---
_id: '17278'
abstract:
- lang: eng
text: An azeotrope is a constant boiling point mixture, and its behavior is important
for fluid separation processes. Predicting azeotropes from atomistic simulations
is difficult due to the complexities and convergence problems of Monte Carlo and
free-energy perturbation techniques. Here, we present a methodology for predicting
the azeotropes of binary mixtures, which computes the compositional dependence
of chemical potentials from molecular dynamics simulations using the S0 method
and employs experimental boiling point and vaporization enthalpy data. Using this
methodology, we reproduce the azeotropes, or lack thereof, in five case studies,
including ethanol/water, ethanol/isooctane, methanol/water, hydrazine/water, and
acetone/chloroform mixtures. We find that it is crucial to use the experimental
boiling point and vaporization enthalpy for reliable azeotrope predictions, as
empirical force fields are not accurate enough for these quantities. Finally,
we use regular solution models to rationalize the azeotropes and reveal that they
tend to form when the mixture components have similar boiling points and strong
interactions.
acknowledgement: B.C. thanks Alessandro Laio, who introduced the phenomenon of azeotrope
and suggested using the S0 method to compute it. B.C. and X.W. thank Felix Wodaczek
for the insightful comments and suggestions on the manuscript. B.C. and X.W. acknowledge
the 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).
article_number: '034111'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Xiaoyu
full_name: Wang, Xiaoyu
id: 8dff9c62-32b0-11ee-9fa8-fc73025e10f3
last_name: Wang
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: Wang X, Cheng B. Integrating molecular dynamics simulations and experimental
data for azeotrope predictions in binary mixtures. Journal of Chemical Physics.
2024;161(3). doi:10.1063/5.0217232
apa: Wang, X., & Cheng, B. (2024). Integrating molecular dynamics simulations
and experimental data for azeotrope predictions in binary mixtures. Journal
of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0217232
chicago: Wang, Xiaoyu, and Bingqing Cheng. “Integrating Molecular Dynamics Simulations
and Experimental Data for Azeotrope Predictions in Binary Mixtures.” Journal
of Chemical Physics. AIP Publishing, 2024. https://doi.org/10.1063/5.0217232.
ieee: X. Wang and B. Cheng, “Integrating molecular dynamics simulations and experimental
data for azeotrope predictions in binary mixtures,” Journal of Chemical Physics,
vol. 161, no. 3. AIP Publishing, 2024.
ista: Wang X, Cheng B. 2024. Integrating molecular dynamics simulations and experimental
data for azeotrope predictions in binary mixtures. Journal of Chemical Physics.
161(3), 034111.
mla: Wang, Xiaoyu, and Bingqing Cheng. “Integrating Molecular Dynamics Simulations
and Experimental Data for Azeotrope Predictions in Binary Mixtures.” Journal
of Chemical Physics, vol. 161, no. 3, 034111, AIP Publishing, 2024, doi:10.1063/5.0217232.
short: X. Wang, B. Cheng, Journal of Chemical Physics 161 (2024).
corr_author: '1'
date_created: 2024-07-21T22:01:00Z
date_published: 2024-07-14T00:00:00Z
date_updated: 2025-09-08T08:26:09Z
day: '14'
department:
- _id: BiCh
- _id: GradSch
doi: 10.1063/5.0217232
external_id:
arxiv:
- '2405.02216'
isi:
- '001281819100016'
pmid:
- '39007379'
intvolume: ' 161'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2405.02216
month: '07'
oa: 1
oa_version: Preprint
pmid: 1
publication: Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/Xiaoyu-Wang-Stone/Azeotrope_S0
scopus_import: '1'
status: public
title: Integrating molecular dynamics simulations and experimental data for azeotrope
predictions in binary mixtures
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 161
year: '2024'
...
---
_id: '17279'
abstract:
- lang: eng
text: In a recent issue of Cell, Zhang et al.1 demonstrate that mechanical features
of a solid tumor can drive T cells into dysfunctionality and identify pathways
that revert this “exhausted” state.
article_processing_charge: No
article_type: review
author:
- first_name: Mario
full_name: Avellaneda Sarrió, Mario
id: DC4BA84C-56E6-11EA-AD5D-348C3DDC885E
last_name: Avellaneda Sarrió
orcid: 0000-0001-6406-524X
- 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: Avellaneda Sarrió M, Sixt MK. Rescuing T cells from stiff tumors. Cell Chemical
Biology. 2024;31(7):1242-1243. doi:10.1016/j.chembiol.2024.06.011
apa: Avellaneda Sarrió, M., & Sixt, M. K. (2024). Rescuing T cells from stiff
tumors. Cell Chemical Biology. Elsevier. https://doi.org/10.1016/j.chembiol.2024.06.011
chicago: Avellaneda Sarrió, Mario, and Michael K Sixt. “Rescuing T Cells from Stiff
Tumors.” Cell Chemical Biology. Elsevier, 2024. https://doi.org/10.1016/j.chembiol.2024.06.011.
ieee: M. Avellaneda Sarrió and M. K. Sixt, “Rescuing T cells from stiff tumors,”
Cell Chemical Biology, vol. 31, no. 7. Elsevier, pp. 1242–1243, 2024.
ista: Avellaneda Sarrió M, Sixt MK. 2024. Rescuing T cells from stiff tumors. Cell
Chemical Biology. 31(7), 1242–1243.
mla: Avellaneda Sarrió, Mario, and Michael K. Sixt. “Rescuing T Cells from Stiff
Tumors.” Cell Chemical Biology, vol. 31, no. 7, Elsevier, 2024, pp. 1242–43,
doi:10.1016/j.chembiol.2024.06.011.
short: M. Avellaneda Sarrió, M.K. Sixt, Cell Chemical Biology 31 (2024) 1242–1243.
corr_author: '1'
date_created: 2024-07-21T22:01:00Z
date_published: 2024-07-18T00:00:00Z
date_updated: 2025-09-08T08:27:03Z
day: '18'
department:
- _id: MiSi
doi: 10.1016/j.chembiol.2024.06.011
external_id:
isi:
- '001275725000001'
pmid:
- '39029454'
intvolume: ' 31'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa_version: None
page: 1242-1243
pmid: 1
publication: Cell Chemical Biology
publication_identifier:
eissn:
- 2451-9448
issn:
- 2451-9456
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Rescuing T cells from stiff tumors
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 31
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '17280'
abstract:
- lang: eng
text: Adherens junction–associated protein 1 (AJAP1) has been implicated in brain
diseases; however, a pathogenic mechanism has not been identified. AJAP1 is widely
expressed in neurons and binds to γ-aminobutyric acid type B receptors (GBRs),
which inhibit neurotransmitter release at most synapses in the brain. Here, we
show that AJAP1 is selectively expressed in dendrites and trans-synaptically recruits
GBRs to presynaptic sites of neurons expressing AJAP1. We have identified several
monoallelic AJAP1 variants in individuals with epilepsy and/or neurodevelopmental
disorders. Specifically, we show that the variant p.(W183C) lacks binding to GBRs,
resulting in the inability to recruit them. Ultrastructural analysis revealed
significantly decreased presynaptic GBR levels in Ajap1−/− and Ajap1W183C/+ mice.
Consequently, these mice exhibited reduced GBR-mediated presynaptic inhibition
at excitatory and inhibitory synapses, along with impaired synaptic plasticity.
Our study reveals that AJAP1 enables the postsynaptic neuron to regulate the level
of presynaptic GBR-mediated inhibition, supporting the clinical relevance of loss-of-function
AJAP1 variants.
acknowledgement: "Ajap1HA/HA and Ajap1W183C/+ mice were generated in collaboration
with Pawel Pelczar at the center for transgenic models at the University of Basel,
Switzerland. We thank the imaging core facility (IMCF, University of Basel) and
in particular A. Ferrand for the technical assistance provided on the OMX 3D-SIM
microscope.\r\nThis work was supported by a grant from the Swiss National Science
Foundation (SNF) to B.B. (31003A-152970, 310030B-201291), an NIH grant to E.A. and
E.H.S. (R01NS058721), DFG grants to B.F. (TRR 152 project ID 239283807, FA 332/15-1,
16-1), and grants to P.S. from AIMS-2-TRIALS, which are supported by the Innovative
Medicines Initiatives from the European Commission joint undertaking under grant
agreement No 777394."
article_number: adk5462
article_processing_charge: Yes
article_type: original
author:
- first_name: Simon
full_name: Früh, Simon
last_name: Früh
- first_name: Sami
full_name: Boudkkazi, Sami
last_name: Boudkkazi
- first_name: Peter
full_name: Koppensteiner, Peter
id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87
last_name: Koppensteiner
orcid: 0000-0002-3509-1948
- first_name: Vita
full_name: Sereikaite, Vita
last_name: Sereikaite
- first_name: Li Yuan
full_name: Chen, Li Yuan
last_name: Chen
- first_name: Diego
full_name: Fernandez-Fernandez, Diego
last_name: Fernandez-Fernandez
- first_name: Pascal D.
full_name: Rem, Pascal D.
last_name: Rem
- first_name: Daniel
full_name: Ulrich, Daniel
last_name: Ulrich
- first_name: Jochen
full_name: Schwenk, Jochen
last_name: Schwenk
- first_name: Ziyang
full_name: Chen, Ziyang
last_name: Chen
- first_name: Elodie Le
full_name: Monnier, Elodie Le
last_name: Monnier
- first_name: Thorsten
full_name: Fritzius, Thorsten
last_name: Fritzius
- first_name: Sabrina M.
full_name: Innocenti, Sabrina M.
last_name: Innocenti
- first_name: Valérie
full_name: Besseyrias, Valérie
last_name: Besseyrias
- first_name: Luca
full_name: Trovò, Luca
last_name: Trovò
- first_name: Michal
full_name: Stawarski, Michal
last_name: Stawarski
- first_name: Emanuela
full_name: Argilli, Emanuela
last_name: Argilli
- first_name: Elliott H.
full_name: Sherr, Elliott H.
last_name: Sherr
- first_name: Bregje
full_name: Van Bon, Bregje
last_name: Van Bon
- first_name: Erik Jan
full_name: Kamsteeg, Erik Jan
last_name: Kamsteeg
- first_name: Maria
full_name: Iascone, Maria
last_name: Iascone
- first_name: Alba
full_name: Pilotta, Alba
last_name: Pilotta
- first_name: Maria R.
full_name: Cutrì, Maria R.
last_name: Cutrì
- first_name: Mahshid S.
full_name: Azamian, Mahshid S.
last_name: Azamian
- first_name: Andrés
full_name: Hernández-García, Andrés
last_name: Hernández-García
- first_name: Seema R.
full_name: Lalani, Seema R.
last_name: Lalani
- first_name: Jill A.
full_name: Rosenfeld, Jill A.
last_name: Rosenfeld
- first_name: Xiaonan
full_name: Zhao, Xiaonan
last_name: Zhao
- first_name: Tiphanie P.
full_name: Vogel, Tiphanie P.
last_name: Vogel
- first_name: Herda
full_name: Ona, Herda
last_name: Ona
- first_name: Daryl A.
full_name: Scott, Daryl A.
last_name: Scott
- first_name: Peter
full_name: Scheiffele, Peter
last_name: Scheiffele
- first_name: Kristian
full_name: Strømgaard, Kristian
last_name: Strømgaard
- first_name: Mehdi
full_name: Tafti, Mehdi
last_name: Tafti
- first_name: Martin
full_name: Gassmann, Martin
last_name: Gassmann
- first_name: Bernd
full_name: Fakler, Bernd
last_name: Fakler
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Bernhard
full_name: Bettler, Bernhard
last_name: Bettler
citation:
ama: Früh S, Boudkkazi S, Koppensteiner P, et al. Monoallelic de novo AJAP1 loss-of-
function variants disrupt trans-synaptic control of neurotransmitter release.
Science Advances. 2024;10(28). doi:10.1126/sciadv.adk5462
apa: Früh, S., Boudkkazi, S., Koppensteiner, P., Sereikaite, V., Chen, L. Y., Fernandez-Fernandez,
D., … Bettler, B. (2024). Monoallelic de novo AJAP1 loss-of- function variants
disrupt trans-synaptic control of neurotransmitter release. Science Advances.
American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.adk5462
chicago: Früh, Simon, Sami Boudkkazi, Peter Koppensteiner, Vita Sereikaite, Li Yuan
Chen, Diego Fernandez-Fernandez, Pascal D. Rem, et al. “Monoallelic de Novo AJAP1
Loss-of- Function Variants Disrupt Trans-Synaptic Control of Neurotransmitter
Release.” Science Advances. American Association for the Advancement of
Science, 2024. https://doi.org/10.1126/sciadv.adk5462.
ieee: S. Früh et al., “Monoallelic de novo AJAP1 loss-of- function variants
disrupt trans-synaptic control of neurotransmitter release,” Science Advances,
vol. 10, no. 28. American Association for the Advancement of Science, 2024.
ista: Früh S, Boudkkazi S, Koppensteiner P, Sereikaite V, Chen LY, Fernandez-Fernandez
D, Rem PD, Ulrich D, Schwenk J, Chen Z, Monnier EL, Fritzius T, Innocenti SM,
Besseyrias V, Trovò L, Stawarski M, Argilli E, Sherr EH, Van Bon B, Kamsteeg EJ,
Iascone M, Pilotta A, Cutrì MR, Azamian MS, Hernández-García A, Lalani SR, Rosenfeld
JA, Zhao X, Vogel TP, Ona H, Scott DA, Scheiffele P, Strømgaard K, Tafti M, Gassmann
M, Fakler B, Shigemoto R, Bettler B. 2024. Monoallelic de novo AJAP1 loss-of-
function variants disrupt trans-synaptic control of neurotransmitter release.
Science Advances. 10(28), adk5462.
mla: Früh, Simon, et al. “Monoallelic de Novo AJAP1 Loss-of- Function Variants Disrupt
Trans-Synaptic Control of Neurotransmitter Release.” Science Advances,
vol. 10, no. 28, adk5462, American Association for the Advancement of Science,
2024, doi:10.1126/sciadv.adk5462.
short: S. Früh, S. Boudkkazi, P. Koppensteiner, V. Sereikaite, L.Y. Chen, D. Fernandez-Fernandez,
P.D. Rem, D. Ulrich, J. Schwenk, Z. Chen, E.L. Monnier, T. Fritzius, S.M. Innocenti,
V. Besseyrias, L. Trovò, M. Stawarski, E. Argilli, E.H. Sherr, B. Van Bon, E.J.
Kamsteeg, M. Iascone, A. Pilotta, M.R. Cutrì, M.S. Azamian, A. Hernández-García,
S.R. Lalani, J.A. Rosenfeld, X. Zhao, T.P. Vogel, H. Ona, D.A. Scott, P. Scheiffele,
K. Strømgaard, M. Tafti, M. Gassmann, B. Fakler, R. Shigemoto, B. Bettler, Science
Advances 10 (2024).
date_created: 2024-07-21T22:01:01Z
date_published: 2024-07-12T00:00:00Z
date_updated: 2025-09-08T08:15:54Z
day: '12'
ddc:
- '570'
department:
- _id: RySh
- _id: PreCl
doi: 10.1126/sciadv.adk5462
external_id:
isi:
- '001280159000022'
pmid:
- '38985877'
file:
- access_level: open_access
checksum: 9cbc4501fcd4ba1c0811fd244031422b
content_type: application/pdf
creator: dernst
date_created: 2024-07-22T06:29:27Z
date_updated: 2024-07-22T06:29:27Z
file_id: '17287'
file_name: 2024_ScienceAdv_Früh.pdf
file_size: 7241489
relation: main_file
success: 1
file_date_updated: 2024-07-22T06:29:27Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '28'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Science Advances
publication_identifier:
eissn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Monoallelic de novo AJAP1 loss-of- function variants disrupt trans-synaptic
control of neurotransmitter release
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 10
year: '2024'
...
---
_id: '17281'
abstract:
- lang: eng
text: We extend the free convolution of Brown measures of R-diagonal elements introduced
by Kösters and Tikhomirov [ 28] to fractional powers. We then show how this fractional
free convolution arises naturally when studying the roots of random polynomials
with independent coefficients under repeated differentiation. When the proportion
of derivatives to the degree approaches one, we establish central limit theorem-type
behavior and discuss stable distributions.
acknowledgement: This work was supported by the National Science Foundation [Grant
No. DMS-2143142 to S.O.]; and the European Research Council [Grant No. 101020331].The
third author acknowledges the support of the University of Colorado Boulder, where
a portion of this work was completed. The authors thank Martin Auer, Vadim Gorin,
Brian Hall, and Noah Williams for comments, corrections, and references. The authors
also wish to thank the anonymous referees for useful feedback and corrections.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Andrew J
full_name: Campbell, Andrew J
id: 582b06a9-1f1c-11ee-b076-82ffce00dde4
last_name: Campbell
- first_name: Sean
full_name: O'Rourke, Sean
last_name: O'Rourke
- first_name: David T
full_name: Renfrew, David T
id: 4845BF6A-F248-11E8-B48F-1D18A9856A87
last_name: Renfrew
orcid: 0000-0003-3493-121X
citation:
ama: Campbell AJ, O’Rourke S, Renfrew DT. The fractional free convolution of R-diagonal
elements and random polynomials under repeated differentiation. International
Mathematics Research Notices. 2024;2024(13):10189-10218. doi:10.1093/imrn/rnae062
apa: Campbell, A. J., O’Rourke, S., & Renfrew, D. T. (2024). The fractional
free convolution of R-diagonal elements and random polynomials under repeated
differentiation. International Mathematics Research Notices. Oxford University
Press. https://doi.org/10.1093/imrn/rnae062
chicago: Campbell, Andrew J, Sean O’Rourke, and David T Renfrew. “The Fractional
Free Convolution of R-Diagonal Elements and Random Polynomials under Repeated
Differentiation.” International Mathematics Research Notices. Oxford University
Press, 2024. https://doi.org/10.1093/imrn/rnae062.
ieee: A. J. Campbell, S. O’Rourke, and D. T. Renfrew, “The fractional free convolution
of R-diagonal elements and random polynomials under repeated differentiation,”
International Mathematics Research Notices, vol. 2024, no. 13. Oxford University
Press, pp. 10189–10218, 2024.
ista: Campbell AJ, O’Rourke S, Renfrew DT. 2024. The fractional free convolution
of R-diagonal elements and random polynomials under repeated differentiation.
International Mathematics Research Notices. 2024(13), 10189–10218.
mla: Campbell, Andrew J., et al. “The Fractional Free Convolution of R-Diagonal
Elements and Random Polynomials under Repeated Differentiation.” International
Mathematics Research Notices, vol. 2024, no. 13, Oxford University Press,
2024, pp. 10189–218, doi:10.1093/imrn/rnae062.
short: A.J. Campbell, S. O’Rourke, D.T. Renfrew, International Mathematics Research
Notices 2024 (2024) 10189–10218.
corr_author: '1'
date_created: 2024-07-21T22:01:01Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2025-09-08T08:16:32Z
day: '01'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1093/imrn/rnae062
external_id:
isi:
- '001198019500001'
file:
- access_level: open_access
checksum: f36a7dbf53f23d5833db711052e69b49
content_type: application/pdf
creator: dernst
date_created: 2024-07-22T06:40:19Z
date_updated: 2024-07-22T06:40:19Z
file_id: '17288'
file_name: 2024_IMRN_Campbell.pdf
file_size: 1233508
relation: main_file
success: 1
file_date_updated: 2024-07-22T06:40:19Z
has_accepted_license: '1'
intvolume: ' 2024'
isi: 1
issue: '13'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 10189-10218
publication: International Mathematics Research Notices
publication_identifier:
eissn:
- 1687-0247
issn:
- 1073-7928
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: The fractional free convolution of R-diagonal elements and random polynomials
under repeated differentiation
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 2024
year: '2024'
...
---
_id: '17282'
abstract:
- lang: eng
text: Let X be a vector field and Y be a co-vector field on a smooth manifold M.
Does there exist a smooth Riemannian metric gαβ on M such that Yβ=gαβXα ?
The main result of this note gives necessary and sufficient conditions for this
to be true. As an application of this result we show that a finite-dimensional
ergodic Lindblad equation admits a gradient flow structure for the von Neumann
relative entropy if and only if the condition of BKM-detailed balance holds.
acknowledgement: Open access funding provided by Institute of Science and Technology
(IST Austria).J. M. gratefully acknowledges support by the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreement No 716117), and by the Austrian Science Fund (FWF), Project SFB
F65. We thank the anonymous referee for valuable comments on the paper.
article_number: '153'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Morris
full_name: Brooks, Morris
id: B7ECF9FC-AA38-11E9-AC9A-0930E6697425
last_name: Brooks
orcid: 0000-0002-6249-0928
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
citation:
ama: Brooks M, Maas J. Characterisation of gradient flows for a given functional.
Calculus of Variations and Partial Differential Equations. 2024;63(6).
doi:10.1007/s00526-024-02755-z
apa: Brooks, M., & Maas, J. (2024). Characterisation of gradient flows for a
given functional. Calculus of Variations and Partial Differential Equations.
Springer Nature. https://doi.org/10.1007/s00526-024-02755-z
chicago: Brooks, Morris, and Jan Maas. “Characterisation of Gradient Flows for a
given Functional.” Calculus of Variations and Partial Differential Equations.
Springer Nature, 2024. https://doi.org/10.1007/s00526-024-02755-z.
ieee: M. Brooks and J. Maas, “Characterisation of gradient flows for a given functional,”
Calculus of Variations and Partial Differential Equations, vol. 63, no.
6. Springer Nature, 2024.
ista: Brooks M, Maas J. 2024. Characterisation of gradient flows for a given functional.
Calculus of Variations and Partial Differential Equations. 63(6), 153.
mla: Brooks, Morris, and Jan Maas. “Characterisation of Gradient Flows for a given
Functional.” Calculus of Variations and Partial Differential Equations,
vol. 63, no. 6, 153, Springer Nature, 2024, doi:10.1007/s00526-024-02755-z.
short: M. Brooks, J. Maas, Calculus of Variations and Partial Differential Equations
63 (2024).
corr_author: '1'
date_created: 2024-07-21T22:01:01Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2025-09-08T08:24:51Z
day: '01'
ddc:
- '510'
department:
- _id: JaMa
doi: 10.1007/s00526-024-02755-z
ec_funded: 1
external_id:
arxiv:
- '2209.11149'
isi:
- '001258097800003'
pmid:
- '38947856'
file:
- access_level: open_access
checksum: a0cf0e0ba2157aabb287cb597be17dac
content_type: application/pdf
creator: dernst
date_created: 2024-07-22T07:05:32Z
date_updated: 2024-07-22T07:05:32Z
file_id: '17289'
file_name: 2024_CalculusVariations_Brooks.pdf
file_size: 416622
relation: main_file
success: 1
file_date_updated: 2024-07-22T07:05:32Z
has_accepted_license: '1'
intvolume: ' 63'
isi: 1
issue: '6'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
publication: Calculus of Variations and Partial Differential Equations
publication_identifier:
eissn:
- 1432-0835
issn:
- 0944-2669
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Characterisation of gradient flows for a given functional
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 63
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '17283'
abstract:
- lang: eng
text: 'We consider the problems of statically refuting equivalence and similarity
of output distributions defined by a pair of probabilistic programs. Equivalence
and similarity are two fundamental relational properties of probabilistic programs
that are essential for their correctness both in implementation and in compilation.
In this work, we present a new method for static equivalence and similarity refutation.
Our method refutes equivalence and similarity by computing a function over program
outputs whose expected value with respect to the output distributions of two programs
is different. The function is computed simultaneously with an upper expectation
supermartingale and a lower expectation submartingale for the two programs, which
we show to together provide a formal certificate for refuting equivalence and
similarity. To the best of our knowledge, our method is the first approach to
relational program analysis to offer the combination of the following desirable
features: (1) it is fully automated, (2) it is applicable to infinite-state probabilistic
programs, and (3) it provides formal guarantees on the correctness of its results.
We implement a prototype of our method and our experiments demonstrate the effectiveness
of our method to refute equivalence and similarity for a number of examples collected
from the literature.'
acknowledgement: "This research was partially supported by the ERC CoG 863818 (ForM-SMArt)
grant. Petr Novotný\r\nis supported by the Czech Science Foundation grant no. GA23-06963S.\r\n"
article_number: '232'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Ehsan
full_name: Kafshdar Goharshadi, Ehsan
id: 103b4fa0-896a-11ed-bdf8-87b697bef40d
last_name: Kafshdar Goharshadi
orcid: 0000-0002-8595-0587
- first_name: Petr
full_name: Novotný, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotný
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
citation:
ama: Chatterjee K, Goharshady E, Novotný P, Zikelic D. Equivalence and similarity
refutation for probabilistic programs. Proceedings of the ACM on Programming
Languages. 2024;8. doi:10.1145/3656462
apa: Chatterjee, K., Goharshady, E., Novotný, P., & Zikelic, D. (2024). Equivalence
and similarity refutation for probabilistic programs. Proceedings of the ACM
on Programming Languages. Association for Computing Machinery. https://doi.org/10.1145/3656462
chicago: Chatterjee, Krishnendu, Ehsan Goharshady, Petr Novotný, and Dorde Zikelic.
“Equivalence and Similarity Refutation for Probabilistic Programs.” Proceedings
of the ACM on Programming Languages. Association for Computing Machinery,
2024. https://doi.org/10.1145/3656462.
ieee: K. Chatterjee, E. Goharshady, P. Novotný, and D. Zikelic, “Equivalence and
similarity refutation for probabilistic programs,” Proceedings of the ACM on
Programming Languages, vol. 8. Association for Computing Machinery, 2024.
ista: Chatterjee K, Goharshady E, Novotný P, Zikelic D. 2024. Equivalence and similarity
refutation for probabilistic programs. Proceedings of the ACM on Programming Languages.
8, 232.
mla: Chatterjee, Krishnendu, et al. “Equivalence and Similarity Refutation for Probabilistic
Programs.” Proceedings of the ACM on Programming Languages, vol. 8, 232,
Association for Computing Machinery, 2024, doi:10.1145/3656462.
short: K. Chatterjee, E. Goharshady, P. Novotný, D. Zikelic, Proceedings of the
ACM on Programming Languages 8 (2024).
corr_author: '1'
date_created: 2024-07-21T22:01:01Z
date_published: 2024-06-20T00:00:00Z
date_updated: 2025-04-14T07:52:47Z
day: '20'
ddc:
- '000'
department:
- _id: KrCh
- _id: GradSch
doi: 10.1145/3656462
ec_funded: 1
external_id:
arxiv:
- '2404.03430'
file:
- access_level: open_access
checksum: 8cbf220f284a4a87d093db5320c5afdd
content_type: application/pdf
creator: dernst
date_created: 2024-07-22T07:17:14Z
date_updated: 2024-07-22T07:17:14Z
file_id: '17290'
file_name: 2024_ACMProgLang_Chatterjee.pdf
file_size: 355421
relation: main_file
success: 1
file_date_updated: 2024-07-22T07:17:14Z
has_accepted_license: '1'
intvolume: ' 8'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Proceedings of the ACM on Programming Languages
publication_identifier:
eissn:
- 2475-1421
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Equivalence and similarity refutation for probabilistic programs
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: 8
year: '2024'
...
---
_id: '17284'
abstract:
- lang: eng
text: Platelet homeostasis is essential for vascular integrity and immune defence1,2.
Although the process of platelet formation by fragmenting megakaryocytes (MKs;
thrombopoiesis) has been extensively studied, the cellular and molecular mechanisms
required to constantly replenish the pool of MKs by their progenitor cells (megakaryopoiesis)
remains unclear3,4. Here we use intravital imaging to track the cellular dynamics
of megakaryopoiesis over days. We identify plasmacytoid dendritic cells (pDCs)
as homeostatic sensors that monitor the bone marrow for apoptotic MKs and deliver
IFNα to the MK niche triggering local on-demand proliferation and maturation of
MK progenitors. This pDC-dependent feedback loop is crucial for MK and platelet
homeostasis at steady state and under stress. pDCs are best known for their ability
to function as vigilant detectors of viral infection5. We show that virus-induced
activation of pDCs interferes with their function as homeostatic sensors of megakaryopoiesis.
Consequently, activation of pDCs by SARS-CoV-2 leads to excessive megakaryopoiesis.
Together, we identify a pDC-dependent homeostatic circuit that involves innate
immune sensing and demand-adapted release of inflammatory mediators to maintain
homeostasis of the megakaryocytic lineage.
acknowledgement: 'We thank S. Helmer, N. Blount, E. Raatz and Z. Sisic for technical
assistance. This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German
Research Foundation) SFB 1123 (S.M. project B06); SFB 914 (S.M. projects B02 and
Z01, H.I.-A. project Z01, S.S. project A06, K.S. project B02, C. Schulz project
A10, B.W. project A02, C. Scheiermann project B09); SFB 1054 (T.B. project B03);
FOR2033 (F.G., R.A.J.O., S.M.); Individual research grant project ID: 514478744
(F.G.); Heisenberg Programme project ID: 514477451 (F.G.); the DZHK (German Center
for Cardiovascular Research) (MHA 1.4VD (S.M.), Postdoc Start-up Grant, 81×3600213
(F.G.)); and LMUexcellence NFF (F.G.). W.F. received funding from China Scholarship
Council (CSC, no. 201306270012). P.B. is supported by the German Research Foundation
(DFG, project IDs 322900939, 432698239 and 445703531), European Research Council
(ERC Consolidator grant no. 101001791) and the Federal Ministry of Education and
Research (BMBF, STOP-FSGS-01GM2202C and NATON within the framework of the Network
of University Medicine, no. 01KX2121). S.v.S. is supported by the START-Program
of the Faculty of Medicine of the RWTH Aachen University (AZ 125/17). A.D. and S.E.
are supported by the German Research Foundation (SFB TRR 267); S.E. by the BMBF
in the framework of the Cluster4future program (CNATM—Cluster for Nucleic Acid Therapeutics
Munich). 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. 833440 to S.M.). F.G. received funding from the European Union’s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement
no. 747687. The project is funded by the European Union (ERC, MEKanics, 101078110).
Views and opinions expressed are those of the author(s) only and do not necessarily
reflect those of the European Union or the European Research Council Executive Agency.
Neither the European Union nor the granting authority can be held responsible for
them.'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Florian R
full_name: Gärtner, Florian R
id: 397A88EE-F248-11E8-B48F-1D18A9856A87
last_name: Gärtner
orcid: 0000-0001-6120-3723
- first_name: Hellen
full_name: Ishikawa-Ankerhold, Hellen
last_name: Ishikawa-Ankerhold
- first_name: Susanne
full_name: Stutte, Susanne
last_name: Stutte
- first_name: Wenwen
full_name: Fu, Wenwen
last_name: Fu
- first_name: Jutta
full_name: Weitz, Jutta
last_name: Weitz
- first_name: Anne
full_name: Dueck, Anne
last_name: Dueck
- first_name: Bhavishya
full_name: Nelakuditi, Bhavishya
last_name: Nelakuditi
- first_name: Valeria
full_name: Fumagalli, Valeria
last_name: Fumagalli
- first_name: Dominic
full_name: Van Den Heuvel, Dominic
last_name: Van Den Heuvel
- first_name: Larissa
full_name: Belz, Larissa
last_name: Belz
- first_name: Gulnoza
full_name: Sobirova, Gulnoza
last_name: Sobirova
- first_name: Zhe
full_name: Zhang, Zhe
last_name: Zhang
- first_name: Anna
full_name: Titova, Anna
last_name: Titova
- first_name: Alejandro Martinez
full_name: Navarro, Alejandro Martinez
last_name: Navarro
- first_name: Kami
full_name: Pekayvaz, Kami
last_name: Pekayvaz
- first_name: Michael
full_name: Lorenz, Michael
last_name: Lorenz
- first_name: Louisa
full_name: Von Baumgarten, Louisa
last_name: Von Baumgarten
- first_name: Jan
full_name: Kranich, Jan
last_name: Kranich
- first_name: Tobias
full_name: Straub, Tobias
last_name: Straub
- first_name: Bastian
full_name: Popper, Bastian
last_name: Popper
- first_name: Vanessa
full_name: Zheden, Vanessa
id: 39C5A68A-F248-11E8-B48F-1D18A9856A87
last_name: Zheden
orcid: 0000-0002-9438-4783
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: Chenglong
full_name: Guo, Chenglong
last_name: Guo
- first_name: Guido
full_name: Piontek, Guido
last_name: Piontek
- first_name: Saskia
full_name: Von Stillfried, Saskia
last_name: Von Stillfried
- first_name: Peter
full_name: Boor, Peter
last_name: Boor
- first_name: Marco
full_name: Colonna, Marco
last_name: Colonna
- first_name: Sebastian
full_name: Clauß, Sebastian
last_name: Clauß
- first_name: Christian
full_name: Schulz, Christian
last_name: Schulz
- first_name: Thomas
full_name: Brocker, Thomas
last_name: Brocker
- first_name: Barbara
full_name: Walzog, Barbara
last_name: Walzog
- first_name: Christoph
full_name: Scheiermann, Christoph
last_name: Scheiermann
- first_name: William C.
full_name: Aird, William C.
last_name: Aird
- first_name: Claus
full_name: Nerlov, Claus
last_name: Nerlov
- first_name: Konstantin
full_name: Stark, Konstantin
last_name: Stark
- first_name: Tobias
full_name: Petzold, Tobias
last_name: Petzold
- first_name: Stefan
full_name: Engelhardt, Stefan
last_name: Engelhardt
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Martina
full_name: Rudelius, Martina
last_name: Rudelius
- first_name: Robert A.J.
full_name: Oostendorp, Robert A.J.
last_name: Oostendorp
- first_name: Matteo
full_name: Iannacone, Matteo
last_name: Iannacone
- first_name: Matthias
full_name: Heinig, Matthias
last_name: Heinig
- first_name: Steffen
full_name: Massberg, Steffen
last_name: Massberg
citation:
ama: Gärtner FR, Ishikawa-Ankerhold H, Stutte S, et al. Plasmacytoid dendritic cells
control homeostasis of megakaryopoiesis. Nature. 2024;631:645-653. doi:10.1038/s41586-024-07671-y
apa: Gärtner, F. R., Ishikawa-Ankerhold, H., Stutte, S., Fu, W., Weitz, J., Dueck,
A., … Massberg, S. (2024). Plasmacytoid dendritic cells control homeostasis of
megakaryopoiesis. Nature. Springer Nature. https://doi.org/10.1038/s41586-024-07671-y
chicago: Gärtner, Florian R, Hellen Ishikawa-Ankerhold, Susanne Stutte, Wenwen Fu,
Jutta Weitz, Anne Dueck, Bhavishya Nelakuditi, et al. “Plasmacytoid Dendritic
Cells Control Homeostasis of Megakaryopoiesis.” Nature. Springer Nature,
2024. https://doi.org/10.1038/s41586-024-07671-y.
ieee: F. R. Gärtner et al., “Plasmacytoid dendritic cells control homeostasis
of megakaryopoiesis,” Nature, vol. 631. Springer Nature, pp. 645–653, 2024.
ista: Gärtner FR, Ishikawa-Ankerhold H, Stutte S, Fu W, Weitz J, Dueck A, Nelakuditi
B, Fumagalli V, Van Den Heuvel D, Belz L, Sobirova G, Zhang Z, Titova A, Navarro
AM, Pekayvaz K, Lorenz M, Von Baumgarten L, Kranich J, Straub T, Popper B, Zheden
V, Kaufmann W, Guo C, Piontek G, Von Stillfried S, Boor P, Colonna M, Clauß S,
Schulz C, Brocker T, Walzog B, Scheiermann C, Aird WC, Nerlov C, Stark K, Petzold
T, Engelhardt S, Sixt MK, Hauschild R, Rudelius M, Oostendorp RAJ, Iannacone M,
Heinig M, Massberg S. 2024. Plasmacytoid dendritic cells control homeostasis of
megakaryopoiesis. Nature. 631, 645–653.
mla: Gärtner, Florian R., et al. “Plasmacytoid Dendritic Cells Control Homeostasis
of Megakaryopoiesis.” Nature, vol. 631, Springer Nature, 2024, pp. 645–53,
doi:10.1038/s41586-024-07671-y.
short: F.R. Gärtner, H. Ishikawa-Ankerhold, S. Stutte, W. Fu, J. Weitz, A. Dueck,
B. Nelakuditi, V. Fumagalli, D. Van Den Heuvel, L. Belz, G. Sobirova, Z. Zhang,
A. Titova, A.M. Navarro, K. Pekayvaz, M. Lorenz, L. Von Baumgarten, J. Kranich,
T. Straub, B. Popper, V. Zheden, W. Kaufmann, C. Guo, G. Piontek, S. Von Stillfried,
P. Boor, M. Colonna, S. Clauß, C. Schulz, T. Brocker, B. Walzog, C. Scheiermann,
W.C. Aird, C. Nerlov, K. Stark, T. Petzold, S. Engelhardt, M.K. Sixt, R. Hauschild,
M. Rudelius, R.A.J. Oostendorp, M. Iannacone, M. Heinig, S. Massberg, Nature 631
(2024) 645–653.
corr_author: '1'
date_created: 2024-07-21T22:01:02Z
date_published: 2024-07-18T00:00:00Z
date_updated: 2025-09-08T08:14:25Z
day: '18'
ddc:
- '570'
department:
- _id: EM-Fac
- _id: MiSi
- _id: Bio
doi: 10.1038/s41586-024-07671-y
ec_funded: 1
external_id:
isi:
- '001281636500020'
pmid:
- '38987596'
file:
- access_level: open_access
checksum: aa004afc72d2489f0fb0fcbc9919fbbd
content_type: application/pdf
creator: dernst
date_created: 2024-07-22T06:16:11Z
date_updated: 2024-07-22T06:16:11Z
file_id: '17286'
file_name: 2024_Nature_Gaertner.pdf
file_size: 15704819
relation: main_file
success: 1
file_date_updated: 2024-07-22T06:16:11Z
has_accepted_license: '1'
intvolume: ' 631'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 645-653
pmid: 1
project:
- _id: 260AA4E2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '747687'
name: Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/heiniglab/gaertner_megakaryocytes
scopus_import: '1'
status: public
title: Plasmacytoid dendritic cells control homeostasis of megakaryopoiesis
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 631
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '17285'
abstract:
- lang: eng
text: Winter plants rely on vernalization, a crucial process for adapting to cold
conditions and ensuring successful reproduction. However, understanding the role
of histone modifications in guiding the vernalization process in winter wheat
remains limited. In this study, we investigated the transcriptome and chromatin
dynamics in the shoot apex throughout the life cycle of winter wheat in the field.
Two core histone modifications, H3K27me3 and H3K36me3, exhibited opposite patterns
on the key vernalization gene VERNALIZATION1 (VRN1), correlating with its induction
during cold exposure. Moreover, the H3K36me3 level remained high at VRN1 after
cold exposure, which may maintain its active state. Mutations in FERTILIZATION-INDEPENDENT
ENDOSPERM (TaFIE) and SET DOMAIN GROUP 8/EARLY FLOWERING IN SHORT DAYS (TaSDG8/TaEFS),
components of the writer complex for H3K27me3 and H3K36me3, respectively, affected
flowering time. Intriguingly, VRN1 lost its high expression after the cold exposure
memory in the absence of H3K36me3. During embryo development, VRN1 was silenced
with the removal of active histone modifications in both winter and spring wheat,
with selective restoration of H3K27me3 in winter wheat. The mutant of Tafie-cr-87,
a component of H3K27me3 “writer” complex, did not influence the silence of VRN1
during embryo development, but rather attenuated the cold exposure requirement
of winter wheat. Integrating gene expression with H3K27me3 and H3K36me3 patterns
identified potential regulators of flowering. This study unveils distinct roles
of H3K27me3 and H3K36me3 in controlling vernalization response, maintenance, and
resetting in winter wheat.
acknowledgement: We thank Prof. Kang Chong from Institute of Botany, the Chinese Academy
of Science for valuable comments, Dr. Haoran Li for the help with western blot of
H3K36me3 in Tasdg8-cr lines. This research was supported by National Natural Science
Foundation (31970529), Beijing Natural Science Foundation Outstanding Youth Project
(JQ23026), National Key Research and Development Program of China (2021YFD1201500),
and the Major Basic Research Program of Shandong Natural Science Foundation (ZR2019ZD15).
article_processing_charge: No
article_type: original
author:
- first_name: Xuemei
full_name: Liu, Xuemei
last_name: Liu
- first_name: Min
full_name: Deng, Min
last_name: Deng
- first_name: Bingxin
full_name: Shi, Bingxin
last_name: Shi
- first_name: Kehui
full_name: Zhu, Kehui
last_name: Zhu
- first_name: Jinchao
full_name: Chen, Jinchao
last_name: Chen
- first_name: Shujuan
full_name: Xu, Shujuan
id: 9724dd9d-f591-11ee-bd51-e97ed0652286
last_name: Xu
- first_name: Xiaomin
full_name: Bie, Xiaomin
last_name: Bie
- first_name: Xiansheng
full_name: Zhang, Xiansheng
last_name: Zhang
- first_name: Xuelei
full_name: Lin, Xuelei
last_name: Lin
- first_name: Jun
full_name: Xiao, Jun
last_name: Xiao
citation:
ama: Liu X, Deng M, Shi B, et al. Distinct roles of H3K27me3 and H3K36me3 in vernalization
response, maintenance, and resetting in winter wheat. Science China Life Sciences.
2024;67:2251-2266. doi:10.1007/s11427-024-2664-0
apa: Liu, X., Deng, M., Shi, B., Zhu, K., Chen, J., Xu, S., … Xiao, J. (2024). Distinct
roles of H3K27me3 and H3K36me3 in vernalization response, maintenance, and resetting
in winter wheat. Science China Life Sciences. Springer Nature. https://doi.org/10.1007/s11427-024-2664-0
chicago: Liu, Xuemei, Min Deng, Bingxin Shi, Kehui Zhu, Jinchao Chen, Shujuan Xu,
Xiaomin Bie, Xiansheng Zhang, Xuelei Lin, and Jun Xiao. “Distinct Roles of H3K27me3
and H3K36me3 in Vernalization Response, Maintenance, and Resetting in Winter Wheat.”
Science China Life Sciences. Springer Nature, 2024. https://doi.org/10.1007/s11427-024-2664-0.
ieee: X. Liu et al., “Distinct roles of H3K27me3 and H3K36me3 in vernalization
response, maintenance, and resetting in winter wheat,” Science China Life Sciences,
vol. 67. Springer Nature, pp. 2251–2266, 2024.
ista: Liu X, Deng M, Shi B, Zhu K, Chen J, Xu S, Bie X, Zhang X, Lin X, Xiao J.
2024. Distinct roles of H3K27me3 and H3K36me3 in vernalization response, maintenance,
and resetting in winter wheat. Science China Life Sciences. 67, 2251–2266.
mla: Liu, Xuemei, et al. “Distinct Roles of H3K27me3 and H3K36me3 in Vernalization
Response, Maintenance, and Resetting in Winter Wheat.” Science China Life Sciences,
vol. 67, Springer Nature, 2024, pp. 2251–66, doi:10.1007/s11427-024-2664-0.
short: X. Liu, M. Deng, B. Shi, K. Zhu, J. Chen, S. Xu, X. Bie, X. Zhang, X. Lin,
J. Xiao, Science China Life Sciences 67 (2024) 2251–2266.
date_created: 2024-07-21T22:01:02Z
date_published: 2024-10-01T00:00:00Z
date_updated: 2025-09-08T08:15:08Z
day: '01'
department:
- _id: XiFe
doi: 10.1007/s11427-024-2664-0
external_id:
isi:
- '001268807700002'
pmid:
- '38987431'
intvolume: ' 67'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2023.12.19.572364
month: '10'
oa: 1
oa_version: Preprint
page: 2251-2266
pmid: 1
publication: Science China Life Sciences
publication_identifier:
eissn:
- 1869-1889
issn:
- 1674-7305
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Distinct roles of H3K27me3 and H3K36me3 in vernalization response, maintenance,
and resetting in winter wheat
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 67
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '17291'
abstract:
- lang: eng
text: Bacterial cell walls are gigadalton-large cross-linked polymers with a wide
range of motional amplitudes, including rather rigid as well as highly flexible
parts. Magic-angle spinning NMR is a powerful method to obtain atomic-level information
about intact cell walls. Here we investigate sensitivity and information content
of different homonuclear 13Csingle bond13C and heteronuclear 1Hsingle bond15N,
1Hsingle bond13C and 15Nsingle bond13C correlation experiments. We demonstrate
that a CPMAS CryoProbe yields ca. 8-fold increased signal-to-noise over a room-temperature
probe, or a ca. 3–4-fold larger per-mass sensitivity. The increased sensitivity
allowed to obtain high-resolution spectra even on intact bacteria. Moreover, we
compare resolution and sensitivity of 1H MAS experiments obtained at 100 kHz vs.
55 kHz. Our study provides useful hints for choosing experiments to extract atomic-level
details on cell-wall samples.
acknowledgement: "This research was supported by the French Agence Nationale de la
Recherche (\r\nANR-16-CE11-0030-12, TransPepNMR). This work used the platforms of
the Grenoble Instruct-ERIC center (ISBG; UAR 3518 CNRS-CEA-UGA-EMBL) within the
Grenoble Partnership for Structural Biology (PSB), supported by FRISBI, France (ANR-10-INBS-0005-02\r\n)
and GRAL, financed within the University Grenoble Alpes graduate school (Ecoles
Universitaires de Recherche), CBH-EUR-GS (ANR-17-EURE-0003). Financial support from
the IR INFRANALYTICS FR2054 for conducting the research and intramural funding by
the Institute of Science and Technology Austria (ISTA) are gratefully acknowledged."
article_number: '107708'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Alicia
full_name: Vallet, Alicia
last_name: Vallet
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Barbara
full_name: Perrone, Barbara
last_name: Perrone
- first_name: Alia
full_name: Hassan, Alia
last_name: Hassan
- first_name: Jean-Pierre
full_name: Simorre, Jean-Pierre
last_name: Simorre
- first_name: Catherine
full_name: Bougault, Catherine
last_name: Bougault
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: 'Vallet A, Ayala I, Perrone B, et al. MAS NMR experiments of corynebacterial
cell walls: Complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments.
Journal of Magnetic Resonance. 2024;364. doi:10.1016/j.jmr.2024.107708'
apa: 'Vallet, A., Ayala, I., Perrone, B., Hassan, A., Simorre, J.-P., Bougault,
C., & Schanda, P. (2024). MAS NMR experiments of corynebacterial cell walls:
Complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments. Journal
of Magnetic Resonance. Elsevier. https://doi.org/10.1016/j.jmr.2024.107708'
chicago: 'Vallet, Alicia, Isabel Ayala, Barbara Perrone, Alia Hassan, Jean-Pierre
Simorre, Catherine Bougault, and Paul Schanda. “MAS NMR Experiments of Corynebacterial
Cell Walls: Complementary 1H- and CPMAS CryoProbe-Enhanced 13C-Detected Experiments.”
Journal of Magnetic Resonance. Elsevier, 2024. https://doi.org/10.1016/j.jmr.2024.107708.'
ieee: 'A. Vallet et al., “MAS NMR experiments of corynebacterial cell walls:
Complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments,” Journal
of Magnetic Resonance, vol. 364. Elsevier, 2024.'
ista: 'Vallet A, Ayala I, Perrone B, Hassan A, Simorre J-P, Bougault C, Schanda
P. 2024. MAS NMR experiments of corynebacterial cell walls: Complementary 1H-
and CPMAS CryoProbe-enhanced 13C-detected experiments. Journal of Magnetic Resonance.
364, 107708.'
mla: 'Vallet, Alicia, et al. “MAS NMR Experiments of Corynebacterial Cell Walls:
Complementary 1H- and CPMAS CryoProbe-Enhanced 13C-Detected Experiments.” Journal
of Magnetic Resonance, vol. 364, 107708, Elsevier, 2024, doi:10.1016/j.jmr.2024.107708.'
short: A. Vallet, I. Ayala, B. Perrone, A. Hassan, J.-P. Simorre, C. Bougault, P.
Schanda, Journal of Magnetic Resonance 364 (2024).
corr_author: '1'
date_created: 2024-07-22T07:44:10Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2025-09-09T12:01:41Z
day: '01'
ddc:
- '570'
department:
- _id: PaSc
doi: 10.1016/j.jmr.2024.107708
external_id:
isi:
- '001259302800001'
pmid:
- '38901173'
file:
- access_level: open_access
checksum: 4b59f4f0c287ecbafd808da1212ced38
content_type: application/pdf
creator: dernst
date_created: 2024-07-23T06:23:51Z
date_updated: 2024-07-23T06:23:51Z
file_id: '17316'
file_name: 2024_JourMagneticResonance_Vallet.pdf
file_size: 2236665
relation: main_file
success: 1
file_date_updated: 2024-07-23T06:23:51Z
has_accepted_license: '1'
intvolume: ' 364'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Journal of Magnetic Resonance
publication_identifier:
issn:
- 1090-7807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '17042'
relation: research_data
status: public
scopus_import: '1'
status: public
title: 'MAS NMR experiments of corynebacterial cell walls: Complementary 1H- and CPMAS
CryoProbe-enhanced 13C-detected experiments'
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 364
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '17292'
abstract:
- lang: eng
text: The Gibbons-Hawking ansatz provides a large family of circle-invariant hyperkähler
4-manifolds, and thus Calabi-Yau 2-folds. In this setting, we prove versions of
the Thomas conjecture on existence of special Lagrangian representatives of Hamiltonian
isotopy classes of Lagrangians, and the Thomas-Yau conjecture on longtime existence
of the Lagrangian mean curvature ow. We also make observations concerning closed
geodesics, curve shortening flow and minimal surfaces.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Jason D.
full_name: Lotay, Jason D.
last_name: Lotay
- first_name: Goncalo
full_name: Oliveira, Goncalo
id: 58abbde8-f455-11eb-a497-98c8fd71b905
last_name: Oliveira
citation:
ama: Lotay JD, Oliveira G. Special Lagrangians, Lagrangian mean curvature flow and
the Gibbons-Hawking ansatz. Journal of Differential Geometry. 2024;126(3):1121-1184.
doi:10.4310/jdg/1717348872
apa: Lotay, J. D., & Oliveira, G. (2024). Special Lagrangians, Lagrangian mean
curvature flow and the Gibbons-Hawking ansatz. Journal of Differential Geometry.
International Press. https://doi.org/10.4310/jdg/1717348872
chicago: Lotay, Jason D., and Goncalo Oliveira. “Special Lagrangians, Lagrangian
Mean Curvature Flow and the Gibbons-Hawking Ansatz.” Journal of Differential
Geometry. International Press, 2024. https://doi.org/10.4310/jdg/1717348872.
ieee: J. D. Lotay and G. Oliveira, “Special Lagrangians, Lagrangian mean curvature
flow and the Gibbons-Hawking ansatz,” Journal of Differential Geometry,
vol. 126, no. 3. International Press, pp. 1121–1184, 2024.
ista: Lotay JD, Oliveira G. 2024. Special Lagrangians, Lagrangian mean curvature
flow and the Gibbons-Hawking ansatz. Journal of Differential Geometry. 126(3),
1121–1184.
mla: Lotay, Jason D., and Goncalo Oliveira. “Special Lagrangians, Lagrangian Mean
Curvature Flow and the Gibbons-Hawking Ansatz.” Journal of Differential Geometry,
vol. 126, no. 3, International Press, 2024, pp. 1121–84, doi:10.4310/jdg/1717348872.
short: J.D. Lotay, G. Oliveira, Journal of Differential Geometry 126 (2024) 1121–1184.
corr_author: '1'
date_created: 2024-07-22T07:45:31Z
date_published: 2024-03-01T00:00:00Z
date_updated: 2025-09-08T08:27:51Z
day: '01'
department:
- _id: TaHa
doi: 10.4310/jdg/1717348872
external_id:
arxiv:
- '2002.10391'
isi:
- '001271790200007'
intvolume: ' 126'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2002.10391
month: '03'
oa: 1
oa_version: Preprint
page: 1121-1184
publication: Journal of Differential Geometry
publication_identifier:
issn:
- 0022-040X
publication_status: published
publisher: International Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Special Lagrangians, Lagrangian mean curvature flow and the Gibbons-Hawking
ansatz
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 126
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '17302'
abstract:
- lang: eng
text: The mountain cryosphere and groundwater play pivotal roles in shaping the
hydrological cycle, yet their connectivity remains incompletely understood. Current
knowledge on meltwater recharge and consequent groundwater discharge processes
is better developed for snow–groundwater connectivity than for glacier–groundwater
connectivity. Estimates of meltwater recharge vary considerably, which is probably
a function of not only inherent catchment characteristics but also of the different
spatio-temporal scales involved and the uncertainties in the methods used. This
hinders a comprehensive understanding of the mountain water cycle. As glaciers
retreat, permafrost thaws and snowpack diminishes, the relative importance of
mountain groundwater is expected to increase. However, shifting and declining
recharge from the cryosphere may decrease absolute groundwater amounts and fluxes
with as-yet unknown effects on catchment-scale hydrological processes. We therefore
stress the need to better quantify mountain cryosphere–groundwater connectivity
to predict climate change impacts on mountain water supply and to support sustainable
water resource management of downstream socio-ecological systems.
acknowledgement: 'We acknowledge the Mountain Research Initiative (MRI) for sponsoring
the workshop ‘Cryosphere-groundwater Interactions: A Missing Link in Mountain Water
Research’ via their funding from the Swiss Academy of Sciences (SCNAT) under project
no. FNW0004 004-2019-00. M.v.T. was supported by a Walter Benjamin fellowship from
the German Research Foundation (DFG) under project no. 510684314. C.A.-W. was supported
by the Banting Postdoctoral Fellowships programme, administered by the government
of Canada. G.C. acknowledges the support of the DFG research unit (FOR2793/2) investigating
the ‘Sensitivity of High Alpine Geosystems to Climate Change since 1850’ (SEHAG)
under grant CH981/3-2. F.D. acknowledges funding from the Dirección de Fomento de
la Investigación at PUCP. I.d.G. acknowledges funding from the European Research
Council (ERC) under grant agreement GROW-101041110. V.Y. was supported by Nazarbayev
University under CRP research grant no. 021220CRP2122. We thank D. Masovic of VAW,
ETH Zurich, for drawing Fig. 1.'
article_processing_charge: No
article_type: original
author:
- first_name: Marit
full_name: van Tiel, Marit
last_name: van Tiel
- first_name: Caroline
full_name: Aubry-Wake, Caroline
last_name: Aubry-Wake
- first_name: Lauren
full_name: Somers, Lauren
last_name: Somers
- first_name: Christoff
full_name: Andermann, Christoff
last_name: Andermann
- first_name: Francesco
full_name: Avanzi, Francesco
last_name: Avanzi
- first_name: Michel
full_name: Baraer, Michel
last_name: Baraer
- first_name: Gabriele
full_name: Chiogna, Gabriele
last_name: Chiogna
- first_name: Clémence
full_name: Daigre, Clémence
last_name: Daigre
- first_name: Soumik
full_name: Das, Soumik
last_name: Das
- first_name: Fabian
full_name: Drenkhan, Fabian
last_name: Drenkhan
- first_name: Daniel
full_name: Farinotti, Daniel
last_name: Farinotti
- first_name: Catriona Louise
full_name: Fyffe, Catriona Louise
id: 001b0422-8d15-11ed-bc51-cab6c037a228
last_name: Fyffe
- first_name: Inge
full_name: de Graaf, Inge
last_name: de Graaf
- first_name: Sarah
full_name: Hanus, Sarah
last_name: Hanus
- first_name: Walter
full_name: Immerzeel, Walter
last_name: Immerzeel
- first_name: Franziska
full_name: Koch, Franziska
last_name: Koch
- first_name: Jeffrey M.
full_name: McKenzie, Jeffrey M.
last_name: McKenzie
- first_name: Tom
full_name: Müller, Tom
last_name: Müller
- first_name: Andrea L.
full_name: Popp, Andrea L.
last_name: Popp
- first_name: Zarina
full_name: Saidaliyeva, Zarina
last_name: Saidaliyeva
- first_name: Bettina
full_name: Schaefli, Bettina
last_name: Schaefli
- first_name: Oliver S.
full_name: Schilling, Oliver S.
last_name: Schilling
- first_name: Kapiolani
full_name: Teagai, Kapiolani
last_name: Teagai
- first_name: James M.
full_name: Thornton, James M.
last_name: Thornton
- first_name: Vadim
full_name: Yapiyev, Vadim
last_name: Yapiyev
citation:
ama: van Tiel M, Aubry-Wake C, Somers L, et al. Cryosphere–groundwater connectivity
is a missing link in the mountain water cycle. Nature Water. 2024;2:624-637.
doi:10.1038/s44221-024-00277-8
apa: van Tiel, M., Aubry-Wake, C., Somers, L., Andermann, C., Avanzi, F., Baraer,
M., … Yapiyev, V. (2024). Cryosphere–groundwater connectivity is a missing link
in the mountain water cycle. Nature Water. Springer Nature. https://doi.org/10.1038/s44221-024-00277-8
chicago: Tiel, Marit van, Caroline Aubry-Wake, Lauren Somers, Christoff Andermann,
Francesco Avanzi, Michel Baraer, Gabriele Chiogna, et al. “Cryosphere–Groundwater
Connectivity Is a Missing Link in the Mountain Water Cycle.” Nature Water.
Springer Nature, 2024. https://doi.org/10.1038/s44221-024-00277-8.
ieee: M. van Tiel et al., “Cryosphere–groundwater connectivity is a missing
link in the mountain water cycle,” Nature Water, vol. 2. Springer Nature,
pp. 624–637, 2024.
ista: van Tiel M, Aubry-Wake C, Somers L, Andermann C, Avanzi F, Baraer M, Chiogna
G, Daigre C, Das S, Drenkhan F, Farinotti D, Fyffe CL, de Graaf I, Hanus S, Immerzeel
W, Koch F, McKenzie JM, Müller T, Popp AL, Saidaliyeva Z, Schaefli B, Schilling
OS, Teagai K, Thornton JM, Yapiyev V. 2024. Cryosphere–groundwater connectivity
is a missing link in the mountain water cycle. Nature Water. 2, 624–637.
mla: van Tiel, Marit, et al. “Cryosphere–Groundwater Connectivity Is a Missing Link
in the Mountain Water Cycle.” Nature Water, vol. 2, Springer Nature, 2024,
pp. 624–37, doi:10.1038/s44221-024-00277-8.
short: M. van Tiel, C. Aubry-Wake, L. Somers, C. Andermann, F. Avanzi, M. Baraer,
G. Chiogna, C. Daigre, S. Das, F. Drenkhan, D. Farinotti, C.L. Fyffe, I. de Graaf,
S. Hanus, W. Immerzeel, F. Koch, J.M. McKenzie, T. Müller, A.L. Popp, Z. Saidaliyeva,
B. Schaefli, O.S. Schilling, K. Teagai, J.M. Thornton, V. Yapiyev, Nature Water
2 (2024) 624–637.
date_created: 2024-07-22T09:46:52Z
date_published: 2024-07-19T00:00:00Z
date_updated: 2025-12-02T13:42:28Z
day: '19'
department:
- _id: FrPe
doi: 10.1038/s44221-024-00277-8
external_id:
isi:
- '001390137500016'
intvolume: ' 2'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://insu.hal.science/insu-04674297
month: '07'
oa: 1
oa_version: Submitted Version
page: 624-637
publication: Nature Water
publication_identifier:
issn:
- 2731-6084
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cryosphere–groundwater connectivity is a missing link in the mountain water
cycle
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '17322'
abstract:
- lang: eng
text: Machine learning interatomic potentials are revolutionizing large-scale, accurate
atomistic modeling in material science and chemistry. Many potentials use atomic
cluster expansion or equivariant message-passing frameworks. Such frameworks typically
use spherical harmonics as angular basis functions, followed by Clebsch-Gordan
contraction to maintain rotational symmetry. We propose a mathematically equivalent
and simple alternative that performs all operations in the Cartesian coordinates.
This approach provides a complete set of polynormially independent features of
atomic environments while maintaining interaction body orders. Additionally, we
integrate low-dimensional embeddings of various chemical elements, trainable radial
channel coupling, and inter-atomic message passing. The resulting potential, named
Cartesian Atomic Cluster Expansion (CACE), exhibits good accuracy, stability,
and generalizability. We validate its performance in diverse systems, including
bulk water, small molecules, and 25-element high-entropy alloys.
acknowledgement: B.C. thanks Ralf Drautz and Ngoc Cuong Nguyen for illuminating discussions.
article_number: '157'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: Cheng B. Cartesian atomic cluster expansion for machine learning interatomic
potentials. npj Computational Materials. 2024;10. doi:10.1038/s41524-024-01332-4
apa: Cheng, B. (2024). Cartesian atomic cluster expansion for machine learning interatomic
potentials. Npj Computational Materials. Springer Nature. https://doi.org/10.1038/s41524-024-01332-4
chicago: Cheng, Bingqing. “Cartesian Atomic Cluster Expansion for Machine Learning
Interatomic Potentials.” Npj Computational Materials. Springer Nature,
2024. https://doi.org/10.1038/s41524-024-01332-4.
ieee: B. Cheng, “Cartesian atomic cluster expansion for machine learning interatomic
potentials,” npj Computational Materials, vol. 10. Springer Nature, 2024.
ista: Cheng B. 2024. Cartesian atomic cluster expansion for machine learning interatomic
potentials. npj Computational Materials. 10, 157.
mla: Cheng, Bingqing. “Cartesian Atomic Cluster Expansion for Machine Learning Interatomic
Potentials.” Npj Computational Materials, vol. 10, 157, Springer Nature,
2024, doi:10.1038/s41524-024-01332-4.
short: B. Cheng, Npj Computational Materials 10 (2024).
corr_author: '1'
date_created: 2024-07-28T22:01:08Z
date_published: 2024-07-18T00:00:00Z
date_updated: 2025-09-08T08:43:34Z
day: '18'
ddc:
- '000'
department:
- _id: BiCh
doi: 10.1038/s41524-024-01332-4
external_id:
arxiv:
- '2402.07472'
isi:
- '001271730700001'
file:
- access_level: open_access
checksum: e6b4d1a45a9ef1e9be35b313d96ebd6f
content_type: application/pdf
creator: dernst
date_created: 2025-01-09T12:36:48Z
date_updated: 2025-01-09T12:36:48Z
file_id: '18813'
file_name: 2024_npjComputationalMaterials_Cheng.pdf
file_size: 1659509
relation: main_file
success: 1
file_date_updated: 2025-01-09T12:36:48Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: npj Computational Materials
publication_identifier:
eissn:
- 2057-3960
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cartesian atomic cluster expansion for machine learning interatomic potentials
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 10
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '17323'
abstract:
- lang: eng
text: We investigate strong divisibility sequences and produce lower and upper bounds
for the density of integers in the sequence that only have (somewhat) large prime
factors. We focus on the special cases of Fibonacci numbers and elliptic divisibility
sequences, discussing the limitations of our methods. At the end of the paper,
there is an appendix by Sandro Bettin on divisor closed sets that we use to study
the density of prime terms that appear in strong divisibility sequences.
acknowledgement: The authors are very grateful to Andrew Granville, Dimitris Koukoulopoulos,
Davide Lombardo,Florian Luca, Igor Shparlinski and Joni Teräväinen for useful comments.
While working on thispaper, the first author was supported by a FWF Grant (DOI 10.55776/P36278)
and the secondauthor was supported by the European Union’s Horizon 2020 research
and innovation programunder the Marie Skłodowska-Curie Grant Agreement Number 101034413.
article_number: e12269
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Matteo
full_name: Verzobio, Matteo
id: 7aa8f170-131e-11ed-88e1-a9efd01027cb
last_name: Verzobio
orcid: 0000-0002-0854-0306
citation:
ama: Browning TD, Verzobio M. Strong divisibility sequences and sieve methods. Mathematika.
2024;70(4). doi:10.1112/mtk.12269
apa: Browning, T. D., & Verzobio, M. (2024). Strong divisibility sequences and
sieve methods. Mathematika. London Mathematical Society. https://doi.org/10.1112/mtk.12269
chicago: Browning, Timothy D, and Matteo Verzobio. “Strong Divisibility Sequences
and Sieve Methods.” Mathematika. London Mathematical Society, 2024. https://doi.org/10.1112/mtk.12269.
ieee: T. D. Browning and M. Verzobio, “Strong divisibility sequences and sieve methods,”
Mathematika, vol. 70, no. 4. London Mathematical Society, 2024.
ista: Browning TD, Verzobio M. 2024. Strong divisibility sequences and sieve methods.
Mathematika. 70(4), e12269.
mla: Browning, Timothy D., and Matteo Verzobio. “Strong Divisibility Sequences and
Sieve Methods.” Mathematika, vol. 70, no. 4, e12269, London Mathematical
Society, 2024, doi:10.1112/mtk.12269.
short: T.D. Browning, M. Verzobio, Mathematika 70 (2024).
corr_author: '1'
date_created: 2024-07-28T22:01:08Z
date_published: 2024-10-01T00:00:00Z
date_updated: 2025-09-08T08:44:11Z
day: '01'
ddc:
- '510'
department:
- _id: TiBr
doi: 10.1112/mtk.12269
ec_funded: 1
external_id:
isi:
- '001273912800001'
file:
- access_level: open_access
checksum: 0b1518bdc1a901413005c19202cfa497
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creator: dernst
date_created: 2025-01-13T11:06:25Z
date_updated: 2025-01-13T11:06:25Z
file_id: '18842'
file_name: 2024_Mathematika_Browning.pdf
file_size: 273006
relation: main_file
success: 1
file_date_updated: 2025-01-13T11:06:25Z
has_accepted_license: '1'
intvolume: ' 70'
isi: 1
issue: '4'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: bd8a4fdc-d553-11ed-ba76-80a0167441a3
grant_number: P36278
name: Rational curves via function field analytic number theory
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Mathematika
publication_identifier:
eissn:
- 2041-7942
issn:
- 0025-5793
publication_status: published
publisher: London Mathematical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Strong divisibility sequences and sieve methods
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 70
year: '2024'
...
---
_id: '17325'
abstract:
- lang: eng
text: Bacterial ion fluxes are involved in the generation of energy, transport,
and motility. As such, bacterial electrophysiology is fundamentally important
for the bacterial life cycle, but it is often neglected and consequently, by and
large, not understood. Arguably, the two main reasons for this are the complexity
of measuring relevant variables in small cells with a cell envelope that contains
the cell wall and the fact that, in a unicellular organism, relevant variables
become intertwined in a nontrivial manner. To help give bacterial electrophysiology
studies a firm footing, in this review, we go back to basics. We look first at
the biophysics of bacterial membrane potential, and then at the approaches and
models developed mostly for the study of neurons and eukaryotic mitochondria.
We discuss their applicability to bacterial cells. Finally, we connect bacterial
membrane potential with other relevant (electro)physiological variables and summarize
methods that can be used to both measure and influence bacterial electrophysiology.
acknowledgement: We would like to thank all members of the Pilizota lab, as well as
Calin Guet, Orkun Soyer, Munehiro Asally, Peter Swain, and in particular Matt Scott
and Ariel Amir, for their support, comments, and useful discussions. T.P. and W.-C.L.
were supported by the Leverhulme Trust, grant RPG-2019-187, and T.P. is supported
by EPSRC Fellowship EP/V03264X/1. E.K. was supported by a European Molecular Biology
Organization Long-Term Postdoctoral Fellowship, ALTF 44-2021.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Wei Chang
full_name: Lo, Wei Chang
last_name: Lo
- first_name: Ekaterina
full_name: Krasnopeeva, Ekaterina
id: 1F1EE44A-BF83-11EA-B3C1-BB9CC619BF3A
last_name: Krasnopeeva
- first_name: Teuta
full_name: Pilizota, Teuta
last_name: Pilizota
citation:
ama: Lo WC, Krasnopeeva E, Pilizota T. Bacterial Electrophysiology. Annual Review
of Biophysics. 2024;53:487-510. doi:10.1146/annurev-biophys-030822-032215
apa: Lo, W. C., Krasnopeeva, E., & Pilizota, T. (2024). Bacterial Electrophysiology.
Annual Review of Biophysics. Annual Reviews. https://doi.org/10.1146/annurev-biophys-030822-032215
chicago: Lo, Wei Chang, Ekaterina Krasnopeeva, and Teuta Pilizota. “Bacterial Electrophysiology.”
Annual Review of Biophysics. Annual Reviews, 2024. https://doi.org/10.1146/annurev-biophys-030822-032215.
ieee: W. C. Lo, E. Krasnopeeva, and T. Pilizota, “Bacterial Electrophysiology,”
Annual Review of Biophysics, vol. 53. Annual Reviews, pp. 487–510, 2024.
ista: Lo WC, Krasnopeeva E, Pilizota T. 2024. Bacterial Electrophysiology. Annual
Review of Biophysics. 53, 487–510.
mla: Lo, Wei Chang, et al. “Bacterial Electrophysiology.” Annual Review of Biophysics,
vol. 53, Annual Reviews, 2024, pp. 487–510, doi:10.1146/annurev-biophys-030822-032215.
short: W.C. Lo, E. Krasnopeeva, T. Pilizota, Annual Review of Biophysics 53 (2024)
487–510.
date_created: 2024-07-28T22:01:09Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2025-09-08T08:34:43Z
day: '01'
ddc:
- '570'
department:
- _id: CaGu
doi: 10.1146/annurev-biophys-030822-032215
external_id:
isi:
- '001278237500021'
pmid:
- '38382113'
file:
- access_level: open_access
checksum: e0505553b3cee624fa865f0cc5a99ecc
content_type: application/pdf
creator: dernst
date_created: 2024-07-29T10:56:01Z
date_updated: 2024-07-29T10:56:01Z
file_id: '17339'
file_name: 2024_AnnualReviewBiophys_Lo.pdf
file_size: 1276645
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success: 1
file_date_updated: 2024-07-29T10:56:01Z
has_accepted_license: '1'
intvolume: ' 53'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 487-510
pmid: 1
project:
- _id: eb872896-77a9-11ec-83b8-f59a38ec17f8
grant_number: ALTF 44-2021
name: 'Bacterial cytoplasm glass transition: passive physiological switch or active
survival strategy'
publication: Annual Review of Biophysics
publication_identifier:
eissn:
- 1936-1238
issn:
- 1936-122X
publication_status: published
publisher: Annual Reviews
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bacterial Electrophysiology
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 53
year: '2024'
...
---
DOAJ_listed: '1'
_id: '17326'
abstract:
- lang: eng
text: Magnetic fields in the stellar interiors are key candidates to explain observed
core rotation rates inside solar-like stars along their evolution. Recently, asteroseismic
estimates of radial magnetic field amplitudes near the hydrogen-burning shell
(H-shell) inside about 24 red giants (RGs) have been obtained by measuring frequency
splittings from their power spectra. Using general Lorentz-stress (magnetic) kernels,
we investigated the potential for detectability of near-surface magnetism in a
1.3 M⊙ star of supersolar metallicity as it evolves from a mid subgiant to a late
subgiant into an RG. Based on these sensitivity kernels, we decompose an RG into
three zones—deep core, H-shell, and near-surface. The subgiants instead required
decomposition into an inner core, an outer core, and a near-surface layer. Additionally,
we find that for a low-frequency g-dominated dipolar mode in the presence of a
typical stable magnetic field, ∼25% of the frequency shift comes from the H-shell
and the remaining from deeper layers. The ratio of the subsurface tangential field
to the radial field in the H-burning shell decides if subsurface fields may be
potentially detectable. For p-dominated dipole modes close to vmax, this ratio
is around two orders of magnitude smaller in subgiant phases than the corresponding
RG. Further, with the availability of magnetic kernels, we propose lower limits
of field strengths in crucial layers in our stellar model during its evolutionary
phases. The theoretical prescription outlined here provides the first formal way
to devise inverse problems for stellar magnetism and can be seamlessly employed
for slow rotators.
acknowledgement: "This project has received funding from the European Union's Horizon
2020 research and innovation program under the Marie Skłodowska-Curie grant agreement
No. 101034413. S.\r\nB.D. acknowledges Prof. Jeroen Tromp at Princeton University
for supporting a part of this work. S.M.H., S.B., and S.P. acknowledge support from
the Department of Atomic Energy,\r\nGovernment of India, under Project Identification
No. RTI 4002. The authors would like to thank the reviewer(s) and data editor for
their constructive comments and suggestions. The\r\ngeneration of the stellar models
was done using the Modules for Experiments in Stellar Astrophysics (MESA Paxton
et al. 2011, 2013, 2015, 2018, 2019; we have used MESA version\r\nr22.05.1 for RG
and r23.05.1 for SG models, MESA-SDK version x86_64-linux-22.6.1). The eigenfrequencies
and eigenfunctions for this model were calculated using the GYRE\r\n(Townsend &
Teitler 2013) code. The code to calculate the kernels and the splittings has been
written completely in Python 3.8.16."
article_number: '42'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Shatanik
full_name: Bhattacharya, Shatanik
last_name: Bhattacharya
- first_name: Srijan B
full_name: Das, Srijan B
id: 9ce7c423-dacf-11ed-8942-e09c6cb27149
last_name: Das
orcid: 0000-0003-0896-7972
- first_name: Lisa Annabelle
full_name: Bugnet, Lisa Annabelle
id: d9edb345-f866-11ec-9b37-d119b5234501
last_name: Bugnet
orcid: 0000-0003-0142-4000
- first_name: Subrata
full_name: Panda, Subrata
last_name: Panda
- first_name: Shravan M.
full_name: Hanasoge, Shravan M.
last_name: Hanasoge
citation:
ama: Bhattacharya S, Das SB, Bugnet LA, Panda S, Hanasoge SM. Detectability of axisymmetric
magnetic fields from the core to the surface of oscillating post-main-sequence
stars. Astrophysical Journal. 2024;970(1). doi:10.3847/1538-4357/ad4708
apa: Bhattacharya, S., Das, S. B., Bugnet, L. A., Panda, S., & Hanasoge, S.
M. (2024). Detectability of axisymmetric magnetic fields from the core to the
surface of oscillating post-main-sequence stars. Astrophysical Journal.
IOP Publishing. https://doi.org/10.3847/1538-4357/ad4708
chicago: Bhattacharya, Shatanik, Srijan B Das, Lisa Annabelle Bugnet, Subrata Panda,
and Shravan M. Hanasoge. “Detectability of Axisymmetric Magnetic Fields from the
Core to the Surface of Oscillating Post-Main-Sequence Stars.” Astrophysical
Journal. IOP Publishing, 2024. https://doi.org/10.3847/1538-4357/ad4708.
ieee: S. Bhattacharya, S. B. Das, L. A. Bugnet, S. Panda, and S. M. Hanasoge, “Detectability
of axisymmetric magnetic fields from the core to the surface of oscillating post-main-sequence
stars,” Astrophysical Journal, vol. 970, no. 1. IOP Publishing, 2024.
ista: Bhattacharya S, Das SB, Bugnet LA, Panda S, Hanasoge SM. 2024. Detectability
of axisymmetric magnetic fields from the core to the surface of oscillating post-main-sequence
stars. Astrophysical Journal. 970(1), 42.
mla: Bhattacharya, Shatanik, et al. “Detectability of Axisymmetric Magnetic Fields
from the Core to the Surface of Oscillating Post-Main-Sequence Stars.” Astrophysical
Journal, vol. 970, no. 1, 42, IOP Publishing, 2024, doi:10.3847/1538-4357/ad4708.
short: S. Bhattacharya, S.B. Das, L.A. Bugnet, S. Panda, S.M. Hanasoge, Astrophysical
Journal 970 (2024).
date_created: 2024-07-28T22:01:09Z
date_published: 2024-07-15T00:00:00Z
date_updated: 2025-09-08T08:42:20Z
day: '15'
ddc:
- '520'
department:
- _id: LiBu
doi: 10.3847/1538-4357/ad4708
ec_funded: 1
external_id:
arxiv:
- '2404.17167'
isi:
- '001270972500001'
file:
- access_level: open_access
checksum: acb42a87deecbc9228fbbe6a48a37ec6
content_type: application/pdf
creator: dernst
date_created: 2024-07-29T11:02:48Z
date_updated: 2024-07-29T11:02:48Z
file_id: '17340'
file_name: 2024_AstrophysicalJourn_Bhattacharya.pdf
file_size: 3912290
relation: main_file
success: 1
file_date_updated: 2024-07-29T11:02:48Z
has_accepted_license: '1'
intvolume: ' 970'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Astrophysical Journal
publication_identifier:
eissn:
- 1538-4357
issn:
- 0004-637X
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Detectability of axisymmetric magnetic fields from the core to the surface
of oscillating post-main-sequence stars
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 970
year: '2024'
...
---
_id: '17327'
abstract:
- lang: eng
text: Sequential decision-making in probabilistic environments is a fundamental
problem with many applications in AI and economics. In this paper, we present
an algorithm for synthesizing sequential decision-making agents that optimize
statistical properties such as maximum and average response times. In the general
setting of sequential decision-making, the environment is modeled as a random
process that generates inputs. The agent responds to each input, aiming to maximize
rewards and minimize costs within a specified time horizon. The corresponding
synthesis problem is known to be PSPACE-hard. We consider the special case where
the input distribution, reward, and cost depend on input-output statistics specified
by counter automata. For such problems, this paper presents the first PTIME synthesis
algorithms. We introduce the notion of statistical abstraction, which clusters
statistically indistinguishable input-output sequences into equivalence classes.
This abstraction allows for a dynamic programming algorithm whose complexity grows
polynomially with the considered horizon, making the statistical case exponentially
more efficient than the general case. We evaluate our algorithm on three different
application scenarios of a client-server protocol, where multiple clients compete
via bidding to gain access to the service offered by the server. The synthesized
policies optimize profit while guaranteeing that none of the server’s clients
is disproportionately starved of the service.
acknowledgement: "This work is partly supported by the European Research Council under
Grant No.: ERC2020-AdG 101020093. It is also partially supported by the State Government
of Styria, Austria –\r\nDepartment Zukunftsfonds Steiermark."
alternative_title:
- LIPIcs
article_number: '2'
article_processing_charge: Yes
author:
- first_name: Filip
full_name: Cano, Filip
last_name: Cano
- 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: Bettina
full_name: Könighofer, Bettina
last_name: Könighofer
- first_name: Konstantin
full_name: Kueffner, Konstantin
id: 8121a2d0-dc85-11ea-9058-af578f3b4515
last_name: Kueffner
orcid: 0000-0001-8974-2542
- first_name: Kaushik
full_name: Mallik, Kaushik
id: 0834ff3c-6d72-11ec-94e0-b5b0a4fb8598
last_name: Mallik
orcid: 0000-0001-9864-7475
citation:
ama: 'Cano F, Henzinger TA, Könighofer B, Kueffner K, Mallik K. Abstraction-based
decision making for statistical properties. In: 9th International Conference
on Formal Structures for Computation and Deduction. Vol 299. Schloss Dagstuhl
- Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.FSCD.2024.2'
apa: 'Cano, F., Henzinger, T. A., Könighofer, B., Kueffner, K., & Mallik, K.
(2024). Abstraction-based decision making for statistical properties. In 9th
International Conference on Formal Structures for Computation and Deduction
(Vol. 299). Tallinn, Estonia: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPIcs.FSCD.2024.2'
chicago: Cano, Filip, Thomas A Henzinger, Bettina Könighofer, Konstantin Kueffner,
and Kaushik Mallik. “Abstraction-Based Decision Making for Statistical Properties.”
In 9th International Conference on Formal Structures for Computation and Deduction,
Vol. 299. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.FSCD.2024.2.
ieee: F. Cano, T. A. Henzinger, B. Könighofer, K. Kueffner, and K. Mallik, “Abstraction-based
decision making for statistical properties,” in 9th International Conference
on Formal Structures for Computation and Deduction, Tallinn, Estonia, 2024,
vol. 299.
ista: 'Cano F, Henzinger TA, Könighofer B, Kueffner K, Mallik K. 2024. Abstraction-based
decision making for statistical properties. 9th International Conference on Formal
Structures for Computation and Deduction. FSCD: Conference on Formal Structures
for Computation and Deduction, LIPIcs, vol. 299, 2.'
mla: Cano, Filip, et al. “Abstraction-Based Decision Making for Statistical Properties.”
9th International Conference on Formal Structures for Computation and Deduction,
vol. 299, 2, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.FSCD.2024.2.
short: F. Cano, T.A. Henzinger, B. Könighofer, K. Kueffner, K. Mallik, in:, 9th
International Conference on Formal Structures for Computation and Deduction, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2024.
conference:
end_date: 2024-07-13
location: Tallinn, Estonia
name: 'FSCD: Conference on Formal Structures for Computation and Deduction'
start_date: 2024-07-10
corr_author: '1'
date_created: 2024-07-28T22:01:09Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2025-12-02T13:43:50Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.4230/LIPIcs.FSCD.2024.2
ec_funded: 1
external_id:
isi:
- '001587746100002'
file:
- access_level: open_access
checksum: cc6bb89be0eaa404a6ce019392cd293e
content_type: application/pdf
creator: dernst
date_created: 2024-07-29T11:15:59Z
date_updated: 2024-07-29T11:15:59Z
file_id: '17341'
file_name: 2024_LIPICs_Cano.pdf
file_size: 1391381
relation: main_file
success: 1
file_date_updated: 2024-07-29T11:15:59Z
has_accepted_license: '1'
intvolume: ' 299'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 9th International Conference on Formal Structures for Computation and
Deduction
publication_identifier:
isbn:
- '9783959773232'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Abstraction-based decision making for statistical properties
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: 299
year: '2024'
...
---
_id: '17328'
abstract:
- lang: eng
text: "We study selfish mining attacks in longest-chain blockchains like Bitcoin,
but where the proof of work is replaced with efficient proof systems - like proofs
of stake or proofs of space - and consider the problem of computing an optimal
selfish mining attack which maximizes expected relative revenue of the adversary,
thus minimizing the chain quality. To this end, we propose a novel selfish mining
attack that aims to maximize this objective and formally model the attack as a
Markov decision process (MDP). We then present a formal analysis procedure which
computes an ϵ-tight lower bound on the optimal expected relative revenue in the
MDP and a strategy that achieves this ϵ-tight lower bound, where ϵ > 0 may be
any specified precision. Our analysis is fully automated and provides formal guarantees
on the correctness. We evaluate our selfish mining attack and observe that it
achieves superior expected relative revenue compared to two considered baselines.\r\nIn
concurrent work [Sarenche FC'24] does an automated analysis on selfish mining
in predictable longest-chain blockchains based on efficient proof systems. Predictable
means the randomness for the challenges is fixed for many blocks (as used e.g.,
in Ouroboros), while we consider unpredictable (Bitcoin-like) chains where the
challenge is derived from the previous block."
acknowledgement: "This work was supported in part by the ERC-2020-CoG 863818 (FoRM-SMArt)
grant and the MOE-T2EP20122-0014 (Data-Driven Distributed Algorithms) grant.\r\n"
article_processing_charge: Yes (via OA deal)
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amirali
full_name: Ebrahimzadeh, Amirali
last_name: Ebrahimzadeh
- first_name: Mehrdad
full_name: Karrabi, Mehrdad
id: 67638922-f394-11eb-9cf6-f20423e08757
last_name: Karrabi
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Michelle X
full_name: Yeo, Michelle X
id: 2D82B818-F248-11E8-B48F-1D18A9856A87
last_name: Yeo
orcid: 0009-0001-3676-4809
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
citation:
ama: 'Chatterjee K, Ebrahimzadeh A, Karrabi M, Pietrzak KZ, Yeo MX, Zikelic D. Fully
automated selfish mining analysis in efficient proof systems blockchains. In:
Proceedings of the 43rd Annual ACM Symposium on Principles of Distributed
Computing. Association for Computing Machinery; 2024:268-278. doi:10.1145/3662158.3662769'
apa: 'Chatterjee, K., Ebrahimzadeh, A., Karrabi, M., Pietrzak, K. Z., Yeo, M. X.,
& Zikelic, D. (2024). Fully automated selfish mining analysis in efficient
proof systems blockchains. In Proceedings of the 43rd Annual ACM Symposium
on Principles of Distributed Computing (pp. 268–278). Nantes, France: Association
for Computing Machinery. https://doi.org/10.1145/3662158.3662769'
chicago: Chatterjee, Krishnendu, Amirali Ebrahimzadeh, Mehrdad Karrabi, Krzysztof
Z Pietrzak, Michelle X Yeo, and Dorde Zikelic. “Fully Automated Selfish Mining
Analysis in Efficient Proof Systems Blockchains.” In Proceedings of the 43rd
Annual ACM Symposium on Principles of Distributed Computing, 268–78. Association
for Computing Machinery, 2024. https://doi.org/10.1145/3662158.3662769.
ieee: K. Chatterjee, A. Ebrahimzadeh, M. Karrabi, K. Z. Pietrzak, M. X. Yeo, and
D. Zikelic, “Fully automated selfish mining analysis in efficient proof systems
blockchains,” in Proceedings of the 43rd Annual ACM Symposium on Principles
of Distributed Computing, Nantes, France, 2024, pp. 268–278.
ista: 'Chatterjee K, Ebrahimzadeh A, Karrabi M, Pietrzak KZ, Yeo MX, Zikelic D.
2024. Fully automated selfish mining analysis in efficient proof systems blockchains. Proceedings
of the 43rd Annual ACM Symposium on Principles of Distributed Computing. PODC:
Symposium on Principles of Distributed Computing, 268–278.'
mla: Chatterjee, Krishnendu, et al. “Fully Automated Selfish Mining Analysis in
Efficient Proof Systems Blockchains.” Proceedings of the 43rd Annual ACM Symposium
on Principles of Distributed Computing, Association for Computing Machinery,
2024, pp. 268–78, doi:10.1145/3662158.3662769.
short: K. Chatterjee, A. Ebrahimzadeh, M. Karrabi, K.Z. Pietrzak, M.X. Yeo, D. Zikelic,
in:, Proceedings of the 43rd Annual ACM Symposium on Principles of Distributed
Computing, Association for Computing Machinery, 2024, pp. 268–278.
conference:
end_date: 2024-06-21
location: Nantes, France
name: 'PODC: Symposium on Principles of Distributed Computing'
start_date: 2024-06-17
corr_author: '1'
date_created: 2024-07-28T22:01:10Z
date_published: 2024-06-17T00:00:00Z
date_updated: 2025-04-14T07:52:47Z
day: '17'
ddc:
- '000'
department:
- _id: KrCh
- _id: KrPi
doi: 10.1145/3662158.3662769
ec_funded: 1
external_id:
arxiv:
- '2405.04420'
file:
- access_level: open_access
checksum: 6122bd97b42751ff81c452a19970f67d
content_type: application/pdf
creator: dernst
date_created: 2024-07-29T07:18:12Z
date_updated: 2024-07-29T07:18:12Z
file_id: '17334'
file_name: 2024_ACM_Chatterjee.pdf
file_size: 832034
relation: main_file
success: 1
file_date_updated: 2024-07-29T07:18:12Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 268-278
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: ' Proceedings of the 43rd Annual ACM Symposium on Principles of Distributed
Computing'
publication_identifier:
isbn:
- '9798400706684'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fully automated selfish mining analysis in efficient proof systems blockchains
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
year: '2024'
...
---
_id: '17329'
abstract:
- lang: eng
text: 'We initiate the study of game dynamics in the population protocol model:
n agents each maintain a current local strategy and interact in pairs uniformly
at random. Upon each interaction, the agents play a two-person game and receive
a payoff from an underlying utility function, and they can subsequently update
their strategies according to a fixed local algorithm. In this setting, we ask
how the distribution over agent strategies evolves over a sequence of interactions,
and we introduce a new distributional equilibrium concept to quantify the quality
of such distributions. As an initial example, we study a class of repeated prisoner''s
dilemma games, and we consider a family of simple local update algorithms that
yield non-trivial dynamics over the distribution of agent strategies. We show
that these dynamics are related to a new class of high-dimensional Ehrenfest random
walks, and we derive exact characterizations of their stationary distributions,
bounds on their mixing times, and prove their convergence to approximate distributional
equilibria. Our results highlight trade-offs between the local state space of
each agent, and the convergence rate and approximation factor of the underlying
dynamics. Our approach opens the door towards the further characterization of
equilibrium computation for other classes of games and dynamics in the population
setting.'
acknowledgement: This work was supported in part by the ERC-2020-CoG 863818 (FoRM-SMArt)
grant. We thank James Aspnes and Thomas Sauerwald for several helpful discussions
on Ehrenfest random walks.
article_processing_charge: Yes (via OA deal)
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Mehrdad
full_name: Karrabi, Mehrdad
id: 67638922-f394-11eb-9cf6-f20423e08757
last_name: Karrabi
- first_name: John M
full_name: Lazarsfeld, John M
id: 17ce3656-183e-11ef-84c3-8932383e1b23
last_name: Lazarsfeld
citation:
ama: 'Alistarh D-A, Chatterjee K, Karrabi M, Lazarsfeld JM. Game dynamics and equilibrium
computation in the population protocol model. In: Proceedings of the 43rd Annual
ACM Symposium on Principles of Distributed Computing. Association for Computing
Machinery; 2024:40-49. doi:10.1145/3662158.3662768'
apa: 'Alistarh, D.-A., Chatterjee, K., Karrabi, M., & Lazarsfeld, J. M. (2024).
Game dynamics and equilibrium computation in the population protocol model. In
Proceedings of the 43rd Annual ACM Symposium on Principles of Distributed Computing
(pp. 40–49). Nantes, France: Association for Computing Machinery. https://doi.org/10.1145/3662158.3662768'
chicago: Alistarh, Dan-Adrian, Krishnendu Chatterjee, Mehrdad Karrabi, and John
M Lazarsfeld. “Game Dynamics and Equilibrium Computation in the Population Protocol
Model.” In Proceedings of the 43rd Annual ACM Symposium on Principles of Distributed
Computing, 40–49. Association for Computing Machinery, 2024. https://doi.org/10.1145/3662158.3662768.
ieee: D.-A. Alistarh, K. Chatterjee, M. Karrabi, and J. M. Lazarsfeld, “Game dynamics
and equilibrium computation in the population protocol model,” in Proceedings
of the 43rd Annual ACM Symposium on Principles of Distributed Computing, Nantes,
France, 2024, pp. 40–49.
ista: 'Alistarh D-A, Chatterjee K, Karrabi M, Lazarsfeld JM. 2024. Game dynamics
and equilibrium computation in the population protocol model. Proceedings of the
43rd Annual ACM Symposium on Principles of Distributed Computing. PODC: Symposium
on Principles of Distributed Computing, 40–49.'
mla: Alistarh, Dan-Adrian, et al. “Game Dynamics and Equilibrium Computation in
the Population Protocol Model.” Proceedings of the 43rd Annual ACM Symposium
on Principles of Distributed Computing, Association for Computing Machinery,
2024, pp. 40–49, doi:10.1145/3662158.3662768.
short: D.-A. Alistarh, K. Chatterjee, M. Karrabi, J.M. Lazarsfeld, in:, Proceedings
of the 43rd Annual ACM Symposium on Principles of Distributed Computing, Association
for Computing Machinery, 2024, pp. 40–49.
conference:
end_date: 2024-06-21
location: Nantes, France
name: 'PODC: Symposium on Principles of Distributed Computing'
start_date: 2024-06-17
corr_author: '1'
date_created: 2024-07-28T22:01:10Z
date_published: 2024-06-17T00:00:00Z
date_updated: 2025-04-14T07:52:47Z
day: '17'
ddc:
- '000'
department:
- _id: DaAl
- _id: KrCh
doi: 10.1145/3662158.3662768
ec_funded: 1
file:
- access_level: open_access
checksum: 65a40437f83373fa79dd999d5287509e
content_type: application/pdf
creator: dernst
date_created: 2024-07-29T07:37:31Z
date_updated: 2024-07-29T07:37:31Z
file_id: '17335'
file_name: 2024_ACMPODC_Alistarh.pdf
file_size: 750908
relation: main_file
success: 1
file_date_updated: 2024-07-29T07:37:31Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 40-49
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Proceedings of the 43rd Annual ACM Symposium on Principles of Distributed
Computing
publication_identifier:
isbn:
- '9798400706684'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Game dynamics and equilibrium computation in the population protocol model
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
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '17330'
abstract:
- lang: eng
text: In this work we consider the list-decodability and list-recoverability of
arbitrary q -ary codes, for all integer values of q ⩾ 2. A code is called ( p
, L ) q -list-decodable if every radius pn Hamming ball contains less than L codewords;
( p , ℓ, L ) q -recoverability is a generalization where we place radius pn Hamming
balls on every point of a combinatorial rectangle with side length ℓ and again
stipulate that there be less than L codewords. Our main contribution is to precisely
calculate the maximum value of p for which there exist infinite families of positive
rate ( p , ℓ, L ) q -list-recoverable codes, the quantity we call the zero-rate
threshold . Denoting this value by p *, we in fact show that codes correcting
a p * + ε fraction of errors must have size O ε (1), i.e., independent of n .
Such a result is typically referred to as a “Plotkin bound.” To complement this,
a standard random code with expurgation construction shows that there exist positive
rate codes correcting a p * − ε fraction of errors. We also follow a classical
proof template (typically attributed to Elias and Bassalygo) to derive from the
zero-rate threshold other tradeoffs between rate and decoding radius for list-decoding
and list-recovery. Technically, proving the Plotkin bound boils down to demon-strating
the Schur convexity of a certain function defined on the q -simplex as well as
the convexity of a univariate function derived from it. We remark that an earlier
argument claimed similar results for q -ary list-decoding; however, we point out
that this earlier proof is flawed.
acknowledgement: Part of this work was done while Nicolas Resch was affiliated with
the Centrum Wiskunde & Informatica and supported in part by ERC H2020 grant No.74079
(ALGSTRONGCRYPTO). Chen Yuan is supported in part by the National Key Research and
Development Projects under Grant 2022YFA1004900 and Grant 2021YFE0109900, the National
Natural Science Foundation of China under Grant 12101403 and Grant 12031011.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Nicolas
full_name: Resch, Nicolas
last_name: Resch
- first_name: Chen
full_name: Yuan, Chen
last_name: Yuan
- first_name: Yihan
full_name: Zhang, Yihan
id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c
last_name: Zhang
orcid: 0000-0002-6465-6258
citation:
ama: Resch N, Yuan C, Zhang Y. Zero-rate thresholds and new capacity bounds for
list-decoding and list-recovery. IEEE Transactions on Information Theory.
2024;70(9):6211-6238. doi:10.1109/TIT.2024.3430842
apa: Resch, N., Yuan, C., & Zhang, Y. (2024). Zero-rate thresholds and new capacity
bounds for list-decoding and list-recovery. IEEE Transactions on Information
Theory. IEEE. https://doi.org/10.1109/TIT.2024.3430842
chicago: Resch, Nicolas, Chen Yuan, and Yihan Zhang. “Zero-Rate Thresholds and New
Capacity Bounds for List-Decoding and List-Recovery.” IEEE Transactions on
Information Theory. IEEE, 2024. https://doi.org/10.1109/TIT.2024.3430842.
ieee: N. Resch, C. Yuan, and Y. Zhang, “Zero-rate thresholds and new capacity bounds
for list-decoding and list-recovery,” IEEE Transactions on Information Theory,
vol. 70, no. 9. IEEE, pp. 6211–6238, 2024.
ista: Resch N, Yuan C, Zhang Y. 2024. Zero-rate thresholds and new capacity bounds
for list-decoding and list-recovery. IEEE Transactions on Information Theory.
70(9), 6211–6238.
mla: Resch, Nicolas, et al. “Zero-Rate Thresholds and New Capacity Bounds for List-Decoding
and List-Recovery.” IEEE Transactions on Information Theory, vol. 70, no.
9, IEEE, 2024, pp. 6211–38, doi:10.1109/TIT.2024.3430842.
short: N. Resch, C. Yuan, Y. Zhang, IEEE Transactions on Information Theory 70 (2024)
6211–6238.
corr_author: '1'
date_created: 2024-07-28T22:01:10Z
date_published: 2024-09-01T00:00:00Z
date_updated: 2025-09-08T08:31:53Z
day: '01'
department:
- _id: MaMo
doi: 10.1109/TIT.2024.3430842
external_id:
arxiv:
- '2210.07754'
isi:
- '001299623600019'
intvolume: ' 70'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2210.07754
month: '09'
oa: 1
oa_version: Preprint
page: 6211-6238
publication: IEEE Transactions on Information Theory
publication_identifier:
eissn:
- 1557-9654
issn:
- 0018-9448
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '14083'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 70
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '17331'
abstract:
- lang: eng
text: Amyloidosis are a group of diseases in which soluble proteins aggregate and
deposit in fibrillar conformation extracellularly in tissues. The effectiveness
of therapeutic strategies depends on the specific protein involved, being crucial
to accurately determine its nature. Moreover, following the diagnosis, the search
for the mutation within relatives allows the clinical advice. Here we report the
precise diagnosis and explored the possible reasons of the structural pathogenicity
for a renal amyloidosis related to a fibrinogen Aα-chain variant. Whole-exome
sequencing and GATK calling pipeline were leveraged to characterize the protein
variant present in a patient with kidney failure. Bioinformatics strategies were
applied to suggest potential explanations of the variants aggregation. Our pipeline
allowed the identification of a single-point variant of fibrinogen Aα-chain, which
opened the possibility of curative transplantation. In silico structural analysis
suggested that the pathogenicity of the variant may be attributed to a heightened
susceptibility to yield a peptide prone to deposit as an oligomer with a β-sheet
structure. Exploiting the comprehensive coverage of whole-genome sequencing, we
managed to fill a vacant stage in the diagnosis of hereditary amyloidosis and
to stimulate the advancement in biomedicine.
acknowledgement: The authors acknowledge Rosana del Cid for her help with English
corrections, Mario Ramos for the figure editions, and Gabriela Finarelli for technical
assistance. S.A. Rosú, N.A. Ramella, and M.A. Tricerri acknowledge support from
Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) (Grant PIP
11220200102381), Agencia Nacional de Promoción Científica y Tecnológica (PICT 2019-03592),
Universidad Nacional de La Plata (UNLP) (Grants M234 and PPID M014), and Fundación
Florencio Fiorini. The authors warmly thank M.P. for her willingness to conduct
these studies.
article_processing_charge: No
article_type: original
author:
- first_name: Elizabeth R
full_name: Cattaneo, Elizabeth R
last_name: Cattaneo
- first_name: Romina A
full_name: Gisonno, Romina A
id: a9e08d76-6a98-11ec-8f7b-c777fe5ca519
last_name: Gisonno
- first_name: Martín C
full_name: Abba, Martín C
last_name: Abba
- first_name: Marianela
full_name: Santana, Marianela
last_name: Santana
- first_name: Silvana A
full_name: Rosú, Silvana A
last_name: Rosú
- first_name: Elsa
full_name: Nucifora, Elsa
last_name: Nucifora
- first_name: María A
full_name: Aguirre, María A
last_name: Aguirre
- first_name: María C
full_name: Giordani, María C
last_name: Giordani
- first_name: M. Alejandra
full_name: Tricerri, M. Alejandra
last_name: Tricerri
- first_name: Nahuel A
full_name: Ramella, Nahuel A
last_name: Ramella
citation:
ama: 'Cattaneo ER, Gisonno RA, Abba MC, et al. Hereditary amyloidosis: Insights
into a fibrinogen A variant protein. Proteins: Structure, Function and Bioinformatics.
2024;92(12):1366-1374. doi:10.1002/prot.26732'
apa: 'Cattaneo, E. R., Gisonno, R. A., Abba, M. C., Santana, M., Rosú, S. A., Nucifora,
E., … Ramella, N. A. (2024). Hereditary amyloidosis: Insights into a fibrinogen
A variant protein. Proteins: Structure, Function and Bioinformatics. Wiley.
https://doi.org/10.1002/prot.26732'
chicago: 'Cattaneo, Elizabeth R, Romina A Gisonno, Martín C Abba, Marianela Santana,
Silvana A Rosú, Elsa Nucifora, María A Aguirre, María C Giordani, M. Alejandra
Tricerri, and Nahuel A Ramella. “Hereditary Amyloidosis: Insights into a Fibrinogen
A Variant Protein.” Proteins: Structure, Function and Bioinformatics. Wiley,
2024. https://doi.org/10.1002/prot.26732.'
ieee: 'E. R. Cattaneo et al., “Hereditary amyloidosis: Insights into a fibrinogen
A variant protein,” Proteins: Structure, Function and Bioinformatics, vol.
92, no. 12. Wiley, pp. 1366–1374, 2024.'
ista: 'Cattaneo ER, Gisonno RA, Abba MC, Santana M, Rosú SA, Nucifora E, Aguirre
MA, Giordani MC, Tricerri MA, Ramella NA. 2024. Hereditary amyloidosis: Insights
into a fibrinogen A variant protein. Proteins: Structure, Function and Bioinformatics.
92(12), 1366–1374.'
mla: 'Cattaneo, Elizabeth R., et al. “Hereditary Amyloidosis: Insights into a Fibrinogen
A Variant Protein.” Proteins: Structure, Function and Bioinformatics, vol.
92, no. 12, Wiley, 2024, pp. 1366–74, doi:10.1002/prot.26732.'
short: 'E.R. Cattaneo, R.A. Gisonno, M.C. Abba, M. Santana, S.A. Rosú, E. Nucifora,
M.A. Aguirre, M.C. Giordani, M.A. Tricerri, N.A. Ramella, Proteins: Structure,
Function and Bioinformatics 92 (2024) 1366–1374.'
date_created: 2024-07-28T22:01:10Z
date_published: 2024-12-01T00:00:00Z
date_updated: 2025-09-08T08:33:53Z
day: '01'
department:
- _id: GaNo
doi: 10.1002/prot.26732
external_id:
isi:
- '001272128100001'
pmid:
- '39031927'
intvolume: ' 92'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.22541/au.171804763.37967262/v1
month: '12'
oa: 1
oa_version: Preprint
page: 1366-1374
pmid: 1
publication: 'Proteins: Structure, Function and Bioinformatics'
publication_identifier:
eissn:
- 1097-0134
issn:
- 0887-3585
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Hereditary amyloidosis: Insights into a fibrinogen A variant protein'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 92
year: '2024'
...