---
_id: '10338'
abstract:
- lang: eng
text: In the nuclear pore complex, intrinsically disordered proteins (FG Nups),
along with their interactions with more globular proteins called nuclear transport
receptors (NTRs), are vital to the selectivity of transport into and out of the
cell nucleus. Although such interactions can be modeled at different levels of
coarse graining, in vitro experimental data have been quantitatively described
by minimal models that describe FG Nups as cohesive homogeneous polymers and NTRs
as uniformly cohesive spheres, in which the heterogeneous effects have been smeared
out. By definition, these minimal models do not account for the explicit heterogeneities
in FG Nup sequences, essentially a string of cohesive and noncohesive polymer
units, and at the NTR surface. Here, we develop computational and analytical models
that do take into account such heterogeneity in a minimal fashion and compare
them with experimental data on single-molecule interactions between FG Nups and
NTRs. Overall, we find that the heterogeneous nature of FG Nups and NTRs does
play a role in determining equilibrium binding properties but is of much greater
significance when it comes to unbinding and binding kinetics. Using our models,
we predict how binding equilibria and kinetics depend on the distribution of cohesive
blocks in the FG Nup sequences and of the binding pockets at the NTR surface,
with multivalency playing a key role. Finally, we observe that single-molecule
binding kinetics has a rather minor influence on the diffusion of NTRs in polymer
melts consisting of FG-Nup-like sequences.
article_processing_charge: No
article_type: original
author:
- first_name: Luke K.
full_name: Davis, Luke K.
last_name: Davis
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Bart W.
full_name: Hoogenboom, Bart W.
last_name: Hoogenboom
- first_name: Anton
full_name: Zilman, Anton
last_name: Zilman
citation:
ama: Davis LK, Šarić A, Hoogenboom BW, Zilman A. Physical modeling of multivalent
interactions in the nuclear pore complex. Biophysical Journal. 2021;120(9):1565-1577.
doi:10.1016/j.bpj.2021.01.039
apa: Davis, L. K., Šarić, A., Hoogenboom, B. W., & Zilman, A. (2021). Physical
modeling of multivalent interactions in the nuclear pore complex. Biophysical
Journal. Elsevier. https://doi.org/10.1016/j.bpj.2021.01.039
chicago: Davis, Luke K., Anđela Šarić, Bart W. Hoogenboom, and Anton Zilman. “Physical
Modeling of Multivalent Interactions in the Nuclear Pore Complex.” Biophysical
Journal. Elsevier, 2021. https://doi.org/10.1016/j.bpj.2021.01.039.
ieee: L. K. Davis, A. Šarić, B. W. Hoogenboom, and A. Zilman, “Physical modeling
of multivalent interactions in the nuclear pore complex,” Biophysical Journal,
vol. 120, no. 9. Elsevier, pp. 1565–1577, 2021.
ista: Davis LK, Šarić A, Hoogenboom BW, Zilman A. 2021. Physical modeling of multivalent
interactions in the nuclear pore complex. Biophysical Journal. 120(9), 1565–1577.
mla: Davis, Luke K., et al. “Physical Modeling of Multivalent Interactions in the
Nuclear Pore Complex.” Biophysical Journal, vol. 120, no. 9, Elsevier,
2021, pp. 1565–77, doi:10.1016/j.bpj.2021.01.039.
short: L.K. Davis, A. Šarić, B.W. Hoogenboom, A. Zilman, Biophysical Journal 120
(2021) 1565–1577.
date_created: 2021-11-25T15:36:36Z
date_published: 2021-02-19T00:00:00Z
date_updated: 2022-04-01T10:34:38Z
day: '19'
doi: 10.1016/j.bpj.2021.01.039
extern: '1'
external_id:
pmid:
- '33617830'
fulldoi: https://doi.org/10.1016/j.bpj.2021.01.039
intvolume: ' 120'
issue: '9'
keyword:
- biophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2020.10.01.322156
month: '02'
oa: 1
oa_version: Preprint
page: 1565-1577
pmid: 1
publication: Biophysical Journal
publication_identifier:
issn:
- 0006-3495
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Physical modeling of multivalent interactions in the nuclear pore complex
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 120
year: '2021'
...
---
OA_place: publisher
OA_type: hybrid
_id: '10339'
abstract:
- lang: eng
text: We study the effects of osmotic shocks on lipid vesicles via coarse-grained
molecular dynamics simulations by explicitly considering the solute in the system.
We find that depending on their nature (hypo- or hypertonic) such shocks can lead
to bursting events or engulfing of external material into inner compartments,
among other morphology transformations. We characterize the dynamics of these
processes and observe a separation of time scales between the osmotic shock absorption
and the shape relaxation. Our work consequently provides an insight into the dynamics
of compartmentalization in vesicular systems as a result of osmotic shocks, which
can be of interest in the context of early proto-cell development and proto-cell
compartmentalisation.
acknowledgement: We acknowledge support from the Royal Society (C. V. C. and A. Sˇ.),
the Medical Research Council (C. V. C. and A. Sˇ.), and the European Research Council
(Starting grant ‘‘NEPA’’ 802960 to A. Sˇ.). We thank Johannes Krausser and Ivan
Palaia for fruitful discussions.
article_processing_charge: No
article_type: original
author:
- first_name: Christian
full_name: Vanhille-Campos, Christian
last_name: Vanhille-Campos
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
citation:
ama: Vanhille-Campos C, Šarić A. Modelling the dynamics of vesicle reshaping and
scission under osmotic shocks. Soft Matter. 2021;17(14):3798-3806. doi:10.1039/d0sm02012e
apa: Vanhille-Campos, C., & Šarić, A. (2021). Modelling the dynamics of vesicle
reshaping and scission under osmotic shocks. Soft Matter. Royal Society
of Chemistry. https://doi.org/10.1039/d0sm02012e
chicago: Vanhille-Campos, Christian, and Anđela Šarić. “Modelling the Dynamics of
Vesicle Reshaping and Scission under Osmotic Shocks.” Soft Matter. Royal
Society of Chemistry, 2021. https://doi.org/10.1039/d0sm02012e.
ieee: C. Vanhille-Campos and A. Šarić, “Modelling the dynamics of vesicle reshaping
and scission under osmotic shocks,” Soft Matter, vol. 17, no. 14. Royal
Society of Chemistry, pp. 3798–3806, 2021.
ista: Vanhille-Campos C, Šarić A. 2021. Modelling the dynamics of vesicle reshaping
and scission under osmotic shocks. Soft Matter. 17(14), 3798–3806.
mla: Vanhille-Campos, Christian, and Anđela Šarić. “Modelling the Dynamics of Vesicle
Reshaping and Scission under Osmotic Shocks.” Soft Matter, vol. 17, no.
14, Royal Society of Chemistry, 2021, pp. 3798–806, doi:10.1039/d0sm02012e.
short: C. Vanhille-Campos, A. Šarić, Soft Matter 17 (2021) 3798–3806.
date_created: 2021-11-25T16:06:42Z
date_published: 2021-02-16T00:00:00Z
date_updated: 2024-10-14T14:20:59Z
day: '16'
doi: 10.1039/d0sm02012e
extern: '1'
external_id:
pmid:
- '33629089'
fulldoi: https://doi.org/10.1039/d0sm02012e
intvolume: ' 17'
issue: '14'
keyword:
- condensed matter physics
- general chemistry
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/3.0/
main_file_link:
- open_access: '1'
url: https://pubs.rsc.org/en/content/articlehtml/2021/sm/d0sm02012e
month: '02'
oa: 1
oa_version: Published Version
page: 3798-3806
pmid: 1
publication: Soft Matter
publication_identifier:
eissn:
- 1744-6848
issn:
- 1744-683X
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
related_material:
link:
- relation: earlier_version
url: https://www.biorxiv.org/content/10.1101/2020.11.16.384602v2
scopus_import: '1'
status: public
title: Modelling the dynamics of vesicle reshaping and scission under osmotic shocks
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/3.0/legalcode
name: Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)
short: CC BY-NC (3.0)
type: journal_article
user_id: 0043cee0-e5fc-11ee-9736-f83bc23afbf0
volume: 17
year: '2021'
...
---
_id: '10340'
abstract:
- lang: eng
text: 'The cell membrane is an inhomogeneous system composed of phospholipids, sterols,
carbohydrates, and proteins that can be directly attached to underlying cytoskeleton.
The protein linkers between the membrane and the cytoskeleton are believed to
have a profound effect on the mechanical properties of the cell membrane and its
ability to reshape. Here, we investigate the role of membrane-cortex linkers on
the extrusion of membrane tubes using computer simulations and experiments. In
simulations, we find that the force for tube extrusion has a nonlinear dependence
on the density of membrane-cortex attachments: at a range of low and intermediate
linker densities, the force is not significantly influenced by the presence of
the membrane-cortex attachments and resembles that of the bare membrane. For large
concentrations of linkers, however, the force substantially increases compared
with the bare membrane. In both cases, the linkers provided membrane tubes with
increased stability against coalescence. We then pulled tubes from HEK cells using
optical tweezers for varying expression levels of the membrane-cortex attachment
protein Ezrin. In line with simulations, we observed that overexpression of Ezrin
led to an increased extrusion force, while Ezrin depletion had a negligible effect
on the force. Our results shed light on the importance of local protein rearrangements
for membrane reshaping at nanoscopic scales.'
acknowledgement: We thank Ewa Paluch, Alba Diz-Muñoz, Guillaume Salbreux, Guillaume
Charras, and Shiladitya Banerjee for helpful discussions. We acknowledge support
from the Engineering and Physical Sciences Research Council (A.P. and A.Š.), the
UCL Institute for the Physics of Living Systems (A.P., C.V.C., and A.Š.), the Royal
Society (C.V.C. and A.Š.), and the European Research Council (Starting grant EP/R011818/1
to A.Š.; E.C. and P.B. are partners of the advanced grant, project 339847) and from
Institut Curie (E.C. and P.B.) and Centre National de la Recherche Scientifique
(CNRS) (E.C. and P.B.). The P.B. and E.C. groups belong to Labex CelTisPhyBio (ANR-11-LABX0038)
and to Paris Sciences et Lettres (ANR-10-IDEX-0001-02). T.L. received a PhD grant
from Paris Sciences et Lettres Research University and support from the Institut
Curie.
article_processing_charge: No
article_type: original
author:
- first_name: Alexandru
full_name: Paraschiv, Alexandru
last_name: Paraschiv
- first_name: Thibaut J.
full_name: Lagny, Thibaut J.
last_name: Lagny
- first_name: Christian Vanhille
full_name: Campos, Christian Vanhille
last_name: Campos
- first_name: Evelyne
full_name: Coudrier, Evelyne
last_name: Coudrier
- first_name: Patricia
full_name: Bassereau, Patricia
last_name: Bassereau
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
citation:
ama: Paraschiv A, Lagny TJ, Campos CV, Coudrier E, Bassereau P, Šarić A. Influence
of membrane-cortex linkers on the extrusion of membrane tubes. Biophysical
Journal. 2021;120(4):598-606. doi:10.1016/j.bpj.2020.12.028
apa: Paraschiv, A., Lagny, T. J., Campos, C. V., Coudrier, E., Bassereau, P., &
Šarić, A. (2021). Influence of membrane-cortex linkers on the extrusion of membrane
tubes. Biophysical Journal. Cell Press. https://doi.org/10.1016/j.bpj.2020.12.028
chicago: Paraschiv, Alexandru, Thibaut J. Lagny, Christian Vanhille Campos, Evelyne
Coudrier, Patricia Bassereau, and Anđela Šarić. “Influence of Membrane-Cortex
Linkers on the Extrusion of Membrane Tubes.” Biophysical Journal. Cell
Press, 2021. https://doi.org/10.1016/j.bpj.2020.12.028.
ieee: A. Paraschiv, T. J. Lagny, C. V. Campos, E. Coudrier, P. Bassereau, and A.
Šarić, “Influence of membrane-cortex linkers on the extrusion of membrane tubes,”
Biophysical Journal, vol. 120, no. 4. Cell Press, pp. 598–606, 2021.
ista: Paraschiv A, Lagny TJ, Campos CV, Coudrier E, Bassereau P, Šarić A. 2021.
Influence of membrane-cortex linkers on the extrusion of membrane tubes. Biophysical
Journal. 120(4), 598–606.
mla: Paraschiv, Alexandru, et al. “Influence of Membrane-Cortex Linkers on the Extrusion
of Membrane Tubes.” Biophysical Journal, vol. 120, no. 4, Cell Press, 2021,
pp. 598–606, doi:10.1016/j.bpj.2020.12.028.
short: A. Paraschiv, T.J. Lagny, C.V. Campos, E. Coudrier, P. Bassereau, A. Šarić,
Biophysical Journal 120 (2021) 598–606.
date_created: 2021-11-25T16:18:23Z
date_published: 2021-01-16T00:00:00Z
date_updated: 2024-10-14T11:13:03Z
day: '16'
doi: 10.1016/j.bpj.2020.12.028
extern: '1'
external_id:
pmid:
- '33460596'
fulldoi: https://doi.org/10.1016/j.bpj.2020.12.028
intvolume: ' 120'
issue: '4'
keyword:
- biophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2020.07.28.224741
month: '01'
oa: 1
oa_version: Preprint
page: 598-606
pmid: 1
publication: Biophysical Journal
publication_identifier:
issn:
- 0006-3495
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Influence of membrane-cortex linkers on the extrusion of membrane tubes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 120
year: '2021'
...
---
_id: '10365'
abstract:
- lang: eng
text: The early development of many organisms involves the folding of cell monolayers,
but this behaviour is difficult to reproduce in vitro; therefore, both mechanistic
causes and effects of local curvature remain unclear. Here we study epithelial
cell monolayers on corrugated hydrogels engineered into wavy patterns, examining
how concave and convex curvatures affect cellular and nuclear shape. We find that
substrate curvature affects monolayer thickness, which is larger in valleys than
crests. We show that this feature generically arises in a vertex model, leading
to the hypothesis that cells may sense curvature by modifying the thickness of
the tissue. We find that local curvature also affects nuclear morphology and positioning,
which we explain by extending the vertex model to take into account membrane–nucleus
interactions, encoding thickness modulation in changes to nuclear deformation
and position. We propose that curvature governs the spatial distribution of yes-associated
proteins via nuclear shape and density changes. We show that curvature also induces
significant variations in lamins, chromatin condensation and cell proliferation
rate in folded epithelial tissues. Together, this work identifies active cell
mechanics and nuclear mechanoadaptation as the key players of the mechanistic
regulation of epithelia to substrate curvature.
acknowledgement: S.G. acknowledges funding from FEDER Prostem Research Project no.
1510614 (Wallonia DG06), F.R.S.-FNRS Epiforce Research Project no. T.0092.21 and
Interreg MAT(T)ISSE project, which is financially supported by Interreg France-Wallonie-Vlaanderen
(Fonds Européen de Développement Régional, FEDER-ERDF). This project was supported
by the European Research Council under the European Union’s Horizon 2020 Research
and Innovation Programme grant agreement 851288 (to E.H.), and by the Austrian Science
Fund (FWF) (P 31639; to E.H.). L.R.M. acknowledges funding from the Agence National
de la Recherche (ANR), as part of the ‘Investments d’Avenir’ Programme (I-SITE ULNE/ANR-16-IDEX-0004
ULNE). This work benefited from ANR-10-EQPX-04-01 and FEDER 12001407 grants to F.L.
W.D.V. is supported by the Research Foundation Flanders (FWO 1516619N, FWO GOO5819N,
FWO I003420N, FWO IRI I000321N) and is member of the Research Excellence Consortium
µNEURO at the University of Antwerp. M.L. is financially supported by FRIA (F.R.S.-FNRS).
M.S. is a Senior Research Associate of the Fund for Scientific Research (F.R.S.-FNRS)
and acknowledges EOS grant no. 30650939 (PRECISION). Sketches in Figs. 1a and 5e
and Extended Data Fig. 9 were drawn by C. Levicek.
article_processing_charge: No
article_type: original
author:
- first_name: Marine
full_name: Luciano, Marine
last_name: Luciano
- first_name: Shi-lei
full_name: Xue, Shi-lei
id: 31D2C804-F248-11E8-B48F-1D18A9856A87
last_name: Xue
- first_name: Winnok H.
full_name: De Vos, Winnok H.
last_name: De Vos
- first_name: Lorena
full_name: Redondo-Morata, Lorena
last_name: Redondo-Morata
- first_name: Mathieu
full_name: Surin, Mathieu
last_name: Surin
- first_name: Frank
full_name: Lafont, Frank
last_name: Lafont
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Sylvain
full_name: Gabriele, Sylvain
last_name: Gabriele
citation:
ama: Luciano M, Xue S, De Vos WH, et al. Cell monolayers sense curvature by exploiting
active mechanics and nuclear mechanoadaptation. Nature Physics. 2021;17(12):1382–1390.
doi:10.1038/s41567-021-01374-1
apa: Luciano, M., Xue, S., De Vos, W. H., Redondo-Morata, L., Surin, M., Lafont,
F., … Gabriele, S. (2021). Cell monolayers sense curvature by exploiting active
mechanics and nuclear mechanoadaptation. Nature Physics. Springer Nature.
https://doi.org/10.1038/s41567-021-01374-1
chicago: Luciano, Marine, Shi-lei Xue, Winnok H. De Vos, Lorena Redondo-Morata,
Mathieu Surin, Frank Lafont, Edouard B Hannezo, and Sylvain Gabriele. “Cell Monolayers
Sense Curvature by Exploiting Active Mechanics and Nuclear Mechanoadaptation.”
Nature Physics. Springer Nature, 2021. https://doi.org/10.1038/s41567-021-01374-1.
ieee: M. Luciano et al., “Cell monolayers sense curvature by exploiting active
mechanics and nuclear mechanoadaptation,” Nature Physics, vol. 17, no.
12. Springer Nature, pp. 1382–1390, 2021.
ista: Luciano M, Xue S, De Vos WH, Redondo-Morata L, Surin M, Lafont F, Hannezo
EB, Gabriele S. 2021. Cell monolayers sense curvature by exploiting active mechanics
and nuclear mechanoadaptation. Nature Physics. 17(12), 1382–1390.
mla: Luciano, Marine, et al. “Cell Monolayers Sense Curvature by Exploiting Active
Mechanics and Nuclear Mechanoadaptation.” Nature Physics, vol. 17, no.
12, Springer Nature, 2021, pp. 1382–1390, doi:10.1038/s41567-021-01374-1.
short: M. Luciano, S. Xue, W.H. De Vos, L. Redondo-Morata, M. Surin, F. Lafont,
E.B. Hannezo, S. Gabriele, Nature Physics 17 (2021) 1382–1390.
corr_author: '1'
date_created: 2021-11-28T23:01:29Z
date_published: 2021-11-18T00:00:00Z
date_updated: 2025-04-14T07:52:26Z
day: '18'
ddc:
- '530'
department:
- _id: EdHa
doi: 10.1038/s41567-021-01374-1
ec_funded: 1
external_id:
isi:
- '000720204300004'
file:
- access_level: open_access
checksum: 5d6d76750a71d7cb632bb15417c38ef7
content_type: application/pdf
creator: channezo
date_created: 2023-10-11T09:31:43Z
date_updated: 2023-10-11T09:31:43Z
file_id: '14420'
file_name: 50145_4_merged_1630498627.pdf
file_size: 40285498
relation: main_file
success: 1
file_date_updated: 2023-10-11T09:31:43Z
fulldoi: https://doi.org/10.1038/s41567-021-01374-1
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '12'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 1382–1390
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
- _id: 268294B6-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31639
name: Active mechano-chemical description of the cell cytoskeleton
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Webpage
relation: press_release
url: https://ist.ac.at/en/news/how-cells-feel-curvature/
scopus_import: '1'
status: public
title: Cell monolayers sense curvature by exploiting active mechanics and nuclear
mechanoadaptation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2021'
...
---
_id: '10366'
article_number: '203758'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Ana Maria
full_name: Lennon, Ana Maria
last_name: Lennon
- first_name: Roberto
full_name: Mayor, Roberto
last_name: Mayor
- first_name: Guillaume
full_name: Salbreux, Guillaume
last_name: Salbreux
citation:
ama: 'Heisenberg C-PJ, Lennon AM, Mayor R, Salbreux G. Special rebranding issue:
“Quantitative cell and developmental biology.” Cells and Development. 2021;168(12).
doi:10.1016/j.cdev.2021.203758'
apa: 'Heisenberg, C.-P. J., Lennon, A. M., Mayor, R., & Salbreux, G. (2021).
Special rebranding issue: “Quantitative cell and developmental biology.” Cells
and Development. Elsevier. https://doi.org/10.1016/j.cdev.2021.203758'
chicago: 'Heisenberg, Carl-Philipp J, Ana Maria Lennon, Roberto Mayor, and Guillaume
Salbreux. “Special Rebranding Issue: ‘Quantitative Cell and Developmental Biology.’”
Cells and Development. Elsevier, 2021. https://doi.org/10.1016/j.cdev.2021.203758.'
ieee: 'C.-P. J. Heisenberg, A. M. Lennon, R. Mayor, and G. Salbreux, “Special rebranding
issue: ‘Quantitative cell and developmental biology,’” Cells and Development,
vol. 168, no. 12. Elsevier, 2021.'
ista: 'Heisenberg C-PJ, Lennon AM, Mayor R, Salbreux G. 2021. Special rebranding
issue: “Quantitative cell and developmental biology”. Cells and Development. 168(12),
203758.'
mla: 'Heisenberg, Carl-Philipp J., et al. “Special Rebranding Issue: ‘Quantitative
Cell and Developmental Biology.’” Cells and Development, vol. 168, no.
12, 203758, Elsevier, 2021, doi:10.1016/j.cdev.2021.203758.'
short: C.-P.J. Heisenberg, A.M. Lennon, R. Mayor, G. Salbreux, Cells and Development
168 (2021).
corr_author: '1'
date_created: 2021-11-28T23:01:30Z
date_published: 2021-11-17T00:00:00Z
date_updated: 2026-06-18T08:37:21Z
day: '17'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1016/j.cdev.2021.203758
external_id:
isi:
- '000974771600028'
pmid:
- '34800748'
fulldoi: https://doi.org/10.1016/j.cdev.2021.203758
intvolume: ' 168'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cdev.2021.203758
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: Cells and Development
publication_identifier:
issn:
- 2667-2901
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Special rebranding issue: “Quantitative cell and developmental biology”'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 168
year: '2021'
...
---
_id: '10367'
abstract:
- lang: eng
text: How information is created, shared and consumed has changed rapidly in recent
decades, in part thanks to new social platforms and technologies on the web. With
ever-larger amounts of unstructured and limited labels, organizing and reconciling
information from different sources and modalities is a central challenge in machine
learning. This cutting-edge tutorial aims to introduce the multimodal entailment
task, which can be useful for detecting semantic alignments when a single modality
alone does not suffice for a whole content understanding. Starting with a brief
overview of natural language processing, computer vision, structured data and
neural graph learning, we lay the foundations for the multimodal sections to follow.
We then discuss recent multimodal learning literature covering visual, audio and
language streams, and explore case studies focusing on tasks which require fine-grained
understanding of visual and linguistic semantics question answering, veracity
and hatred classification. Finally, we introduce a new dataset for recognizing
multimodal entailment, exploring it in a hands-on collaborative section. Overall,
this tutorial gives an overview of multimodal learning, introduces a multimodal
entailment dataset, and encourages future research in the topic.
acknowledgement: "We would like to thank Abby Schantz, Abe Ittycheriah, Aliaksei Severyn,
Allan Heydon, Aly\r\nGrealish, Andrey Vlasov, Arkaitz Zubiaga, Ashwin Kakarla, Chen
Sun, Clayton Williams, Cong\r\nYu, Cordelia Schmid, Da-Cheng Juan, Dan Finnie, Dani
Valevski, Daniel Rocha, David Price, David Sklar, Devi Krishna, Elena Kochkina,
Enrique Alfonseca, Franc¸oise Beaufays, Isabelle Augenstein, Jialu Liu, John Cantwell,
John Palowitch, Jordan Boyd-Graber, Lei Shi, Luis Valente, Maria Voitovich, Mehmet
Aktuna, Mogan Brown, Mor Naaman, Natalia P, Nidhi Hebbar, Pete Aykroyd, Rahul Sukthankar,
Richa Dixit, Steve Pucci, Tania Bedrax-Weiss, Tobias Kaufmann, Tom Boulos, Tu Tsao,
Vladimir Chtchetkine, Yair Kurzion, Yifan Xu and Zach Hynes."
article_processing_charge: No
author:
- first_name: Cesar
full_name: Ilharco, Cesar
last_name: Ilharco
- first_name: Afsaneh
full_name: Shirazi, Afsaneh
last_name: Shirazi
- first_name: Arjun
full_name: Gopalan, Arjun
last_name: Gopalan
- first_name: Arsha
full_name: Nagrani, Arsha
last_name: Nagrani
- first_name: Blaž
full_name: Bratanič, Blaž
last_name: Bratanič
- first_name: Chris
full_name: Bregler, Chris
last_name: Bregler
- first_name: Christina
full_name: Liu, Christina
last_name: Liu
- first_name: Felipe
full_name: Ferreira, Felipe
last_name: Ferreira
- first_name: Gabriek
full_name: Barcik, Gabriek
last_name: Barcik
- first_name: Gabriel
full_name: Ilharco, Gabriel
last_name: Ilharco
- first_name: Georg F
full_name: Osang, Georg F
id: 464B40D6-F248-11E8-B48F-1D18A9856A87
last_name: Osang
- first_name: Jannis
full_name: Bulian, Jannis
last_name: Bulian
- first_name: Jared
full_name: Frank, Jared
last_name: Frank
- first_name: Lucas
full_name: Smaira, Lucas
last_name: Smaira
- first_name: Qin
full_name: Cao, Qin
last_name: Cao
- first_name: Ricardo
full_name: Marino, Ricardo
last_name: Marino
- first_name: Roma
full_name: Patel, Roma
last_name: Patel
- first_name: Thomas
full_name: Leung, Thomas
last_name: Leung
- first_name: Vaiva
full_name: Imbrasaite, Vaiva
last_name: Imbrasaite
citation:
ama: 'Ilharco C, Shirazi A, Gopalan A, et al. Recognizing multimodal entailment.
In: 59th Annual Meeting of the Association for Computational Linguistics and
the 11th International Joint Conference on Natural Language Processing, Tutorial
Abstracts. Association for Computational Linguistics; 2021:29-30. doi:10.18653/v1/2021.acl-tutorials.6'
apa: 'Ilharco, C., Shirazi, A., Gopalan, A., Nagrani, A., Bratanič, B., Bregler,
C., … Imbrasaite, V. (2021). Recognizing multimodal entailment. In 59th Annual
Meeting of the Association for Computational Linguistics and the 11th International
Joint Conference on Natural Language Processing, Tutorial Abstracts (pp. 29–30).
Bangkok, Thailand: Association for Computational Linguistics. https://doi.org/10.18653/v1/2021.acl-tutorials.6'
chicago: Ilharco, Cesar, Afsaneh Shirazi, Arjun Gopalan, Arsha Nagrani, Blaž Bratanič,
Chris Bregler, Christina Liu, et al. “Recognizing Multimodal Entailment.” In 59th
Annual Meeting of the Association for Computational Linguistics and the 11th International
Joint Conference on Natural Language Processing, Tutorial Abstracts, 29–30.
Association for Computational Linguistics, 2021. https://doi.org/10.18653/v1/2021.acl-tutorials.6.
ieee: C. Ilharco et al., “Recognizing multimodal entailment,” in 59th
Annual Meeting of the Association for Computational Linguistics and the 11th International
Joint Conference on Natural Language Processing, Tutorial Abstracts, Bangkok,
Thailand, 2021, pp. 29–30.
ista: 'Ilharco C, Shirazi A, Gopalan A, Nagrani A, Bratanič B, Bregler C, Liu C,
Ferreira F, Barcik G, Ilharco G, Osang GF, Bulian J, Frank J, Smaira L, Cao Q,
Marino R, Patel R, Leung T, Imbrasaite V. 2021. Recognizing multimodal entailment.
59th Annual Meeting of the Association for Computational Linguistics and the 11th
International Joint Conference on Natural Language Processing, Tutorial Abstracts.
ACL: Association for Computational Linguistics ; IJCNLP: International Joint Conference
on Natural Language Processing, 29–30.'
mla: Ilharco, Cesar, et al. “Recognizing Multimodal Entailment.” 59th Annual
Meeting of the Association for Computational Linguistics and the 11th International
Joint Conference on Natural Language Processing, Tutorial Abstracts, Association
for Computational Linguistics, 2021, pp. 29–30, doi:10.18653/v1/2021.acl-tutorials.6.
short: C. Ilharco, A. Shirazi, A. Gopalan, A. Nagrani, B. Bratanič, C. Bregler,
C. Liu, F. Ferreira, G. Barcik, G. Ilharco, G.F. Osang, J. Bulian, J. Frank, L.
Smaira, Q. Cao, R. Marino, R. Patel, T. Leung, V. Imbrasaite, in:, 59th Annual
Meeting of the Association for Computational Linguistics and the 11th International
Joint Conference on Natural Language Processing, Tutorial Abstracts, Association
for Computational Linguistics, 2021, pp. 29–30.
conference:
end_date: 2021-08-06
location: Bangkok, Thailand
name: 'ACL: Association for Computational Linguistics ; IJCNLP: International Joint
Conference on Natural Language Processing'
start_date: 2021-08-01
date_created: 2021-11-28T23:01:30Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2022-01-26T14:26:36Z
day: '01'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.18653/v1/2021.acl-tutorials.6
file:
- access_level: open_access
checksum: b14052a025a6ecf675bdfe51db98c0d7
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-29T08:41:00Z
date_updated: 2021-11-29T08:41:00Z
file_id: '10368'
file_name: 2021_ACL_Ilharco.pdf
file_size: 1227703
relation: main_file
success: 1
file_date_updated: 2021-11-29T08:41:00Z
fulldoi: https://doi.org/10.18653/v1/2021.acl-tutorials.6
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://aclanthology.org/2021.acl-tutorials.6/
month: '08'
oa: 1
oa_version: Published Version
page: 29-30
publication: 59th Annual Meeting of the Association for Computational Linguistics
and the 11th International Joint Conference on Natural Language Processing, Tutorial
Abstracts
publication_identifier:
isbn:
- 9-781-9540-8557-2
publication_status: published
publisher: Association for Computational Linguistics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Recognizing multimodal entailment
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2021'
...
---
_id: '10401'
abstract:
- lang: eng
text: Theoretical and experimental studies of the interaction between spins and
temperature are vital for the development of spin caloritronics, as they dictate
the design of future devices. In this work, we propose a two-terminal cold-atom
simulator to study that interaction. The proposed quantum simulator consists of
strongly interacting atoms that occupy two temperature reservoirs connected by
a one-dimensional link. First, we argue that the dynamics in the link can be described
using an inhomogeneous Heisenberg spin chain whose couplings are defined by the
local temperature. Second, we show the existence of a spin current in a system
with a temperature difference by studying the dynamics that follows the spin-flip
of an atom in the link. A temperature gradient accelerates the impurity in one
direction more than in the other, leading to an overall spin current similar to
the spin Seebeck effect.
acknowledgement: The authors acknowledge support from the European QuantERA ERA-NET
Cofund in Quantum Technologies (Project QTFLAG Grant Agreement No. 731473) (R.E.B),
CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico) Brazil (A.F.),
the European Union’s Horizon 2020 research and innovation programme under the Marie
Skłodowska-Curie Grant Agreement No. 754411 (A.G.V.), the Independent Research Fund
Denmark, the Carlsberg Foundation, and Aarhus University Research Foundation under
the Jens Christian Skou fellowship program (N.T.Z).
article_number: '252'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Rafael E.
full_name: Barfknecht, Rafael E.
last_name: Barfknecht
- first_name: Angela
full_name: Foerster, Angela
last_name: Foerster
- first_name: Nikolaj T.
full_name: Zinner, Nikolaj T.
last_name: Zinner
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Barfknecht RE, Foerster A, Zinner NT, Volosniev A. Generation of spin currents
by a temperature gradient in a two-terminal device. Communications Physics.
2021;4(1). doi:10.1038/s42005-021-00753-7
apa: Barfknecht, R. E., Foerster, A., Zinner, N. T., & Volosniev, A. (2021).
Generation of spin currents by a temperature gradient in a two-terminal device.
Communications Physics. Springer Nature. https://doi.org/10.1038/s42005-021-00753-7
chicago: Barfknecht, Rafael E., Angela Foerster, Nikolaj T. Zinner, and Artem Volosniev.
“Generation of Spin Currents by a Temperature Gradient in a Two-Terminal Device.”
Communications Physics. Springer Nature, 2021. https://doi.org/10.1038/s42005-021-00753-7.
ieee: R. E. Barfknecht, A. Foerster, N. T. Zinner, and A. Volosniev, “Generation
of spin currents by a temperature gradient in a two-terminal device,” Communications
Physics, vol. 4, no. 1. Springer Nature, 2021.
ista: Barfknecht RE, Foerster A, Zinner NT, Volosniev A. 2021. Generation of spin
currents by a temperature gradient in a two-terminal device. Communications Physics.
4(1), 252.
mla: Barfknecht, Rafael E., et al. “Generation of Spin Currents by a Temperature
Gradient in a Two-Terminal Device.” Communications Physics, vol. 4, no.
1, 252, Springer Nature, 2021, doi:10.1038/s42005-021-00753-7.
short: R.E. Barfknecht, A. Foerster, N.T. Zinner, A. Volosniev, Communications Physics
4 (2021).
date_created: 2021-12-05T23:01:39Z
date_published: 2021-11-26T00:00:00Z
date_updated: 2026-04-02T14:05:00Z
day: '26'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1038/s42005-021-00753-7
ec_funded: 1
external_id:
arxiv:
- '2101.02020'
isi:
- '000722867600002'
file:
- access_level: open_access
checksum: 9097319952cb9a3d96e7fd3aa9813a03
content_type: application/pdf
creator: alisjak
date_created: 2021-12-06T14:53:41Z
date_updated: 2021-12-06T14:53:41Z
file_id: '10420'
file_name: 2021_NatComm_Barfknecht.pdf
file_size: 1068984
relation: main_file
success: 1
file_date_updated: 2021-12-06T14:53:41Z
fulldoi: https://doi.org/10.1038/s42005-021-00753-7
has_accepted_license: '1'
intvolume: ' 4'
isi: 1
issue: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Communications Physics
publication_identifier:
eissn:
- 2399-3650
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Generation of spin currents by a temperature gradient in a two-terminal device
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 4
year: '2021'
...
---
_id: '10402'
abstract:
- lang: eng
text: Branching morphogenesis governs the formation of many organs such as lung,
kidney, and the neurovascular system. Many studies have explored system-specific
molecular and cellular regulatory mechanisms, as well as self-organizing rules
underlying branching morphogenesis. However, in addition to local cues, branched
tissue growth can also be influenced by global guidance. Here, we develop a theoretical
framework for a stochastic self-organized branching process in the presence of
external cues. Combining analytical theory with numerical simulations, we predict
differential signatures of global vs. local regulatory mechanisms on the branching
pattern, such as angle distributions, domain size, and space-filling efficiency.
We find that branch alignment follows a generic scaling law determined by the
strength of global guidance, while local interactions influence the tissue density
but not its overall territory. Finally, using zebrafish innervation as a model
system, we test these key features of the model experimentally. Our work thus
provides quantitative predictions to disentangle the role of different types of
cues in shaping branched structures across scales.
acknowledgement: We thank all members of our respective groups for helpful discussion
on the paper. The authors are also grateful to Prof. Abdel El. Manira for support
and sharing Tg(HUC:Gal4;UAS:Synaptohysin-GFP), to Haohao Wu for discussion, and
thank Elena Zabalueva for the zebrafish schematic. The authors also acknowledge
Zebrafish core facility, Genome Engineering Zebrafish and Biomedicum Imaging Core
from the Karolinska Institutet for technical support. This work received funding
from the ERC under the European Union’s Horizon 2020 research and innovation programme
(grant agreement No. 851288 to E.H.) and under the Marie Skłodowska-Curie grant
agreement No. 754411 (to M.C.U.); Swedish Research Council (to F.L., I.A. and S.H.);
Knut and Alice Wallenberg Foundation (F.L. and I.A.); Swedish Brain Foundation (F.L.
and S.H.); Ming Wai Lau Foundation (to F.L.); StratRegen (to F.L.); ERC Consolidator
grant STEMMING-FROM-NERVE and ERC Synergy Grant KILL-OR-DIFFERENTIATE (to I.A.);
Bertil Hallsten Research Foundation (to I.A.); Cancerfonden (to I.A.); the Paradifference
Foundation (to I.A.); Austrian Science Fund (to I.A.); and StratNeuro (to S.H.).
article_number: '6830'
article_processing_charge: No
article_type: original
author:
- first_name: Mehmet C
full_name: Ucar, Mehmet C
id: 50B2A802-6007-11E9-A42B-EB23E6697425
last_name: Ucar
orcid: 0000-0003-0506-4217
- first_name: Dmitrii
full_name: Kamenev, Dmitrii
last_name: Kamenev
- first_name: Kazunori
full_name: Sunadome, Kazunori
last_name: Sunadome
- first_name: Dominik C
full_name: Fachet, Dominik C
id: 14FDD550-AA41-11E9-A0E5-1ACCE5697425
last_name: Fachet
- first_name: Francois
full_name: Lallemend, Francois
last_name: Lallemend
- first_name: Igor
full_name: Adameyko, Igor
last_name: Adameyko
- first_name: Saida
full_name: Hadjab, Saida
last_name: Hadjab
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
citation:
ama: Ucar MC, Kamenev D, Sunadome K, et al. Theory of branching morphogenesis by
local interactions and global guidance. Nature Communications. 2021;12.
doi:10.1038/s41467-021-27135-5
apa: Ucar, M. C., Kamenev, D., Sunadome, K., Fachet, D. C., Lallemend, F., Adameyko,
I., … Hannezo, E. B. (2021). Theory of branching morphogenesis by local interactions
and global guidance. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-27135-5
chicago: Ucar, Mehmet C, Dmitrii Kamenev, Kazunori Sunadome, Dominik C Fachet, Francois
Lallemend, Igor Adameyko, Saida Hadjab, and Edouard B Hannezo. “Theory of Branching
Morphogenesis by Local Interactions and Global Guidance.” Nature Communications.
Springer Nature, 2021. https://doi.org/10.1038/s41467-021-27135-5.
ieee: M. C. Ucar et al., “Theory of branching morphogenesis by local interactions
and global guidance,” Nature Communications, vol. 12. Springer Nature,
2021.
ista: Ucar MC, Kamenev D, Sunadome K, Fachet DC, Lallemend F, Adameyko I, Hadjab
S, Hannezo EB. 2021. Theory of branching morphogenesis by local interactions and
global guidance. Nature Communications. 12, 6830.
mla: Ucar, Mehmet C., et al. “Theory of Branching Morphogenesis by Local Interactions
and Global Guidance.” Nature Communications, vol. 12, 6830, Springer Nature,
2021, doi:10.1038/s41467-021-27135-5.
short: M.C. Ucar, D. Kamenev, K. Sunadome, D.C. Fachet, F. Lallemend, I. Adameyko,
S. Hadjab, E.B. Hannezo, Nature Communications 12 (2021).
date_created: 2021-12-05T23:01:40Z
date_published: 2021-11-24T00:00:00Z
date_updated: 2025-04-14T07:43:47Z
day: '24'
ddc:
- '573'
department:
- _id: EdHa
doi: 10.1038/s41467-021-27135-5
ec_funded: 1
external_id:
isi:
- '000722322900020'
pmid:
- '34819507'
file:
- access_level: open_access
checksum: 63c56ec75314a71e63e7dd2920b3c5b5
content_type: application/pdf
creator: cchlebak
date_created: 2021-12-10T08:54:09Z
date_updated: 2021-12-10T08:54:09Z
file_id: '10529'
file_name: 2021_NatComm_Ucar.pdf
file_size: 2303405
relation: main_file
success: 1
file_date_updated: 2021-12-10T08:54:09Z
fulldoi: https://doi.org/10.1038/s41467-021-27135-5
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '13058'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Theory of branching morphogenesis by local interactions and global guidance
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: 12
year: '2021'
...
---
_id: '10403'
abstract:
- lang: eng
text: Synaptic transmission, connectivity, and dendritic morphology mature in parallel
during brain development and are often disrupted in neurodevelopmental disorders.
Yet how these changes influence the neuronal computations necessary for normal
brain function are not well understood. To identify cellular mechanisms underlying
the maturation of synaptic integration in interneurons, we combined patch-clamp
recordings of excitatory inputs in mouse cerebellar stellate cells (SCs), three-dimensional
reconstruction of SC morphology with excitatory synapse location, and biophysical
modeling. We found that postnatal maturation of postsynaptic strength was homogeneously
reduced along the somatodendritic axis, but dendritic integration was always sublinear.
However, dendritic branching increased without changes in synapse density, leading
to a substantial gain in distal inputs. Thus, changes in synapse distribution,
rather than dendrite cable properties, are the dominant mechanism underlying the
maturation of neuronal computation. These mechanisms favor the emergence of a
spatially compartmentalized two-stage integration model promoting location-dependent
integration within dendritic subunits.
acknowledgement: This study was supported by the Centre National de la Recherche Scientifique
and the Agence Nationale de la Recherche (ANR-13-BSV4-00166, to LC and DAD). TA
was supported by fellowships from the Fondation pour la Recherche Medicale and the
Swedish Research Council. We thank Dmitry Ershov from the Image Analysis Hub of
the Institut Pasteur, Elodie Le Monnier, Elena Hollergschwandtner, Vanessa Zheden,
and Corinne Nantet for technical support and Haining Zhong for providing the Venus-tagged
PSD95 mouse line. We would like to thank Alberto Bacci, Ann Lohof, and Nelson Rebola
for comments on the manuscript.
article_number: e65954
article_processing_charge: No
article_type: original
author:
- first_name: Celia
full_name: Biane, Celia
last_name: Biane
- first_name: Florian
full_name: Rückerl, Florian
last_name: Rückerl
- first_name: Therese
full_name: Abrahamsson, Therese
last_name: Abrahamsson
- first_name: Cécile
full_name: Saint-Cloment, Cécile
last_name: Saint-Cloment
- first_name: Jean
full_name: Mariani, Jean
last_name: Mariani
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: David A.
full_name: Digregorio, David A.
last_name: Digregorio
- first_name: Rachel M.
full_name: Sherrard, Rachel M.
last_name: Sherrard
- first_name: Laurence
full_name: Cathala, Laurence
last_name: Cathala
citation:
ama: Biane C, Rückerl F, Abrahamsson T, et al. Developmental emergence of two-stage
nonlinear synaptic integration in cerebellar interneurons. eLife. 2021;10.
doi:10.7554/eLife.65954
apa: Biane, C., Rückerl, F., Abrahamsson, T., Saint-Cloment, C., Mariani, J., Shigemoto,
R., … Cathala, L. (2021). Developmental emergence of two-stage nonlinear synaptic
integration in cerebellar interneurons. ELife. eLife Sciences Publications.
https://doi.org/10.7554/eLife.65954
chicago: Biane, Celia, Florian Rückerl, Therese Abrahamsson, Cécile Saint-Cloment,
Jean Mariani, Ryuichi Shigemoto, David A. Digregorio, Rachel M. Sherrard, and
Laurence Cathala. “Developmental Emergence of Two-Stage Nonlinear Synaptic Integration
in Cerebellar Interneurons.” ELife. eLife Sciences Publications, 2021.
https://doi.org/10.7554/eLife.65954.
ieee: C. Biane et al., “Developmental emergence of two-stage nonlinear synaptic
integration in cerebellar interneurons,” eLife, vol. 10. eLife Sciences
Publications, 2021.
ista: Biane C, Rückerl F, Abrahamsson T, Saint-Cloment C, Mariani J, Shigemoto R,
Digregorio DA, Sherrard RM, Cathala L. 2021. Developmental emergence of two-stage
nonlinear synaptic integration in cerebellar interneurons. eLife. 10, e65954.
mla: Biane, Celia, et al. “Developmental Emergence of Two-Stage Nonlinear Synaptic
Integration in Cerebellar Interneurons.” ELife, vol. 10, e65954, eLife
Sciences Publications, 2021, doi:10.7554/eLife.65954.
short: C. Biane, F. Rückerl, T. Abrahamsson, C. Saint-Cloment, J. Mariani, R. Shigemoto,
D.A. Digregorio, R.M. Sherrard, L. Cathala, ELife 10 (2021).
date_created: 2021-12-05T23:01:40Z
date_published: 2021-11-03T00:00:00Z
date_updated: 2025-03-07T08:12:39Z
day: '03'
ddc:
- '570'
department:
- _id: RySh
doi: 10.7554/eLife.65954
external_id:
isi:
- '000715789500001'
pmid:
- '34730085'
file:
- access_level: open_access
checksum: c7c33c3319428d56e332e22349c50ed3
content_type: application/pdf
creator: cchlebak
date_created: 2021-12-10T08:31:41Z
date_updated: 2021-12-10T08:31:41Z
file_id: '10528'
file_name: 2021_eLife_Biane.pdf
file_size: 13131322
relation: main_file
success: 1
file_date_updated: 2021-12-10T08:31:41Z
fulldoi: https://doi.org/10.7554/eLife.65954
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Developmental emergence of two-stage nonlinear synaptic integration in cerebellar
interneurons
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: 10
year: '2021'
...
---
_id: '10404'
abstract:
- lang: eng
text: While convolutional neural networks (CNNs) have found wide adoption as state-of-the-art
models for image-related tasks, their predictions are often highly sensitive to
small input perturbations, which the human vision is robust against. This paper
presents Perturber, a web-based application that allows users to instantaneously
explore how CNN activations and predictions evolve when a 3D input scene is interactively
perturbed. Perturber offers a large variety of scene modifications, such as camera
controls, lighting and shading effects, background modifications, object morphing,
as well as adversarial attacks, to facilitate the discovery of potential vulnerabilities.
Fine-tuned model versions can be directly compared for qualitative evaluation
of their robustness. Case studies with machine learning experts have shown that
Perturber helps users to quickly generate hypotheses about model vulnerabilities
and to qualitatively compare model behavior. Using quantitative analyses, we could
replicate users’ insights with other CNN architectures and input images, yielding
new insights about the vulnerability of adversarially trained models.
acknowledgement: "We thank Robert Geirhos and Roland Zimmermann for their participation
in the case study and valuable feedback, Chris Olah and Nick Cammarata for valuable
discussions in the early phase of the project, as well as the Distill Slack workspace
as a platform for discussions. M.L. is supported in part by the Austrian Science
Fund (FWF) under grant Z211-N23 (Wittgenstein Award). J.B. is supported by the German
Federal Ministry of Education and Research\r\n(BMBF) through the Competence Center
for Machine Learning (TUE.AI, FKZ 01IS18039A) and the International Max Planck Research
School for Intelligent Systems (IMPRS-IS). R.H. is partially supported by Boeing
and Horizon-2020 ECSEL (grant 783163, iDev40).\r\n"
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Stefan
full_name: Sietzen, Stefan
last_name: Sietzen
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Judy
full_name: Borowski, Judy
last_name: Borowski
- first_name: Ramin
full_name: Hasani, Ramin
last_name: Hasani
- first_name: Manuela
full_name: Waldner, Manuela
last_name: Waldner
citation:
ama: Sietzen S, Lechner M, Borowski J, Hasani R, Waldner M. Interactive analysis
of CNN robustness. Computer Graphics Forum. 2021;40(7):253-264. doi:10.1111/cgf.14418
apa: Sietzen, S., Lechner, M., Borowski, J., Hasani, R., & Waldner, M. (2021).
Interactive analysis of CNN robustness. Computer Graphics Forum. Wiley.
https://doi.org/10.1111/cgf.14418
chicago: Sietzen, Stefan, Mathias Lechner, Judy Borowski, Ramin Hasani, and Manuela
Waldner. “Interactive Analysis of CNN Robustness.” Computer Graphics Forum.
Wiley, 2021. https://doi.org/10.1111/cgf.14418.
ieee: S. Sietzen, M. Lechner, J. Borowski, R. Hasani, and M. Waldner, “Interactive
analysis of CNN robustness,” Computer Graphics Forum, vol. 40, no. 7. Wiley,
pp. 253–264, 2021.
ista: Sietzen S, Lechner M, Borowski J, Hasani R, Waldner M. 2021. Interactive analysis
of CNN robustness. Computer Graphics Forum. 40(7), 253–264.
mla: Sietzen, Stefan, et al. “Interactive Analysis of CNN Robustness.” Computer
Graphics Forum, vol. 40, no. 7, Wiley, 2021, pp. 253–64, doi:10.1111/cgf.14418.
short: S. Sietzen, M. Lechner, J. Borowski, R. Hasani, M. Waldner, Computer Graphics
Forum 40 (2021) 253–264.
date_created: 2021-12-05T23:01:40Z
date_published: 2021-11-27T00:00:00Z
date_updated: 2025-04-15T06:25:55Z
day: '27'
department:
- _id: ToHe
doi: 10.1111/cgf.14418
external_id:
arxiv:
- '2110.07667'
isi:
- '000722952000024'
fulldoi: https://doi.org/10.1111/cgf.14418
intvolume: ' 40'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2110.07667
month: '11'
oa: 1
oa_version: Preprint
page: 253-264
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
publication: Computer Graphics Forum
publication_identifier:
eissn:
- 1467-8659
issn:
- 0167-7055
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Interactive analysis of CNN robustness
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 40
year: '2021'
...
---
OA_place: publisher
OA_type: free access
_id: '10406'
abstract:
- lang: eng
text: Multicellular organisms develop complex shapes from much simpler, single-celled
zygotes through a process commonly called morphogenesis. Morphogenesis involves
an interplay between several factors, ranging from the gene regulatory networks
determining cell fate and differentiation to the mechanical processes underlying
cell and tissue shape changes. Thus, the study of morphogenesis has historically
been based on multidisciplinary approaches at the interface of biology with physics
and mathematics. Recent technological advances have further improved our ability
to study morphogenesis by bridging the gap between the genetic and biophysical
factors through the development of new tools for visualizing, analyzing, and perturbing
these factors and their biochemical intermediaries. Here, we review how a combination
of genetic, microscopic, biophysical, and biochemical approaches has aided our
attempts to understand morphogenesis and discuss potential approaches that may
be beneficial to such an inquiry in the future.
acknowledgement: The authors would like to thank Feyza Nur Arslan, Suyash Naik, Diana
Pinheiro, Alexandra Schauer, and Shayan Shamipour for their comments on the draft.
N.M. is supported by an ISTplus postdoctoral fellowship (H2020 Marie-Sklodowska-Curie
COFUND Action).
article_processing_charge: No
article_type: original
author:
- first_name: Nikhil
full_name: Mishra, Nikhil
id: C4D70E82-1081-11EA-B3ED-9A4C3DDC885E
last_name: Mishra
orcid: 0000-0002-6425-5788
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Mishra N, Heisenberg C-PJ. Dissecting organismal morphogenesis by bridging
genetics and biophysics. Annual Review of Genetics. 2021;55:209-233. doi:10.1146/annurev-genet-071819-103748
apa: Mishra, N., & Heisenberg, C.-P. J. (2021). Dissecting organismal morphogenesis
by bridging genetics and biophysics. Annual Review of Genetics. Annual
Reviews. https://doi.org/10.1146/annurev-genet-071819-103748
chicago: Mishra, Nikhil, and Carl-Philipp J Heisenberg. “Dissecting Organismal Morphogenesis
by Bridging Genetics and Biophysics.” Annual Review of Genetics. Annual
Reviews, 2021. https://doi.org/10.1146/annurev-genet-071819-103748.
ieee: N. Mishra and C.-P. J. Heisenberg, “Dissecting organismal morphogenesis by
bridging genetics and biophysics,” Annual Review of Genetics, vol. 55.
Annual Reviews, pp. 209–233, 2021.
ista: Mishra N, Heisenberg C-PJ. 2021. Dissecting organismal morphogenesis by bridging
genetics and biophysics. Annual Review of Genetics. 55, 209–233.
mla: Mishra, Nikhil, and Carl-Philipp J. Heisenberg. “Dissecting Organismal Morphogenesis
by Bridging Genetics and Biophysics.” Annual Review of Genetics, vol. 55,
Annual Reviews, 2021, pp. 209–33, doi:10.1146/annurev-genet-071819-103748.
short: N. Mishra, C.-P.J. Heisenberg, Annual Review of Genetics 55 (2021) 209–233.
corr_author: '1'
date_created: 2021-12-05T23:01:41Z
date_published: 2021-08-30T00:00:00Z
date_updated: 2026-06-18T08:39:48Z
day: '30'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1146/annurev-genet-071819-103748
ec_funded: 1
external_id:
isi:
- '000747220900010'
pmid:
- '34460295'
fulldoi: https://doi.org/10.1146/annurev-genet-071819-103748
intvolume: ' 55'
isi: 1
keyword:
- morphogenesis
- forward genetics
- high-resolution microscopy
- biophysics
- biochemistry
- patterning
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1146/annurev-genet-071819-103748
month: '08'
oa: 1
oa_version: Published Version
page: 209-233
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Annual Review of Genetics
publication_identifier:
eissn:
- 1545-2948
issn:
- 0066-4197
publication_status: published
publisher: Annual Reviews
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dissecting organismal morphogenesis by bridging genetics and biophysics
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2021'
...
---
_id: '10407'
abstract:
- lang: eng
text: Digital hardware Trojans are integrated circuits whose implementation differ
from the specification in an arbitrary and malicious way. For example, the circuit
can differ from its specified input/output behavior after some fixed number of
queries (known as “time bombs”) or on some particular input (known as “cheat codes”).
To detect such Trojans, countermeasures using multiparty computation (MPC) or
verifiable computation (VC) have been proposed. On a high level, to realize a
circuit with specification F one has more sophisticated circuits F⋄ manufactured
(where F⋄ specifies a MPC or VC of F ), and then embeds these F⋄ ’s into
a master circuit which must be trusted but is relatively simple compared to F
. Those solutions impose a significant overhead as F⋄ is much more complex
than F , also the master circuits are not exactly trivial. In this work, we
show that in restricted settings, where F has no evolving state and is queried
on independent inputs, we can achieve a relaxed security notion using very simple
constructions. In particular, we do not change the specification of the circuit
at all (i.e., F=F⋄ ). Moreover the master circuit basically just queries a subset
of its manufactured circuits and checks if they’re all the same. The security
we achieve guarantees that, if the manufactured circuits are initially tested
on up to T inputs, the master circuit will catch Trojans that try to deviate on
significantly more than a 1/T fraction of the inputs. This bound is optimal for
the type of construction considered, and we provably achieve it using a construction
where 12 instantiations of F need to be embedded into the master. We also discuss
an extremely simple construction with just 2 instantiations for which we conjecture
that it already achieves the optimal bound.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Suvradip
full_name: Chakraborty, Suvradip
id: B9CD0494-D033-11E9-B219-A439E6697425
last_name: Chakraborty
- first_name: Stefan
full_name: Dziembowski, Stefan
last_name: Dziembowski
- first_name: Małgorzata
full_name: Gałązka, Małgorzata
last_name: Gałązka
- first_name: Tomasz
full_name: Lizurej, Tomasz
last_name: Lizurej
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Michelle X
full_name: Yeo, Michelle X
id: 2D82B818-F248-11E8-B48F-1D18A9856A87
last_name: Yeo
orcid: 0009-0001-3676-4809
citation:
ama: 'Chakraborty S, Dziembowski S, Gałązka M, Lizurej T, Pietrzak KZ, Yeo MX. Trojan-resilience
without cryptography. In: Vol 13043. Springer Nature; 2021:397-428. doi:10.1007/978-3-030-90453-1_14'
apa: 'Chakraborty, S., Dziembowski, S., Gałązka, M., Lizurej, T., Pietrzak, K. Z.,
& Yeo, M. X. (2021). Trojan-resilience without cryptography (Vol. 13043, pp.
397–428). Presented at the TCC: Theory of Cryptography Conference, Raleigh, NC,
United States: Springer Nature. https://doi.org/10.1007/978-3-030-90453-1_14'
chicago: Chakraborty, Suvradip, Stefan Dziembowski, Małgorzata Gałązka, Tomasz Lizurej,
Krzysztof Z Pietrzak, and Michelle X Yeo. “Trojan-Resilience without Cryptography,”
13043:397–428. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-90453-1_14.
ieee: 'S. Chakraborty, S. Dziembowski, M. Gałązka, T. Lizurej, K. Z. Pietrzak, and
M. X. Yeo, “Trojan-resilience without cryptography,” presented at the TCC: Theory
of Cryptography Conference, Raleigh, NC, United States, 2021, vol. 13043, pp.
397–428.'
ista: 'Chakraborty S, Dziembowski S, Gałązka M, Lizurej T, Pietrzak KZ, Yeo MX.
2021. Trojan-resilience without cryptography. TCC: Theory of Cryptography Conference,
LNCS, vol. 13043, 397–428.'
mla: Chakraborty, Suvradip, et al. Trojan-Resilience without Cryptography.
Vol. 13043, Springer Nature, 2021, pp. 397–428, doi:10.1007/978-3-030-90453-1_14.
short: S. Chakraborty, S. Dziembowski, M. Gałązka, T. Lizurej, K.Z. Pietrzak, M.X.
Yeo, in:, Springer Nature, 2021, pp. 397–428.
conference:
end_date: 2021-11-11
location: Raleigh, NC, United States
name: 'TCC: Theory of Cryptography Conference'
start_date: 2021-11-08
date_created: 2021-12-05T23:01:42Z
date_published: 2021-11-04T00:00:00Z
date_updated: 2025-04-14T07:22:05Z
day: '04'
department:
- _id: KrPi
doi: 10.1007/978-3-030-90453-1_14
ec_funded: 1
external_id:
isi:
- '000728364000014'
fulldoi: https://doi.org/10.1007/978-3-030-90453-1_14
intvolume: ' 13043'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2021/1224
month: '11'
oa: 1
oa_version: Preprint
page: 397-428
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_identifier:
eissn:
- 1611-3349
isbn:
- 9-783-0309-0452-4
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Trojan-resilience without cryptography
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13043
year: '2021'
...
---
_id: '10414'
abstract:
- lang: eng
text: 'We consider the almost-sure (a.s.) termination problem for probabilistic
programs, which are a stochastic extension of classical imperative programs. Lexicographic
ranking functions provide a sound and practical approach for termination of non-probabilistic
programs, and their extension to probabilistic programs is achieved via lexicographic
ranking supermartingales (LexRSMs). However, LexRSMs introduced in the previous
work have a limitation that impedes their automation: all of their components
have to be non-negative in all reachable states. This might result in LexRSM not
existing even for simple terminating programs. Our contributions are twofold:
First, we introduce a generalization of LexRSMs which allows for some components
to be negative. This standard feature of non-probabilistic termination proofs
was hitherto not known to be sound in the probabilistic setting, as the soundness
proof requires a careful analysis of the underlying stochastic process. Second,
we present polynomial-time algorithms using our generalized LexRSMs for proving
a.s. termination in broad classes of linear-arithmetic programs.'
acknowledgement: This research was partially supported by the ERC CoG 863818 (ForM-SMArt),
the Czech Science Foundation grant No. GJ19-15134Y, and the European Union’s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement
No. 665385.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Ehsan
full_name: Kafshdar Goharshadi, Ehsan
id: 103b4fa0-896a-11ed-bdf8-87b697bef40d
last_name: Kafshdar Goharshadi
orcid: 0000-0002-8595-0587
- first_name: Petr
full_name: Novotný, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotný
- first_name: Jiří
full_name: Zárevúcky, Jiří
last_name: Zárevúcky
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
citation:
ama: 'Chatterjee K, Goharshady E, Novotný P, Zárevúcky J, Zikelic D. On lexicographic
proof rules for probabilistic termination. In: 24th International Symposium
on Formal Methods. Vol 13047. Springer Nature; 2021:619-639. doi:10.1007/978-3-030-90870-6_33'
apa: 'Chatterjee, K., Goharshady, E., Novotný, P., Zárevúcky, J., & Zikelic,
D. (2021). On lexicographic proof rules for probabilistic termination. In 24th
International Symposium on Formal Methods (Vol. 13047, pp. 619–639). Virtual:
Springer Nature. https://doi.org/10.1007/978-3-030-90870-6_33'
chicago: Chatterjee, Krishnendu, Ehsan Goharshady, Petr Novotný, Jiří Zárevúcky,
and Dorde Zikelic. “On Lexicographic Proof Rules for Probabilistic Termination.”
In 24th International Symposium on Formal Methods, 13047:619–39. Springer
Nature, 2021. https://doi.org/10.1007/978-3-030-90870-6_33.
ieee: K. Chatterjee, E. Goharshady, P. Novotný, J. Zárevúcky, and D. Zikelic, “On
lexicographic proof rules for probabilistic termination,” in 24th International
Symposium on Formal Methods, Virtual, 2021, vol. 13047, pp. 619–639.
ista: 'Chatterjee K, Goharshady E, Novotný P, Zárevúcky J, Zikelic D. 2021. On lexicographic
proof rules for probabilistic termination. 24th International Symposium on Formal
Methods. FM: Formal Methods, LNCS, vol. 13047, 619–639.'
mla: Chatterjee, Krishnendu, et al. “On Lexicographic Proof Rules for Probabilistic
Termination.” 24th International Symposium on Formal Methods, vol. 13047,
Springer Nature, 2021, pp. 619–39, doi:10.1007/978-3-030-90870-6_33.
short: K. Chatterjee, E. Goharshady, P. Novotný, J. Zárevúcky, D. Zikelic, in:,
24th International Symposium on Formal Methods, Springer Nature, 2021, pp. 619–639.
conference:
end_date: 2021-11-26
location: Virtual
name: 'FM: Formal Methods'
start_date: 2021-11-20
date_created: 2021-12-05T23:01:45Z
date_published: 2021-11-10T00:00:00Z
date_updated: 2026-04-07T13:27:55Z
day: '10'
department:
- _id: KrCh
doi: 10.1007/978-3-030-90870-6_33
ec_funded: 1
external_id:
arxiv:
- '2108.02188'
isi:
- '000758218600033'
fulldoi: https://doi.org/10.1007/978-3-030-90870-6_33
intvolume: ' 13047'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2108.02188
month: '11'
oa: 1
oa_version: Preprint
page: 619-639
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: 24th International Symposium on Formal Methods
publication_identifier:
eisbn:
- 978-3-030-90870-6
eissn:
- 1611-3349
isbn:
- 9-783-0309-0869-0
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '14778'
relation: later_version
status: public
- id: '14539'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: On lexicographic proof rules for probabilistic termination
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13047
year: '2021'
...
---
_id: '10415'
abstract:
- lang: eng
text: The Hardy–Littlewood circle method was invented over a century ago to study
integer solutions to special Diophantine equations, but it has since proven to
be one of the most successful all-purpose tools available to number theorists.
Not only is it capable of handling remarkably general systems of polynomial equations
defined over arbitrary global fields, but it can also shed light on the space
of rational curves that lie on algebraic varieties. This book, in which the arithmetic
of cubic polynomials takes centre stage, is aimed at bringing beginning graduate
students into contact with some of the many facets of the circle method, both
classical and modern. This monograph is the winner of the 2021 Ferran Sunyer i
Balaguer Prize, a prestigious award for books of expository nature presenting
the latest developments in an active area of research in mathematics.
alternative_title:
- Progress in Mathematics
article_processing_charge: No
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
citation:
ama: 'Browning TD. Cubic Forms and the Circle Method. Vol 343. Cham: Springer
Nature; 2021. doi:10.1007/978-3-030-86872-7'
apa: 'Browning, T. D. (2021). Cubic Forms and the Circle Method (Vol. 343).
Cham: Springer Nature. https://doi.org/10.1007/978-3-030-86872-7'
chicago: 'Browning, Timothy D. Cubic Forms and the Circle Method. Vol. 343.
Cham: Springer Nature, 2021. https://doi.org/10.1007/978-3-030-86872-7.'
ieee: 'T. D. Browning, Cubic Forms and the Circle Method, vol. 343. Cham:
Springer Nature, 2021.'
ista: 'Browning TD. 2021. Cubic Forms and the Circle Method, Cham: Springer Nature,
XIV, 166p.'
mla: Browning, Timothy D. Cubic Forms and the Circle Method. Vol. 343, Springer
Nature, 2021, doi:10.1007/978-3-030-86872-7.
short: T.D. Browning, Cubic Forms and the Circle Method, Springer Nature, Cham,
2021.
corr_author: '1'
date_created: 2021-12-05T23:01:46Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2024-10-09T21:01:16Z
day: '01'
department:
- _id: TiBr
doi: 10.1007/978-3-030-86872-7
fulldoi: https://doi.org/10.1007/978-3-030-86872-7
intvolume: ' 343'
language:
- iso: eng
month: '12'
oa_version: None
page: XIV, 166
place: Cham
publication_identifier:
eisbn:
- 978-3-030-86872-7
eissn:
- 2296-505X
isbn:
- 978-3-030-86871-0
issn:
- 0743-1643
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cubic Forms and the Circle Method
type: book
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 343
year: '2021'
...
---
OA_place: publisher
_id: '10422'
abstract:
- lang: eng
text: Those who aim to devise new materials with desirable properties usually examine
present methods first. However, they will find out that some approaches can exist
only conceptually without high chances to become practically useful. It seems
that a numerical technique called automatic differentiation together with increasing
supply of computational accelerators will soon shift many methods of the material
design from the category ”unimaginable” to the category ”expensive but possible”.
Approach we suggest is not an exception. Our overall goal is to have an efficient
and generalizable approach allowing to solve inverse design problems. In this
thesis we scratch its surface. We consider jammed systems of identical particles.
And ask ourselves how the shape of those particles (or the parameters codifying
it) may affect mechanical properties of the system. An indispensable part of reaching
the answer is an appropriate particle parametrization. We come up with a simple,
yet generalizable and purposeful scheme for it. Using our generalizable shape
parameterization, we simulate the formation of a solid composed of pentagonal-like
particles and measure anisotropy in the resulting elastic response. Through automatic
differentiation techniques, we directly connect the shape parameters with the
elastic response. Interestingly, for our system we find that less isotropic particles
lead to a more isotropic elastic response. Together with other results known about
our method it seems that it can be successfully generalized for different inverse
design problems.
alternative_title:
- ISTA Master's Thesis
article_processing_charge: No
author:
- first_name: Anton
full_name: Piankov, Anton
id: 865E3C26-AA8C-11E9-A409-C4C4E5697425
last_name: Piankov
citation:
ama: Piankov A. Towards designer materials using customizable particle shape. 2021.
doi:10.15479/at:ista:10422
apa: Piankov, A. (2021). Towards designer materials using customizable particle
shape. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10422
chicago: Piankov, Anton. “Towards Designer Materials Using Customizable Particle
Shape.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10422.
ieee: A. Piankov, “Towards designer materials using customizable particle shape,”
Institute of Science and Technology Austria, 2021.
ista: Piankov A. 2021. Towards designer materials using customizable particle shape.
Institute of Science and Technology Austria.
mla: Piankov, Anton. Towards Designer Materials Using Customizable Particle Shape.
Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10422.
short: A. Piankov, Towards Designer Materials Using Customizable Particle Shape,
Institute of Science and Technology Austria, 2021.
corr_author: '1'
date_created: 2021-12-07T10:48:06Z
date_published: 2021-12-07T00:00:00Z
date_updated: 2026-04-08T06:58:55Z
day: '07'
ddc:
- '530'
degree_awarded: MS
department:
- _id: GradSch
- _id: CaGo
doi: 10.15479/at:ista:10422
file:
- access_level: closed
checksum: 114e8f4b2c002c6c352416c12de2c695
content_type: application/x-zip-compressed
creator: cchlebak
date_created: 2021-12-07T11:13:52Z
date_updated: 2022-03-10T12:10:25Z
file_id: '10424'
file_name: Thesis.zip
file_size: 394018
relation: source_file
- access_level: closed
checksum: cd15ae991ced352a9959815f794e657c
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: cchlebak
date_created: 2021-12-07T11:14:01Z
date_updated: 2022-03-10T12:10:25Z
file_id: '10425'
file_name: Preliminary_pages_Piankov.docx
file_size: 47638
relation: source_file
- access_level: open_access
checksum: e6899c798b75ba42fab9822bce309050
content_type: application/pdf
creator: cchlebak
date_created: 2021-12-07T11:20:35Z
date_updated: 2021-12-07T11:20:35Z
file_id: '10426'
file_name: 2021_Piankov_combined.pdf
file_size: 484965
relation: main_file
success: 1
file_date_updated: 2022-03-10T12:10:25Z
fulldoi: https://doi.org/10.15479/at:ista:10422
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication_identifier:
issn:
- 2791-4585
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
title: Towards designer materials using customizable particle shape
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2021'
...
---
_id: '10435'
abstract:
- lang: eng
text: Decentralized optimization is emerging as a viable alternative for scalable
distributed machine learning, but also introduces new challenges in terms of synchronization
costs. To this end, several communication-reduction techniques, such as non-blocking
communication, quantization, and local steps, have been explored in the decentralized
setting. Due to the complexity of analyzing optimization in such a relaxed setting,
this line of work often assumes \emph{global} communication rounds, which require
additional synchronization. In this paper, we consider decentralized optimization
in the simpler, but harder to analyze, \emph{asynchronous gossip} model, in which
communication occurs in discrete, randomly chosen pairings among nodes. Perhaps
surprisingly, we show that a variant of SGD called \emph{SwarmSGD} still converges
in this setting, even if \emph{non-blocking communication}, \emph{quantization},
and \emph{local steps} are all applied \emph{in conjunction}, and even if the
node data distributions and underlying graph topology are both \emph{heterogenous}.
Our analysis is based on a new connection with multi-dimensional load-balancing
processes. We implement this algorithm and deploy it in a super-computing environment,
showing that it can outperform previous decentralized methods in terms of end-to-end
training time, and that it can even rival carefully-tuned large-batch SGD for
certain tasks.
acknowledgement: "We gratefully acknowledge funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreement No 805223 ScaleML). PD partly conducted this work while at IST
Austria and was supported by the European Union’s Horizon 2020 programme under the
Marie Skłodowska-Curie grant agreement No. 754411. SL was funded in part by European
Research Council (ERC) under the European Union’s Horizon 2020 programme (grant
agreement DAPP, No. 678880, and EPiGRAM-HS, No. 801039).\r\n"
article_processing_charge: No
arxiv: 1
author:
- first_name: Giorgi
full_name: Nadiradze, Giorgi
id: 3279A00C-F248-11E8-B48F-1D18A9856A87
last_name: Nadiradze
orcid: 0000-0001-5634-0731
- first_name: Amirmojtaba
full_name: Sabour, Amirmojtaba
id: bcc145fd-e77f-11ea-ae8b-80d661dbff67
last_name: Sabour
- first_name: Peter
full_name: Davies, Peter
id: 11396234-BB50-11E9-B24C-90FCE5697425
last_name: Davies
orcid: 0000-0002-5646-9524
- first_name: Shigang
full_name: Li, Shigang
last_name: Li
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Nadiradze G, Sabour A, Davies P, Li S, Alistarh D-A. Asynchronous decentralized
SGD with quantized and local updates. In: 35th Conference on Neural Information
Processing Systems. Neural Information Processing Systems Foundation; 2021.'
apa: 'Nadiradze, G., Sabour, A., Davies, P., Li, S., & Alistarh, D.-A. (2021).
Asynchronous decentralized SGD with quantized and local updates. In 35th Conference
on Neural Information Processing Systems. Sydney, Australia: Neural Information
Processing Systems Foundation.'
chicago: Nadiradze, Giorgi, Amirmojtaba Sabour, Peter Davies, Shigang Li, and Dan-Adrian
Alistarh. “Asynchronous Decentralized SGD with Quantized and Local Updates.” In
35th Conference on Neural Information Processing Systems. Neural Information
Processing Systems Foundation, 2021.
ieee: G. Nadiradze, A. Sabour, P. Davies, S. Li, and D.-A. Alistarh, “Asynchronous
decentralized SGD with quantized and local updates,” in 35th Conference on
Neural Information Processing Systems, Sydney, Australia, 2021.
ista: 'Nadiradze G, Sabour A, Davies P, Li S, Alistarh D-A. 2021. Asynchronous decentralized
SGD with quantized and local updates. 35th Conference on Neural Information Processing
Systems. NeurIPS: Neural Information Processing Systems.'
mla: Nadiradze, Giorgi, et al. “Asynchronous Decentralized SGD with Quantized and
Local Updates.” 35th Conference on Neural Information Processing Systems,
Neural Information Processing Systems Foundation, 2021.
short: G. Nadiradze, A. Sabour, P. Davies, S. Li, D.-A. Alistarh, in:, 35th Conference
on Neural Information Processing Systems, Neural Information Processing Systems
Foundation, 2021.
conference:
end_date: 2021-12-14
location: Sydney, Australia
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2021-12-06
date_created: 2021-12-09T10:59:12Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2026-06-18T08:41:40Z
day: '01'
ddc:
- '000'
department:
- _id: DaAl
ec_funded: 1
external_id:
arxiv:
- '1910.12308'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://papers.nips.cc/paper/2021/hash/362c99307cdc3f2d8b410652386a9dd1-Abstract.html
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: 35th Conference on Neural Information Processing Systems
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
related_material:
record:
- id: '10429'
relation: dissertation_contains
status: public
status: public
title: Asynchronous decentralized SGD with quantized and local updates
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '10527'
abstract:
- lang: eng
text: We show that in a two-dimensional electron gas with an annular Fermi surface,
long-range Coulomb interactions can lead to unconventional superconductivity by
the Kohn-Luttinger mechanism. Superconductivity is strongly enhanced when the
inner and outer Fermi surfaces are close to each other. The most prevalent state
has chiral p-wave symmetry, but d-wave and extended s-wave pairing are also possible.
We discuss these results in the context of rhombohedral trilayer graphene, where
superconductivity was recently discovered in regimes where the normal state has
an annular Fermi surface. Using realistic parameters, our mechanism can account
for the order of magnitude of Tc, as well as its trends as a function of electron
density and perpendicular displacement field. Moreover, it naturally explains
some of the outstanding puzzles in this material, that include the weak temperature
dependence of the resistivity above Tc, and the proximity of spin singlet superconductivity
to the ferromagnetic phase.
acknowledgement: We thank Yang-Zhi Chou, Andrey Chubukov, Johannes Hofmann, Steve
Kivelson, Sri Raghu, and Sankar das Sarma, Jay Sau, Fengcheng Wu, and Andrea Young
for many stimulating discussions and for their comments on the manuscript. E.B.
thanks S. Chatterjee, T. Wang, and M. Zaletel for a collaboration on a related topic.
A.G. acknowledges support by the European Unions Horizon 2020 research and innovation
program under the Marie Sklodowska-Curie Grant Agreement No. 754411. E.B. and T.H.
were supported by the European Research Council (ERC) under grant HQMAT (Grant Agreement
No. 817799), by the Israel-USA Binational Science Foundation (BSF), and by a Research
grant from Irving and Cherna Moskowitz.
article_number: '247001'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: Tobias
full_name: Holder, Tobias
last_name: Holder
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Erez
full_name: Berg, Erez
last_name: Berg
citation:
ama: 'Ghazaryan A, Holder T, Serbyn M, Berg E. Unconventional superconductivity
in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene.
Physical Review Letters. 2021;127(24). doi:10.1103/physrevlett.127.247001'
apa: 'Ghazaryan, A., Holder, T., Serbyn, M., & Berg, E. (2021). Unconventional
superconductivity in systems with annular Fermi surfaces: Application to rhombohedral
trilayer graphene. Physical Review Letters. American Physical Society.
https://doi.org/10.1103/physrevlett.127.247001'
chicago: 'Ghazaryan, Areg, Tobias Holder, Maksym Serbyn, and Erez Berg. “Unconventional
Superconductivity in Systems with Annular Fermi Surfaces: Application to Rhombohedral
Trilayer Graphene.” Physical Review Letters. American Physical Society,
2021. https://doi.org/10.1103/physrevlett.127.247001.'
ieee: 'A. Ghazaryan, T. Holder, M. Serbyn, and E. Berg, “Unconventional superconductivity
in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene,”
Physical Review Letters, vol. 127, no. 24. American Physical Society, 2021.'
ista: 'Ghazaryan A, Holder T, Serbyn M, Berg E. 2021. Unconventional superconductivity
in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene.
Physical Review Letters. 127(24), 247001.'
mla: 'Ghazaryan, Areg, et al. “Unconventional Superconductivity in Systems with
Annular Fermi Surfaces: Application to Rhombohedral Trilayer Graphene.” Physical
Review Letters, vol. 127, no. 24, 247001, American Physical Society, 2021,
doi:10.1103/physrevlett.127.247001.'
short: A. Ghazaryan, T. Holder, M. Serbyn, E. Berg, Physical Review Letters 127
(2021).
date_created: 2021-12-10T07:51:33Z
date_published: 2021-12-09T00:00:00Z
date_updated: 2025-04-14T07:43:47Z
day: '09'
department:
- _id: MaSe
doi: 10.1103/physrevlett.127.247001
ec_funded: 1
external_id:
arxiv:
- '2109.00011'
isi:
- '000923819400004'
fulldoi: https://doi.org/10.1103/physrevlett.127.247001
intvolume: ' 127'
isi: 1
issue: '24'
keyword:
- general physics and astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2109.00011
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
link:
- description: News on IST Webpage
relation: press_release
url: https://ist.ac.at/en/news/resolving-the-puzzles-of-graphene-superconductivity/
scopus_import: '1'
status: public
title: 'Unconventional superconductivity in systems with annular Fermi surfaces: Application
to rhombohedral trilayer graphene'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 127
year: '2021'
...
---
_id: '10533'
abstract:
- lang: eng
text: Flowering plants utilize small RNA molecules to guide DNA methyltransferases
to genomic sequences. This RNA-directed DNA methylation (RdDM) pathway preferentially
targets euchromatic transposable elements. However, RdDM is thought to be recruited
by methylation of histone H3 at lysine 9 (H3K9me), a hallmark of heterochromatin.
How RdDM is targeted to euchromatin despite an affinity for H3K9me is unclear.
Here we show that loss of histone H1 enhances heterochromatic RdDM, preferentially
at nucleosome linker DNA. Surprisingly, this does not require SHH1, the RdDM component
that binds H3K9me. Furthermore, H3K9me is dispensable for RdDM, as is CG DNA methylation.
Instead, we find that non-CG methylation is specifically associated with small
RNA biogenesis, and without H1 small RNA production quantitatively expands to
non-CG methylated loci. Our results demonstrate that H1 enforces the separation
of euchromatic and heterochromatic DNA methylation pathways by excluding the small
RNA-generating branch of RdDM from non-CG methylated heterochromatin.
acknowledgement: We thank X Feng for helpful comments on the manuscript. This work
was supported by a European Research Council grant MaintainMeth (725746) to DZ.
article_number: e72676
article_processing_charge: No
article_type: original
author:
- first_name: Jaemyung
full_name: Choi, Jaemyung
last_name: Choi
- first_name: David B
full_name: Lyons, David B
last_name: Lyons
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Choi J, Lyons DB, Zilberman D. Histone H1 prevents non-CG methylation-mediated
small RNA biogenesis in Arabidopsis heterochromatin. eLife. 2021;10. doi:10.7554/elife.72676
apa: Choi, J., Lyons, D. B., & Zilberman, D. (2021). Histone H1 prevents non-CG
methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. ELife.
eLife Sciences Publications. https://doi.org/10.7554/elife.72676
chicago: Choi, Jaemyung, David B Lyons, and Daniel Zilberman. “Histone H1 Prevents
Non-CG Methylation-Mediated Small RNA Biogenesis in Arabidopsis Heterochromatin.”
ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.72676.
ieee: J. Choi, D. B. Lyons, and D. Zilberman, “Histone H1 prevents non-CG methylation-mediated
small RNA biogenesis in Arabidopsis heterochromatin,” eLife, vol. 10. eLife
Sciences Publications, 2021.
ista: Choi J, Lyons DB, Zilberman D. 2021. Histone H1 prevents non-CG methylation-mediated
small RNA biogenesis in Arabidopsis heterochromatin. eLife. 10, e72676.
mla: Choi, Jaemyung, et al. “Histone H1 Prevents Non-CG Methylation-Mediated Small
RNA Biogenesis in Arabidopsis Heterochromatin.” ELife, vol. 10, e72676,
eLife Sciences Publications, 2021, doi:10.7554/elife.72676.
short: J. Choi, D.B. Lyons, D. Zilberman, ELife 10 (2021).
corr_author: '1'
date_created: 2021-12-10T13:12:08Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2025-04-14T07:57:42Z
day: '01'
ddc:
- '570'
department:
- _id: DaZi
doi: 10.7554/elife.72676
ec_funded: 1
external_id:
isi:
- '000754832000001'
pmid:
- '34850679'
file:
- access_level: open_access
checksum: 22ed4c55fb550f6da02ae55c359be651
content_type: application/pdf
creator: dernst
date_created: 2022-05-16T10:42:22Z
date_updated: 2022-05-16T10:42:22Z
file_id: '11384'
file_name: 2021_eLife_Choi.pdf
file_size: 2715200
relation: main_file
success: 1
file_date_updated: 2022-05-16T10:42:22Z
fulldoi: https://doi.org/10.7554/elife.72676
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
keyword:
- genetics and molecular biology
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 62935a00-2b32-11ec-9570-eff30fa39068
call_identifier: H2020
grant_number: '725746'
name: Quantitative analysis of DNA methylation maintenance with chromatin
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis
heterochromatin
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: 10
year: '2021'
...
---
_id: '10534'
abstract:
- lang: eng
text: For many years, fullerene derivatives have been the main n-type material of
organic electronics and optoelectronics. Recently, fullerene derivatives functionalized
with ethylene glycol (EG) side chains have been showing important properties such
as enhanced dielectric constants, facile doping and enhanced self-assembly capabilities.
Here, we have prepared field-effect transistors using a series of these fullerene
derivatives equipped with EG side chains of different lengths. Transport data
show the beneficial effect of increasing the EG side chain. In order to understand
the material properties, full structural determination of these fullerene derivatives
has been achieved by coupling the X-ray data with molecular dynamics (MD) simulations.
The increase in transport properties is paired with the formation of extended
layered structures, efficient molecular packing and an increase in the crystallite
alignment. The layer-like structure is composed of conducting layers, containing
of closely packed C60 balls approaching the inter-distance of 1 nm, that are separated
by well-defined EG layers, where the EG chains are rather splayed with the chain
direction almost perpendicular to the layer normal. Such a layered structure appears
highly ordered and highly aligned with the C60 planes oriented parallel to the
substrate in the thin film configuration. The order inside the thin film increases
with the EG chain length, allowing the systems to achieve mobilities as high as
0.053 cm2 V−1 s−1. Our work elucidates the structure of these interesting semiconducting
organic molecules and shows that the synergistic use of X-ray structural analysis
and MD simulations is a powerful tool to identify the structure of thin organic
films for optoelectronic applications.
acknowledgement: J. D. gratefully acknowledges the China Scholarship Council (CSC
No. 201606340158) for supporting his PhD studies. S. S. thanks J. Antoja-Lleonart
for insightful discussions on simulating the X-ray diffraction patterns. Part of
the work was sponsored by NWO Exact and Natural Sciences for the use of supercomputer
facilities (Contract no. 17197 7095). Regarding S. S., R. A., R. W. A. H., J. C.
H., and M. A. L., this is a publication by the FOM Focus Group “Next Generation
Organic Photovoltaics”, participating in the Dutch Institute for Fundamental Energy
Research (DIFFER). The ESRF is acknowledged for providing the beamtime. J. D. and
G. P. are grateful to the BM26B staff for their great support during the beamtime.
M. A. L., D. M. B. are grateful for the financial support of the European Research
Council via a Starting Grant (HySPOD, No. 306983).
article_processing_charge: No
article_type: original
author:
- first_name: Jingjin
full_name: Dong, Jingjin
last_name: Dong
- first_name: Selim
full_name: Sami, Selim
last_name: Sami
- first_name: Daniel
full_name: Balazs, Daniel
id: 302BADF6-85FC-11EA-9E3B-B9493DDC885E
last_name: Balazs
orcid: 0000-0001-7597-043X
- first_name: Riccardo
full_name: Alessandri, Riccardo
last_name: Alessandri
- first_name: Fatimeh
full_name: Jahani, Fatimeh
last_name: Jahani
- first_name: Li
full_name: Qiu, Li
last_name: Qiu
- first_name: Siewert J.
full_name: Marrink, Siewert J.
last_name: Marrink
- first_name: Remco W.A.
full_name: Havenith, Remco W.A.
last_name: Havenith
- first_name: Jan C.
full_name: Hummelen, Jan C.
last_name: Hummelen
- first_name: Maria A.
full_name: Loi, Maria A.
last_name: Loi
- first_name: Giuseppe
full_name: Portale, Giuseppe
last_name: Portale
citation:
ama: 'Dong J, Sami S, Balazs D, et al. Fullerene derivatives with oligoethylene-glycol
side chains: An investigation on the origin of their outstanding transport properties.
Journal of Materials Chemistry C. 2021;9(45):16217-16225. doi:10.1039/d1tc02753k'
apa: 'Dong, J., Sami, S., Balazs, D., Alessandri, R., Jahani, F., Qiu, L., … Portale,
G. (2021). Fullerene derivatives with oligoethylene-glycol side chains: An investigation
on the origin of their outstanding transport properties. Journal of Materials
Chemistry C. Royal Society of Chemistry. https://doi.org/10.1039/d1tc02753k'
chicago: 'Dong, Jingjin, Selim Sami, Daniel Balazs, Riccardo Alessandri, Fatimeh
Jahani, Li Qiu, Siewert J. Marrink, et al. “Fullerene Derivatives with Oligoethylene-Glycol
Side Chains: An Investigation on the Origin of Their Outstanding Transport Properties.”
Journal of Materials Chemistry C. Royal Society of Chemistry, 2021. https://doi.org/10.1039/d1tc02753k.'
ieee: 'J. Dong et al., “Fullerene derivatives with oligoethylene-glycol side
chains: An investigation on the origin of their outstanding transport properties,”
Journal of Materials Chemistry C, vol. 9, no. 45. Royal Society of Chemistry,
pp. 16217–16225, 2021.'
ista: 'Dong J, Sami S, Balazs D, Alessandri R, Jahani F, Qiu L, Marrink SJ, Havenith
RWA, Hummelen JC, Loi MA, Portale G. 2021. Fullerene derivatives with oligoethylene-glycol
side chains: An investigation on the origin of their outstanding transport properties.
Journal of Materials Chemistry C. 9(45), 16217–16225.'
mla: 'Dong, Jingjin, et al. “Fullerene Derivatives with Oligoethylene-Glycol Side
Chains: An Investigation on the Origin of Their Outstanding Transport Properties.”
Journal of Materials Chemistry C, vol. 9, no. 45, Royal Society of Chemistry,
2021, pp. 16217–25, doi:10.1039/d1tc02753k.'
short: J. Dong, S. Sami, D. Balazs, R. Alessandri, F. Jahani, L. Qiu, S.J. Marrink,
R.W.A. Havenith, J.C. Hummelen, M.A. Loi, G. Portale, Journal of Materials Chemistry
C 9 (2021) 16217–16225.
date_created: 2021-12-12T23:01:27Z
date_published: 2021-12-07T00:00:00Z
date_updated: 2023-08-17T06:18:44Z
day: '07'
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doi: 10.1039/d1tc02753k
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issue: '45'
language:
- iso: eng
month: '12'
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oa_version: Published Version
page: 16217-16225
publication: Journal of Materials Chemistry C
publication_identifier:
eissn:
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issn:
- 2050-7534
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
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title: 'Fullerene derivatives with oligoethylene-glycol side chains: An investigation
on the origin of their outstanding transport properties'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
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...
---
_id: '10535'
abstract:
- lang: eng
text: Realistic models of biological processes typically involve interacting components
on multiple scales, driven by changing environment and inherent stochasticity.
Such models are often analytically and numerically intractable. We revisit a dynamic
maximum entropy method that combines a static maximum entropy with a quasi-stationary
approximation. This allows us to reduce stochastic non-equilibrium dynamics expressed
by the Fokker-Planck equation to a simpler low-dimensional deterministic dynamics,
without the need to track microscopic details. Although the method has been previously
applied to a few (rather complicated) applications in population genetics, our
main goal here is to explain and to better understand how the method works. We
demonstrate the usefulness of the method for two widely studied stochastic problems,
highlighting its accuracy in capturing important macroscopic quantities even in
rapidly changing non-stationary conditions. For the Ornstein-Uhlenbeck process,
the method recovers the exact dynamics whilst for a stochastic island model with
migration from other habitats, the approximation retains high macroscopic accuracy
under a wide range of scenarios in a dynamic environment.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "Computational resources for the study were provided by the Institute
of Science and Technology, Austria.\r\nKB received funding from the Scientific Grant
Agency of the Slovak Republic under the Grants Nos. 1/0755/19 and 1/0521/20."
article_number: e1009661
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Katarína
full_name: Bod'ová, Katarína
id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87
last_name: Bod'ová
orcid: 0000-0002-7214-0171
- first_name: Eniko
full_name: Szep, Eniko
id: 485BB5A4-F248-11E8-B48F-1D18A9856A87
last_name: Szep
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Bodova K, Szep E, Barton NH. Dynamic maximum entropy provides accurate approximation
of structured population dynamics. PLoS Computational Biology. 2021;17(12).
doi:10.1371/journal.pcbi.1009661
apa: Bodova, K., Szep, E., & Barton, N. H. (2021). Dynamic maximum entropy provides
accurate approximation of structured population dynamics. PLoS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1009661
chicago: Bodova, Katarina, Eniko Szep, and Nicholas H Barton. “Dynamic Maximum Entropy
Provides Accurate Approximation of Structured Population Dynamics.” PLoS Computational
Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1009661.
ieee: K. Bodova, E. Szep, and N. H. Barton, “Dynamic maximum entropy provides accurate
approximation of structured population dynamics,” PLoS Computational Biology,
vol. 17, no. 12. Public Library of Science, 2021.
ista: Bodova K, Szep E, Barton NH. 2021. Dynamic maximum entropy provides accurate
approximation of structured population dynamics. PLoS Computational Biology. 17(12),
e1009661.
mla: Bodova, Katarina, et al. “Dynamic Maximum Entropy Provides Accurate Approximation
of Structured Population Dynamics.” PLoS Computational Biology, vol. 17,
no. 12, e1009661, Public Library of Science, 2021, doi:10.1371/journal.pcbi.1009661.
short: K. Bodova, E. Szep, N.H. Barton, PLoS Computational Biology 17 (2021).
corr_author: '1'
date_created: 2021-12-12T23:01:27Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2024-10-09T21:01:16Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1371/journal.pcbi.1009661
external_id:
arxiv:
- '2102.03669'
pmid:
- '34851948'
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checksum: dcd185d4f7e0acee25edf1d6537f447e
content_type: application/pdf
creator: dernst
date_created: 2022-05-16T08:53:11Z
date_updated: 2022-05-16T08:53:11Z
file_id: '11383'
file_name: 2021_PLOsComBio_Bodova.pdf
file_size: 2299486
relation: main_file
success: 1
file_date_updated: 2022-05-16T08:53:11Z
fulldoi: https://doi.org/10.1371/journal.pcbi.1009661
has_accepted_license: '1'
intvolume: ' 17'
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Computational Biology
publication_identifier:
eissn:
- 1553-7358
issn:
- 1553-734X
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamic maximum entropy provides accurate approximation of structured population
dynamics
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'
...