Christina
last_name: Hetzmannseder
- first_name: Gertrude
full_name: Zisser, Gertrude
last_name: Zisser
- first_name: Christian C.
full_name: Gruber, Christian C.
last_name: Gruber
- first_name: Karl
full_name: Gruber, Karl
last_name: Gruber
- first_name: David
full_name: Haselbach, David
last_name: Haselbach
- first_name: Helmut
full_name: Bergler, Helmut
last_name: Bergler
citation:
ama: Prattes M, Grishkovskaya I, Hodirnau V-V, et al. Structural basis for inhibition
of the AAA-ATPase Drg1 by diazaborine. Nature Communications. 2021;12(1).
doi:10.1038/s41467-021-23854-x
apa: Prattes, M., Grishkovskaya, I., Hodirnau, V.-V., Rössler, I., Klein, I., Hetzmannseder,
C., … Bergler, H. (2021). Structural basis for inhibition of the AAA-ATPase Drg1
by diazaborine. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-23854-x
chicago: Prattes, Michael, Irina Grishkovskaya, Victor-Valentin Hodirnau, Ingrid
Rössler, Isabella Klein, Christina Hetzmannseder, Gertrude Zisser, et al. “Structural
Basis for Inhibition of the AAA-ATPase Drg1 by Diazaborine.” Nature Communications.
Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23854-x.
ieee: M. Prattes et al., “Structural basis for inhibition of the AAA-ATPase
Drg1 by diazaborine,” Nature Communications, vol. 12, no. 1. Springer Nature,
2021.
ista: Prattes M, Grishkovskaya I, Hodirnau V-V, Rössler I, Klein I, Hetzmannseder
C, Zisser G, Gruber CC, Gruber K, Haselbach D, Bergler H. 2021. Structural basis
for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. 12(1),
3483.
mla: Prattes, Michael, et al. “Structural Basis for Inhibition of the AAA-ATPase
Drg1 by Diazaborine.” Nature Communications, vol. 12, no. 1, 3483, Springer
Nature, 2021, doi:10.1038/s41467-021-23854-x.
short: M. Prattes, I. Grishkovskaya, V.-V. Hodirnau, I. Rössler, I. Klein, C. Hetzmannseder,
G. Zisser, C.C. Gruber, K. Gruber, D. Haselbach, H. Bergler, Nature Communications
12 (2021).
date_created: 2021-06-10T14:57:45Z
date_published: 2021-06-09T00:00:00Z
date_updated: 2023-08-08T14:05:26Z
day: '09'
ddc:
- '570'
department:
- _id: EM-Fac
doi: 10.1038/s41467-021-23854-x
external_id:
isi:
- '000664874700014'
pmid:
- '34108481'
file:
- access_level: open_access
checksum: 40fc24c1310930990b52a8ad1142ee97
content_type: application/pdf
creator: cziletti
date_created: 2021-06-15T18:55:59Z
date_updated: 2021-06-15T18:55:59Z
file_id: '9556'
file_name: 2021_NatureComm_Prattes.pdf
file_size: 3397292
relation: main_file
success: 1
file_date_updated: 2021-06-15T18:55:59Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Physics and Astronomy
- General Chemistry
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '9549'
abstract:
- lang: eng
text: 'AMPA receptors (AMPARs) mediate the majority of excitatory transmission in
the brain and enable the synaptic plasticity that underlies learning1. A diverse
array of AMPAR signalling complexes are established by receptor auxiliary subunits,
which associate with the AMPAR in various combinations to modulate trafficking,
gating and synaptic strength2. However, their mechanisms of action are poorly
understood. Here we determine cryo-electron microscopy structures of the heteromeric
GluA1–GluA2 receptor assembled with both TARP-γ8 and CNIH2, the predominant AMPAR
complex in the forebrain, in both resting and active states. Two TARP-γ8 and two
CNIH2 subunits insert at distinct sites beneath the ligand-binding domains of
the receptor, with site-specific lipids shaping each interaction and affecting
the gating regulation of the AMPARs. Activation of the receptor leads to asymmetry
between GluA1 and GluA2 along the ion conduction path and an outward expansion
of the channel triggers counter-rotations of both auxiliary subunit pairs, promoting
the active-state conformation. In addition, both TARP-γ8 and CNIH2 pivot towards
the pore exit upon activation, extending their reach for cytoplasmic receptor
elements. CNIH2 achieves this through its uniquely extended M2 helix, which has
transformed this endoplasmic reticulum-export factor into a powerful AMPAR modulator
that is capable of providing hippocampal pyramidal neurons with their integrative
synaptic properties. '
acknowledgement: We thank members of the Greger laboratory, B. Herguedas, J. Krieger
and J.-N. Dohrke for comments on the manuscript; J. Krieger and J.-N. Dohrke for
discussion, J. Krieger for help with the normal mode analysis, B. Köhegyi for help
with cryo-EM imaging, V. Chang and K. Suzuki for helping to generate the CNIH2-1D4-HA
stable cell line, M. Carvalho for assistance at early stages of this project, the
LMB scientific computing and the cryo-EM facility for support, P. Emsley for help
with model building, T. Nakane for helpful comments with RELION 3.1 and R. Warshamanage
for helping with EMDA cryo-EM-map processing. We acknowledge the Diamond Light Source
for access and support of the Cryo-EM facilities at the UK national electron bio10
imaging centre (eBIC), proposal EM17434, funded by the Wellcome Trust, MRC and BBSRC.
This work was supported by grants from the Medical Research Council, as part of
United Kingdom Research and Innovation (also known as UK Research and Innovation)
(MC_U105174197) and BBSRC (BB/N002113/1) to I.H.G.
article_processing_charge: No
article_type: original
author:
- first_name: Danyang
full_name: Zhang, Danyang
last_name: Zhang
- first_name: Jake
full_name: Watson, Jake
id: 63836096-4690-11EA-BD4E-32803DDC885E
last_name: Watson
orcid: 0000-0002-8698-3823
- first_name: Peter M.
full_name: Matthews, Peter M.
last_name: Matthews
- first_name: Ondrej
full_name: Cais, Ondrej
last_name: Cais
- first_name: Ingo H.
full_name: Greger, Ingo H.
last_name: Greger
citation:
ama: Zhang D, Watson J, Matthews PM, Cais O, Greger IH. Gating and modulation of
a hetero-octameric AMPA glutamate receptor. Nature. 2021;594:454-458. doi:10.1038/s41586-021-03613-0
apa: Zhang, D., Watson, J., Matthews, P. M., Cais, O., & Greger, I. H. (2021).
Gating and modulation of a hetero-octameric AMPA glutamate receptor. Nature.
Springer Nature. https://doi.org/10.1038/s41586-021-03613-0
chicago: Zhang, Danyang, Jake Watson, Peter M. Matthews, Ondrej Cais, and Ingo H.
Greger. “Gating and Modulation of a Hetero-Octameric AMPA Glutamate Receptor.”
Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-021-03613-0.
ieee: D. Zhang, J. Watson, P. M. Matthews, O. Cais, and I. H. Greger, “Gating and
modulation of a hetero-octameric AMPA glutamate receptor,” Nature, vol.
594. Springer Nature, pp. 454–458, 2021.
ista: Zhang D, Watson J, Matthews PM, Cais O, Greger IH. 2021. Gating and modulation
of a hetero-octameric AMPA glutamate receptor. Nature. 594, 454–458.
mla: Zhang, Danyang, et al. “Gating and Modulation of a Hetero-Octameric AMPA Glutamate
Receptor.” Nature, vol. 594, Springer Nature, 2021, pp. 454–58, doi:10.1038/s41586-021-03613-0.
short: D. Zhang, J. Watson, P.M. Matthews, O. Cais, I.H. Greger, Nature 594 (2021)
454–458.
date_created: 2021-06-13T22:01:33Z
date_published: 2021-06-02T00:00:00Z
date_updated: 2023-08-08T13:59:51Z
day: '02'
department:
- _id: PeJo
doi: 10.1038/s41586-021-03613-0
external_id:
isi:
- '000657238100003'
pmid:
- '34079129'
intvolume: ' 594'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41586-021-03613-0
month: '06'
oa: 1
oa_version: Published Version
page: 454-458
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Gating and modulation of a hetero-octameric AMPA glutamate receptor
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 594
year: '2021'
...
---
_id: '9550'
abstract:
- lang: eng
text: 'We prove that the energy of any eigenvector of a sum of several independent
large Wigner matrices is equally distributed among these matrices with very high
precision. This shows a particularly strong microcanonical form of the equipartition
principle for quantum systems whose components are modelled by Wigner matrices. '
acknowledgement: The first author is supported in part by Hong Kong RGC Grant GRF
16301519 and NSFC 11871425. The second author is supported in part by ERC Advanced
Grant RANMAT 338804. The third author is supported in part by Swedish Research Council
Grant VR-2017-05195 and the Knut and Alice Wallenberg Foundation
article_number: e44
article_processing_charge: No
article_type: original
author:
- first_name: Zhigang
full_name: Bao, Zhigang
id: 442E6A6C-F248-11E8-B48F-1D18A9856A87
last_name: Bao
orcid: 0000-0003-3036-1475
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Kevin
full_name: Schnelli, Kevin
id: 434AD0AE-F248-11E8-B48F-1D18A9856A87
last_name: Schnelli
orcid: 0000-0003-0954-3231
citation:
ama: Bao Z, Erdös L, Schnelli K. Equipartition principle for Wigner matrices. Forum
of Mathematics, Sigma. 2021;9. doi:10.1017/fms.2021.38
apa: Bao, Z., Erdös, L., & Schnelli, K. (2021). Equipartition principle for
Wigner matrices. Forum of Mathematics, Sigma. Cambridge University Press.
https://doi.org/10.1017/fms.2021.38
chicago: Bao, Zhigang, László Erdös, and Kevin Schnelli. “Equipartition Principle
for Wigner Matrices.” Forum of Mathematics, Sigma. Cambridge University
Press, 2021. https://doi.org/10.1017/fms.2021.38.
ieee: Z. Bao, L. Erdös, and K. Schnelli, “Equipartition principle for Wigner matrices,”
Forum of Mathematics, Sigma, vol. 9. Cambridge University Press, 2021.
ista: Bao Z, Erdös L, Schnelli K. 2021. Equipartition principle for Wigner matrices.
Forum of Mathematics, Sigma. 9, e44.
mla: Bao, Zhigang, et al. “Equipartition Principle for Wigner Matrices.” Forum
of Mathematics, Sigma, vol. 9, e44, Cambridge University Press, 2021, doi:10.1017/fms.2021.38.
short: Z. Bao, L. Erdös, K. Schnelli, Forum of Mathematics, Sigma 9 (2021).
date_created: 2021-06-13T22:01:33Z
date_published: 2021-05-27T00:00:00Z
date_updated: 2023-08-08T14:03:40Z
day: '27'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1017/fms.2021.38
ec_funded: 1
external_id:
arxiv:
- '2008.07061'
isi:
- '000654960800001'
file:
- access_level: open_access
checksum: 47c986578de132200d41e6d391905519
content_type: application/pdf
creator: cziletti
date_created: 2021-06-15T14:40:45Z
date_updated: 2021-06-15T14:40:45Z
file_id: '9555'
file_name: 2021_ForumMath_Bao.pdf
file_size: 483458
relation: main_file
success: 1
file_date_updated: 2021-06-15T14:40:45Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Forum of Mathematics, Sigma
publication_identifier:
eissn:
- '20505094'
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Equipartition principle for Wigner matrices
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2021'
...
---
_id: '9570'
abstract:
- lang: eng
text: We present conductance-matrix measurements in long, three-terminal hybrid
superconductor-semiconductor nanowires, and compare with theoretical predictions
of a magnetic-field-driven, topological quantum phase transition. By examining
the nonlocal conductance, we identify the closure of the excitation gap in the
bulk of the semiconductor before the emergence of zero-bias peaks, ruling out
spurious gap-closure signatures from localized states. We observe that after the
gap closes, nonlocal signals and zero-bias peaks fluctuate strongly at both ends,
inconsistent with a simple picture of clean topological superconductivity.
acknowledgement: We acknowledge insightful discussions with K. Flensberg, E. B. Hansen,
T. Karzig, R. Lutchyn, D. Pikulin, E. Prada, and R. Aguado. This work was supported
by Microsoft Project Q and the Danmarks Grundforskningsfond. C.M.M. acknowledges
support from the Villum Fonden. A.P.H. and L.C. contributed equally to this work.
article_number: '235201'
article_processing_charge: No
article_type: original
author:
- first_name: Denise
full_name: Puglia, Denise
id: 4D495994-AE37-11E9-AC72-31CAE5697425
last_name: Puglia
- first_name: E. A.
full_name: Martinez, E. A.
last_name: Martinez
- first_name: G. C.
full_name: Ménard, G. C.
last_name: Ménard
- first_name: A.
full_name: Pöschl, A.
last_name: Pöschl
- first_name: S.
full_name: Gronin, S.
last_name: Gronin
- first_name: G. C.
full_name: Gardner, G. C.
last_name: Gardner
- first_name: R.
full_name: Kallaher, R.
last_name: Kallaher
- first_name: M. J.
full_name: Manfra, M. J.
last_name: Manfra
- first_name: C. M.
full_name: Marcus, C. M.
last_name: Marcus
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: L.
full_name: Casparis, L.
last_name: Casparis
citation:
ama: Puglia D, Martinez EA, Ménard GC, et al. Closing of the induced gap in a hybrid
superconductor-semiconductor nanowire. Physical Review B. 2021;103(23).
doi:10.1103/PhysRevB.103.235201
apa: Puglia, D., Martinez, E. A., Ménard, G. C., Pöschl, A., Gronin, S., Gardner,
G. C., … Casparis, L. (2021). Closing of the induced gap in a hybrid superconductor-semiconductor
nanowire. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.103.235201
chicago: Puglia, Denise, E. A. Martinez, G. C. Ménard, A. Pöschl, S. Gronin, G.
C. Gardner, R. Kallaher, et al. “Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor
Nanowire.” Physical Review B. American Physical Society, 2021. https://doi.org/10.1103/PhysRevB.103.235201.
ieee: D. Puglia et al., “Closing of the induced gap in a hybrid superconductor-semiconductor
nanowire,” Physical Review B, vol. 103, no. 23. American Physical Society,
2021.
ista: Puglia D, Martinez EA, Ménard GC, Pöschl A, Gronin S, Gardner GC, Kallaher
R, Manfra MJ, Marcus CM, Higginbotham AP, Casparis L. 2021. Closing of the induced
gap in a hybrid superconductor-semiconductor nanowire. Physical Review B. 103(23),
235201.
mla: Puglia, Denise, et al. “Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor
Nanowire.” Physical Review B, vol. 103, no. 23, 235201, American Physical
Society, 2021, doi:10.1103/PhysRevB.103.235201.
short: D. Puglia, E.A. Martinez, G.C. Ménard, A. Pöschl, S. Gronin, G.C. Gardner,
R. Kallaher, M.J. Manfra, C.M. Marcus, A.P. Higginbotham, L. Casparis, Physical
Review B 103 (2021).
date_created: 2021-06-20T22:01:33Z
date_published: 2021-06-15T00:00:00Z
date_updated: 2023-08-08T14:08:08Z
day: '15'
department:
- _id: AnHi
doi: 10.1103/PhysRevB.103.235201
external_id:
arxiv:
- '2006.01275'
isi:
- '000661512500002'
intvolume: ' 103'
isi: 1
issue: '23'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2006.01275
month: '06'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- '24699969'
issn:
- '24699950'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '13080'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Closing of the induced gap in a hybrid superconductor-semiconductor nanowire
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 103
year: '2021'
...