---
_id: '12723'
abstract:
- lang: eng
text: 'Lead halide perovskites enjoy a number of remarkable optoelectronic properties.
To explain their origin, it is necessary to study how electromagnetic fields interact
with these systems. We address this problem here by studying two classical quantities:
Faraday rotation and the complex refractive index in a paradigmatic perovskite
CH3NH3PbBr3 in a broad wavelength range. We find that the minimal coupling of
electromagnetic fields to the k⋅p Hamiltonian is insufficient to describe the
observed data even on the qualitative level. To amend this, we demonstrate that
there exists a relevant atomic-level coupling between electromagnetic fields and
the spin degree of freedom. This spin-electric coupling allows for quantitative
description of a number of previous as well as present experimental data. In particular,
we use it here to show that the Faraday effect in lead halide perovskites is dominated
by the Zeeman splitting of the energy levels and has a substantial beyond-Becquerel
contribution. Finally, we present general symmetry-based phenomenological arguments
that in the low-energy limit our effective model includes all basis coupling terms
to the electromagnetic field in the linear order.'
article_number: '106901'
article_processing_charge: No
article_type: original
author:
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
- first_name: Abhishek
full_name: Shiva Kumar, Abhishek
id: 5e9a6931-eb97-11eb-a6c2-e96f7058d77a
last_name: Shiva Kumar
- first_name: Dusan
full_name: Lorenc, Dusan
id: 40D8A3E6-F248-11E8-B48F-1D18A9856A87
last_name: Lorenc
- first_name: Younes
full_name: Ashourishokri, Younes
id: e32c111f-f6e0-11ea-865d-eb955baea334
last_name: Ashourishokri
- first_name: Ayan A.
full_name: Zhumekenov, Ayan A.
last_name: Zhumekenov
- first_name: Osman M.
full_name: Bakr, Osman M.
last_name: Bakr
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Zhanybek
full_name: Alpichshev, Zhanybek
id: 45E67A2A-F248-11E8-B48F-1D18A9856A87
last_name: Alpichshev
orcid: 0000-0002-7183-5203
citation:
ama: Volosniev A, Shiva Kumar A, Lorenc D, et al. Spin-electric coupling in lead
halide perovskites. Physical Review Letters. 2023;130(10). doi:10.1103/physrevlett.130.106901
apa: Volosniev, A., Shiva Kumar, A., Lorenc, D., Ashourishokri, Y., Zhumekenov,
A. A., Bakr, O. M., … Alpichshev, Z. (2023). Spin-electric coupling in lead halide
perovskites. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.130.106901
chicago: Volosniev, Artem, Abhishek Shiva Kumar, Dusan Lorenc, Younes Ashourishokri,
Ayan A. Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev.
“Spin-Electric Coupling in Lead Halide Perovskites.” Physical Review Letters.
American Physical Society, 2023. https://doi.org/10.1103/physrevlett.130.106901.
ieee: A. Volosniev et al., “Spin-electric coupling in lead halide perovskites,”
Physical Review Letters, vol. 130, no. 10. American Physical Society, 2023.
ista: Volosniev A, Shiva Kumar A, Lorenc D, Ashourishokri Y, Zhumekenov AA, Bakr
OM, Lemeshko M, Alpichshev Z. 2023. Spin-electric coupling in lead halide perovskites.
Physical Review Letters. 130(10), 106901.
mla: Volosniev, Artem, et al. “Spin-Electric Coupling in Lead Halide Perovskites.”
Physical Review Letters, vol. 130, no. 10, 106901, American Physical Society,
2023, doi:10.1103/physrevlett.130.106901.
short: A. Volosniev, A. Shiva Kumar, D. Lorenc, Y. Ashourishokri, A.A. Zhumekenov,
O.M. Bakr, M. Lemeshko, Z. Alpichshev, Physical Review Letters 130 (2023).
date_created: 2023-03-14T13:11:59Z
date_published: 2023-03-10T00:00:00Z
date_updated: 2023-08-01T13:39:04Z
day: '10'
department:
- _id: GradSch
- _id: ZhAl
- _id: MiLe
doi: 10.1103/physrevlett.130.106901
external_id:
arxiv:
- '2203.09443'
isi:
- '000982435900002'
intvolume: ' 130'
isi: 1
issue: '10'
keyword:
- General Physics and Astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2203.09443
month: '03'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spin-electric coupling in lead halide perovskites
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 130
year: '2023'
...
---
_id: '12724'
abstract:
- lang: eng
text: 'We use general symmetry-based arguments to construct an effective model suitable
for studying optical properties of lead halide perovskites. To build the model,
we identify an atomic-level interaction between electromagnetic fields and the
spin degree of freedom that should be added to a minimally coupled k⋅p Hamiltonian.
As a first application, we study two basic optical characteristics of the material:
the Verdet constant and the refractive index. Beyond these linear characteristics
of the material, the model is suitable for calculating nonlinear effects such
as the third-order optical susceptibility. Analysis of this quantity shows that
the geometrical properties of the spin-electric term imply isotropic optical response
of the system, and that optical anisotropy of lead halide perovskites is a manifestation
of hopping of charge carriers. To illustrate this, we discuss third-harmonic generation.'
article_number: '125201'
article_processing_charge: No
article_type: original
author:
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
- first_name: Abhishek
full_name: Shiva Kumar, Abhishek
id: 5e9a6931-eb97-11eb-a6c2-e96f7058d77a
last_name: Shiva Kumar
- first_name: Dusan
full_name: Lorenc, Dusan
id: 40D8A3E6-F248-11E8-B48F-1D18A9856A87
last_name: Lorenc
- first_name: Younes
full_name: Ashourishokri, Younes
id: e32c111f-f6e0-11ea-865d-eb955baea334
last_name: Ashourishokri
- first_name: Ayan
full_name: Zhumekenov, Ayan
last_name: Zhumekenov
- first_name: Osman M.
full_name: Bakr, Osman M.
last_name: Bakr
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Zhanybek
full_name: Alpichshev, Zhanybek
id: 45E67A2A-F248-11E8-B48F-1D18A9856A87
last_name: Alpichshev
orcid: 0000-0002-7183-5203
citation:
ama: Volosniev A, Shiva Kumar A, Lorenc D, et al. Effective model for studying optical
properties of lead halide perovskites. Physical Review B. 2023;107(12).
doi:10.1103/physrevb.107.125201
apa: Volosniev, A., Shiva Kumar, A., Lorenc, D., Ashourishokri, Y., Zhumekenov,
A., Bakr, O. M., … Alpichshev, Z. (2023). Effective model for studying optical
properties of lead halide perovskites. Physical Review B. American Physical
Society. https://doi.org/10.1103/physrevb.107.125201
chicago: Volosniev, Artem, Abhishek Shiva Kumar, Dusan Lorenc, Younes Ashourishokri,
Ayan Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Effective
Model for Studying Optical Properties of Lead Halide Perovskites.” Physical
Review B. American Physical Society, 2023. https://doi.org/10.1103/physrevb.107.125201.
ieee: A. Volosniev et al., “Effective model for studying optical properties
of lead halide perovskites,” Physical Review B, vol. 107, no. 12. American
Physical Society, 2023.
ista: Volosniev A, Shiva Kumar A, Lorenc D, Ashourishokri Y, Zhumekenov A, Bakr
OM, Lemeshko M, Alpichshev Z. 2023. Effective model for studying optical properties
of lead halide perovskites. Physical Review B. 107(12), 125201.
mla: Volosniev, Artem, et al. “Effective Model for Studying Optical Properties of
Lead Halide Perovskites.” Physical Review B, vol. 107, no. 12, 125201,
American Physical Society, 2023, doi:10.1103/physrevb.107.125201.
short: A. Volosniev, A. Shiva Kumar, D. Lorenc, Y. Ashourishokri, A. Zhumekenov,
O.M. Bakr, M. Lemeshko, Z. Alpichshev, Physical Review B 107 (2023).
date_created: 2023-03-14T13:13:05Z
date_published: 2023-03-15T00:00:00Z
date_updated: 2023-08-01T13:39:47Z
day: '15'
department:
- _id: GradSch
- _id: ZhAl
- _id: MiLe
doi: 10.1103/physrevb.107.125201
external_id:
arxiv:
- '2204.04022'
isi:
- '000972602200006'
intvolume: ' 107'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2204.04022
month: '03'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Effective model for studying optical properties of lead halide perovskites
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 107
year: '2023'
...
---
_id: '12759'
abstract:
- lang: eng
text: Stereological methods for estimating the 3D particle size and density from
2D projections are essential to many research fields. These methods are, however,
prone to errors arising from undetected particle profiles due to sectioning and
limited resolution, known as ‘lost caps’. A potential solution developed by Keiding,
Jensen, and Ranek in 1972, which we refer to as the Keiding model, accounts for
lost caps by quantifying the smallest detectable profile in terms of its limiting
‘cap angle’ (ϕ), a size-independent measure of a particle’s distance from the
section surface. However, this simple solution has not been widely adopted nor
tested. Rather, model-independent design-based stereological methods, which do
not explicitly account for lost caps, have come to the fore. Here, we provide
the first experimental validation of the Keiding model by comparing the size and
density of particles estimated from 2D projections with direct measurement from
3D EM reconstructions of the same tissue. We applied the Keiding model to estimate
the size and density of somata, nuclei and vesicles in the cerebellum of mice
and rats, where high packing density can be problematic for design-based methods.
Our analysis reveals a Gaussian distribution for ϕ rather than a single value.
Nevertheless, curve fits of the Keiding model to the 2D diameter distribution
accurately estimate the mean ϕ and 3D diameter distribution. While systematic
testing using simulations revealed an upper limit to determining ϕ, our analysis
shows that estimated ϕ can be used to determine the 3D particle density from the
2D density under a wide range of conditions, and this method is potentially more
accurate than minimum-size-based lost-cap corrections and disector methods. Our
results show the Keiding model provides an efficient means of accurately estimating
the size and density of particles from 2D projections even under conditions of
a high density.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: "We thank the IST Austria Electron Microscopy Facility for technical
support, and Diccon Coyle, Andrea Lőrincz and Zoltan Nusser for their helpful comments
and discussions.\r\nFunding for JSR and RAS was from the Wellcome Trust (203048;
224499; https://\r\nwellcome.org/). RAS is in receipt of a Wellcome Trust Principal
Research Fellowship (224499).\r\nFunding for CBM and PJ was from Fond zur Förderung
der Wissenschaftlichen Forschung (V\r\n739-B27 Elise-Richter Programme to CBM, Z
312-B27 Wittgenstein Award to PJ; \r\nhttps://www.fwf.ac.at). PJ received funding
from the European Research Council (ERC; https://erc.europa.eu) under the European
Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692).
NH was supported by a European\r\nResearch Council Advanced Grant (ERC-AG787157)."
article_number: e0277148
article_processing_charge: No
article_type: original
author:
- first_name: Jason Seth
full_name: Rothman, Jason Seth
last_name: Rothman
- first_name: Carolina
full_name: Borges Merjane, Carolina
id: 4305C450-F248-11E8-B48F-1D18A9856A87
last_name: Borges Merjane
orcid: 0000-0003-0005-401X
- first_name: Noemi
full_name: Holderith, Noemi
last_name: Holderith
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: R.
full_name: Angus Silver, R.
last_name: Angus Silver
citation:
ama: Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. Validation
of a stereological method for estimating particle size and density from 2D projections
with high accuracy. PLoS ONE. 2023;18(3 March). doi:10.1371/journal.pone.0277148
apa: Rothman, J. S., Borges Merjane, C., Holderith, N., Jonas, P. M., & Angus
Silver, R. (2023). Validation of a stereological method for estimating particle
size and density from 2D projections with high accuracy. PLoS ONE. Public
Library of Science. https://doi.org/10.1371/journal.pone.0277148
chicago: Rothman, Jason Seth, Carolina Borges Merjane, Noemi Holderith, Peter M
Jonas, and R. Angus Silver. “Validation of a Stereological Method for Estimating
Particle Size and Density from 2D Projections with High Accuracy.” PLoS ONE.
Public Library of Science, 2023. https://doi.org/10.1371/journal.pone.0277148.
ieee: J. S. Rothman, C. Borges Merjane, N. Holderith, P. M. Jonas, and R. Angus
Silver, “Validation of a stereological method for estimating particle size and
density from 2D projections with high accuracy,” PLoS ONE, vol. 18, no.
3 March. Public Library of Science, 2023.
ista: Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. 2023.
Validation of a stereological method for estimating particle size and density
from 2D projections with high accuracy. PLoS ONE. 18(3 March), e0277148.
mla: Rothman, Jason Seth, et al. “Validation of a Stereological Method for Estimating
Particle Size and Density from 2D Projections with High Accuracy.” PLoS ONE,
vol. 18, no. 3 March, e0277148, Public Library of Science, 2023, doi:10.1371/journal.pone.0277148.
short: J.S. Rothman, C. Borges Merjane, N. Holderith, P.M. Jonas, R. Angus Silver,
PLoS ONE 18 (2023).
date_created: 2023-03-26T22:01:07Z
date_published: 2023-03-17T00:00:00Z
date_updated: 2023-08-01T13:46:39Z
day: '17'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1371/journal.pone.0277148
ec_funded: 1
external_id:
isi:
- '001024737400001'
file:
- access_level: open_access
checksum: 2380331ec27cc87808826fc64419ac1c
content_type: application/pdf
creator: dernst
date_created: 2023-03-27T06:51:09Z
date_updated: 2023-03-27T06:51:09Z
file_id: '12770'
file_name: 2023_PLoSOne_Rothman.pdf
file_size: 7290413
relation: main_file
success: 1
file_date_updated: 2023-03-27T06:51:09Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: 3 March
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: The Wittgenstein Prize
- _id: 2696E7FE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: V00739
name: Structural plasticity at mossy fiber-CA3 synapses
publication: PLoS ONE
publication_identifier:
eissn:
- 1932-6203
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Validation of a stereological method for estimating particle size and density
from 2D projections with high accuracy
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 18
year: '2023'
...
---
_id: '12756'
abstract:
- lang: eng
text: ESCRT-III family proteins form composite polymers that deform and cut membrane
tubes in the context of a wide range of cell biological processes across the tree
of life. In reconstituted systems, sequential changes in the composition of ESCRT-III
polymers induced by the AAA–adenosine triphosphatase Vps4 have been shown to remodel
membranes. However, it is not known how composite ESCRT-III polymers are organized
and remodeled in space and time in a cellular context. Taking advantage of the
relative simplicity of the ESCRT-III–dependent division system in Sulfolobus acidocaldarius,
one of the closest experimentally tractable prokaryotic relatives of eukaryotes,
we use super-resolution microscopy, electron microscopy, and computational modeling
to show how CdvB/CdvB1/CdvB2 proteins form a precisely patterned composite ESCRT-III
division ring, which undergoes stepwise Vps4-dependent disassembly and contracts
to cut cells into two. These observations lead us to suggest sequential changes
in a patterned composite polymer as a general mechanism of ESCRT-III–dependent
membrane remodeling.
acknowledgement: "We thank Y. Liu and V. Hale for help with electron cryotomography;
the Medical Research Council (MRC) LMB Electron Microscopy Facility for access,
training, and support; and T. Darling and J. Grimmett at the MRC LMB for help with
computing infrastructure. We also thank the Flow Cytometry Facility and the MRC
LMB for training and support.\r\n F.H. and G.T.-R. were supported by a grant from
the Wellcome Trust (203276/Z/16/Z). A.C. was supported by an EMBO long-term fellowship:
ALTF_1041-2021. J.T. was supported by a grant from the VW Foundation (94933). A.A.P.
was supported by the Wellcome Trust (203276/Z/16/Z) and the HFSP (LT001027/2019).
B.B. received support from the MRC LMB, the Wellcome Trust (203276/Z/16/Z), the
VW Foundation (94933), the Life Sciences–Moore-Simons Foundation (735929LPI), and
a Gordon and Betty Moore Foundation’s Symbiosis in Aquatic Systems Initiative (9346).
A.Š. and X.J. acknowledge funding from the European Research Council (ERC) under
the European Union’s Horizon 2020 research and innovation programme (grant no. 802960).
L.H.-K. acknowledges support from Biotechnology and Biological Sciences Research
Council LIDo Programme. T.N. and J.L. were supported by the MRC (U105184326) and
the Wellcome Trust (203276/Z/16/Z)."
article_number: eade5224
article_processing_charge: No
article_type: original
author:
- first_name: Fredrik
full_name: Hurtig, Fredrik
last_name: Hurtig
- first_name: Thomas C.Q.
full_name: Burgers, Thomas C.Q.
last_name: Burgers
- first_name: Alice
full_name: Cezanne, Alice
last_name: Cezanne
- first_name: Xiuyun
full_name: Jiang, Xiuyun
last_name: Jiang
- first_name: Frank N.
full_name: Mol, Frank N.
last_name: Mol
- first_name: Jovan
full_name: Traparić, Jovan
last_name: Traparić
- first_name: Andre Arashiro
full_name: Pulschen, Andre Arashiro
last_name: Pulschen
- first_name: Tim
full_name: Nierhaus, Tim
last_name: Nierhaus
- first_name: Gabriel
full_name: Tarrason-Risa, Gabriel
last_name: Tarrason-Risa
- first_name: Lena
full_name: Harker-Kirschneck, Lena
last_name: Harker-Kirschneck
- first_name: Jan
full_name: Löwe, Jan
last_name: Löwe
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Rifka
full_name: Vlijm, Rifka
last_name: Vlijm
- first_name: Buzz
full_name: Baum, Buzz
last_name: Baum
citation:
ama: Hurtig F, Burgers TCQ, Cezanne A, et al. The patterned assembly and stepwise
Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell
division. Science Advances. 2023;9(11). doi:10.1126/sciadv.ade5224
apa: Hurtig, F., Burgers, T. C. Q., Cezanne, A., Jiang, X., Mol, F. N., Traparić,
J., … Baum, B. (2023). The patterned assembly and stepwise Vps4-mediated disassembly
of composite ESCRT-III polymers drives archaeal cell division. Science Advances.
American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.ade5224
chicago: Hurtig, Fredrik, Thomas C.Q. Burgers, Alice Cezanne, Xiuyun Jiang, Frank
N. Mol, Jovan Traparić, Andre Arashiro Pulschen, et al. “The Patterned Assembly
and Stepwise Vps4-Mediated Disassembly of Composite ESCRT-III Polymers Drives
Archaeal Cell Division.” Science Advances. American Association for the
Advancement of Science, 2023. https://doi.org/10.1126/sciadv.ade5224.
ieee: F. Hurtig et al., “The patterned assembly and stepwise Vps4-mediated
disassembly of composite ESCRT-III polymers drives archaeal cell division,” Science
Advances, vol. 9, no. 11. American Association for the Advancement of Science,
2023.
ista: Hurtig F, Burgers TCQ, Cezanne A, Jiang X, Mol FN, Traparić J, Pulschen AA,
Nierhaus T, Tarrason-Risa G, Harker-Kirschneck L, Löwe J, Šarić A, Vlijm R, Baum
B. 2023. The patterned assembly and stepwise Vps4-mediated disassembly of composite
ESCRT-III polymers drives archaeal cell division. Science Advances. 9(11), eade5224.
mla: Hurtig, Fredrik, et al. “The Patterned Assembly and Stepwise Vps4-Mediated
Disassembly of Composite ESCRT-III Polymers Drives Archaeal Cell Division.” Science
Advances, vol. 9, no. 11, eade5224, American Association for the Advancement
of Science, 2023, doi:10.1126/sciadv.ade5224.
short: F. Hurtig, T.C.Q. Burgers, A. Cezanne, X. Jiang, F.N. Mol, J. Traparić, A.A.
Pulschen, T. Nierhaus, G. Tarrason-Risa, L. Harker-Kirschneck, J. Löwe, A. Šarić,
R. Vlijm, B. Baum, Science Advances 9 (2023).
date_created: 2023-03-26T22:01:06Z
date_published: 2023-03-17T00:00:00Z
date_updated: 2023-08-01T13:45:54Z
day: '17'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.1126/sciadv.ade5224
ec_funded: 1
external_id:
isi:
- '000968083500010'
file:
- access_level: open_access
checksum: 6d7dbe9ed86a116c8a002d62971202c5
content_type: application/pdf
creator: dernst
date_created: 2023-03-27T06:24:49Z
date_updated: 2023-03-27T06:24:49Z
file_id: '12768'
file_name: 2023_ScienceAdvances_Hurtig.pdf
file_size: 1826471
relation: main_file
success: 1
file_date_updated: 2023-03-27T06:24:49Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '11'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
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: The patterned assembly and stepwise Vps4-mediated disassembly of composite
ESCRT-III polymers drives archaeal cell division
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2023'
...
---
_id: '12758'
abstract:
- lang: eng
text: AlphaFold changed the field of structural biology by achieving three-dimensional
(3D) structure prediction from protein sequence at experimental quality. The astounding
success even led to claims that the protein folding problem is “solved”. However,
protein folding problem is more than just structure prediction from sequence.
Presently, it is unknown if the AlphaFold-triggered revolution could help to solve
other problems related to protein folding. Here we assay the ability of AlphaFold
to predict the impact of single mutations on protein stability (ΔΔG) and function.
To study the question we extracted the pLDDT and metrics from AlphaFold
predictions before and after single mutation in a protein and correlated the predicted
change with the experimentally known ΔΔG values. Additionally, we correlated the
same AlphaFold pLDDT metrics with the impact of a single mutation on structure
using a large scale dataset of single mutations in GFP with the experimentally
assayed levels of fluorescence. We found a very weak or no correlation between
AlphaFold output metrics and change of protein stability or fluorescence. Our
results imply that AlphaFold may not be immediately applied to other problems
or applications in protein folding.
acknowledgement: The authors acknowledge the use of Zhores supercomputer [28] for
obtaining the results presented in this paper.The authors thank Zimin Foundation
and Petrovax for support of the presented study at the School of Molecular and Theoretical
Biology 2021.
article_number: e0282689
article_processing_charge: No
article_type: original
author:
- first_name: Marina A.
full_name: Pak, Marina A.
last_name: Pak
- first_name: Karina A.
full_name: Markhieva, Karina A.
last_name: Markhieva
- first_name: Mariia S.
full_name: Novikova, Mariia S.
last_name: Novikova
- first_name: Dmitry S.
full_name: Petrov, Dmitry S.
last_name: Petrov
- first_name: Ilya S.
full_name: Vorobyev, Ilya S.
last_name: Vorobyev
- first_name: Ekaterina
full_name: Maksimova, Ekaterina
id: 2FBE0DE4-F248-11E8-B48F-1D18A9856A87
last_name: Maksimova
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Dmitry N.
full_name: Ivankov, Dmitry N.
last_name: Ivankov
citation:
ama: Pak MA, Markhieva KA, Novikova MS, et al. Using AlphaFold to predict the impact
of single mutations on protein stability and function. PLoS ONE. 2023;18(3).
doi:10.1371/journal.pone.0282689
apa: Pak, M. A., Markhieva, K. A., Novikova, M. S., Petrov, D. S., Vorobyev, I.
S., Maksimova, E., … Ivankov, D. N. (2023). Using AlphaFold to predict the impact
of single mutations on protein stability and function. PLoS ONE. Public
Library of Science. https://doi.org/10.1371/journal.pone.0282689
chicago: Pak, Marina A., Karina A. Markhieva, Mariia S. Novikova, Dmitry S. Petrov,
Ilya S. Vorobyev, Ekaterina Maksimova, Fyodor Kondrashov, and Dmitry N. Ivankov.
“Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability
and Function.” PLoS ONE. Public Library of Science, 2023. https://doi.org/10.1371/journal.pone.0282689.
ieee: M. A. Pak et al., “Using AlphaFold to predict the impact of single
mutations on protein stability and function,” PLoS ONE, vol. 18, no. 3.
Public Library of Science, 2023.
ista: Pak MA, Markhieva KA, Novikova MS, Petrov DS, Vorobyev IS, Maksimova E, Kondrashov
F, Ivankov DN. 2023. Using AlphaFold to predict the impact of single mutations
on protein stability and function. PLoS ONE. 18(3), e0282689.
mla: Pak, Marina A., et al. “Using AlphaFold to Predict the Impact of Single Mutations
on Protein Stability and Function.” PLoS ONE, vol. 18, no. 3, e0282689,
Public Library of Science, 2023, doi:10.1371/journal.pone.0282689.
short: M.A. Pak, K.A. Markhieva, M.S. Novikova, D.S. Petrov, I.S. Vorobyev, E. Maksimova,
F. Kondrashov, D.N. Ivankov, PLoS ONE 18 (2023).
date_created: 2023-03-26T22:01:07Z
date_published: 2023-03-16T00:00:00Z
date_updated: 2023-08-01T13:47:14Z
day: '16'
ddc:
- '570'
department:
- _id: FyKo
- _id: MaRo
doi: 10.1371/journal.pone.0282689
external_id:
isi:
- '000985134400106'
file:
- access_level: open_access
checksum: 0281bdfccf8d76c4e08dd011c603f6b6
content_type: application/pdf
creator: dernst
date_created: 2023-03-27T07:09:08Z
date_updated: 2023-03-27T07:09:08Z
file_id: '12771'
file_name: 2023_PLoSOne_Pak.pdf
file_size: 856625
relation: main_file
success: 1
file_date_updated: 2023-03-27T07:09:08Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: PLoS ONE
publication_identifier:
eissn:
- 1932-6203
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Using AlphaFold to predict the impact of single mutations on protein stability
and function
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 18
year: '2023'
...
---
_id: '12757'
abstract:
- lang: eng
text: My group and myself have studied respiratory complex I for almost 30 years,
starting in 1994 when it was known as a L-shaped giant ‘black box' of bioenergetics.
First breakthrough was the X-ray structure of the peripheral arm, followed by
structures of the membrane arm and finally the entire complex from Thermus thermophilus.
The developments in cryo-EM technology allowed us to solve the first complete
structure of the twice larger, ∼1 MDa mammalian enzyme in 2016. However, the mechanism
coupling, over large distances, the transfer of two electrons to pumping of four
protons across the membrane remained an enigma. Recently we have solved high-resolution
structures of mammalian and bacterial complex I under a range of redox conditions,
including catalytic turnover. This allowed us to propose a robust and universal
mechanism for complex I and related protein families. Redox reactions initially
drive conformational changes around the quinone cavity and a long-distance transfer
of substrate protons. These set up a stage for a series of electrostatically driven
proton transfers along the membrane arm (‘domino effect'), eventually resulting
in proton expulsion from the distal antiporter-like subunit. The mechanism radically
differs from previous suggestions, however, it naturally explains all the unusual
structural features of complex I. In this review I discuss the state of knowledge
on complex I, including the current most controversial issues.
article_processing_charge: No
article_type: review
author:
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: 'Sazanov LA. From the “black box” to “domino effect” mechanism: What have we
learned from the structures of respiratory complex I. The Biochemical Journal.
2023;480(5):319-333. doi:10.1042/BCJ20210285'
apa: 'Sazanov, L. A. (2023). From the “black box” to “domino effect” mechanism:
What have we learned from the structures of respiratory complex I. The Biochemical
Journal. Portland Press. https://doi.org/10.1042/BCJ20210285'
chicago: 'Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism:
What Have We Learned from the Structures of Respiratory Complex I.” The Biochemical
Journal. Portland Press, 2023. https://doi.org/10.1042/BCJ20210285.'
ieee: 'L. A. Sazanov, “From the ‘black box’ to ‘domino effect’ mechanism: What have
we learned from the structures of respiratory complex I,” The Biochemical Journal,
vol. 480, no. 5. Portland Press, pp. 319–333, 2023.'
ista: 'Sazanov LA. 2023. From the ‘black box’ to ‘domino effect’ mechanism: What
have we learned from the structures of respiratory complex I. The Biochemical
Journal. 480(5), 319–333.'
mla: 'Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism: What
Have We Learned from the Structures of Respiratory Complex I.” The Biochemical
Journal, vol. 480, no. 5, Portland Press, 2023, pp. 319–33, doi:10.1042/BCJ20210285.'
short: L.A. Sazanov, The Biochemical Journal 480 (2023) 319–333.
date_created: 2023-03-26T22:01:06Z
date_published: 2023-03-15T00:00:00Z
date_updated: 2023-08-01T13:45:12Z
day: '15'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1042/BCJ20210285
external_id:
isi:
- '000957065700001'
pmid:
- '36920092'
has_accepted_license: '1'
intvolume: ' 480'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1042/BCJ20210285
month: '03'
oa: 1
oa_version: Published Version
page: 319-333
pmid: 1
publication: The Biochemical Journal
publication_identifier:
eissn:
- 1470-8728
issn:
- 0264-6021
publication_status: published
publisher: Portland Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'From the ''black box'' to ''domino effect'' mechanism: What have we learned
from the structures of respiratory complex I'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 480
year: '2023'
...
---
_id: '12787'
abstract:
- lang: eng
text: "Populations evolve in spatially heterogeneous environments. While a certain
trait might bring a fitness advantage in some patch of the environment, a different
trait might be advantageous in another patch. Here, we study the Moran birth–death
process with two types of individuals in a population stretched across two patches
of size N, each patch favouring one of the two types. We show that the long-term
fate of such populations crucially depends on the migration rate μ\r\n between
the patches. To classify the possible fates, we use the distinction between polynomial
(short) and exponential (long) timescales. We show that when μ is high then one
of the two types fixates on the whole population after a number of steps that
is only polynomial in N. By contrast, when μ is low then each type holds majority
in the patch where it is favoured for a number of steps that is at least exponential
in N. Moreover, we precisely identify the threshold migration rate μ⋆ that separates
those two scenarios, thereby exactly delineating the situations that support long-term
coexistence of the two types. We also discuss the case of various cycle graphs
and we present computer simulations that perfectly match our analytical results."
acknowledgement: J.S. and K.C. acknowledge support from the ERC CoG 863818 (ForM-SMArt)
article_number: '20220685'
article_processing_charge: No
article_type: original
author:
- first_name: Jakub
full_name: Svoboda, Jakub
id: 130759D2-D7DD-11E9-87D2-DE0DE6697425
last_name: Svoboda
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Kamran
full_name: Kaveh, Kamran
last_name: Kaveh
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: 'Svoboda J, Tkadlec J, Kaveh K, Chatterjee K. Coexistence times in the Moran
process with environmental heterogeneity. Proceedings of the Royal Society
A: Mathematical, Physical and Engineering Sciences. 2023;479(2271). doi:10.1098/rspa.2022.0685'
apa: 'Svoboda, J., Tkadlec, J., Kaveh, K., & Chatterjee, K. (2023). Coexistence
times in the Moran process with environmental heterogeneity. Proceedings of
the Royal Society A: Mathematical, Physical and Engineering Sciences. The
Royal Society. https://doi.org/10.1098/rspa.2022.0685'
chicago: 'Svoboda, Jakub, Josef Tkadlec, Kamran Kaveh, and Krishnendu Chatterjee.
“Coexistence Times in the Moran Process with Environmental Heterogeneity.” Proceedings
of the Royal Society A: Mathematical, Physical and Engineering Sciences. The
Royal Society, 2023. https://doi.org/10.1098/rspa.2022.0685.'
ieee: 'J. Svoboda, J. Tkadlec, K. Kaveh, and K. Chatterjee, “Coexistence times in
the Moran process with environmental heterogeneity,” Proceedings of the Royal
Society A: Mathematical, Physical and Engineering Sciences, vol. 479, no.
2271. The Royal Society, 2023.'
ista: 'Svoboda J, Tkadlec J, Kaveh K, Chatterjee K. 2023. Coexistence times in the
Moran process with environmental heterogeneity. Proceedings of the Royal Society
A: Mathematical, Physical and Engineering Sciences. 479(2271), 20220685.'
mla: 'Svoboda, Jakub, et al. “Coexistence Times in the Moran Process with Environmental
Heterogeneity.” Proceedings of the Royal Society A: Mathematical, Physical
and Engineering Sciences, vol. 479, no. 2271, 20220685, The Royal Society,
2023, doi:10.1098/rspa.2022.0685.'
short: 'J. Svoboda, J. Tkadlec, K. Kaveh, K. Chatterjee, Proceedings of the Royal
Society A: Mathematical, Physical and Engineering Sciences 479 (2023).'
date_created: 2023-04-02T22:01:09Z
date_published: 2023-03-29T00:00:00Z
date_updated: 2023-08-01T13:58:34Z
day: '29'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1098/rspa.2022.0685
ec_funded: 1
external_id:
isi:
- '000957125500002'
file:
- access_level: open_access
checksum: 13953d349fbefcb5d21ccc6b303297eb
content_type: application/pdf
creator: dernst
date_created: 2023-04-03T06:25:29Z
date_updated: 2023-04-03T06:25:29Z
file_id: '12796'
file_name: 2023_ProceedingsRoyalSocietyA_Svoboda.pdf
file_size: 827784
relation: main_file
success: 1
file_date_updated: 2023-04-03T06:25:29Z
has_accepted_license: '1'
intvolume: ' 479'
isi: 1
issue: '2271'
language:
- iso: eng
month: '03'
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 Royal Society A: Mathematical, Physical and Engineering
Sciences'
publication_identifier:
eissn:
- 1471-2946
issn:
- 1364-5021
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
related_material:
link:
- relation: research_data
url: https://doi.org/10.6084/m9.figshare.21261771.v1
scopus_import: '1'
status: public
title: Coexistence times in the Moran process with environmental heterogeneity
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 479
year: '2023'
...
---
_id: '12788'
abstract:
- lang: eng
text: We show that the simplest of existing molecules—closed-shell diatomics not
interacting with one another—host topological charges when driven by periodic
far-off-resonant laser pulses. A periodically kicked molecular rotor can be mapped
onto a “crystalline” lattice in angular momentum space. This allows us to define
quasimomenta and the band structure in the Floquet representation, by analogy
with the Bloch waves of solid-state physics. Applying laser pulses spaced by 1/3
of the molecular rotational period creates a lattice with three atoms per unit
cell with staggered hopping. Within the synthetic dimension of the laser strength,
we discover Dirac cones with topological charges. These Dirac cones, topologically
protected by reflection and time-reversal symmetry, are reminiscent of (although
not equivalent to) that seen in graphene. They—and the corresponding edge states—are
broadly tunable by adjusting the laser strength and can be observed in present-day
experiments by measuring molecular alignment and populations of rotational levels.
This paves the way to study controllable topological physics in gas-phase experiments
with small molecules as well as to classify dynamical molecular states by their
topological invariants.
acknowledgement: M. L. acknowledges support by the European Research Council (ERC)
Starting Grant No. 801770 (ANGULON).
article_number: '103202'
article_processing_charge: No
article_type: original
author:
- first_name: Volker
full_name: Karle, Volker
id: D7C012AE-D7ED-11E9-95E8-1EC5E5697425
last_name: Karle
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Karle V, Ghazaryan A, Lemeshko M. Topological charges of periodically kicked
molecules. Physical Review Letters. 2023;130(10). doi:10.1103/PhysRevLett.130.103202
apa: Karle, V., Ghazaryan, A., & Lemeshko, M. (2023). Topological charges of
periodically kicked molecules. Physical Review Letters. American Physical
Society. https://doi.org/10.1103/PhysRevLett.130.103202
chicago: Karle, Volker, Areg Ghazaryan, and Mikhail Lemeshko. “Topological Charges
of Periodically Kicked Molecules.” Physical Review Letters. American Physical
Society, 2023. https://doi.org/10.1103/PhysRevLett.130.103202.
ieee: V. Karle, A. Ghazaryan, and M. Lemeshko, “Topological charges of periodically
kicked molecules,” Physical Review Letters, vol. 130, no. 10. American
Physical Society, 2023.
ista: Karle V, Ghazaryan A, Lemeshko M. 2023. Topological charges of periodically
kicked molecules. Physical Review Letters. 130(10), 103202.
mla: Karle, Volker, et al. “Topological Charges of Periodically Kicked Molecules.”
Physical Review Letters, vol. 130, no. 10, 103202, American Physical Society,
2023, doi:10.1103/PhysRevLett.130.103202.
short: V. Karle, A. Ghazaryan, M. Lemeshko, Physical Review Letters 130 (2023).
date_created: 2023-04-02T22:01:10Z
date_published: 2023-03-10T00:00:00Z
date_updated: 2023-08-01T14:02:06Z
day: '10'
department:
- _id: MiLe
doi: 10.1103/PhysRevLett.130.103202
ec_funded: 1
external_id:
arxiv:
- '2206.07067'
isi:
- '000957635500003'
intvolume: ' 130'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2206.07067
month: '03'
oa: 1
oa_version: Preprint
project:
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
link:
- description: News on the ISTA website
relation: press_release
url: https://ista.ac.at/en/news/topology-of-rotating-molecules/
scopus_import: '1'
status: public
title: Topological charges of periodically kicked molecules
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 130
year: '2023'
...
---
_id: '12790'
abstract:
- lang: eng
text: Motivated by the recent discoveries of superconductivity in bilayer and trilayer
graphene, we theoretically investigate superconductivity and other interaction-driven
phases in multilayer graphene stacks. To this end, we study the density of states
of multilayer graphene with up to four layers at the single-particle band structure
level in the presence of a transverse electric field. Among the considered structures,
tetralayer graphene with rhombohedral (ABCA) stacking reaches the highest density
of states. We study the phases that can arise in ABCA graphene by tuning the carrier
density and transverse electric field. For a broad region of the tuning parameters,
the presence of strong Coulomb repulsion leads to a spontaneous spin and valley
symmetry breaking via Stoner transitions. Using a model that incorporates the
spontaneous spin and valley polarization, we explore the Kohn-Luttinger mechanism
for superconductivity driven by repulsive Coulomb interactions. We find that the
strongest superconducting instability is in the p-wave channel, and occurs in
proximity to the onset of Stoner transitions. Interestingly, we find a range of
densities and transverse electric fields where superconductivity develops out
of a strongly corrugated, singly connected Fermi surface in each valley, leading
to a topologically nontrivial chiral p+ip superconducting state with an even number
of copropagating chiral Majorana edge modes. Our work establishes ABCA-stacked
tetralayer graphene as a promising platform for observing strongly correlated
physics and topological superconductivity.
acknowledgement: E.B. and T.H. were supported by the European Research Council (ERC)
under grant HQMAT (Grant Agreement No. 817799), by the Israel-USA Binational Science
Foundation (BSF), and by a Research grant from Irving and Cherna Moskowitz.
article_number: '104502'
article_processing_charge: No
article_type: original
author:
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: Tobias
full_name: Holder, Tobias
last_name: Holder
- first_name: Erez
full_name: Berg, Erez
last_name: Berg
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Ghazaryan A, Holder T, Berg E, Serbyn M. Multilayer graphenes as a platform
for interaction-driven physics and topological superconductivity. Physical
Review B. 2023;107(10). doi:10.1103/PhysRevB.107.104502
apa: Ghazaryan, A., Holder, T., Berg, E., & Serbyn, M. (2023). Multilayer graphenes
as a platform for interaction-driven physics and topological superconductivity.
Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.107.104502
chicago: Ghazaryan, Areg, Tobias Holder, Erez Berg, and Maksym Serbyn. “Multilayer
Graphenes as a Platform for Interaction-Driven Physics and Topological Superconductivity.”
Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.107.104502.
ieee: A. Ghazaryan, T. Holder, E. Berg, and M. Serbyn, “Multilayer graphenes as
a platform for interaction-driven physics and topological superconductivity,”
Physical Review B, vol. 107, no. 10. American Physical Society, 2023.
ista: Ghazaryan A, Holder T, Berg E, Serbyn M. 2023. Multilayer graphenes as a platform
for interaction-driven physics and topological superconductivity. Physical Review
B. 107(10), 104502.
mla: Ghazaryan, Areg, et al. “Multilayer Graphenes as a Platform for Interaction-Driven
Physics and Topological Superconductivity.” Physical Review B, vol. 107,
no. 10, 104502, American Physical Society, 2023, doi:10.1103/PhysRevB.107.104502.
short: A. Ghazaryan, T. Holder, E. Berg, M. Serbyn, Physical Review B 107 (2023).
date_created: 2023-04-02T22:01:10Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-08-01T13:59:29Z
day: '01'
department:
- _id: MaSe
- _id: MiLe
doi: 10.1103/PhysRevB.107.104502
external_id:
arxiv:
- '2211.02492'
isi:
- '000945526400003'
intvolume: ' 107'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2211.02492
month: '03'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
link:
- description: News on the ISTA website
relation: press_release
url: https://ista.ac.at/en/news/reaching-superconductivity-layer-by-layer/
scopus_import: '1'
status: public
title: Multilayer graphenes as a platform for interaction-driven physics and topological
superconductivity
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 107
year: '2023'
...
---
_id: '12791'
abstract:
- lang: eng
text: We investigate the capabilities of Physics-Informed Neural Networks (PINNs)
to reconstruct turbulent Rayleigh–Bénard flows using only temperature information.
We perform a quantitative analysis of the quality of the reconstructions at various
amounts of low-passed-filtered information and turbulent intensities. We compare
our results with those obtained via nudging, a classical equation-informed data
assimilation technique. At low Rayleigh numbers, PINNs are able to reconstruct
with high precision, comparable to the one achieved with nudging. At high Rayleigh
numbers, PINNs outperform nudging and are able to achieve satisfactory reconstruction
of the velocity fields only when data for temperature is provided with high spatial
and temporal density. When data becomes sparse, the PINNs performance worsens,
not only in a point-to-point error sense but also, and contrary to nudging, in
a statistical sense, as can be seen in the probability density functions and energy
spectra.
acknowledgement: This project has received partial funding from the European Research
Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme
(Grant Agreement No. 882340))
article_number: '16'
article_processing_charge: No
article_type: original
author:
- first_name: Patricio
full_name: Clark Di Leoni, Patricio
last_name: Clark Di Leoni
- first_name: Lokahith N
full_name: Agasthya, Lokahith N
id: cd100965-0804-11ed-9c55-f4878ff4e877
last_name: Agasthya
- first_name: Michele
full_name: Buzzicotti, Michele
last_name: Buzzicotti
- first_name: Luca
full_name: Biferale, Luca
last_name: Biferale
citation:
ama: Clark Di Leoni P, Agasthya LN, Buzzicotti M, Biferale L. Reconstructing Rayleigh–Bénard
flows out of temperature-only measurements using Physics-Informed Neural Networks.
The European Physical Journal E. 2023;46(3). doi:10.1140/epje/s10189-023-00276-9
apa: Clark Di Leoni, P., Agasthya, L. N., Buzzicotti, M., & Biferale, L. (2023).
Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using
Physics-Informed Neural Networks. The European Physical Journal E. Springer
Nature. https://doi.org/10.1140/epje/s10189-023-00276-9
chicago: Clark Di Leoni, Patricio, Lokahith N Agasthya, Michele Buzzicotti, and
Luca Biferale. “Reconstructing Rayleigh–Bénard Flows out of Temperature-Only Measurements
Using Physics-Informed Neural Networks.” The European Physical Journal E.
Springer Nature, 2023. https://doi.org/10.1140/epje/s10189-023-00276-9.
ieee: P. Clark Di Leoni, L. N. Agasthya, M. Buzzicotti, and L. Biferale, “Reconstructing
Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed
Neural Networks,” The European Physical Journal E, vol. 46, no. 3. Springer
Nature, 2023.
ista: Clark Di Leoni P, Agasthya LN, Buzzicotti M, Biferale L. 2023. Reconstructing
Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed
Neural Networks. The European Physical Journal E. 46(3), 16.
mla: Clark Di Leoni, Patricio, et al. “Reconstructing Rayleigh–Bénard Flows out
of Temperature-Only Measurements Using Physics-Informed Neural Networks.” The
European Physical Journal E, vol. 46, no. 3, 16, Springer Nature, 2023, doi:10.1140/epje/s10189-023-00276-9.
short: P. Clark Di Leoni, L.N. Agasthya, M. Buzzicotti, L. Biferale, The European
Physical Journal E 46 (2023).
date_created: 2023-04-02T22:01:11Z
date_published: 2023-03-20T00:00:00Z
date_updated: 2023-08-01T14:03:47Z
day: '20'
department:
- _id: CaMu
doi: 10.1140/epje/s10189-023-00276-9
external_id:
arxiv:
- '2301.07769'
isi:
- '000956387200001'
intvolume: ' 46'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2301.07769'
month: '03'
oa: 1
oa_version: Preprint
publication: The European Physical Journal E
publication_identifier:
eissn:
- 1292-895X
issn:
- 1292-8941
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using
Physics-Informed Neural Networks
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 46
year: '2023'
...