---
_id: '14494'
abstract:
- lang: eng
text: "We provide i) gridded initial conditions (.tif), ii) modeled gridded monthly
outputs (.tif), and iii) modeled hourly outputs at the station locations (.txt)
for the hydrological year 2019. Information about the variables and units can
be found in the figures (.png) associated to each dataset. Details about the datasets
can be found in the original publication by Buri and others (2023).\r\n\r\nBuri,
P., Fatichi, S., Shaw, T. E., Miles, E. S., McCarthy, M. J., Fyffe, C. L., ...
& Pellicciotti, F. (2023). Land Surface Modeling in the Himalayas: On the Importance
of Evaporative Fluxes for the Water Balance of a High‐Elevation Catchment. Water
Resources Research, 59(10), e2022WR033841. DOI: 10.1029/2022WR033841"
article_processing_charge: No
author:
- first_name: Pascal
full_name: Buri, Pascal
last_name: Buri
- first_name: Simone
full_name: Fatichi, Simone
last_name: Fatichi
- first_name: Thomas
full_name: Shaw, Thomas
id: 3caa3f91-1f03-11ee-96ce-e0e553054d6e
last_name: Shaw
- first_name: 'Evan '
full_name: 'Miles, Evan '
last_name: Miles
- first_name: Michael
full_name: McCarthy, Michael
id: 22a2674a-61ce-11ee-94b5-d18813baf16f
last_name: McCarthy
- first_name: Catriona Louise
full_name: Fyffe, Catriona Louise
id: 001b0422-8d15-11ed-bc51-cab6c037a228
last_name: Fyffe
- first_name: Stefan
full_name: Fugger, Stefan
last_name: Fugger
- first_name: Shaoting
full_name: Ren, Shaoting
last_name: Ren
- first_name: Marin
full_name: Kneib, Marin
last_name: Kneib
- first_name: Achille
full_name: Jouberton, Achille
last_name: Jouberton
- first_name: Jakob
full_name: Steiner, Jakob
last_name: Steiner
- first_name: Koji
full_name: Fujita, Koji
last_name: Fujita
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
orcid: 0000-0002-5554-8087
citation:
ama: 'Buri P, Fatichi S, Shaw T, et al. Model output data to “Land surface modeling
in the Himalayas: on the importance of evaporative fluxes for the water balance
of a high elevation catchment.” 2023. doi:10.5281/ZENODO.8402426'
apa: 'Buri, P., Fatichi, S., Shaw, T., Miles, E., McCarthy, M., Fyffe, C. L., …
Pellicciotti, F. (2023). Model output data to “Land surface modeling in the Himalayas:
on the importance of evaporative fluxes for the water balance of a high elevation
catchment.” Zenodo. https://doi.org/10.5281/ZENODO.8402426'
chicago: 'Buri, Pascal, Simone Fatichi, Thomas Shaw, Evan Miles, Michael McCarthy,
Catriona Louise Fyffe, Stefan Fugger, et al. “Model Output Data to ‘Land Surface
Modeling in the Himalayas: On the Importance of Evaporative Fluxes for the Water
Balance of a High Elevation Catchment.’” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8402426.'
ieee: 'P. Buri et al., “Model output data to ‘Land surface modeling in the
Himalayas: on the importance of evaporative fluxes for the water balance of a
high elevation catchment.’” Zenodo, 2023.'
ista: 'Buri P, Fatichi S, Shaw T, Miles E, McCarthy M, Fyffe CL, Fugger S, Ren S,
Kneib M, Jouberton A, Steiner J, Fujita K, Pellicciotti F. 2023. Model output
data to ‘Land surface modeling in the Himalayas: on the importance of evaporative
fluxes for the water balance of a high elevation catchment’, Zenodo, 10.5281/ZENODO.8402426.'
mla: 'Buri, Pascal, et al. Model Output Data to “Land Surface Modeling in the
Himalayas: On the Importance of Evaporative Fluxes for the Water Balance of a
High Elevation Catchment.” Zenodo, 2023, doi:10.5281/ZENODO.8402426.'
short: P. Buri, S. Fatichi, T. Shaw, E. Miles, M. McCarthy, C.L. Fyffe, S. Fugger,
S. Ren, M. Kneib, A. Jouberton, J. Steiner, K. Fujita, F. Pellicciotti, (2023).
date_created: 2023-11-07T08:01:39Z
date_published: 2023-10-03T00:00:00Z
date_updated: 2023-11-07T08:12:35Z
day: '03'
ddc:
- '550'
department:
- _id: FrPe
doi: 10.5281/ZENODO.8402426
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://10.5281/ZENODO.8402426
month: '10'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '14487'
relation: used_in_publication
status: public
status: public
title: 'Model output data to "Land surface modeling in the Himalayas: on the importance
of evaporative fluxes for the water balance of a high elevation catchment"'
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14499'
abstract:
- lang: eng
text: "An n-vertex graph is called C-Ramsey if it has no clique or independent set
of size Clog2n (i.e., if it has near-optimal Ramsey behavior). In this paper,
we study edge statistics in Ramsey graphs, in particular obtaining very precise
control of the distribution of the number of edges in a random vertex subset of
a C-Ramsey graph. This brings together two ongoing lines of research: the study
of ‘random-like’ properties of Ramsey graphs and the study of small-ball probability
for low-degree polynomials of independent random variables.\r\n\r\nThe proof proceeds
via an ‘additive structure’ dichotomy on the degree sequence and involves a wide
range of different tools from Fourier analysis, random matrix theory, the theory
of Boolean functions, probabilistic combinatorics and low-rank approximation.
In particular, a key ingredient is a new sharpened version of the quadratic Carbery–Wright
theorem on small-ball probability for polynomials of Gaussians, which we believe
is of independent interest. One of the consequences of our result is the resolution
of an old conjecture of Erdős and McKay, for which Erdős reiterated in several
of his open problem collections and for which he offered one of his notorious
monetary prizes."
acknowledgement: Kwan was supported for part of this work by ERC Starting Grant ‘RANDSTRUCT’
No. 101076777. Sah and Sawhney were supported by NSF Graduate Research Fellowship
Program DGE-2141064. Sah was supported by the PD Soros Fellowship. Sauermann was
supported by NSF Award DMS-2100157, and for part of this work by a Sloan Research
Fellowship.
article_number: e21
article_processing_charge: Yes
article_type: original
author:
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Ashwin
full_name: Sah, Ashwin
last_name: Sah
- first_name: Lisa
full_name: Sauermann, Lisa
last_name: Sauermann
- first_name: Mehtaab
full_name: Sawhney, Mehtaab
last_name: Sawhney
citation:
ama: Kwan MA, Sah A, Sauermann L, Sawhney M. Anticoncentration in Ramsey graphs
and a proof of the Erdős–McKay conjecture. Forum of Mathematics, Pi. 2023;11.
doi:10.1017/fmp.2023.17
apa: Kwan, M. A., Sah, A., Sauermann, L., & Sawhney, M. (2023). Anticoncentration
in Ramsey graphs and a proof of the Erdős–McKay conjecture. Forum of Mathematics,
Pi. Cambridge University Press. https://doi.org/10.1017/fmp.2023.17
chicago: Kwan, Matthew Alan, Ashwin Sah, Lisa Sauermann, and Mehtaab Sawhney. “Anticoncentration
in Ramsey Graphs and a Proof of the Erdős–McKay Conjecture.” Forum of Mathematics,
Pi. Cambridge University Press, 2023. https://doi.org/10.1017/fmp.2023.17.
ieee: M. A. Kwan, A. Sah, L. Sauermann, and M. Sawhney, “Anticoncentration in Ramsey
graphs and a proof of the Erdős–McKay conjecture,” Forum of Mathematics, Pi,
vol. 11. Cambridge University Press, 2023.
ista: Kwan MA, Sah A, Sauermann L, Sawhney M. 2023. Anticoncentration in Ramsey
graphs and a proof of the Erdős–McKay conjecture. Forum of Mathematics, Pi. 11,
e21.
mla: Kwan, Matthew Alan, et al. “Anticoncentration in Ramsey Graphs and a Proof
of the Erdős–McKay Conjecture.” Forum of Mathematics, Pi, vol. 11, e21,
Cambridge University Press, 2023, doi:10.1017/fmp.2023.17.
short: M.A. Kwan, A. Sah, L. Sauermann, M. Sawhney, Forum of Mathematics, Pi 11
(2023).
date_created: 2023-11-07T09:02:48Z
date_published: 2023-08-24T00:00:00Z
date_updated: 2023-11-07T09:18:57Z
day: '24'
ddc:
- '510'
department:
- _id: MaKw
doi: 10.1017/fmp.2023.17
external_id:
arxiv:
- '2208.02874'
file:
- access_level: open_access
checksum: 54b824098d59073cc87a308d458b0a3e
content_type: application/pdf
creator: dernst
date_created: 2023-11-07T09:16:23Z
date_updated: 2023-11-07T09:16:23Z
file_id: '14500'
file_name: 2023_ForumMathematics_Kwan.pdf
file_size: 1218719
relation: main_file
success: 1
file_date_updated: 2023-11-07T09:16:23Z
has_accepted_license: '1'
intvolume: ' 11'
keyword:
- Discrete Mathematics and Combinatorics
- Geometry and Topology
- Mathematical Physics
- Statistics and Probability
- Algebra and Number Theory
- Analysis
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: bd95085b-d553-11ed-ba76-e55d3349be45
grant_number: '101076777'
name: Randomness and structure in combinatorics
publication: Forum of Mathematics, Pi
publication_identifier:
issn:
- 2050-5086
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Anticoncentration in Ramsey graphs and a proof of the Erdős–McKay conjecture
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2023'
...
---
_id: '14281'
abstract:
- lang: eng
text: In nature, proteins that switch between two conformations in response to environmental
stimuli structurally transduce biochemical information in a manner analogous to
how transistors control information flow in computing devices. Designing proteins
with two distinct but fully structured conformations is a challenge for protein
design as it requires sculpting an energy landscape with two distinct minima.
Here we describe the design of “hinge” proteins that populate one designed state
in the absence of ligand and a second designed state in the presence of ligand.
X-ray crystallography, electron microscopy, double electron-electron resonance
spectroscopy, and binding measurements demonstrate that despite the significant
structural differences the two states are designed with atomic level accuracy
and that the conformational and binding equilibria are closely coupled.
article_processing_charge: No
article_type: original
author:
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: Philip J. Y.
full_name: Leung, Philip J. Y.
last_name: Leung
- first_name: Maxx H.
full_name: Tessmer, Maxx H.
last_name: Tessmer
- first_name: Adam
full_name: Broerman, Adam
last_name: Broerman
- first_name: Cullen
full_name: Demakis, Cullen
last_name: Demakis
- first_name: Acacia F.
full_name: Dishman, Acacia F.
last_name: Dishman
- first_name: Arvind
full_name: Pillai, Arvind
last_name: Pillai
- first_name: Abbas
full_name: Idris, Abbas
last_name: Idris
- first_name: David
full_name: Juergens, David
last_name: Juergens
- first_name: Justas
full_name: Dauparas, Justas
last_name: Dauparas
- first_name: Xinting
full_name: Li, Xinting
last_name: Li
- first_name: Paul M.
full_name: Levine, Paul M.
last_name: Levine
- first_name: Mila
full_name: Lamb, Mila
last_name: Lamb
- first_name: Ryanne K.
full_name: Ballard, Ryanne K.
last_name: Ballard
- first_name: Stacey R.
full_name: Gerben, Stacey R.
last_name: Gerben
- first_name: Hannah
full_name: Nguyen, Hannah
last_name: Nguyen
- first_name: Alex
full_name: Kang, Alex
last_name: Kang
- first_name: Banumathi
full_name: Sankaran, Banumathi
last_name: Sankaran
- first_name: Asim K.
full_name: Bera, Asim K.
last_name: Bera
- first_name: Brian F.
full_name: Volkman, Brian F.
last_name: Volkman
- first_name: Jeff
full_name: Nivala, Jeff
last_name: Nivala
- first_name: Stefan
full_name: Stoll, Stefan
last_name: Stoll
- first_name: David
full_name: Baker, David
last_name: Baker
citation:
ama: Praetorius FM, Leung PJY, Tessmer MH, et al. Design of stimulus-responsive
two-state hinge proteins. Science. 2023;381(6659):754-760. doi:10.1126/science.adg7731
apa: Praetorius, F. M., Leung, P. J. Y., Tessmer, M. H., Broerman, A., Demakis,
C., Dishman, A. F., … Baker, D. (2023). Design of stimulus-responsive two-state
hinge proteins. Science. American Association for the Advancement of Science.
https://doi.org/10.1126/science.adg7731
chicago: Praetorius, Florian M, Philip J. Y. Leung, Maxx H. Tessmer, Adam Broerman,
Cullen Demakis, Acacia F. Dishman, Arvind Pillai, et al. “Design of Stimulus-Responsive
Two-State Hinge Proteins.” Science. American Association for the Advancement
of Science, 2023. https://doi.org/10.1126/science.adg7731.
ieee: F. M. Praetorius et al., “Design of stimulus-responsive two-state hinge
proteins,” Science, vol. 381, no. 6659. American Association for the Advancement
of Science, pp. 754–760, 2023.
ista: Praetorius FM, Leung PJY, Tessmer MH, Broerman A, Demakis C, Dishman AF, Pillai
A, Idris A, Juergens D, Dauparas J, Li X, Levine PM, Lamb M, Ballard RK, Gerben
SR, Nguyen H, Kang A, Sankaran B, Bera AK, Volkman BF, Nivala J, Stoll S, Baker
D. 2023. Design of stimulus-responsive two-state hinge proteins. Science. 381(6659),
754–760.
mla: Praetorius, Florian M., et al. “Design of Stimulus-Responsive Two-State Hinge
Proteins.” Science, vol. 381, no. 6659, American Association for the Advancement
of Science, 2023, pp. 754–60, doi:10.1126/science.adg7731.
short: F.M. Praetorius, P.J.Y. Leung, M.H. Tessmer, A. Broerman, C. Demakis, A.F.
Dishman, A. Pillai, A. Idris, D. Juergens, J. Dauparas, X. Li, P.M. Levine, M.
Lamb, R.K. Ballard, S.R. Gerben, H. Nguyen, A. Kang, B. Sankaran, A.K. Bera, B.F.
Volkman, J. Nivala, S. Stoll, D. Baker, Science 381 (2023) 754–760.
date_created: 2023-09-06T12:04:23Z
date_published: 2023-08-17T00:00:00Z
date_updated: 2023-11-07T12:42:09Z
day: '17'
doi: 10.1126/science.adg7731
extern: '1'
external_id:
pmid:
- '37590357'
intvolume: ' 381'
issue: '6659'
language:
- iso: eng
month: '08'
oa_version: None
page: 754-760
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: Design of stimulus-responsive two-state hinge proteins
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 381
year: '2023'
...
---
_id: '14294'
abstract:
- lang: eng
text: Growth factors and cytokines signal by binding to the extracellular domains
of their receptors and drive association and transphosphorylation of the receptor
intracellular tyrosine kinase domains, initiating downstream signaling cascades.
To enable systematic exploration of how receptor valency and geometry affects
signaling outcomes, we designed cyclic homo-oligomers with up to 8 subunits using
repeat protein building blocks that can be modularly extended. By incorporating
a de novo designed fibroblast growth-factor receptor (FGFR) binding module into
these scaffolds, we generated a series of synthetic signaling ligands that exhibit
potent valency- and geometry-dependent Ca2+ release and MAPK pathway activation.
The high specificity of the designed agonists reveal distinct roles for two FGFR
splice variants in driving endothelial and mesenchymal cell fates during early
vascular development. The ability to incorporate receptor binding domains and
repeat extensions in a modular fashion makes our designed scaffolds broadly useful
for probing and manipulating cellular signaling pathways.
article_processing_charge: No
author:
- first_name: Natasha I
full_name: Edman, Natasha I
last_name: Edman
- first_name: Rachel L
full_name: Redler, Rachel L
last_name: Redler
- first_name: Ashish
full_name: Phal, Ashish
last_name: Phal
- first_name: Thomas
full_name: Schlichthaerle, Thomas
last_name: Schlichthaerle
- first_name: Sanjay R
full_name: Srivatsan, Sanjay R
last_name: Srivatsan
- first_name: Ali
full_name: Etemadi, Ali
last_name: Etemadi
- first_name: Seong
full_name: An, Seong
last_name: An
- first_name: Andrew
full_name: Favor, Andrew
last_name: Favor
- first_name: Devon
full_name: Ehnes, Devon
last_name: Ehnes
- first_name: Zhe
full_name: Li, Zhe
last_name: Li
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: Max
full_name: Gordon, Max
last_name: Gordon
- first_name: Wei
full_name: Yang, Wei
last_name: Yang
- first_name: Brian
full_name: Coventry, Brian
last_name: Coventry
- first_name: Derrick R
full_name: Hicks, Derrick R
last_name: Hicks
- first_name: Longxing
full_name: Cao, Longxing
last_name: Cao
- first_name: Neville
full_name: Bethel, Neville
last_name: Bethel
- first_name: Piper
full_name: Heine, Piper
last_name: Heine
- first_name: Analisa N
full_name: Murray, Analisa N
last_name: Murray
- first_name: Stacey
full_name: Gerben, Stacey
last_name: Gerben
- first_name: Lauren
full_name: Carter, Lauren
last_name: Carter
- first_name: Marcos
full_name: Miranda, Marcos
last_name: Miranda
- first_name: Babak
full_name: Negahdari, Babak
last_name: Negahdari
- first_name: Sangwon
full_name: Lee, Sangwon
last_name: Lee
- first_name: Cole
full_name: Trapnell, Cole
last_name: Trapnell
- first_name: Lance
full_name: Stewart, Lance
last_name: Stewart
- first_name: Damian C
full_name: Ekiert, Damian C
last_name: Ekiert
- first_name: Joseph
full_name: Schlessinger, Joseph
last_name: Schlessinger
- first_name: Jay
full_name: Shendure, Jay
last_name: Shendure
- first_name: Gira
full_name: Bhabha, Gira
last_name: Bhabha
- first_name: Hannele
full_name: Ruohola-Baker, Hannele
last_name: Ruohola-Baker
- first_name: David
full_name: Baker, David
last_name: Baker
citation:
ama: Edman NI, Redler RL, Phal A, et al. Modulation of FGF pathway signaling and
vascular differentiation using designed oligomeric assemblies. bioRxiv.
doi:10.1101/2023.03.14.532666
apa: Edman, N. I., Redler, R. L., Phal, A., Schlichthaerle, T., Srivatsan, S. R.,
Etemadi, A., … Baker, D. (n.d.). Modulation of FGF pathway signaling and vascular
differentiation using designed oligomeric assemblies. bioRxiv. https://doi.org/10.1101/2023.03.14.532666
chicago: Edman, Natasha I, Rachel L Redler, Ashish Phal, Thomas Schlichthaerle,
Sanjay R Srivatsan, Ali Etemadi, Seong An, et al. “Modulation of FGF Pathway Signaling
and Vascular Differentiation Using Designed Oligomeric Assemblies.” BioRxiv,
n.d. https://doi.org/10.1101/2023.03.14.532666.
ieee: N. I. Edman et al., “Modulation of FGF pathway signaling and vascular
differentiation using designed oligomeric assemblies,” bioRxiv. .
ista: Edman NI, Redler RL, Phal A, Schlichthaerle T, Srivatsan SR, Etemadi A, An
S, Favor A, Ehnes D, Li Z, Praetorius FM, Gordon M, Yang W, Coventry B, Hicks
DR, Cao L, Bethel N, Heine P, Murray AN, Gerben S, Carter L, Miranda M, Negahdari
B, Lee S, Trapnell C, Stewart L, Ekiert DC, Schlessinger J, Shendure J, Bhabha
G, Ruohola-Baker H, Baker D. Modulation of FGF pathway signaling and vascular
differentiation using designed oligomeric assemblies. bioRxiv, 10.1101/2023.03.14.532666.
mla: Edman, Natasha I., et al. “Modulation of FGF Pathway Signaling and Vascular
Differentiation Using Designed Oligomeric Assemblies.” BioRxiv, doi:10.1101/2023.03.14.532666.
short: N.I. Edman, R.L. Redler, A. Phal, T. Schlichthaerle, S.R. Srivatsan, A. Etemadi,
S. An, A. Favor, D. Ehnes, Z. Li, F.M. Praetorius, M. Gordon, W. Yang, B. Coventry,
D.R. Hicks, L. Cao, N. Bethel, P. Heine, A.N. Murray, S. Gerben, L. Carter, M.
Miranda, B. Negahdari, S. Lee, C. Trapnell, L. Stewart, D.C. Ekiert, J. Schlessinger,
J. Shendure, G. Bhabha, H. Ruohola-Baker, D. Baker, BioRxiv (n.d.).
date_created: 2023-09-06T12:31:49Z
date_published: 2023-03-15T00:00:00Z
date_updated: 2023-11-07T12:21:58Z
day: '15'
doi: 10.1101/2023.03.14.532666
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2023.03.14.532666
month: '03'
oa: 1
oa_version: Preprint
publication: bioRxiv
publication_status: submitted
status: public
title: Modulation of FGF pathway signaling and vascular differentiation using designed
oligomeric assemblies
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14513'
abstract:
- lang: eng
text: Cold atomic gases have become a paradigmatic system for exploring fundamental
physics, which at the same time allows for applications in quantum technologies.
The accelerating developments in the field have led to a highly advanced set of
engineering techniques that, for example, can tune interactions, shape the external
geometry, select among a large set of atomic species with different properties,
or control the number of atoms. In particular, it is possible to operate in lower
dimensions and drive atomic systems into the strongly correlated regime. In this
review, we discuss recent advances in few-body cold atom systems confined in low
dimensions from a theoretical viewpoint. We mainly focus on bosonic systems in
one dimension and provide an introduction to the static properties before we review
the state-of-the-art research into quantum dynamical processes stimulated by the
presence of correlations. Besides discussing the fundamental physical phenomena
arising in these systems, we also provide an overview of the calculational and
numerical tools and methods that are commonly used, thus delivering a balanced
and comprehensive overview of the field. We conclude by giving an outlook on possible
future directions that are interesting to explore in these correlated systems.
acknowledgement: This review could not have been written without the many fruitful
discussions and great collaborations with colleagues throughout the years, there
are too many to mention. Here we acknowledge conversations regarding the context
of the review with Joachim Brand, Fabian Brauneis, Adolfo del Campo, Alberto Cappellaro,
Panagiotis Giannakeas, Tommaso Macrí, Oleksandr Marchukov, Lukas Rammelmüller and
Manuel Valiente. S. I. M. acknowledges support from the NSF through a grant for
ITAMP at Harvard University. T.F. acknowledges support from JSPS KAKENHI Grant Number
JP23K03290 and T.F. and Th.B. acknowledge support from the Okinawa Institute for
Science and Technology Graduate University, and JST Grant Number JPMJPF2221. A.F.
and R. E. B. acknowledge support from CNPq (Conselho Nacional de Desenvolvimento
Científico e Tecnológico) - Edital Universal 406563/2021-7. A. G. V. acknowledges
support by European Union’s Horizon 2020 research and innovation programme under
the Marie Skłodowska-Curie Grant Agreement No. 754411. P. S. is supported by the
Cluster of Excellence ‘Advanced Imaging of Matter’ of the Deutsche Forschungsgemeinschaft
(DFG) - EXC2056 - project ID 390715994. N. T. Z. is partially supported by the Independent
Research Fund Denmark .
article_processing_charge: No
article_type: original
author:
- first_name: S. I.
full_name: Mistakidis, S. I.
last_name: Mistakidis
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
- first_name: R. E.
full_name: Barfknecht, R. E.
last_name: Barfknecht
- first_name: T.
full_name: Fogarty, T.
last_name: Fogarty
- first_name: Th
full_name: Busch, Th
last_name: Busch
- first_name: A.
full_name: Foerster, A.
last_name: Foerster
- first_name: P.
full_name: Schmelcher, P.
last_name: Schmelcher
- first_name: N. T.
full_name: Zinner, N. T.
last_name: Zinner
citation:
ama: Mistakidis SI, Volosniev A, Barfknecht RE, et al. Few-body Bose gases in low
dimensions - A laboratory for quantum dynamics. Physics Reports. 2023;1042:1-108.
doi:10.1016/j.physrep.2023.10.004
apa: Mistakidis, S. I., Volosniev, A., Barfknecht, R. E., Fogarty, T., Busch, T.,
Foerster, A., … Zinner, N. T. (2023). Few-body Bose gases in low dimensions -
A laboratory for quantum dynamics. Physics Reports. Elsevier. https://doi.org/10.1016/j.physrep.2023.10.004
chicago: Mistakidis, S. I., Artem Volosniev, R. E. Barfknecht, T. Fogarty, Th Busch,
A. Foerster, P. Schmelcher, and N. T. Zinner. “Few-Body Bose Gases in Low Dimensions
- A Laboratory for Quantum Dynamics.” Physics Reports. Elsevier, 2023.
https://doi.org/10.1016/j.physrep.2023.10.004.
ieee: S. I. Mistakidis et al., “Few-body Bose gases in low dimensions - A
laboratory for quantum dynamics,” Physics Reports, vol. 1042. Elsevier,
pp. 1–108, 2023.
ista: Mistakidis SI, Volosniev A, Barfknecht RE, Fogarty T, Busch T, Foerster A,
Schmelcher P, Zinner NT. 2023. Few-body Bose gases in low dimensions - A laboratory
for quantum dynamics. Physics Reports. 1042, 1–108.
mla: Mistakidis, S. I., et al. “Few-Body Bose Gases in Low Dimensions - A Laboratory
for Quantum Dynamics.” Physics Reports, vol. 1042, Elsevier, 2023, pp.
1–108, doi:10.1016/j.physrep.2023.10.004.
short: S.I. Mistakidis, A. Volosniev, R.E. Barfknecht, T. Fogarty, T. Busch, A.
Foerster, P. Schmelcher, N.T. Zinner, Physics Reports 1042 (2023) 1–108.
date_created: 2023-11-12T23:00:54Z
date_published: 2023-11-29T00:00:00Z
date_updated: 2023-11-13T08:01:57Z
day: '29'
department:
- _id: MiLe
doi: 10.1016/j.physrep.2023.10.004
ec_funded: 1
external_id:
arxiv:
- '2202.11071'
intvolume: ' 1042'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2202.11071
month: '11'
oa: 1
oa_version: Preprint
page: 1-108
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Physics Reports
publication_identifier:
issn:
- 0370-1573
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Few-body Bose gases in low dimensions - A laboratory for quantum dynamics
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1042
year: '2023'
...
---
_id: '12869'
abstract:
- lang: eng
text: 'We introduce a stochastic cellular automaton as a model for culture and border
formation. The model can be conceptualized as a game where the expansion rate
of cultures is quantified in terms of their area and perimeter in such a way that
approximately round cultures get a competitive advantage. We first analyse the
model with periodic boundary conditions, where we study how the model can end
up in a fixed state, i.e. freezes. Then we implement the model on the European
geography with mountains and rivers. We see how the model reproduces some qualitative
features of European culture formation, namely that rivers and mountains are more
frequently borders between cultures, mountainous regions tend to have higher cultural
diversity and the central European plain has less clear cultural borders. '
acknowledgement: 'FRK acknowledges support from the Villum Foundation for support
through the QMATH center of Excellence (Grant No. 10059) and the Villum Young Investigator
(Grant No. 25452) programs. '
article_processing_charge: No
author:
- first_name: Frederik Ravn
full_name: Klausen, Frederik Ravn
last_name: Klausen
- first_name: Asbjørn Bækgaard
full_name: Lauritsen, Asbjørn Bækgaard
id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1
last_name: Lauritsen
orcid: 0000-0003-4476-2288
citation:
ama: 'Klausen FR, Lauritsen AB. Research data for: A stochastic cellular automaton
model of culture formation. 2023. doi:10.15479/AT:ISTA:12869'
apa: 'Klausen, F. R., & Lauritsen, A. B. (2023). Research data for: A stochastic
cellular automaton model of culture formation. Institute of Science and Technology
Austria. https://doi.org/10.15479/AT:ISTA:12869'
chicago: 'Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Research Data
for: A Stochastic Cellular Automaton Model of Culture Formation.” Institute of
Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12869.'
ieee: 'F. R. Klausen and A. B. Lauritsen, “Research data for: A stochastic cellular
automaton model of culture formation.” Institute of Science and Technology Austria,
2023.'
ista: 'Klausen FR, Lauritsen AB. 2023. Research data for: A stochastic cellular
automaton model of culture formation, Institute of Science and Technology Austria,
10.15479/AT:ISTA:12869.'
mla: 'Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. Research Data for:
A Stochastic Cellular Automaton Model of Culture Formation. Institute of Science
and Technology Austria, 2023, doi:10.15479/AT:ISTA:12869.'
short: F.R. Klausen, A.B. Lauritsen, (2023).
date_created: 2023-04-26T12:34:49Z
date_published: 2023-04-26T00:00:00Z
date_updated: 2023-11-13T07:47:29Z
day: '26'
ddc:
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department:
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- _id: RoSe
doi: 10.15479/AT:ISTA:12869
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status: public
title: 'Research data for: A stochastic cellular automaton model of culture formation'
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12890'
abstract:
- lang: eng
text: We introduce a stochastic cellular automaton as a model for culture and border
formation. The model can be conceptualized as a game where the expansion rate
of cultures is quantified in terms of their area and perimeter in such a way that
approximately geometrically round cultures get a competitive advantage. We first
analyze the model with periodic boundary conditions, where we study how the model
can end up in a fixed state, i.e., freezes. Then we implement the model on the
European geography with mountains and rivers. We see how the model reproduces
some qualitative features of European culture formation, namely, that rivers and
mountains are more frequently borders between cultures, mountainous regions tend
to have higher cultural diversity, and the central European plain has less clear
cultural borders.
acknowledgement: Thanks to Kim Sneppen, Svend Krøjer, Peter Wildemann, Peter Rasmussen
and Kent Bækgaard Lauritsen for discussions and suggestions. FRK acknowledges support
from the Villum Foundation for support through the QMATH center of Excellence (Grant
No. 10059) and the Villum Young Investigator (Grant No. 25452) programs.
article_number: '054307'
article_processing_charge: No
article_type: original
author:
- first_name: Frederik Ravn
full_name: Klausen, Frederik Ravn
last_name: Klausen
- first_name: Asbjørn Bækgaard
full_name: Lauritsen, Asbjørn Bækgaard
id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1
last_name: Lauritsen
orcid: 0000-0003-4476-2288
citation:
ama: Klausen FR, Lauritsen AB. Stochastic cellular automaton model of culture formation.
Physical Review E. 2023;108(5). doi:10.1103/PhysRevE.108.054307
apa: Klausen, F. R., & Lauritsen, A. B. (2023). Stochastic cellular automaton
model of culture formation. Physical Review E. American Physical Society.
https://doi.org/10.1103/PhysRevE.108.054307
chicago: Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular
Automaton Model of Culture Formation.” Physical Review E. American Physical
Society, 2023. https://doi.org/10.1103/PhysRevE.108.054307.
ieee: F. R. Klausen and A. B. Lauritsen, “Stochastic cellular automaton model of
culture formation,” Physical Review E, vol. 108, no. 5. American Physical
Society, 2023.
ista: Klausen FR, Lauritsen AB. 2023. Stochastic cellular automaton model of culture
formation. Physical Review E. 108(5), 054307.
mla: Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular
Automaton Model of Culture Formation.” Physical Review E, vol. 108, no.
5, 054307, American Physical Society, 2023, doi:10.1103/PhysRevE.108.054307.
short: F.R. Klausen, A.B. Lauritsen, Physical Review E 108 (2023).
date_created: 2023-05-04T08:35:01Z
date_published: 2023-11-08T00:00:00Z
date_updated: 2023-11-13T07:47:30Z
day: '08'
department:
- _id: GradSch
- _id: RoSe
doi: 10.1103/PhysRevE.108.054307
external_id:
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intvolume: ' 108'
issue: '5'
language:
- iso: eng
main_file_link:
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url: https://doi.org/10.48550/arXiv.2305.02153
month: '11'
oa: 1
oa_version: Preprint
publication: Physical Review E
publication_identifier:
eissn:
- 2470-0053
issn:
- 2470-0045
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/FrederikRavnKlausen/model-for-culture-formation
record:
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relation: research_data
status: public
scopus_import: '1'
status: public
title: Stochastic cellular automaton model of culture formation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2023'
...
---
_id: '14516'
abstract:
- lang: eng
text: 'We revisit decentralized random beacons with a focus on practical distributed
applications. Decentralized random beacons (Beaver and So, Eurocrypt''93) provide
the functionality for n parties to generate an unpredictable sequence of bits
in a way that cannot be biased, which is useful for any decentralized protocol
requiring trusted randomness. Existing beacon constructions are highly inefficient
in practical settings where protocol parties need to rejoin after crashes or disconnections,
and more significantly where smart contracts may rely on arbitrary index points
in high-volume streams. For this, we introduce a new notion of history-generating
decentralized random beacons (HGDRBs). Roughly, the history-generation property
of HGDRBs allows for previous beacon outputs to be efficiently generated knowing
only the current value and the public key. At application layers, history-generation
supports registering a sparser set of on-chain values if desired, so that apps
like lotteries can utilize on-chain values without incurring high-frequency costs,
enjoying all the benefits of DRBs implemented off-chain or with decoupled, special-purpose
chains. Unlike rollups, HG is tailored specifically to recovering and verifying
pseudorandom bit sequences and thus enjoys unique optimizations investigated in
this work. We introduce STROBE: an efficient HGDRB construction which generalizes
the original squaring-based RSA approach of Beaver and So. STROBE enjoys several
useful properties that make it suited for practical applications that use beacons:
1) history-generating: it can regenerate and verify high-throughput beacon streams,
supporting sparse (thus cost-effective) ledger entries; 2) concisely self-verifying:
NIZK-free, with state and validation employing a single ring element; 3) eco-friendly:
stake-based rather than work based; 4) unbounded: refresh-free, addressing limitations
of Beaver and So; 5) delay-free: results are immediately available. 6) storage-efficient:
the last beacon suffices to derive all past outputs, thus O(1) storage requirements
for nodes serving the whole history.'
acknowledgement: Work done when all the authors were at Novi Research, Meta.
alternative_title:
- LIPIcs
article_number: '7'
article_processing_charge: Yes
author:
- first_name: Donald
full_name: Beaver, Donald
last_name: Beaver
- first_name: Mahimna
full_name: Kelkar, Mahimna
last_name: Kelkar
- first_name: Kevin
full_name: Lewi, Kevin
last_name: Lewi
- first_name: Valeria
full_name: Nikolaenko, Valeria
last_name: Nikolaenko
- first_name: Alberto
full_name: Sonnino, Alberto
last_name: Sonnino
- first_name: Konstantinos
full_name: Chalkias, Konstantinos
last_name: Chalkias
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Ladi De
full_name: Naurois, Ladi De
last_name: Naurois
- first_name: Arnab
full_name: Roy, Arnab
last_name: Roy
citation:
ama: 'Beaver D, Kelkar M, Lewi K, et al. STROBE: Streaming Threshold Random Beacons.
In: 5th Conference on Advances in Financial Technologies. Vol 282. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.AFT.2023.7'
apa: 'Beaver, D., Kelkar, M., Lewi, K., Nikolaenko, V., Sonnino, A., Chalkias, K.,
… Roy, A. (2023). STROBE: Streaming Threshold Random Beacons. In 5th Conference
on Advances in Financial Technologies (Vol. 282). Princeton, NJ, United States:
Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.AFT.2023.7'
chicago: 'Beaver, Donald, Mahimna Kelkar, Kevin Lewi, Valeria Nikolaenko, Alberto
Sonnino, Konstantinos Chalkias, Eleftherios Kokoris Kogias, Ladi De Naurois, and
Arnab Roy. “STROBE: Streaming Threshold Random Beacons.” In 5th Conference
on Advances in Financial Technologies, Vol. 282. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2023. https://doi.org/10.4230/LIPIcs.AFT.2023.7.'
ieee: 'D. Beaver et al., “STROBE: Streaming Threshold Random Beacons,” in
5th Conference on Advances in Financial Technologies, Princeton, NJ, United
States, 2023, vol. 282.'
ista: 'Beaver D, Kelkar M, Lewi K, Nikolaenko V, Sonnino A, Chalkias K, Kokoris
Kogias E, Naurois LD, Roy A. 2023. STROBE: Streaming Threshold Random Beacons.
5th Conference on Advances in Financial Technologies. AFT: Conference on Advances
in Financial Technologies, LIPIcs, vol. 282, 7.'
mla: 'Beaver, Donald, et al. “STROBE: Streaming Threshold Random Beacons.” 5th
Conference on Advances in Financial Technologies, vol. 282, 7, Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.AFT.2023.7.'
short: D. Beaver, M. Kelkar, K. Lewi, V. Nikolaenko, A. Sonnino, K. Chalkias, E.
Kokoris Kogias, L.D. Naurois, A. Roy, in:, 5th Conference on Advances in Financial
Technologies, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.
conference:
end_date: 2023-10-25
location: Princeton, NJ, United States
name: 'AFT: Conference on Advances in Financial Technologies'
start_date: 2023-10-23
date_created: 2023-11-12T23:00:55Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2023-11-13T08:52:01Z
day: '01'
ddc:
- '000'
department:
- _id: ElKo
doi: 10.4230/LIPIcs.AFT.2023.7
file:
- access_level: open_access
checksum: c1f98831cb5149d6c030c41999e6e960
content_type: application/pdf
creator: dernst
date_created: 2023-11-13T08:44:34Z
date_updated: 2023-11-13T08:44:34Z
file_id: '14521'
file_name: 2023_LIPIcs_Beaver.pdf
file_size: 793495
relation: main_file
success: 1
file_date_updated: 2023-11-13T08:44:34Z
has_accepted_license: '1'
intvolume: ' 282'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2021/1643
month: '10'
oa: 1
oa_version: Published Version
publication: 5th Conference on Advances in Financial Technologies
publication_identifier:
isbn:
- '9783959773034'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'STROBE: Streaming Threshold Random Beacons'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 282
year: '2023'
...
---
_id: '14517'
abstract:
- lang: eng
text: 'State-of-the-art transmon qubits rely on large capacitors, which systematically
improve their coherence due to reduced surface-loss participation. However, this
approach increases both the footprint and the parasitic cross-coupling and is
ultimately limited by radiation losses—a potential roadblock for scaling up quantum
processors to millions of qubits. In this work we present transmon qubits with
sizes as low as 36 × 39 µm2 with 100-nm-wide vacuum-gap capacitors that are micromachined
from commercial silicon-on-insulator wafers and shadow evaporated with aluminum.
We achieve a vacuum participation ratio up to 99.6% in an in-plane design that
is compatible with standard coplanar circuits. Qubit relaxationtime measurements
for small gaps with high zero-point electric field variance of up to 22 V/m reveal
a double exponential decay indicating comparably strong qubit interaction with
long-lived two-level systems. The exceptionally high selectivity of up to 20 dB
to the superconductor-vacuum interface allows us to precisely back out the sub-single-photon
dielectric loss tangent of aluminum oxide previously exposed to ambient conditions.
In terms of future scaling potential, we achieve a ratio of qubit quality factor
to a footprint area equal to 20 µm−2, which is comparable with the highest T1
devices relying on larger geometries, a value that could improve substantially
for lower surface-loss superconductors. '
acknowledged_ssus:
- _id: NanoFab
acknowledgement: "This work was supported by the Austrian Science Fund (FWF) through
BeyondC (F7105), the European Research Council under Grant Agreement No. 758053
(ERC StG QUNNECT) and a NOMIS foundation research grant. M.Z. was the recipient
of a SAIA scholarship, E.R. of\r\na DOC fellowship of the Austrian Academy of Sciences,
and M.P. of a Pöttinger scholarship at IST Austria. S.B. acknowledges support from
Marie Skłodowska Curie Program No. 707438 (MSC-IF SUPEREOM). J.M.F. acknowledges
support from the Horizon Europe Program HORIZON-CL4-2022-QUANTUM-01-SGA via Project
No. 101113946 OpenSuperQPlus100 and the ISTA Nanofabrication Facility."
article_number: '044054'
article_processing_charge: No
article_type: original
author:
- first_name: Martin
full_name: Zemlicka, Martin
id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87
last_name: Zemlicka
- first_name: Elena
full_name: Redchenko, Elena
id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87
last_name: Redchenko
- first_name: Matilda
full_name: Peruzzo, Matilda
id: 3F920B30-F248-11E8-B48F-1D18A9856A87
last_name: Peruzzo
orcid: 0000-0002-3415-4628
- first_name: Farid
full_name: Hassani, Farid
id: 2AED110C-F248-11E8-B48F-1D18A9856A87
last_name: Hassani
orcid: 0000-0001-6937-5773
- first_name: Andrea
full_name: Trioni, Andrea
id: 42F71B44-F248-11E8-B48F-1D18A9856A87
last_name: Trioni
- first_name: Shabir
full_name: Barzanjeh, Shabir
id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87
last_name: Barzanjeh
orcid: 0000-0003-0415-1423
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
citation:
ama: 'Zemlicka M, Redchenko E, Peruzzo M, et al. Compact vacuum-gap transmon qubits:
Selective and sensitive probes for superconductor surface losses. Physical
Review Applied. 2023;20(4). doi:10.1103/PhysRevApplied.20.044054'
apa: 'Zemlicka, M., Redchenko, E., Peruzzo, M., Hassani, F., Trioni, A., Barzanjeh,
S., & Fink, J. M. (2023). Compact vacuum-gap transmon qubits: Selective and
sensitive probes for superconductor surface losses. Physical Review Applied.
American Physical Society. https://doi.org/10.1103/PhysRevApplied.20.044054'
chicago: 'Zemlicka, Martin, Elena Redchenko, Matilda Peruzzo, Farid Hassani, Andrea
Trioni, Shabir Barzanjeh, and Johannes M Fink. “Compact Vacuum-Gap Transmon Qubits:
Selective and Sensitive Probes for Superconductor Surface Losses.” Physical
Review Applied. American Physical Society, 2023. https://doi.org/10.1103/PhysRevApplied.20.044054.'
ieee: 'M. Zemlicka et al., “Compact vacuum-gap transmon qubits: Selective
and sensitive probes for superconductor surface losses,” Physical Review Applied,
vol. 20, no. 4. American Physical Society, 2023.'
ista: 'Zemlicka M, Redchenko E, Peruzzo M, Hassani F, Trioni A, Barzanjeh S, Fink
JM. 2023. Compact vacuum-gap transmon qubits: Selective and sensitive probes for
superconductor surface losses. Physical Review Applied. 20(4), 044054.'
mla: 'Zemlicka, Martin, et al. “Compact Vacuum-Gap Transmon Qubits: Selective and
Sensitive Probes for Superconductor Surface Losses.” Physical Review Applied,
vol. 20, no. 4, 044054, American Physical Society, 2023, doi:10.1103/PhysRevApplied.20.044054.'
short: M. Zemlicka, E. Redchenko, M. Peruzzo, F. Hassani, A. Trioni, S. Barzanjeh,
J.M. Fink, Physical Review Applied 20 (2023).
date_created: 2023-11-12T23:00:55Z
date_published: 2023-10-20T00:00:00Z
date_updated: 2023-11-13T09:22:47Z
day: '20'
department:
- _id: JoFi
doi: 10.1103/PhysRevApplied.20.044054
ec_funded: 1
external_id:
arxiv:
- '2206.14104'
intvolume: ' 20'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2206.14104
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 26927A52-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: F07105
name: Integrating superconducting quantum circuits
- _id: 26336814-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '758053'
name: A Fiber Optic Transceiver for Superconducting Qubits
- _id: eb9b30ac-77a9-11ec-83b8-871f581d53d2
name: Protected states of quantum matter
- _id: 258047B6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '707438'
name: 'Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination
with cavity Optomechanics SUPEREOM'
- _id: bdb7cfc1-d553-11ed-ba76-d2eaab167738
grant_number: '101080139'
name: Open Superconducting Quantum Computers (OpenSuperQPlus)
publication: Physical Review Applied
publication_identifier:
eissn:
- 2331-7019
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '14520'
relation: research_data
status: public
scopus_import: '1'
status: public
title: 'Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor
surface losses'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2023'
...
---
_id: '14515'
abstract:
- lang: eng
text: Most natural and engineered information-processing systems transmit information
via signals that vary in time. Computing the information transmission rate or
the information encoded in the temporal characteristics of these signals requires
the mutual information between the input and output signals as a function of time,
i.e., between the input and output trajectories. Yet, this is notoriously difficult
because of the high-dimensional nature of the trajectory space, and all existing
techniques require approximations. We present an exact Monte Carlo technique called
path weight sampling (PWS) that, for the first time, makes it possible to compute
the mutual information between input and output trajectories for any stochastic
system that is described by a master equation. The principal idea is to use the
master equation to evaluate the exact conditional probability of an individual
output trajectory for a given input trajectory and average this via Monte Carlo
sampling in trajectory space to obtain the mutual information. We present three
variants of PWS, which all generate the trajectories using the standard stochastic
simulation algorithm. While direct PWS is a brute-force method, Rosenbluth-Rosenbluth
PWS exploits the analogy between signal trajectory sampling and polymer sampling,
and thermodynamic integration PWS is based on a reversible work calculation in
trajectory space. PWS also makes it possible to compute the mutual information
between input and output trajectories for systems with hidden internal states
as well as systems with feedback from output to input. Applying PWS to the bacterial
chemotaxis system, consisting of 182 coupled chemical reactions, demonstrates
not only that the scheme is highly efficient but also that the number of receptor
clusters is much smaller than hitherto believed, while their size is much larger.
acknowledgement: "We thank Bela Mulder, Tom Shimizu, Fotios Avgidis, Peter Bolhuis,
and Daan Frenkel for useful discussions and a careful reading of the manuscript,
and we thank Age Tjalma for support with obtaining the Gaussian approximation of
the chemotaxis system. This work is part of the Dutch Research Council (NWO) and
was performed at the research institute AMOLF. This project has received funding
from the European Research Council (ERC) under the European Union’s Horizon 2020
research and innovation program (Grant Agreement No. 885065) and was\r\nfinancially
supported by NWO through the “Building a Synthetic Cell (BaSyC)” Gravitation Grant
(024.003.019)."
article_number: '041017'
article_processing_charge: Yes
article_type: original
author:
- first_name: Manuel
full_name: Reinhardt, Manuel
last_name: Reinhardt
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Pieter Rein
full_name: Ten Wolde, Pieter Rein
last_name: Ten Wolde
citation:
ama: 'Reinhardt M, Tkačik G, Ten Wolde PR. Path weight sampling: Exact Monte Carlo
computation of the mutual information between stochastic trajectories. Physical
Review X. 2023;13(4). doi:10.1103/PhysRevX.13.041017'
apa: 'Reinhardt, M., Tkačik, G., & Ten Wolde, P. R. (2023). Path weight sampling:
Exact Monte Carlo computation of the mutual information between stochastic trajectories.
Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.13.041017'
chicago: 'Reinhardt, Manuel, Gašper Tkačik, and Pieter Rein Ten Wolde. “Path Weight
Sampling: Exact Monte Carlo Computation of the Mutual Information between Stochastic
Trajectories.” Physical Review X. American Physical Society, 2023. https://doi.org/10.1103/PhysRevX.13.041017.'
ieee: 'M. Reinhardt, G. Tkačik, and P. R. Ten Wolde, “Path weight sampling: Exact
Monte Carlo computation of the mutual information between stochastic trajectories,”
Physical Review X, vol. 13, no. 4. American Physical Society, 2023.'
ista: 'Reinhardt M, Tkačik G, Ten Wolde PR. 2023. Path weight sampling: Exact Monte
Carlo computation of the mutual information between stochastic trajectories. Physical
Review X. 13(4), 041017.'
mla: 'Reinhardt, Manuel, et al. “Path Weight Sampling: Exact Monte Carlo Computation
of the Mutual Information between Stochastic Trajectories.” Physical Review
X, vol. 13, no. 4, 041017, American Physical Society, 2023, doi:10.1103/PhysRevX.13.041017.'
short: M. Reinhardt, G. Tkačik, P.R. Ten Wolde, Physical Review X 13 (2023).
date_created: 2023-11-12T23:00:55Z
date_published: 2023-10-26T00:00:00Z
date_updated: 2023-11-13T09:03:30Z
day: '26'
ddc:
- '530'
department:
- _id: GaTk
doi: 10.1103/PhysRevX.13.041017
external_id:
arxiv:
- '2203.03461'
file:
- access_level: open_access
checksum: 32574aeebcca7347a4152c611b66b3d5
content_type: application/pdf
creator: dernst
date_created: 2023-11-13T09:00:19Z
date_updated: 2023-11-13T09:00:19Z
file_id: '14522'
file_name: 2023_PhysReviewX_Reinhardt.pdf
file_size: 1595223
relation: main_file
success: 1
file_date_updated: 2023-11-13T09:00:19Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '4'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: Physical Review X
publication_identifier:
eissn:
- 2160-3308
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Path weight sampling: Exact Monte Carlo computation of the mutual information
between stochastic trajectories'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2023'
...
---
_id: '14514'
abstract:
- lang: eng
text: 'The elastic Leidenfrost effect occurs when a vaporizable soft solid is lowered
onto a hot surface. Evaporative flow couples to elastic deformation, giving spontaneous
bouncing or steady-state floating. The effect embodies an unexplored interplay
between thermodynamics, elasticity, and lubrication: despite being observed, its
basic theoretical description remains a challenge. Here, we provide a theory of
elastic Leidenfrost floating. As weight increases, a rigid solid sits closer to
the hot surface. By contrast, we discover an elasticity-dominated regime where
the heavier the solid, the higher it floats. This geometry-governed behavior is
reminiscent of the dynamics of large liquid Leidenfrost drops. We show that this
elastic regime is characterized by Hertzian behavior of the solid’s underbelly
and derive how the float height scales with materials parameters. Introducing
a dimensionless elastic Leidenfrost number, we capture the crossover between rigid
and Hertzian behavior. Our results provide theoretical underpinning for recent
experiments, and point to the design of novel soft machines.'
acknowledgement: "We are grateful to Dominic Vella, Jens Eggers, John Kolinski, Joshua
Dijksman, and Daniel Bonn for insightful discussions. J. B. and A. S. acknowledge
the support of the Engineering and Physical Sciences Research Council (EPSRC) through
New Investigator Award No. EP/\r\nT000961/1. A. S. acknowledges the support of Royal
Society under Grant No. RGS/R2/202135. J. E. S. acknowledges EPSRC Grants No. EP/N016602/1,
EP/S022848/1, EP/S029966/1, and EP/P031684/1."
article_number: '168201'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Jack
full_name: Binysh, Jack
last_name: Binysh
- first_name: Indrajit
full_name: Chakraborty, Indrajit
last_name: Chakraborty
- first_name: Mykyta V.
full_name: Chubynsky, Mykyta V.
last_name: Chubynsky
- first_name: Vicente L
full_name: Diaz Melian, Vicente L
id: b6798902-eea0-11ea-9cbc-a8e14286c631
last_name: Diaz Melian
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
- first_name: James E.
full_name: Sprittles, James E.
last_name: Sprittles
- first_name: Anton
full_name: Souslov, Anton
last_name: Souslov
citation:
ama: Binysh J, Chakraborty I, Chubynsky MV, et al. Modeling Leidenfrost levitation
of soft elastic solids. Physical Review Letters. 2023;131(16). doi:10.1103/PhysRevLett.131.168201
apa: Binysh, J., Chakraborty, I., Chubynsky, M. V., Diaz Melian, V. L., Waitukaitis,
S. R., Sprittles, J. E., & Souslov, A. (2023). Modeling Leidenfrost levitation
of soft elastic solids. Physical Review Letters. American Physical Society.
https://doi.org/10.1103/PhysRevLett.131.168201
chicago: Binysh, Jack, Indrajit Chakraborty, Mykyta V. Chubynsky, Vicente L Diaz
Melian, Scott R Waitukaitis, James E. Sprittles, and Anton Souslov. “Modeling
Leidenfrost Levitation of Soft Elastic Solids.” Physical Review Letters.
American Physical Society, 2023. https://doi.org/10.1103/PhysRevLett.131.168201.
ieee: J. Binysh et al., “Modeling Leidenfrost levitation of soft elastic
solids,” Physical Review Letters, vol. 131, no. 16. American Physical Society,
2023.
ista: Binysh J, Chakraborty I, Chubynsky MV, Diaz Melian VL, Waitukaitis SR, Sprittles
JE, Souslov A. 2023. Modeling Leidenfrost levitation of soft elastic solids. Physical
Review Letters. 131(16), 168201.
mla: Binysh, Jack, et al. “Modeling Leidenfrost Levitation of Soft Elastic Solids.”
Physical Review Letters, vol. 131, no. 16, 168201, American Physical Society,
2023, doi:10.1103/PhysRevLett.131.168201.
short: J. Binysh, I. Chakraborty, M.V. Chubynsky, V.L. Diaz Melian, S.R. Waitukaitis,
J.E. Sprittles, A. Souslov, Physical Review Letters 131 (2023).
date_created: 2023-11-12T23:00:55Z
date_published: 2023-10-20T00:00:00Z
date_updated: 2023-11-13T09:21:30Z
day: '20'
ddc:
- '530'
department:
- _id: ScWa
doi: 10.1103/PhysRevLett.131.168201
file:
- access_level: open_access
checksum: 1a419e25b762aadffbcc8eb2e609bd97
content_type: application/pdf
creator: dernst
date_created: 2023-11-13T09:12:58Z
date_updated: 2023-11-13T09:12:58Z
file_id: '14524'
file_name: 2023_PhysRevLetters_Binysh.pdf
file_size: 724098
relation: main_file
success: 1
file_date_updated: 2023-11-13T09:12:58Z
has_accepted_license: '1'
intvolume: ' 131'
issue: '16'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '14523'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Modeling Leidenfrost levitation of soft elastic solids
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 131
year: '2023'
...
---
_id: '14523'
abstract:
- lang: eng
text: see Readme file
article_processing_charge: No
author:
- first_name: Jack
full_name: Binysh, Jack
last_name: Binysh
- first_name: Indrajit
full_name: Chakraborty, Indrajit
last_name: Chakraborty
- first_name: Mykyta
full_name: Chubynsky, Mykyta
last_name: Chubynsky
- first_name: Vicente L
full_name: Diaz Melian, Vicente L
id: b6798902-eea0-11ea-9cbc-a8e14286c631
last_name: Diaz Melian
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
- first_name: James
full_name: Sprittles, James
last_name: Sprittles
- first_name: Anton
full_name: Souslov, Anton
last_name: Souslov
citation:
ama: 'Binysh J, Chakraborty I, Chubynsky M, et al. SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids:
v1.0.1. 2023. doi:10.5281/ZENODO.8329143'
apa: 'Binysh, J., Chakraborty, I., Chubynsky, M., Diaz Melian, V. L., Waitukaitis,
S. R., Sprittles, J., & Souslov, A. (2023). SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids:
v1.0.1. Zenodo. https://doi.org/10.5281/ZENODO.8329143'
chicago: 'Binysh, Jack, Indrajit Chakraborty, Mykyta Chubynsky, Vicente L Diaz Melian,
Scott R Waitukaitis, James Sprittles, and Anton Souslov. “SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids:
V1.0.1.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8329143.'
ieee: 'J. Binysh et al., “SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids:
v1.0.1.” Zenodo, 2023.'
ista: 'Binysh J, Chakraborty I, Chubynsky M, Diaz Melian VL, Waitukaitis SR, Sprittles
J, Souslov A. 2023. SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids:
v1.0.1, Zenodo, 10.5281/ZENODO.8329143.'
mla: 'Binysh, Jack, et al. SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids:
V1.0.1. Zenodo, 2023, doi:10.5281/ZENODO.8329143.'
short: J. Binysh, I. Chakraborty, M. Chubynsky, V.L. Diaz Melian, S.R. Waitukaitis,
J. Sprittles, A. Souslov, (2023).
date_created: 2023-11-13T09:12:11Z
date_published: 2023-09-08T00:00:00Z
date_updated: 2023-11-13T09:21:31Z
day: '08'
ddc:
- '530'
department:
- _id: ScWa
doi: 10.5281/ZENODO.8329143
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/ZENODO.8329143
month: '09'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '14514'
relation: used_in_publication
status: public
status: public
title: 'SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1'
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14518'
abstract:
- lang: eng
text: We consider bidding games, a class of two-player zero-sum graph games. The
game proceeds as follows. Both players have bounded budgets. A token is placed
on a vertex of a graph, in each turn the players simultaneously submit bids, and
the higher bidder moves the token, where we break bidding ties in favor of Player
1. Player 1 wins the game iff the token visits a designated target vertex. We
consider, for the first time, poorman discrete-bidding in which the granularity
of the bids is restricted and the higher bid is paid to the bank. Previous work
either did not impose granularity restrictions or considered Richman bidding (bids
are paid to the opponent). While the latter mechanisms are technically more accessible,
the former is more appealing from a practical standpoint. Our study focuses on
threshold budgets, which is the necessary and sufficient initial budget required
for Player 1 to ensure winning against a given Player 2 budget. We first show
existence of thresholds. In DAGs, we show that threshold budgets can be approximated
with error bounds by thresholds under continuous-bidding and that they exhibit
a periodic behavior. We identify closed-form solutions in special cases. We implement
and experiment with an algorithm to find threshold budgets.
acknowledgement: This research was supported in part by ISF grant no. 1679/21, ERC
CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation
programme under the Marie SkłodowskaCurie Grant Agreement No. 665385.
article_processing_charge: No
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Tobias
full_name: Meggendorfer, Tobias
id: b21b0c15-30a2-11eb-80dc-f13ca25802e1
last_name: Meggendorfer
orcid: 0000-0002-1712-2165
- first_name: Suman
full_name: Sadhukhan, Suman
last_name: Sadhukhan
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
citation:
ama: 'Avni G, Meggendorfer T, Sadhukhan S, Tkadlec J, Zikelic D. Reachability poorman
discrete-bidding games. In: Frontiers in Artificial Intelligence and Applications.
Vol 372. IOS Press; 2023:141-148. doi:10.3233/FAIA230264'
apa: 'Avni, G., Meggendorfer, T., Sadhukhan, S., Tkadlec, J., & Zikelic, D.
(2023). Reachability poorman discrete-bidding games. In Frontiers in Artificial
Intelligence and Applications (Vol. 372, pp. 141–148). Krakow, Poland: IOS
Press. https://doi.org/10.3233/FAIA230264'
chicago: Avni, Guy, Tobias Meggendorfer, Suman Sadhukhan, Josef Tkadlec, and Dorde
Zikelic. “Reachability Poorman Discrete-Bidding Games.” In Frontiers in Artificial
Intelligence and Applications, 372:141–48. IOS Press, 2023. https://doi.org/10.3233/FAIA230264.
ieee: G. Avni, T. Meggendorfer, S. Sadhukhan, J. Tkadlec, and D. Zikelic, “Reachability
poorman discrete-bidding games,” in Frontiers in Artificial Intelligence and
Applications, Krakow, Poland, 2023, vol. 372, pp. 141–148.
ista: 'Avni G, Meggendorfer T, Sadhukhan S, Tkadlec J, Zikelic D. 2023. Reachability
poorman discrete-bidding games. Frontiers in Artificial Intelligence and Applications.
ECAI: European Conference on Artificial Intelligence vol. 372, 141–148.'
mla: Avni, Guy, et al. “Reachability Poorman Discrete-Bidding Games.” Frontiers
in Artificial Intelligence and Applications, vol. 372, IOS Press, 2023, pp.
141–48, doi:10.3233/FAIA230264.
short: G. Avni, T. Meggendorfer, S. Sadhukhan, J. Tkadlec, D. Zikelic, in:, Frontiers
in Artificial Intelligence and Applications, IOS Press, 2023, pp. 141–148.
conference:
end_date: 2023-10-04
location: Krakow, Poland
name: 'ECAI: European Conference on Artificial Intelligence'
start_date: 2023-09-30
date_created: 2023-11-12T23:00:56Z
date_published: 2023-09-28T00:00:00Z
date_updated: 2023-11-13T10:18:45Z
day: '28'
ddc:
- '000'
department:
- _id: ToHe
- _id: KrCh
doi: 10.3233/FAIA230264
ec_funded: 1
external_id:
arxiv:
- '2307.15218'
file:
- access_level: open_access
checksum: 1390ca38480fa4cf286b0f1a42e8c12f
content_type: application/pdf
creator: dernst
date_created: 2023-11-13T10:16:10Z
date_updated: 2023-11-13T10:16:10Z
file_id: '14529'
file_name: 2023_FAIA_Avni.pdf
file_size: 501011
relation: main_file
success: 1
file_date_updated: 2023-11-13T10:16:10Z
has_accepted_license: '1'
intvolume: ' 372'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '09'
oa: 1
oa_version: Published Version
page: 141-148
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Frontiers in Artificial Intelligence and Applications
publication_identifier:
isbn:
- '9781643684369'
issn:
- 0922-6389
publication_status: published
publisher: IOS Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reachability poorman discrete-bidding games
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 372
year: '2023'
...
---
_id: '13096'
abstract:
- lang: eng
text: Eukaryotic cells can undergo different forms of programmed cell death, many
of which culminate in plasma membrane rupture as the defining terminal event1,2,3,4,5,6,7.
Plasma membrane rupture was long thought to be driven by osmotic pressure, but
it has recently been shown to be in many cases an active process, mediated by
the protein ninjurin-18 (NINJ1). Here we resolve the structure of NINJ1 and the
mechanism by which it ruptures membranes. Super-resolution microscopy reveals
that NINJ1 clusters into structurally diverse assemblies in the membranes of dying
cells, in particular large, filamentous assemblies with branched morphology. A
cryo-electron microscopy structure of NINJ1 filaments shows a tightly packed fence-like
array of transmembrane α-helices. Filament directionality and stability is defined
by two amphipathic α-helices that interlink adjacent filament subunits. The NINJ1
filament features a hydrophilic side and a hydrophobic side, and molecular dynamics
simulations show that it can stably cap membrane edges. The function of the resulting
supramolecular arrangement was validated by site-directed mutagenesis. Our data
thus suggest that, during lytic cell death, the extracellular α-helices of NINJ1
insert into the plasma membrane to polymerize NINJ1 monomers into amphipathic
filaments that rupture the plasma membrane. The membrane protein NINJ1 is therefore
an interactive component of the eukaryotic cell membrane that functions as an
in-built breaking point in response to activation of cell death.
acknowledged_ssus:
- _id: NMR
- _id: LifeSc
acknowledgement: "This work was supported by the Deutsche Forschungsgemeinschaft under
Germany’s Excellence Strategy EXC 2075–390740016 and the Stuttgart Center for Simulation
Science (SC SimTech) to K.P., by ERC-CoG 770988 (InflamCellDeath) and SNF Project
funding (310030B_198005, 310030B_192523) to P.B., by the Swiss Nanoscience Institute
and the Swiss National Science Foundation via the NCCR AntiResist (180541) to S.H.
and the NCCR Molecular Systems Engineering (51NF40-205608) to D.J.M., by the Helmholtz
Young Investigator Program of the Helmholtz Association to C.S., by the SNF Professorship
funding (PP00P3_198903) to C.P., EMBO postdoctoral fellowship ALTF 27-2022 to E.H.
and by the Scientific Service Units of IST Austria through resources provided by
the NMR and Life Science Facilities to P.S. Molecular dynamics simulations were
performed on the HoreKa supercomputer funded by the Ministry of Science, Research
and the Arts Baden-Württemberg and by the Federal Ministry of Education and Research.
The authors thank the BioEM Lab of the Biozentrum, University of Basel for support;
V. Mack, K. Shkarina and J. Fricke for technical support; D. Ricklin and S. Vogt
for peptide synthesis; P. Pelczar for support with animals; S.-J. Marrink and P.
Telles de Souza for supply with Martini3 parameters and scripts; and P. Radler und
M. Loose for help with QCM. Fig. 4g and Extended Data Fig. 1a were in part created
with BioRender.com.\r\nOpen access funding provided by University of Basel."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Morris
full_name: Degen, Morris
last_name: Degen
- first_name: José Carlos
full_name: Santos, José Carlos
last_name: Santos
- first_name: Kristyna
full_name: Pluhackova, Kristyna
last_name: Pluhackova
- first_name: Gonzalo
full_name: Cebrero, Gonzalo
last_name: Cebrero
- first_name: Saray
full_name: Ramos, Saray
last_name: Ramos
- first_name: Gytis
full_name: Jankevicius, Gytis
last_name: Jankevicius
- first_name: Ella
full_name: Hartenian, Ella
last_name: Hartenian
- first_name: Undina
full_name: Guillerm, Undina
id: bb74f472-ae54-11eb-9835-bc9c22fb1183
last_name: Guillerm
- first_name: Stefania A.
full_name: Mari, Stefania A.
last_name: Mari
- first_name: Bastian
full_name: Kohl, Bastian
last_name: Kohl
- first_name: Daniel J.
full_name: Müller, Daniel J.
last_name: Müller
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Timm
full_name: Maier, Timm
last_name: Maier
- first_name: Camilo
full_name: Perez, Camilo
last_name: Perez
- first_name: Christian
full_name: Sieben, Christian
last_name: Sieben
- first_name: Petr
full_name: Broz, Petr
last_name: Broz
- first_name: Sebastian
full_name: Hiller, Sebastian
last_name: Hiller
citation:
ama: Degen M, Santos JC, Pluhackova K, et al. Structural basis of NINJ1-mediated
plasma membrane rupture in cell death. Nature. 2023;618:1065-1071. doi:10.1038/s41586-023-05991-z
apa: Degen, M., Santos, J. C., Pluhackova, K., Cebrero, G., Ramos, S., Jankevicius,
G., … Hiller, S. (2023). Structural basis of NINJ1-mediated plasma membrane rupture
in cell death. Nature. Springer Nature. https://doi.org/10.1038/s41586-023-05991-z
chicago: Degen, Morris, José Carlos Santos, Kristyna Pluhackova, Gonzalo Cebrero,
Saray Ramos, Gytis Jankevicius, Ella Hartenian, et al. “Structural Basis of NINJ1-Mediated
Plasma Membrane Rupture in Cell Death.” Nature. Springer Nature, 2023.
https://doi.org/10.1038/s41586-023-05991-z.
ieee: M. Degen et al., “Structural basis of NINJ1-mediated plasma membrane
rupture in cell death,” Nature, vol. 618. Springer Nature, pp. 1065–1071,
2023.
ista: Degen M, Santos JC, Pluhackova K, Cebrero G, Ramos S, Jankevicius G, Hartenian
E, Guillerm U, Mari SA, Kohl B, Müller DJ, Schanda P, Maier T, Perez C, Sieben
C, Broz P, Hiller S. 2023. Structural basis of NINJ1-mediated plasma membrane
rupture in cell death. Nature. 618, 1065–1071.
mla: Degen, Morris, et al. “Structural Basis of NINJ1-Mediated Plasma Membrane Rupture
in Cell Death.” Nature, vol. 618, Springer Nature, 2023, pp. 1065–71, doi:10.1038/s41586-023-05991-z.
short: M. Degen, J.C. Santos, K. Pluhackova, G. Cebrero, S. Ramos, G. Jankevicius,
E. Hartenian, U. Guillerm, S.A. Mari, B. Kohl, D.J. Müller, P. Schanda, T. Maier,
C. Perez, C. Sieben, P. Broz, S. Hiller, Nature 618 (2023) 1065–1071.
date_created: 2023-05-28T22:01:04Z
date_published: 2023-06-29T00:00:00Z
date_updated: 2023-11-14T11:49:21Z
day: '29'
ddc:
- '570'
department:
- _id: PaSc
doi: 10.1038/s41586-023-05991-z
external_id:
isi:
- '000991386800011'
file:
- access_level: open_access
checksum: 0fab69252453bff1de7f0e2eceb76d34
content_type: application/pdf
creator: dernst
date_created: 2023-11-14T11:48:18Z
date_updated: 2023-11-14T11:48:18Z
file_id: '14533'
file_name: 2023_Nature_Degen.pdf
file_size: 12292188
relation: main_file
success: 1
file_date_updated: 2023-11-14T11:48:18Z
has_accepted_license: '1'
intvolume: ' 618'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 1065-1071
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: Structural basis of NINJ1-mediated plasma membrane rupture in cell death
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 618
year: '2023'
...
---
_id: '13041'
abstract:
- lang: eng
text: A series of triarylamines was synthesised and screened for their suitability
as catholytes in redox flow batteries using cyclic voltammetry (CV). Tris(4-aminophenyl)amine
was found to be the strongest candidate. Solubility and initial electrochemical
performance were promising; however, polymerisation was observed during electrochemical
cycling leading to rapid capacity fade prescribed to a loss of accessible active
material and the limitation of ion transport processes within the cell. A mixed
electrolyte system of H3PO4 and HCl was found to inhibit polymerisation producing
oligomers that consumed less active material reducing rates of degradation in
the redox flow battery. Under these conditions Coulombic efficiency improved by
over 4 %, the maximum number of cycles more than quadrupled and an additional
theoretical capacity of 20 % was accessed. This paper is, to our knowledge, the
first example of triarylamines as catholytes in all-aqueous redox flow batteries
and emphasises the impact supporting electrolytes can have on electrochemical
performance.
acknowledgement: The authors (N.L.F and R.B.J) would like to acknowledge the funding
contributions of Shell and the EPRSC via I–Case studentships (grants no. EP/V519662/1
and EP/R511870/1 respectively). T.I would like to thank the ERC advanced Investigator
Grant for CPG (EC H2020 835073). Thank you to Zhen Wang from the University of Cambridge
for measuring GPC, the Yusuf Hamied Department of Chemistry's mass spectrometry
service for MS measurements and analysis and Dr Andrew Bond from the University
of Cambridge for XRD measurement and analysis.
article_number: e202300128
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Nadia L.
full_name: Farag, Nadia L.
last_name: Farag
- first_name: Rajesh B
full_name: Jethwa, Rajesh B
id: 4cc538d5-803f-11ed-ab7e-8139573aad8f
last_name: Jethwa
orcid: 0000-0002-0404-4356
- first_name: Alice E.
full_name: Beardmore, Alice E.
last_name: Beardmore
- first_name: Teresa
full_name: Insinna, Teresa
last_name: Insinna
- first_name: Christopher A.
full_name: O'Keefe, Christopher A.
last_name: O'Keefe
- first_name: Peter A.A.
full_name: Klusener, Peter A.A.
last_name: Klusener
- first_name: Clare P.
full_name: Grey, Clare P.
last_name: Grey
- first_name: Dominic S.
full_name: Wright, Dominic S.
last_name: Wright
citation:
ama: Farag NL, Jethwa RB, Beardmore AE, et al. Triarylamines as catholytes in aqueous
organic redox flow batteries. ChemSusChem. 2023;16(13). doi:10.1002/cssc.202300128
apa: Farag, N. L., Jethwa, R. B., Beardmore, A. E., Insinna, T., O’Keefe, C. A.,
Klusener, P. A. A., … Wright, D. S. (2023). Triarylamines as catholytes in aqueous
organic redox flow batteries. ChemSusChem. Wiley. https://doi.org/10.1002/cssc.202300128
chicago: Farag, Nadia L., Rajesh B Jethwa, Alice E. Beardmore, Teresa Insinna, Christopher
A. O’Keefe, Peter A.A. Klusener, Clare P. Grey, and Dominic S. Wright. “Triarylamines
as Catholytes in Aqueous Organic Redox Flow Batteries.” ChemSusChem. Wiley,
2023. https://doi.org/10.1002/cssc.202300128.
ieee: N. L. Farag et al., “Triarylamines as catholytes in aqueous organic
redox flow batteries,” ChemSusChem, vol. 16, no. 13. Wiley, 2023.
ista: Farag NL, Jethwa RB, Beardmore AE, Insinna T, O’Keefe CA, Klusener PAA, Grey
CP, Wright DS. 2023. Triarylamines as catholytes in aqueous organic redox flow
batteries. ChemSusChem. 16(13), e202300128.
mla: Farag, Nadia L., et al. “Triarylamines as Catholytes in Aqueous Organic Redox
Flow Batteries.” ChemSusChem, vol. 16, no. 13, e202300128, Wiley, 2023,
doi:10.1002/cssc.202300128.
short: N.L. Farag, R.B. Jethwa, A.E. Beardmore, T. Insinna, C.A. O’Keefe, P.A.A.
Klusener, C.P. Grey, D.S. Wright, ChemSusChem 16 (2023).
date_created: 2023-05-21T22:01:05Z
date_published: 2023-07-06T00:00:00Z
date_updated: 2023-11-14T11:28:23Z
day: '06'
ddc:
- '540'
department:
- _id: StFr
doi: 10.1002/cssc.202300128
external_id:
isi:
- '000985051300001'
pmid:
- '36970847'
file:
- access_level: open_access
checksum: efa0713289995af83a2147b3e8e1d6a6
content_type: application/pdf
creator: dernst
date_created: 2023-11-14T11:27:16Z
date_updated: 2023-11-14T11:27:16Z
file_id: '14532'
file_name: 2023_ChemSusChem_Farag.pdf
file_size: 1168683
relation: main_file
success: 1
file_date_updated: 2023-11-14T11:27:16Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '13'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: ChemSusChem
publication_identifier:
eissn:
- 1864-564X
issn:
- 1864-5631
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Triarylamines as catholytes in aqueous organic redox flow batteries
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2023'
...
---
_id: '13118'
abstract:
- lang: eng
text: Under high pressures and temperatures, molecular systems with substantial
polarization charges, such as ammonia and water, are predicted to form superionic
phases and dense fluid states with dissociating molecules and high electrical
conductivity. This behaviour potentially plays a role in explaining the origin
of the multipolar magnetic fields of Uranus and Neptune, whose mantles are thought
to result from a mixture of H2O, NH3 and CH4 ices. Determining the stability domain,
melting curve and electrical conductivity of these superionic phases is therefore
crucial for modelling planetary interiors and dynamos. Here we report the melting
curve of superionic ammonia up to 300 GPa from laser-driven shock compression
of pre-compressed samples and atomistic calculations. We show that ammonia melts
at lower temperatures than water above 100 GPa and that fluid ammonia’s electrical
conductivity exceeds that of water at conditions predicted by hot, super-adiabatic
models for Uranus and Neptune, and enhances the conductivity in their fluid water-rich
dynamo layers.
acknowledgement: We acknowledge the crucial contribution of the LULI2000 laser and
support teams to the success of the experiments. We also thank S. Brygoo and P.
Loubeyre for useful discussions. This research was supported by the French National
Research Agency (ANR) through the projects POMPEI (grant no. ANR-16-CE31-0008) and
SUPER-ICES (grant ANR-15-CE30-008-01), and by the PLAS@PAR Federation. M.F. and
R.R. gratefully acknowledge support by the DFG within the Research Unit FOR 2440.
M.B. was supported by the European Union within the Marie Skłodowska-Curie actions
(xICE grant 894725) and the NOMIS foundation. The DFT-MD calculations were performed
at the North-German Supercomputing Alliance facilities.
article_processing_charge: No
article_type: original
author:
- first_name: J.-A.
full_name: Hernandez, J.-A.
last_name: Hernandez
- first_name: Mandy
full_name: Bethkenhagen, Mandy
id: 201939f4-803f-11ed-ab7e-d8da4bd1517f
last_name: Bethkenhagen
orcid: 0000-0002-1838-2129
- first_name: S.
full_name: Ninet, S.
last_name: Ninet
- first_name: M.
full_name: French, M.
last_name: French
- first_name: A.
full_name: Benuzzi-Mounaix, A.
last_name: Benuzzi-Mounaix
- first_name: F.
full_name: Datchi, F.
last_name: Datchi
- first_name: M.
full_name: Guarguaglini, M.
last_name: Guarguaglini
- first_name: F.
full_name: Lefevre, F.
last_name: Lefevre
- first_name: F.
full_name: Occelli, F.
last_name: Occelli
- first_name: R.
full_name: Redmer, R.
last_name: Redmer
- first_name: T.
full_name: Vinci, T.
last_name: Vinci
- first_name: A.
full_name: Ravasio, A.
last_name: Ravasio
citation:
ama: Hernandez J-A, Bethkenhagen M, Ninet S, et al. Melting curve of superionic
ammonia at planetary interior conditions. Nature Physics. 2023;19:1280-1285.
doi:10.1038/s41567-023-02074-8
apa: Hernandez, J.-A., Bethkenhagen, M., Ninet, S., French, M., Benuzzi-Mounaix,
A., Datchi, F., … Ravasio, A. (2023). Melting curve of superionic ammonia at planetary
interior conditions. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02074-8
chicago: Hernandez, J.-A., Mandy Bethkenhagen, S. Ninet, M. French, A. Benuzzi-Mounaix,
F. Datchi, M. Guarguaglini, et al. “Melting Curve of Superionic Ammonia at Planetary
Interior Conditions.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02074-8.
ieee: J.-A. Hernandez et al., “Melting curve of superionic ammonia at planetary
interior conditions,” Nature Physics, vol. 19. Springer Nature, pp. 1280–1285,
2023.
ista: Hernandez J-A, Bethkenhagen M, Ninet S, French M, Benuzzi-Mounaix A, Datchi
F, Guarguaglini M, Lefevre F, Occelli F, Redmer R, Vinci T, Ravasio A. 2023. Melting
curve of superionic ammonia at planetary interior conditions. Nature Physics.
19, 1280–1285.
mla: Hernandez, J. A., et al. “Melting Curve of Superionic Ammonia at Planetary
Interior Conditions.” Nature Physics, vol. 19, Springer Nature, 2023, pp.
1280–85, doi:10.1038/s41567-023-02074-8.
short: J.-A. Hernandez, M. Bethkenhagen, S. Ninet, M. French, A. Benuzzi-Mounaix,
F. Datchi, M. Guarguaglini, F. Lefevre, F. Occelli, R. Redmer, T. Vinci, A. Ravasio,
Nature Physics 19 (2023) 1280–1285.
date_created: 2023-06-04T22:01:02Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2023-11-14T12:58:31Z
day: '01'
department:
- _id: BiCh
doi: 10.1038/s41567-023-02074-8
external_id:
isi:
- '000996921200001'
intvolume: ' 19'
isi: 1
language:
- iso: eng
month: '09'
oa_version: None
page: 1280-1285
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: 10.1038/s41567-023-02130-3
scopus_import: '1'
status: public
title: Melting curve of superionic ammonia at planetary interior conditions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2023'
...
---
_id: '13119'
abstract:
- lang: eng
text: A density wave (DW) is a fundamental type of long-range order in quantum matter
tied to self-organization into a crystalline structure. The interplay of DW order
with superfluidity can lead to complex scenarios that pose a great challenge to
theoretical analysis. In the past decades, tunable quantum Fermi gases have served
as model systems for exploring the physics of strongly interacting fermions, including
most notably magnetic ordering1, pairing and superfluidity2, and the crossover
from a Bardeen–Cooper–Schrieffer superfluid to a Bose–Einstein condensate3. Here,
we realize a Fermi gas featuring both strong, tunable contact interactions and
photon-mediated, spatially structured long-range interactions in a transversely
driven high-finesse optical cavity. Above a critical long-range interaction strength,
DW order is stabilized in the system, which we identify via its superradiant light-scattering
properties. We quantitatively measure the variation of the onset of DW order as
the contact interaction is varied across the Bardeen–Cooper–Schrieffer superfluid
and Bose–Einstein condensate crossover, in qualitative agreement with a mean-field
theory. The atomic DW susceptibility varies over an order of magnitude upon tuning
the strength and the sign of the long-range interactions below the self-ordering
threshold, demonstrating independent and simultaneous control over the contact
and long-range interactions. Therefore, our experimental setup provides a fully
tunable and microscopically controllable platform for the experimental study of
the interplay of superfluidity and DW order.
acknowledgement: Open access funding provided by EPFL Lausanne.We acknowledge discussions
with T. Donner and T. Esslinger. We thank G. del Pace and T. Bühler for their assistance
in the final stages of the experiment. We acknowledge funding from the European
Research Council under the European Union Horizon 2020 Research and Innovation Programme
(Grant no. 714309) and the Swiss National Science Foundation (Grant no. 184654).
F.M. acknowledges financial support from the Austrian Science Fund (Stand-Alone
Project P 35891-N).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Victor
full_name: Helson, Victor
last_name: Helson
- first_name: Timo
full_name: Zwettler, Timo
last_name: Zwettler
- first_name: Farokh
full_name: Mivehvar, Farokh
last_name: Mivehvar
- first_name: Elvia
full_name: Colella, Elvia
last_name: Colella
- first_name: Kevin Etienne Robert
full_name: Roux, Kevin Etienne Robert
id: 53f93ea2-803f-11ed-ab7e-b283135794ef
last_name: Roux
- first_name: Hideki
full_name: Konishi, Hideki
last_name: Konishi
- first_name: Helmut
full_name: Ritsch, Helmut
last_name: Ritsch
- first_name: Jean Philippe
full_name: Brantut, Jean Philippe
last_name: Brantut
citation:
ama: Helson V, Zwettler T, Mivehvar F, et al. Density-wave ordering in a unitary
Fermi gas with photon-mediated interactions. Nature. 2023;618:716-720.
doi:10.1038/s41586-023-06018-3
apa: Helson, V., Zwettler, T., Mivehvar, F., Colella, E., Roux, K. E. R., Konishi,
H., … Brantut, J. P. (2023). Density-wave ordering in a unitary Fermi gas with
photon-mediated interactions. Nature. Springer Nature. https://doi.org/10.1038/s41586-023-06018-3
chicago: Helson, Victor, Timo Zwettler, Farokh Mivehvar, Elvia Colella, Kevin Etienne
Robert Roux, Hideki Konishi, Helmut Ritsch, and Jean Philippe Brantut. “Density-Wave
Ordering in a Unitary Fermi Gas with Photon-Mediated Interactions.” Nature.
Springer Nature, 2023. https://doi.org/10.1038/s41586-023-06018-3.
ieee: V. Helson et al., “Density-wave ordering in a unitary Fermi gas with
photon-mediated interactions,” Nature, vol. 618. Springer Nature, pp. 716–720,
2023.
ista: Helson V, Zwettler T, Mivehvar F, Colella E, Roux KER, Konishi H, Ritsch H,
Brantut JP. 2023. Density-wave ordering in a unitary Fermi gas with photon-mediated
interactions. Nature. 618, 716–720.
mla: Helson, Victor, et al. “Density-Wave Ordering in a Unitary Fermi Gas with Photon-Mediated
Interactions.” Nature, vol. 618, Springer Nature, 2023, pp. 716–20, doi:10.1038/s41586-023-06018-3.
short: V. Helson, T. Zwettler, F. Mivehvar, E. Colella, K.E.R. Roux, H. Konishi,
H. Ritsch, J.P. Brantut, Nature 618 (2023) 716–720.
date_created: 2023-06-04T22:01:03Z
date_published: 2023-06-22T00:00:00Z
date_updated: 2023-11-14T13:02:50Z
day: '22'
ddc:
- '530'
department:
- _id: GeKa
doi: 10.1038/s41586-023-06018-3
external_id:
isi:
- '001001139300008'
file:
- access_level: open_access
checksum: 4887a296e3b6f54e8c0b946cbfd24f49
content_type: application/pdf
creator: dernst
date_created: 2023-11-14T13:00:19Z
date_updated: 2023-11-14T13:00:19Z
file_id: '14534'
file_name: 2023_Nature_Helson.pdf
file_size: 8156497
relation: main_file
success: 1
file_date_updated: 2023-11-14T13:00:19Z
has_accepted_license: '1'
intvolume: ' 618'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 716-720
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: Density-wave ordering in a unitary Fermi gas with photon-mediated interactions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 618
year: '2023'
...
---
_id: '12911'
abstract:
- lang: eng
text: 'This paper establishes new connections between many-body quantum systems,
One-body Reduced Density Matrices Functional Theory (1RDMFT) and Optimal Transport
(OT), by interpreting the problem of computing the ground-state energy of a finite-dimensional
composite quantum system at positive temperature as a non-commutative entropy
regularized Optimal Transport problem. We develop a new approach to fully characterize
the dual-primal solutions in such non-commutative setting. The mathematical formalism
is particularly relevant in quantum chemistry: numerical realizations of the many-electron
ground-state energy can be computed via a non-commutative version of Sinkhorn
algorithm. Our approach allows to prove convergence and robustness of this algorithm,
which, to our best knowledge, were unknown even in the two marginal case. Our
methods are based on a priori estimates in the dual problem, which we believe
to be of independent interest. Finally, the above results are extended in 1RDMFT
setting, where bosonic or fermionic symmetry conditions are enforced on the problem.'
acknowledgement: "This work started when A.G. was visiting the Erwin Schrödinger Institute
and then continued when D.F. and L.P visited the Theoretical Chemistry Department
of the Vrije Universiteit Amsterdam. The authors thank the hospitality of both places
and, especially, P. Gori-Giorgi and K. Giesbertz for fruitful discussions and literature
suggestions in the early state of the project. The authors also thank J. Maas and
R. Seiringer for their feedback and useful comments to a first draft of the article.
Finally, we acknowledge the high quality review done by the anonymous referee of
our paper, who we would like to thank for the excellent work and constructive feedback.\r\nD.F
acknowledges support by the European Research Council (ERC) under the European Union's
Horizon 2020 research and innovation programme (grant agreements No 716117 and No
694227). A.G. acknowledges funding by the HORIZON EUROPE European Research Council
under H2020/MSCA-IF “OTmeetsDFT” [grant ID: 795942] as well as partial support of
his research by the Canada Research Chairs Program (ID 2021-00234) and Natural Sciences
and Engineering Research Council of Canada, RGPIN-2022-05207. L.P. acknowledges
support by the Austrian Science Fund (FWF), grants No W1245 and No F65, and by the
Deutsche Forschungsgemeinschaft (DFG) - Project number 390685813."
article_number: '109963'
article_processing_charge: No
article_type: original
author:
- first_name: Dario
full_name: Feliciangeli, Dario
id: 41A639AA-F248-11E8-B48F-1D18A9856A87
last_name: Feliciangeli
orcid: 0000-0003-0754-8530
- first_name: Augusto
full_name: Gerolin, Augusto
last_name: Gerolin
- first_name: Lorenzo
full_name: Portinale, Lorenzo
id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87
last_name: Portinale
citation:
ama: Feliciangeli D, Gerolin A, Portinale L. A non-commutative entropic optimal
transport approach to quantum composite systems at positive temperature. Journal
of Functional Analysis. 2023;285(4). doi:10.1016/j.jfa.2023.109963
apa: Feliciangeli, D., Gerolin, A., & Portinale, L. (2023). A non-commutative
entropic optimal transport approach to quantum composite systems at positive temperature.
Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2023.109963
chicago: Feliciangeli, Dario, Augusto Gerolin, and Lorenzo Portinale. “A Non-Commutative
Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.”
Journal of Functional Analysis. Elsevier, 2023. https://doi.org/10.1016/j.jfa.2023.109963.
ieee: D. Feliciangeli, A. Gerolin, and L. Portinale, “A non-commutative entropic
optimal transport approach to quantum composite systems at positive temperature,”
Journal of Functional Analysis, vol. 285, no. 4. Elsevier, 2023.
ista: Feliciangeli D, Gerolin A, Portinale L. 2023. A non-commutative entropic optimal
transport approach to quantum composite systems at positive temperature. Journal
of Functional Analysis. 285(4), 109963.
mla: Feliciangeli, Dario, et al. “A Non-Commutative Entropic Optimal Transport Approach
to Quantum Composite Systems at Positive Temperature.” Journal of Functional
Analysis, vol. 285, no. 4, 109963, Elsevier, 2023, doi:10.1016/j.jfa.2023.109963.
short: D. Feliciangeli, A. Gerolin, L. Portinale, Journal of Functional Analysis
285 (2023).
date_created: 2023-05-07T22:01:02Z
date_published: 2023-08-15T00:00:00Z
date_updated: 2023-11-14T13:21:01Z
day: '15'
department:
- _id: RoSe
- _id: JaMa
doi: 10.1016/j.jfa.2023.109963
ec_funded: 1
external_id:
arxiv:
- '2106.11217'
isi:
- '000990804300001'
intvolume: ' 285'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2106.11217
month: '08'
oa: 1
oa_version: Preprint
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: 260482E2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: ' F06504'
name: Taming Complexity in Partial Di erential Systems
publication: Journal of Functional Analysis
publication_identifier:
eissn:
- 1096-0783
issn:
- 0022-1236
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '9792'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: A non-commutative entropic optimal transport approach to quantum composite
systems at positive temperature
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 285
year: '2023'
...
---
_id: '13177'
abstract:
- lang: eng
text: In this note we study the eigenvalue growth of infinite graphs with discrete
spectrum. We assume that the corresponding Dirichlet forms satisfy certain Sobolev-type
inequalities and that the total measure is finite. In this sense, the associated
operators on these graphs display similarities to elliptic operators on bounded
domains in the continuum. Specifically, we prove lower bounds on the eigenvalue
growth and show by examples that corresponding upper bounds cannot be established.
acknowledgement: The second author was supported by the priority program SPP2026 of
the German Research Foundation (DFG). The fourth author was supported by the German
Academic Scholarship Foundation (Studienstiftung des deutschen Volkes) and by the
German Research Foundation (DFG) via RTG 1523/2.
article_processing_charge: No
article_type: original
author:
- first_name: Bobo
full_name: Hua, Bobo
last_name: Hua
- first_name: Matthias
full_name: Keller, Matthias
last_name: Keller
- first_name: Michael
full_name: Schwarz, Michael
last_name: Schwarz
- first_name: Melchior
full_name: Wirth, Melchior
id: 88644358-0A0E-11EA-8FA5-49A33DDC885E
last_name: Wirth
orcid: 0000-0002-0519-4241
citation:
ama: Hua B, Keller M, Schwarz M, Wirth M. Sobolev-type inequalities and eigenvalue
growth on graphs with finite measure. Proceedings of the American Mathematical
Society. 2023;151(8):3401-3414. doi:10.1090/proc/14361
apa: Hua, B., Keller, M., Schwarz, M., & Wirth, M. (2023). Sobolev-type inequalities
and eigenvalue growth on graphs with finite measure. Proceedings of the American
Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/14361
chicago: Hua, Bobo, Matthias Keller, Michael Schwarz, and Melchior Wirth. “Sobolev-Type
Inequalities and Eigenvalue Growth on Graphs with Finite Measure.” Proceedings
of the American Mathematical Society. American Mathematical Society, 2023.
https://doi.org/10.1090/proc/14361.
ieee: B. Hua, M. Keller, M. Schwarz, and M. Wirth, “Sobolev-type inequalities and
eigenvalue growth on graphs with finite measure,” Proceedings of the American
Mathematical Society, vol. 151, no. 8. American Mathematical Society, pp.
3401–3414, 2023.
ista: Hua B, Keller M, Schwarz M, Wirth M. 2023. Sobolev-type inequalities and eigenvalue
growth on graphs with finite measure. Proceedings of the American Mathematical
Society. 151(8), 3401–3414.
mla: Hua, Bobo, et al. “Sobolev-Type Inequalities and Eigenvalue Growth on Graphs
with Finite Measure.” Proceedings of the American Mathematical Society,
vol. 151, no. 8, American Mathematical Society, 2023, pp. 3401–14, doi:10.1090/proc/14361.
short: B. Hua, M. Keller, M. Schwarz, M. Wirth, Proceedings of the American Mathematical
Society 151 (2023) 3401–3414.
date_created: 2023-07-02T22:00:43Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2023-11-14T13:07:09Z
day: '01'
department:
- _id: JaMa
doi: 10.1090/proc/14361
external_id:
arxiv:
- '1804.08353'
isi:
- '000988204400001'
intvolume: ' 151'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.1804.08353'
month: '08'
oa: 1
oa_version: Preprint
page: 3401-3414
publication: Proceedings of the American Mathematical Society
publication_identifier:
eissn:
- 1088-6826
issn:
- 0002-9939
publication_status: published
publisher: American Mathematical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sobolev-type inequalities and eigenvalue growth on graphs with finite measure
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 151
year: '2023'
...
---
_id: '14558'
abstract:
- lang: eng
text: "n the dynamic minimum set cover problem, the challenge is to minimize the
update time while guaranteeing a close-to-optimal min{O(log n), f} approximation
factor. (Throughout, n, m, f , and C are parameters denoting the maximum number
of elements, the number of sets, the frequency, and the cost range.) In the high-frequency
range, when f = Ω(log n) , this was achieved by a deterministic O(log n) -approximation
algorithm with O(f log n) amortized update time by Gupta et al. [Online and dynamic
algorithms for set cover, in Proceedings STOC 2017, ACM, pp. 537–550]. In this
paper we consider the low-frequency range, when f = O(log n) , and obtain deterministic
algorithms with a (1 + ∈)f -approximation ratio and the following guarantees on
the update time. (1) O ((f/∈)-log(Cn)) amortized update time: Prior to our work,
the best approximation ratio guaranteed by deterministic algorithms was O(f2)
of Bhattacharya, Henzinger, and Italiano [Design of dynamic algorithms via primal-dual
method, in Proceedings ICALP 2015, Springer, pp. 206–218]. In contrast, the only
result with O(f) -approximation was that of Abboud et al. [Dynamic set cover:
Improved algorithms and lower bounds, in Proceedings STOC 2019, ACM, pp. 114–125],
who designed a randomized (1+∈)f -approximation algorithm with amortized update
time. (2) O(f2/∈3 + (f/∈2).logC) amortized update time: This result improves the
above update time bound for most values of f\r\n in the low-frequency range, i.e.,
f=o(log n) . It is also the first result that is independent of m\r\n and n. It
subsumes the constant amortized update time of Bhattacharya and Kulkarni [Deterministically
maintaining a (2 + ∈) -approximate minimum vertex cover in O(1/∈2) amortized update
time, in Proceedings SODA 2019, SIAM, pp. 1872–1885] for unweighted dynamic vertex
cover (i.e., when f = 2 and C = 1). (3) O((f/∈3).log2(Cn)) worst-case update time:
No nontrivial worst-case update time was previously known for the dynamic set
cover problem. Our bound subsumes and improves by a logarithmic factor the O(log3n/poly
(∈)) \r\n worst-case update time for the unweighted dynamic vertex cover problem
(i.e., when f = 2\r\n and C =1) of Bhattacharya, Henzinger, and Nanongkai [Fully
dynamic approximate maximum matching and minimum vertex cover in O(log3)n worst
case update time, in Proceedings SODA 2017, SIAM, pp. 470–489]. We achieve our
results via the primal-dual approach, by maintaining a fractional packing solution
as a dual certificate. Prior work in dynamic algorithms that employs the primal-dual
approach uses a local update scheme that maintains relaxed complementary slackness
conditions for every set. For our first result we use instead a global update
scheme that does not always maintain complementary slackness conditions. For our
second result we combine the global and the local update schema. To achieve our
third result we use a hierarchy of background schedulers. It is an interesting
open question whether this background scheduler technique can also be used to
transform algorithms with amortized running time bounds into algorithms with worst-case
running time bounds."
acknowledgement: "This project has received funding from the European Research Council
(ERC) under the European Union's Horizon 2020 research and innovation programme
(grants 715672 and\r\n101019564 ``The Design of Modern Fully Dynamic Data Structures
(MoDynStruct)\"\") and from the Engineering and Physical Sciences Research Council,
UK (EPSRC) under grant EP/S03353X/1. The second author was also supported by the
Austrian Science Fund (FWF) project ``Fast Algorithms for a Reactive Network Layer
(ReactNet),\"\" P 33775-N, with additional funding from the netidee SCIENCE Stiftung,
2020--2024, project ``Static and Dynamic Hierarchical Graph Decompositions,\"\"I
5982-N, and project Z 422-N. The third author was also supported by the Swedish
Research Council (Reg. No. 2015-04659). The fourth author was also supported by
the Science and Technology Development Fund (FDCT), Macau SAR (file 0014/2022/AFJ,
0085/2022/A, 0143/2020/A3, and SKL-IOTSC-2021-2023)."
article_processing_charge: No
article_type: original
author:
- first_name: Sayan
full_name: Bhattacharya, Sayan
last_name: Bhattacharya
- 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: Danupon
full_name: Nanongkai, Danupon
last_name: Nanongkai
- first_name: Xiaowei
full_name: Wu, Xiaowei
last_name: Wu
citation:
ama: Bhattacharya S, Henzinger MH, Nanongkai D, Wu X. Deterministic near-optimal
approximation algorithms for dynamic set cover. SIAM Journal on Computing.
2023;52(5):1132-1192. doi:10.1137/21M1428649
apa: Bhattacharya, S., Henzinger, M. H., Nanongkai, D., & Wu, X. (2023). Deterministic
near-optimal approximation algorithms for dynamic set cover. SIAM Journal on
Computing. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/21M1428649
chicago: Bhattacharya, Sayan, Monika H Henzinger, Danupon Nanongkai, and Xiaowei
Wu. “Deterministic Near-Optimal Approximation Algorithms for Dynamic Set Cover.”
SIAM Journal on Computing. Society for Industrial and Applied Mathematics,
2023. https://doi.org/10.1137/21M1428649.
ieee: S. Bhattacharya, M. H. Henzinger, D. Nanongkai, and X. Wu, “Deterministic
near-optimal approximation algorithms for dynamic set cover,” SIAM Journal
on Computing, vol. 52, no. 5. Society for Industrial and Applied Mathematics,
pp. 1132–1192, 2023.
ista: Bhattacharya S, Henzinger MH, Nanongkai D, Wu X. 2023. Deterministic near-optimal
approximation algorithms for dynamic set cover. SIAM Journal on Computing. 52(5),
1132–1192.
mla: Bhattacharya, Sayan, et al. “Deterministic Near-Optimal Approximation Algorithms
for Dynamic Set Cover.” SIAM Journal on Computing, vol. 52, no. 5, Society
for Industrial and Applied Mathematics, 2023, pp. 1132–92, doi:10.1137/21M1428649.
short: S. Bhattacharya, M.H. Henzinger, D. Nanongkai, X. Wu, SIAM Journal on Computing
52 (2023) 1132–1192.
date_created: 2023-11-19T23:00:56Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2023-11-20T08:21:07Z
day: '01'
department:
- _id: MoHe
doi: 10.1137/21M1428649
ec_funded: 1
intvolume: ' 52'
issue: '5'
language:
- iso: eng
month: '10'
oa_version: None
page: 1132-1192
project:
- _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62
call_identifier: H2020
grant_number: '101019564'
name: The design and evaluation of modern fully dynamic data structures
- _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe
grant_number: 'P33775 '
name: Fast Algorithms for a Reactive Network Layer
- _id: 34def286-11ca-11ed-8bc3-da5948e1613c
grant_number: Z00422
name: Wittgenstein Award - Monika Henzinger
- _id: bda196b2-d553-11ed-ba76-8e8ee6c21103
grant_number: I05982
name: Static and Dynamic Hierarchical Graph Decompositions
publication: SIAM Journal on Computing
publication_identifier:
eissn:
- 1095-7111
issn:
- 0097-5397
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Deterministic near-optimal approximation algorithms for dynamic set cover
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 52
year: '2023'
...
---
_id: '14559'
abstract:
- lang: eng
text: We consider the problem of learning control policies in discrete-time stochastic
systems which guarantee that the system stabilizes within some specified stabilization
region with probability 1. Our approach is based on the novel notion of stabilizing
ranking supermartingales (sRSMs) that we introduce in this work. Our sRSMs overcome
the limitation of methods proposed in previous works whose applicability is restricted
to systems in which the stabilizing region cannot be left once entered under any
control policy. We present a learning procedure that learns a control policy together
with an sRSM that formally certifies probability 1 stability, both learned as
neural networks. We show that this procedure can also be adapted to formally verifying
that, under a given Lipschitz continuous control policy, the stochastic system
stabilizes within some stabilizing region with probability 1. Our experimental
evaluation shows that our learning procedure can successfully learn provably stabilizing
policies in practice.
acknowledgement: This work was supported in part by the ERC-2020-AdG 101020093, ERC
CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Matin
full_name: Ansaripour, Matin
last_name: Ansaripour
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
citation:
ama: 'Ansaripour M, Chatterjee K, Henzinger TA, Lechner M, Zikelic D. Learning provably
stabilizing neural controllers for discrete-time stochastic systems. In: 21st
International Symposium on Automated Technology for Verification and Analysis.
Vol 14215. Springer Nature; 2023:357-379. doi:10.1007/978-3-031-45329-8_17'
apa: 'Ansaripour, M., Chatterjee, K., Henzinger, T. A., Lechner, M., & Zikelic,
D. (2023). Learning provably stabilizing neural controllers for discrete-time
stochastic systems. In 21st International Symposium on Automated Technology
for Verification and Analysis (Vol. 14215, pp. 357–379). Singapore, Singapore:
Springer Nature. https://doi.org/10.1007/978-3-031-45329-8_17'
chicago: Ansaripour, Matin, Krishnendu Chatterjee, Thomas A Henzinger, Mathias Lechner,
and Dorde Zikelic. “Learning Provably Stabilizing Neural Controllers for Discrete-Time
Stochastic Systems.” In 21st International Symposium on Automated Technology
for Verification and Analysis, 14215:357–79. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-45329-8_17.
ieee: M. Ansaripour, K. Chatterjee, T. A. Henzinger, M. Lechner, and D. Zikelic,
“Learning provably stabilizing neural controllers for discrete-time stochastic
systems,” in 21st International Symposium on Automated Technology for Verification
and Analysis, Singapore, Singapore, 2023, vol. 14215, pp. 357–379.
ista: 'Ansaripour M, Chatterjee K, Henzinger TA, Lechner M, Zikelic D. 2023. Learning
provably stabilizing neural controllers for discrete-time stochastic systems.
21st International Symposium on Automated Technology for Verification and Analysis.
ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 14215, 357–379.'
mla: Ansaripour, Matin, et al. “Learning Provably Stabilizing Neural Controllers
for Discrete-Time Stochastic Systems.” 21st International Symposium on Automated
Technology for Verification and Analysis, vol. 14215, Springer Nature, 2023,
pp. 357–79, doi:10.1007/978-3-031-45329-8_17.
short: M. Ansaripour, K. Chatterjee, T.A. Henzinger, M. Lechner, D. Zikelic, in:,
21st International Symposium on Automated Technology for Verification and Analysis,
Springer Nature, 2023, pp. 357–379.
conference:
end_date: 2023-10-27
location: Singapore, Singapore
name: 'ATVA: Automated Technology for Verification and Analysis'
start_date: 2023-10-24
date_created: 2023-11-19T23:00:56Z
date_published: 2023-10-22T00:00:00Z
date_updated: 2023-11-20T08:30:20Z
day: '22'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1007/978-3-031-45329-8_17
ec_funded: 1
intvolume: ' 14215'
language:
- iso: eng
month: '10'
oa_version: None
page: 357-379
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: 21st International Symposium on Automated Technology for Verification
and Analysis
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031453281'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Learning provably stabilizing neural controllers for discrete-time stochastic
systems
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14215
year: '2023'
...
---
_id: '14554'
abstract:
- lang: eng
text: 'The Regularised Inertial Dean–Kawasaki model (RIDK) – introduced by the authors
and J. Zimmer in earlier works – is a nonlinear stochastic PDE capturing fluctuations
around the meanfield limit for large-scale particle systems in both particle density
and momentum density. We focus on the following two aspects. Firstly, we set up
a Discontinuous Galerkin (DG) discretisation scheme for the RIDK model: we provide
suitable definitions of numerical fluxes at the interface of the mesh elements
which are consistent with the wave-type nature of the RIDK model and grant stability
of the simulations, and we quantify the rate of convergence in mean square to
the continuous RIDK model. Secondly, we introduce modifications of the RIDK model
in order to preserve positivity of the density (such a feature only holds in a
“high-probability sense” for the original RIDK model). By means of numerical simulations,
we show that the modifications lead to physically realistic and positive density
profiles. In one case, subject to additional regularity constraints, we also prove
positivity. Finally, we present an application of our methodology to a system
of diffusing and reacting particles. Our Python code is available in open-source
format.'
acknowledgement: "The authors thank the anonymous referees for their careful reading
of the manuscript and their\r\nvaluable suggestions. FC gratefully acknowledges
funding from the Austrian Science Fund (FWF) through the project F65, and from the
European Union’s Horizon 2020 research and innovation programme under the Marie
Sk lodowska-Curie grant agreement No. 754411 (the latter funding source covered
the first part of this project)."
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Federico
full_name: Cornalba, Federico
id: 2CEB641C-A400-11E9-A717-D712E6697425
last_name: Cornalba
orcid: 0000-0002-6269-5149
- first_name: Tony
full_name: Shardlow, Tony
last_name: Shardlow
citation:
ama: 'Cornalba F, Shardlow T. The regularised inertial Dean’ Kawasaki equation:
Discontinuous Galerkin approximation and modelling for low-density regime. ESAIM:
Mathematical Modelling and Numerical Analysis. 2023;57(5):3061-3090. doi:10.1051/m2an/2023077'
apa: 'Cornalba, F., & Shardlow, T. (2023). The regularised inertial Dean’ Kawasaki
equation: Discontinuous Galerkin approximation and modelling for low-density regime.
ESAIM: Mathematical Modelling and Numerical Analysis. EDP Sciences. https://doi.org/10.1051/m2an/2023077'
chicago: 'Cornalba, Federico, and Tony Shardlow. “The Regularised Inertial Dean’
Kawasaki Equation: Discontinuous Galerkin Approximation and Modelling for Low-Density
Regime.” ESAIM: Mathematical Modelling and Numerical Analysis. EDP Sciences,
2023. https://doi.org/10.1051/m2an/2023077.'
ieee: 'F. Cornalba and T. Shardlow, “The regularised inertial Dean’ Kawasaki equation:
Discontinuous Galerkin approximation and modelling for low-density regime,” ESAIM:
Mathematical Modelling and Numerical Analysis, vol. 57, no. 5. EDP Sciences,
pp. 3061–3090, 2023.'
ista: 'Cornalba F, Shardlow T. 2023. The regularised inertial Dean’ Kawasaki equation:
Discontinuous Galerkin approximation and modelling for low-density regime. ESAIM:
Mathematical Modelling and Numerical Analysis. 57(5), 3061–3090.'
mla: 'Cornalba, Federico, and Tony Shardlow. “The Regularised Inertial Dean’ Kawasaki
Equation: Discontinuous Galerkin Approximation and Modelling for Low-Density Regime.”
ESAIM: Mathematical Modelling and Numerical Analysis, vol. 57, no. 5, EDP
Sciences, 2023, pp. 3061–90, doi:10.1051/m2an/2023077.'
short: 'F. Cornalba, T. Shardlow, ESAIM: Mathematical Modelling and Numerical Analysis
57 (2023) 3061–3090.'
date_created: 2023-11-19T23:00:55Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2023-11-20T08:38:47Z
day: '01'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1051/m2an/2023077
ec_funded: 1
file:
- access_level: open_access
checksum: 3aef1475b1882c8dec112df9a5167c39
content_type: application/pdf
creator: dernst
date_created: 2023-11-20T08:34:57Z
date_updated: 2023-11-20T08:34:57Z
file_id: '14560'
file_name: 2023_ESAIM_Cornalba.pdf
file_size: 1508534
relation: main_file
success: 1
file_date_updated: 2023-11-20T08:34:57Z
has_accepted_license: '1'
intvolume: ' 57'
issue: '5'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 3061-3090
project:
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: 'ESAIM: Mathematical Modelling and Numerical Analysis'
publication_identifier:
eissn:
- 2804-7214
issn:
- 2822-7840
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/tonyshardlow/RIDK-FD
scopus_import: '1'
status: public
title: 'The regularised inertial Dean'' Kawasaki equation: Discontinuous Galerkin
approximation and modelling for low-density regime'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 57
year: '2023'
...
---
_id: '14556'
abstract:
- lang: eng
text: Inversions are structural mutations that reverse the sequence of a chromosome
segment and reduce the effective rate of recombination in the heterozygous state.
They play a major role in adaptation, as well as in other evolutionary processes
such as speciation. Although inversions have been studied since the 1920s, they
remain difficult to investigate because the reduced recombination conferred by
them strengthens the effects of drift and hitchhiking, which in turn can obscure
signatures of selection. Nonetheless, numerous inversions have been found to be
under selection. Given recent advances in population genetic theory and empirical
study, here we review how different mechanisms of selection affect the evolution
of inversions. A key difference between inversions and other mutations, such as
single nucleotide variants, is that the fitness of an inversion may be affected
by a larger number of frequently interacting processes. This considerably complicates
the analysis of the causes underlying the evolution of inversions. We discuss
the extent to which these mechanisms can be disentangled, and by which approach.
acknowledgement: 'We are grateful to two referees and Luke Holman for valuable comments
on a previous version of our manuscript. This paper was conceived at the ESEB Progress
Meeting ‘Disentangling neutral versus adaptive evolution in chromosomal inversions’,
organized by ELB, KJ and TF and held at Tjärnö Marine Laboratory (Sweden) between
28 February and 3 March 2022. We are indebted to ESEB for sponsoring our workshop
and to the following funding bodies for supporting our research: ERC AdG 101055327
to NHB; Swedish Research Council (VR) 2018-03695 and Leverhulme Trust RPG-2021-141
to RKB; Fundação para a Ciência e a Tecnologia (FCT) contract 2020.00275.CEECIND
and research project PTDC/BIA-1232 EVL/1614/2021 to RF; Fundação para a Ciência
e a Tecnologia (FCT) junior researcher contract CEECIND/02616/2018 to IF; Swiss
National Science Foundation (SNSF) Ambizione #PZ00P3_185952 to KJG; National Science
Foundation NSF-OCE 2043905 and NSF-DEB 1655701 to KEL; Swiss National Science Foundation
(SNSF) 310030_204681 to CLP; Swedish Research Council (VR) 2021-05243 to MR; Norwegian
Research Council grant 315287 to AMW; Swiss National Science Foundation (SNSF) 31003A-182262
and FZEB-0-214654 to TF. We also thank Luca Ferretti for the discussion and Eliane
Zinn (Flatt lab) for help with reference formatting.'
article_number: '14242'
article_processing_charge: No
article_type: review
author:
- first_name: Emma L.
full_name: Berdan, Emma L.
last_name: Berdan
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Roger
full_name: Butlin, Roger
last_name: Butlin
- first_name: Brian
full_name: Charlesworth, Brian
last_name: Charlesworth
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Inês
full_name: Fragata, Inês
last_name: Fragata
- first_name: Kimberly J.
full_name: Gilbert, Kimberly J.
last_name: Gilbert
- first_name: Paul
full_name: Jay, Paul
last_name: Jay
- first_name: Martin
full_name: Kapun, Martin
last_name: Kapun
- first_name: Katie E.
full_name: Lotterhos, Katie E.
last_name: Lotterhos
- first_name: Claire
full_name: Mérot, Claire
last_name: Mérot
- first_name: Esra
full_name: Durmaz Mitchell, Esra
last_name: Durmaz Mitchell
- first_name: Marta
full_name: Pascual, Marta
last_name: Pascual
- first_name: Catherine L.
full_name: Peichel, Catherine L.
last_name: Peichel
- first_name: Marina
full_name: Rafajlović, Marina
last_name: Rafajlović
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Stephen W.
full_name: Schaeffer, Stephen W.
last_name: Schaeffer
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Thomas
full_name: Flatt, Thomas
last_name: Flatt
citation:
ama: Berdan EL, Barton NH, Butlin R, et al. How chromosomal inversions reorient
the evolutionary process. Journal of Evolutionary Biology. 2023. doi:10.1111/jeb.14242
apa: Berdan, E. L., Barton, N. H., Butlin, R., Charlesworth, B., Faria, R., Fragata,
I., … Flatt, T. (2023). How chromosomal inversions reorient the evolutionary process.
Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.14242
chicago: Berdan, Emma L., Nicholas H Barton, Roger Butlin, Brian Charlesworth, Rui
Faria, Inês Fragata, Kimberly J. Gilbert, et al. “How Chromosomal Inversions Reorient
the Evolutionary Process.” Journal of Evolutionary Biology. Wiley, 2023.
https://doi.org/10.1111/jeb.14242.
ieee: E. L. Berdan et al., “How chromosomal inversions reorient the evolutionary
process,” Journal of Evolutionary Biology. Wiley, 2023.
ista: Berdan EL, Barton NH, Butlin R, Charlesworth B, Faria R, Fragata I, Gilbert
KJ, Jay P, Kapun M, Lotterhos KE, Mérot C, Durmaz Mitchell E, Pascual M, Peichel
CL, Rafajlović M, Westram AM, Schaeffer SW, Johannesson K, Flatt T. 2023. How
chromosomal inversions reorient the evolutionary process. Journal of Evolutionary
Biology., 14242.
mla: Berdan, Emma L., et al. “How Chromosomal Inversions Reorient the Evolutionary
Process.” Journal of Evolutionary Biology, 14242, Wiley, 2023, doi:10.1111/jeb.14242.
short: E.L. Berdan, N.H. Barton, R. Butlin, B. Charlesworth, R. Faria, I. Fragata,
K.J. Gilbert, P. Jay, M. Kapun, K.E. Lotterhos, C. Mérot, E. Durmaz Mitchell,
M. Pascual, C.L. Peichel, M. Rafajlović, A.M. Westram, S.W. Schaeffer, K. Johannesson,
T. Flatt, Journal of Evolutionary Biology (2023).
date_created: 2023-11-19T23:00:55Z
date_published: 2023-11-08T00:00:00Z
date_updated: 2023-11-20T08:51:09Z
day: '08'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/jeb.14242
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/jeb.14242
month: '11'
oa: 1
oa_version: Published Version
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- 1420-9101
issn:
- 1010-061X
publication_status: epub_ahead
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: How chromosomal inversions reorient the evolutionary process
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14555'
abstract:
- lang: eng
text: The intricate regulatory processes behind actin polymerization play a crucial
role in cellular biology, including essential mechanisms such as cell migration
or cell division. However, the self-organizing principles governing actin polymerization
are still poorly understood. In this perspective article, we compare the Belousov-Zhabotinsky
(BZ) reaction, a classic and well understood chemical oscillator known for its
self-organizing spatiotemporal dynamics, with the excitable dynamics of polymerizing
actin. While the BZ reaction originates from the domain of inorganic chemistry,
it shares remarkable similarities with actin polymerization, including the characteristic
propagating waves, which are influenced by geometry and external fields, and the
emergent collective behavior. Starting with a general description of emerging
patterns, we elaborate on single droplets or cell-level dynamics, the influence
of geometric confinements and conclude with collective interactions. Comparing
these two systems sheds light on the universal nature of self-organization principles
in both living and inanimate systems.
acknowledgement: The author(s) declare that no financial support was received for
the research, authorship, and/or publication of this article.
article_number: '1287420'
article_processing_charge: Yes
article_type: original
author:
- first_name: Michael
full_name: Riedl, Michael
id: 3BE60946-F248-11E8-B48F-1D18A9856A87
last_name: Riedl
orcid: 0000-0003-4844-6311
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Riedl M, Sixt MK. The excitable nature of polymerizing actin and the Belousov-Zhabotinsky
reaction. Frontiers in Cell and Developmental Biology. 2023;11. doi:10.3389/fcell.2023.1287420
apa: Riedl, M., & Sixt, M. K. (2023). The excitable nature of polymerizing actin
and the Belousov-Zhabotinsky reaction. Frontiers in Cell and Developmental
Biology. Frontiers. https://doi.org/10.3389/fcell.2023.1287420
chicago: Riedl, Michael, and Michael K Sixt. “The Excitable Nature of Polymerizing
Actin and the Belousov-Zhabotinsky Reaction.” Frontiers in Cell and Developmental
Biology. Frontiers, 2023. https://doi.org/10.3389/fcell.2023.1287420.
ieee: M. Riedl and M. K. Sixt, “The excitable nature of polymerizing actin and the
Belousov-Zhabotinsky reaction,” Frontiers in Cell and Developmental Biology,
vol. 11. Frontiers, 2023.
ista: Riedl M, Sixt MK. 2023. The excitable nature of polymerizing actin and the
Belousov-Zhabotinsky reaction. Frontiers in Cell and Developmental Biology. 11,
1287420.
mla: Riedl, Michael, and Michael K. Sixt. “The Excitable Nature of Polymerizing
Actin and the Belousov-Zhabotinsky Reaction.” Frontiers in Cell and Developmental
Biology, vol. 11, 1287420, Frontiers, 2023, doi:10.3389/fcell.2023.1287420.
short: M. Riedl, M.K. Sixt, Frontiers in Cell and Developmental Biology 11 (2023).
date_created: 2023-11-19T23:00:55Z
date_published: 2023-10-31T00:00:00Z
date_updated: 2023-11-20T08:44:17Z
day: '31'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.3389/fcell.2023.1287420
file:
- access_level: open_access
checksum: 61857fc3ebf019354932e7ee684658ce
content_type: application/pdf
creator: dernst
date_created: 2023-11-20T08:41:15Z
date_updated: 2023-11-20T08:41:15Z
file_id: '14561'
file_name: 2023_FrontiersCellDevBio_Riedl.pdf
file_size: 2047622
relation: main_file
success: 1
file_date_updated: 2023-11-20T08:41:15Z
has_accepted_license: '1'
intvolume: ' 11'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: Frontiers in Cell and Developmental Biology
publication_identifier:
eissn:
- 2296-634X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2023'
...
---
_id: '14543'
abstract:
- lang: eng
text: The acyl-CoA-binding domain-containing protein 6 (ACBD6) is ubiquitously expressed,
plays a role in the acylation of lipids and proteins, and regulates the N-myristoylation
of proteins via N-myristoyltransferase enzymes (NMTs). However, its precise function
in cells is still unclear, as is the consequence of ACBD6 defects on human pathophysiology.
Utilizing exome sequencing and extensive international data sharing efforts, we
identified 45 affected individuals from 28 unrelated families (consanguinity 93%)
with bi-allelic pathogenic, predominantly loss-of-function (18/20) variants in
ACBD6. We generated zebrafish and Xenopus tropicalis acbd6 knockouts by CRISPR/Cas9
and characterized the role of ACBD6 on protein N-myristoylation with YnMyr chemical
proteomics in the model organisms and human cells, with the latter also being
subjected further to ACBD6 peroxisomal localization studies. The affected individuals
(23 males and 22 females), with ages ranging from 1 to 50 years old, typically
present with a complex and progressive disease involving moderate-to-severe global
developmental delay/intellectual disability (100%) with significant expressive
language impairment (98%), movement disorders (97%), facial dysmorphism (95%),
and mild cerebellar ataxia (85%) associated with gait impairment (94%), limb spasticity/hypertonia
(76%), oculomotor (71%) and behavioural abnormalities (65%), overweight (59%),
microcephaly (39%) and epilepsy (33%). The most conspicuous and common movement
disorder was dystonia (94%), frequently leading to early-onset progressive postural
deformities (97%), limb dystonia (55%), and cervical dystonia (31%). A jerky tremor
in the upper limbs (63%), a mild head tremor (59%), parkinsonism/hypokinesia developing
with advancing age (32%), and simple motor and vocal tics were among other frequent
movement disorders. Midline brain malformations including corpus callosum abnormalities
(70%), hypoplasia/agenesis of the anterior commissure (66%), short midbrain and
small inferior cerebellar vermis (38% each), as well as hypertrophy of the clava
(24%) were common neuroimaging findings. acbd6-deficient zebrafish and Xenopus
models effectively recapitulated many clinical phenotypes reported in patients
including movement disorders, progressive neuromotor impairment, seizures, microcephaly,
craniofacial dysmorphism, and midbrain defects accompanied by developmental delay
with increased mortality over time. Unlike ACBD5, ACBD6 did not show a peroxisomal
localisation and ACBD6-deficiency was not associated with altered peroxisomal
parameters in patient fibroblasts. Significant differences in YnMyr-labelling
were observed for 68 co- and 18 post-translationally N-myristoylated proteins
in patient-derived fibroblasts. N-Myristoylation was similarly affected in acbd6-deficient
zebrafish and Xenopus tropicalis models, including Fus, Marcks, and Chchd-related
proteins implicated in neurological diseases. The present study provides evidence
that bi-allelic pathogenic variants in ACBD6 lead to a distinct neurodevelopmental
syndrome accompanied by complex and progressive cognitive and movement disorders.
article_number: awad380
article_processing_charge: No
article_type: original
author:
- first_name: Rauan
full_name: Kaiyrzhanov, Rauan
last_name: Kaiyrzhanov
- first_name: Aboulfazl
full_name: Rad, Aboulfazl
last_name: Rad
- first_name: Sheng-Jia
full_name: Lin, Sheng-Jia
last_name: Lin
- first_name: Aida
full_name: Bertoli-Avella, Aida
last_name: Bertoli-Avella
- first_name: Wouter W
full_name: Kallemeijn, Wouter W
last_name: Kallemeijn
- first_name: Annie
full_name: Godwin, Annie
last_name: Godwin
- first_name: Maha S
full_name: Zaki, Maha S
last_name: Zaki
- first_name: Kevin
full_name: Huang, Kevin
id: 3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3
last_name: Huang
orcid: 0000-0002-2512-7812
- first_name: Tracy
full_name: Lau, Tracy
last_name: Lau
- first_name: Cassidy
full_name: Petree, Cassidy
last_name: Petree
- first_name: Stephanie
full_name: Efthymiou, Stephanie
last_name: Efthymiou
- first_name: Ehsan
full_name: Ghayoor Karimiani, Ehsan
last_name: Ghayoor Karimiani
- first_name: Maja
full_name: Hempel, Maja
last_name: Hempel
- first_name: Elizabeth A
full_name: Normand, Elizabeth A
last_name: Normand
- first_name: Sabine
full_name: Rudnik-Schöneborn, Sabine
last_name: Rudnik-Schöneborn
- first_name: Ulrich A
full_name: Schatz, Ulrich A
last_name: Schatz
- first_name: Marc P
full_name: Baggelaar, Marc P
last_name: Baggelaar
- first_name: Muhammad
full_name: Ilyas, Muhammad
last_name: Ilyas
- first_name: Tipu
full_name: Sultan, Tipu
last_name: Sultan
- first_name: Javeria Raza
full_name: Alvi, Javeria Raza
last_name: Alvi
- first_name: Manizha
full_name: Ganieva, Manizha
last_name: Ganieva
- first_name: Ben
full_name: Fowler, Ben
last_name: Fowler
- first_name: Ruxandra
full_name: Aanicai, Ruxandra
last_name: Aanicai
- first_name: Gulsen
full_name: Akay Tayfun, Gulsen
last_name: Akay Tayfun
- first_name: Abdulaziz
full_name: Al Saman, Abdulaziz
last_name: Al Saman
- first_name: Abdulrahman
full_name: Alswaid, Abdulrahman
last_name: Alswaid
- first_name: Nafise
full_name: Amiri, Nafise
last_name: Amiri
- first_name: Nilufar
full_name: Asilova, Nilufar
last_name: Asilova
- first_name: Vorasuk
full_name: Shotelersuk, Vorasuk
last_name: Shotelersuk
- first_name: Patra
full_name: Yeetong, Patra
last_name: Yeetong
- first_name: Matloob
full_name: Azam, Matloob
last_name: Azam
- first_name: Meisam
full_name: Babaei, Meisam
last_name: Babaei
- first_name: Gholamreza
full_name: Bahrami Monajemi, Gholamreza
last_name: Bahrami Monajemi
- first_name: Pouria
full_name: Mohammadi, Pouria
last_name: Mohammadi
- first_name: Saeed
full_name: Samie, Saeed
last_name: Samie
- first_name: Selina Husna
full_name: Banu, Selina Husna
last_name: Banu
- first_name: Jorge Pinto
full_name: Basto, Jorge Pinto
last_name: Basto
- first_name: Fanny
full_name: Kortüm, Fanny
last_name: Kortüm
- first_name: Mislen
full_name: Bauer, Mislen
last_name: Bauer
- first_name: Peter
full_name: Bauer, Peter
last_name: Bauer
- first_name: Christian
full_name: Beetz, Christian
last_name: Beetz
- first_name: Masoud
full_name: Garshasbi, Masoud
last_name: Garshasbi
- first_name: Awatif
full_name: Hameed Issa, Awatif
last_name: Hameed Issa
- first_name: Wafaa
full_name: Eyaid, Wafaa
last_name: Eyaid
- first_name: Hind
full_name: Ahmed, Hind
last_name: Ahmed
- first_name: Narges
full_name: Hashemi, Narges
last_name: Hashemi
- first_name: Kazem
full_name: Hassanpour, Kazem
last_name: Hassanpour
- first_name: Isabella
full_name: Herman, Isabella
last_name: Herman
- first_name: Sherozjon
full_name: Ibrohimov, Sherozjon
last_name: Ibrohimov
- first_name: Ban A
full_name: Abdul-Majeed, Ban A
last_name: Abdul-Majeed
- first_name: Maria
full_name: Imdad, Maria
last_name: Imdad
- first_name: Maksudjon
full_name: Isrofilov, Maksudjon
last_name: Isrofilov
- first_name: Qassem
full_name: Kaiyal, Qassem
last_name: Kaiyal
- first_name: Suliman
full_name: Khan, Suliman
last_name: Khan
- first_name: Brian
full_name: Kirmse, Brian
last_name: Kirmse
- first_name: Janet
full_name: Koster, Janet
last_name: Koster
- first_name: Charles Marques
full_name: Lourenço, Charles Marques
last_name: Lourenço
- first_name: Tadahiro
full_name: Mitani, Tadahiro
last_name: Mitani
- first_name: Oana
full_name: Moldovan, Oana
last_name: Moldovan
- first_name: David
full_name: Murphy, David
last_name: Murphy
- first_name: Maryam
full_name: Najafi, Maryam
last_name: Najafi
- first_name: Davut
full_name: Pehlivan, Davut
last_name: Pehlivan
- first_name: Maria Eugenia
full_name: Rocha, Maria Eugenia
last_name: Rocha
- first_name: Vincenzo
full_name: Salpietro, Vincenzo
last_name: Salpietro
- first_name: Miriam
full_name: Schmidts, Miriam
last_name: Schmidts
- first_name: Adel
full_name: Shalata, Adel
last_name: Shalata
- first_name: Mohammad
full_name: Mahroum, Mohammad
last_name: Mahroum
- first_name: Jawabreh Kassem
full_name: Talbeya, Jawabreh Kassem
last_name: Talbeya
- first_name: Robert W
full_name: Taylor, Robert W
last_name: Taylor
- first_name: Dayana
full_name: Vazquez, Dayana
last_name: Vazquez
- first_name: Annalisa
full_name: Vetro, Annalisa
last_name: Vetro
- first_name: Hans R
full_name: Waterham, Hans R
last_name: Waterham
- first_name: Mashaya
full_name: Zaman, Mashaya
last_name: Zaman
- first_name: Tina A
full_name: Schrader, Tina A
last_name: Schrader
- first_name: Wendy K
full_name: Chung, Wendy K
last_name: Chung
- first_name: Renzo
full_name: Guerrini, Renzo
last_name: Guerrini
- first_name: James R
full_name: Lupski, James R
last_name: Lupski
- first_name: Joseph
full_name: Gleeson, Joseph
last_name: Gleeson
- first_name: Mohnish
full_name: Suri, Mohnish
last_name: Suri
- first_name: Yalda
full_name: Jamshidi, Yalda
last_name: Jamshidi
- first_name: Kailash P
full_name: Bhatia, Kailash P
last_name: Bhatia
- first_name: Barbara
full_name: Vona, Barbara
last_name: Vona
- first_name: Michael
full_name: Schrader, Michael
last_name: Schrader
- first_name: Mariasavina
full_name: Severino, Mariasavina
last_name: Severino
- first_name: Matthew
full_name: Guille, Matthew
last_name: Guille
- first_name: Edward W
full_name: Tate, Edward W
last_name: Tate
- first_name: Gaurav K
full_name: Varshney, Gaurav K
last_name: Varshney
- first_name: Henry
full_name: Houlden, Henry
last_name: Houlden
- first_name: Reza
full_name: Maroofian, Reza
last_name: Maroofian
citation:
ama: Kaiyrzhanov R, Rad A, Lin S-J, et al. Bi-allelic ACBD6 variants lead to a neurodevelopmental
syndrome with progressive and complex movement disorders. Brain. 2023.
doi:10.1093/brain/awad380
apa: Kaiyrzhanov, R., Rad, A., Lin, S.-J., Bertoli-Avella, A., Kallemeijn, W. W.,
Godwin, A., … Maroofian, R. (2023). Bi-allelic ACBD6 variants lead to a neurodevelopmental
syndrome with progressive and complex movement disorders. Brain. Oxford
University Press. https://doi.org/10.1093/brain/awad380
chicago: Kaiyrzhanov, Rauan, Aboulfazl Rad, Sheng-Jia Lin, Aida Bertoli-Avella,
Wouter W Kallemeijn, Annie Godwin, Maha S Zaki, et al. “Bi-Allelic ACBD6 Variants
Lead to a Neurodevelopmental Syndrome with Progressive and Complex Movement Disorders.”
Brain. Oxford University Press, 2023. https://doi.org/10.1093/brain/awad380.
ieee: R. Kaiyrzhanov et al., “Bi-allelic ACBD6 variants lead to a neurodevelopmental
syndrome with progressive and complex movement disorders,” Brain. Oxford
University Press, 2023.
ista: Kaiyrzhanov R, Rad A, Lin S-J, Bertoli-Avella A, Kallemeijn WW, Godwin A,
Zaki MS, Huang K, Lau T, Petree C, Efthymiou S, Ghayoor Karimiani E, Hempel M,
Normand EA, Rudnik-Schöneborn S, Schatz UA, Baggelaar MP, Ilyas M, Sultan T, Alvi
JR, Ganieva M, Fowler B, Aanicai R, Akay Tayfun G, Al Saman A, Alswaid A, Amiri
N, Asilova N, Shotelersuk V, Yeetong P, Azam M, Babaei M, Bahrami Monajemi G,
Mohammadi P, Samie S, Banu SH, Basto JP, Kortüm F, Bauer M, Bauer P, Beetz C,
Garshasbi M, Hameed Issa A, Eyaid W, Ahmed H, Hashemi N, Hassanpour K, Herman
I, Ibrohimov S, Abdul-Majeed BA, Imdad M, Isrofilov M, Kaiyal Q, Khan S, Kirmse
B, Koster J, Lourenço CM, Mitani T, Moldovan O, Murphy D, Najafi M, Pehlivan D,
Rocha ME, Salpietro V, Schmidts M, Shalata A, Mahroum M, Talbeya JK, Taylor RW,
Vazquez D, Vetro A, Waterham HR, Zaman M, Schrader TA, Chung WK, Guerrini R, Lupski
JR, Gleeson J, Suri M, Jamshidi Y, Bhatia KP, Vona B, Schrader M, Severino M,
Guille M, Tate EW, Varshney GK, Houlden H, Maroofian R. 2023. Bi-allelic ACBD6
variants lead to a neurodevelopmental syndrome with progressive and complex movement
disorders. Brain., awad380.
mla: Kaiyrzhanov, Rauan, et al. “Bi-Allelic ACBD6 Variants Lead to a Neurodevelopmental
Syndrome with Progressive and Complex Movement Disorders.” Brain, awad380,
Oxford University Press, 2023, doi:10.1093/brain/awad380.
short: R. Kaiyrzhanov, A. Rad, S.-J. Lin, A. Bertoli-Avella, W.W. Kallemeijn, A.
Godwin, M.S. Zaki, K. Huang, T. Lau, C. Petree, S. Efthymiou, E. Ghayoor Karimiani,
M. Hempel, E.A. Normand, S. Rudnik-Schöneborn, U.A. Schatz, M.P. Baggelaar, M.
Ilyas, T. Sultan, J.R. Alvi, M. Ganieva, B. Fowler, R. Aanicai, G. Akay Tayfun,
A. Al Saman, A. Alswaid, N. Amiri, N. Asilova, V. Shotelersuk, P. Yeetong, M.
Azam, M. Babaei, G. Bahrami Monajemi, P. Mohammadi, S. Samie, S.H. Banu, J.P.
Basto, F. Kortüm, M. Bauer, P. Bauer, C. Beetz, M. Garshasbi, A. Hameed Issa,
W. Eyaid, H. Ahmed, N. Hashemi, K. Hassanpour, I. Herman, S. Ibrohimov, B.A. Abdul-Majeed,
M. Imdad, M. Isrofilov, Q. Kaiyal, S. Khan, B. Kirmse, J. Koster, C.M. Lourenço,
T. Mitani, O. Moldovan, D. Murphy, M. Najafi, D. Pehlivan, M.E. Rocha, V. Salpietro,
M. Schmidts, A. Shalata, M. Mahroum, J.K. Talbeya, R.W. Taylor, D. Vazquez, A.
Vetro, H.R. Waterham, M. Zaman, T.A. Schrader, W.K. Chung, R. Guerrini, J.R. Lupski,
J. Gleeson, M. Suri, Y. Jamshidi, K.P. Bhatia, B. Vona, M. Schrader, M. Severino,
M. Guille, E.W. Tate, G.K. Varshney, H. Houlden, R. Maroofian, Brain (2023).
date_created: 2023-11-16T12:36:51Z
date_published: 2023-11-10T00:00:00Z
date_updated: 2023-11-20T10:17:32Z
day: '10'
department:
- _id: GradSch
doi: 10.1093/brain/awad380
extern: '1'
keyword:
- Neurology (clinical)
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/brain/awad380
month: '11'
oa: 1
oa_version: Submitted Version
publication: Brain
publication_identifier:
eissn:
- 1460-2156
issn:
- 0006-8950
publication_status: epub_ahead
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive
and complex movement disorders
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14542'
abstract:
- lang: eng
text: "It is a remarkable property of BCS theory that the ratio of the energy gap
at zero temperature Ξ\r\n and the critical temperature Tc is (approximately) given
by a universal constant, independent of the microscopic details of the fermionic
interaction. This universality has rigorously been proven quite recently in three
spatial dimensions and three different limiting regimes: weak coupling, low density
and high density. The goal of this short note is to extend the universal behavior
to lower dimensions d=1,2 and give an exemplary proof in the weak coupling limit."
acknowledgement: We thank Robert Seiringer for comments on the paper. J. H. gratefully
acknowledges partial financial support by the ERC Advanced Grant “RMTBeyond”No.
101020331.This research was funded in part by the Austrian Science Fund (FWF) grantnumber
I6427.
article_number: '2360005 '
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Sven Joscha
full_name: Henheik, Sven Joscha
id: 31d731d7-d235-11ea-ad11-b50331c8d7fb
last_name: Henheik
orcid: 0000-0003-1106-327X
- first_name: Asbjørn Bækgaard
full_name: Lauritsen, Asbjørn Bækgaard
id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1
last_name: Lauritsen
orcid: 0000-0003-4476-2288
- first_name: Barbara
full_name: Roos, Barbara
id: 5DA90512-D80F-11E9-8994-2E2EE6697425
last_name: Roos
orcid: 0000-0002-9071-5880
citation:
ama: Henheik SJ, Lauritsen AB, Roos B. Universality in low-dimensional BCS theory.
Reviews in Mathematical Physics. 2023. doi:10.1142/s0129055x2360005x
apa: Henheik, S. J., Lauritsen, A. B., & Roos, B. (2023). Universality in low-dimensional
BCS theory. Reviews in Mathematical Physics. World Scientific Publishing.
https://doi.org/10.1142/s0129055x2360005x
chicago: Henheik, Sven Joscha, Asbjørn Bækgaard Lauritsen, and Barbara Roos. “Universality
in Low-Dimensional BCS Theory.” Reviews in Mathematical Physics. World
Scientific Publishing, 2023. https://doi.org/10.1142/s0129055x2360005x.
ieee: S. J. Henheik, A. B. Lauritsen, and B. Roos, “Universality in low-dimensional
BCS theory,” Reviews in Mathematical Physics. World Scientific Publishing,
2023.
ista: Henheik SJ, Lauritsen AB, Roos B. 2023. Universality in low-dimensional BCS
theory. Reviews in Mathematical Physics., 2360005.
mla: Henheik, Sven Joscha, et al. “Universality in Low-Dimensional BCS Theory.”
Reviews in Mathematical Physics, 2360005, World Scientific Publishing,
2023, doi:10.1142/s0129055x2360005x.
short: S.J. Henheik, A.B. Lauritsen, B. Roos, Reviews in Mathematical Physics (2023).
date_created: 2023-11-15T23:48:14Z
date_published: 2023-10-31T00:00:00Z
date_updated: 2023-11-20T10:04:38Z
day: '31'
department:
- _id: GradSch
- _id: LaEr
- _id: RoSe
doi: 10.1142/s0129055x2360005x
ec_funded: 1
external_id:
arxiv:
- '2301.05621'
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1142/S0129055X2360005X
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 62796744-2b32-11ec-9570-940b20777f1d
call_identifier: H2020
grant_number: '101020331'
name: Random matrices beyond Wigner-Dyson-Mehta
- _id: bda63fe5-d553-11ed-ba76-a16e3d2f256b
grant_number: I06427
name: Mathematical Challenges in BCS Theory of Superconductivity
publication: Reviews in Mathematical Physics
publication_identifier:
eissn:
- 1793-6659
issn:
- 0129-055X
publication_status: epub_ahead
publisher: World Scientific Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Universality in low-dimensional BCS theory
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14553'
abstract:
- lang: eng
text: Quantum state tomography is an essential component of modern quantum technology.
In application to continuous-variable harmonic-oscillator systems, such as the
electromagnetic field, existing tomography methods typically reconstruct the state
in discrete bases, and are hence limited to states with relatively low amplitudes
and energies. Here, we overcome this limitation by utilizing a feed-forward neural
network to obtain the density matrix directly in the continuous position basis.
An important benefit of our approach is the ability to choose specific regions
in the phase space for detailed reconstruction. This results in a relatively slow
scaling of the amount of resources required for the reconstruction with the state
amplitude, and hence allows us to dramatically increase the range of amplitudes
accessible with our method.
article_number: '042430'
article_processing_charge: No
article_type: original
author:
- first_name: Ekaterina
full_name: Fedotova, Ekaterina
id: c1bea5e1-878e-11ee-9dff-d7404e4422ab
last_name: Fedotova
orcid: 0000-0001-7242-015X
- first_name: Nikolai
full_name: Kuznetsov, Nikolai
last_name: Kuznetsov
- first_name: Egor
full_name: Tiunov, Egor
last_name: Tiunov
- first_name: A. E.
full_name: Ulanov, A. E.
last_name: Ulanov
- first_name: A. I.
full_name: Lvovsky, A. I.
last_name: Lvovsky
citation:
ama: Fedotova E, Kuznetsov N, Tiunov E, Ulanov AE, Lvovsky AI. Continuous-variable
quantum tomography of high-amplitude states. Physical Review A. 2023;108(4).
doi:10.1103/PhysRevA.108.042430
apa: Fedotova, E., Kuznetsov, N., Tiunov, E., Ulanov, A. E., & Lvovsky, A. I.
(2023). Continuous-variable quantum tomography of high-amplitude states. Physical
Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.108.042430
chicago: Fedotova, Ekaterina, Nikolai Kuznetsov, Egor Tiunov, A. E. Ulanov, and
A. I. Lvovsky. “Continuous-Variable Quantum Tomography of High-Amplitude States.”
Physical Review A. American Physical Society, 2023. https://doi.org/10.1103/PhysRevA.108.042430.
ieee: E. Fedotova, N. Kuznetsov, E. Tiunov, A. E. Ulanov, and A. I. Lvovsky, “Continuous-variable
quantum tomography of high-amplitude states,” Physical Review A, vol. 108,
no. 4. American Physical Society, 2023.
ista: Fedotova E, Kuznetsov N, Tiunov E, Ulanov AE, Lvovsky AI. 2023. Continuous-variable
quantum tomography of high-amplitude states. Physical Review A. 108(4), 042430.
mla: Fedotova, Ekaterina, et al. “Continuous-Variable Quantum Tomography of High-Amplitude
States.” Physical Review A, vol. 108, no. 4, 042430, American Physical
Society, 2023, doi:10.1103/PhysRevA.108.042430.
short: E. Fedotova, N. Kuznetsov, E. Tiunov, A.E. Ulanov, A.I. Lvovsky, Physical
Review A 108 (2023).
date_created: 2023-11-19T23:00:54Z
date_published: 2023-10-30T00:00:00Z
date_updated: 2023-11-20T10:26:51Z
day: '30'
department:
- _id: JoFi
doi: 10.1103/PhysRevA.108.042430
external_id:
arxiv:
- '2212.07406'
intvolume: ' 108'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2212.07406
month: '10'
oa: 1
oa_version: Preprint
publication: Physical Review A
publication_identifier:
eissn:
- 2469-9934
issn:
- 2469-9926
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Continuous-variable quantum tomography of high-amplitude states
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2023'
...
---
_id: '14557'
abstract:
- lang: eng
text: Motivated by a problem posed in [10], we investigate the closure operators
of the category SLatt of join semilattices and its subcategory SLattO of join
semilattices with bottom element. In particular, we show that there are only finitely
many closure operators of both categories, and provide a complete classification.
We use this result to deduce the known fact that epimorphisms of SLatt and SLattO
are surjective. We complement the paper with two different proofs of this result
using either generators or Isbell’s zigzag theorem.
acknowledgement: "The first and second named authors are members of GNSAGA – INdAM.\r\nThe
third named author was supported by the FWF Grant, Project number I4245–N35"
article_processing_charge: No
article_type: original
author:
- first_name: D.
full_name: Dikranjan, D.
last_name: Dikranjan
- first_name: A.
full_name: Giordano Bruno, A.
last_name: Giordano Bruno
- first_name: Nicolò
full_name: Zava, Nicolò
id: c8b3499c-7a77-11eb-b046-aa368cbbf2ad
last_name: Zava
orcid: 0000-0001-8686-1888
citation:
ama: Dikranjan D, Giordano Bruno A, Zava N. Epimorphisms and closure operators of
categories of semilattices. Quaestiones Mathematicae. 2023;46(S1):191-221.
doi:10.2989/16073606.2023.2247731
apa: Dikranjan, D., Giordano Bruno, A., & Zava, N. (2023). Epimorphisms and
closure operators of categories of semilattices. Quaestiones Mathematicae.
Taylor & Francis. https://doi.org/10.2989/16073606.2023.2247731
chicago: Dikranjan, D., A. Giordano Bruno, and Nicolò Zava. “Epimorphisms and Closure
Operators of Categories of Semilattices.” Quaestiones Mathematicae. Taylor
& Francis, 2023. https://doi.org/10.2989/16073606.2023.2247731.
ieee: D. Dikranjan, A. Giordano Bruno, and N. Zava, “Epimorphisms and closure operators
of categories of semilattices,” Quaestiones Mathematicae, vol. 46, no.
S1. Taylor & Francis, pp. 191–221, 2023.
ista: Dikranjan D, Giordano Bruno A, Zava N. 2023. Epimorphisms and closure operators
of categories of semilattices. Quaestiones Mathematicae. 46(S1), 191–221.
mla: Dikranjan, D., et al. “Epimorphisms and Closure Operators of Categories of
Semilattices.” Quaestiones Mathematicae, vol. 46, no. S1, Taylor &
Francis, 2023, pp. 191–221, doi:10.2989/16073606.2023.2247731.
short: D. Dikranjan, A. Giordano Bruno, N. Zava, Quaestiones Mathematicae 46 (2023)
191–221.
date_created: 2023-11-19T23:00:55Z
date_published: 2023-11-01T00:00:00Z
date_updated: 2023-11-20T09:24:48Z
day: '01'
department:
- _id: HeEd
doi: 10.2989/16073606.2023.2247731
intvolume: ' 46'
issue: S1
language:
- iso: eng
month: '11'
oa_version: None
page: 191-221
project:
- _id: 26AD5D90-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I04245
name: Algebraic Footprints of Geometric Features in Homology
publication: Quaestiones Mathematicae
publication_identifier:
eissn:
- 1727-933X
issn:
- 1607-3606
publication_status: published
publisher: Taylor & Francis
quality_controlled: '1'
scopus_import: '1'
status: public
title: Epimorphisms and closure operators of categories of semilattices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 46
year: '2023'
...
---
_id: '14552'
abstract:
- lang: eng
text: Interactions between plants and herbivores are central in most ecosystems,
but their strength is highly variable. The amount of variability within a system
is thought to influence most aspects of plant-herbivore biology, from ecological
stability to plant defense evolution. Our understanding of what influences variability,
however, is limited by sparse data. We collected standardized surveys of herbivory
for 503 plant species at 790 sites across 116° of latitude. With these data, we
show that within-population variability in herbivory increases with latitude,
decreases with plant size, and is phylogenetically structured. Differences in
the magnitude of variability are thus central to how plant-herbivore biology varies
across macroscale gradients. We argue that increased focus on interaction variability
will advance understanding of patterns of life on Earth.
acknowledgement: The authors acknowledge funding for central project coordination
from NSF Research Coordination Network grant DEB-2203582; the Ecology, Evolution,
and Behavior Program at Michigan State University; and AgBioResearch at Michigan
State University. Site-specific funding is listed in the supplementary materials.
article_processing_charge: No
article_type: original
author:
- first_name: M. L.
full_name: Robinson, M. L.
last_name: Robinson
- first_name: P. G.
full_name: Hahn, P. G.
last_name: Hahn
- first_name: B. D.
full_name: Inouye, B. D.
last_name: Inouye
- first_name: N.
full_name: Underwood, N.
last_name: Underwood
- first_name: S. R.
full_name: Whitehead, S. R.
last_name: Whitehead
- first_name: K. C.
full_name: Abbott, K. C.
last_name: Abbott
- first_name: E. M.
full_name: Bruna, E. M.
last_name: Bruna
- first_name: N. I.
full_name: Cacho, N. I.
last_name: Cacho
- first_name: L. A.
full_name: Dyer, L. A.
last_name: Dyer
- first_name: L.
full_name: Abdala-Roberts, L.
last_name: Abdala-Roberts
- first_name: W. J.
full_name: Allen, W. J.
last_name: Allen
- first_name: J. F.
full_name: Andrade, J. F.
last_name: Andrade
- first_name: D. F.
full_name: Angulo, D. F.
last_name: Angulo
- first_name: D.
full_name: Anjos, D.
last_name: Anjos
- first_name: D. N.
full_name: Anstett, D. N.
last_name: Anstett
- first_name: R.
full_name: Bagchi, R.
last_name: Bagchi
- first_name: S.
full_name: Bagchi, S.
last_name: Bagchi
- first_name: M.
full_name: Barbosa, M.
last_name: Barbosa
- first_name: S.
full_name: Barrett, S.
last_name: Barrett
- first_name: Carina
full_name: Baskett, Carina
id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87
last_name: Baskett
orcid: 0000-0002-7354-8574
- first_name: E.
full_name: Ben-Simchon, E.
last_name: Ben-Simchon
- first_name: K. J.
full_name: Bloodworth, K. J.
last_name: Bloodworth
- first_name: J. L.
full_name: Bronstein, J. L.
last_name: Bronstein
- first_name: Y. M.
full_name: Buckley, Y. M.
last_name: Buckley
- first_name: K. T.
full_name: Burghardt, K. T.
last_name: Burghardt
- first_name: C.
full_name: Bustos-Segura, C.
last_name: Bustos-Segura
- first_name: E. S.
full_name: Calixto, E. S.
last_name: Calixto
- first_name: R. L.
full_name: Carvalho, R. L.
last_name: Carvalho
- first_name: B.
full_name: Castagneyrol, B.
last_name: Castagneyrol
- first_name: M. C.
full_name: Chiuffo, M. C.
last_name: Chiuffo
- first_name: D.
full_name: Cinoğlu, D.
last_name: Cinoğlu
- first_name: E.
full_name: Cinto Mejía, E.
last_name: Cinto Mejía
- first_name: M. C.
full_name: Cock, M. C.
last_name: Cock
- first_name: R.
full_name: Cogni, R.
last_name: Cogni
- first_name: O. L.
full_name: Cope, O. L.
last_name: Cope
- first_name: T.
full_name: Cornelissen, T.
last_name: Cornelissen
- first_name: D. R.
full_name: Cortez, D. R.
last_name: Cortez
- first_name: D. W.
full_name: Crowder, D. W.
last_name: Crowder
- first_name: C.
full_name: Dallstream, C.
last_name: Dallstream
- first_name: W.
full_name: Dáttilo, W.
last_name: Dáttilo
- first_name: J. K.
full_name: Davis, J. K.
last_name: Davis
- first_name: R. D.
full_name: Dimarco, R. D.
last_name: Dimarco
- first_name: H. E.
full_name: Dole, H. E.
last_name: Dole
- first_name: I. N.
full_name: Egbon, I. N.
last_name: Egbon
- first_name: M.
full_name: Eisenring, M.
last_name: Eisenring
- first_name: A.
full_name: Ejomah, A.
last_name: Ejomah
- first_name: B. D.
full_name: Elderd, B. D.
last_name: Elderd
- first_name: M. J.
full_name: Endara, M. J.
last_name: Endara
- first_name: M. D.
full_name: Eubanks, M. D.
last_name: Eubanks
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full_name: Everingham, S. E.
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citation:
ama: Robinson ML, Hahn PG, Inouye BD, et al. Plant size, latitude, and phylogeny
explain within-population variability in herbivory. Science. 2023;382(6671):679-683.
doi:10.1126/science.adh8830
apa: Robinson, M. L., Hahn, P. G., Inouye, B. D., Underwood, N., Whitehead, S. R.,
Abbott, K. C., … Wetzel, W. C. (2023). Plant size, latitude, and phylogeny explain
within-population variability in herbivory. Science. AAAS. https://doi.org/10.1126/science.adh8830
chicago: Robinson, M. L., P. G. Hahn, B. D. Inouye, N. Underwood, S. R. Whitehead,
K. C. Abbott, E. M. Bruna, et al. “Plant Size, Latitude, and Phylogeny Explain
within-Population Variability in Herbivory.” Science. AAAS, 2023. https://doi.org/10.1126/science.adh8830.
ieee: M. L. Robinson et al., “Plant size, latitude, and phylogeny explain
within-population variability in herbivory,” Science, vol. 382, no. 6671.
AAAS, pp. 679–683, 2023.
ista: Robinson ML et al. 2023. Plant size, latitude, and phylogeny explain within-population
variability in herbivory. Science. 382(6671), 679–683.
mla: Robinson, M. L., et al. “Plant Size, Latitude, and Phylogeny Explain within-Population
Variability in Herbivory.” Science, vol. 382, no. 6671, AAAS, 2023, pp.
679–83, doi:10.1126/science.adh8830.
short: M.L. Robinson, P.G. Hahn, B.D. Inouye, N. Underwood, S.R. Whitehead, K.C.
Abbott, E.M. Bruna, N.I. Cacho, L.A. Dyer, L. Abdala-Roberts, W.J. Allen, J.F.
Andrade, D.F. Angulo, D. Anjos, D.N. Anstett, R. Bagchi, S. Bagchi, M. Barbosa,
S. Barrett, C. Baskett, E. Ben-Simchon, K.J. Bloodworth, J.L. Bronstein, Y.M.
Buckley, K.T. Burghardt, C. Bustos-Segura, E.S. Calixto, R.L. Carvalho, B. Castagneyrol,
M.C. Chiuffo, D. Cinoğlu, E. Cinto Mejía, M.C. Cock, R. Cogni, O.L. Cope, T. Cornelissen,
D.R. Cortez, D.W. Crowder, C. Dallstream, W. Dáttilo, J.K. Davis, R.D. Dimarco,
H.E. Dole, I.N. Egbon, M. Eisenring, A. Ejomah, B.D. Elderd, M.J. Endara, M.D.
Eubanks, S.E. Everingham, K.N. Farah, R.P. Farias, A.P. Fernandes, G.W. Fernandes,
M. Ferrante, A. Finn, G.A. Florjancic, M.L. Forister, Q.N. Fox, E. Frago, F.M.
França, A.S. Getman-Pickering, Z. Getman-Pickering, E. Gianoli, B. Gooden, M.M.
Gossner, K.A. Greig, S. Gripenberg, R. Groenteman, P. Grof-Tisza, N. Haack, L.
Hahn, S.M. Haq, A.M. Helms, J. Hennecke, S.L. Hermann, L.M. Holeski, S. Holm,
M.C. Hutchinson, E.E. Jackson, S. Kagiya, A. Kalske, M. Kalwajtys, R. Karban,
R. Kariyat, T. Keasar, M.F. Kersch-Becker, H.M. Kharouba, T.N. Kim, D.M. Kimuyu,
J. Kluse, S.E. Koerner, K.J. Komatsu, S. Krishnan, M. Laihonen, L. Lamelas-López,
M.C. Lascaleia, N. Lecomte, C.R. Lehn, X. Li, R.L. Lindroth, E.F. Lopresti, M.
Losada, A.M. Louthan, V.J. Luizzi, S.C. Lynch, J.S. Lynn, N.J. Lyon, L.F. Maia,
R.A. Maia, T.L. Mannall, B.S. Martin, T.J. Massad, A.C. Mccall, K. Mcgurrin, A.C.
Merwin, Z. Mijango-Ramos, C.H. Mills, A.T. Moles, C.M. Moore, X. Moreira, C.R.
Morrison, M.C. Moshobane, A. Muola, R. Nakadai, K. Nakajima, S. Novais, C.O. Ogbebor,
H. Ohsaki, V.S. Pan, N.A. Pardikes, M. Pareja, N. Parthasarathy, R.R. Pawar, Q.
Paynter, I.S. Pearse, R.M. Penczykowski, A.A. Pepi, C.C. Pereira, S.S. Phartyal,
F.I. Piper, K. Poveda, E.G. Pringle, J. Puy, T. Quijano, C. Quintero, S. Rasmann,
C. Rosche, L.Y. Rosenheim, J.A. Rosenheim, J.B. Runyon, A. Sadeh, Y. Sakata, D.M.
Salcido, C. Salgado-Luarte, B.A. Santos, Y. Sapir, Y. Sasal, Y. Sato, M. Sawant,
H. Schroeder, I. Schumann, M. Segoli, H. Segre, O. Shelef, N. Shinohara, R.P.
Singh, D.S. Smith, M. Sobral, G.C. Stotz, A.J.M. Tack, M. Tayal, J.F. Tooker,
D. Torrico-Bazoberry, K. Tougeron, A.M. Trowbridge, S. Utsumi, O. Uyi, J.L. Vaca-Uribe,
A. Valtonen, L.J.A. Van Dijk, V. Vandvik, J. Villellas, L.P. Waller, M.G. Weber,
A. Yamawo, S. Yim, P.L. Zarnetske, L.N. Zehr, Z. Zhong, W.C. Wetzel, Science 382
(2023) 679–683.
date_created: 2023-11-19T23:00:54Z
date_published: 2023-11-09T00:00:00Z
date_updated: 2023-11-20T11:17:34Z
day: '09'
department:
- _id: NiBa
doi: 10.1126/science.adh8830
external_id:
pmid:
- '37943897'
intvolume: ' 382'
issue: '6671'
language:
- iso: eng
month: '11'
oa_version: None
page: 679-683
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
publication_status: published
publisher: AAAS
quality_controlled: '1'
related_material:
record:
- id: '14579'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Plant size, latitude, and phylogeny explain within-population variability in
herbivory
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 382
year: '2023'
...
---
_id: '14551'
abstract:
- lang: eng
text: Methylation of CG dinucleotides (mCGs), which regulates eukaryotic genome
functions, is epigenetically propagated by Dnmt1/MET1 methyltransferases. How
mCG is established and transmitted across generations despite imperfect enzyme
fidelity is unclear. Whether mCG variation in natural populations is governed
by genetic or epigenetic inheritance also remains mysterious. Here, we show that
MET1 de novo activity, which is enhanced by existing proximate methylation, seeds
and stabilizes mCG in Arabidopsis thaliana genes. MET1 activity is restricted
by active demethylation and suppressed by histone variant H2A.Z, producing localized
mCG patterns. Based on these observations, we develop a stochastic mathematical
model that precisely recapitulates mCG inheritance dynamics and predicts intragenic
mCG patterns and their population-scale variation given only CG site spacing.
Our results demonstrate that intragenic mCG establishment, inheritance, and variance
constitute a unified epigenetic process, revealing that intragenic mCG undergoes
large, millennia-long epigenetic fluctuations and can therefore mediate evolution
on this timescale.
acknowledgement: We would like to thank Xiaoqi Feng, Ander Movilla Miangolarra, and
Suzanne de Bruijn for discussions. This work was supported by BBSRC Institute Strategic
Programme GEN (BB/P013511/1) to M.H. and D.Z. and by a European Research Council
grant MaintainMeth (725746) to D.Z.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Amy
full_name: Briffa, Amy
last_name: Briffa
- first_name: Elizabeth
full_name: Hollwey, Elizabeth
id: b8c4f54b-e484-11eb-8fdc-a54df64ef6dd
last_name: Hollwey
- first_name: Zaigham
full_name: Shahzad, Zaigham
last_name: Shahzad
- first_name: Jonathan D.
full_name: Moore, Jonathan D.
last_name: Moore
- first_name: David B.
full_name: Lyons, David B.
last_name: Lyons
- first_name: Martin
full_name: Howard, Martin
last_name: Howard
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Briffa A, Hollwey E, Shahzad Z, et al. Millennia-long epigenetic fluctuations
generate intragenic DNA methylation variance in Arabidopsis populations. Cell
Systems. 2023;14(11):953-967. doi:10.1016/j.cels.2023.10.007
apa: Briffa, A., Hollwey, E., Shahzad, Z., Moore, J. D., Lyons, D. B., Howard, M.,
& Zilberman, D. (2023). Millennia-long epigenetic fluctuations generate intragenic
DNA methylation variance in Arabidopsis populations. Cell Systems. Elsevier.
https://doi.org/10.1016/j.cels.2023.10.007
chicago: Briffa, Amy, Elizabeth Hollwey, Zaigham Shahzad, Jonathan D. Moore, David
B. Lyons, Martin Howard, and Daniel Zilberman. “Millennia-Long Epigenetic Fluctuations
Generate Intragenic DNA Methylation Variance in Arabidopsis Populations.” Cell
Systems. Elsevier, 2023. https://doi.org/10.1016/j.cels.2023.10.007.
ieee: A. Briffa et al., “Millennia-long epigenetic fluctuations generate
intragenic DNA methylation variance in Arabidopsis populations,” Cell Systems,
vol. 14, no. 11. Elsevier, pp. 953–967, 2023.
ista: Briffa A, Hollwey E, Shahzad Z, Moore JD, Lyons DB, Howard M, Zilberman D.
2023. Millennia-long epigenetic fluctuations generate intragenic DNA methylation
variance in Arabidopsis populations. Cell Systems. 14(11), 953–967.
mla: Briffa, Amy, et al. “Millennia-Long Epigenetic Fluctuations Generate Intragenic
DNA Methylation Variance in Arabidopsis Populations.” Cell Systems, vol.
14, no. 11, Elsevier, 2023, pp. 953–67, doi:10.1016/j.cels.2023.10.007.
short: A. Briffa, E. Hollwey, Z. Shahzad, J.D. Moore, D.B. Lyons, M. Howard, D.
Zilberman, Cell Systems 14 (2023) 953–967.
date_created: 2023-11-19T23:00:54Z
date_published: 2023-11-15T00:00:00Z
date_updated: 2023-11-20T11:24:34Z
day: '15'
ddc:
- '570'
department:
- _id: DaZi
doi: 10.1016/j.cels.2023.10.007
ec_funded: 1
external_id:
pmid:
- '37944515'
file:
- access_level: open_access
checksum: 101fdac59e6f1102d68ef91f2b5bd51a
content_type: application/pdf
creator: dernst
date_created: 2023-11-20T11:22:52Z
date_updated: 2023-11-20T11:22:52Z
file_id: '14580'
file_name: 2023_CellSystems_Briffa.pdf
file_size: 5587897
relation: main_file
success: 1
file_date_updated: 2023-11-20T11:22:52Z
has_accepted_license: '1'
intvolume: ' 14'
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 953-967
pmid: 1
project:
- _id: 62935a00-2b32-11ec-9570-eff30fa39068
call_identifier: H2020
grant_number: '725746'
name: Quantitative analysis of DNA methylation maintenance with chromatin
publication: Cell Systems
publication_identifier:
eissn:
- 2405-4720
issn:
- 2405-4712
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Millennia-long epigenetic fluctuations generate intragenic DNA methylation
variance in Arabidopsis populations
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2023'
...
---
_id: '14579'
abstract:
- lang: eng
text: "This is associated with our paper \"Plant size, latitude, and phylogeny explain
within-population variability in herbivory\" published in Science.\r\n"
article_processing_charge: No
author:
- first_name: William
full_name: Wetzel, William
last_name: Wetzel
citation:
ama: 'Wetzel W. HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0. 2023. doi:10.5281/ZENODO.8133117'
apa: 'Wetzel, W. (2023). HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0. Zenodo.
https://doi.org/10.5281/ZENODO.8133117'
chicago: 'Wetzel, William. “HerbVar-Network/HV-Large-Patterns-MS-Public: V1.0.0.”
Zenodo, 2023. https://doi.org/10.5281/ZENODO.8133117.'
ieee: 'W. Wetzel, “HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0.” Zenodo,
2023.'
ista: 'Wetzel W. 2023. HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0, Zenodo,
10.5281/ZENODO.8133117.'
mla: 'Wetzel, William. HerbVar-Network/HV-Large-Patterns-MS-Public: V1.0.0.
Zenodo, 2023, doi:10.5281/ZENODO.8133117.'
short: W. Wetzel, (2023).
date_created: 2023-11-20T11:07:45Z
date_published: 2023-07-11T00:00:00Z
date_updated: 2023-11-20T11:17:33Z
day: '11'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.5281/ZENODO.8133117
main_file_link:
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month: '07'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
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relation: used_in_publication
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status: public
title: 'HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0'
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12334'
abstract:
- lang: eng
text: Regulation of the Arp2/3 complex is required for productive nucleation of
branched actin networks. An emerging aspect of regulation is the incorporation
of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit
isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity
and branch junction stability. We have combined reverse genetics and cellular
structural biology to describe how ArpC5 and ArpC5L differentially affect cell
migration. Both define the structural stability of ArpC1 in branch junctions and,
in turn, by determining protrusion characteristics, affect protein dynamics and
actin network ultrastructure. ArpC5 isoforms also affect the positioning of members
of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament
elongators, which mediate ArpC5 isoform–specific effects on the actin assembly
level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling
pathway enhancing cell migration.
acknowledged_ssus:
- _id: ScienComp
- _id: LifeSc
- _id: Bio
- _id: EM-Fac
acknowledgement: "We would like to thank K. von Peinen and B. Denker (Helmholtz Centre
for Infection Research, Braunschweig, Germany) for experimental and technical assistance,
respectively.\r\nThis research was supported by the Scientific Service Units (SSUs)
of ISTA through resources provided by Scientific Computing (SciComp), the Life Science
Facility (LSF), the Imaging and Optics facility (IOF), and the Electron Microscopy
Facility (EMF). We acknowledge support from ISTA and from the Austrian Science Fund
(FWF) (P33367) to F.K.M.S., from the Research Training Group GRK2223 and the Helmholtz
Society to K.R,. and from the Deutsche Forschungsgemeinschaft (DFG) to J.F. and
K.R."
article_number: add6495
article_processing_charge: No
article_type: original
author:
- first_name: Florian
full_name: Fäßler, Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- first_name: Manjunath
full_name: Javoor, Manjunath
id: 305ab18b-dc7d-11ea-9b2f-b58195228ea2
last_name: Javoor
- first_name: Julia
full_name: Datler, Julia
id: 3B12E2E6-F248-11E8-B48F-1D18A9856A87
last_name: Datler
orcid: 0000-0002-3616-8580
- first_name: Hermann
full_name: Döring, Hermann
last_name: Döring
- first_name: Florian
full_name: Hofer, Florian
id: b9d234ba-9e33-11ed-95b6-cd561df280e6
last_name: Hofer
- first_name: Georgi A
full_name: Dimchev, Georgi A
id: 38C393BE-F248-11E8-B48F-1D18A9856A87
last_name: Dimchev
orcid: 0000-0001-8370-6161
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
- first_name: Jan
full_name: Faix, Jan
last_name: Faix
- first_name: Klemens
full_name: Rottner, Klemens
last_name: Rottner
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Fäßler F, Javoor M, Datler J, et al. ArpC5 isoforms regulate Arp2/3 complex–dependent
protrusion through differential Ena/VASP positioning. Science Advances.
2023;9(3). doi:10.1126/sciadv.add6495
apa: Fäßler, F., Javoor, M., Datler, J., Döring, H., Hofer, F., Dimchev, G. A.,
… Schur, F. K. (2023). ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion
through differential Ena/VASP positioning. Science Advances. American Association
for the Advancement of Science. https://doi.org/10.1126/sciadv.add6495
chicago: Fäßler, Florian, Manjunath Javoor, Julia Datler, Hermann Döring, Florian
Hofer, Georgi A Dimchev, Victor-Valentin Hodirnau, Jan Faix, Klemens Rottner,
and Florian KM Schur. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion
through Differential Ena/VASP Positioning.” Science Advances. American
Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciadv.add6495.
ieee: F. Fäßler et al., “ArpC5 isoforms regulate Arp2/3 complex–dependent
protrusion through differential Ena/VASP positioning,” Science Advances,
vol. 9, no. 3. American Association for the Advancement of Science, 2023.
ista: Fäßler F, Javoor M, Datler J, Döring H, Hofer F, Dimchev GA, Hodirnau V-V,
Faix J, Rottner K, Schur FK. 2023. ArpC5 isoforms regulate Arp2/3 complex–dependent
protrusion through differential Ena/VASP positioning. Science Advances. 9(3),
add6495.
mla: Fäßler, Florian, et al. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion
through Differential Ena/VASP Positioning.” Science Advances, vol. 9, no.
3, add6495, American Association for the Advancement of Science, 2023, doi:10.1126/sciadv.add6495.
short: F. Fäßler, M. Javoor, J. Datler, H. Döring, F. Hofer, G.A. Dimchev, V.-V.
Hodirnau, J. Faix, K. Rottner, F.K. Schur, Science Advances 9 (2023).
date_created: 2023-01-23T07:26:42Z
date_published: 2023-01-20T00:00:00Z
date_updated: 2023-11-21T08:05:35Z
day: '20'
ddc:
- '570'
department:
- _id: FlSc
- _id: EM-Fac
doi: 10.1126/sciadv.add6495
external_id:
isi:
- '000964550100015'
file:
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checksum: ce81a6d0b84170e5e8c62f6acfa15d9e
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success: 1
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intvolume: ' 9'
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keyword:
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language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
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grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
publication: Science Advances
publication_identifier:
issn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
record:
- id: '14562'
relation: research_data
status: public
scopus_import: '1'
status: public
title: ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential
Ena/VASP positioning
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2023'
...
---
_id: '14562'
abstract:
- lang: eng
text: "Regulation of the Arp2/3 complex is required for productive nucleation of
branched actin networks. An emerging aspect of regulation is the incorporation
of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit
isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity
and branch junction stability. We have combined reverse genetics and cellular
structural biology to describe how ArpC5 and ArpC5L differentially affect cell
migration. Both define the structural stability of ArpC1 in branch junctions and,
in turn, by determining protrusion characteristics, affect protein dynamics and
actin network ultrastructure. ArpC5 isoforms also affect the positioning of members
of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament
elongators, which mediate ArpC5 isoform–specific effects on the actin assembly
level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling
pathway enhancing cell migration.\r\n"
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
- _id: ScienComp
- _id: EM-Fac
acknowledgement: "We would like to thank K. von Peinen and B. Denker (Helmholtz Centre
for Infection Research, Braunschweig, Germany) for experimental and technical assistance,
respectively.\r\nFunding: This research was supported by the Scientific Service
Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp),
the Life Science Facility (LSF), the Imaging and Optics facility (IOF), and the
Electron Microscopy Facility (EMF). We acknowledge support from ISTA and from the
Austrian Science Fund (FWF) (P33367) to F.K.M.S., from the Research Training Group
GRK2223 and the Helmholtz Society to K.R,. and from the Deutsche Forschungsgemeinschaft
(DFG) to J.F. and K.R."
article_processing_charge: No
author:
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Schur FK. Research data of the publication “ArpC5 isoforms regulate Arp2/3
complex-dependent protrusion through differential Ena/VASP positioning.” 2023.
doi:10.15479/AT:ISTA:14562
apa: Schur, F. K. (2023). Research data of the publication “ArpC5 isoforms regulate
Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.”
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14562
chicago: Schur, Florian KM. “Research Data of the Publication ‘ArpC5 Isoforms Regulate
Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.’”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14562.
ieee: F. K. Schur, “Research data of the publication ‘ArpC5 isoforms regulate Arp2/3
complex-dependent protrusion through differential Ena/VASP positioning.’” Institute
of Science and Technology Austria, 2023.
ista: Schur FK. 2023. Research data of the publication ‘ArpC5 isoforms regulate
Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning’,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:14562.
mla: Schur, Florian KM. Research Data of the Publication “ArpC5 Isoforms Regulate
Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.”
Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:14562.
short: F.K. Schur, (2023).
contributor:
- contributor_type: researcher
first_name: Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- contributor_type: researcher
first_name: Manjunath
id: 305ab18b-dc7d-11ea-9b2f-b58195228ea2
last_name: Javoor
- contributor_type: researcher
first_name: Julia
id: 3B12E2E6-F248-11E8-B48F-1D18A9856A87
last_name: Datler
orcid: 0000-0002-3616-8580
- contributor_type: researcher
first_name: Hermann
last_name: Döring
- contributor_type: researcher
first_name: Florian
id: b9d234ba-9e33-11ed-95b6-cd561df280e6
last_name: Hofer
- contributor_type: researcher
first_name: Georgi A
id: 38C393BE-F248-11E8-B48F-1D18A9856A87
last_name: Dimchev
orcid: 0000-0001-8370-6161
- contributor_type: researcher
first_name: Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
- contributor_type: researcher
first_name: Jan
last_name: Faix
- contributor_type: researcher
first_name: Klemens
last_name: Rottner
- contributor_type: researcher
first_name: Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
date_created: 2023-11-20T09:22:33Z
date_published: 2023-11-21T00:00:00Z
date_updated: 2023-11-21T08:05:34Z
day: '21'
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month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A
grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
publisher: Institute of Science and Technology Austria
related_material:
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relation: used_in_publication
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status: public
title: Research data of the publication "ArpC5 isoforms regulate Arp2/3 complex-dependent
protrusion through differential Ena/VASP positioning"
tmp:
image: /images/cc_by_sa.png
legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC
BY-SA 4.0)
short: CC BY-SA (4.0)
type: research_data
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...
---
_id: '14502'
abstract:
- lang: eng
text: A precise quantitative description of the ultrastructural characteristics
underlying biological mechanisms is often key to their understanding. This is
particularly true for dynamic extra- and intracellular filamentous assemblies,
playing a role in cell motility, cell integrity, cytokinesis, tissue formation
and maintenance. For example, genetic manipulation or modulation of actin regulatory
proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural
architecture of actin filament-rich cell peripheral structures, such as lamellipodia
or filopodia. However, the observed ultrastructural effects often remain subtle
and require sufficiently large datasets for appropriate quantitative analysis.
The acquisition of such large datasets has been enabled by recent advances in
high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates
the development of complementary approaches to maximize the extraction of relevant
biological information. We have developed a computational toolbox for the semi-automatic
quantification of segmented and vectorized fila- mentous networks from pre-processed
cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple
experimental conditions. GUI-based components simplify the processing of data
and allow users to obtain a large number of ultrastructural parameters describing
filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing
cryo-ET data of untreated and chemically perturbed branched actin filament networks
and that of parallel actin filament arrays. In principle, the computational toolbox
presented here is applicable for data analysis comprising any type of filaments
in regular (i.e. parallel) or random arrangement. We show that it can ease the
identification of key differences between experimental groups and facilitate the
in-depth analysis of ultrastructural data in a time-efficient manner.
author:
- first_name: Georgi A
full_name: Dimchev, Georgi A
id: 38C393BE-F248-11E8-B48F-1D18A9856A87
last_name: Dimchev
orcid: 0000-0001-8370-6161
- first_name: Behnam
full_name: Amiri, Behnam
last_name: Amiri
- first_name: Florian
full_name: Fäßler, Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- first_name: Martin
full_name: Falcke, Martin
last_name: Falcke
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for
ultrastructural quantitative analysis of filament networks in cryo-ET data. 2023.
doi:10.15479/AT:ISTA:14502
apa: Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., & Schur, F. K. (2023).
Computational toolbox for ultrastructural quantitative analysis of filament networks
in cryo-ET data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14502
chicago: Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian
KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of
Filament Networks in Cryo-ET Data.” Institute of Science and Technology Austria,
2023. https://doi.org/10.15479/AT:ISTA:14502.
ieee: G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational
toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET
data.” Institute of Science and Technology Austria, 2023.
ista: Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2023. Computational toolbox
for ultrastructural quantitative analysis of filament networks in cryo-ET data,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:14502.
mla: Dimchev, Georgi A., et al. Computational Toolbox for Ultrastructural Quantitative
Analysis of Filament Networks in Cryo-ET Data. Institute of Science and Technology
Austria, 2023, doi:10.15479/AT:ISTA:14502.
short: G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, (2023).
date_created: 2023-11-08T19:40:54Z
date_published: 2023-11-21T00:00:00Z
date_updated: 2023-11-21T08:36:02Z
day: '21'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.15479/AT:ISTA:14502
file:
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creator: dernst
date_created: 2023-11-21T08:20:23Z
date_updated: 2023-11-21T08:20:23Z
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file_name: Readme.txt
file_size: 1522
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success: 1
file_date_updated: 2023-11-21T08:20:23Z
has_accepted_license: '1'
keyword:
- cryo-electron tomography
- actin cytoskeleton
- toolbox
license: https://choosealicense.com/licenses/agpl-3.0/
month: '11'
oa: 1
project:
- _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A
grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
publisher: Institute of Science and Technology Austria
related_material:
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relation: used_for_analysis_in
status: public
status: public
title: Computational toolbox for ultrastructural quantitative analysis of filament
networks in cryo-ET data
tmp:
legal_code_url: https://www.gnu.org/licenses/agpl-3.0.html
name: GNU Affero General Public License v3.0
short: 'GNU AGPLv3 '
type: software
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13342'
abstract:
- lang: eng
text: Motile cells moving in multicellular organisms encounter microenvironments
of locally heterogeneous mechanochemical composition. Individual compositional
parameters like chemotactic signals, adhesiveness, and pore sizes are well known
to be sensed by motile cells, providing individual guidance cues for cellular
pathfinding. However, motile cells encounter diverse mechanochemical signals at
the same time, raising the question of how cells respond to locally diverse and
potentially competing signals on their migration routes. Here, we reveal that
motile amoeboid cells require nuclear repositioning, termed nucleokinesis, for
adaptive pathfinding in heterogeneous mechanochemical microenvironments. Using
mammalian immune cells and the amoebaDictyostelium discoideum,
we discover that frequent, rapid and long-distance nucleokinesis is a basic component
of amoeboid pathfinding, enabling cells to reorientate quickly between locally
competing cues. Amoeboid nucleokinesis comprises a two-step cell polarity switch
and is driven by myosin II-forces, sliding the nucleus from a ‘losing’ to the
‘winning’ leading edge to re-adjust the nuclear to the cellular path. Impaired
nucleokinesis distorts fast path adaptions and causes cellular arrest in the microenvironment.
Our findings establish that nucleokinesis is required for amoeboid cell navigation.
Given that motile single-cell amoebae, many immune cells, and some cancer cells
utilize an amoeboid migration strategy, these results suggest that amoeboid nucleokinesis
underlies cellular navigation during unicellular biology, immunity, and disease.
acknowledgement: We thank Christoph Mayr and Bingzhi Wang for initial experiments
on amoeboid nucleokinesis, Ana-Maria Lennon-Duménil and Aline Yatim for bone marrow
from MyoIIA-Flox*CD11c-Cre mice, Michael Sixt and Aglaja Kopf for EMTB-mCherry,
EB3-mCherry, Lifeact-GFP, Lfc knockout, and Myh9-GFP expressing HoxB8 cells, Malte
Benjamin Braun, Mauricio Ruiz, and Madeleine T. Schmitt for critical reading of
the manuscript, and the Core Facility Bioimaging, the Core Facility Flow Cytometry,
and the Animal Core Facility of the Biomedical Center (BMC) for excellent support.
This study was supported by the Peter Hans Hofschneider Professorship of the foundation
“Stiftung Experimentelle Biomedizin” (to JR), the LMU Institutional Strategy LMU-Excellent
within the framework of the German Excellence Initiative (to JR), and the Deutsche
Forschungsgemeinschaft (DFG; German Research Foundation; SFB914 project A12, to
JR), and the CZI grant DAF2020-225401 (https://doi.org/10.37921/120055ratwvi) from
the Chan Zuckerberg Initiative DAF (to RH; an advised fund of Silicon Valley Community
Foundation (funder https://doi.org/10.13039/100014989)). Open Access funding enabled
and organized by Projekt DEAL.
article_number: e114557
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Janina
full_name: Kroll, Janina
last_name: Kroll
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Arthur
full_name: Kuznetcov, Arthur
last_name: Kuznetcov
- first_name: Kasia
full_name: Stefanowski, Kasia
last_name: Stefanowski
- first_name: Monika D.
full_name: Hermann, Monika D.
last_name: Hermann
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Lubuna B
full_name: Shafeek, Lubuna B
id: 3CD37A82-F248-11E8-B48F-1D18A9856A87
last_name: Shafeek
orcid: 0000-0001-7180-6050
- first_name: Annette
full_name: Müller-Taubenberger, Annette
last_name: Müller-Taubenberger
- first_name: Jörg
full_name: Renkawitz, Jörg
id: 3F0587C8-F248-11E8-B48F-1D18A9856A87
last_name: Renkawitz
orcid: 0000-0003-2856-3369
citation:
ama: Kroll J, Hauschild R, Kuznetcov A, et al. Adaptive pathfinding by nucleokinesis
during amoeboid migration. EMBO Journal. 2023. doi:10.15252/embj.2023114557
apa: Kroll, J., Hauschild, R., Kuznetcov, A., Stefanowski, K., Hermann, M. D., Merrin,
J., … Renkawitz, J. (2023). Adaptive pathfinding by nucleokinesis during amoeboid
migration. EMBO Journal. Embo Press. https://doi.org/10.15252/embj.2023114557
chicago: Kroll, Janina, Robert Hauschild, Arthur Kuznetcov, Kasia Stefanowski, Monika
D. Hermann, Jack Merrin, Lubuna B Shafeek, Annette Müller-Taubenberger, and Jörg
Renkawitz. “Adaptive Pathfinding by Nucleokinesis during Amoeboid Migration.”
EMBO Journal. Embo Press, 2023. https://doi.org/10.15252/embj.2023114557.
ieee: J. Kroll et al., “Adaptive pathfinding by nucleokinesis during amoeboid
migration,” EMBO Journal. Embo Press, 2023.
ista: Kroll J, Hauschild R, Kuznetcov A, Stefanowski K, Hermann MD, Merrin J, Shafeek
LB, Müller-Taubenberger A, Renkawitz J. 2023. Adaptive pathfinding by nucleokinesis
during amoeboid migration. EMBO Journal., e114557.
mla: Kroll, Janina, et al. “Adaptive Pathfinding by Nucleokinesis during Amoeboid
Migration.” EMBO Journal, e114557, Embo Press, 2023, doi:10.15252/embj.2023114557.
short: J. Kroll, R. Hauschild, A. Kuznetcov, K. Stefanowski, M.D. Hermann, J. Merrin,
L.B. Shafeek, A. Müller-Taubenberger, J. Renkawitz, EMBO Journal (2023).
date_created: 2023-08-01T08:59:06Z
date_published: 2023-11-21T00:00:00Z
date_updated: 2023-11-27T08:47:45Z
day: '21'
ddc:
- '570'
department:
- _id: NanoFab
- _id: Bio
doi: 10.15252/embj.2023114557
external_id:
pmid:
- '37987147'
file:
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checksum: 6261d0041c7e8d284c39712c40079730
content_type: application/pdf
creator: dernst
date_created: 2023-11-27T08:45:56Z
date_updated: 2023-11-27T08:45:56Z
file_id: '14611'
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success: 1
file_date_updated: 2023-11-27T08:45:56Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: EMBO Journal
publication_identifier:
eissn:
- 1460-2075
issn:
- 0261-4189
publication_status: published
publisher: Embo Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Adaptive pathfinding by nucleokinesis during amoeboid migration
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14610'
abstract:
- lang: eng
text: AbstractEndomembrane damage represents a
form of stress that is detrimental for eukaryotic cells1,2.
To cope with this threat, cells possess mechanisms that repair the damage and
restore cellular homeostasis3–7. Endomembrane damage also
results in organelle instability and the mechanisms by which cells stabilize damaged
endomembranes to enable membrane repair remains unknown. Here, by combining in
vitro and in cellulo studies with computational modelling we uncover a biological
function for stress granules whereby these biomolecular condensates form rapidly
at endomembrane damage sites and act as a plug that stabilizes the ruptured membrane.
Functionally, we demonstrate that stress granule formation and membrane stabilization
enable efficient repair of damaged endolysosomes, through both ESCRT (endosomal
sorting complex required for transport)-dependent and independent mechanisms.
We also show that blocking stress granule formation in human macrophages creates
a permissive environment for Mycobacterium tuberculosis,
a human pathogen that exploits endomembrane damage to survive within the host.
acknowledgement: "We thank the Human Embryonic Stem Cell Unit, Advanced Light Microscopy
and High-throughput Screening facilities at the Crick for their support in various
aspects of the work. We thank the laboratory of P. Anderson for providing the G3BP-DKO
U2OS cells. The authors thank N. Chen for providing the purified glycinin protein;
Z. Zhao for providing the microfluidic chip wafers; and M. Amaral and F. Frey for
helpful discussions and valuable input regarding analysis methods. This work was
supported by the Francis Crick Institute (to M.G.G.), which receives its core funding
from Cancer Research UK (FC001092), the UK Medical Research Council (FC001092) and
the Wellcome Trust (FC001092). This project has received funding from the European
Research Council (ERC) under the European Union’s Horizon 2020 research and innovation
programme (grant agreement no. 772022 to M.G.G.). C.B. has received funding from
the European Respiratory Society and the European Union’s H2020 research and innovation
programme under the Marie Sklodowska-Curie grant agreement no. 713406. A.M. acknowledges
support from Alexander von Humboldt Foundation and C.V.-C. acknowledges funding
by the Royal Society and the European Research Council under the European Union’s
Horizon 2020 Research and Innovation Programme (grant no. 802960 to A.S.). All simulations
were carried out on the high-performance computing cluster at the Institute of Science
and Technology Austria. For the purpose of Open Access, the author has applied a
CC BY public copyright licence to any Author Accepted Manuscript version arising
from this submission.\r\nOpen Access funding provided by The Francis Crick Institute."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Claudio
full_name: Bussi, Claudio
last_name: Bussi
- first_name: Agustín
full_name: Mangiarotti, Agustín
last_name: Mangiarotti
- first_name: Christian Eduardo
full_name: Vanhille-Campos, Christian Eduardo
id: 3adeca52-9313-11ed-b1ac-c170b2505714
last_name: Vanhille-Campos
- first_name: Beren
full_name: Aylan, Beren
last_name: Aylan
- first_name: Enrica
full_name: Pellegrino, Enrica
last_name: Pellegrino
- first_name: Natalia
full_name: Athanasiadi, Natalia
last_name: Athanasiadi
- first_name: Antony
full_name: Fearns, Antony
last_name: Fearns
- first_name: Angela
full_name: Rodgers, Angela
last_name: Rodgers
- first_name: Titus M.
full_name: Franzmann, Titus M.
last_name: Franzmann
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Rumiana
full_name: Dimova, Rumiana
last_name: Dimova
- first_name: Maximiliano G.
full_name: Gutierrez, Maximiliano G.
last_name: Gutierrez
citation:
ama: Bussi C, Mangiarotti A, Vanhille-Campos CE, et al. Stress granules plug and
stabilize damaged endolysosomal membranes. Nature. 2023. doi:10.1038/s41586-023-06726-w
apa: Bussi, C., Mangiarotti, A., Vanhille-Campos, C. E., Aylan, B., Pellegrino,
E., Athanasiadi, N., … Gutierrez, M. G. (2023). Stress granules plug and stabilize
damaged endolysosomal membranes. Nature. Springer Nature. https://doi.org/10.1038/s41586-023-06726-w
chicago: Bussi, Claudio, Agustín Mangiarotti, Christian Eduardo Vanhille-Campos,
Beren Aylan, Enrica Pellegrino, Natalia Athanasiadi, Antony Fearns, et al. “Stress
Granules Plug and Stabilize Damaged Endolysosomal Membranes.” Nature. Springer
Nature, 2023. https://doi.org/10.1038/s41586-023-06726-w.
ieee: C. Bussi et al., “Stress granules plug and stabilize damaged endolysosomal
membranes,” Nature. Springer Nature, 2023.
ista: Bussi C, Mangiarotti A, Vanhille-Campos CE, Aylan B, Pellegrino E, Athanasiadi
N, Fearns A, Rodgers A, Franzmann TM, Šarić A, Dimova R, Gutierrez MG. 2023. Stress
granules plug and stabilize damaged endolysosomal membranes. Nature.
mla: Bussi, Claudio, et al. “Stress Granules Plug and Stabilize Damaged Endolysosomal
Membranes.” Nature, Springer Nature, 2023, doi:10.1038/s41586-023-06726-w.
short: C. Bussi, A. Mangiarotti, C.E. Vanhille-Campos, B. Aylan, E. Pellegrino,
N. Athanasiadi, A. Fearns, A. Rodgers, T.M. Franzmann, A. Šarić, R. Dimova, M.G.
Gutierrez, Nature (2023).
date_created: 2023-11-27T07:56:37Z
date_published: 2023-11-15T00:00:00Z
date_updated: 2023-11-27T09:05:08Z
day: '15'
department:
- _id: AnSa
doi: 10.1038/s41586-023-06726-w
external_id:
pmid:
- '37968398'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41586-023-06726-w
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41586-023-06882-z
record:
- id: '14472'
relation: research_data
status: public
status: public
title: Stress granules plug and stabilize damaged endolysosomal membranes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14472'
abstract:
- lang: eng
text: "Data related to the following paper:\r\n\"Stress granules plug and stabilize
damaged endolysosomal membranes\" (https://doi.org/10.1038/s41586-023-06726-w)\r\n\r\nAbstract:
\r\nEndomembrane damage represents a form of stress that is detrimental for eukaryotic
cells. To cope with this threat, cells possess mechanisms that repair the damage
and restore cellular homeostasis. Endomembrane damage also results in organelle
instability and the mechanisms by which cells stabilize damaged endomembranes
to enable membrane repair remains unknown. In this work we use a minimal coarse-grained
molecular dynamics system to explore how lipid vesicles undergoing poration in
a protein-rich medium can be plugged and stabilised by condensate formation. The
solution of proteins in and out of the vesicle is described by beads dispersed
in implicit solvent. The membrane is described as a one-bead-thick fluid elastic
layer of mechanical properties that mimic biological membranes. We tune the interactions
between solution beads in the different compartments to capture the differences
between the cytoplasmic and endosomal protein solutions and explore how the system
responds to different degrees of membrane poration. We find that, in the right
interaction regime, condensates form rapidly at the damage site upon solution
mixing and act as a plug that prevents futher mixing and destabilisation of the
vesicle. Further, when the condensate can interact with the membrane (wetting
interactions) we find that it mediates pore sealing and membrane repair. This
research is part of the work published in \"Stress granules plug and stabilize
damaged endolysosomal membranes\", Bussi et al, Nature, 2023 - 10.1038/s41586-023-06726-w."
article_processing_charge: No
author:
- first_name: Christian Eduardo
full_name: Vanhille-Campos, Christian Eduardo
id: 3adeca52-9313-11ed-b1ac-c170b2505714
last_name: Vanhille-Campos
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
citation:
ama: Vanhille-Campos CE, Šarić A. Stress granules plug and stabilize damaged endolysosomal
membranes. 2023. doi:10.15479/AT:ISTA:14472
apa: Vanhille-Campos, C. E., & Šarić, A. (2023). Stress granules plug and stabilize
damaged endolysosomal membranes. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:14472
chicago: Vanhille-Campos, Christian Eduardo, and Anđela Šarić. “Stress Granules
Plug and Stabilize Damaged Endolysosomal Membranes.” Institute of Science and
Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14472.
ieee: C. E. Vanhille-Campos and A. Šarić, “Stress granules plug and stabilize damaged
endolysosomal membranes.” Institute of Science and Technology Austria, 2023.
ista: Vanhille-Campos CE, Šarić A. 2023. Stress granules plug and stabilize damaged
endolysosomal membranes, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14472.
mla: Vanhille-Campos, Christian Eduardo, and Anđela Šarić. Stress Granules Plug
and Stabilize Damaged Endolysosomal Membranes. Institute of Science and Technology
Austria, 2023, doi:10.15479/AT:ISTA:14472.
short: C.E. Vanhille-Campos, A. Šarić, (2023).
date_created: 2023-10-30T16:38:32Z
date_published: 2023-10-31T00:00:00Z
date_updated: 2023-11-27T09:05:07Z
day: '31'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.15479/AT:ISTA:14472
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publisher: Institute of Science and Technology Austria
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title: Stress granules plug and stabilize damaged endolysosomal membranes
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12747'
abstract:
- lang: eng
text: Muscle degeneration is the most prevalent cause for frailty and dependency
in inherited diseases and ageing. Elucidation of pathophysiological mechanisms,
as well as effective treatments for muscle diseases, represents an important goal
in improving human health. Here, we show that the lipid synthesis enzyme phosphatidylethanolamine
cytidyltransferase (PCYT2/ECT) is critical to muscle health. Human deficiency
in PCYT2 causes a severe disease with failure to thrive and progressive weakness.
pcyt2-mutant zebrafish and muscle-specific Pcyt2-knockout mice recapitulate the
participant phenotypes, with failure to thrive, progressive muscle weakness and
accelerated ageing. Mechanistically, muscle Pcyt2 deficiency affects cellular
bioenergetics and membrane lipid bilayer structure and stability. PCYT2 activity
declines in ageing muscles of mice and humans, and adeno-associated virus-based
delivery of PCYT2 ameliorates muscle weakness in Pcyt2-knockout and old mice,
offering a therapy for individuals with a rare disease and muscle ageing. Thus,
PCYT2 plays a fundamental and conserved role in vertebrate muscle health, linking
PCYT2 and PCYT2-synthesized lipids to severe muscle dystrophy and ageing.
acknowledgement: 'The authors thank the participants and their families for participating
in the study. We thank all members of our laboratories for helpful discussions.
We are grateful to Vienna BioCenter Core Facilities: Mouse Phenotyping Unit, Histopathology
Unit, Bioinformatics Unit, BioOptics Unit, Electron Microscopy Unit and Comparative
Medicine Unit. We are grateful to the Lipidomics Facility, and K. Klavins and T.
Hannich at the CeMM Research Center for Molecular Medicine of the Austrian Academy
of Sciences for assistance with lipidomics analysis. We also thank T. Huan and A.
Hui (UBC Vancouver) for mouse tissue and mitochondria lipidomics analysis. We thank
A. Klymchenko (Laboratoire de Bioimagerie et Pathologies Université de Strasbourg,
Strasbourg, France) for providing the NR12S probe. We are thankful to the Sen. Paul
D. Wellstone Muscular Dystrophy Cooperative Specialized Research Center Viral Vector
Core Facility for AAV6 production. We also thank K. P. Campbell and M. E. Anderson
(University of Iowa, Carver College of Medicine) for advice on muscle tissue handling.
We thank A. Al-Qassabi from the Sultan Qaboos University for the clinical assessment
of the participants. D.C. and J.M.P. are supported by the Austrian Federal Ministry
of Education, Science and Research, the Austrian Academy of Sciences, and the City
of Vienna, and grants from the Austrian Science Fund (FWF) Wittgenstein award (Z
271-B19), the T. von Zastrow Foundation, and a Canada 150 Research Chairs Program
(F18-01336). J.S.C. is supported by grants RO1AR44533 and P50AR065139 from the US
National Institutes of Health. C.K. is supported by a grant from the Agence Nationale
de la Recherche (ANR-18-CE14-0007-01). A.V.K. is supported by European Union’s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement
no. 67544, and an Austrian Science Fund (FWF; no P-33799). A.W. is supported by
Austrian Research Promotion Agency (FFG) project no 867674. E.S. is supported by
a SciLifeLab fellowship and Karolinska Institutet Foundation Grants. Work in the
laboratory of G.S.-F. is supported by the Austrian Academy of Sciences, the European
Research Council (ERC AdG 695214 GameofGates) and the Innovative Medicines Initiative
2 Joint Undertaking (grant agreement no. 777372, ReSOLUTE). S.B., M.L. and R.Y.
acknowledge the support of the Spastic Paraplegia Foundation.'
article_processing_charge: No
article_type: original
author:
- first_name: Domagoj
full_name: Cikes, Domagoj
last_name: Cikes
- first_name: Kareem
full_name: Elsayad, Kareem
last_name: Elsayad
- first_name: Erdinc
full_name: Sezgin, Erdinc
last_name: Sezgin
- first_name: Erika
full_name: Koitai, Erika
last_name: Koitai
- first_name: Torma
full_name: Ferenc, Torma
last_name: Ferenc
- first_name: Michael
full_name: Orthofer, Michael
last_name: Orthofer
- first_name: Rebecca
full_name: Yarwood, Rebecca
last_name: Yarwood
- first_name: Leonhard X.
full_name: Heinz, Leonhard X.
last_name: Heinz
- first_name: Vitaly
full_name: Sedlyarov, Vitaly
last_name: Sedlyarov
- first_name: Nasser
full_name: Darwish-Miranda, Nasser
id: 39CD9926-F248-11E8-B48F-1D18A9856A87
last_name: Darwish-Miranda
orcid: 0000-0002-8821-8236
- first_name: Adrian
full_name: Taylor, Adrian
last_name: Taylor
- first_name: Sophie
full_name: Grapentine, Sophie
last_name: Grapentine
- first_name: Fathiya
full_name: al-Murshedi, Fathiya
last_name: al-Murshedi
- first_name: Anne
full_name: Abot, Anne
last_name: Abot
- first_name: Adelheid
full_name: Weidinger, Adelheid
last_name: Weidinger
- first_name: Candice
full_name: Kutchukian, Candice
last_name: Kutchukian
- first_name: Colline
full_name: Sanchez, Colline
last_name: Sanchez
- first_name: Shane J. F.
full_name: Cronin, Shane J. F.
last_name: Cronin
- first_name: Maria
full_name: Novatchkova, Maria
last_name: Novatchkova
- first_name: Anoop
full_name: Kavirayani, Anoop
last_name: Kavirayani
- first_name: Thomas
full_name: Schuetz, Thomas
last_name: Schuetz
- first_name: Bernhard
full_name: Haubner, Bernhard
last_name: Haubner
- first_name: Lisa
full_name: Haas, Lisa
last_name: Haas
- first_name: Astrid
full_name: Hagelkruys, Astrid
last_name: Hagelkruys
- first_name: Suzanne
full_name: Jackowski, Suzanne
last_name: Jackowski
- first_name: Andrey
full_name: Kozlov, Andrey
last_name: Kozlov
- first_name: Vincent
full_name: Jacquemond, Vincent
last_name: Jacquemond
- first_name: Claude
full_name: Knauf, Claude
last_name: Knauf
- first_name: Giulio
full_name: Superti-Furga, Giulio
last_name: Superti-Furga
- first_name: Eric
full_name: Rullman, Eric
last_name: Rullman
- first_name: Thomas
full_name: Gustafsson, Thomas
last_name: Gustafsson
- first_name: John
full_name: McDermot, John
last_name: McDermot
- first_name: Martin
full_name: Lowe, Martin
last_name: Lowe
- first_name: Zsolt
full_name: Radak, Zsolt
last_name: Radak
- first_name: Jeffrey S.
full_name: Chamberlain, Jeffrey S.
last_name: Chamberlain
- first_name: Marica
full_name: Bakovic, Marica
last_name: Bakovic
- first_name: Siddharth
full_name: Banka, Siddharth
last_name: Banka
- first_name: Josef M.
full_name: Penninger, Josef M.
last_name: Penninger
citation:
ama: Cikes D, Elsayad K, Sezgin E, et al. PCYT2-regulated lipid biosynthesis is
critical to muscle health and ageing. Nature Metabolism. 2023;5:495-515.
doi:10.1038/s42255-023-00766-2
apa: Cikes, D., Elsayad, K., Sezgin, E., Koitai, E., Ferenc, T., Orthofer, M., …
Penninger, J. M. (2023). PCYT2-regulated lipid biosynthesis is critical to muscle
health and ageing. Nature Metabolism. Springer Nature. https://doi.org/10.1038/s42255-023-00766-2
chicago: Cikes, Domagoj, Kareem Elsayad, Erdinc Sezgin, Erika Koitai, Torma Ferenc,
Michael Orthofer, Rebecca Yarwood, et al. “PCYT2-Regulated Lipid Biosynthesis
Is Critical to Muscle Health and Ageing.” Nature Metabolism. Springer Nature,
2023. https://doi.org/10.1038/s42255-023-00766-2.
ieee: D. Cikes et al., “PCYT2-regulated lipid biosynthesis is critical to
muscle health and ageing,” Nature Metabolism, vol. 5. Springer Nature,
pp. 495–515, 2023.
ista: Cikes D, Elsayad K, Sezgin E, Koitai E, Ferenc T, Orthofer M, Yarwood R, Heinz
LX, Sedlyarov V, Darwish-Miranda N, Taylor A, Grapentine S, al-Murshedi F, Abot
A, Weidinger A, Kutchukian C, Sanchez C, Cronin SJF, Novatchkova M, Kavirayani
A, Schuetz T, Haubner B, Haas L, Hagelkruys A, Jackowski S, Kozlov A, Jacquemond
V, Knauf C, Superti-Furga G, Rullman E, Gustafsson T, McDermot J, Lowe M, Radak
Z, Chamberlain JS, Bakovic M, Banka S, Penninger JM. 2023. PCYT2-regulated lipid
biosynthesis is critical to muscle health and ageing. Nature Metabolism. 5, 495–515.
mla: Cikes, Domagoj, et al. “PCYT2-Regulated Lipid Biosynthesis Is Critical to Muscle
Health and Ageing.” Nature Metabolism, vol. 5, Springer Nature, 2023, pp.
495–515, doi:10.1038/s42255-023-00766-2.
short: D. Cikes, K. Elsayad, E. Sezgin, E. Koitai, T. Ferenc, M. Orthofer, R. Yarwood,
L.X. Heinz, V. Sedlyarov, N. Darwish-Miranda, A. Taylor, S. Grapentine, F. al-Murshedi,
A. Abot, A. Weidinger, C. Kutchukian, C. Sanchez, S.J.F. Cronin, M. Novatchkova,
A. Kavirayani, T. Schuetz, B. Haubner, L. Haas, A. Hagelkruys, S. Jackowski, A.
Kozlov, V. Jacquemond, C. Knauf, G. Superti-Furga, E. Rullman, T. Gustafsson,
J. McDermot, M. Lowe, Z. Radak, J.S. Chamberlain, M. Bakovic, S. Banka, J.M. Penninger,
Nature Metabolism 5 (2023) 495–515.
date_created: 2023-03-23T12:58:43Z
date_published: 2023-03-20T00:00:00Z
date_updated: 2023-11-28T07:31:33Z
day: '20'
department:
- _id: Bio
doi: 10.1038/s42255-023-00766-2
external_id:
isi:
- '000992064000002'
pmid:
- '36941451'
intvolume: ' 5'
isi: 1
keyword:
- Cell Biology
- Physiology (medical)
- Endocrinology
- Diabetes and Metabolism
- Internal Medicine
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2022.03.02.482658
month: '03'
oa: 1
oa_version: Preprint
page: 495-515
pmid: 1
publication: Nature Metabolism
publication_identifier:
issn:
- 2522-5812
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s42255-023-00791-1
scopus_import: '1'
status: public
title: PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2023'
...
---
_id: '14605'
abstract:
- lang: eng
text: The phonon transport mechanisms and ultralow lattice thermal conductivities
(κL) in silver halide AgX (X=Cl,Br,I) compounds are not yet well understood. Herein,
we study the lattice dynamics and thermal property of AgX under the framework
of perturbation theory and the two-channel Wigner thermal transport model based
on accurate machine learning potentials. We find that an accurate extraction of
the third-order atomic force constants from largely displaced configurations is
significant for the calculation of the κL of AgX, and the coherence thermal transport
is also non-negligible. In AgI, however, the calculated κL still considerably
overestimates the experimental values even including four-phonon scatterings.
Molecular dynamics (MD) simulations using machine learning potential suggest an
important role of the higher-than-fourth-order lattice anharmonicity in the low-frequency
phonon linewidths of AgI at room temperature, which can be related to the simultaneous
restrictions of the three- and four-phonon phase spaces. The κL of AgI calculated
using MD phonon lifetimes including full-order lattice anharmonicity shows a better
agreement with experiments.
acknowledgement: This work is supported by the Research Grants Council of Hong Kong
(Grants No. 17318122 and No. 17306721). The authors are grateful for the research
computing facilities offered by ITS, HKU. Z.Z. acknowledges the European Union’s
Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant
Agreement No. 101034413.
article_number: '174302'
article_processing_charge: No
article_type: original
author:
- first_name: Niuchang
full_name: Ouyang, Niuchang
last_name: Ouyang
- first_name: Zezhu
full_name: Zeng, Zezhu
id: 54a2c730-803f-11ed-ab7e-95b29d2680e7
last_name: Zeng
- first_name: Chen
full_name: Wang, Chen
last_name: Wang
- first_name: Qi
full_name: Wang, Qi
last_name: Wang
- first_name: Yue
full_name: Chen, Yue
last_name: Chen
citation:
ama: Ouyang N, Zeng Z, Wang C, Wang Q, Chen Y. Role of high-order lattice anharmonicity
in the phonon thermal transport of silver halide AgX (X=Cl,Br, I). Physical
Review B. 2023;108(17). doi:10.1103/PhysRevB.108.174302
apa: Ouyang, N., Zeng, Z., Wang, C., Wang, Q., & Chen, Y. (2023). Role of high-order
lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br,
I). Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.108.174302
chicago: Ouyang, Niuchang, Zezhu Zeng, Chen Wang, Qi Wang, and Yue Chen. “Role of
High-Order Lattice Anharmonicity in the Phonon Thermal Transport of Silver Halide
AgX (X=Cl,Br, I).” Physical Review B. American Physical Society, 2023.
https://doi.org/10.1103/PhysRevB.108.174302.
ieee: N. Ouyang, Z. Zeng, C. Wang, Q. Wang, and Y. Chen, “Role of high-order lattice
anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I),”
Physical Review B, vol. 108, no. 17. American Physical Society, 2023.
ista: Ouyang N, Zeng Z, Wang C, Wang Q, Chen Y. 2023. Role of high-order lattice
anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I).
Physical Review B. 108(17), 174302.
mla: Ouyang, Niuchang, et al. “Role of High-Order Lattice Anharmonicity in the Phonon
Thermal Transport of Silver Halide AgX (X=Cl,Br, I).” Physical Review B,
vol. 108, no. 17, 174302, American Physical Society, 2023, doi:10.1103/PhysRevB.108.174302.
short: N. Ouyang, Z. Zeng, C. Wang, Q. Wang, Y. Chen, Physical Review B 108 (2023).
date_created: 2023-11-26T23:00:54Z
date_published: 2023-11-01T00:00:00Z
date_updated: 2023-11-28T07:48:55Z
day: '01'
department:
- _id: BiCh
doi: 10.1103/PhysRevB.108.174302
ec_funded: 1
intvolume: ' 108'
issue: '17'
language:
- iso: eng
month: '11'
oa_version: None
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Role of high-order lattice anharmonicity in the phonon thermal transport of
silver halide AgX (X=Cl,Br, I)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2023'
...
---
_id: '14609'
abstract:
- lang: eng
text: "Distributed Key Generation (DKG) is a technique to bootstrap threshold cryptosystems
without a trusted party. DKG is an essential building block to many decentralized
protocols such as randomness beacons, threshold signatures, Byzantine consensus,
and multiparty computation. While significant progress has been made recently,
existing asynchronous DKG constructions are inefficient when the reconstruction
threshold is larger than one-third of the total nodes. In this paper, we present
a simple and concretely efficient asynchronous DKG (ADKG) protocol among n = 3t
+ 1 nodes that can tolerate up to t malicious nodes and support any reconstruction
threshold ℓ ≥ t. Our protocol has an expected O(κn3) communication cost, where
κ is the security parameter, and only assumes the hardness of the Discrete Logarithm.
The\r\ncore ingredient of our ADKG protocol is an asynchronous protocol to secret
share a random polynomial of degree ℓ ≥ t, which has other applications, such
as asynchronous proactive secret sharing and asynchronous multiparty computation.
We implement our high-threshold ADKG protocol and evaluate it using a network
of up to 128 geographically distributed nodes. Our evaluation shows that our high-threshold
ADKG protocol reduces the running time by 90% and bandwidth usage by 80% over
the state-of-the-art."
acknowledgement: The authors would like to thank Amit Agarwal, Andrew Miller, and
Tom Yurek for the helpful discussions related to the paper. This work is funded
in part by a VMware early career faculty grant, a Chainlink Labs Ph.D. fellowship,
the National Science Foundation, and the Austrian Science Fund (FWF) F8512-N.
article_processing_charge: No
author:
- first_name: Sourav
full_name: Das, Sourav
last_name: Das
- first_name: Zhuolun
full_name: Xiang, Zhuolun
last_name: Xiang
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Ling
full_name: Ren, Ling
last_name: Ren
citation:
ama: 'Das S, Xiang Z, Kokoris Kogias E, Ren L. Practical asynchronous high-threshold
distributed key generation and distributed polynomial sampling. In: 32nd USENIX
Security Symposium. Vol 8. Usenix; 2023:5359-5376.'
apa: 'Das, S., Xiang, Z., Kokoris Kogias, E., & Ren, L. (2023). Practical asynchronous
high-threshold distributed key generation and distributed polynomial sampling.
In 32nd USENIX Security Symposium (Vol. 8, pp. 5359–5376). Anaheim, CA,
United States: Usenix.'
chicago: Das, Sourav, Zhuolun Xiang, Eleftherios Kokoris Kogias, and Ling Ren. “Practical
Asynchronous High-Threshold Distributed Key Generation and Distributed Polynomial
Sampling.” In 32nd USENIX Security Symposium, 8:5359–76. Usenix, 2023.
ieee: S. Das, Z. Xiang, E. Kokoris Kogias, and L. Ren, “Practical asynchronous high-threshold
distributed key generation and distributed polynomial sampling,” in 32nd USENIX
Security Symposium, Anaheim, CA, United States, 2023, vol. 8, pp. 5359–5376.
ista: Das S, Xiang Z, Kokoris Kogias E, Ren L. 2023. Practical asynchronous high-threshold
distributed key generation and distributed polynomial sampling. 32nd USENIX Security
Symposium. USENIX Security Symposium vol. 8, 5359–5376.
mla: Das, Sourav, et al. “Practical Asynchronous High-Threshold Distributed Key
Generation and Distributed Polynomial Sampling.” 32nd USENIX Security Symposium,
vol. 8, Usenix, 2023, pp. 5359–76.
short: S. Das, Z. Xiang, E. Kokoris Kogias, L. Ren, in:, 32nd USENIX Security Symposium,
Usenix, 2023, pp. 5359–5376.
conference:
end_date: 2023-08-11
location: Anaheim, CA, United States
name: USENIX Security Symposium
start_date: 2023-08-09
date_created: 2023-11-26T23:00:55Z
date_published: 2023-08-15T00:00:00Z
date_updated: 2023-11-28T09:17:38Z
day: '15'
ddc:
- '000'
department:
- _id: ElKo
file:
- access_level: open_access
checksum: 1a730765930138e23c6efd2575872641
content_type: application/pdf
creator: dernst
date_created: 2023-11-28T09:14:34Z
date_updated: 2023-11-28T09:14:34Z
file_id: '14621'
file_name: 2023_USENIX_Das.pdf
file_size: 704331
relation: main_file
success: 1
file_date_updated: 2023-11-28T09:14:34Z
has_accepted_license: '1'
intvolume: ' 8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2022/1389
month: '08'
oa: 1
oa_version: Published Version
page: 5359-5376
project:
- _id: 34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f
grant_number: F8512
name: Secure Network and Hardware for Efficient Blockchains
publication: 32nd USENIX Security Symposium
publication_identifier:
isbn:
- '9781713879497'
publication_status: published
publisher: Usenix
quality_controlled: '1'
scopus_import: '1'
status: public
title: Practical asynchronous high-threshold distributed key generation and distributed
polynomial sampling
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2023'
...
---
_id: '14603'
abstract:
- lang: eng
text: Computing the solubility of crystals in a solvent using atomistic simulations
is notoriously challenging due to the complexities and convergence issues associated
with free-energy methods, as well as the slow equilibration in direct-coexistence
simulations. This paper introduces a molecular-dynamics workflow that simplifies
and robustly computes the solubility of molecular or ionic crystals. This method
is considerably more straightforward than the state-of-the-art, as we have streamlined
and optimised each step of the process. Specifically, we calculate the chemical
potential of the crystal using the gas-phase molecule as a reference state, and
employ the S0 method to determine the concentration dependence of the chemical
potential of the solute. We use this workflow to predict the solubilities of sodium
chloride in water, urea polymorphs in water, and paracetamol polymorphs in both
water and ethanol. Our findings indicate that the predicted solubility is sensitive
to the chosen potential energy surface. Furthermore, we note that the harmonic
approximation often fails for both molecular crystals and gas molecules at or
above room temperature, and that the assumption of an ideal solution becomes less
valid for highly soluble substances.
acknowledgement: A.R. and B.C. acknowledge resources provided by the Cambridge Tier-2
system operated by the University of Cambridge Research Computing Service funded
by EPSRC Tier-2 capital Grant No. EP/P020259/1. P.Y.C. acknowledges support from
the Ernest Oppenheimer Fund and the Winton Programme for the Physics of Sustainability.
article_number: '184110'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Aleks
full_name: Reinhardt, Aleks
last_name: Reinhardt
- first_name: Pin Yu
full_name: Chew, Pin Yu
last_name: Chew
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: Reinhardt A, Chew PY, Cheng B. A streamlined molecular-dynamics workflow for
computing solubilities of molecular and ionic crystals. Journal of Chemical
Physics. 2023;159(18). doi:10.1063/5.0173341
apa: Reinhardt, A., Chew, P. Y., & Cheng, B. (2023). A streamlined molecular-dynamics
workflow for computing solubilities of molecular and ionic crystals. Journal
of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0173341
chicago: Reinhardt, Aleks, Pin Yu Chew, and Bingqing Cheng. “A Streamlined Molecular-Dynamics
Workflow for Computing Solubilities of Molecular and Ionic Crystals.” Journal
of Chemical Physics. AIP Publishing, 2023. https://doi.org/10.1063/5.0173341.
ieee: A. Reinhardt, P. Y. Chew, and B. Cheng, “A streamlined molecular-dynamics
workflow for computing solubilities of molecular and ionic crystals,” Journal
of Chemical Physics, vol. 159, no. 18. AIP Publishing, 2023.
ista: Reinhardt A, Chew PY, Cheng B. 2023. A streamlined molecular-dynamics workflow
for computing solubilities of molecular and ionic crystals. Journal of Chemical
Physics. 159(18), 184110.
mla: Reinhardt, Aleks, et al. “A Streamlined Molecular-Dynamics Workflow for Computing
Solubilities of Molecular and Ionic Crystals.” Journal of Chemical Physics,
vol. 159, no. 18, 184110, AIP Publishing, 2023, doi:10.1063/5.0173341.
short: A. Reinhardt, P.Y. Chew, B. Cheng, Journal of Chemical Physics 159 (2023).
date_created: 2023-11-26T23:00:54Z
date_published: 2023-11-14T00:00:00Z
date_updated: 2023-11-28T08:39:23Z
day: '14'
ddc:
- '530'
- '540'
department:
- _id: BiCh
doi: 10.1063/5.0173341
external_id:
arxiv:
- '2308.10886'
file:
- access_level: open_access
checksum: f668ee0d07096eef81159d05bc27aabc
content_type: application/pdf
creator: dernst
date_created: 2023-11-28T08:39:06Z
date_updated: 2023-11-28T08:39:06Z
file_id: '14620'
file_name: 2023_JourChemicalPhysics_Reinhardt.pdf
file_size: 6276059
relation: main_file
success: 1
file_date_updated: 2023-11-28T08:39:06Z
has_accepted_license: '1'
intvolume: ' 159'
issue: '18'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
related_material:
record:
- id: '14619'
relation: research_data
status: public
scopus_import: '1'
status: public
title: A streamlined molecular-dynamics workflow for computing solubilities of molecular
and ionic crystals
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 159
year: '2023'
...
---
_id: '14604'
abstract:
- lang: eng
text: Sex chromosomes have evolved independently multiple times, but why some are
conserved for more than 100 million years whereas others turnover rapidly remains
an open question. Here, we examine the homology of sex chromosomes across nine
orders of insects, plus the outgroup springtails. We find that the X chromosome
is likely homologous across insects and springtails; the only exception is in
the Lepidoptera, which has lost the X and now has a ZZ/ZW sex-chromosome system.
These results suggest the ancestral insect X chromosome has persisted for more
than 450 million years—the oldest known sex chromosome to date. Further, we propose
that the shrinking of gene content the dipteran X chromosome has allowed for a
burst of sex-chromosome turnover that is absent from other speciose insect orders.
acknowledgement: All computational analyses were performed on the server at Institute
of Science and Technology Austria. We thank Marwan Elkrewi and Vincent Bett for
analytical advice, and Tanja Schwander and Vincent Merel for useful discussions.
We also thank Matthew Hahn for comments on an earlier version of the manuscript.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Toups MA, Vicoso B. The X chromosome of insects likely predates the origin
of class Insecta. Evolution. 2023;77(11):2504-2511. doi:10.1093/evolut/qpad169
apa: Toups, M. A., & Vicoso, B. (2023). The X chromosome of insects likely predates
the origin of class Insecta. Evolution. Oxford University Press. https://doi.org/10.1093/evolut/qpad169
chicago: Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely
Predates the Origin of Class Insecta.” Evolution. Oxford University Press,
2023. https://doi.org/10.1093/evolut/qpad169.
ieee: M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the
origin of class Insecta,” Evolution, vol. 77, no. 11. Oxford University
Press, pp. 2504–2511, 2023.
ista: Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the
origin of class Insecta. Evolution. 77(11), 2504–2511.
mla: Toups, Melissa A., and Beatriz Vicoso. “The X Chromosome of Insects Likely
Predates the Origin of Class Insecta.” Evolution, vol. 77, no. 11, Oxford
University Press, 2023, pp. 2504–11, doi:10.1093/evolut/qpad169.
short: M.A. Toups, B. Vicoso, Evolution 77 (2023) 2504–2511.
date_created: 2023-11-26T23:00:54Z
date_published: 2023-11-02T00:00:00Z
date_updated: 2023-11-28T08:25:28Z
day: '02'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/evolut/qpad169
external_id:
pmid:
- '37738212'
file:
- access_level: open_access
checksum: b66dc10edae92d38918d534e64dda77c
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creator: dernst
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date_updated: 2023-11-28T08:12:15Z
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file_size: 1399102
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intvolume: ' 77'
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language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 2504-2511
pmid: 1
publication: Evolution
publication_identifier:
eissn:
- 1558-5646
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://git.ista.ac.at/bvicoso/veryoldx
record:
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relation: research_data
status: public
- id: '14617'
relation: research_data
status: public
scopus_import: '1'
status: public
title: The X chromosome of insects likely predates the origin of class Insecta
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 77
year: '2023'
...
---
_id: '14616'
abstract:
- lang: eng
text: Sex chromosomes have evolved independently multiple times, but why some are
conserved for more than 100 million years whereas others turnover rapidly remains
an open question. Here, we examine the homology of sex chromosomes across nine
orders of insects, plus the outgroup springtails. We find that the X chromosome
is likely homologous across insects and springtails; the only exception is in
the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system.
These results suggest the ancestral insect X chromosome has persisted for more
than 450 million years – the oldest known sex chromosome to date. Further, we
propose that the shrinking of gene content of the Dipteran X chromosome has allowed
for a burst of sex-chromosome turnover that is absent from other speciose insect
orders.
article_processing_charge: No
author:
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Toups MA, Vicoso B. The X chromosome of insects likely predates the origin
of Class Insecta. 2023. doi:10.5061/DRYAD.HX3FFBGKT
apa: Toups, M. A., & Vicoso, B. (2023). The X chromosome of insects likely predates
the origin of Class Insecta. Dryad. https://doi.org/10.5061/DRYAD.HX3FFBGKT
chicago: Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely
Predates the Origin of Class Insecta.” Dryad, 2023. https://doi.org/10.5061/DRYAD.HX3FFBGKT.
ieee: M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the
origin of Class Insecta.” Dryad, 2023.
ista: Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the
origin of Class Insecta, Dryad, 10.5061/DRYAD.HX3FFBGKT.
mla: Toups, Melissa A., and Beatriz Vicoso. The X Chromosome of Insects Likely
Predates the Origin of Class Insecta. Dryad, 2023, doi:10.5061/DRYAD.HX3FFBGKT.
short: M.A. Toups, B. Vicoso, (2023).
date_created: 2023-11-28T08:01:53Z
date_published: 2023-09-15T00:00:00Z
date_updated: 2023-11-28T08:17:31Z
day: '15'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.5061/DRYAD.HX3FFBGKT
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.hx3ffbgkt
month: '09'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '14604'
relation: used_in_publication
status: public
status: public
title: The X chromosome of insects likely predates the origin of Class Insecta
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14617'
abstract:
- lang: eng
text: Sex chromosomes have evolved independently multiple times, but why some are
conserved for more than 100 million years whereas others turnover rapidly remains
an open question. Here, we examine the homology of sex chromosomes across nine
orders of insects, plus the outgroup springtails. We find that the X chromosome
is likely homologous across insects and springtails; the only exception is in
the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system.
These results suggest the ancestral insect X chromosome has persisted for more
than 450 million years – the oldest known sex chromosome to date. Further, we
propose that the shrinking of gene content of the Dipteran X chromosome has allowed
for a burst of sex-chromosome turnover that is absent from other speciose insect
orders.
article_processing_charge: No
author:
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Toups MA, Vicoso B. The X chromosome of insects likely predates the origin
of Class Insecta. 2023. doi:10.5281/ZENODO.8138705
apa: Toups, M. A., & Vicoso, B. (2023). The X chromosome of insects likely predates
the origin of Class Insecta. Zenodo. https://doi.org/10.5281/ZENODO.8138705
chicago: Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely
Predates the Origin of Class Insecta.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8138705.
ieee: M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the
origin of Class Insecta.” Zenodo, 2023.
ista: Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the
origin of Class Insecta, Zenodo, 10.5281/ZENODO.8138705.
mla: Toups, Melissa A., and Beatriz Vicoso. The X Chromosome of Insects Likely
Predates the Origin of Class Insecta. Zenodo, 2023, doi:10.5281/ZENODO.8138705.
short: M.A. Toups, B. Vicoso, (2023).
date_created: 2023-11-28T08:04:03Z
date_published: 2023-09-15T00:00:00Z
date_updated: 2023-11-28T08:25:28Z
day: '15'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.5281/ZENODO.8138705
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.8138705
month: '09'
oa: 1
oa_version: Published Version
other_data_license: MIT License
publisher: Zenodo
related_material:
record:
- id: '14604'
relation: used_in_publication
status: public
status: public
title: The X chromosome of insects likely predates the origin of Class Insecta
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14619'
abstract:
- lang: eng
text: Data underlying the publication "A streamlined molecular-dynamics workflow
for computing solubilities of molecular and ionic crystals" (DOI https://doi.org/10.1063/5.0173341).
article_processing_charge: No
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: 'Cheng B. BingqingCheng/solubility: V1.0. 2023. doi:10.5281/ZENODO.8398094'
apa: 'Cheng, B. (2023). BingqingCheng/solubility: V1.0. Zenodo. https://doi.org/10.5281/ZENODO.8398094'
chicago: 'Cheng, Bingqing. “BingqingCheng/Solubility: V1.0.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8398094.'
ieee: 'B. Cheng, “BingqingCheng/solubility: V1.0.” Zenodo, 2023.'
ista: 'Cheng B. 2023. BingqingCheng/solubility: V1.0, Zenodo, 10.5281/ZENODO.8398094.'
mla: 'Cheng, Bingqing. BingqingCheng/Solubility: V1.0. Zenodo, 2023, doi:10.5281/ZENODO.8398094.'
short: B. Cheng, (2023).
date_created: 2023-11-28T08:32:18Z
date_published: 2023-10-02T00:00:00Z
date_updated: 2023-11-28T08:39:22Z
day: '02'
ddc:
- '530'
department:
- _id: BiCh
doi: 10.5281/ZENODO.8398094
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.8398094
month: '10'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '14603'
relation: used_in_publication
status: public
status: public
title: 'BingqingCheng/solubility: V1.0'
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14564'
abstract:
- lang: eng
text: Cumulus parameterization (CP) in state‐of‐the‐art global climate models is
based on the quasi‐equilibrium assumption (QEA), which views convection as the
action of an ensemble of cumulus clouds, in a state of equilibrium with respect
to a slowly varying atmospheric state. This view is not compatible with the organization
and dynamical interactions across multiple scales of cloud systems in the tropics
and progress in this research area was slow over decades despite the widely recognized
major shortcomings. Novel ideas on how to represent key physical processes of
moist convection‐large‐scale interaction to overcome the QEA have surged recently.
The stochastic multicloud model (SMCM) CP in particular mimics the dynamical interactions
of multiple cloud types that characterize organized tropical convection. Here,
the SMCM is used to modify the Zhang‐McFarlane (ZM) CP by changing the way in
which the bulk mass flux and bulk entrainment and detrainment rates are calculated.
This is done by introducing a stochastic ensemble of plumes characterized by randomly
varying detrainment level distributions based on the cloud area fraction of the
SMCM. The SMCM is here extended to include shallow cumulus clouds resulting in
a unified shallow‐deep CP. The new stochastic multicloud plume CP is validated
against the control ZM scheme in the context of the single column Community Climate
Model of the National Center for Atmospheric Research using data from both tropical
ocean and midlatitude land convection. Some key features of the SMCM CP such as
it capability to represent the tri‐modal nature of organized convection are emphasized.
acknowledgement: The research of B.K. is supported in part by a Discovery Grant from
the Natural Sciences and Engineering Research Council of Canada (RGPIN-04246-2020).
This research was conducted during the visits of P.M. Krishna to the Center for
Prototype Climate Models at NYU Abu Dhabi and University of Victoria from November
2018 to June 2019 and July 2019 and October 2019, respectively. The authors are
very grateful to the three anonymous reviewers who provided very thoughtful and
constructive comments during the review process that helped greatly improve and
shape the final version of the manuscript.
article_number: e2022MS003391
article_processing_charge: Yes
article_type: original
author:
- first_name: B.
full_name: Khouider, B.
last_name: Khouider
- first_name: BIDYUT B
full_name: GOSWAMI, BIDYUT B
id: 3a4ac09c-6d61-11ec-bf66-884cde66b64b
last_name: GOSWAMI
orcid: 0000-0001-8602-3083
- first_name: R.
full_name: Phani, R.
last_name: Phani
- first_name: A. J.
full_name: Majda, A. J.
last_name: Majda
citation:
ama: Khouider B, GOSWAMI BB, Phani R, Majda AJ. A shallow‐deep unified stochastic
mass flux cumulus parameterization in the single column community climate model.
Journal of Advances in Modeling Earth Systems. 2023;15(11). doi:10.1029/2022ms003391
apa: Khouider, B., GOSWAMI, B. B., Phani, R., & Majda, A. J. (2023). A shallow‐deep
unified stochastic mass flux cumulus parameterization in the single column community
climate model. Journal of Advances in Modeling Earth Systems. American
Geophysical Union. https://doi.org/10.1029/2022ms003391
chicago: Khouider, B., BIDYUT B GOSWAMI, R. Phani, and A. J. Majda. “A Shallow‐deep
Unified Stochastic Mass Flux Cumulus Parameterization in the Single Column Community
Climate Model.” Journal of Advances in Modeling Earth Systems. American
Geophysical Union, 2023. https://doi.org/10.1029/2022ms003391.
ieee: B. Khouider, B. B. GOSWAMI, R. Phani, and A. J. Majda, “A shallow‐deep unified
stochastic mass flux cumulus parameterization in the single column community climate
model,” Journal of Advances in Modeling Earth Systems, vol. 15, no. 11.
American Geophysical Union, 2023.
ista: Khouider B, GOSWAMI BB, Phani R, Majda AJ. 2023. A shallow‐deep unified stochastic
mass flux cumulus parameterization in the single column community climate model.
Journal of Advances in Modeling Earth Systems. 15(11), e2022MS003391.
mla: Khouider, B., et al. “A Shallow‐deep Unified Stochastic Mass Flux Cumulus Parameterization
in the Single Column Community Climate Model.” Journal of Advances in Modeling
Earth Systems, vol. 15, no. 11, e2022MS003391, American Geophysical Union,
2023, doi:10.1029/2022ms003391.
short: B. Khouider, B.B. GOSWAMI, R. Phani, A.J. Majda, Journal of Advances in Modeling
Earth Systems 15 (2023).
date_created: 2023-11-20T09:18:21Z
date_published: 2023-11-01T00:00:00Z
date_updated: 2023-11-28T12:04:42Z
day: '01'
ddc:
- '550'
department:
- _id: CaMu
doi: 10.1029/2022ms003391
file:
- access_level: open_access
checksum: e30329dd985559de0ddc7021ca7382b4
content_type: application/pdf
creator: dernst
date_created: 2023-11-20T11:29:16Z
date_updated: 2023-11-20T11:29:16Z
file_id: '14582'
file_name: 2023_JAMES_Khoulder.pdf
file_size: 6435697
relation: main_file
success: 1
file_date_updated: 2023-11-20T11:29:16Z
has_accepted_license: '1'
intvolume: ' 15'
issue: '11'
keyword:
- General Earth and Planetary Sciences
- Environmental Chemistry
- Global and Planetary Change
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Journal of Advances in Modeling Earth Systems
publication_identifier:
eissn:
- 1942-2466
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
scopus_import: '1'
status: public
title: A shallow‐deep unified stochastic mass flux cumulus parameterization in the
single column community climate model
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2023'
...
---
_id: '12789'
abstract:
- lang: eng
text: Experiments have shown that charge distributions of granular materials are
non-Gaussian, with broad tails that indicate many particles with high charge.
This observation has consequences for the behavior of granular materials in many
settings, and may bear relevance to the underlying charge transfer mechanism.
However, there is the unaddressed possibility that broad tails arise due to experimental
uncertainties, as determining the shapes of tails is nontrivial. Here we show
that measurement uncertainties can indeed account for most of the tail broadening
previously observed. The clue that reveals this is that distributions are sensitive
to the electric field at which they are measured; ones measured at low (high)
fields have larger (smaller) tails. Accounting for sources of uncertainty, we
reproduce this broadening in silico. Finally, we use our results to back out the
true charge distribution without broadening, which we find is still non-Guassian,
though with substantially different behavior at the tails and indicating significantly
fewer highly charged particles. These results have implications in many natural
settings where electrostatic interactions, especially among highly charged particles,
strongly affect granular behavior.
acknowledged_ssus:
- _id: M-Shop
acknowledgement: This research was supported by Grants QUIMAL 160001 and Fondecyt
1221597. This project has received funding from the European Research Council (ERC)
under the European Union's Horizon 2020 research and innovation programme (Grant
Agreement No. 949120). This research was supported by the Scientific Service Units
of The Institute of Science and Technology Austria (ISTA) through resources provided
by the Miba Machine Shop. We thank the machine shop technical assistance of Ricardo
Silva and Andrés Espinosa at Departamento de Física, Universidad de Chile.
article_number: '034901'
article_processing_charge: No
article_type: original
author:
- first_name: Nicolás
full_name: Mujica, Nicolás
last_name: Mujica
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
citation:
ama: Mujica N, Waitukaitis SR. Accurate determination of the shapes of granular
charge distributions. Physical Review E. 2023;107(3). doi:10.1103/PhysRevE.107.034901
apa: Mujica, N., & Waitukaitis, S. R. (2023). Accurate determination of the
shapes of granular charge distributions. Physical Review E. American Physical
Society. https://doi.org/10.1103/PhysRevE.107.034901
chicago: Mujica, Nicolás, and Scott R Waitukaitis. “Accurate Determination of the
Shapes of Granular Charge Distributions.” Physical Review E. American Physical
Society, 2023. https://doi.org/10.1103/PhysRevE.107.034901.
ieee: N. Mujica and S. R. Waitukaitis, “Accurate determination of the shapes of
granular charge distributions,” Physical Review E, vol. 107, no. 3. American
Physical Society, 2023.
ista: Mujica N, Waitukaitis SR. 2023. Accurate determination of the shapes of granular
charge distributions. Physical Review E. 107(3), 034901.
mla: Mujica, Nicolás, and Scott R. Waitukaitis. “Accurate Determination of the Shapes
of Granular Charge Distributions.” Physical Review E, vol. 107, no. 3,
034901, American Physical Society, 2023, doi:10.1103/PhysRevE.107.034901.
short: N. Mujica, S.R. Waitukaitis, Physical Review E 107 (2023).
date_created: 2023-04-02T22:01:10Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-11-28T09:22:25Z
day: '01'
ddc:
- '530'
department:
- _id: ScWa
doi: 10.1103/PhysRevE.107.034901
ec_funded: 1
external_id:
isi:
- '000992142700001'
file:
- access_level: open_access
checksum: 48f5dfe4e5f1c46c3c86805cd8f84bea
content_type: application/pdf
creator: swaituka
date_created: 2023-11-27T09:51:48Z
date_updated: 2023-11-27T09:51:48Z
file_id: '14612'
file_name: PhysRevE.107.034901 (1).pdf
file_size: 1428631
relation: main_file
success: 1
file_date_updated: 2023-11-27T09:51:48Z
has_accepted_license: '1'
intvolume: ' 107'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 0aa60e99-070f-11eb-9043-a6de6bdc3afa
call_identifier: H2020
grant_number: '949120'
name: 'Tribocharge: a multi-scale approach to an enduring problem in physics'
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: Accurate determination of the shapes of granular charge distributions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 107
year: '2023'
...
---
_id: '13238'
abstract:
- lang: eng
text: "We consider a natural problem dealing with weighted packet selection across
a rechargeable link, which e.g., finds applications in cryptocurrency networks.
The capacity of a link (u, v) is determined by how much nodes u and v allocate
for this link. Specifically, the input is a finite ordered sequence of packets
that arrive in both directions along a link. Given (u, v) and a packet of weight
x going from u to v, node u can either accept or reject the packet. If u accepts
the packet, the capacity on link (u, v) decreases by x. Correspondingly, v’s capacity
on (u, v) increases by x. If a node rejects the packet, this will entail a cost
affinely linear in the weight of the packet. A link is “rechargeable” in the sense
that the total capacity of the link has to remain constant, but the allocation
of capacity at the ends of the link can depend arbitrarily on the nodes’ decisions.
The goal is to minimise the sum of the capacity injected into the link and the
cost of rejecting packets. We show that the problem is NP-hard, but can be approximated
efficiently with a ratio of (1+ε)⋅(1+3–√) for some arbitrary ε>0.\r\n."
acknowledgement: We thank Mahsa Bastankhah and Mohammad Ali Maddah-Ali for fruitful
discussions about different variants of the problem. This work is supported by the
European Research Council (ERC) Consolidator Project 864228 (AdjustNet), 2020-2025,
the ERC CoG 863818 (ForM-SMArt), and the German Research Foundation (DFG) grant
470029389 (FlexNets), 2021–2024.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Stefan
full_name: Schmid, Stefan
last_name: Schmid
- first_name: Jakub
full_name: Svoboda, Jakub
id: 130759D2-D7DD-11E9-87D2-DE0DE6697425
last_name: Svoboda
orcid: 0000-0002-1419-3267
- first_name: Michelle X
full_name: Yeo, Michelle X
id: 2D82B818-F248-11E8-B48F-1D18A9856A87
last_name: Yeo
citation:
ama: 'Schmid S, Svoboda J, Yeo MX. Weighted packet selection for rechargeable links
in cryptocurrency networks: Complexity and approximation. In: SIROCCO 2023:
Structural Information and Communication Complexity . Vol 13892. Springer
Nature; 2023:576-594. doi:10.1007/978-3-031-32733-9_26'
apa: 'Schmid, S., Svoboda, J., & Yeo, M. X. (2023). Weighted packet selection
for rechargeable links in cryptocurrency networks: Complexity and approximation.
In SIROCCO 2023: Structural Information and Communication Complexity (Vol.
13892, pp. 576–594). Alcala de Henares, Spain: Springer Nature. https://doi.org/10.1007/978-3-031-32733-9_26'
chicago: 'Schmid, Stefan, Jakub Svoboda, and Michelle X Yeo. “Weighted Packet Selection
for Rechargeable Links in Cryptocurrency Networks: Complexity and Approximation.”
In SIROCCO 2023: Structural Information and Communication Complexity ,
13892:576–94. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-32733-9_26.'
ieee: 'S. Schmid, J. Svoboda, and M. X. Yeo, “Weighted packet selection for rechargeable
links in cryptocurrency networks: Complexity and approximation,” in SIROCCO
2023: Structural Information and Communication Complexity , Alcala de Henares,
Spain, 2023, vol. 13892, pp. 576–594.'
ista: 'Schmid S, Svoboda J, Yeo MX. 2023. Weighted packet selection for rechargeable
links in cryptocurrency networks: Complexity and approximation. SIROCCO 2023:
Structural Information and Communication Complexity . SIROCCO: Structural Information
and Communication Complexity, LNCS, vol. 13892, 576–594.'
mla: 'Schmid, Stefan, et al. “Weighted Packet Selection for Rechargeable Links in Cryptocurrency
Networks: Complexity and Approximation.” SIROCCO 2023: Structural Information
and Communication Complexity , vol. 13892, Springer Nature, 2023, pp. 576–94,
doi:10.1007/978-3-031-32733-9_26.'
short: 'S. Schmid, J. Svoboda, M.X. Yeo, in:, SIROCCO 2023: Structural Information
and Communication Complexity , Springer Nature, 2023, pp. 576–594.'
conference:
end_date: 2023-06-09
location: Alcala de Henares, Spain
name: 'SIROCCO: Structural Information and Communication Complexity'
start_date: 2023-06-06
date_created: 2023-07-16T22:01:12Z
date_published: 2023-05-25T00:00:00Z
date_updated: 2023-11-30T10:54:51Z
day: '25'
department:
- _id: KrPi
- _id: KrCh
doi: 10.1007/978-3-031-32733-9_26
ec_funded: 1
external_id:
arxiv:
- '2204.13459'
intvolume: ' 13892'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2204.13459
month: '05'
oa: 1
oa_version: Preprint
page: 576-594
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: 'SIROCCO 2023: Structural Information and Communication Complexity '
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031327322'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '14506'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'Weighted packet selection for rechargeable links in cryptocurrency networks:
Complexity and approximation'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13892
year: '2023'
...
---
_id: '14506'
abstract:
- lang: eng
text: "Payment channel networks are a promising approach to improve the scalability
bottleneck\r\nof cryptocurrencies. Two design principles behind payment channel
networks are\r\nefficiency and privacy. Payment channel networks improve efficiency
by allowing users\r\nto transact in a peer-to-peer fashion along multi-hop routes
in the network, avoiding\r\nthe lengthy process of consensus on the blockchain.
Transacting over payment channel\r\nnetworks also improves privacy as these transactions
are not broadcast to the blockchain.\r\nDespite the influx of recent protocols
built on top of payment channel networks and\r\ntheir analysis, a common shortcoming
of many of these protocols is that they typically\r\nfocus only on either improving
efficiency or privacy, but not both. Another limitation\r\non the efficiency front
is that the models used to model actions, costs and utilities of\r\nusers are
limited or come with unrealistic assumptions.\r\nThis thesis aims to address some
of the shortcomings of recent protocols and algorithms\r\non payment channel networks,
particularly in their privacy and efficiency aspects. We\r\nfirst present a payment
route discovery protocol based on hub labelling and private\r\ninformation retrieval
that hides the route query and is also efficient. We then present\r\na rebalancing
protocol that formulates the rebalancing problem as a linear program\r\nand solves
the linear program using multiparty computation so as to hide the channel\r\nbalances.
The rebalancing solution as output by our protocol is also globally optimal.\r\nWe
go on to develop more realistic models of the action space, costs, and utilities
of\r\nboth existing and new users that want to join the network. In each of these
settings,\r\nwe also develop algorithms to optimise the utility of these users
with good guarantees\r\non the approximation and competitive ratios."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Michelle X
full_name: Yeo, Michelle X
id: 2D82B818-F248-11E8-B48F-1D18A9856A87
last_name: Yeo
citation:
ama: Yeo MX. Advances in efficiency and privacy in payment channel network analysis.
2023. doi:10.15479/14506
apa: Yeo, M. X. (2023). Advances in efficiency and privacy in payment channel
network analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/14506
chicago: Yeo, Michelle X. “Advances in Efficiency and Privacy in Payment Channel
Network Analysis.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14506.
ieee: M. X. Yeo, “Advances in efficiency and privacy in payment channel network
analysis,” Institute of Science and Technology Austria, 2023.
ista: Yeo MX. 2023. Advances in efficiency and privacy in payment channel network
analysis. Institute of Science and Technology Austria.
mla: Yeo, Michelle X. Advances in Efficiency and Privacy in Payment Channel Network
Analysis. Institute of Science and Technology Austria, 2023, doi:10.15479/14506.
short: M.X. Yeo, Advances in Efficiency and Privacy in Payment Channel Network Analysis,
Institute of Science and Technology Austria, 2023.
date_created: 2023-11-10T08:10:43Z
date_published: 2023-11-10T00:00:00Z
date_updated: 2023-11-30T10:54:51Z
day: '10'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: GradSch
- _id: KrPi
doi: 10.15479/14506
ec_funded: 1
file:
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creator: cchlebak
date_created: 2023-11-23T10:29:55Z
date_updated: 2023-11-23T10:29:55Z
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file_name: thesis_yeo.zip
file_size: 3037720
relation: source_file
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checksum: 0ed5d16899687aecf13d843c9878c9f2
content_type: application/pdf
creator: cchlebak
date_created: 2023-11-23T10:30:08Z
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file_id: '14599'
file_name: thesis_yeo.pdf
file_size: 2717256
relation: main_file
success: 1
file_date_updated: 2023-11-23T10:30:08Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '162'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9969'
relation: part_of_dissertation
status: public
- id: '13238'
relation: part_of_dissertation
status: public
- id: '14490'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
title: Advances in efficiency and privacy in payment channel network analysis
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14490'
abstract:
- lang: eng
text: Payment channel networks (PCNs) are a promising solution to the scalability
problem of cryptocurrencies. Any two users connected by a payment channel in the
network can theoretically send an unbounded number of instant, costless transactions
between them. Users who are not directly connected can also transact with each
other in a multi-hop fashion. In this work, we study the incentive structure behind
the creation of payment channel networks, particularly from the point of view
of a single user that wants to join the network. We define a utility function
for a new user in terms of expected revenue, expected fees, and the cost of creating
channels, and then provide constant factor approximation algorithms that optimise
the utility function given a certain budget. Additionally, we take a step back
from a single user to the whole network and examine the parameter spaces under
which simple graph topologies form a Nash equilibrium.
acknowledgement: The work was partially supported by the Austrian Science Fund (FWF)
through the project CoRaF (grant 2020388). It was also partially supported by NCN
Grant 2019/35/B/ST6/04138 and ERC Grant 885666.
article_processing_charge: No
author:
- first_name: Zeta
full_name: Avarikioti, Zeta
last_name: Avarikioti
- first_name: Tomasz
full_name: Lizurej, Tomasz
last_name: Lizurej
- first_name: Tomasz
full_name: Michalak, Tomasz
last_name: Michalak
- first_name: Michelle X
full_name: Yeo, Michelle X
id: 2D82B818-F248-11E8-B48F-1D18A9856A87
last_name: Yeo
citation:
ama: 'Avarikioti Z, Lizurej T, Michalak T, Yeo MX. Lightning creation games. In:
43rd International Conference on Distributed Computing Systems. Vol 2023.
IEEE; 2023:603-613. doi:10.1109/ICDCS57875.2023.00037'
apa: 'Avarikioti, Z., Lizurej, T., Michalak, T., & Yeo, M. X. (2023). Lightning
creation games. In 43rd International Conference on Distributed Computing Systems
(Vol. 2023, pp. 603–613). Hong Kong, China: IEEE. https://doi.org/10.1109/ICDCS57875.2023.00037'
chicago: Avarikioti, Zeta, Tomasz Lizurej, Tomasz Michalak, and Michelle X Yeo.
“Lightning Creation Games.” In 43rd International Conference on Distributed
Computing Systems, 2023:603–13. IEEE, 2023. https://doi.org/10.1109/ICDCS57875.2023.00037.
ieee: Z. Avarikioti, T. Lizurej, T. Michalak, and M. X. Yeo, “Lightning creation
games,” in 43rd International Conference on Distributed Computing Systems,
Hong Kong, China, 2023, vol. 2023, pp. 603–613.
ista: 'Avarikioti Z, Lizurej T, Michalak T, Yeo MX. 2023. Lightning creation games.
43rd International Conference on Distributed Computing Systems. ICDCS: International
Conference on Distributed Computing Systems vol. 2023, 603–613.'
mla: Avarikioti, Zeta, et al. “Lightning Creation Games.” 43rd International
Conference on Distributed Computing Systems, vol. 2023, IEEE, 2023, pp. 603–13,
doi:10.1109/ICDCS57875.2023.00037.
short: Z. Avarikioti, T. Lizurej, T. Michalak, M.X. Yeo, in:, 43rd International
Conference on Distributed Computing Systems, IEEE, 2023, pp. 603–613.
conference:
end_date: 2023-07-21
location: Hong Kong, China
name: 'ICDCS: International Conference on Distributed Computing Systems'
start_date: 2023-07-18
date_created: 2023-11-05T23:00:54Z
date_published: 2023-10-11T00:00:00Z
date_updated: 2023-11-30T10:54:51Z
day: '11'
department:
- _id: KrPi
doi: 10.1109/ICDCS57875.2023.00037
external_id:
arxiv:
- '2306.16006'
intvolume: ' 2023'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2306.16006
month: '10'
oa: 1
oa_version: Preprint
page: 603-613
publication: 43rd International Conference on Distributed Computing Systems
publication_identifier:
eissn:
- 2575-8411
isbn:
- '9798350339864'
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '14506'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Lightning creation games
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2023
year: '2023'
...