---
_id: '9631'
abstract:
- lang: eng
text: The ability to leverage large-scale hardware parallelism has been one of the
key enablers of the accelerated recent progress in machine learning. Consequently,
there has been considerable effort invested into developing efficient parallel
variants of classic machine learning algorithms. However, despite the wealth of
knowledge on parallelization, some classic machine learning algorithms often prove
hard to parallelize efficiently while maintaining convergence. In this paper,
we focus on efficient parallel algorithms for the key machine learning task of
inference on graphical models, in particular on the fundamental belief propagation
algorithm. We address the challenge of efficiently parallelizing this classic
paradigm by showing how to leverage scalable relaxed schedulers in this context.
We present an extensive empirical study, showing that our approach outperforms
previous parallel belief propagation implementations both in terms of scalability
and in terms of wall-clock convergence time, on a range of practical applications.
acknowledgement: "We thank Marco Mondelli for discussions related to LDPC decoding,
and Giorgi Nadiradze for discussions on analysis of relaxed schedulers. This project
has received funding from the European Research Council (ERC) under the European\r\nUnion’s
Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML)."
article_processing_charge: No
arxiv: 1
author:
- first_name: Vitaly
full_name: Aksenov, Vitaly
last_name: Aksenov
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Janne
full_name: Korhonen, Janne
id: C5402D42-15BC-11E9-A202-CA2BE6697425
last_name: Korhonen
citation:
ama: 'Aksenov V, Alistarh D-A, Korhonen J. Scalable belief propagation via relaxed
scheduling. In: Advances in Neural Information Processing Systems. Vol
33. Curran Associates; 2020:22361-22372.'
apa: 'Aksenov, V., Alistarh, D.-A., & Korhonen, J. (2020). Scalable belief propagation
via relaxed scheduling. In Advances in Neural Information Processing Systems
(Vol. 33, pp. 22361–22372). Vancouver, Canada: Curran Associates.'
chicago: Aksenov, Vitaly, Dan-Adrian Alistarh, and Janne Korhonen. “Scalable Belief
Propagation via Relaxed Scheduling.” In Advances in Neural Information Processing
Systems, 33:22361–72. Curran Associates, 2020.
ieee: V. Aksenov, D.-A. Alistarh, and J. Korhonen, “Scalable belief propagation
via relaxed scheduling,” in Advances in Neural Information Processing Systems,
Vancouver, Canada, 2020, vol. 33, pp. 22361–22372.
ista: 'Aksenov V, Alistarh D-A, Korhonen J. 2020. Scalable belief propagation via
relaxed scheduling. Advances in Neural Information Processing Systems. NeurIPS:
Conference on Neural Information Processing Systems vol. 33, 22361–22372.'
mla: Aksenov, Vitaly, et al. “Scalable Belief Propagation via Relaxed Scheduling.”
Advances in Neural Information Processing Systems, vol. 33, Curran Associates,
2020, pp. 22361–72.
short: V. Aksenov, D.-A. Alistarh, J. Korhonen, in:, Advances in Neural Information
Processing Systems, Curran Associates, 2020, pp. 22361–22372.
conference:
end_date: 2020-12-12
location: Vancouver, Canada
name: 'NeurIPS: Conference on Neural Information Processing Systems'
start_date: 2020-12-06
date_created: 2021-07-04T22:01:26Z
date_published: 2020-12-06T00:00:00Z
date_updated: 2023-02-23T14:03:03Z
day: '06'
department:
- _id: DaAl
ec_funded: 1
external_id:
arxiv:
- '2002.11505'
intvolume: ' 33'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://proceedings.neurips.cc/paper/2020/hash/fdb2c3bab9d0701c4a050a4d8d782c7f-Abstract.html
month: '12'
oa: 1
oa_version: Published Version
page: 22361-22372
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: Advances in Neural Information Processing Systems
publication_identifier:
isbn:
- '9781713829546'
issn:
- '10495258'
publication_status: published
publisher: Curran Associates
quality_controlled: '1'
scopus_import: '1'
status: public
title: Scalable belief propagation via relaxed scheduling
type: conference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 33
year: '2020'
...
---
_id: '9632'
abstract:
- lang: eng
text: "Second-order information, in the form of Hessian- or Inverse-Hessian-vector
products, is a fundamental tool for solving optimization problems. Recently, there
has been significant interest in utilizing this information in the context of
deep\r\nneural networks; however, relatively little is known about the quality
of existing approximations in this context. Our work examines this question, identifies
issues with existing approaches, and proposes a method called WoodFisher to compute
a faithful and efficient estimate of the inverse Hessian. Our main application
is to neural network compression, where we build on the classic Optimal Brain
Damage/Surgeon framework. We demonstrate that WoodFisher significantly outperforms
popular state-of-the-art methods for oneshot pruning. Further, even when iterative,
gradual pruning is allowed, our method results in a gain in test accuracy over
the state-of-the-art approaches, for standard image classification datasets such
as ImageNet ILSVRC. We examine how our method can be extended to take into account
first-order information, as well as\r\nillustrate its ability to automatically
set layer-wise pruning thresholds and perform compression in the limited-data
regime. The code is available at the following link, https://github.com/IST-DASLab/WoodFisher."
acknowledgement: This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreement No 805223 ScaleML). Also, we would like to thank Alexander Shevchenko,
Alexandra Peste, and other members of the group for fruitful discussions.
article_processing_charge: No
arxiv: 1
author:
- first_name: Sidak Pal
full_name: Singh, Sidak Pal
id: DD138E24-D89D-11E9-9DC0-DEF6E5697425
last_name: Singh
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Singh SP, Alistarh D-A. WoodFisher: Efficient second-order approximation for
neural network compression. In: Advances in Neural Information Processing Systems.
Vol 33. Curran Associates; 2020:18098-18109.'
apa: 'Singh, S. P., & Alistarh, D.-A. (2020). WoodFisher: Efficient second-order
approximation for neural network compression. In Advances in Neural Information
Processing Systems (Vol. 33, pp. 18098–18109). Vancouver, Canada: Curran Associates.'
chicago: 'Singh, Sidak Pal, and Dan-Adrian Alistarh. “WoodFisher: Efficient Second-Order
Approximation for Neural Network Compression.” In Advances in Neural Information
Processing Systems, 33:18098–109. Curran Associates, 2020.'
ieee: 'S. P. Singh and D.-A. Alistarh, “WoodFisher: Efficient second-order approximation
for neural network compression,” in Advances in Neural Information Processing
Systems, Vancouver, Canada, 2020, vol. 33, pp. 18098–18109.'
ista: 'Singh SP, Alistarh D-A. 2020. WoodFisher: Efficient second-order approximation
for neural network compression. Advances in Neural Information Processing Systems.
NeurIPS: Conference on Neural Information Processing Systems vol. 33, 18098–18109.'
mla: 'Singh, Sidak Pal, and Dan-Adrian Alistarh. “WoodFisher: Efficient Second-Order
Approximation for Neural Network Compression.” Advances in Neural Information
Processing Systems, vol. 33, Curran Associates, 2020, pp. 18098–109.'
short: S.P. Singh, D.-A. Alistarh, in:, Advances in Neural Information Processing
Systems, Curran Associates, 2020, pp. 18098–18109.
conference:
end_date: 2020-12-12
location: Vancouver, Canada
name: 'NeurIPS: Conference on Neural Information Processing Systems'
start_date: 2020-12-06
date_created: 2021-07-04T22:01:26Z
date_published: 2020-12-06T00:00:00Z
date_updated: 2023-02-23T14:03:06Z
day: '06'
department:
- _id: DaAl
- _id: ToHe
ec_funded: 1
external_id:
arxiv:
- '2004.14340'
intvolume: ' 33'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://proceedings.neurips.cc/paper/2020/hash/d1ff1ec86b62cd5f3903ff19c3a326b2-Abstract.html
month: '12'
oa: 1
oa_version: Published Version
page: 18098-18109
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: Advances in Neural Information Processing Systems
publication_identifier:
isbn:
- '9781713829546'
issn:
- '10495258'
publication_status: published
publisher: Curran Associates
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'WoodFisher: Efficient second-order approximation for neural network compression'
type: conference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 33
year: '2020'
...
---
_id: '9633'
abstract:
- lang: eng
text: The search for biologically faithful synaptic plasticity rules has resulted
in a large body of models. They are usually inspired by – and fitted to – experimental
data, but they rarely produce neural dynamics that serve complex functions. These
failures suggest that current plasticity models are still under-constrained by
existing data. Here, we present an alternative approach that uses meta-learning
to discover plausible synaptic plasticity rules. Instead of experimental data,
the rules are constrained by the functions they implement and the structure they
are meant to produce. Briefly, we parameterize synaptic plasticity rules by a
Volterra expansion and then use supervised learning methods (gradient descent
or evolutionary strategies) to minimize a problem-dependent loss function that
quantifies how effectively a candidate plasticity rule transforms an initially
random network into one with the desired function. We first validate our approach
by re-discovering previously described plasticity rules, starting at the single-neuron
level and “Oja’s rule”, a simple Hebbian plasticity rule that captures the direction
of most variability of inputs to a neuron (i.e., the first principal component).
We expand the problem to the network level and ask the framework to find Oja’s
rule together with an anti-Hebbian rule such that an initially random two-layer
firing-rate network will recover several principal components of the input space
after learning. Next, we move to networks of integrate-and-fire neurons with plastic
inhibitory afferents. We train for rules that achieve a target firing rate by
countering tuned excitation. Our algorithm discovers a specific subset of the
manifold of rules that can solve this task. Our work is a proof of principle of
an automated and unbiased approach to unveil synaptic plasticity rules that obey
biological constraints and can solve complex functions.
acknowledgement: We would like to thank Chaitanya Chintaluri, Georgia Christodoulou,
Bill Podlaski and Merima Šabanovic for useful discussions and comments. This work
was supported by a Wellcome Trust ´ Senior Research Fellowship (214316/Z/18/Z),
a BBSRC grant (BB/N019512/1), an ERC consolidator Grant (SYNAPSEEK), a Leverhulme
Trust Project Grant (RPG-2016-446), and funding from École Polytechnique, Paris.
article_processing_charge: No
author:
- first_name: Basile J
full_name: Confavreux, Basile J
id: C7610134-B532-11EA-BD9F-F5753DDC885E
last_name: Confavreux
- first_name: Friedemann
full_name: Zenke, Friedemann
last_name: Zenke
- first_name: Everton J.
full_name: Agnes, Everton J.
last_name: Agnes
- first_name: Timothy
full_name: Lillicrap, Timothy
last_name: Lillicrap
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: 'Confavreux BJ, Zenke F, Agnes EJ, Lillicrap T, Vogels TP. A meta-learning
approach to (re)discover plasticity rules that carve a desired function into a
neural network. In: Advances in Neural Information Processing Systems.
Vol 33. ; 2020:16398-16408.'
apa: Confavreux, B. J., Zenke, F., Agnes, E. J., Lillicrap, T., & Vogels, T.
P. (2020). A meta-learning approach to (re)discover plasticity rules that carve
a desired function into a neural network. In Advances in Neural Information
Processing Systems (Vol. 33, pp. 16398–16408). Vancouver, Canada.
chicago: Confavreux, Basile J, Friedemann Zenke, Everton J. Agnes, Timothy Lillicrap,
and Tim P Vogels. “A Meta-Learning Approach to (Re)Discover Plasticity Rules That
Carve a Desired Function into a Neural Network.” In Advances in Neural Information
Processing Systems, 33:16398–408, 2020.
ieee: B. J. Confavreux, F. Zenke, E. J. Agnes, T. Lillicrap, and T. P. Vogels, “A
meta-learning approach to (re)discover plasticity rules that carve a desired function
into a neural network,” in Advances in Neural Information Processing Systems,
Vancouver, Canada, 2020, vol. 33, pp. 16398–16408.
ista: 'Confavreux BJ, Zenke F, Agnes EJ, Lillicrap T, Vogels TP. 2020. A meta-learning
approach to (re)discover plasticity rules that carve a desired function into a
neural network. Advances in Neural Information Processing Systems. NeurIPS: Conference
on Neural Information Processing Systems vol. 33, 16398–16408.'
mla: Confavreux, Basile J., et al. “A Meta-Learning Approach to (Re)Discover Plasticity
Rules That Carve a Desired Function into a Neural Network.” Advances in Neural
Information Processing Systems, vol. 33, 2020, pp. 16398–408.
short: B.J. Confavreux, F. Zenke, E.J. Agnes, T. Lillicrap, T.P. Vogels, in:, Advances
in Neural Information Processing Systems, 2020, pp. 16398–16408.
conference:
end_date: 2020-12-12
location: Vancouver, Canada
name: 'NeurIPS: Conference on Neural Information Processing Systems'
start_date: 2020-12-06
date_created: 2021-07-04T22:01:27Z
date_published: 2020-12-06T00:00:00Z
date_updated: 2023-10-18T09:20:55Z
day: '06'
department:
- _id: TiVo
ec_funded: 1
intvolume: ' 33'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://proceedings.neurips.cc/paper/2020/hash/bdbd5ebfde4934142c8a88e7a3796cd5-Abstract.html
month: '12'
oa: 1
oa_version: Published Version
page: 16398-16408
project:
- _id: c084a126-5a5b-11eb-8a69-d75314a70a87
grant_number: 214316/Z/18/Z
name: What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent
neuronal networks.
- _id: 0aacfa84-070f-11eb-9043-d7eb2c709234
call_identifier: H2020
grant_number: '819603'
name: Learning the shape of synaptic plasticity rules for neuronal architectures
and function through machine learning.
publication: Advances in Neural Information Processing Systems
publication_identifier:
issn:
- 1049-5258
publication_status: published
quality_controlled: '1'
related_material:
link:
- relation: is_continued_by
url: https://doi.org/10.1101/2020.10.24.353409
record:
- id: '14422'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: A meta-learning approach to (re)discover plasticity rules that carve a desired
function into a neural network
type: conference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 33
year: '2020'
...
---
_id: '9658'
abstract:
- lang: eng
text: Macroscopic models of nucleation provide powerful tools for understanding
activated phase transition processes. These models do not provide atomistic insights
and can thus sometimes lack material-specific descriptions. Here, we provide a
comprehensive framework for constructing a continuum picture from an atomistic
simulation of homogeneous nucleation. We use this framework to determine the equilibrium
shape of the solid nucleus that forms inside bulk liquid for a Lennard-Jones potential.
From this shape, we then extract the anisotropy of the solid-liquid interfacial
free energy, by performing a reverse Wulff construction in the space of spherical
harmonic expansions. We find that the shape of the nucleus is nearly spherical
and that its anisotropy can be perfectly described using classical models.
article_number: '044103'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
- first_name: Gareth A.
full_name: Tribello, Gareth A.
last_name: Tribello
citation:
ama: Cheng B, Ceriotti M, Tribello GA. Classical nucleation theory predicts the
shape of the nucleus in homogeneous solidification. The Journal of Chemical
Physics. 2020;152(4). doi:10.1063/1.5134461
apa: Cheng, B., Ceriotti, M., & Tribello, G. A. (2020). Classical nucleation
theory predicts the shape of the nucleus in homogeneous solidification. The
Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.5134461
chicago: Cheng, Bingqing, Michele Ceriotti, and Gareth A. Tribello. “Classical Nucleation
Theory Predicts the Shape of the Nucleus in Homogeneous Solidification.” The
Journal of Chemical Physics. AIP Publishing, 2020. https://doi.org/10.1063/1.5134461.
ieee: B. Cheng, M. Ceriotti, and G. A. Tribello, “Classical nucleation theory predicts
the shape of the nucleus in homogeneous solidification,” The Journal of Chemical
Physics, vol. 152, no. 4. AIP Publishing, 2020.
ista: Cheng B, Ceriotti M, Tribello GA. 2020. Classical nucleation theory predicts
the shape of the nucleus in homogeneous solidification. The Journal of Chemical
Physics. 152(4), 044103.
mla: Cheng, Bingqing, et al. “Classical Nucleation Theory Predicts the Shape of
the Nucleus in Homogeneous Solidification.” The Journal of Chemical Physics,
vol. 152, no. 4, 044103, AIP Publishing, 2020, doi:10.1063/1.5134461.
short: B. Cheng, M. Ceriotti, G.A. Tribello, The Journal of Chemical Physics 152
(2020).
date_created: 2021-07-15T07:22:24Z
date_published: 2020-01-31T00:00:00Z
date_updated: 2023-02-23T14:03:55Z
day: '31'
doi: 10.1063/1.5134461
extern: '1'
external_id:
arxiv:
- '1910.13481'
pmid:
- '32007057'
intvolume: ' 152'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://pure.qub.ac.uk/en/publications/classical-nucleation-theory-predicts-the-shape-of-the-nucleus-in-homogeneous-solidification(56af848b-eee8-4e9b-93cf-667373e4a49b).html
month: '01'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Classical nucleation theory predicts the shape of the nucleus in homogeneous
solidification
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 152
year: '2020'
...
---
_id: '9664'
abstract:
- lang: eng
text: Equilibrium molecular dynamics simulations, in combination with the Green-Kubo
(GK) method, have been extensively used to compute the thermal conductivity of
liquids. However, the GK method relies on an ambiguous definition of the microscopic
heat flux, which depends on how one chooses to distribute energies over atoms.
This ambiguity makes it problematic to employ the GK method for systems with nonpairwise
interactions. In this work, we show that the hydrodynamic description of thermally
driven density fluctuations can be used to obtain the thermal conductivity of
a bulk fluid unambiguously, thereby bypassing the need to define the heat flux.
We verify that, for a model fluid with only pairwise interactions, our method
yields estimates of thermal conductivity consistent with the GK approach. We apply
our approach to compute the thermal conductivity of a nonpairwise additive water
model at supercritical conditions, and of a liquid hydrogen system described by
a machine-learning interatomic potential, at 33 GPa and 2000 K.
article_number: '130602'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Daan
full_name: Frenkel, Daan
last_name: Frenkel
citation:
ama: Cheng B, Frenkel D. Computing the heat conductivity of fluids from density
fluctuations. Physical Review Letters. 2020;125(13). doi:10.1103/physrevlett.125.130602
apa: Cheng, B., & Frenkel, D. (2020). Computing the heat conductivity of fluids
from density fluctuations. Physical Review Letters. American Physical Society.
https://doi.org/10.1103/physrevlett.125.130602
chicago: Cheng, Bingqing, and Daan Frenkel. “Computing the Heat Conductivity of
Fluids from Density Fluctuations.” Physical Review Letters. American Physical
Society, 2020. https://doi.org/10.1103/physrevlett.125.130602.
ieee: B. Cheng and D. Frenkel, “Computing the heat conductivity of fluids from density
fluctuations,” Physical Review Letters, vol. 125, no. 13. American Physical
Society, 2020.
ista: Cheng B, Frenkel D. 2020. Computing the heat conductivity of fluids from density
fluctuations. Physical Review Letters. 125(13), 130602.
mla: Cheng, Bingqing, and Daan Frenkel. “Computing the Heat Conductivity of Fluids
from Density Fluctuations.” Physical Review Letters, vol. 125, no. 13,
130602, American Physical Society, 2020, doi:10.1103/physrevlett.125.130602.
short: B. Cheng, D. Frenkel, Physical Review Letters 125 (2020).
date_created: 2021-07-15T12:15:14Z
date_published: 2020-09-25T00:00:00Z
date_updated: 2021-08-09T12:35:58Z
day: '25'
doi: 10.1103/physrevlett.125.130602
extern: '1'
external_id:
arxiv:
- '2005.07562'
pmid:
- '33034481'
intvolume: ' 125'
issue: '13'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2005.07562
month: '09'
oa: 1
oa_version: Preprint
pmid: 1
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Computing the heat conductivity of fluids from density fluctuations
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 125
year: '2020'
...
---
_id: '9666'
abstract:
- lang: eng
text: Predicting phase stabilities of crystal polymorphs is central to computational
materials science and chemistry. Such predictions are challenging because they
first require searching for potential energy minima and then performing arduous
free-energy calculations to account for entropic effects at finite temperatures.
Here, we develop a framework that facilitates such predictions by exploiting all
the information obtained from random searches of crystal structures. This framework
combines automated clustering, classification and visualisation of crystal structures
with machine-learning estimation of their enthalpy and entropy. We demonstrate
the framework on the technologically important system of TiO2, which has many
polymorphs, without relying on prior knowledge of known phases. We find a number
of new phases and predict the phase diagram and metastabilities of crystal polymorphs
at 1600 K, benchmarking the results against full free-energy calculations.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Aleks
full_name: Reinhardt, Aleks
last_name: Reinhardt
- first_name: Chris J.
full_name: Pickard, Chris J.
last_name: Pickard
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: Reinhardt A, Pickard CJ, Cheng B. Predicting the phase diagram of titanium
dioxide with random search and pattern recognition. Physical Chemistry Chemical
Physics. 2020;22(22):12697-12705. doi:10.1039/d0cp02513e
apa: Reinhardt, A., Pickard, C. J., & Cheng, B. (2020). Predicting the phase
diagram of titanium dioxide with random search and pattern recognition. Physical
Chemistry Chemical Physics. Royal Society of Chemistry. https://doi.org/10.1039/d0cp02513e
chicago: Reinhardt, Aleks, Chris J. Pickard, and Bingqing Cheng. “Predicting the
Phase Diagram of Titanium Dioxide with Random Search and Pattern Recognition.”
Physical Chemistry Chemical Physics. Royal Society of Chemistry, 2020.
https://doi.org/10.1039/d0cp02513e.
ieee: A. Reinhardt, C. J. Pickard, and B. Cheng, “Predicting the phase diagram of
titanium dioxide with random search and pattern recognition,” Physical Chemistry
Chemical Physics, vol. 22, no. 22. Royal Society of Chemistry, pp. 12697–12705,
2020.
ista: Reinhardt A, Pickard CJ, Cheng B. 2020. Predicting the phase diagram of titanium
dioxide with random search and pattern recognition. Physical Chemistry Chemical
Physics. 22(22), 12697–12705.
mla: Reinhardt, Aleks, et al. “Predicting the Phase Diagram of Titanium Dioxide
with Random Search and Pattern Recognition.” Physical Chemistry Chemical Physics,
vol. 22, no. 22, Royal Society of Chemistry, 2020, pp. 12697–705, doi:10.1039/d0cp02513e.
short: A. Reinhardt, C.J. Pickard, B. Cheng, Physical Chemistry Chemical Physics
22 (2020) 12697–12705.
date_created: 2021-07-15T12:37:27Z
date_published: 2020-06-14T00:00:00Z
date_updated: 2023-02-23T14:04:16Z
day: '14'
ddc:
- '530'
doi: 10.1039/d0cp02513e
extern: '1'
external_id:
arxiv:
- '1909.08934'
pmid:
- '32459228'
file:
- access_level: open_access
checksum: 0a6872972b1b2e60f9095d39b01753fa
content_type: application/pdf
creator: asandaue
date_created: 2021-07-15T12:43:51Z
date_updated: 2021-07-15T12:43:51Z
file_id: '9667'
file_name: 202_PhysicalChemistryChemicalPhysics_Reinhardt.pdf
file_size: 3151206
relation: main_file
success: 1
file_date_updated: 2021-07-15T12:43:51Z
has_accepted_license: '1'
intvolume: ' 22'
issue: '22'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 12697-12705
pmid: 1
publication: Physical Chemistry Chemical Physics
publication_identifier:
eissn:
- 1463-9084
issn:
- 1463-9076
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Predicting the phase diagram of titanium dioxide with random search and pattern
recognition
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 22
year: '2020'
...
---
_id: '9671'
abstract:
- lang: eng
text: Water molecules can arrange into a liquid with complex hydrogen-bond networks
and at least 17 experimentally confirmed ice phases with enormous structural diversity.
It remains a puzzle how or whether this multitude of arrangements in different
phases of water are related. Here we investigate the structural similarities between
liquid water and a comprehensive set of 54 ice phases in simulations, by directly
comparing their local environments using general atomic descriptors, and also
by demonstrating that a machine-learning potential trained on liquid water alone
can predict the densities, lattice energies, and vibrational properties of the
ices. The finding that the local environments characterising the different ice
phases are found in water sheds light on the phase behavior of water, and rationalizes
the transferability of water models between different phases.
article_number: '5757'
article_processing_charge: No
article_type: original
author:
- first_name: Bartomeu
full_name: Monserrat, Bartomeu
last_name: Monserrat
- first_name: Jan Gerit
full_name: Brandenburg, Jan Gerit
last_name: Brandenburg
- first_name: Edgar A.
full_name: Engel, Edgar A.
last_name: Engel
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: Monserrat B, Brandenburg JG, Engel EA, Cheng B. Liquid water contains the building
blocks of diverse ice phases. Nature Communications. 2020;11(1). doi:10.1038/s41467-020-19606-y
apa: Monserrat, B., Brandenburg, J. G., Engel, E. A., & Cheng, B. (2020). Liquid
water contains the building blocks of diverse ice phases. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-020-19606-y
chicago: Monserrat, Bartomeu, Jan Gerit Brandenburg, Edgar A. Engel, and Bingqing
Cheng. “Liquid Water Contains the Building Blocks of Diverse Ice Phases.” Nature
Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-19606-y.
ieee: B. Monserrat, J. G. Brandenburg, E. A. Engel, and B. Cheng, “Liquid water
contains the building blocks of diverse ice phases,” Nature Communications,
vol. 11, no. 1. Springer Nature, 2020.
ista: Monserrat B, Brandenburg JG, Engel EA, Cheng B. 2020. Liquid water contains
the building blocks of diverse ice phases. Nature Communications. 11(1), 5757.
mla: Monserrat, Bartomeu, et al. “Liquid Water Contains the Building Blocks of Diverse
Ice Phases.” Nature Communications, vol. 11, no. 1, 5757, Springer Nature,
2020, doi:10.1038/s41467-020-19606-y.
short: B. Monserrat, J.G. Brandenburg, E.A. Engel, B. Cheng, Nature Communications
11 (2020).
date_created: 2021-07-15T14:01:35Z
date_published: 2020-11-13T00:00:00Z
date_updated: 2023-02-23T14:04:25Z
day: '13'
ddc:
- '530'
- '540'
doi: 10.1038/s41467-020-19606-y
extern: '1'
file:
- access_level: open_access
checksum: 1edd9b6d8fa791f8094d87bd6453955b
content_type: application/pdf
creator: asandaue
date_created: 2021-07-15T14:05:45Z
date_updated: 2021-07-15T14:05:45Z
file_id: '9672'
file_name: 2020_NatureCommunications_Monserrat.pdf
file_size: 1385954
relation: main_file
success: 1
file_date_updated: 2021-07-15T14:05:45Z
has_accepted_license: '1'
intvolume: ' 11'
issue: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Liquid water contains the building blocks of diverse ice phases
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: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 11
year: '2020'
...
---
_id: '9675'
abstract:
- lang: eng
text: The visualization of data is indispensable in scientific research, from the
early stages when human insight forms to the final step of communicating results.
In computational physics, chemistry and materials science, it can be as simple
as making a scatter plot or as straightforward as looking through the snapshots
of atomic positions manually. However, as a result of the "big data" revolution,
these conventional approaches are often inadequate. The widespread adoption of
high-throughput computation for materials discovery and the associated community-wide
repositories have given rise to data sets that contain an enormous number of compounds
and atomic configurations. A typical data set contains thousands to millions of
atomic structures, along with a diverse range of properties such as formation
energies, band gaps, or bioactivities.It would thus be desirable to have a data-driven
and automated framework for visualizing and analyzing such structural data sets.
The key idea is to construct a low-dimensional representation of the data, which
facilitates navigation, reveals underlying patterns, and helps to identify data
points with unusual attributes. Such data-intensive maps, often employing machine
learning methods, are appearing more and more frequently in the literature. However,
to the wider community, it is not always transparent how these maps are made and
how they should be interpreted. Furthermore, while these maps undoubtedly serve
a decorative purpose in academic publications, it is not always apparent what
extra information can be garnered from reading or making them.This Account attempts
to answer such questions. We start with a concise summary of the theory of representing
chemical environments, followed by the introduction of a simple yet practical
conceptual approach for generating structure maps in a generic and automated manner.
Such analysis and mapping is made nearly effortless by employing the newly developed
software tool ASAP. To showcase the applicability to a wide variety of systems
in chemistry and materials science, we provide several illustrative examples,
including crystalline and amorphous materials, interfaces, and organic molecules.
In these examples, the maps not only help to sift through large data sets but
also reveal hidden patterns that could be easily missed using conventional analyses.The
explosion in the amount of computed information in chemistry and materials science
has made visualization into a science in itself. Not only have we benefited from
exploiting these visualization methods in previous works, we also believe that
the automated mapping of data sets will in turn stimulate further creativity and
exploration, as well as ultimately feed back into future advances in the respective
fields.
article_processing_charge: No
article_type: original
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Ryan-Rhys
full_name: Griffiths, Ryan-Rhys
last_name: Griffiths
- first_name: Simon
full_name: Wengert, Simon
last_name: Wengert
- first_name: Christian
full_name: Kunkel, Christian
last_name: Kunkel
- first_name: Tamas
full_name: Stenczel, Tamas
last_name: Stenczel
- first_name: Bonan
full_name: Zhu, Bonan
last_name: Zhu
- first_name: Volker L.
full_name: Deringer, Volker L.
last_name: Deringer
- first_name: Noam
full_name: Bernstein, Noam
last_name: Bernstein
- first_name: Johannes T.
full_name: Margraf, Johannes T.
last_name: Margraf
- first_name: Karsten
full_name: Reuter, Karsten
last_name: Reuter
- first_name: Gabor
full_name: Csanyi, Gabor
last_name: Csanyi
citation:
ama: Cheng B, Griffiths R-R, Wengert S, et al. Mapping materials and molecules.
Accounts of Chemical Research. 2020;53(9):1981-1991. doi:10.1021/acs.accounts.0c00403
apa: Cheng, B., Griffiths, R.-R., Wengert, S., Kunkel, C., Stenczel, T., Zhu, B.,
… Csanyi, G. (2020). Mapping materials and molecules. Accounts of Chemical
Research. American Chemical Society. https://doi.org/10.1021/acs.accounts.0c00403
chicago: Cheng, Bingqing, Ryan-Rhys Griffiths, Simon Wengert, Christian Kunkel,
Tamas Stenczel, Bonan Zhu, Volker L. Deringer, et al. “Mapping Materials and Molecules.”
Accounts of Chemical Research. American Chemical Society, 2020. https://doi.org/10.1021/acs.accounts.0c00403.
ieee: B. Cheng et al., “Mapping materials and molecules,” Accounts of
Chemical Research, vol. 53, no. 9. American Chemical Society, pp. 1981–1991,
2020.
ista: Cheng B, Griffiths R-R, Wengert S, Kunkel C, Stenczel T, Zhu B, Deringer VL,
Bernstein N, Margraf JT, Reuter K, Csanyi G. 2020. Mapping materials and molecules.
Accounts of Chemical Research. 53(9), 1981–1991.
mla: Cheng, Bingqing, et al. “Mapping Materials and Molecules.” Accounts of Chemical
Research, vol. 53, no. 9, American Chemical Society, 2020, pp. 1981–91, doi:10.1021/acs.accounts.0c00403.
short: B. Cheng, R.-R. Griffiths, S. Wengert, C. Kunkel, T. Stenczel, B. Zhu, V.L.
Deringer, N. Bernstein, J.T. Margraf, K. Reuter, G. Csanyi, Accounts of Chemical
Research 53 (2020) 1981–1991.
date_created: 2021-07-16T06:25:53Z
date_published: 2020-08-14T00:00:00Z
date_updated: 2021-11-24T15:54:41Z
day: '14'
doi: 10.1021/acs.accounts.0c00403
extern: '1'
external_id:
pmid:
- '32794697'
intvolume: ' 53'
issue: '9'
language:
- iso: eng
month: '08'
oa_version: None
page: 1981-1991
pmid: 1
publication: Accounts of Chemical Research
publication_identifier:
eissn:
- 1520-4898
issn:
- 0001-4842
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mapping materials and molecules
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 53
year: '2020'
...
---
_id: '9685'
abstract:
- lang: eng
text: Hydrogen, the simplest and most abundant element in the Universe, develops
a remarkably complex behaviour upon compression^1. Since Wigner predicted the
dissociation and metallization of solid hydrogen at megabar pressures almost a
century ago^2, several efforts have been made to explain the many unusual properties
of dense hydrogen, including a rich and poorly understood solid polymorphism^1,3-5,
an anomalous melting line6 and the possible transition to a superconducting state^7.
Experiments at such extreme conditions are challenging and often lead to hard-to-interpret
and controversial observations, whereas theoretical investigations are constrained
by the huge computational cost of sufficiently accurate quantum mechanical calculations.
Here we present a theoretical study of the phase diagram of dense hydrogen that
uses machine learning to 'learn' potential-energy surfaces and interatomic forces
from reference calculations and then predict them at low computational cost, overcoming
length- and timescale limitations. We reproduce both the re-entrant melting behaviour
and the polymorphism of the solid phase. Simulations using our machine-learning-based
potentials provide evidence for a continuous molecular-to-atomic transition in
the liquid, with no first-order transition observed above the melting line. This
suggests a smooth transition between insulating and metallic layers in giant gas
planets, and reconciles existing discrepancies between experiments as a manifestation
of supercritical behaviour.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Guglielmo
full_name: Mazzola, Guglielmo
last_name: Mazzola
- first_name: Chris J.
full_name: Pickard, Chris J.
last_name: Pickard
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: Cheng B, Mazzola G, Pickard CJ, Ceriotti M. Evidence for supercritical behaviour
of high-pressure liquid hydrogen. Nature. 2020;585(7824):217-220. doi:10.1038/s41586-020-2677-y
apa: Cheng, B., Mazzola, G., Pickard, C. J., & Ceriotti, M. (2020). Evidence
for supercritical behaviour of high-pressure liquid hydrogen. Nature. Springer
Nature. https://doi.org/10.1038/s41586-020-2677-y
chicago: Cheng, Bingqing, Guglielmo Mazzola, Chris J. Pickard, and Michele Ceriotti.
“Evidence for Supercritical Behaviour of High-Pressure Liquid Hydrogen.” Nature.
Springer Nature, 2020. https://doi.org/10.1038/s41586-020-2677-y.
ieee: B. Cheng, G. Mazzola, C. J. Pickard, and M. Ceriotti, “Evidence for supercritical
behaviour of high-pressure liquid hydrogen,” Nature, vol. 585, no. 7824.
Springer Nature, pp. 217–220, 2020.
ista: Cheng B, Mazzola G, Pickard CJ, Ceriotti M. 2020. Evidence for supercritical
behaviour of high-pressure liquid hydrogen. Nature. 585(7824), 217–220.
mla: Cheng, Bingqing, et al. “Evidence for Supercritical Behaviour of High-Pressure
Liquid Hydrogen.” Nature, vol. 585, no. 7824, Springer Nature, 2020, pp.
217–20, doi:10.1038/s41586-020-2677-y.
short: B. Cheng, G. Mazzola, C.J. Pickard, M. Ceriotti, Nature 585 (2020) 217–220.
date_created: 2021-07-19T09:17:49Z
date_published: 2020-09-10T00:00:00Z
date_updated: 2021-08-09T12:38:01Z
day: '10'
doi: 10.1038/s41586-020-2677-y
extern: '1'
external_id:
arxiv:
- '1906.03341'
pmid:
- '32908269'
intvolume: ' 585'
issue: '7824'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1906.03341
month: '09'
oa: 1
oa_version: Preprint
page: 217-220
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: Evidence for supercritical behaviour of high-pressure liquid hydrogen
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 585
year: '2020'
...
---
_id: '10012'
abstract:
- lang: eng
text: We prove that in the absence of topological changes, the notion of BV solutions
to planar multiphase mean curvature flow does not allow for a mechanism for (unphysical)
non-uniqueness. Our approach is based on the local structure of the energy landscape
near a classical evolution by mean curvature. Mean curvature flow being the gradient
flow of the surface energy functional, we develop a gradient-flow analogue of
the notion of calibrations. Just like the existence of a calibration guarantees
that one has reached a global minimum in the energy landscape, the existence of
a "gradient flow calibration" ensures that the route of steepest descent in the
energy landscape is unique and stable.
acknowledgement: Parts of the paper were written during the visit of the authors to
the Hausdorff Research Institute for Mathematics (HIM), University of Bonn, in the
framework of the trimester program “Evolution of Interfaces”. The support and the
hospitality of HIM are gratefully acknowledged. This project has received funding
from the European Union’s Horizon 2020 research and innovation programme under the
Marie Sklodowska-Curie Grant Agreement No. 665385.
article_number: '2003.05478'
article_processing_charge: No
arxiv: 1
author:
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
- first_name: Sebastian
full_name: Hensel, Sebastian
id: 4D23B7DA-F248-11E8-B48F-1D18A9856A87
last_name: Hensel
orcid: 0000-0001-7252-8072
- first_name: Tim
full_name: Laux, Tim
last_name: Laux
- first_name: Thilo
full_name: Simon, Thilo
last_name: Simon
citation:
ama: 'Fischer JL, Hensel S, Laux T, Simon T. The local structure of the energy landscape
in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions.
arXiv.'
apa: 'Fischer, J. L., Hensel, S., Laux, T., & Simon, T. (n.d.). The local structure
of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness
and stability of evolutions. arXiv.'
chicago: 'Fischer, Julian L, Sebastian Hensel, Tim Laux, and Thilo Simon. “The Local
Structure of the Energy Landscape in Multiphase Mean Curvature Flow: Weak-Strong
Uniqueness and Stability of Evolutions.” ArXiv, n.d.'
ieee: 'J. L. Fischer, S. Hensel, T. Laux, and T. Simon, “The local structure of
the energy landscape in multiphase mean curvature flow: weak-strong uniqueness
and stability of evolutions,” arXiv. .'
ista: 'Fischer JL, Hensel S, Laux T, Simon T. The local structure of the energy
landscape in multiphase mean curvature flow: weak-strong uniqueness and stability
of evolutions. arXiv, 2003.05478.'
mla: 'Fischer, Julian L., et al. “The Local Structure of the Energy Landscape in
Multiphase Mean Curvature Flow: Weak-Strong Uniqueness and Stability of Evolutions.”
ArXiv, 2003.05478.'
short: J.L. Fischer, S. Hensel, T. Laux, T. Simon, ArXiv (n.d.).
date_created: 2021-09-13T12:17:11Z
date_published: 2020-03-11T00:00:00Z
date_updated: 2023-09-07T13:30:45Z
day: '11'
department:
- _id: JuFi
ec_funded: 1
external_id:
arxiv:
- '2003.05478'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2003.05478
month: '03'
oa: 1
oa_version: Preprint
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: arXiv
publication_status: submitted
related_material:
record:
- id: '10007'
relation: dissertation_contains
status: public
status: public
title: 'The local structure of the energy landscape in multiphase mean curvature flow:
weak-strong uniqueness and stability of evolutions'
type: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2020'
...
---
_id: '10022'
abstract:
- lang: eng
text: We consider finite-volume approximations of Fokker-Planck equations on bounded
convex domains in R^d and study the corresponding gradient flow structures. We
reprove the convergence of the discrete to continuous Fokker-Planck equation via
the method of Evolutionary Γ-convergence, i.e., we pass to the limit at the level
of the gradient flow structures, generalising the one-dimensional result obtained
by Disser and Liero. The proof is of variational nature and relies on a Mosco
convergence result for functionals in the discrete-to-continuum limit that is
of independent interest. Our results apply to arbitrary regular meshes, even though
the associated discrete transport distances may fail to converge to the Wasserstein
distance in this generality.
acknowledgement: This work is supported by the European Research Council (ERC) under
the European Union’s Horizon 2020 research and innovation programme (grant agreement
No 716117) and by the Austrian Science Fund (FWF), grants No F65 and W1245.
article_number: '2008.10962'
article_processing_charge: No
arxiv: 1
author:
- first_name: Dominik L
full_name: Forkert, Dominik L
id: 35C79D68-F248-11E8-B48F-1D18A9856A87
last_name: Forkert
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
- first_name: Lorenzo
full_name: Portinale, Lorenzo
id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87
last_name: Portinale
citation:
ama: Forkert DL, Maas J, Portinale L. Evolutionary Γ-convergence of entropic gradient
flow structures for Fokker-Planck equations in multiple dimensions. arXiv.
apa: Forkert, D. L., Maas, J., & Portinale, L. (n.d.). Evolutionary Γ-convergence
of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions.
arXiv.
chicago: Forkert, Dominik L, Jan Maas, and Lorenzo Portinale. “Evolutionary Γ-Convergence
of Entropic Gradient Flow Structures for Fokker-Planck Equations in Multiple Dimensions.”
ArXiv, n.d.
ieee: D. L. Forkert, J. Maas, and L. Portinale, “Evolutionary Γ-convergence of entropic
gradient flow structures for Fokker-Planck equations in multiple dimensions,”
arXiv. .
ista: Forkert DL, Maas J, Portinale L. Evolutionary Γ-convergence of entropic gradient
flow structures for Fokker-Planck equations in multiple dimensions. arXiv, 2008.10962.
mla: Forkert, Dominik L., et al. “Evolutionary Γ-Convergence of Entropic Gradient
Flow Structures for Fokker-Planck Equations in Multiple Dimensions.” ArXiv,
2008.10962.
short: D.L. Forkert, J. Maas, L. Portinale, ArXiv (n.d.).
date_created: 2021-09-17T10:57:27Z
date_published: 2020-08-25T00:00:00Z
date_updated: 2023-09-07T13:31:05Z
day: '25'
department:
- _id: JaMa
ec_funded: 1
external_id:
arxiv:
- '2008.10962'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2008.10962
month: '08'
oa: 1
oa_version: Preprint
page: '33'
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
publication: arXiv
publication_status: submitted
related_material:
record:
- id: '11739'
relation: later_version
status: public
- id: '10030'
relation: dissertation_contains
status: public
status: public
title: Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck
equations in multiple dimensions
type: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2020'
...
---
_id: '10328'
abstract:
- lang: eng
text: We discus noise channels in coherent electro-optic up-conversion between microwave
and optical fields, in particular due to optical heating. We also report on a
novel configuration, which promises to be flexible and highly efficient.
alternative_title:
- OSA Technical Digest
article_number: QTu8A.1
article_processing_charge: No
author:
- first_name: Nicholas J.
full_name: Lambert, Nicholas J.
last_name: Lambert
- first_name: Sonia
full_name: Mobassem, Sonia
last_name: Mobassem
- first_name: Alfredo R
full_name: Rueda Sanchez, Alfredo R
id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87
last_name: Rueda Sanchez
orcid: 0000-0001-6249-5860
- first_name: Harald G.L.
full_name: Schwefel, Harald G.L.
last_name: Schwefel
citation:
ama: 'Lambert NJ, Mobassem S, Rueda Sanchez AR, Schwefel HGL. New designs and noise
channels in electro-optic microwave to optical up-conversion. In: OSA Quantum
2.0 Conference. Optica Publishing Group; 2020. doi:10.1364/QUANTUM.2020.QTu8A.1'
apa: 'Lambert, N. J., Mobassem, S., Rueda Sanchez, A. R., & Schwefel, H. G.
L. (2020). New designs and noise channels in electro-optic microwave to optical
up-conversion. In OSA Quantum 2.0 Conference. Washington, DC, United States:
Optica Publishing Group. https://doi.org/10.1364/QUANTUM.2020.QTu8A.1'
chicago: Lambert, Nicholas J., Sonia Mobassem, Alfredo R Rueda Sanchez, and Harald
G.L. Schwefel. “New Designs and Noise Channels in Electro-Optic Microwave to Optical
up-Conversion.” In OSA Quantum 2.0 Conference. Optica Publishing Group,
2020. https://doi.org/10.1364/QUANTUM.2020.QTu8A.1.
ieee: N. J. Lambert, S. Mobassem, A. R. Rueda Sanchez, and H. G. L. Schwefel, “New
designs and noise channels in electro-optic microwave to optical up-conversion,”
in OSA Quantum 2.0 Conference, Washington, DC, United States, 2020.
ista: 'Lambert NJ, Mobassem S, Rueda Sanchez AR, Schwefel HGL. 2020. New designs
and noise channels in electro-optic microwave to optical up-conversion. OSA Quantum
2.0 Conference. OSA: Optical Society of America, OSA Technical Digest, , QTu8A.1.'
mla: Lambert, Nicholas J., et al. “New Designs and Noise Channels in Electro-Optic
Microwave to Optical up-Conversion.” OSA Quantum 2.0 Conference, QTu8A.1,
Optica Publishing Group, 2020, doi:10.1364/QUANTUM.2020.QTu8A.1.
short: N.J. Lambert, S. Mobassem, A.R. Rueda Sanchez, H.G.L. Schwefel, in:, OSA
Quantum 2.0 Conference, Optica Publishing Group, 2020.
conference:
end_date: 2020-09-17
location: Washington, DC, United States
name: 'OSA: Optical Society of America'
start_date: 2020-09-14
date_created: 2021-11-21T23:01:31Z
date_published: 2020-01-01T00:00:00Z
date_updated: 2023-10-18T08:32:34Z
day: '01'
department:
- _id: JoFi
doi: 10.1364/QUANTUM.2020.QTu8A.1
language:
- iso: eng
month: '01'
oa_version: None
publication: OSA Quantum 2.0 Conference
publication_identifier:
isbn:
- 9-781-5575-2820-9
publication_status: published
publisher: Optica Publishing Group
quality_controlled: '1'
scopus_import: '1'
status: public
title: New designs and noise channels in electro-optic microwave to optical up-conversion
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '10336'
abstract:
- lang: eng
text: Biological membranes can dramatically accelerate the aggregation of normally
soluble protein molecules into amyloid fibrils and alter the fibril morphologies,
yet the molecular mechanisms through which this accelerated nucleation takes place
are not yet understood. Here, we develop a coarse-grained model to systematically
explore the effect that the structural properties of the lipid membrane and the
nature of protein–membrane interactions have on the nucleation rates of amyloid
fibrils. We identify two physically distinct nucleation pathways—protein-rich
and lipid-rich—and quantify how the membrane fluidity and protein–membrane affinity
control the relative importance of those molecular pathways. We find that the
membrane’s susceptibility to reshaping and being incorporated into the fibrillar
aggregates is a key determinant of its ability to promote protein aggregation.
We then characterize the rates and the free-energy profile associated with this
heterogeneous nucleation process, in which the surface itself participates in
the aggregate structure. Finally, we compare quantitatively our data to experiments
on membrane-catalyzed amyloid aggregation of α-synuclein, a protein implicated
in Parkinson’s disease that predominately nucleates on membranes. More generally,
our results provide a framework for understanding macromolecular aggregation on
lipid membranes in a broad biological and biotechnological context.
acknowledgement: We thank T. C. T. Michaels for reading the manuscript. This work
was supported by the Academy of Medical Science (J.K. and A.Š.), the Cambridge Center
for Misfolding Diseases (T.P.J.K.), the Biotechnology and Biological Sciences Research
Council (T.P.J.K.), the Frances and Augustus Newman Foundation (T.P.J.K.), the European
Research Council Grant PhysProt Agreement 337969, the Wellcome Trust (A.Š. and T.P.J.K.),
the Royal Society (A.Š.), the Medical Research Council (J.K. and A.Š.), and the
UK Materials and Molecular Modeling Hub for computational resources, which is partially
funded by Engineering and Physical Sciences Research Council Grant EP/P020194/1.
article_processing_charge: No
article_type: original
author:
- first_name: Johannes
full_name: Krausser, Johannes
last_name: Krausser
- first_name: Tuomas P. J.
full_name: Knowles, Tuomas P. J.
last_name: Knowles
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
citation:
ama: Krausser J, Knowles TPJ, Šarić A. Physical mechanisms of amyloid nucleation
on fluid membranes. Proceedings of the National Academy of Sciences. 2020;117(52):33090-33098.
doi:10.1073/pnas.2007694117
apa: Krausser, J., Knowles, T. P. J., & Šarić, A. (2020). Physical mechanisms
of amyloid nucleation on fluid membranes. Proceedings of the National Academy
of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2007694117
chicago: Krausser, Johannes, Tuomas P. J. Knowles, and Anđela Šarić. “Physical Mechanisms
of Amyloid Nucleation on Fluid Membranes.” Proceedings of the National Academy
of Sciences. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2007694117.
ieee: J. Krausser, T. P. J. Knowles, and A. Šarić, “Physical mechanisms of amyloid
nucleation on fluid membranes,” Proceedings of the National Academy of Sciences,
vol. 117, no. 52. National Academy of Sciences, pp. 33090–33098, 2020.
ista: Krausser J, Knowles TPJ, Šarić A. 2020. Physical mechanisms of amyloid nucleation
on fluid membranes. Proceedings of the National Academy of Sciences. 117(52),
33090–33098.
mla: Krausser, Johannes, et al. “Physical Mechanisms of Amyloid Nucleation on Fluid
Membranes.” Proceedings of the National Academy of Sciences, vol. 117,
no. 52, National Academy of Sciences, 2020, pp. 33090–98, doi:10.1073/pnas.2007694117.
short: J. Krausser, T.P.J. Knowles, A. Šarić, Proceedings of the National Academy
of Sciences 117 (2020) 33090–33098.
date_created: 2021-11-25T15:07:09Z
date_published: 2020-12-16T00:00:00Z
date_updated: 2021-11-25T15:35:58Z
day: '16'
doi: 10.1073/pnas.2007694117
extern: '1'
external_id:
pmid:
- '33328273'
intvolume: ' 117'
issue: '52'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/2019.12.22.886267v2
month: '12'
oa: 1
oa_version: Published Version
page: 33090-33098
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Physical mechanisms of amyloid nucleation on fluid membranes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 117
year: '2020'
...
---
_id: '10341'
abstract:
- lang: eng
text: Tracing the motion of macromolecules, viruses, and nanoparticles adsorbed
onto cell membranes is currently the most direct way of probing the complex dynamic
interactions behind vital biological processes, including cell signalling, trafficking,
and viral infection. The resulting trajectories are usually consistent with some
type of anomalous diffusion, but the molecular origins behind the observed anomalous
behaviour are usually not obvious. Here we use coarse-grained molecular dynamics
simulations to help identify the physical mechanisms that can give rise to experimentally
observed trajectories of nanoscopic objects moving on biological membranes. We
find that diffusion on membranes of high fluidities typically results in normal
diffusion of the adsorbed nanoparticle, irrespective of the concentration of receptors,
receptor clustering, or multivalent interactions between the particle and membrane
receptors. Gel-like membranes on the other hand result in anomalous diffusion
of the particle, which becomes more pronounced at higher receptor concentrations.
This anomalous diffusion is characterised by local particle trapping in the regions
of high receptor concentrations and fast hopping between such regions. The normal
diffusion is recovered in the limit where the gel membrane is saturated with receptors.
We conclude that hindered receptor diffusivity can be a common reason behind the
observed anomalous diffusion of viruses, vesicles, and nanoparticles adsorbed
on cell and model membranes. Our results enable direct comparison with experiments
and offer a new route for interpreting motility experiments on cell membranes.
acknowledgement: We thank Jessica McQuade for her input at the start of the project.
We acknowledge support from the ERASMUS Placement Programme (V. E. D.), the UCL
Institute for the Physics of Living Systems (V. E. D. and A. Š.), the UCL Global
Engagement Fund (L. M. C. J.), and the Royal Society (A. Š.).
article_processing_charge: No
article_type: original
author:
- first_name: V. E.
full_name: Debets, V. E.
last_name: Debets
- first_name: L. M. C.
full_name: Janssen, L. M. C.
last_name: Janssen
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
citation:
ama: Debets VE, Janssen LMC, Šarić A. Characterising the diffusion of biological
nanoparticles on fluid and cross-linked membranes. Soft Matter. 2020;16(47):10628-10639.
doi:10.1039/d0sm00712a
apa: Debets, V. E., Janssen, L. M. C., & Šarić, A. (2020). Characterising the
diffusion of biological nanoparticles on fluid and cross-linked membranes. Soft
Matter. Royal Society of Chemistry. https://doi.org/10.1039/d0sm00712a
chicago: Debets, V. E., L. M. C. Janssen, and Anđela Šarić. “Characterising the
Diffusion of Biological Nanoparticles on Fluid and Cross-Linked Membranes.” Soft
Matter. Royal Society of Chemistry, 2020. https://doi.org/10.1039/d0sm00712a.
ieee: V. E. Debets, L. M. C. Janssen, and A. Šarić, “Characterising the diffusion
of biological nanoparticles on fluid and cross-linked membranes,” Soft Matter,
vol. 16, no. 47. Royal Society of Chemistry, pp. 10628–10639, 2020.
ista: Debets VE, Janssen LMC, Šarić A. 2020. Characterising the diffusion of biological
nanoparticles on fluid and cross-linked membranes. Soft Matter. 16(47), 10628–10639.
mla: Debets, V. E., et al. “Characterising the Diffusion of Biological Nanoparticles
on Fluid and Cross-Linked Membranes.” Soft Matter, vol. 16, no. 47, Royal
Society of Chemistry, 2020, pp. 10628–39, doi:10.1039/d0sm00712a.
short: V.E. Debets, L.M.C. Janssen, A. Šarić, Soft Matter 16 (2020) 10628–10639.
date_created: 2021-11-26T06:29:41Z
date_published: 2020-10-06T00:00:00Z
date_updated: 2021-11-26T07:00:33Z
day: '06'
doi: 10.1039/d0sm00712a
extern: '1'
external_id:
pmid:
- '33084724'
intvolume: ' 16'
issue: '47'
keyword:
- condensed matter physics
- general chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/2020.05.01.071761v1
month: '10'
oa: 1
oa_version: Published Version
page: 10628-10639
pmid: 1
publication: Soft Matter
publication_identifier:
issn:
- 1744-683X
- 1744-6848
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Characterising the diffusion of biological nanoparticles on fluid and cross-linked
membranes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 16
year: '2020'
...
---
_id: '10342'
abstract:
- lang: eng
text: The blood-brain barrier is made of polarized brain endothelial cells (BECs)
phenotypically conditioned by the central nervous system (CNS). Although transport
across BECs is of paramount importance for nutrient uptake as well as ridding
the brain of waste products, the intracellular sorting mechanisms that regulate
successful receptor-mediated transcytosis in BECs remain to be elucidated. Here,
we used a synthetic multivalent system with tunable avidity to the low-density
lipoprotein receptor–related protein 1 (LRP1) to investigate the mechanisms of
transport across BECs. We used a combination of conventional and super-resolution
microscopy, both in vivo and in vitro, accompanied with biophysical modeling of
transport kinetics and membrane-bound interactions to elucidate the role of membrane-sculpting
protein syndapin-2 on fast transport via tubule formation. We show that high-avidity
cargo biases the LRP1 toward internalization associated with fast degradation,
while mid-avidity augments the formation of syndapin-2 tubular carriers promoting
a fast shuttling across.
acknowledgement: 'Funding: G.B. thanks the ERC for the starting grant (MEViC 278793)
and consolidator award (CheSSTaG 769798), EPSRC/BTG Healthcare Partnership (EP/I001697/1),
EPSRC Established Career Fellowship (EP/N026322/1), EPSRC/SomaNautix Healthcare
Partnership EP/R024723/1, and Children with Cancer UK for the research project (16-227).
X.T. and G.B. thank that Anhui 100 Talent program for facilitating data sharing
and research visits. A.D.-C. and L.R. acknowledge the Royal Society for a Newton
fellowship and the Marie Skłodowska-Curie Actions for a European Fellowship. Author
contributions: X.T. prepared and characterized POs, performed all the fast imaging
in both conventional and STED microscopy, set up the initial BBB model, encapsulated
the PtA2 in POs, and supervised the PtA2-PO animal work. D.M.L. prepared and characterized
POs; performed all the permeability studies, PLA assays, WB and associated data
analysis, and part of the colocalization assays; and performed experiments with
the shRNA for knockdown of syndapin-2. E.S. prepared and characterized POs and performed
part of colocalization assays and Cy7-labeled PO animal experiments. S.N. prepared
and characterized POs and performed part of the colocalization and inhibition assays.
G.F. designed, performed, and analyzed the agent-based simulations of transcytosis.
J.F. designed the image-based algorithm to analyze the PLA data. D.M. prepared and
characterized POs and helped with Cy7-labeled PO animal experiments. A.A. performed
TEM imaging of the POs. A.P. and A.D.-C. synthesized the dye- and peptide-functionalized
and pristine copolymers. M.V., L.H.-K., and A.Š. designed, performed, and analyzed
the MD simulations. Z.Z. supervised and supported STED imaging. P.X., B.F., and
Y.T. synthesized and characterized the PtA2 compound. L.L. performed some of the
animal work. L.R. supported and helped with the BBB characterization. G.B. analyzed
all fast imaging and supervised and coordinated the overall work. X.T., D.M.L.,
E.S., and G.B. wrote the manuscript. Competing interests: The authors declare that
part of the work is associated with the UCL spin-out company SomaNautix Ltd. Data
and materials availability: All data needed to evaluate the conclusions in the paper
are present in the paper and/or the Supplementary Materials. Additional data related
to this paper may be requested from the authors.'
article_number: 'eabc4397 '
article_processing_charge: No
article_type: original
author:
- first_name: Xiaohe
full_name: Tian, Xiaohe
last_name: Tian
- first_name: Diana M.
full_name: Leite, Diana M.
last_name: Leite
- first_name: Edoardo
full_name: Scarpa, Edoardo
last_name: Scarpa
- first_name: Sophie
full_name: Nyberg, Sophie
last_name: Nyberg
- first_name: Gavin
full_name: Fullstone, Gavin
last_name: Fullstone
- first_name: Joe
full_name: Forth, Joe
last_name: Forth
- first_name: Diana
full_name: Matias, Diana
last_name: Matias
- first_name: Azzurra
full_name: Apriceno, Azzurra
last_name: Apriceno
- first_name: Alessandro
full_name: Poma, Alessandro
last_name: Poma
- first_name: Aroa
full_name: Duro-Castano, Aroa
last_name: Duro-Castano
- first_name: Manish
full_name: Vuyyuru, Manish
last_name: Vuyyuru
- first_name: Lena
full_name: Harker-Kirschneck, Lena
last_name: Harker-Kirschneck
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Zhongping
full_name: Zhang, Zhongping
last_name: Zhang
- first_name: Pan
full_name: Xiang, Pan
last_name: Xiang
- first_name: Bin
full_name: Fang, Bin
last_name: Fang
- first_name: Yupeng
full_name: Tian, Yupeng
last_name: Tian
- first_name: Lei
full_name: Luo, Lei
last_name: Luo
- first_name: Loris
full_name: Rizzello, Loris
last_name: Rizzello
- first_name: Giuseppe
full_name: Battaglia, Giuseppe
last_name: Battaglia
citation:
ama: 'Tian X, Leite DM, Scarpa E, et al. On the shuttling across the blood-brain
barrier via tubule formation: Mechanism and cargo avidity bias. Science Advances.
2020;6(48). doi:10.1126/sciadv.abc4397'
apa: 'Tian, X., Leite, D. M., Scarpa, E., Nyberg, S., Fullstone, G., Forth, J.,
… Battaglia, G. (2020). On the shuttling across the blood-brain barrier via tubule
formation: Mechanism and cargo avidity bias. Science Advances. American
Association for the Advancement of Science. https://doi.org/10.1126/sciadv.abc4397'
chicago: 'Tian, Xiaohe, Diana M. Leite, Edoardo Scarpa, Sophie Nyberg, Gavin Fullstone,
Joe Forth, Diana Matias, et al. “On the Shuttling across the Blood-Brain Barrier
via Tubule Formation: Mechanism and Cargo Avidity Bias.” Science Advances.
American Association for the Advancement of Science, 2020. https://doi.org/10.1126/sciadv.abc4397.'
ieee: 'X. Tian et al., “On the shuttling across the blood-brain barrier via
tubule formation: Mechanism and cargo avidity bias,” Science Advances,
vol. 6, no. 48. American Association for the Advancement of Science, 2020.'
ista: 'Tian X, Leite DM, Scarpa E, Nyberg S, Fullstone G, Forth J, Matias D, Apriceno
A, Poma A, Duro-Castano A, Vuyyuru M, Harker-Kirschneck L, Šarić A, Zhang Z, Xiang
P, Fang B, Tian Y, Luo L, Rizzello L, Battaglia G. 2020. On the shuttling across
the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias.
Science Advances. 6(48), eabc4397.'
mla: 'Tian, Xiaohe, et al. “On the Shuttling across the Blood-Brain Barrier via
Tubule Formation: Mechanism and Cargo Avidity Bias.” Science Advances,
vol. 6, no. 48, eabc4397, American Association for the Advancement of Science,
2020, doi:10.1126/sciadv.abc4397.'
short: X. Tian, D.M. Leite, E. Scarpa, S. Nyberg, G. Fullstone, J. Forth, D. Matias,
A. Apriceno, A. Poma, A. Duro-Castano, M. Vuyyuru, L. Harker-Kirschneck, A. Šarić,
Z. Zhang, P. Xiang, B. Fang, Y. Tian, L. Luo, L. Rizzello, G. Battaglia, Science
Advances 6 (2020).
date_created: 2021-11-26T06:40:28Z
date_published: 2020-11-27T00:00:00Z
date_updated: 2021-11-26T07:00:24Z
day: '27'
ddc:
- '611'
doi: 10.1126/sciadv.abc4397
extern: '1'
external_id:
pmid:
- '33246953'
file:
- access_level: open_access
checksum: 3ba2eca975930cdb0b1ce1ae876885a7
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-26T06:50:09Z
date_updated: 2021-11-26T06:50:09Z
file_id: '10343'
file_name: 2020_SciAdv_Tian.pdf
file_size: 10381298
relation: main_file
success: 1
file_date_updated: 2021-11-26T06:50:09Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '48'
keyword:
- multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/2020.04.04.025866v1
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: Science Advances
publication_identifier:
issn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'On the shuttling across the blood-brain barrier via tubule formation: Mechanism
and cargo avidity bias'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 6
year: '2020'
...
---
_id: '10344'
abstract:
- lang: eng
text: In this study, we investigate the role of the surface patterning of nanostructures
for cell membrane reshaping. To accomplish this, we combine an evolutionary algorithm
with coarse-grained molecular dynamics simulations and explore the solution space
of ligand patterns on a nanoparticle that promote efficient and reliable cell
uptake. Surprisingly, we find that in the regime of low ligand number the best-performing
structures are characterized by ligands arranged into long one-dimensional chains
that pattern the surface of the particle. We show that these chains of ligands
provide particles with high rotational freedom and they lower the free energy
barrier for membrane crossing. Our approach reveals a set of nonintuitive design
rules that can be used to inform artificial nanoparticle construction and the
search for inhibitors of viral entry.
acknowledgement: We acknowledge support from EPSRC (J. C. F.), MRC (B. B. and A. Š.),
the ERC StG 802960 “NEPA” (J. K. and A. Š.), the Royal Society (A. Š.), and the
United Kingdom Materials and Molecular Modelling Hub for computational resources,
which is partially funded by EPSRC (EP/P020194/1).
article_number: '228101'
article_processing_charge: No
article_type: original
author:
- first_name: Joel C.
full_name: Forster, Joel C.
last_name: Forster
- first_name: Johannes
full_name: Krausser, Johannes
last_name: Krausser
- first_name: Manish R.
full_name: Vuyyuru, Manish R.
last_name: Vuyyuru
- first_name: Buzz
full_name: Baum, Buzz
last_name: Baum
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
citation:
ama: Forster JC, Krausser J, Vuyyuru MR, Baum B, Šarić A. Exploring the design rules
for efficient membrane-reshaping nanostructures. Physical Review Letters.
2020;125(22). doi:10.1103/physrevlett.125.228101
apa: Forster, J. C., Krausser, J., Vuyyuru, M. R., Baum, B., & Šarić, A. (2020).
Exploring the design rules for efficient membrane-reshaping nanostructures. Physical
Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.125.228101
chicago: Forster, Joel C., Johannes Krausser, Manish R. Vuyyuru, Buzz Baum, and
Anđela Šarić. “Exploring the Design Rules for Efficient Membrane-Reshaping Nanostructures.”
Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/physrevlett.125.228101.
ieee: J. C. Forster, J. Krausser, M. R. Vuyyuru, B. Baum, and A. Šarić, “Exploring
the design rules for efficient membrane-reshaping nanostructures,” Physical
Review Letters, vol. 125, no. 22. American Physical Society, 2020.
ista: Forster JC, Krausser J, Vuyyuru MR, Baum B, Šarić A. 2020. Exploring the design
rules for efficient membrane-reshaping nanostructures. Physical Review Letters.
125(22), 228101.
mla: Forster, Joel C., et al. “Exploring the Design Rules for Efficient Membrane-Reshaping
Nanostructures.” Physical Review Letters, vol. 125, no. 22, 228101, American
Physical Society, 2020, doi:10.1103/physrevlett.125.228101.
short: J.C. Forster, J. Krausser, M.R. Vuyyuru, B. Baum, A. Šarić, Physical Review
Letters 125 (2020).
date_created: 2021-11-26T07:10:43Z
date_published: 2020-11-23T00:00:00Z
date_updated: 2021-11-30T08:33:14Z
day: '23'
ddc:
- '530'
doi: 10.1103/physrevlett.125.228101
extern: '1'
external_id:
pmid:
- '33315453'
file:
- access_level: open_access
checksum: fbf2e1415e332d6add90222d60401a1d
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-26T07:16:49Z
date_updated: 2021-11-26T07:16:49Z
file_id: '10345'
file_name: 2020_PhysRevLett_Forster.pdf
file_size: 844353
relation: main_file
success: 1
file_date_updated: 2021-11-26T07:16:49Z
has_accepted_license: '1'
intvolume: ' 125'
issue: '22'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/2020.02.27.968149v1
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Exploring the design rules for efficient membrane-reshaping nanostructures
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 125
year: '2020'
...
---
_id: '10346'
abstract:
- lang: eng
text: One of the most robust examples of self-assembly in living organisms is the
formation of collagen architectures. Collagen type I molecules are a crucial component
of the extracellular matrix, where they self-assemble into fibrils of well-defined
axial striped patterns. This striped fibrillar pattern is preserved across the
animal kingdom and is important for the determination of cell phenotype, cell
adhesion, and tissue regulation and signaling. The understanding of the physical
processes that determine such a robust morphology of self-assembled collagen fibrils
is currently almost completely missing. Here, we develop a minimal coarse-grained
computational model to identify the physical principles of the assembly of collagen-mimetic
molecules. We find that screened electrostatic interactions can drive the formation
of collagen-like filaments of well-defined striped morphologies. The fibril axial
pattern is determined solely by the distribution of charges on the molecule and
is robust to the changes in protein concentration, monomer rigidity, and environmental
conditions. We show that the striped fibrillar pattern cannot be easily predicted
from the interactions between two monomers but is an emergent result of multibody
interactions. Our results can help address collagen remodeling in diseases and
aging and guide the design of collagen scaffolds for biotechnological applications.
acknowledgement: We thank Melinda Duer, Patrick Mesquida, Lucy Colwell, Lucie Liu,
Daan Frenkel, and Ivan Palaia for helpful discussions. We acknowledge support from
the Engineering and Physical Sciences Research Council (A.E.H., L.K.D., and A.Š.),
Biotechnology and Biological Sciences Research Council LIDo programme (N.G.G. and
C.A.B.), the Royal Society (A.Š.), and the UK Materials and Molecular Modelling
Hub for computational resources, which is partially funded by EPSRC ( EP/P020194/1).
article_processing_charge: No
article_type: original
author:
- first_name: Anne E.
full_name: Hafner, Anne E.
last_name: Hafner
- first_name: Noemi G.
full_name: Gyori, Noemi G.
last_name: Gyori
- first_name: Ciaran A.
full_name: Bench, Ciaran A.
last_name: Bench
- first_name: Luke K.
full_name: Davis, Luke K.
last_name: Davis
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
citation:
ama: Hafner AE, Gyori NG, Bench CA, Davis LK, Šarić A. Modeling fibrillogenesis
of collagen-mimetic molecules. Biophysical Journal. 2020;119(9):1791-1799.
doi:10.1016/j.bpj.2020.09.013
apa: Hafner, A. E., Gyori, N. G., Bench, C. A., Davis, L. K., & Šarić, A. (2020).
Modeling fibrillogenesis of collagen-mimetic molecules. Biophysical Journal.
Cell Press. https://doi.org/10.1016/j.bpj.2020.09.013
chicago: Hafner, Anne E., Noemi G. Gyori, Ciaran A. Bench, Luke K. Davis, and Anđela
Šarić. “Modeling Fibrillogenesis of Collagen-Mimetic Molecules.” Biophysical
Journal. Cell Press, 2020. https://doi.org/10.1016/j.bpj.2020.09.013.
ieee: A. E. Hafner, N. G. Gyori, C. A. Bench, L. K. Davis, and A. Šarić, “Modeling
fibrillogenesis of collagen-mimetic molecules,” Biophysical Journal, vol.
119, no. 9. Cell Press, pp. 1791–1799, 2020.
ista: Hafner AE, Gyori NG, Bench CA, Davis LK, Šarić A. 2020. Modeling fibrillogenesis
of collagen-mimetic molecules. Biophysical Journal. 119(9), 1791–1799.
mla: Hafner, Anne E., et al. “Modeling Fibrillogenesis of Collagen-Mimetic Molecules.”
Biophysical Journal, vol. 119, no. 9, Cell Press, 2020, pp. 1791–99, doi:10.1016/j.bpj.2020.09.013.
short: A.E. Hafner, N.G. Gyori, C.A. Bench, L.K. Davis, A. Šarić, Biophysical Journal
119 (2020) 1791–1799.
date_created: 2021-11-26T07:27:24Z
date_published: 2020-09-23T00:00:00Z
date_updated: 2021-11-26T07:45:24Z
day: '23'
doi: 10.1016/j.bpj.2020.09.013
extern: '1'
external_id:
pmid:
- '33049216'
intvolume: ' 119'
issue: '9'
keyword:
- biophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/2020.06.08.140061v1
month: '09'
oa: 1
oa_version: Published Version
page: 1791-1799
pmid: 1
publication: Biophysical Journal
publication_identifier:
issn:
- 0006-3495
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Modeling fibrillogenesis of collagen-mimetic molecules
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 119
year: '2020'
...
---
_id: '10347'
abstract:
- lang: eng
text: Understanding the mechanism of action of compounds capable of inhibiting amyloid-fibril
formation is critical to the development of potential therapeutics against protein-misfolding
diseases. A fundamental challenge for progress is the range of possible target
species and the disparate timescales involved, since the aggregating proteins
are simultaneously the reactants, products, intermediates, and catalysts of the
reaction. It is a complex problem, therefore, to choose the states of the aggregating
proteins that should be bound by the compounds to achieve the most potent inhibition.
We present here a comprehensive kinetic theory of amyloid-aggregation inhibition
that reveals the fundamental thermodynamic and kinetic signatures characterizing
effective inhibitors by identifying quantitative relationships between the aggregation
and binding rate constants. These results provide general physical laws to guide
the design and optimization of inhibitors of amyloid-fibril formation, revealing
in particular the important role of on-rates in the binding of the inhibitors.
acknowledgement: We acknowledge support from Peterhouse, Cambridge (T.C.T.M.); the
Swiss National Science Foundation (T.C.T.M.); the Royal Society (A.S. and S.C.);
the Academy of Medical Sciences (A.S.); Sidney Sussex College, Cambridge (G.M.);
Newnham College, Cambridge (G.T.H.); the Wellcome Trust (T.P.J.K.); the Cambridge
Center for Misfolding Diseases (T.P.J.K. and M.V.); the Biotechnology and Biological
Sciences Research Council (T.P.J.K.); the Frances and Augustus Newman Foundation
(T.P.J.K.); and the Synapsis Foundation for Alzheimer’s disease (P.A.). The research
leading to these results has received funding from the European Research Council
(ERC) under the European Union’s Seventh Framework Program (FP7/2007-2013) through
the ERC Grant PhysProt (Agreement 337969).
article_processing_charge: No
article_type: original
author:
- first_name: Thomas C. T.
full_name: Michaels, Thomas C. T.
last_name: Michaels
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Georg
full_name: Meisl, Georg
last_name: Meisl
- first_name: Gabriella T.
full_name: Heller, Gabriella T.
last_name: Heller
- first_name: Samo
full_name: Curk, Samo
last_name: Curk
- first_name: Paolo
full_name: Arosio, Paolo
last_name: Arosio
- first_name: Sara
full_name: Linse, Sara
last_name: Linse
- first_name: Christopher M.
full_name: Dobson, Christopher M.
last_name: Dobson
- first_name: Michele
full_name: Vendruscolo, Michele
last_name: Vendruscolo
- first_name: Tuomas P. J.
full_name: Knowles, Tuomas P. J.
last_name: Knowles
citation:
ama: Michaels TCT, Šarić A, Meisl G, et al. Thermodynamic and kinetic design principles
for amyloid-aggregation inhibitors. Proceedings of the National Academy of
Sciences. 2020;117(39):24251-24257. doi:10.1073/pnas.2006684117
apa: Michaels, T. C. T., Šarić, A., Meisl, G., Heller, G. T., Curk, S., Arosio,
P., … Knowles, T. P. J. (2020). Thermodynamic and kinetic design principles for
amyloid-aggregation inhibitors. Proceedings of the National Academy of Sciences.
National Academy of Sciences. https://doi.org/10.1073/pnas.2006684117
chicago: Michaels, Thomas C. T., Anđela Šarić, Georg Meisl, Gabriella T. Heller,
Samo Curk, Paolo Arosio, Sara Linse, Christopher M. Dobson, Michele Vendruscolo,
and Tuomas P. J. Knowles. “Thermodynamic and Kinetic Design Principles for Amyloid-Aggregation
Inhibitors.” Proceedings of the National Academy of Sciences. National
Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2006684117.
ieee: T. C. T. Michaels et al., “Thermodynamic and kinetic design principles
for amyloid-aggregation inhibitors,” Proceedings of the National Academy of
Sciences, vol. 117, no. 39. National Academy of Sciences, pp. 24251–24257,
2020.
ista: Michaels TCT, Šarić A, Meisl G, Heller GT, Curk S, Arosio P, Linse S, Dobson
CM, Vendruscolo M, Knowles TPJ. 2020. Thermodynamic and kinetic design principles
for amyloid-aggregation inhibitors. Proceedings of the National Academy of Sciences.
117(39), 24251–24257.
mla: Michaels, Thomas C. T., et al. “Thermodynamic and Kinetic Design Principles
for Amyloid-Aggregation Inhibitors.” Proceedings of the National Academy of
Sciences, vol. 117, no. 39, National Academy of Sciences, 2020, pp. 24251–57,
doi:10.1073/pnas.2006684117.
short: T.C.T. Michaels, A. Šarić, G. Meisl, G.T. Heller, S. Curk, P. Arosio, S.
Linse, C.M. Dobson, M. Vendruscolo, T.P.J. Knowles, Proceedings of the National
Academy of Sciences 117 (2020) 24251–24257.
date_created: 2021-11-26T07:48:27Z
date_published: 2020-09-14T00:00:00Z
date_updated: 2021-11-26T08:59:06Z
day: '14'
doi: 10.1073/pnas.2006684117
extern: '1'
external_id:
pmid:
- '32929030'
intvolume: ' 117'
issue: '39'
keyword:
- multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/2020.02.22.960716
month: '09'
oa: 1
oa_version: Published Version
page: 24251-24257
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 117
year: '2020'
...
---
_id: '10348'
abstract:
- lang: eng
text: The endosomal sorting complex required for transport-III (ESCRT-III) catalyzes
membrane fission from within membrane necks, a process that is essential for many
cellular functions, from cell division to lysosome degradation and autophagy.
How it breaks membranes, though, remains unknown. Here, we characterize a sequential
polymerization of ESCRT-III subunits that, driven by a recruitment cascade and
by continuous subunit-turnover powered by the ATPase Vps4, induces membrane deformation
and fission. During this process, the exchange of Vps24 for Did2 induces a tilt
in the polymer-membrane interface, which triggers transition from flat spiral
polymers to helical filament to drive the formation of membrane protrusions, and
ends with the formation of a highly constricted Did2-Ist1 co-polymer that we show
is competent to promote fission when bound on the inside of membrane necks. Overall,
our results suggest a mechanism of stepwise changes in ESCRT-III filament structure
and mechanical properties via exchange of the filament subunits to catalyze ESCRT-III
activity.
acknowledgement: The authors thank Nicolas Chiaruttini, Jean Gruenberg, and Lena Harker-Kirschneck
for careful correction of this manuscript and helpful discussions. The authors want
to thank the NCCR Chemical Biology for constant support during this project. A.R.
acknowledges funding from the Swiss National Fund for Research (31003A_130520, 31003A_149975,
and 31003A_173087) and the European Research Council Consolidator (311536). A.Š.
acknowledges the European Research Council (802960). B.B. thanks the BBSRC (BB/K009001/1)
and Wellcome Trust (203276/Z/16/Z) for support. J.M.v.F. acknowledges funding through
an EMBO Long-Term Fellowship (ALTF 1065-2015), the European Commission FP7 (Marie
Curie Actions, LTFCOFUND2013, and GA-2013-609409), and a Transitional Postdoc fellowship
(2015/345) from the Swiss SystemsX.ch initiative, evaluated by the Swiss National
Science Foundation and Swiss National Science Foundation Research (SNSF SINERGIA
160728/1 [leader, Sophie Martin]).
article_processing_charge: No
article_type: original
author:
- first_name: Anna-Katharina
full_name: Pfitzner, Anna-Katharina
last_name: Pfitzner
- first_name: Vincent
full_name: Mercier, Vincent
last_name: Mercier
- first_name: Xiuyun
full_name: Jiang, Xiuyun
last_name: Jiang
- first_name: Joachim
full_name: Moser von Filseck, Joachim
last_name: Moser von Filseck
- first_name: Buzz
full_name: Baum, Buzz
last_name: Baum
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Aurélien
full_name: Roux, Aurélien
last_name: Roux
citation:
ama: Pfitzner A-K, Mercier V, Jiang X, et al. An ESCRT-III polymerization sequence
drives membrane deformation and fission. Cell. 2020;182(5):1140-1155.e18.
doi:10.1016/j.cell.2020.07.021
apa: Pfitzner, A.-K., Mercier, V., Jiang, X., Moser von Filseck, J., Baum, B., Šarić,
A., & Roux, A. (2020). An ESCRT-III polymerization sequence drives membrane
deformation and fission. Cell. Elsevier. https://doi.org/10.1016/j.cell.2020.07.021
chicago: Pfitzner, Anna-Katharina, Vincent Mercier, Xiuyun Jiang, Joachim Moser
von Filseck, Buzz Baum, Anđela Šarić, and Aurélien Roux. “An ESCRT-III Polymerization
Sequence Drives Membrane Deformation and Fission.” Cell. Elsevier, 2020.
https://doi.org/10.1016/j.cell.2020.07.021.
ieee: A.-K. Pfitzner et al., “An ESCRT-III polymerization sequence drives
membrane deformation and fission,” Cell, vol. 182, no. 5. Elsevier, p.
1140–1155.e18, 2020.
ista: Pfitzner A-K, Mercier V, Jiang X, Moser von Filseck J, Baum B, Šarić A, Roux
A. 2020. An ESCRT-III polymerization sequence drives membrane deformation and
fission. Cell. 182(5), 1140–1155.e18.
mla: Pfitzner, Anna-Katharina, et al. “An ESCRT-III Polymerization Sequence Drives
Membrane Deformation and Fission.” Cell, vol. 182, no. 5, Elsevier, 2020,
p. 1140–1155.e18, doi:10.1016/j.cell.2020.07.021.
short: A.-K. Pfitzner, V. Mercier, X. Jiang, J. Moser von Filseck, B. Baum, A. Šarić,
A. Roux, Cell 182 (2020) 1140–1155.e18.
date_created: 2021-11-26T08:02:27Z
date_published: 2020-08-18T00:00:00Z
date_updated: 2021-11-26T08:58:37Z
day: '18'
doi: 10.1016/j.cell.2020.07.021
extern: '1'
external_id:
pmid:
- '32814015'
intvolume: ' 182'
issue: '5'
keyword:
- general biochemistry
- genetics and molecular biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.sciencedirect.com/science/article/pii/S0092867420309296
month: '08'
oa: 1
oa_version: Published Version
page: 1140-1155.e18
pmid: 1
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: An ESCRT-III polymerization sequence drives membrane deformation and fission
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 182
year: '2020'
...
---
_id: '10349'
abstract:
- lang: eng
text: Sulfolobus acidocaldarius is the closest experimentally tractable archaeal
relative of eukaryotes and, despite lacking obvious cyclin-dependent kinase and
cyclin homologs, has an ordered eukaryote-like cell cycle with distinct phases
of DNA replication and division. Here, in exploring the mechanism of cell division
in S. acidocaldarius, we identify a role for the archaeal proteasome in regulating
the transition from the end of one cell cycle to the beginning of the next. Further,
we identify the archaeal ESCRT-III homolog, CdvB, as a key target of the proteasome
and show that its degradation triggers division by allowing constriction of the
CdvB1:CdvB2 ESCRT-III division ring. These findings offer a minimal mechanism
for ESCRT-III–mediated membrane remodeling and point to a conserved role for the
proteasome in eukaryotic and archaeal cell cycle control.
acknowledgement: "We thank the MRC LMCB at UCL for their support; the flow cytometry
STP at the Francis Crick Institute for assistance, with special thanks to S. Purewal
and D. Davis; C. Bertoli for mentorship\r\nand advice; J. M. Garcia-Arcos for help
early on in this project; the entire Baum lab for their input throughout the project;
the Albers lab for advice and reagents, with special thanks to M. Van Wolferen and
S. Albers; the members of the Wellcome consortium for archaeal cytoskeleton studies
for advice and comments; and J. Löwe, S. Oliferenko, M. Balasubramanian, and D.
Gerlich for discussions and advice on the manuscript. N.P.R. and S.B. would like
to thank N. Rzechorzek, A. Simon, and S. Anjum for discussion and advice."
article_processing_charge: No
article_type: original
author:
- first_name: Gabriel
full_name: Tarrason Risa, Gabriel
last_name: Tarrason Risa
- first_name: Fredrik
full_name: Hurtig, Fredrik
last_name: Hurtig
- first_name: Sian
full_name: Bray, Sian
last_name: Bray
- first_name: Anne E.
full_name: Hafner, Anne E.
last_name: Hafner
- first_name: Lena
full_name: Harker-Kirschneck, Lena
last_name: Harker-Kirschneck
- first_name: Peter
full_name: Faull, Peter
last_name: Faull
- first_name: Colin
full_name: Davis, Colin
last_name: Davis
- first_name: Dimitra
full_name: Papatziamou, Dimitra
last_name: Papatziamou
- first_name: Delyan R.
full_name: Mutavchiev, Delyan R.
last_name: Mutavchiev
- first_name: Catherine
full_name: Fan, Catherine
last_name: Fan
- first_name: Leticia
full_name: Meneguello, Leticia
last_name: Meneguello
- first_name: Andre
full_name: Arashiro Pulschen, Andre
last_name: Arashiro Pulschen
- first_name: Gautam
full_name: Dey, Gautam
last_name: Dey
- first_name: Siân
full_name: Culley, Siân
last_name: Culley
- first_name: Mairi
full_name: Kilkenny, Mairi
last_name: Kilkenny
- first_name: Diorge P.
full_name: Souza, Diorge P.
last_name: Souza
- first_name: Luca
full_name: Pellegrini, Luca
last_name: Pellegrini
- first_name: Robertus A. M.
full_name: de Bruin, Robertus A. M.
last_name: de Bruin
- first_name: Ricardo
full_name: Henriques, Ricardo
last_name: Henriques
- first_name: Ambrosius P.
full_name: Snijders, Ambrosius P.
last_name: Snijders
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Ann-Christin
full_name: Lindås, Ann-Christin
last_name: Lindås
- first_name: Nicholas P.
full_name: Robinson, Nicholas P.
last_name: Robinson
- first_name: Buzz
full_name: Baum, Buzz
last_name: Baum
citation:
ama: Tarrason Risa G, Hurtig F, Bray S, et al. The proteasome controls ESCRT-III–mediated
cell division in an archaeon. Science. 2020;369(6504). doi:10.1126/science.aaz2532
apa: Tarrason Risa, G., Hurtig, F., Bray, S., Hafner, A. E., Harker-Kirschneck,
L., Faull, P., … Baum, B. (2020). The proteasome controls ESCRT-III–mediated cell
division in an archaeon. Science. American Association for the Advancement
of Science. https://doi.org/10.1126/science.aaz2532
chicago: Tarrason Risa, Gabriel, Fredrik Hurtig, Sian Bray, Anne E. Hafner, Lena
Harker-Kirschneck, Peter Faull, Colin Davis, et al. “The Proteasome Controls ESCRT-III–Mediated
Cell Division in an Archaeon.” Science. American Association for the Advancement
of Science, 2020. https://doi.org/10.1126/science.aaz2532.
ieee: G. Tarrason Risa et al., “The proteasome controls ESCRT-III–mediated
cell division in an archaeon,” Science, vol. 369, no. 6504. American Association
for the Advancement of Science, 2020.
ista: Tarrason Risa G, Hurtig F, Bray S, Hafner AE, Harker-Kirschneck L, Faull P,
Davis C, Papatziamou D, Mutavchiev DR, Fan C, Meneguello L, Arashiro Pulschen
A, Dey G, Culley S, Kilkenny M, Souza DP, Pellegrini L, de Bruin RAM, Henriques
R, Snijders AP, Šarić A, Lindås A-C, Robinson NP, Baum B. 2020. The proteasome
controls ESCRT-III–mediated cell division in an archaeon. Science. 369(6504).
mla: Tarrason Risa, Gabriel, et al. “The Proteasome Controls ESCRT-III–Mediated
Cell Division in an Archaeon.” Science, vol. 369, no. 6504, American Association
for the Advancement of Science, 2020, doi:10.1126/science.aaz2532.
short: G. Tarrason Risa, F. Hurtig, S. Bray, A.E. Hafner, L. Harker-Kirschneck,
P. Faull, C. Davis, D. Papatziamou, D.R. Mutavchiev, C. Fan, L. Meneguello, A.
Arashiro Pulschen, G. Dey, S. Culley, M. Kilkenny, D.P. Souza, L. Pellegrini,
R.A.M. de Bruin, R. Henriques, A.P. Snijders, A. Šarić, A.-C. Lindås, N.P. Robinson,
B. Baum, Science 369 (2020).
date_created: 2021-11-26T08:21:34Z
date_published: 2020-08-07T00:00:00Z
date_updated: 2021-11-26T08:58:33Z
day: '07'
doi: 10.1126/science.aaz2532
extern: '1'
external_id:
pmid:
- '32764038'
intvolume: ' 369'
issue: '6504'
keyword:
- multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/774273v1
month: '08'
oa: 1
oa_version: Preprint
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: The proteasome controls ESCRT-III–mediated cell division in an archaeon
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 369
year: '2020'
...