---
_id: '8817'
abstract:
- lang: eng
text: The paper introduces an inertial extragradient subgradient method with self-adaptive
step sizes for solving equilibrium problems in real Hilbert spaces. Weak convergence
of the proposed method is obtained under the condition that the bifunction is
pseudomonotone and Lipchitz continuous. Linear convergence is also given when
the bifunction is strongly pseudomonotone and Lipchitz continuous. Numerical implementations
and comparisons with other related inertial methods are given using test problems
including a real-world application to Nash–Cournot oligopolistic electricity market
equilibrium model.
acknowledgement: The authors are grateful to the two referees and the Associate Editor
for their comments and suggestions which have improved the earlier version of the
paper greatly. The project of Yekini Shehu has received funding from the European
Research Council (ERC) under the European Union’s Seventh Framework Program (FP7
- 2007-2013) (Grant agreement No. 616160).
article_processing_charge: No
article_type: original
author:
- first_name: Yekini
full_name: Shehu, Yekini
id: 3FC7CB58-F248-11E8-B48F-1D18A9856A87
last_name: Shehu
orcid: 0000-0001-9224-7139
- first_name: Olaniyi S.
full_name: Iyiola, Olaniyi S.
last_name: Iyiola
- first_name: Duong Viet
full_name: Thong, Duong Viet
last_name: Thong
- first_name: Nguyen Thi Cam
full_name: Van, Nguyen Thi Cam
last_name: Van
citation:
ama: Shehu Y, Iyiola OS, Thong DV, Van NTC. An inertial subgradient extragradient
algorithm extended to pseudomonotone equilibrium problems. Mathematical Methods
of Operations Research. 2021;93(2):213-242. doi:10.1007/s00186-020-00730-w
apa: Shehu, Y., Iyiola, O. S., Thong, D. V., & Van, N. T. C. (2021). An inertial
subgradient extragradient algorithm extended to pseudomonotone equilibrium problems.
Mathematical Methods of Operations Research. Springer Nature. https://doi.org/10.1007/s00186-020-00730-w
chicago: Shehu, Yekini, Olaniyi S. Iyiola, Duong Viet Thong, and Nguyen Thi Cam
Van. “An Inertial Subgradient Extragradient Algorithm Extended to Pseudomonotone
Equilibrium Problems.” Mathematical Methods of Operations Research. Springer
Nature, 2021. https://doi.org/10.1007/s00186-020-00730-w.
ieee: Y. Shehu, O. S. Iyiola, D. V. Thong, and N. T. C. Van, “An inertial subgradient
extragradient algorithm extended to pseudomonotone equilibrium problems,” Mathematical
Methods of Operations Research, vol. 93, no. 2. Springer Nature, pp. 213–242,
2021.
ista: Shehu Y, Iyiola OS, Thong DV, Van NTC. 2021. An inertial subgradient extragradient
algorithm extended to pseudomonotone equilibrium problems. Mathematical Methods
of Operations Research. 93(2), 213–242.
mla: Shehu, Yekini, et al. “An Inertial Subgradient Extragradient Algorithm Extended
to Pseudomonotone Equilibrium Problems.” Mathematical Methods of Operations
Research, vol. 93, no. 2, Springer Nature, 2021, pp. 213–42, doi:10.1007/s00186-020-00730-w.
short: Y. Shehu, O.S. Iyiola, D.V. Thong, N.T.C. Van, Mathematical Methods of Operations
Research 93 (2021) 213–242.
date_created: 2020-11-29T23:01:18Z
date_published: 2021-04-01T00:00:00Z
date_updated: 2024-11-04T13:52:33Z
day: '01'
department:
- _id: VlKo
doi: 10.1007/s00186-020-00730-w
ec_funded: 1
external_id:
isi:
- '000590497300001'
intvolume: ' 93'
isi: 1
issue: '2'
language:
- iso: eng
month: '04'
oa_version: None
page: 213-242
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: Mathematical Methods of Operations Research
publication_identifier:
eissn:
- 1432-5217
issn:
- 1432-2994
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: An inertial subgradient extragradient algorithm extended to pseudomonotone
equilibrium problems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 93
year: '2021'
...
---
_id: '8818'
abstract:
- lang: eng
text: The hippocampus has a major role in encoding and consolidating long-term memories,
and undergoes plastic changes during sleep1. These changes require precise homeostatic
control by subcortical neuromodulatory structures2. The underlying mechanisms
of this phenomenon, however, remain unknown. Here, using multi-structure recordings
in macaque monkeys, we show that the brainstem transiently modulates hippocampal
network events through phasic pontine waves known as pontogeniculooccipital waves
(PGO waves). Two physiologically distinct types of PGO wave appear to occur sequentially,
selectively influencing high-frequency ripples and low-frequency theta events,
respectively. The two types of PGO wave are associated with opposite hippocampal
spike-field coupling, prompting periods of high neural synchrony of neural populations
during periods of ripple and theta instances. The coupling between PGO waves and
ripples, classically associated with distinct sleep stages, supports the notion
that a global coordination mechanism of hippocampal sleep dynamics by cholinergic
pontine transients may promote systems and synaptic memory consolidation as well
as synaptic homeostasis.
acknowledgement: We thank O. Eschenko and M. Constantinou for providing feedback on
earlier versions of this work, and J. Werner and M. Schnabel for technical support
during the development of this study. This research was supported by the Max Planck
Society.
article_processing_charge: No
article_type: original
author:
- first_name: Juan F
full_name: Ramirez Villegas, Juan F
id: 44B06F76-F248-11E8-B48F-1D18A9856A87
last_name: Ramirez Villegas
- first_name: Michel
full_name: Besserve, Michel
last_name: Besserve
- first_name: Yusuke
full_name: Murayama, Yusuke
last_name: Murayama
- first_name: Henry C.
full_name: Evrard, Henry C.
last_name: Evrard
- first_name: Axel
full_name: Oeltermann, Axel
last_name: Oeltermann
- first_name: Nikos K.
full_name: Logothetis, Nikos K.
last_name: Logothetis
citation:
ama: Ramirez Villegas JF, Besserve M, Murayama Y, Evrard HC, Oeltermann A, Logothetis
NK. Coupling of hippocampal theta and ripples with pontogeniculooccipital waves.
Nature. 2021;589(7840):96-102. doi:10.1038/s41586-020-2914-4
apa: Ramirez Villegas, J. F., Besserve, M., Murayama, Y., Evrard, H. C., Oeltermann,
A., & Logothetis, N. K. (2021). Coupling of hippocampal theta and ripples
with pontogeniculooccipital waves. Nature. Springer Nature. https://doi.org/10.1038/s41586-020-2914-4
chicago: Ramirez Villegas, Juan F, Michel Besserve, Yusuke Murayama, Henry C. Evrard,
Axel Oeltermann, and Nikos K. Logothetis. “Coupling of Hippocampal Theta and Ripples
with Pontogeniculooccipital Waves.” Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-020-2914-4.
ieee: J. F. Ramirez Villegas, M. Besserve, Y. Murayama, H. C. Evrard, A. Oeltermann,
and N. K. Logothetis, “Coupling of hippocampal theta and ripples with pontogeniculooccipital
waves,” Nature, vol. 589, no. 7840. Springer Nature, pp. 96–102, 2021.
ista: Ramirez Villegas JF, Besserve M, Murayama Y, Evrard HC, Oeltermann A, Logothetis
NK. 2021. Coupling of hippocampal theta and ripples with pontogeniculooccipital
waves. Nature. 589(7840), 96–102.
mla: Ramirez Villegas, Juan F., et al. “Coupling of Hippocampal Theta and Ripples
with Pontogeniculooccipital Waves.” Nature, vol. 589, no. 7840, Springer
Nature, 2021, pp. 96–102, doi:10.1038/s41586-020-2914-4.
short: J.F. Ramirez Villegas, M. Besserve, Y. Murayama, H.C. Evrard, A. Oeltermann,
N.K. Logothetis, Nature 589 (2021) 96–102.
date_created: 2020-11-29T23:01:19Z
date_published: 2021-01-07T00:00:00Z
date_updated: 2025-07-10T12:01:26Z
day: '07'
department:
- _id: JoCs
doi: 10.1038/s41586-020-2914-4
external_id:
isi:
- '000591047800005'
pmid:
- '33208951'
intvolume: ' 589'
isi: 1
issue: '7840'
language:
- iso: eng
month: '01'
oa_version: None
page: 96-102
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41586-020-03068-9
scopus_import: '1'
status: public
title: Coupling of hippocampal theta and ripples with pontogeniculooccipital waves
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 589
year: '2021'
...
---
_id: '8824'
abstract:
- lang: eng
text: Plants are able to orient their growth according to gravity, which ultimately
controls both shoot and root architecture.1 Gravitropism is a dynamic process
whereby gravistimulation induces the asymmetric distribution of the plant hormone
auxin, leading to asymmetric growth, organ bending, and subsequent reset of auxin
distribution back to the original pre-gravistimulation situation.1, 2, 3 Differential
auxin accumulation during the gravitropic response depends on the activity of
polarly localized PIN-FORMED (PIN) auxin-efflux carriers.1, 2, 3, 4 In particular,
the timing of this dynamic response is regulated by PIN2,5,6 but the underlying
molecular mechanisms are poorly understood. Here, we show that MEMBRANE ASSOCIATED
KINASE REGULATOR2 (MAKR2) controls the pace of the root gravitropic response.
We found that MAKR2 is required for the PIN2 asymmetry during gravitropism by
acting as a negative regulator of the cell-surface signaling mediated by the receptor-like
kinase TRANSMEMBRANE KINASE1 (TMK1).2,7, 8, 9, 10 Furthermore, we show that
the MAKR2 inhibitory effect on TMK1 signaling is antagonized by auxin itself,
which triggers rapid MAKR2 membrane dissociation in a TMK1-dependent manner. Our
findings suggest that the timing of the root gravitropic response is orchestrated
by the reversible inhibition of the TMK1 signaling pathway at the cell surface.
acknowledgement: "We thank the SiCE group for discussions and comments; S. Yalovsky,
B. Scheres, and the NASC/ABRC collection for providing transgenic Arabidopsis lines
and plasmids; L. Kalmbach and M. Barberon for the gift of pLOK180_pFR7m34GW; A.
Lacroix, J. Berger, and P. Bolland for plant care; and M. Fendrych for help with
microfluidics in the J.F. lab. We acknowledge\r\nthe contribution of the SFR Biosciences
(UMS3444/CNRS, US8/Inser m, ENS de Lyon, UCBL) facilities: C. Lionet, E. Chatre,
and J. Brocard at LBIPLATIM-MICROSCOPY for assistance with imaging, and V. GuegenChaignon
and A. Page at the Protein Science Facility (PSF) for assistance with protein purification
and mass spectrometry. Y.J. was funded by ERC\r\ngrant 3363360-APPL under FP/2007–2013.
Y.J. and Z.L.N. were funded by an ANR- and NSF-supported ERA-CAPS project (SICOPID:
ANR-17-CAPS0003-01/NSF PGRP IOS-1841917). A.I.C.-D. is funded by an ERC consolidator
grant (ERC-2015-CoG–683163) and BIO2016-78955 grant from the Spanish Ministry of
Economy and Competitiveness. Exchanges between the Y.J. and T.B. laboratories were
funded by Tournesol grant 35656NB. B.K.M. was\r\nfunded by the Omics@vib Marie Curie
COFUND and Research Foundation Flanders for a postdoctoral fellowship."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: MM
full_name: Marquès-Bueno, MM
last_name: Marquès-Bueno
- first_name: L
full_name: Armengot, L
last_name: Armengot
- first_name: LC
full_name: Noack, LC
last_name: Noack
- first_name: J
full_name: Bareille, J
last_name: Bareille
- first_name: Lesia
full_name: Rodriguez Solovey, Lesia
id: 3922B506-F248-11E8-B48F-1D18A9856A87
last_name: Rodriguez Solovey
orcid: 0000-0002-7244-7237
- first_name: MP
full_name: Platre, MP
last_name: Platre
- first_name: V
full_name: Bayle, V
last_name: Bayle
- first_name: M
full_name: Liu, M
last_name: Liu
- first_name: D
full_name: Opdenacker, D
last_name: Opdenacker
- first_name: S
full_name: Vanneste, S
last_name: Vanneste
- first_name: BK
full_name: Möller, BK
last_name: Möller
- first_name: ZL
full_name: Nimchuk, ZL
last_name: Nimchuk
- first_name: T
full_name: Beeckman, T
last_name: Beeckman
- first_name: AI
full_name: Caño-Delgado, AI
last_name: Caño-Delgado
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Y
full_name: Jaillais, Y
last_name: Jaillais
citation:
ama: Marquès-Bueno M, Armengot L, Noack L, et al. Auxin-regulated reversible inhibition
of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism. Current
Biology. 2021;31(1). doi:10.1016/j.cub.2020.10.011
apa: Marquès-Bueno, M., Armengot, L., Noack, L., Bareille, J., Rodriguez Solovey,
L., Platre, M., … Jaillais, Y. (2021). Auxin-regulated reversible inhibition of
TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism. Current
Biology. Elsevier. https://doi.org/10.1016/j.cub.2020.10.011
chicago: Marquès-Bueno, MM, L Armengot, LC Noack, J Bareille, Lesia Rodriguez Solovey,
MP Platre, V Bayle, et al. “Auxin-Regulated Reversible Inhibition of TMK1 Signaling
by MAKR2 Modulates the Dynamics of Root Gravitropism.” Current Biology.
Elsevier, 2021. https://doi.org/10.1016/j.cub.2020.10.011.
ieee: M. Marquès-Bueno et al., “Auxin-regulated reversible inhibition of
TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism,” Current
Biology, vol. 31, no. 1. Elsevier, 2021.
ista: Marquès-Bueno M, Armengot L, Noack L, Bareille J, Rodriguez Solovey L, Platre
M, Bayle V, Liu M, Opdenacker D, Vanneste S, Möller B, Nimchuk Z, Beeckman T,
Caño-Delgado A, Friml J, Jaillais Y. 2021. Auxin-regulated reversible inhibition
of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism. Current
Biology. 31(1).
mla: Marquès-Bueno, MM, et al. “Auxin-Regulated Reversible Inhibition of TMK1 Signaling
by MAKR2 Modulates the Dynamics of Root Gravitropism.” Current Biology,
vol. 31, no. 1, Elsevier, 2021, doi:10.1016/j.cub.2020.10.011.
short: M. Marquès-Bueno, L. Armengot, L. Noack, J. Bareille, L. Rodriguez Solovey,
M. Platre, V. Bayle, M. Liu, D. Opdenacker, S. Vanneste, B. Möller, Z. Nimchuk,
T. Beeckman, A. Caño-Delgado, J. Friml, Y. Jaillais, Current Biology 31 (2021).
date_created: 2020-12-01T13:39:46Z
date_published: 2021-01-11T00:00:00Z
date_updated: 2024-10-21T06:02:09Z
day: '11'
ddc:
- '570'
department:
- _id: JiFr
doi: 10.1016/j.cub.2020.10.011
external_id:
isi:
- '000614361000039'
pmid:
- '33157019'
file:
- access_level: open_access
checksum: 30b3393d841fb2b1e2b22fb42b5c8fff
content_type: application/pdf
creator: dernst
date_created: 2021-02-04T11:37:50Z
date_updated: 2021-02-04T11:37:50Z
file_id: '9090'
file_name: 2021_CurrentBiology_MarquesBueno.pdf
file_size: 3458646
relation: main_file
success: 1
file_date_updated: 2021-02-04T11:37:50Z
has_accepted_license: '1'
intvolume: ' 31'
isi: 1
issue: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Current Biology
publication_identifier:
eissn:
- 1879-0445
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates
the dynamics of root gravitropism
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 31
year: '2021'
...
---
_id: '8911'
abstract:
- lang: eng
text: "In the worldwide endeavor for disruptive quantum technologies, germanium
is emerging as a versatile material to realize devices capable of encoding, processing,
or transmitting quantum information. These devices leverage special properties
of the germanium valence-band states, commonly known as holes, such as their inherently
strong spin-orbit coupling and the ability to host superconducting pairing correlations.
In this Review, we initially introduce the physics of holes in low-dimensional
germanium structures with key insights from a theoretical perspective. We then
examine the material science progress underpinning germanium-based planar heterostructures
and nanowires. We review the most significant experimental results demonstrating
key building blocks for quantum technology, such as an electrically driven universal
quantum gate set with spin qubits in quantum dots and superconductor-semiconductor
devices for hybrid quantum systems. We conclude by identifying the most promising
prospects\r\ntoward scalable quantum information processing. "
acknowledgement: "G.S., M.W.,F.A.Z acknowledge financial support from The Netherlands
Organization for Scientific Research (NWO). F.Z., D.L., G.K. acknowledge funding
from the European Union’s Horizon 2020 research and innovation programme under Grand
Agreement Nr. 862046. G.K. acknowledges funding from FP7 ERC Starting Grant 335497,
FWF Y 715-N30, FWF P-30207. S.D. acknowledges support from the European Union’s
Horizon 2020 program under Grant\r\nAgreement No. 81050 and from the Agence Nationale
de la Recherche through the TOPONANO and CMOSQSPIN projects. J.Z. acknowledges support
from the National Key R&D Program of China (Grant No. 2016YFA0301701) and Strategic
Priority Research Program of CAS (Grant No. XDB30000000). D.L. and C.K. acknowledge
the Swiss National Science Foundation and NCCR QSIT."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Giordano
full_name: Scappucci, Giordano
last_name: Scappucci
- first_name: Christoph
full_name: Kloeffel, Christoph
last_name: Kloeffel
- first_name: Floris A.
full_name: Zwanenburg, Floris A.
last_name: Zwanenburg
- first_name: Daniel
full_name: Loss, Daniel
last_name: Loss
- first_name: Maksym
full_name: Myronov, Maksym
last_name: Myronov
- first_name: Jian-Jun
full_name: Zhang, Jian-Jun
last_name: Zhang
- first_name: Silvano De
full_name: Franceschi, Silvano De
last_name: Franceschi
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
- first_name: Menno
full_name: Veldhorst, Menno
last_name: Veldhorst
citation:
ama: Scappucci G, Kloeffel C, Zwanenburg FA, et al. The germanium quantum information
route. Nature Reviews Materials. 2021;6:926–943. doi:10.1038/s41578-020-00262-z
apa: Scappucci, G., Kloeffel, C., Zwanenburg, F. A., Loss, D., Myronov, M., Zhang,
J.-J., … Veldhorst, M. (2021). The germanium quantum information route. Nature
Reviews Materials. Springer Nature. https://doi.org/10.1038/s41578-020-00262-z
chicago: Scappucci, Giordano, Christoph Kloeffel, Floris A. Zwanenburg, Daniel Loss,
Maksym Myronov, Jian-Jun Zhang, Silvano De Franceschi, Georgios Katsaros, and
Menno Veldhorst. “The Germanium Quantum Information Route.” Nature Reviews
Materials. Springer Nature, 2021. https://doi.org/10.1038/s41578-020-00262-z.
ieee: G. Scappucci et al., “The germanium quantum information route,” Nature
Reviews Materials, vol. 6. Springer Nature, pp. 926–943, 2021.
ista: Scappucci G, Kloeffel C, Zwanenburg FA, Loss D, Myronov M, Zhang J-J, Franceschi
SD, Katsaros G, Veldhorst M. 2021. The germanium quantum information route. Nature
Reviews Materials. 6, 926–943.
mla: Scappucci, Giordano, et al. “The Germanium Quantum Information Route.” Nature
Reviews Materials, vol. 6, Springer Nature, 2021, pp. 926–943, doi:10.1038/s41578-020-00262-z.
short: G. Scappucci, C. Kloeffel, F.A. Zwanenburg, D. Loss, M. Myronov, J.-J. Zhang,
S.D. Franceschi, G. Katsaros, M. Veldhorst, Nature Reviews Materials 6 (2021)
926–943.
date_created: 2020-12-02T10:52:51Z
date_published: 2021-10-01T00:00:00Z
date_updated: 2024-10-22T09:41:03Z
day: '01'
department:
- _id: GeKa
doi: 10.1038/s41578-020-00262-z
ec_funded: 1
external_id:
arxiv:
- '2004.08133'
isi:
- '000600826100003'
intvolume: ' 6'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2004.08133
month: '10'
oa: 1
oa_version: Preprint
page: '926–943 '
project:
- _id: 25517E86-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '335497'
name: Towards Spin qubits and Majorana fermions in Germanium self assembled hut-wires
- _id: 2552F888-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Y00715
name: Loch Spin-Qubits und Majorana-Fermionen in Germanium
- _id: 2641CE5E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P30207
name: Hole spin orbit qubits in Ge quantum wells
publication: Nature Reviews Materials
publication_identifier:
eissn:
- 2058-8437
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The germanium quantum information route
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2021'
...
---
_id: '8927'
abstract:
- lang: eng
text: The recent outbreak of coronavirus disease 2019 (COVID‐19), caused by the
Severe Acute Respiratory Syndrome Coronavirus‐2 (SARS‐CoV‐2) has resulted in a
world‐wide pandemic. Disseminated lung injury with the development of acute respiratory
distress syndrome (ARDS) is the main cause of mortality in COVID‐19. Although
liver failure does not seem to occur in the absence of pre‐existing liver disease,
hepatic involvement in COVID‐19 may correlate with overall disease severity and
serve as a prognostic factor for the development of ARDS. The spectrum of liver
injury in COVID‐19 may range from direct infection by SARS‐CoV‐2, indirect involvement
by systemic inflammation, hypoxic changes, iatrogenic causes such as drugs and
ventilation to exacerbation of underlying liver disease. This concise review discusses
the potential pathophysiological mechanisms for SARS‐CoV‐2 hepatic tropism as
well as acute and possibly long‐term liver injury in COVID‐19.
acknowledgement: This work was supported by grant F7310‐B21 from the Austrian Science
Foundation (to MT). We thank Jelena Remetic, Claudia D. Fuchs, Veronika Mlitz and
Daniel Steinacher, for their valuable input and discussion. Figure 1 and Figure
2 have been created with BioRender.com.
article_processing_charge: No
article_type: original
author:
- first_name: Alexander D.
full_name: Nardo, Alexander D.
last_name: Nardo
- first_name: Mathias
full_name: Schneeweiss-Gleixner, Mathias
last_name: Schneeweiss-Gleixner
- first_name: May M
full_name: Bakail, May M
id: FB3C3F8E-522F-11EA-B186-22963DDC885E
last_name: Bakail
orcid: 0000-0002-9592-1587
- first_name: Emmanuel D.
full_name: Dixon, Emmanuel D.
last_name: Dixon
- first_name: Sigurd F.
full_name: Lax, Sigurd F.
last_name: Lax
- first_name: Michael
full_name: Trauner, Michael
last_name: Trauner
citation:
ama: Nardo AD, Schneeweiss-Gleixner M, Bakail MM, Dixon ED, Lax SF, Trauner M. Pathophysiological
mechanisms of liver injury in COVID-19. Liver International. 2021;41(1):20-32.
doi:10.1111/liv.14730
apa: Nardo, A. D., Schneeweiss-Gleixner, M., Bakail, M. M., Dixon, E. D., Lax, S.
F., & Trauner, M. (2021). Pathophysiological mechanisms of liver injury in
COVID-19. Liver International. Wiley. https://doi.org/10.1111/liv.14730
chicago: Nardo, Alexander D., Mathias Schneeweiss-Gleixner, May M Bakail, Emmanuel
D. Dixon, Sigurd F. Lax, and Michael Trauner. “Pathophysiological Mechanisms of
Liver Injury in COVID-19.” Liver International. Wiley, 2021. https://doi.org/10.1111/liv.14730.
ieee: A. D. Nardo, M. Schneeweiss-Gleixner, M. M. Bakail, E. D. Dixon, S. F. Lax,
and M. Trauner, “Pathophysiological mechanisms of liver injury in COVID-19,” Liver
International, vol. 41, no. 1. Wiley, pp. 20–32, 2021.
ista: Nardo AD, Schneeweiss-Gleixner M, Bakail MM, Dixon ED, Lax SF, Trauner M.
2021. Pathophysiological mechanisms of liver injury in COVID-19. Liver International.
41(1), 20–32.
mla: Nardo, Alexander D., et al. “Pathophysiological Mechanisms of Liver Injury
in COVID-19.” Liver International, vol. 41, no. 1, Wiley, 2021, pp. 20–32,
doi:10.1111/liv.14730.
short: A.D. Nardo, M. Schneeweiss-Gleixner, M.M. Bakail, E.D. Dixon, S.F. Lax, M.
Trauner, Liver International 41 (2021) 20–32.
date_created: 2020-12-06T23:01:16Z
date_published: 2021-01-01T00:00:00Z
date_updated: 2025-06-12T06:33:00Z
day: '01'
ddc:
- '570'
department:
- _id: CampIT
doi: 10.1111/liv.14730
external_id:
isi:
- '000594239200001'
pmid:
- '33190346'
file:
- access_level: open_access
checksum: 6e4f21b77ef22c854e016240974fc473
content_type: application/pdf
creator: dernst
date_created: 2021-02-04T12:01:45Z
date_updated: 2021-02-04T12:01:45Z
file_id: '9091'
file_name: 2021_Liver_Nardo.pdf
file_size: 930414
relation: main_file
success: 1
file_date_updated: 2021-02-04T12:01:45Z
has_accepted_license: '1'
intvolume: ' 41'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 20-32
pmid: 1
publication: Liver International
publication_identifier:
eissn:
- 1478-3231
issn:
- 1478-3223
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Pathophysiological mechanisms of liver injury in COVID-19
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: 41
year: '2021'
...
---
_id: '8928'
abstract:
- lang: eng
text: Domestication is a human‐induced selection process that imprints the genomes
of domesticated populations over a short evolutionary time scale and that occurs
in a given demographic context. Reconstructing historical gene flow, effective
population size changes and their timing is therefore of fundamental interest
to understand how plant demography and human selection jointly shape genomic divergence
during domestication. Yet, the comparison under a single statistical framework
of independent domestication histories across different crop species has been
little evaluated so far. Thus, it is unclear whether domestication leads to convergent
demographic changes that similarly affect crop genomes. To address this question,
we used existing and new transcriptome data on three crop species of Solanaceae
(eggplant, pepper and tomato), together with their close wild relatives. We fitted
twelve demographic models of increasing complexity on the unfolded joint allele
frequency spectrum for each wild/crop pair, and we found evidence for both shared
and species‐specific demographic processes between species. A convergent history
of domestication with gene flow was inferred for all three species, along with
evidence of strong reduction in the effective population size during the cultivation
stage of tomato and pepper. The absence of any reduction in size of the crop in
eggplant stands out from the classical view of the domestication process; as does
the existence of a “protracted period” of management before cultivation. Our results
also suggest divergent management strategies of modern cultivars among species
as their current demography substantially differs. Finally, the timing of domestication
is species‐specific and supported by the few historical records available.
acknowledgement: This work was supported by the EU Marie Curie Career Integration
grant (FP7‐PEOPLE‐2011‐CIG grant agreement PCIG10‐GA‐2011‐304164) attributed to
CS. SA was supported by a PhD fellowship from the French Région PACA and the Plant
Breeding division of INRA, in partnership with Gautier Semences. CF was supported
by an Austrian Science Foundation FWF grant (Project M 2463‐B29). Authors thank
Mathilde Causse and Beatriz Vicoso for their team leading. Thanks to the Italian
Eggplant Genome Consortium, which includes the DISAFA, Plant Genetics and Breeding
(University of Torino), the Biotechnology Department (University of Verona), the
CREA‐ORL in Montanaso Lombardo (LO) and the ENEA in Rome for providing access to
the eggplant genome reference. Thanks to CRB‐lég ( https://www6.paca.inra.fr/gafl_eng/Vegetables-GRC
) for managing and providing the genetic resources, to Marie‐Christine Daunay and
Alain Palloix (INRA UR1052) for assistance in choosing the biological material used,
to Muriel Latreille and Sylvain Santoni from the UMR AGAP (INRA Montpellier, France)
for their help with RNAseq library preparation, to Jean‐Paul Bouchet and Jacques
Lagnel (INRA UR1052) for their Bioinformatics assistance.
article_processing_charge: No
article_type: original
author:
- first_name: Stéphanie
full_name: Arnoux, Stéphanie
last_name: Arnoux
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Christopher
full_name: Sauvage, Christopher
last_name: Sauvage
citation:
ama: Arnoux S, Fraisse C, Sauvage C. Genomic inference of complex domestication
histories in three Solanaceae species. Journal of Evolutionary Biology.
2021;34(2):270-283. doi:10.1111/jeb.13723
apa: Arnoux, S., Fraisse, C., & Sauvage, C. (2021). Genomic inference of complex
domestication histories in three Solanaceae species. Journal of Evolutionary
Biology. Wiley. https://doi.org/10.1111/jeb.13723
chicago: Arnoux, Stéphanie, Christelle Fraisse, and Christopher Sauvage. “Genomic
Inference of Complex Domestication Histories in Three Solanaceae Species.” Journal
of Evolutionary Biology. Wiley, 2021. https://doi.org/10.1111/jeb.13723.
ieee: S. Arnoux, C. Fraisse, and C. Sauvage, “Genomic inference of complex domestication
histories in three Solanaceae species,” Journal of Evolutionary Biology,
vol. 34, no. 2. Wiley, pp. 270–283, 2021.
ista: Arnoux S, Fraisse C, Sauvage C. 2021. Genomic inference of complex domestication
histories in three Solanaceae species. Journal of Evolutionary Biology. 34(2),
270–283.
mla: Arnoux, Stéphanie, et al. “Genomic Inference of Complex Domestication Histories
in Three Solanaceae Species.” Journal of Evolutionary Biology, vol. 34,
no. 2, Wiley, 2021, pp. 270–83, doi:10.1111/jeb.13723.
short: S. Arnoux, C. Fraisse, C. Sauvage, Journal of Evolutionary Biology 34 (2021)
270–283.
date_created: 2020-12-06T23:01:16Z
date_published: 2021-02-01T00:00:00Z
date_updated: 2025-07-10T12:01:26Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/jeb.13723
external_id:
isi:
- '000587769700001'
pmid:
- '33107098'
intvolume: ' 34'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/jeb.13723
month: '02'
oa: 1
oa_version: Published Version
page: 270-283
pmid: 1
project:
- _id: 2662AADE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02463
name: Sex chromosomes and species barriers
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- 1420-9101
issn:
- 1010-061X
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '13065'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Genomic inference of complex domestication histories in three Solanaceae species
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2021'
...
---
_id: '8940'
abstract:
- lang: eng
text: We quantise Whitney’s construction to prove the existence of a triangulation
for any C^2 manifold, so that we get an algorithm with explicit bounds. We also
give a new elementary proof, which is completely geometric.
acknowledgement: This work has been funded by the European Research Council under
the European Union’s ERC Grant Agreement Number 339025 GUDHI (Algorithmic Foundations
of Geometric Understanding in Higher Dimensions). The third author also received
funding from the European Union’s Horizon 2020 research and innovation programme
under the Marie Skłodowska-Curie Grant Agreement No. 754411. Open access funding
provided by the Institute of Science and Technology (IST Austria).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Jean-Daniel
full_name: Boissonnat, Jean-Daniel
last_name: Boissonnat
- first_name: Siargey
full_name: Kachanovich, Siargey
last_name: Kachanovich
- first_name: Mathijs
full_name: Wintraecken, Mathijs
id: 307CFBC8-F248-11E8-B48F-1D18A9856A87
last_name: Wintraecken
orcid: 0000-0002-7472-2220
citation:
ama: 'Boissonnat J-D, Kachanovich S, Wintraecken M. Triangulating submanifolds:
An elementary and quantified version of Whitney’s method. Discrete & Computational
Geometry. 2021;66(1):386-434. doi:10.1007/s00454-020-00250-8'
apa: 'Boissonnat, J.-D., Kachanovich, S., & Wintraecken, M. (2021). Triangulating
submanifolds: An elementary and quantified version of Whitney’s method. Discrete
& Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00250-8'
chicago: 'Boissonnat, Jean-Daniel, Siargey Kachanovich, and Mathijs Wintraecken.
“Triangulating Submanifolds: An Elementary and Quantified Version of Whitney’s
Method.” Discrete & Computational Geometry. Springer Nature, 2021.
https://doi.org/10.1007/s00454-020-00250-8.'
ieee: 'J.-D. Boissonnat, S. Kachanovich, and M. Wintraecken, “Triangulating submanifolds:
An elementary and quantified version of Whitney’s method,” Discrete & Computational
Geometry, vol. 66, no. 1. Springer Nature, pp. 386–434, 2021.'
ista: 'Boissonnat J-D, Kachanovich S, Wintraecken M. 2021. Triangulating submanifolds:
An elementary and quantified version of Whitney’s method. Discrete & Computational
Geometry. 66(1), 386–434.'
mla: 'Boissonnat, Jean-Daniel, et al. “Triangulating Submanifolds: An Elementary
and Quantified Version of Whitney’s Method.” Discrete & Computational Geometry,
vol. 66, no. 1, Springer Nature, 2021, pp. 386–434, doi:10.1007/s00454-020-00250-8.'
short: J.-D. Boissonnat, S. Kachanovich, M. Wintraecken, Discrete & Computational
Geometry 66 (2021) 386–434.
corr_author: '1'
date_created: 2020-12-12T11:07:02Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2025-04-14T07:43:50Z
day: '01'
ddc:
- '516'
department:
- _id: HeEd
doi: 10.1007/s00454-020-00250-8
ec_funded: 1
external_id:
isi:
- '000597770300001'
file:
- access_level: open_access
checksum: c848986091e56699dc12de85adb1e39c
content_type: application/pdf
creator: kschuh
date_created: 2021-08-06T09:52:29Z
date_updated: 2021-08-06T09:52:29Z
file_id: '9795'
file_name: 2021_DescreteCompGeopmetry_Boissonnat.pdf
file_size: 983307
relation: main_file
success: 1
file_date_updated: 2021-08-06T09:52:29Z
has_accepted_license: '1'
intvolume: ' 66'
isi: 1
issue: '1'
keyword:
- Theoretical Computer Science
- Computational Theory and Mathematics
- Geometry and Topology
- Discrete Mathematics and Combinatorics
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 386-434
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Discrete & Computational Geometry
publication_identifier:
eissn:
- 1432-0444
issn:
- 0179-5376
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Triangulating submanifolds: An elementary and quantified version of Whitney’s
method'
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 66
year: '2021'
...
---
_id: '8988'
abstract:
- lang: eng
text: The differentiation of cells depends on a precise control of their internal
organization, which is the result of a complex dynamic interplay between the cytoskeleton,
molecular motors, signaling molecules, and membranes. For example, in the developing
neuron, the protein ADAP1 (ADP-ribosylation factor GTPase-activating protein [ArfGAP]
with dual pleckstrin homology [PH] domains 1) has been suggested to control dendrite
branching by regulating the small GTPase ARF6. Together with the motor protein
KIF13B, ADAP1 is also thought to mediate delivery of the second messenger phosphatidylinositol
(3,4,5)-trisphosphate (PIP3) to the axon tip, thus contributing to PIP3 polarity.
However, what defines the function of ADAP1 and how its different roles are coordinated
are still not clear. Here, we studied ADAP1’s functions using in vitro reconstitutions.
We found that KIF13B transports ADAP1 along microtubules, but that PIP3 as well
as PI(3,4)P2 act as stop signals for this transport instead of being transported.
We also demonstrate that these phosphoinositides activate ADAP1’s enzymatic activity
to catalyze GTP hydrolysis by ARF6. Together, our results support a model for
the cellular function of ADAP1, where KIF13B transports ADAP1 until it encounters
high PIP3/PI(3,4)P2 concentrations in the plasma membrane. Here, ADAP1 disassociates
from the motor to inactivate ARF6, promoting dendrite branching.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: EM-Fac
acknowledgement: "We thank Urban Bezeljak, Natalia Baranova, Mar Lopez-Pelegrin, Catarina
Alcarva, and Victoria Faas for sharing reagents and helpful discussions. We thank
Veronika Szentirmai for help with protein purifications. We thank Carrie Bernecky,
Sascha Martens, and the M.L. lab for comments on the manuscript. We thank the bioimaging
facility, the life science facility, and Armel Nicolas from the mass spec facility
at the Institute of Science and Technology (IST) Austria for technical support.
C.D. acknowledges funding from the IST fellowship program; this work was supported
by Human Frontier Science Program Young Investigator Grant\r\nRGY0083/2016. "
article_number: e2010054118
article_processing_charge: No
article_type: original
author:
- first_name: Christian F
full_name: Düllberg, Christian F
id: 459064DC-F248-11E8-B48F-1D18A9856A87
last_name: Düllberg
orcid: 0000-0001-6335-9748
- first_name: Albert
full_name: Auer, Albert
id: 3018E8C2-F248-11E8-B48F-1D18A9856A87
last_name: Auer
orcid: 0000-0002-3580-2906
- first_name: Nikola
full_name: Canigova, Nikola
id: 3795523E-F248-11E8-B48F-1D18A9856A87
last_name: Canigova
orcid: 0000-0002-8518-5926
- first_name: Katrin
full_name: Loibl, Katrin
id: 3760F32C-F248-11E8-B48F-1D18A9856A87
last_name: Loibl
orcid: 0000-0002-2429-7668
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
citation:
ama: Düllberg CF, Auer A, Canigova N, Loibl K, Loose M. In vitro reconstitution
reveals phosphoinositides as cargo-release factors and activators of the ARF6
GAP ADAP1. Proceedings of the National Academy of Sciences of the United States
of America. 2021;118(1). doi:10.1073/pnas.2010054118
apa: Düllberg, C. F., Auer, A., Canigova, N., Loibl, K., & Loose, M. (2021).
In vitro reconstitution reveals phosphoinositides as cargo-release factors and
activators of the ARF6 GAP ADAP1. Proceedings of the National Academy of Sciences
of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2010054118
chicago: Düllberg, Christian F, Albert Auer, Nikola Canigova, Katrin Loibl, and
Martin Loose. “In Vitro Reconstitution Reveals Phosphoinositides as Cargo-Release
Factors and Activators of the ARF6 GAP ADAP1.” Proceedings of the National
Academy of Sciences of the United States of America. National Academy of Sciences,
2021. https://doi.org/10.1073/pnas.2010054118.
ieee: C. F. Düllberg, A. Auer, N. Canigova, K. Loibl, and M. Loose, “In vitro reconstitution
reveals phosphoinositides as cargo-release factors and activators of the ARF6
GAP ADAP1,” Proceedings of the National Academy of Sciences of the United States
of America, vol. 118, no. 1. National Academy of Sciences, 2021.
ista: Düllberg CF, Auer A, Canigova N, Loibl K, Loose M. 2021. In vitro reconstitution
reveals phosphoinositides as cargo-release factors and activators of the ARF6
GAP ADAP1. Proceedings of the National Academy of Sciences of the United States
of America. 118(1), e2010054118.
mla: Düllberg, Christian F., et al. “In Vitro Reconstitution Reveals Phosphoinositides
as Cargo-Release Factors and Activators of the ARF6 GAP ADAP1.” Proceedings
of the National Academy of Sciences of the United States of America, vol.
118, no. 1, e2010054118, National Academy of Sciences, 2021, doi:10.1073/pnas.2010054118.
short: C.F. Düllberg, A. Auer, N. Canigova, K. Loibl, M. Loose, Proceedings of the
National Academy of Sciences of the United States of America 118 (2021).
corr_author: '1'
date_created: 2021-01-03T23:01:23Z
date_published: 2021-01-05T00:00:00Z
date_updated: 2025-05-14T10:59:29Z
day: '05'
department:
- _id: MaLo
- _id: MiSi
doi: 10.1073/pnas.2010054118
external_id:
isi:
- '000607270100018'
pmid:
- '33443153'
intvolume: ' 118'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.2010054118
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2599F062-B435-11E9-9278-68D0E5697425
grant_number: RGY0083/2016
name: Reconstitution of cell polarity and axis determination in a cell-free system
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: In vitro reconstitution reveals phosphoinositides as cargo-release factors
and activators of the ARF6 GAP ADAP1
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 118
year: '2021'
...
---
_id: '8992'
abstract:
- lang: eng
text: The phytohormone auxin plays a central role in shaping plant growth and development.
With decades of genetic and biochemical studies, numerous core molecular components
and their networks, underlying auxin biosynthesis, transport, and signaling, have
been identified. Notably, protein phosphorylation, catalyzed by kinases and oppositely
hydrolyzed by phosphatases, has been emerging to be a crucial type of post-translational
modification, regulating physiological and developmental auxin output at all levels.
In this review, we comprehensively discuss earlier and recent advances in our
understanding of genetics, biochemistry, and cell biology of the kinases and phosphatases
participating in auxin action. We provide insights into the mechanisms by which
reversible protein phosphorylation defines developmental auxin responses, discuss
current challenges, and provide our perspectives on future directions involving
the integration of the control of protein phosphorylation into the molecular auxin
network.
acknowledgement: This work was supported by the European Union’s Horizon 2020 Program
(ERC grant agreement no. 742985 to J.F.). S.T. was funded by a European Molecular
Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). C.L.
is supported by the Austrian Science Fund (FWF; P 31493).
article_processing_charge: No
article_type: original
author:
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: Christian
full_name: Luschnig, Christian
last_name: Luschnig
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Tan S, Luschnig C, Friml J. Pho-view of auxin: Reversible protein phosphorylation
in auxin biosynthesis, transport and signaling. Molecular Plant. 2021;14(1):151-165.
doi:10.1016/j.molp.2020.11.004'
apa: 'Tan, S., Luschnig, C., & Friml, J. (2021). Pho-view of auxin: Reversible
protein phosphorylation in auxin biosynthesis, transport and signaling. Molecular
Plant. Elsevier. https://doi.org/10.1016/j.molp.2020.11.004'
chicago: 'Tan, Shutang, Christian Luschnig, and Jiří Friml. “Pho-View of Auxin:
Reversible Protein Phosphorylation in Auxin Biosynthesis, Transport and Signaling.”
Molecular Plant. Elsevier, 2021. https://doi.org/10.1016/j.molp.2020.11.004.'
ieee: 'S. Tan, C. Luschnig, and J. Friml, “Pho-view of auxin: Reversible protein
phosphorylation in auxin biosynthesis, transport and signaling,” Molecular
Plant, vol. 14, no. 1. Elsevier, pp. 151–165, 2021.'
ista: 'Tan S, Luschnig C, Friml J. 2021. Pho-view of auxin: Reversible protein phosphorylation
in auxin biosynthesis, transport and signaling. Molecular Plant. 14(1), 151–165.'
mla: 'Tan, Shutang, et al. “Pho-View of Auxin: Reversible Protein Phosphorylation
in Auxin Biosynthesis, Transport and Signaling.” Molecular Plant, vol.
14, no. 1, Elsevier, 2021, pp. 151–65, doi:10.1016/j.molp.2020.11.004.'
short: S. Tan, C. Luschnig, J. Friml, Molecular Plant 14 (2021) 151–165.
date_created: 2021-01-03T23:01:23Z
date_published: 2021-01-04T00:00:00Z
date_updated: 2025-07-10T12:01:28Z
day: '04'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1016/j.molp.2020.11.004
ec_funded: 1
external_id:
isi:
- '000605359400014'
pmid:
- '33186755'
file:
- access_level: open_access
checksum: 917e60e57092f22e16beac70b1775ea6
content_type: application/pdf
creator: dernst
date_created: 2021-01-07T14:03:53Z
date_updated: 2021-01-07T14:03:53Z
file_id: '8995'
file_name: 2020_MolecularPlant_Tan.pdf
file_size: 871088
relation: main_file
success: 1
file_date_updated: 2021-01-07T14:03:53Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 151-165
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 256FEF10-B435-11E9-9278-68D0E5697425
grant_number: 723-2015
name: Molecular Mechanism underlying Salicylic Acid Regulation of Endocytic Trafficking
in Arabidopsis
publication: Molecular Plant
publication_identifier:
eissn:
- 1752-9867
issn:
- 1674-2052
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis,
transport and signaling'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2021'
...
---
_id: '8993'
abstract:
- lang: eng
text: N-1-naphthylphthalamic acid (NPA) is a key inhibitor of directional (polar)
transport of the hormone auxin in plants. For decades, it has been a pivotal tool
in elucidating the unique polar auxin transport-based processes underlying plant
growth and development. Its exact mode of action has long been sought after and
is still being debated, with prevailing mechanistic schemes describing only indirect
connections between NPA and the main transporters responsible for directional
transport, namely PIN auxin exporters. Here we present data supporting a model
in which NPA associates with PINs in a more direct manner than hitherto postulated.
We show that NPA inhibits PIN activity in a heterologous oocyte system and that
expression of NPA-sensitive PINs in plant, yeast, and oocyte membranes leads to
specific saturable NPA binding. We thus propose that PINs are a bona fide NPA
target. This offers a straightforward molecular basis for NPA inhibition of PIN-dependent
auxin transport and a logical parsimonious explanation for the known physiological
effects of NPA on plant growth, as well as an alternative hypothesis to interpret
past and future results. We also introduce PIN dimerization and describe an effect
of NPA on this, suggesting that NPA binding could be exploited to gain insights
into structural aspects of PINs related to their transport mechanism.
acknowledgement: "This work was supported by Austrian Science Fund Grant FWF P21533-B20
(to L.A.); German Research Foundation Grant DFG HA3468/6-1 (to U.Z.H.); and European
Research Council Grant 742985 (to J.F.). We thank Herta Steinkellner and Alexandra
Castilho for N. benthamiana plants, Fabian Nagelreiter for statistical advice, Lanassa
Bassukas for help with [ɣ32P]-\r\nATP assays, and Josef Penninger for providing
access to mass spectrometry instruments at the Vienna BioCenter Core Facilities.
We thank PNAS reviewers for the many comments and suggestions that helped to improve
this manuscript."
article_number: e2020857118
article_processing_charge: No
article_type: original
author:
- first_name: Lindy
full_name: Abas, Lindy
last_name: Abas
- first_name: Martina
full_name: Kolb, Martina
last_name: Kolb
- first_name: Johannes
full_name: Stadlmann, Johannes
last_name: Stadlmann
- first_name: Dorina P.
full_name: Janacek, Dorina P.
last_name: Janacek
- first_name: Kristina
full_name: Lukic, Kristina
id: 2B04DB84-F248-11E8-B48F-1D18A9856A87
last_name: Lukic
orcid: 0000-0003-1581-881X
- first_name: Claus
full_name: Schwechheimer, Claus
last_name: Schwechheimer
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
- first_name: Lukas
full_name: Mach, Lukas
last_name: Mach
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Ulrich Z.
full_name: Hammes, Ulrich Z.
last_name: Hammes
citation:
ama: Abas L, Kolb M, Stadlmann J, et al. Naphthylphthalamic acid associates with
and inhibits PIN auxin transporters. Proceedings of the National Academy of
Sciences of the United States of America. 2021;118(1). doi:10.1073/pnas.2020857118
apa: Abas, L., Kolb, M., Stadlmann, J., Janacek, D. P., Lukic, K., Schwechheimer,
C., … Hammes, U. Z. (2021). Naphthylphthalamic acid associates with and inhibits
PIN auxin transporters. Proceedings of the National Academy of Sciences of
the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2020857118
chicago: Abas, Lindy, Martina Kolb, Johannes Stadlmann, Dorina P. Janacek, Kristina
Lukic, Claus Schwechheimer, Leonid A Sazanov, Lukas Mach, Jiří Friml, and Ulrich
Z. Hammes. “Naphthylphthalamic Acid Associates with and Inhibits PIN Auxin Transporters.”
Proceedings of the National Academy of Sciences of the United States of America.
National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2020857118.
ieee: L. Abas et al., “Naphthylphthalamic acid associates with and inhibits
PIN auxin transporters,” Proceedings of the National Academy of Sciences of
the United States of America, vol. 118, no. 1. National Academy of Sciences,
2021.
ista: Abas L, Kolb M, Stadlmann J, Janacek DP, Lukic K, Schwechheimer C, Sazanov
LA, Mach L, Friml J, Hammes UZ. 2021. Naphthylphthalamic acid associates with
and inhibits PIN auxin transporters. Proceedings of the National Academy of Sciences
of the United States of America. 118(1), e2020857118.
mla: Abas, Lindy, et al. “Naphthylphthalamic Acid Associates with and Inhibits PIN
Auxin Transporters.” Proceedings of the National Academy of Sciences of the
United States of America, vol. 118, no. 1, e2020857118, National Academy of
Sciences, 2021, doi:10.1073/pnas.2020857118.
short: L. Abas, M. Kolb, J. Stadlmann, D.P. Janacek, K. Lukic, C. Schwechheimer,
L.A. Sazanov, L. Mach, J. Friml, U.Z. Hammes, Proceedings of the National Academy
of Sciences of the United States of America 118 (2021).
date_created: 2021-01-03T23:01:23Z
date_published: 2021-01-05T00:00:00Z
date_updated: 2025-05-14T10:58:54Z
day: '05'
department:
- _id: JiFr
- _id: LeSa
doi: 10.1073/pnas.2020857118
ec_funded: 1
external_id:
isi:
- '000607270100073'
pmid:
- '33443187'
intvolume: ' 118'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.2020857118
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1073/pnas.2102232118
scopus_import: '1'
status: public
title: Naphthylphthalamic acid associates with and inhibits PIN auxin transporters
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 118
year: '2021'
...
---
_id: '8997'
abstract:
- lang: eng
text: Phenomenological relations such as Ohm’s or Fourier’s law have a venerable
history in physics but are still scarce in biology. This situation restrains predictive
theory. Here, we build on bacterial “growth laws,” which capture physiological
feedback between translation and cell growth, to construct a minimal biophysical
model for the combined action of ribosome-targeting antibiotics. Our model predicts
drug interactions like antagonism or synergy solely from responses to individual
drugs. We provide analytical results for limiting cases, which agree well with
numerical results. We systematically refine the model by including direct physical
interactions of different antibiotics on the ribosome. In a limiting case, our
model provides a mechanistic underpinning for recent predictions of higher-order
interactions that were derived using entropy maximization. We further refine the
model to include the effects of antibiotics that mimic starvation and the presence
of resistance genes. We describe the impact of a starvation-mimicking antibiotic
on drug interactions analytically and verify it experimentally. Our extended model
suggests a change in the type of drug interaction that depends on the strength
of resistance, which challenges established rescaling paradigms. We experimentally
show that the presence of unregulated resistance genes can lead to altered drug
interaction, which agrees with the prediction of the model. While minimal, the
model is readily adaptable and opens the door to predicting interactions of second
and higher-order in a broad range of biological systems.
acknowledgement: 'This work was supported in part by Tum stipend of Knafelj foundation
(to B.K.), Austrian Science Fund (FWF) standalone grants P 27201-B22 (to T.B.) and
P 28844(to G.T.), HFSP program Grant RGP0042/2013 (to T.B.), German Research Foundation
(DFG) individual grant BO 3502/2-1 (to T.B.), and German Research Foundation (DFG)
Collaborative Research Centre (SFB) 1310 (to T.B.). '
article_number: e1008529
article_processing_charge: Yes
article_type: original
author:
- first_name: Bor
full_name: Kavcic, Bor
id: 350F91D2-F248-11E8-B48F-1D18A9856A87
last_name: Kavcic
orcid: 0000-0001-6041-254X
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Tobias
full_name: Bollenbach, Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Kavcic B, Tkačik G, Bollenbach MT. Minimal biophysical model of combined antibiotic
action. PLOS Computational Biology. 2021;17. doi:10.1371/journal.pcbi.1008529
apa: Kavcic, B., Tkačik, G., & Bollenbach, M. T. (2021). Minimal biophysical
model of combined antibiotic action. PLOS Computational Biology. Public
Library of Science. https://doi.org/10.1371/journal.pcbi.1008529
chicago: Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “Minimal Biophysical
Model of Combined Antibiotic Action.” PLOS Computational Biology. Public
Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1008529.
ieee: B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Minimal biophysical model of
combined antibiotic action,” PLOS Computational Biology, vol. 17. Public
Library of Science, 2021.
ista: Kavcic B, Tkačik G, Bollenbach MT. 2021. Minimal biophysical model of combined
antibiotic action. PLOS Computational Biology. 17, e1008529.
mla: Kavcic, Bor, et al. “Minimal Biophysical Model of Combined Antibiotic Action.”
PLOS Computational Biology, vol. 17, e1008529, Public Library of Science,
2021, doi:10.1371/journal.pcbi.1008529.
short: B. Kavcic, G. Tkačik, M.T. Bollenbach, PLOS Computational Biology 17 (2021).
date_created: 2021-01-08T07:16:18Z
date_published: 2021-01-07T00:00:00Z
date_updated: 2025-06-12T06:33:18Z
day: '07'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1008529
external_id:
isi:
- '000608045000010'
pmid:
- '33411759'
file:
- access_level: open_access
checksum: e29f2b42651bef8e034781de8781ffac
content_type: application/pdf
creator: dernst
date_created: 2021-02-04T12:30:48Z
date_updated: 2021-02-04T12:30:48Z
file_id: '9092'
file_name: 2021_PlosComBio_Kavcic.pdf
file_size: 3690053
relation: main_file
success: 1
file_date_updated: 2021-02-04T12:30:48Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
keyword:
- Modelling and Simulation
- Genetics
- Molecular Biology
- Antibiotics
- Drug interactions
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: PLOS Computational Biology
publication_identifier:
issn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
record:
- id: '8930'
relation: research_data
status: public
- id: '7673'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Minimal biophysical model of combined antibiotic action
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: 17
year: '2021'
...
---
_id: '8999'
abstract:
- lang: eng
text: "In many basic shear flows, such as pipe, Couette, and channel flow, turbulence
does not\r\narise from an instability of the laminar state, and both dynamical
states co-exist. With decreasing flow speed (i.e., decreasing Reynolds number)
the fraction of fluid in laminar motion increases while turbulence recedes and
eventually the entire flow relaminarizes. The first step towards understanding
the nature of this transition is to determine if the phase change is of either
first or second order. In the former case, the turbulent fraction would drop discontinuously
to zero as the Reynolds number decreases while in the latter the process would
be continuous. For Couette flow, the flow between two parallel plates, earlier
studies suggest a discontinuous scenario. In the present study we realize a Couette
flow between two concentric cylinders which allows studies to be carried out in
large aspect ratios and for extensive observation times. The presented measurements
show that the transition in this circular Couette geometry is continuous suggesting
that former studies were limited by finite size effects. A further characterization
of this transition, in particular its relation to the directed percolation universality
class, requires even larger system sizes than presently available. "
acknowledgement: "This research was funded by the Central Research Development Fund
of the University of\r\nBremen grant number ZF04B /2019/FB04 Avila_Kerstin (“Independent
Project for Postdocs”). Shreyas Jalikop is acknowledged for recording some of the
lifetime measurements\r\n"
article_number: '58'
article_processing_charge: No
article_type: original
author:
- first_name: Kerstin
full_name: Avila, Kerstin
id: fcf74381-53e1-11eb-a6dc-b0e2acf78757
last_name: Avila
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Avila K, Hof B. Second-order phase transition in counter-rotating taylor-couette
flow experiment. Entropy. 2021;23(1). doi:10.3390/e23010058
apa: Avila, K., & Hof, B. (2021). Second-order phase transition in counter-rotating
taylor-couette flow experiment. Entropy. MDPI. https://doi.org/10.3390/e23010058
chicago: Avila, Kerstin, and Björn Hof. “Second-Order Phase Transition in Counter-Rotating
Taylor-Couette Flow Experiment.” Entropy. MDPI, 2021. https://doi.org/10.3390/e23010058.
ieee: K. Avila and B. Hof, “Second-order phase transition in counter-rotating taylor-couette
flow experiment,” Entropy, vol. 23, no. 1. MDPI, 2021.
ista: Avila K, Hof B. 2021. Second-order phase transition in counter-rotating taylor-couette
flow experiment. Entropy. 23(1), 58.
mla: Avila, Kerstin, and Björn Hof. “Second-Order Phase Transition in Counter-Rotating
Taylor-Couette Flow Experiment.” Entropy, vol. 23, no. 1, 58, MDPI, 2021,
doi:10.3390/e23010058.
short: K. Avila, B. Hof, Entropy 23 (2021).
date_created: 2021-01-10T23:01:17Z
date_published: 2021-01-01T00:00:00Z
date_updated: 2023-08-07T13:31:07Z
day: '01'
ddc:
- '530'
department:
- _id: BjHo
doi: 10.3390/e23010058
external_id:
isi:
- '000610135400001'
pmid:
- '33396499'
file:
- access_level: open_access
checksum: 3ba3dd8b7eecff713b72c5e9ba30d626
content_type: application/pdf
creator: dernst
date_created: 2021-01-11T07:50:32Z
date_updated: 2021-01-11T07:50:32Z
file_id: '9003'
file_name: 2021_Entropy_Avila.pdf
file_size: 9456389
relation: main_file
success: 1
file_date_updated: 2021-01-11T07:50:32Z
has_accepted_license: '1'
intvolume: ' 23'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Entropy
publication_identifier:
eissn:
- 1099-4300
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Second-order phase transition in counter-rotating taylor-couette flow experiment
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: 23
year: '2021'
...
---
OA_place: repository
OA_type: green
_id: '9002'
abstract:
- lang: eng
text: ' We prove that, for the binary erasure channel (BEC), the polar-coding paradigm
gives rise to codes that not only approach the Shannon limit but do so under the
best possible scaling of their block length as a function of the gap to capacity.
This result exhibits the first known family of binary codes that attain both optimal
scaling and quasi-linear complexity of encoding and decoding. Our proof is based
on the construction and analysis of binary polar codes with large kernels. When
communicating reliably at rates within ε>0 of capacity, the code length n often
scales as O(1/εμ), where the constant μ is called the scaling exponent. It is
known that the optimal scaling exponent is μ=2, and it is achieved by random linear
codes. The scaling exponent of conventional polar codes (based on the 2×2 kernel)
on the BEC is μ=3.63. This falls far short of the optimal scaling guaranteed by
random codes. Our main contribution is a rigorous proof of the following result:
for the BEC, there exist ℓ×ℓ binary kernels, such that polar codes constructed
from these kernels achieve scaling exponent μ(ℓ) that tends to the optimal value
of 2 as ℓ grows. We furthermore characterize precisely how large ℓ needs to be
as a function of the gap between μ(ℓ) and 2. The resulting binary codes maintain
the recursive structure of conventional polar codes, and thereby achieve construction
complexity O(n) and encoding/decoding complexity O(nlogn).'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Arman
full_name: Fazeli, Arman
last_name: Fazeli
- first_name: Hamed
full_name: Hassani, Hamed
last_name: Hassani
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Alexander
full_name: Vardy, Alexander
last_name: Vardy
citation:
ama: 'Fazeli A, Hassani H, Mondelli M, Vardy A. Binary linear codes with optimal
scaling: Polar codes with large kernels. IEEE Transactions on Information Theory.
2021;67(9):5693-5710. doi:10.1109/TIT.2020.3038806'
apa: 'Fazeli, A., Hassani, H., Mondelli, M., & Vardy, A. (2021). Binary linear
codes with optimal scaling: Polar codes with large kernels. IEEE Transactions
on Information Theory. IEEE. https://doi.org/10.1109/TIT.2020.3038806'
chicago: 'Fazeli, Arman, Hamed Hassani, Marco Mondelli, and Alexander Vardy. “Binary
Linear Codes with Optimal Scaling: Polar Codes with Large Kernels.” IEEE Transactions
on Information Theory. IEEE, 2021. https://doi.org/10.1109/TIT.2020.3038806.'
ieee: 'A. Fazeli, H. Hassani, M. Mondelli, and A. Vardy, “Binary linear codes with
optimal scaling: Polar codes with large kernels,” IEEE Transactions on Information
Theory, vol. 67, no. 9. IEEE, pp. 5693–5710, 2021.'
ista: 'Fazeli A, Hassani H, Mondelli M, Vardy A. 2021. Binary linear codes with
optimal scaling: Polar codes with large kernels. IEEE Transactions on Information
Theory. 67(9), 5693–5710.'
mla: 'Fazeli, Arman, et al. “Binary Linear Codes with Optimal Scaling: Polar Codes
with Large Kernels.” IEEE Transactions on Information Theory, vol. 67,
no. 9, IEEE, 2021, pp. 5693–710, doi:10.1109/TIT.2020.3038806.'
short: A. Fazeli, H. Hassani, M. Mondelli, A. Vardy, IEEE Transactions on Information
Theory 67 (2021) 5693–5710.
date_created: 2021-01-10T23:01:18Z
date_published: 2021-09-01T00:00:00Z
date_updated: 2025-09-10T09:59:12Z
day: '01'
department:
- _id: MaMo
doi: 10.1109/TIT.2020.3038806
external_id:
arxiv:
- '1711.01339'
isi:
- '000690440100007'
intvolume: ' 67'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1711.01339
month: '09'
oa: 1
oa_version: Preprint
page: 5693-5710
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: '6665'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: 'Binary linear codes with optimal scaling: Polar codes with large kernels'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 67
year: '2021'
...
---
_id: '9009'
abstract:
- lang: eng
text: Recent advancements in live cell imaging technologies have identified the
phenomenon of intracellular propagation of late apoptotic events, such as cytochrome
c release and caspase activation. The mechanism, prevalence, and speed of apoptosis
propagation remain unclear. Additionally, no studies have demonstrated propagation
of the pro-apoptotic protein, BAX. To evaluate the role of BAX in intracellular
apoptotic propagation, we used high speed live-cell imaging to visualize fluorescently
tagged-BAX recruitment to mitochondria in four immortalized cell lines. We show
that propagation of mitochondrial BAX recruitment occurs in parallel to cytochrome
c and SMAC/Diablo release and is affected by cellular morphology, such that cells
with processes are more likely to exhibit propagation. The initiation of propagation
events is most prevalent in the distal tips of processes, while the rate of propagation
is influenced by the 2-dimensional width of the process. Propagation was rarely
observed in the cell soma, which exhibited near synchronous recruitment of BAX.
Propagation velocity is not affected by mitochondrial volume in segments of processes,
but is negatively affected by mitochondrial density. There was no evidence of
a propagating wave of increased levels of intracellular calcium ions. Alternatively,
we did observe a uniform increase in superoxide build-up in cellular mitochondria,
which was released as a propagating wave simultaneously with the propagating recruitment
of BAX to the mitochondrial outer membrane.
acknowledgement: This work was supported by National Institute of Health grants R01
EY030123, P30 EY016665, and T32 GM081061, an unrestricted research grant from Research
to Prevent Blindness, Inc., and the Frederick A. Davis Endowment from the Department
of Ophthalmology and Visual Sciences at the University of Wisconsin-Madison.
article_processing_charge: No
article_type: original
author:
- first_name: Joshua A.
full_name: Grosser, Joshua A.
last_name: Grosser
- first_name: Margaret E
full_name: Maes, Margaret E
id: 3838F452-F248-11E8-B48F-1D18A9856A87
last_name: Maes
orcid: 0000-0001-9642-1085
- first_name: Robert W.
full_name: Nickells, Robert W.
last_name: Nickells
citation:
ama: Grosser JA, Maes ME, Nickells RW. Characteristics of intracellular propagation
of mitochondrial BAX recruitment during apoptosis. Apoptosis. 2021;26(2):132-145.
doi:10.1007/s10495-020-01654-w
apa: Grosser, J. A., Maes, M. E., & Nickells, R. W. (2021). Characteristics
of intracellular propagation of mitochondrial BAX recruitment during apoptosis.
Apoptosis. Springer Nature. https://doi.org/10.1007/s10495-020-01654-w
chicago: Grosser, Joshua A., Margaret E Maes, and Robert W. Nickells. “Characteristics
of Intracellular Propagation of Mitochondrial BAX Recruitment during Apoptosis.”
Apoptosis. Springer Nature, 2021. https://doi.org/10.1007/s10495-020-01654-w.
ieee: J. A. Grosser, M. E. Maes, and R. W. Nickells, “Characteristics of intracellular
propagation of mitochondrial BAX recruitment during apoptosis,” Apoptosis,
vol. 26, no. 2. Springer Nature, pp. 132–145, 2021.
ista: Grosser JA, Maes ME, Nickells RW. 2021. Characteristics of intracellular propagation
of mitochondrial BAX recruitment during apoptosis. Apoptosis. 26(2), 132–145.
mla: Grosser, Joshua A., et al. “Characteristics of Intracellular Propagation of
Mitochondrial BAX Recruitment during Apoptosis.” Apoptosis, vol. 26, no.
2, Springer Nature, 2021, pp. 132–45, doi:10.1007/s10495-020-01654-w.
short: J.A. Grosser, M.E. Maes, R.W. Nickells, Apoptosis 26 (2021) 132–145.
date_created: 2021-01-17T23:01:11Z
date_published: 2021-02-01T00:00:00Z
date_updated: 2023-08-07T13:32:40Z
day: '01'
department:
- _id: SaSi
doi: 10.1007/s10495-020-01654-w
external_id:
isi:
- '000606722600001'
pmid:
- '33426618'
intvolume: ' 26'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8082518/
month: '02'
oa: 1
oa_version: Submitted Version
page: 132-145
pmid: 1
publication: Apoptosis
publication_identifier:
eissn:
- 1573-675X
issn:
- 1360-8185
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Characteristics of intracellular propagation of mitochondrial BAX recruitment
during apoptosis
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 26
year: '2021'
...
---
_id: '9020'
abstract:
- lang: eng
text: 'We study dynamics and thermodynamics of ion transport in narrow, water-filled
channels, considered as effective 1D Coulomb systems. The long range nature of
the inter-ion interactions comes about due to the dielectric constants mismatch
between the water and the surrounding medium, confining the electric filed to
stay mostly within the water-filled channel. Statistical mechanics of such Coulomb
systems is dominated by entropic effects which may be accurately accounted for
by mapping onto an effective quantum mechanics. In presence of multivalent ions
the corresponding quantum mechanics appears to be non-Hermitian. In this review
we discuss a framework for semiclassical calculations for the effective non-Hermitian
Hamiltonians. Non-Hermiticity elevates WKB action integrals from the real line
to closed cycles on a complex Riemann surfaces where direct calculations are not
attainable. We circumvent this issue by applying tools from algebraic topology,
such as the Picard-Fuchs equation. We discuss how its solutions relate to the
thermodynamics and correlation functions of multivalent solutions within narrow,
water-filled channels. '
acknowledgement: "A.K. was supported by NSF grants DMR-2037654. T.G. acknowledges
funding from the Institute of Science and Technology (IST) Austria, and from the
European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie
Grant Agreement No. 754411.\r\nWe are indebted to Boris Shklovskii for introducing
us to the problem, and Alexander Gorsky and Peter Koroteev for introducing us to
the Picard-Fuchs methods. A very special thanks goes to Michael Janas for several
years of excellent collaboration on these topics. TG thanks Michael Kreshchuk for
introduction to the exact WKB method and great collaboration on related projects.
Figure 3 and Figure 4 are reproduced from Reference [25] with friendly permission
by the Russian Academy of Sciences. Figure 2, Figure 4, Figure 5, Figure 6, and
Figure 8 are reproduced from Reference [26] with friendly permission by IOP Publishing."
article_number: e23010125
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Tobias
full_name: Gulden, Tobias
id: 1083E038-9F73-11E9-A4B5-532AE6697425
last_name: Gulden
orcid: 0000-0001-6814-7541
- first_name: Alex
full_name: Kamenev, Alex
last_name: Kamenev
citation:
ama: Gulden T, Kamenev A. Dynamics of ion channels via non-hermitian quantum mechanics.
Entropy. 2021;23(1). doi:10.3390/e23010125
apa: Gulden, T., & Kamenev, A. (2021). Dynamics of ion channels via non-hermitian
quantum mechanics. Entropy. MDPI. https://doi.org/10.3390/e23010125
chicago: Gulden, Tobias, and Alex Kamenev. “Dynamics of Ion Channels via Non-Hermitian
Quantum Mechanics.” Entropy. MDPI, 2021. https://doi.org/10.3390/e23010125.
ieee: T. Gulden and A. Kamenev, “Dynamics of ion channels via non-hermitian quantum
mechanics,” Entropy, vol. 23, no. 1. MDPI, 2021.
ista: Gulden T, Kamenev A. 2021. Dynamics of ion channels via non-hermitian quantum
mechanics. Entropy. 23(1), e23010125.
mla: Gulden, Tobias, and Alex Kamenev. “Dynamics of Ion Channels via Non-Hermitian
Quantum Mechanics.” Entropy, vol. 23, no. 1, e23010125, MDPI, 2021, doi:10.3390/e23010125.
short: T. Gulden, A. Kamenev, Entropy 23 (2021).
date_created: 2021-01-19T11:12:06Z
date_published: 2021-01-19T00:00:00Z
date_updated: 2025-06-12T06:33:38Z
day: '19'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.3390/e23010125
ec_funded: 1
external_id:
arxiv:
- '2012.01390'
isi:
- '000610122000001'
pmid:
- '33477903'
file:
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checksum: 6cd0e706156827c45c740534bd32c179
content_type: application/pdf
creator: tgulden
date_created: 2021-01-19T11:11:14Z
date_updated: 2021-01-19T11:11:14Z
file_id: '9021'
file_name: Final published paper.pdf
file_size: 981285
relation: main_file
file_date_updated: 2021-01-19T11:11:14Z
has_accepted_license: '1'
intvolume: ' 23'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Entropy
publication_identifier:
eissn:
- 1099-4300
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamics of ion channels via non-hermitian quantum mechanics
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: 23
year: '2021'
...
---
_id: '9036'
abstract:
- lang: eng
text: In this short note, we prove that the square root of the quantum Jensen-Shannon
divergence is a true metric on the cone of positive matrices, and hence in particular
on the quantum state space.
acknowledgement: D. Virosztek was supported by the European Union's Horizon 2020 research
and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 846294,
and partially supported by the Hungarian National Research, Development and Innovation
Office (NKFIH) via grants no. K124152, and no. KH129601.
article_number: '107595'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Daniel
full_name: Virosztek, Daniel
id: 48DB45DA-F248-11E8-B48F-1D18A9856A87
last_name: Virosztek
orcid: 0000-0003-1109-5511
citation:
ama: Virosztek D. The metric property of the quantum Jensen-Shannon divergence.
Advances in Mathematics. 2021;380(3). doi:10.1016/j.aim.2021.107595
apa: Virosztek, D. (2021). The metric property of the quantum Jensen-Shannon divergence.
Advances in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2021.107595
chicago: Virosztek, Daniel. “The Metric Property of the Quantum Jensen-Shannon Divergence.”
Advances in Mathematics. Elsevier, 2021. https://doi.org/10.1016/j.aim.2021.107595.
ieee: D. Virosztek, “The metric property of the quantum Jensen-Shannon divergence,”
Advances in Mathematics, vol. 380, no. 3. Elsevier, 2021.
ista: Virosztek D. 2021. The metric property of the quantum Jensen-Shannon divergence.
Advances in Mathematics. 380(3), 107595.
mla: Virosztek, Daniel. “The Metric Property of the Quantum Jensen-Shannon Divergence.”
Advances in Mathematics, vol. 380, no. 3, 107595, Elsevier, 2021, doi:10.1016/j.aim.2021.107595.
short: D. Virosztek, Advances in Mathematics 380 (2021).
date_created: 2021-01-22T17:55:17Z
date_published: 2021-03-26T00:00:00Z
date_updated: 2025-04-14T07:50:40Z
day: '26'
department:
- _id: LaEr
doi: 10.1016/j.aim.2021.107595
ec_funded: 1
external_id:
arxiv:
- '1910.10447'
isi:
- '000619676100035'
intvolume: ' 380'
isi: 1
issue: '3'
keyword:
- General Mathematics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1910.10447
month: '03'
oa: 1
oa_version: Preprint
project:
- _id: 26A455A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '846294'
name: Geometric study of Wasserstein spaces and free probability
publication: Advances in Mathematics
publication_identifier:
issn:
- 0001-8708
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: The metric property of the quantum Jensen-Shannon divergence
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 380
year: '2021'
...
---
_id: '9037'
abstract:
- lang: eng
text: "We continue our study of ‘no‐dimension’ analogues of basic theorems in combinatorial
and convex geometry in Banach spaces. We generalize some results of the paper
(Adiprasito, Bárány and Mustafa, ‘Theorems of Carathéodory, Helly, and Tverberg
without dimension’, Proceedings of the Thirtieth Annual ACM‐SIAM Symposium on
Discrete Algorithms (Society for Industrial and Applied Mathematics, San Diego,
California, 2019) 2350–2360) and prove no‐dimension versions of the colored Tverberg
theorem, the selection lemma and the weak \U0001D700 ‐net theorem in Banach spaces
of type \U0001D45D>1 . To prove these results, we use the original ideas of Adiprasito,
Bárány and Mustafa for the Euclidean case, our no‐dimension version of the Radon
theorem and slightly modified version of the celebrated Maurey lemma."
acknowledgement: "I wish to thank Imre Bárány for bringing the problem to my attention.
I am grateful to Marton Naszódi and Igor Tsiutsiurupa for useful remarks and help
with the text.\r\nThe author acknowledges the financial support from the Ministry
of Educational and Science of the Russian Federation in the framework of MegaGrant
no 075‐15‐2019‐1926."
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Grigory
full_name: Ivanov, Grigory
id: 87744F66-5C6F-11EA-AFE0-D16B3DDC885E
last_name: Ivanov
citation:
ama: Ivanov G. No-dimension Tverberg’s theorem and its corollaries in Banach spaces
of type p. Bulletin of the London Mathematical Society. 2021;53(2):631-641.
doi:10.1112/blms.12449
apa: Ivanov, G. (2021). No-dimension Tverberg’s theorem and its corollaries in Banach
spaces of type p. Bulletin of the London Mathematical Society. London Mathematical
Society. https://doi.org/10.1112/blms.12449
chicago: Ivanov, Grigory. “No-Dimension Tverberg’s Theorem and Its Corollaries in
Banach Spaces of Type P.” Bulletin of the London Mathematical Society.
London Mathematical Society, 2021. https://doi.org/10.1112/blms.12449.
ieee: G. Ivanov, “No-dimension Tverberg’s theorem and its corollaries in Banach
spaces of type p,” Bulletin of the London Mathematical Society, vol. 53,
no. 2. London Mathematical Society, pp. 631–641, 2021.
ista: Ivanov G. 2021. No-dimension Tverberg’s theorem and its corollaries in Banach
spaces of type p. Bulletin of the London Mathematical Society. 53(2), 631–641.
mla: Ivanov, Grigory. “No-Dimension Tverberg’s Theorem and Its Corollaries in Banach
Spaces of Type P.” Bulletin of the London Mathematical Society, vol. 53,
no. 2, London Mathematical Society, 2021, pp. 631–41, doi:10.1112/blms.12449.
short: G. Ivanov, Bulletin of the London Mathematical Society 53 (2021) 631–641.
date_created: 2021-01-24T23:01:08Z
date_published: 2021-04-01T00:00:00Z
date_updated: 2025-07-10T12:01:31Z
day: '01'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.1112/blms.12449
external_id:
arxiv:
- '1912.08561'
isi:
- '000607265100001'
file:
- access_level: open_access
checksum: e6ceaa6470d835eb4c211cbdd38fdfd1
content_type: application/pdf
creator: kschuh
date_created: 2021-08-06T09:59:45Z
date_updated: 2021-08-06T09:59:45Z
file_id: '9796'
file_name: 2021_BLMS_Ivanov.pdf
file_size: 194550
relation: main_file
success: 1
file_date_updated: 2021-08-06T09:59:45Z
has_accepted_license: '1'
intvolume: ' 53'
isi: 1
issue: '2'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '04'
oa: 1
oa_version: Published Version
page: 631-641
publication: Bulletin of the London Mathematical Society
publication_identifier:
eissn:
- 1469-2120
issn:
- 0024-6093
publication_status: published
publisher: London Mathematical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: No-dimension Tverberg's theorem and its corollaries in Banach spaces of type
p
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
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(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
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volume: 53
year: '2021'
...
---
_id: '9046'
acknowledgement: Our work was supported by the Swedish Research Council (grant 2017-01527)
to DIA
article_number: e1009172
article_processing_charge: No
article_type: original
author:
- first_name: Roderich
full_name: Römhild, Roderich
id: 68E56E44-62B0-11EA-B963-444F3DDC885E
last_name: Römhild
orcid: 0000-0001-9480-5261
- first_name: Dan I.
full_name: Andersson, Dan I.
last_name: Andersson
citation:
ama: Römhild R, Andersson DI. Mechanisms and therapeutic potential of collateral
sensitivity to antibiotics. PLoS Pathogens. 2021;17(1). doi:10.1371/journal.ppat.1009172
apa: Römhild, R., & Andersson, D. I. (2021). Mechanisms and therapeutic potential
of collateral sensitivity to antibiotics. PLoS Pathogens. Public Library
of Science. https://doi.org/10.1371/journal.ppat.1009172
chicago: Römhild, Roderich, and Dan I. Andersson. “Mechanisms and Therapeutic Potential
of Collateral Sensitivity to Antibiotics.” PLoS Pathogens. Public Library
of Science, 2021. https://doi.org/10.1371/journal.ppat.1009172.
ieee: R. Römhild and D. I. Andersson, “Mechanisms and therapeutic potential of collateral
sensitivity to antibiotics,” PLoS Pathogens, vol. 17, no. 1. Public Library
of Science, 2021.
ista: Römhild R, Andersson DI. 2021. Mechanisms and therapeutic potential of collateral
sensitivity to antibiotics. PLoS Pathogens. 17(1), e1009172.
mla: Römhild, Roderich, and Dan I. Andersson. “Mechanisms and Therapeutic Potential
of Collateral Sensitivity to Antibiotics.” PLoS Pathogens, vol. 17, no.
1, e1009172, Public Library of Science, 2021, doi:10.1371/journal.ppat.1009172.
short: R. Römhild, D.I. Andersson, PLoS Pathogens 17 (2021).
date_created: 2021-01-31T23:01:21Z
date_published: 2021-01-14T00:00:00Z
date_updated: 2025-07-10T12:01:33Z
day: '14'
ddc:
- '570'
department:
- _id: CaGu
doi: 10.1371/journal.ppat.1009172
external_id:
isi:
- '000610190400007'
pmid:
- '33444399'
file:
- access_level: open_access
checksum: d745d7f8fcbb9b95fea16a36f94dee31
content_type: application/pdf
creator: dernst
date_created: 2021-02-03T12:13:03Z
date_updated: 2021-02-03T12:13:03Z
file_id: '9070'
file_name: 2021_PlosPathogens_Roemhild.pdf
file_size: 570066
relation: main_file
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file_date_updated: 2021-02-03T12:13:03Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Pathogens
publication_identifier:
eissn:
- 1553-7374
issn:
- 1553-7366
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanisms and therapeutic potential of collateral sensitivity to antibiotics
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: 17
year: '2021'
...
---
_id: '9047'
abstract:
- lang: eng
text: This work analyzes the latency of the simplified successive cancellation (SSC)
decoding scheme for polar codes proposed by Alamdar-Yazdi and Kschischang. It
is shown that, unlike conventional successive cancellation decoding, where latency
is linear in the block length, the latency of SSC decoding is sublinear. More
specifically, the latency of SSC decoding is O(N1−1/μ) , where N is the block
length and μ is the scaling exponent of the channel, which captures the speed
of convergence of the rate to capacity. Numerical results demonstrate the tightness
of the bound and show that most of the latency reduction arises from the parallel
decoding of subcodes of rate 0 or 1.
acknowledgement: M. Mondelli was partially supported by grants NSF DMS-1613091, CCF-1714305,
IIS-1741162, and ONR N00014-18-1-2729. S. A. Hashemi is supported by a Postdoctoral
Fellowship from the Natural Sciences and Engineering Research Council of Canada
(NSERC) and by Huawei. The authors would like to thank the anonymous reviewers for
their comments that helped improving the quality of the manuscript.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Seyyed Ali
full_name: Hashemi, Seyyed Ali
last_name: Hashemi
- first_name: John M.
full_name: Cioffi, John M.
last_name: Cioffi
- first_name: Andrea
full_name: Goldsmith, Andrea
last_name: Goldsmith
citation:
ama: Mondelli M, Hashemi SA, Cioffi JM, Goldsmith A. Sublinear latency for simplified
successive cancellation decoding of polar codes. IEEE Transactions on Wireless
Communications. 2021;20(1):18-27. doi:10.1109/TWC.2020.3022922
apa: Mondelli, M., Hashemi, S. A., Cioffi, J. M., & Goldsmith, A. (2021). Sublinear
latency for simplified successive cancellation decoding of polar codes. IEEE
Transactions on Wireless Communications. IEEE. https://doi.org/10.1109/TWC.2020.3022922
chicago: Mondelli, Marco, Seyyed Ali Hashemi, John M. Cioffi, and Andrea Goldsmith.
“Sublinear Latency for Simplified Successive Cancellation Decoding of Polar Codes.”
IEEE Transactions on Wireless Communications. IEEE, 2021. https://doi.org/10.1109/TWC.2020.3022922.
ieee: M. Mondelli, S. A. Hashemi, J. M. Cioffi, and A. Goldsmith, “Sublinear latency
for simplified successive cancellation decoding of polar codes,” IEEE Transactions
on Wireless Communications, vol. 20, no. 1. IEEE, pp. 18–27, 2021.
ista: Mondelli M, Hashemi SA, Cioffi JM, Goldsmith A. 2021. Sublinear latency for
simplified successive cancellation decoding of polar codes. IEEE Transactions
on Wireless Communications. 20(1), 18–27.
mla: Mondelli, Marco, et al. “Sublinear Latency for Simplified Successive Cancellation
Decoding of Polar Codes.” IEEE Transactions on Wireless Communications,
vol. 20, no. 1, IEEE, 2021, pp. 18–27, doi:10.1109/TWC.2020.3022922.
short: M. Mondelli, S.A. Hashemi, J.M. Cioffi, A. Goldsmith, IEEE Transactions on
Wireless Communications 20 (2021) 18–27.
corr_author: '1'
date_created: 2021-01-31T23:01:21Z
date_published: 2021-01-01T00:00:00Z
date_updated: 2025-09-10T10:27:04Z
day: '01'
department:
- _id: MaMo
doi: 10.1109/TWC.2020.3022922
external_id:
arxiv:
- '1909.04892'
isi:
- '000607808800002'
intvolume: ' 20'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1909.04892
month: '01'
oa: 1
oa_version: Preprint
page: 18-27
publication: IEEE Transactions on Wireless Communications
publication_identifier:
eissn:
- 1558-2248
issn:
- 1536-1276
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '8536'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Sublinear latency for simplified successive cancellation decoding of polar
codes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2021'
...
---
_id: '9048'
abstract:
- lang: eng
text: The analogy between an equilibrium partition function and the return probability
in many-body unitary dynamics has led to the concept of dynamical quantum phase
transition (DQPT). DQPTs are defined by nonanalyticities in the return amplitude
and are present in many models. In some cases, DQPTs can be related to equilibrium
concepts, such as order parameters, yet their universal description is an open
question. In this Letter, we provide first steps toward a classification of DQPTs
by using a matrix product state description of unitary dynamics in the thermodynamic
limit. This allows us to distinguish the two limiting cases of “precession” and
“entanglement” DQPTs, which are illustrated using an analytical description in
the quantum Ising model. While precession DQPTs are characterized by a large entanglement
gap and are semiclassical in their nature, entanglement DQPTs occur near avoided
crossings in the entanglement spectrum and can be distinguished by a complex pattern
of nonlocal correlations. We demonstrate the existence of precession and entanglement
DQPTs beyond Ising models, discuss observables that can distinguish them, and
relate their interplay to complex DQPT phenomenology.
acknowledgement: "S. D. N. acknowledges funding from the Institute of Science and
Technology (IST) Austria and from the European Union’s Horizon 2020 Research and
Innovation Programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.
A. M. and M. S. were supported by the European Research Council (ERC) under the
European Union’s Horizon 2020 Research and\r\nInnovation Programme (Grant Agreement
No. 850899)."
article_number: '040602'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Stefano
full_name: De Nicola, Stefano
id: 42832B76-F248-11E8-B48F-1D18A9856A87
last_name: De Nicola
orcid: 0000-0002-4842-6671
- first_name: Alexios
full_name: Michailidis, Alexios
id: 36EBAD38-F248-11E8-B48F-1D18A9856A87
last_name: Michailidis
orcid: 0000-0002-8443-1064
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: De Nicola S, Michailidis A, Serbyn M. Entanglement view of dynamical quantum
phase transitions. Physical Review Letters. 2021;126(4). doi:10.1103/physrevlett.126.040602
apa: De Nicola, S., Michailidis, A., & Serbyn, M. (2021). Entanglement view
of dynamical quantum phase transitions. Physical Review Letters. American
Physical Society. https://doi.org/10.1103/physrevlett.126.040602
chicago: De Nicola, Stefano, Alexios Michailidis, and Maksym Serbyn. “Entanglement
View of Dynamical Quantum Phase Transitions.” Physical Review Letters.
American Physical Society, 2021. https://doi.org/10.1103/physrevlett.126.040602.
ieee: S. De Nicola, A. Michailidis, and M. Serbyn, “Entanglement view of dynamical
quantum phase transitions,” Physical Review Letters, vol. 126, no. 4. American
Physical Society, 2021.
ista: De Nicola S, Michailidis A, Serbyn M. 2021. Entanglement view of dynamical
quantum phase transitions. Physical Review Letters. 126(4), 040602.
mla: De Nicola, Stefano, et al. “Entanglement View of Dynamical Quantum Phase Transitions.”
Physical Review Letters, vol. 126, no. 4, 040602, American Physical Society,
2021, doi:10.1103/physrevlett.126.040602.
short: S. De Nicola, A. Michailidis, M. Serbyn, Physical Review Letters 126 (2021).
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title: Entanglement view of dynamical quantum phase transitions
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