---
_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: '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
license: https://creativecommons.org/licenses/by/4.0/
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'
...
---
_id: '10350'
abstract:
- lang: eng
text: The misfolding and aberrant aggregation of proteins into fibrillar structures
is a key factor in some of the most prevalent human diseases, including diabetes
and dementia. Low molecular weight oligomers are thought to be a central factor
in the pathology of these diseases, as well as critical intermediates in the fibril
formation process, and as such have received much recent attention. Moreover,
on-pathway oligomeric intermediates are potential targets for therapeutic strategies
aimed at interrupting the fibril formation process. However, a consistent framework
for distinguishing on-pathway from off-pathway oligomers has hitherto been lacking
and, in particular, no consensus definition of on- and off-pathway oligomers is
available. In this paper, we argue that a non-binary definition of oligomers'
contribution to fibril-forming pathways may be more informative and we suggest
a quantitative framework, in which each oligomeric species is assigned a value
between 0 and 1 describing its relative contribution to the formation of fibrils.
First, we clarify the distinction between oligomers and fibrils, and then we use
the formalism of reaction networks to develop a general definition for on-pathway
oligomers, that yields meaningful classifications in the context of amyloid formation.
By applying these concepts to Monte Carlo simulations of a minimal aggregating
system, and by revisiting several previous studies of amyloid oligomers in light
of our new framework, we demonstrate how to perform these classifications in practice.
For each oligomeric species we obtain the degree to which it is on-pathway, highlighting
the most effective pharmaceutical targets for the inhibition of amyloid fibril
formation.
acknowledgement: We are grateful to the Schiff Foundation (AJD), Peterhouse, Cambridge
(TCTM), the Swiss National Science foundation (TCTM), Ramon Jenkins Fellowship,
Sidney Sussex, Cambridge (GM), the Royal Society (AŠ), the Academy of Medical Sciences
and Wellcome Trust (AŠ), the Danish Research Council (MK), the Lundbeck Foundation
(MK), the Swedish Research Council (SL), the Wellcome Trust (TPJK), the Cambridge
Centre for Misfolding Diseases (TPJK), the BBSRC (TPJK), the Frances and Augustus
Newman Foundation (TPJK) for financial support. The research leading to these results
has received funding from the European Research Council under the European Union's
Seventh Framework Programme (FP7/2007-2013) through the ERC grants PhysProt (agreement
no. 337969), MAMBA (agreement no. 340890) and NovoNordiskFonden (SL).
article_processing_charge: No
article_type: original
author:
- first_name: Alexander J.
full_name: Dear, Alexander J.
last_name: Dear
- first_name: Georg
full_name: Meisl, Georg
last_name: Meisl
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Thomas C. T.
full_name: Michaels, Thomas C. T.
last_name: Michaels
- first_name: Magnus
full_name: Kjaergaard, Magnus
last_name: Kjaergaard
- first_name: Sara
full_name: Linse, Sara
last_name: Linse
- first_name: Tuomas P. J.
full_name: Knowles, Tuomas P. J.
last_name: Knowles
citation:
ama: Dear AJ, Meisl G, Šarić A, et al. Identification of on- and off-pathway oligomers
in amyloid fibril formation. Chemical Science. 2020;11(24):6236-6247. doi:10.1039/c9sc06501f
apa: Dear, A. J., Meisl, G., Šarić, A., Michaels, T. C. T., Kjaergaard, M., Linse,
S., & Knowles, T. P. J. (2020). Identification of on- and off-pathway oligomers
in amyloid fibril formation. Chemical Science. Royal Society of Chemistry.
https://doi.org/10.1039/c9sc06501f
chicago: Dear, Alexander J., Georg Meisl, Anđela Šarić, Thomas C. T. Michaels, Magnus
Kjaergaard, Sara Linse, and Tuomas P. J. Knowles. “Identification of On- and off-Pathway
Oligomers in Amyloid Fibril Formation.” Chemical Science. Royal Society
of Chemistry, 2020. https://doi.org/10.1039/c9sc06501f.
ieee: A. J. Dear et al., “Identification of on- and off-pathway oligomers
in amyloid fibril formation,” Chemical Science, vol. 11, no. 24. Royal
Society of Chemistry, pp. 6236–6247, 2020.
ista: Dear AJ, Meisl G, Šarić A, Michaels TCT, Kjaergaard M, Linse S, Knowles TPJ.
2020. Identification of on- and off-pathway oligomers in amyloid fibril formation.
Chemical Science. 11(24), 6236–6247.
mla: Dear, Alexander J., et al. “Identification of On- and off-Pathway Oligomers
in Amyloid Fibril Formation.” Chemical Science, vol. 11, no. 24, Royal
Society of Chemistry, 2020, pp. 6236–47, doi:10.1039/c9sc06501f.
short: A.J. Dear, G. Meisl, A. Šarić, T.C.T. Michaels, M. Kjaergaard, S. Linse,
T.P.J. Knowles, Chemical Science 11 (2020) 6236–6247.
date_created: 2021-11-26T09:08:19Z
date_published: 2020-06-08T00:00:00Z
date_updated: 2021-11-26T11:21:20Z
day: '08'
doi: 10.1039/c9sc06501f
extern: '1'
external_id:
pmid:
- '32953019'
intvolume: ' 11'
issue: '24'
keyword:
- general chemistry
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/3.0/
main_file_link:
- open_access: '1'
url: https://pubs.rsc.org/en/content/articlehtml/2020/sc/c9sc06501f
month: '06'
oa: 1
oa_version: Published Version
page: 6236-6247
pmid: 1
publication: Chemical Science
publication_identifier:
eissn:
- 2041-6539
issn:
- 2041-6520
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Identification of on- and off-pathway oligomers in amyloid fibril formation
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/3.0/legalcode
name: Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)
short: CC BY-NC (3.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 11
year: '2020'
...
---
_id: '10351'
abstract:
- lang: eng
text: Oligomeric species populated during the aggregation of the Aβ42 peptide have
been identified as potent cytotoxins linked to Alzheimer’s disease, but the fundamental
molecular pathways that control their dynamics have yet to be elucidated. By developing
a general approach that combines theory, experiment and simulation, we reveal,
in molecular detail, the mechanisms of Aβ42 oligomer dynamics during amyloid fibril
formation. Even though all mature amyloid fibrils must originate as oligomers,
we found that most Aβ42 oligomers dissociate into their monomeric precursors without
forming new fibrils. Only a minority of oligomers converts into fibrillar structures.
Moreover, the heterogeneous ensemble of oligomeric species interconverts on timescales
comparable to those of aggregation. Our results identify fundamentally new steps
that could be targeted by therapeutic interventions designed to combat protein
misfolding diseases.
acknowledgement: We acknowledge support from Peterhouse (T.C.T.M.), the Swiss National
Science foundation (T.C.T.M.), the Royal Society (A.Š.), the Academy of Medical
Sciences (A.Š.), the UCL Institute for the Physics of Living Systems (S.C.), Sidney
Sussex College (G.M.), the Wellcome Trust (A.Š., M.V., C.M.D. and T.P.J.K.), the
Schiff Foundation (A.J.D.), the Cambridge Centre for Misfolding Diseases (M.V.,
C.M.D. and T.P.J.K.), the BBSRC (C.M.D. and T.P.J.K.), the Frances and Augustus
Newman Foundation (T.P.J.K.), the Swedish Research Council (S.L.) and the ERC grant
MAMBA (S.L., agreement no. 340890). The research that led to these results received
funding from the European Research Council under the European Union’s Seventh Framework
Programme (FP7/2007-2013) through the ERC grant PhysProt (agreement no. 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: Samo
full_name: Curk, Samo
last_name: Curk
- first_name: Katja
full_name: Bernfur, Katja
last_name: Bernfur
- first_name: Paolo
full_name: Arosio, Paolo
last_name: Arosio
- first_name: Georg
full_name: Meisl, Georg
last_name: Meisl
- first_name: Alexander J.
full_name: Dear, Alexander J.
last_name: Dear
- first_name: Samuel I. A.
full_name: Cohen, Samuel I. A.
last_name: Cohen
- first_name: Christopher M.
full_name: Dobson, Christopher M.
last_name: Dobson
- first_name: Michele
full_name: Vendruscolo, Michele
last_name: Vendruscolo
- first_name: Sara
full_name: Linse, Sara
last_name: Linse
- first_name: Tuomas P. J.
full_name: Knowles, Tuomas P. J.
last_name: Knowles
citation:
ama: Michaels TCT, Šarić A, Curk S, et al. Dynamics of oligomer populations formed
during the aggregation of Alzheimer’s Aβ42 peptide. Nature Chemistry. 2020;12(5):445-451.
doi:10.1038/s41557-020-0452-1
apa: Michaels, T. C. T., Šarić, A., Curk, S., Bernfur, K., Arosio, P., Meisl, G.,
… Knowles, T. P. J. (2020). Dynamics of oligomer populations formed during the
aggregation of Alzheimer’s Aβ42 peptide. Nature Chemistry. Springer Nature.
https://doi.org/10.1038/s41557-020-0452-1
chicago: Michaels, Thomas C. T., Anđela Šarić, Samo Curk, Katja Bernfur, Paolo Arosio,
Georg Meisl, Alexander J. Dear, et al. “Dynamics of Oligomer Populations Formed
during the Aggregation of Alzheimer’s Aβ42 Peptide.” Nature Chemistry.
Springer Nature, 2020. https://doi.org/10.1038/s41557-020-0452-1.
ieee: T. C. T. Michaels et al., “Dynamics of oligomer populations formed
during the aggregation of Alzheimer’s Aβ42 peptide,” Nature Chemistry,
vol. 12, no. 5. Springer Nature, pp. 445–451, 2020.
ista: Michaels TCT, Šarić A, Curk S, Bernfur K, Arosio P, Meisl G, Dear AJ, Cohen
SIA, Dobson CM, Vendruscolo M, Linse S, Knowles TPJ. 2020. Dynamics of oligomer
populations formed during the aggregation of Alzheimer’s Aβ42 peptide. Nature
Chemistry. 12(5), 445–451.
mla: Michaels, Thomas C. T., et al. “Dynamics of Oligomer Populations Formed during
the Aggregation of Alzheimer’s Aβ42 Peptide.” Nature Chemistry, vol. 12,
no. 5, Springer Nature, 2020, pp. 445–51, doi:10.1038/s41557-020-0452-1.
short: T.C.T. Michaels, A. Šarić, S. Curk, K. Bernfur, P. Arosio, G. Meisl, A.J.
Dear, S.I.A. Cohen, C.M. Dobson, M. Vendruscolo, S. Linse, T.P.J. Knowles, Nature
Chemistry 12 (2020) 445–451.
date_created: 2021-11-26T09:15:13Z
date_published: 2020-04-13T00:00:00Z
date_updated: 2021-11-26T11:21:08Z
day: '13'
doi: 10.1038/s41557-020-0452-1
extern: '1'
external_id:
pmid:
- '32303714'
intvolume: ' 12'
issue: '5'
keyword:
- general chemical engineering
- general chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/2020.01.08.897488
month: '04'
oa: 1
oa_version: None
page: 445-451
pmid: 1
publication: Nature Chemistry
publication_identifier:
eissn:
- 1755-4349
issn:
- 1755-4330
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41557-020-0468-6
scopus_import: '1'
status: public
title: Dynamics of oligomer populations formed during the aggregation of Alzheimer’s
Aβ42 peptide
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 12
year: '2020'
...
---
_id: '10352'
abstract:
- lang: eng
text: In the nuclear pore complex, intrinsically disordered nuclear pore proteins
(FG Nups) form a selective barrier for transport into and out of the cell nucleus,
in a way that remains poorly understood. The collective FG Nup behavior has long
been conceptualized either as a polymer brush, dominated by entropic and excluded-volume
(repulsive) interactions, or as a hydrogel, dominated by cohesive (attractive)
interactions between FG Nups. Here we compare mesoscale computational simulations
with a wide range of experimental data to demonstrate that FG Nups are at the
crossover point between these two regimes. Specifically, we find that repulsive
and attractive interactions are balanced, resulting in morphologies and dynamics
that are close to those of ideal polymer chains. We demonstrate that this property
of FG Nups yields sufficient cohesion to seal the transport barrier, and yet maintains
fast dynamics at the molecular scale, permitting the rapid polymer rearrangements
needed for transport events.
acknowledgement: We thank Dino Osmanović (MIT), Roy Beck (Tel-Aviv), Larissa Kapinos
(Basel), Roderick Lim (Basel), Ralf Richter (Leeds), and Anton Zilman (Toronto)
for discussions. This work was funded by the Royal Society (A.Š.) and the UK Engineering
and Physical Sciences Research Council (EP/L504889/1, B.W.H.).
article_number: '022420'
article_processing_charge: No
article_type: original
author:
- first_name: Luke K.
full_name: Davis, Luke K.
last_name: Davis
- first_name: Ian J.
full_name: Ford, Ian J.
last_name: Ford
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Bart W.
full_name: Hoogenboom, Bart W.
last_name: Hoogenboom
citation:
ama: Davis LK, Ford IJ, Šarić A, Hoogenboom BW. Intrinsically disordered nuclear
pore proteins show ideal-polymer morphologies and dynamics. Physical Review
E. 2020;101(2). doi:10.1103/physreve.101.022420
apa: Davis, L. K., Ford, I. J., Šarić, A., & Hoogenboom, B. W. (2020). Intrinsically
disordered nuclear pore proteins show ideal-polymer morphologies and dynamics.
Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.101.022420
chicago: Davis, Luke K., Ian J. Ford, Anđela Šarić, and Bart W. Hoogenboom. “Intrinsically
Disordered Nuclear Pore Proteins Show Ideal-Polymer Morphologies and Dynamics.”
Physical Review E. American Physical Society, 2020. https://doi.org/10.1103/physreve.101.022420.
ieee: L. K. Davis, I. J. Ford, A. Šarić, and B. W. Hoogenboom, “Intrinsically disordered
nuclear pore proteins show ideal-polymer morphologies and dynamics,” Physical
Review E, vol. 101, no. 2. American Physical Society, 2020.
ista: Davis LK, Ford IJ, Šarić A, Hoogenboom BW. 2020. Intrinsically disordered
nuclear pore proteins show ideal-polymer morphologies and dynamics. Physical Review
E. 101(2), 022420.
mla: Davis, Luke K., et al. “Intrinsically Disordered Nuclear Pore Proteins Show
Ideal-Polymer Morphologies and Dynamics.” Physical Review E, vol. 101,
no. 2, 022420, American Physical Society, 2020, doi:10.1103/physreve.101.022420.
short: L.K. Davis, I.J. Ford, A. Šarić, B.W. Hoogenboom, Physical Review E 101 (2020).
date_created: 2021-11-26T09:41:04Z
date_published: 2020-02-28T00:00:00Z
date_updated: 2021-11-26T11:21:16Z
day: '28'
doi: 10.1103/physreve.101.022420
extern: '1'
external_id:
pmid:
- '32168597'
intvolume: ' 101'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/571687
month: '02'
oa: 1
oa_version: Preprint
pmid: 1
publication: Physical Review E
publication_identifier:
eissn:
- 2470-0053
issn:
- 2470-0045
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies
and dynamics
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 101
year: '2020'
...
---
_id: '10353'
abstract:
- lang: eng
text: Experiments have suggested that bacterial mechanosensitive channels separate
into 2D clusters, the role of which is unclear. By developing a coarse-grained
computer model we find that clustering promotes the channel closure, which is
highly dependent on the channel concentration and membrane stress. This behaviour
yields a tightly regulated gating system, whereby at high tensions channels gate
individually, and at lower tensions the channels spontaneously aggregate and inactivate.
We implement this positive feedback into the model for cell volume regulation,
and find that the channel clustering protects the cell against excessive loss
of cytoplasmic content.
acknowledgement: We thank Samantha Miller, Bert Poolman, and the members of Šarić
and Pilizota laboratories for useful discussion. We acknowledge support from the
Engineering and Physical Sciences Research Council (A.P. and A.Š.), the UCL Institute
for the Physics of Living Systems (A.P. and A.Š.), Darwin Trust of University of
Edinburgh (H.S.), Industrial Biotechnology Innovation Centre (H.S. and T.P.), BBSRC
Council Crossing Biological Membrane Network (H.S. and T.P.), BBSRC/EPSRC/MRC Synthetic
Biology Research Centre (T.P.), and the Royal Society (A.Š.).
article_number: '048102'
article_processing_charge: No
article_type: original
author:
- first_name: Alexandru
full_name: Paraschiv, Alexandru
last_name: Paraschiv
- first_name: Smitha
full_name: Hegde, Smitha
last_name: Hegde
- first_name: Raman
full_name: Ganti, Raman
last_name: Ganti
- first_name: Teuta
full_name: Pilizota, Teuta
last_name: Pilizota
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
citation:
ama: Paraschiv A, Hegde S, Ganti R, Pilizota T, Šarić A. Dynamic clustering regulates
activity of mechanosensitive membrane channels. Physical Review Letters.
2020;124(4). doi:10.1103/physrevlett.124.048102
apa: Paraschiv, A., Hegde, S., Ganti, R., Pilizota, T., & Šarić, A. (2020).
Dynamic clustering regulates activity of mechanosensitive membrane channels. Physical
Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.124.048102
chicago: Paraschiv, Alexandru, Smitha Hegde, Raman Ganti, Teuta Pilizota, and Anđela
Šarić. “Dynamic Clustering Regulates Activity of Mechanosensitive Membrane Channels.”
Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/physrevlett.124.048102.
ieee: A. Paraschiv, S. Hegde, R. Ganti, T. Pilizota, and A. Šarić, “Dynamic clustering
regulates activity of mechanosensitive membrane channels,” Physical Review
Letters, vol. 124, no. 4. American Physical Society, 2020.
ista: Paraschiv A, Hegde S, Ganti R, Pilizota T, Šarić A. 2020. Dynamic clustering
regulates activity of mechanosensitive membrane channels. Physical Review Letters.
124(4), 048102.
mla: Paraschiv, Alexandru, et al. “Dynamic Clustering Regulates Activity of Mechanosensitive
Membrane Channels.” Physical Review Letters, vol. 124, no. 4, 048102, American
Physical Society, 2020, doi:10.1103/physrevlett.124.048102.
short: A. Paraschiv, S. Hegde, R. Ganti, T. Pilizota, A. Šarić, Physical Review
Letters 124 (2020).
date_created: 2021-11-26T09:57:01Z
date_published: 2020-01-31T00:00:00Z
date_updated: 2021-11-26T11:21:12Z
day: '31'
doi: 10.1103/physrevlett.124.048102
extern: '1'
external_id:
pmid:
- '32058787'
intvolume: ' 124'
issue: '4'
keyword:
- general physics and astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/553248
month: '01'
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: Dynamic clustering regulates activity of mechanosensitive membrane channels
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 124
year: '2020'
...
---
_id: '10556'
abstract:
- lang: eng
text: In this paper, we present the first Asynchronous Distributed Key Generation
(ADKG) algorithm which is also the first distributed key generation algorithm
that can generate cryptographic keys with a dual (f,2f+1)-threshold (where f is
the number of faulty parties). As a result, using our ADKG we remove the trusted
setup assumption that the most scalable consensus algorithms make. In order to
create a DKG with a dual (f,2f+1)- threshold we first answer in the affirmative
the open question posed by Cachin et al. [7] on how to create an Asynchronous
Verifiable Secret Sharing (AVSS) protocol with a reconstruction threshold of f+1Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications
Security. Association for Computing Machinery; 2020:1751–1767. doi:10.1145/3372297.3423364'
apa: 'Kokoris Kogias, E., Malkhi, D., & Spiegelman, A. (2020). Asynchronous
distributed key generation for computationally-secure randomness, consensus, and
threshold signatures. In Proceedings of the 2020 ACM SIGSAC Conference on Computer
and Communications Security (pp. 1751–1767). Virtual, United States: Association
for Computing Machinery. https://doi.org/10.1145/3372297.3423364'
chicago: Kokoris Kogias, Eleftherios, Dahlia Malkhi, and Alexander Spiegelman. “Asynchronous
Distributed Key Generation for Computationally-Secure Randomness, Consensus, and
Threshold Signatures.” In Proceedings of the 2020 ACM SIGSAC Conference on
Computer and Communications Security, 1751–1767. Association for Computing
Machinery, 2020. https://doi.org/10.1145/3372297.3423364.
ieee: E. Kokoris Kogias, D. Malkhi, and A. Spiegelman, “Asynchronous distributed
key generation for computationally-secure randomness, consensus, and threshold
signatures,” in Proceedings of the 2020 ACM SIGSAC Conference on Computer and
Communications Security, Virtual, United States, 2020, pp. 1751–1767.
ista: 'Kokoris Kogias E, Malkhi D, Spiegelman A. 2020. Asynchronous distributed
key generation for computationally-secure randomness, consensus, and threshold
signatures. Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications
Security. CCS: Computer and Communications Security, 1751–1767.'
mla: Kokoris Kogias, Eleftherios, et al. “Asynchronous Distributed Key Generation
for Computationally-Secure Randomness, Consensus, and Threshold Signatures.” Proceedings
of the 2020 ACM SIGSAC Conference on Computer and Communications Security,
Association for Computing Machinery, 2020, pp. 1751–1767, doi:10.1145/3372297.3423364.
short: E. Kokoris Kogias, D. Malkhi, A. Spiegelman, in:, Proceedings of the 2020
ACM SIGSAC Conference on Computer and Communications Security, Association for
Computing Machinery, 2020, pp. 1751–1767.
conference:
end_date: 2020-11-13
location: Virtual, United States
name: 'CCS: Computer and Communications Security'
start_date: 2020-11-09
date_created: 2021-12-16T13:23:27Z
date_published: 2020-10-30T00:00:00Z
date_updated: 2024-02-22T13:10:45Z
day: '30'
department:
- _id: ElKo
doi: 10.1145/3372297.3423364
external_id:
isi:
- '000768470400104'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2019/1015
month: '10'
oa: 1
oa_version: Preprint
page: 1751–1767
publication: Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications
Security
publication_identifier:
isbn:
- 978-1-4503-7089-9
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Asynchronous distributed key generation for computationally-secure randomness,
consensus, and threshold signatures
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '10557'
abstract:
- lang: eng
text: Data storage and retrieval systems, methods, and computer-readable media utilize
a cryptographically verifiable data structure that facilitates verification of
a transaction in a decentralized peer-to-peer environment using multi-hop backwards
and forwards links. Backward links are cryptographic hashes of past records. Forward
links are cryptographic signatures of future records that are added retroactively
to records once the target block has been appended to the data structure.
applicant:
- Ecole Polytechnique Federale de Lausanne
application_date: 2017-06-09
article_processing_charge: No
author:
- first_name: Bryan
full_name: Ford, Bryan
last_name: Ford
- first_name: Linus
full_name: Gasse, Linus
last_name: Gasse
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Philipp
full_name: Jovanovic, Philipp
last_name: Jovanovic
citation:
ama: Ford B, Gasse L, Kokoris Kogias E, Jovanovic P. Cryptographically verifiable
data structure having multi-hop forward and backwards links and associated systems
and methods. 2020.
apa: Ford, B., Gasse, L., Kokoris Kogias, E., & Jovanovic, P. (2020). Cryptographically
verifiable data structure having multi-hop forward and backwards links and associated
systems and methods.
chicago: Ford, Bryan, Linus Gasse, Eleftherios Kokoris Kogias, and Philipp Jovanovic.
“Cryptographically Verifiable Data Structure Having Multi-Hop Forward and Backwards
Links and Associated Systems and Methods,” 2020.
ieee: B. Ford, L. Gasse, E. Kokoris Kogias, and P. Jovanovic, “Cryptographically
verifiable data structure having multi-hop forward and backwards links and associated
systems and methods.” 2020.
ista: Ford B, Gasse L, Kokoris Kogias E, Jovanovic P. 2020. Cryptographically verifiable
data structure having multi-hop forward and backwards links and associated systems
and methods.
mla: Ford, Bryan, et al. Cryptographically Verifiable Data Structure Having Multi-Hop
Forward and Backwards Links and Associated Systems and Methods. 2020.
short: B. Ford, L. Gasse, E. Kokoris Kogias, P. Jovanovic, (2020).
date_created: 2021-12-16T13:28:59Z
date_published: 2020-03-03T00:00:00Z
date_updated: 2021-12-21T10:04:50Z
day: '03'
department:
- _id: ElKo
extern: '1'
ipc: ' H04L9/3247 ; G06Q20/29 ; G06Q20/382 ; H04L9/3236'
ipn: '10581613'
main_file_link:
- open_access: '1'
url: https://patents.google.com/patent/US10581613B2/en
month: '03'
oa: 1
oa_version: Published Version
publication_date: 2020-03-03
related_material:
link:
- relation: earlier_version
url: https://patents.google.com/patent/US20180359096A1/en
status: public
title: Cryptographically verifiable data structure having multi-hop forward and backwards
links and associated systems and methods
type: patent
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2020'
...
---
_id: '10618'
abstract:
- lang: eng
text: Magnetism typically arises from the joint effect of Fermi statistics and repulsive
Coulomb interactions, which favours ground states with non-zero electron spin.
As a result, controlling spin magnetism with electric fields—a longstanding technological
goal in spintronics and multiferroics1,2—can be achieved only indirectly. Here
we experimentally demonstrate direct electric-field control of magnetic states
in an orbital Chern insulator3,4,5,6, a magnetic system in which non-trivial band
topology favours long-range order of orbital angular momentum but the spins are
thought to remain disordered7,8,9,10,11,12,13,14. We use van der Waals heterostructures
consisting of a graphene monolayer rotationally faulted with respect to a Bernal-stacked
bilayer to realize narrow and topologically non-trivial valley-projected moiré
minibands15,16,17. At fillings of one and three electrons per moiré unit cell
within these bands, we observe quantized anomalous Hall effects18 with transverse
resistance approximately equal to h/2e2 (where h is Planck’s constant and e is
the charge on the electron), which is indicative of spontaneous polarization of
the system into a single-valley-projected band with a Chern number equal to two.
At a filling of three electrons per moiré unit cell, we find that the sign of
the quantum anomalous Hall effect can be reversed via field-effect control of
the chemical potential; moreover, this transition is hysteretic, which we use
to demonstrate non-volatile electric-field-induced reversal of the magnetic state.
A theoretical analysis19 indicates that the effect arises from the topological
edge states, which drive a change in sign of the magnetization and thus a reversal
in the favoured magnetic state. Voltage control of magnetic states can be used
to electrically pattern non-volatile magnetic-domain structures hosting chiral
edge states, with applications ranging from reconfigurable microwave circuit elements
to ultralow-power magnetic memories.
acknowledgement: We acknowledge discussions with J. Checkelsky, S. Chen, C. Dean,
M. Yankowitz, D. Reilly, I. Sodemann and M. Zaletel. Work at UCSB was primarily
supported by the ARO under MURI W911NF-16-1-0361. Measurements of twisted bilayer
graphene (Extended Data Fig. 8) and measurements at elevated temperatures (Extended
Data Fig. 3) were supported by a SEED grant and made use of shared facilities of
the UCSB MRSEC (NSF DMR 1720256), a member of the Materials Research Facilities
Network (www.mrfn.org). A.F.Y. acknowledges the support of the David and Lucille
Packard Foundation under award 2016-65145. A.H.M. and J.Z. were supported by the
National Science Foundation through the Center for Dynamics and Control of Materials,
an NSF MRSEC under Cooperative Agreement number DMR-1720595, and by the Welch Foundation
under grant TBF1473. C.L.T. acknowledges support from the Hertz Foundation and from
the National Science Foundation Graduate Research Fellowship Program under grant
1650114. K.W. and T.T. acknowledge support from the Elemental Strategy Initiative
conducted by the MEXT, Japan, Grant Number JPMXP0112101001, JSPS KAKENHI grant numbers
JP20H00354 and the CREST(JPMJCR15F3), JST.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Hryhoriy
full_name: Polshyn, Hryhoriy
id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48
last_name: Polshyn
orcid: 0000-0001-8223-8896
- first_name: J.
full_name: Zhu, J.
last_name: Zhu
- first_name: M. A.
full_name: Kumar, M. A.
last_name: Kumar
- first_name: Y.
full_name: Zhang, Y.
last_name: Zhang
- first_name: F.
full_name: Yang, F.
last_name: Yang
- first_name: C. L.
full_name: Tschirhart, C. L.
last_name: Tschirhart
- first_name: M.
full_name: Serlin, M.
last_name: Serlin
- first_name: K.
full_name: Watanabe, K.
last_name: Watanabe
- first_name: T.
full_name: Taniguchi, T.
last_name: Taniguchi
- first_name: A. H.
full_name: MacDonald, A. H.
last_name: MacDonald
- first_name: A. F.
full_name: Young, A. F.
last_name: Young
citation:
ama: Polshyn H, Zhu J, Kumar MA, et al. Electrical switching of magnetic order in
an orbital Chern insulator. Nature. 2020;588(7836):66-70. doi:10.1038/s41586-020-2963-8
apa: Polshyn, H., Zhu, J., Kumar, M. A., Zhang, Y., Yang, F., Tschirhart, C. L.,
… Young, A. F. (2020). Electrical switching of magnetic order in an orbital Chern
insulator. Nature. Springer Nature. https://doi.org/10.1038/s41586-020-2963-8
chicago: Polshyn, Hryhoriy, J. Zhu, M. A. Kumar, Y. Zhang, F. Yang, C. L. Tschirhart,
M. Serlin, et al. “Electrical Switching of Magnetic Order in an Orbital Chern
Insulator.” Nature. Springer Nature, 2020. https://doi.org/10.1038/s41586-020-2963-8.
ieee: H. Polshyn et al., “Electrical switching of magnetic order in an orbital
Chern insulator,” Nature, vol. 588, no. 7836. Springer Nature, pp. 66–70,
2020.
ista: Polshyn H, Zhu J, Kumar MA, Zhang Y, Yang F, Tschirhart CL, Serlin M, Watanabe
K, Taniguchi T, MacDonald AH, Young AF. 2020. Electrical switching of magnetic
order in an orbital Chern insulator. Nature. 588(7836), 66–70.
mla: Polshyn, Hryhoriy, et al. “Electrical Switching of Magnetic Order in an Orbital
Chern Insulator.” Nature, vol. 588, no. 7836, Springer Nature, 2020, pp.
66–70, doi:10.1038/s41586-020-2963-8.
short: H. Polshyn, J. Zhu, M.A. Kumar, Y. Zhang, F. Yang, C.L. Tschirhart, M. Serlin,
K. Watanabe, T. Taniguchi, A.H. MacDonald, A.F. Young, Nature 588 (2020) 66–70.
date_created: 2022-01-13T14:12:17Z
date_published: 2020-11-23T00:00:00Z
date_updated: 2022-01-13T14:21:04Z
day: '23'
doi: 10.1038/s41586-020-2963-8
extern: '1'
external_id:
arxiv:
- '2004.11353'
pmid:
- '33230333'
intvolume: ' 588'
issue: '7836'
keyword:
- multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2004.11353
month: '11'
oa: 1
oa_version: Preprint
page: 66-70
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: Electrical switching of magnetic order in an orbital Chern insulator
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 588
year: '2020'
...
---
_id: '10650'
abstract:
- lang: eng
text: The understanding of material systems with strong electron-electron interactions
is the central problem in modern condensed matter physics. Despite this, the essential
physics of many of these materials is still not understood and we have no overall
perspective on their properties. Moreover, we have very little ability to make
predictions in this class of systems. In this manuscript we share our personal
views of what the major open problems are in correlated electron systems and we
discuss some possible routes to make progress in this rich and fascinating field.
This manuscript is the result of the vigorous discussions and deliberations that
took place at Johns Hopkins University during a three-day workshop January 27,
28, and 29, 2020 that brought together six senior scientists and 46 more junior
scientists. Our hope, is that the topics we have presented will provide inspiration
for others working in this field and motivation for the idea that significant
progress can be made on very hard problems if we focus our collective energies.
acknowledgement: "We thank NSF CMP program for suggestions regarding the topic and
general structure of the workshop. This project was supported by the NSF DMR-2002329
and The Gordon and Betty Moore Foundation (GBMF) EPiQS initiative. We would like
to sincerely thank A. Kapitulnik, A. J. Leggett, M.B. Maple, T.M. McQueen, M. Norman,
P. S. Riseborough, and G. A. Sawatzky for their lectures at the workshop and advice
on the writing of this manuscript. We would also like to thank G. Blumberg, C. Broholm,
S. Crooker, N. Drichko, and A. Patel for helpful consultation on topics discussed\r\nherein.
A number of individuals also had independent support: (AA, EH; GBMF-4305), (IMH;
GBMF-9071), (HJC; NHMFL is supported by the NSF DMR-1644779 and the state of Florida),
(YH, AZ; Miller Institute for Basic Research in Science), (YC; US DOE-BES DEAC02-06CH11357),
(AS; Spallation Neutron Source, a DOE Office of Science User Facility operated by
ORNL), (SAAG; ARO-W911NF-18-1-0290, NSF DMR-1455233), (YW; DOE-BES DE-SC0019331,
GBMF-4532)."
article_processing_charge: No
arxiv: 1
author:
- first_name: A
full_name: Alexandradinata, A
last_name: Alexandradinata
- first_name: N.P.
full_name: Armitage, N.P.
last_name: Armitage
- first_name: Andrey
full_name: Baydin, Andrey
last_name: Baydin
- first_name: Wenli
full_name: Bi, Wenli
last_name: Bi
- first_name: Yue
full_name: Cao, Yue
last_name: Cao
- first_name: Hitesh J.
full_name: Changlani, Hitesh J.
last_name: Changlani
- first_name: Eli
full_name: Chertkov, Eli
last_name: Chertkov
- first_name: Eduardo H.
full_name: da Silva Neto, Eduardo H.
last_name: da Silva Neto
- first_name: Luca
full_name: Delacretaz, Luca
last_name: Delacretaz
- first_name: Ismail
full_name: El Baggari, Ismail
last_name: El Baggari
- first_name: G.M.
full_name: Ferguson, G.M.
last_name: Ferguson
- first_name: William J.
full_name: Gannon, William J.
last_name: Gannon
- first_name: Sayed Ali Akbar
full_name: Ghorashi, Sayed Ali Akbar
last_name: Ghorashi
- first_name: Berit H.
full_name: Goodge, Berit H.
last_name: Goodge
- first_name: Olga
full_name: Goulko, Olga
last_name: Goulko
- first_name: G.
full_name: Grissonnache, G.
last_name: Grissonnache
- first_name: Alannah
full_name: Hallas, Alannah
last_name: Hallas
- first_name: Ian M.
full_name: Hayes, Ian M.
last_name: Hayes
- first_name: Yu
full_name: He, Yu
last_name: He
- first_name: Edwin W.
full_name: Huang, Edwin W.
last_name: Huang
- first_name: Anshu
full_name: Kogar, Anshu
last_name: Kogar
- first_name: Divine
full_name: Kumah, Divine
last_name: Kumah
- first_name: Jong Yeon
full_name: Lee, Jong Yeon
last_name: Lee
- first_name: A.
full_name: Legros, A.
last_name: Legros
- first_name: Fahad
full_name: Mahmood, Fahad
last_name: Mahmood
- first_name: Yulia
full_name: Maximenko, Yulia
last_name: Maximenko
- first_name: Nick
full_name: Pellatz, Nick
last_name: Pellatz
- first_name: Hryhoriy
full_name: Polshyn, Hryhoriy
id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48
last_name: Polshyn
orcid: 0000-0001-8223-8896
- first_name: Tarapada
full_name: Sarkar, Tarapada
last_name: Sarkar
- first_name: Allen
full_name: Scheie, Allen
last_name: Scheie
- first_name: Kyle L.
full_name: Seyler, Kyle L.
last_name: Seyler
- first_name: Zhenzhong
full_name: Shi, Zhenzhong
last_name: Shi
- first_name: Brian
full_name: Skinner, Brian
last_name: Skinner
- first_name: Lucia
full_name: Steinke, Lucia
last_name: Steinke
- first_name: K.
full_name: Thirunavukkuarasu, K.
last_name: Thirunavukkuarasu
- first_name: Thaís Victa
full_name: Trevisan, Thaís Victa
last_name: Trevisan
- first_name: Michael
full_name: Vogl, Michael
last_name: Vogl
- first_name: Pavel A.
full_name: Volkov, Pavel A.
last_name: Volkov
- first_name: Yao
full_name: Wang, Yao
last_name: Wang
- first_name: Yishu
full_name: Wang, Yishu
last_name: Wang
- first_name: Di
full_name: Wei, Di
last_name: Wei
- first_name: Kaya
full_name: Wei, Kaya
last_name: Wei
- first_name: Shuolong
full_name: Yang, Shuolong
last_name: Yang
- first_name: Xian
full_name: Zhang, Xian
last_name: Zhang
- first_name: Ya-Hui
full_name: Zhang, Ya-Hui
last_name: Zhang
- first_name: Liuyan
full_name: Zhao, Liuyan
last_name: Zhao
- first_name: Alfred
full_name: Zong, Alfred
last_name: Zong
citation:
ama: Alexandradinata A, Armitage NP, Baydin A, et al. The future of the correlated
electron problem. arXiv.
apa: Alexandradinata, A., Armitage, N. P., Baydin, A., Bi, W., Cao, Y., Changlani,
H. J., … Zong, A. (n.d.). The future of the correlated electron problem. arXiv.
chicago: Alexandradinata, A, N.P. Armitage, Andrey Baydin, Wenli Bi, Yue Cao, Hitesh
J. Changlani, Eli Chertkov, et al. “The Future of the Correlated Electron Problem.”
ArXiv, n.d.
ieee: A. Alexandradinata et al., “The future of the correlated electron problem,”
arXiv. .
ista: Alexandradinata A, Armitage NP, Baydin A, Bi W, Cao Y, Changlani HJ, Chertkov
E, da Silva Neto EH, Delacretaz L, El Baggari I, Ferguson GM, Gannon WJ, Ghorashi
SAA, Goodge BH, Goulko O, Grissonnache G, Hallas A, Hayes IM, He Y, Huang EW,
Kogar A, Kumah D, Lee JY, Legros A, Mahmood F, Maximenko Y, Pellatz N, Polshyn
H, Sarkar T, Scheie A, Seyler KL, Shi Z, Skinner B, Steinke L, Thirunavukkuarasu
K, Trevisan TV, Vogl M, Volkov PA, Wang Y, Wang Y, Wei D, Wei K, Yang S, Zhang
X, Zhang Y-H, Zhao L, Zong A. The future of the correlated electron problem. arXiv,
.
mla: Alexandradinata, A., et al. “The Future of the Correlated Electron Problem.”
ArXiv.
short: A. Alexandradinata, N.P. Armitage, A. Baydin, W. Bi, Y. Cao, H.J. Changlani,
E. Chertkov, E.H. da Silva Neto, L. Delacretaz, I. El Baggari, G.M. Ferguson,
W.J. Gannon, S.A.A. Ghorashi, B.H. Goodge, O. Goulko, G. Grissonnache, A. Hallas,
I.M. Hayes, Y. He, E.W. Huang, A. Kogar, D. Kumah, J.Y. Lee, A. Legros, F. Mahmood,
Y. Maximenko, N. Pellatz, H. Polshyn, T. Sarkar, A. Scheie, K.L. Seyler, Z. Shi,
B. Skinner, L. Steinke, K. Thirunavukkuarasu, T.V. Trevisan, M. Vogl, P.A. Volkov,
Y. Wang, Y. Wang, D. Wei, K. Wei, S. Yang, X. Zhang, Y.-H. Zhang, L. Zhao, A.
Zong, ArXiv (n.d.).
date_created: 2022-01-20T10:55:36Z
date_published: 2020-10-01T00:00:00Z
date_updated: 2022-01-24T08:05:51Z
day: '01'
extern: '1'
external_id:
arxiv:
- '2010.00584'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2010.00584
month: '10'
oa: 1
oa_version: Preprint
page: '55'
publication: arXiv
publication_status: submitted
status: public
title: The future of the correlated electron problem
type: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2020'
...
---
_id: '11816'
abstract:
- lang: eng
text: In recent years, significant advances have been made in the design and analysis
of fully dynamic maximal matching algorithms. However, these theoretical results
have received very little attention from the practical perspective. Few of the
algorithms are implemented and tested on real datasets, and their practical potential
is far from understood. In this paper, we attempt to bridge the gap between theory
and practice that is currently observed for the fully dynamic maximal matching
problem. We engineer several algorithms and empirically study those algorithms
on an extensive set of dynamic instances.
alternative_title:
- LIPIcs
article_number: '58'
article_processing_charge: No
arxiv: 1
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Khan
full_name: Shahbaz, Khan
last_name: Shahbaz
- first_name: Richard
full_name: Paul, Richard
last_name: Paul
- first_name: Christian
full_name: Schulz, Christian
last_name: Schulz
citation:
ama: 'Henzinger MH, Shahbaz K, Paul R, Schulz C. Dynamic matching algorithms in
practice. In: 8th Annual European Symposium on Algorithms. Vol 173. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.ESA.2020.58'
apa: 'Henzinger, M. H., Shahbaz, K., Paul, R., & Schulz, C. (2020). Dynamic
matching algorithms in practice. In 8th Annual European Symposium on Algorithms
(Vol. 173). Pisa, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ESA.2020.58'
chicago: Henzinger, Monika H, Khan Shahbaz, Richard Paul, and Christian Schulz.
“Dynamic Matching Algorithms in Practice.” In 8th Annual European Symposium
on Algorithms, Vol. 173. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2020. https://doi.org/10.4230/LIPIcs.ESA.2020.58.
ieee: M. H. Henzinger, K. Shahbaz, R. Paul, and C. Schulz, “Dynamic matching algorithms
in practice,” in 8th Annual European Symposium on Algorithms, Pisa, Italy,
2020, vol. 173.
ista: 'Henzinger MH, Shahbaz K, Paul R, Schulz C. 2020. Dynamic matching algorithms
in practice. 8th Annual European Symposium on Algorithms. ESA: Annual European
Symposium on Algorithms, LIPIcs, vol. 173, 58.'
mla: Henzinger, Monika H., et al. “Dynamic Matching Algorithms in Practice.” 8th
Annual European Symposium on Algorithms, vol. 173, 58, Schloss Dagstuhl -
Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.ESA.2020.58.
short: M.H. Henzinger, K. Shahbaz, R. Paul, C. Schulz, in:, 8th Annual European
Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.
conference:
end_date: 2020-09-09
location: Pisa, Italy
name: 'ESA: Annual European Symposium on Algorithms'
start_date: 2020-09-07
date_created: 2022-08-12T07:13:25Z
date_published: 2020-08-26T00:00:00Z
date_updated: 2023-02-14T08:57:55Z
day: '26'
doi: 10.4230/LIPIcs.ESA.2020.58
extern: '1'
external_id:
arxiv:
- '2004.09099'
intvolume: ' 173'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.4230/LIPIcs.ESA.2020.58
month: '08'
oa: 1
oa_version: Published Version
publication: 8th Annual European Symposium on Algorithms
publication_identifier:
isbn:
- '9783959771627'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamic matching algorithms in practice
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 173
year: '2020'
...