---
_id: '8547'
abstract:
- lang: eng
text: The cerebral cortex contains multiple hierarchically organized areas with
distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying
the emergence of this diversity remain unclear. Here, we have quantitatively investigated
the neuronal output of individual progenitor cells in the ventricular zone of
the developing mouse neocortex using a combination of methods that together circumvent
the biases and limitations of individual approaches. We found that individual
cortical progenitor cells show a high degree of stochasticity and generate pyramidal
cell lineages that adopt a wide range of laminar configurations. Mathematical
modelling these lineage data suggests that a small number of progenitor cell populations,
each generating pyramidal cells following different stochastic developmental programs,
suffice to generate the heterogenous complement of pyramidal cell lineages that
collectively build the complex cytoarchitecture of the neocortex.
acknowledgement: We thank I. Andrew and S.E. Bae for excellent technical assistance,
F. Gage for plasmids, and K. Nave (Nex-Cre) for mouse colonies. We thank members
of the Marín and Rico laboratories for stimulating discussions and ideas. Our research
on this topic is supported by grants from the European Research Council (ERC-2017-AdG
787355 to O.M and ERC2016-CoG 725780 to S.H.) and Wellcome Trust (103714MA) to O.M.
L.L. was the recipient of an EMBO long-term postdoctoral fellowship, R.B. received
support from FWF Lise-Meitner program (M 2416) and F.K.W. was supported by an EMBO
postdoctoral fellowship and is currently a Marie Skłodowska-Curie Fellow from the
European Commission under the H2020 Programme.
article_processing_charge: No
author:
- first_name: Alfredo
full_name: Llorca, Alfredo
last_name: Llorca
- first_name: Gabriele
full_name: Ciceri, Gabriele
last_name: Ciceri
- first_name: Robert J
full_name: Beattie, Robert J
id: 2E26DF60-F248-11E8-B48F-1D18A9856A87
last_name: Beattie
orcid: 0000-0002-8483-8753
- first_name: Fong K.
full_name: Wong, Fong K.
last_name: Wong
- first_name: Giovanni
full_name: Diana, Giovanni
last_name: Diana
- first_name: Eleni
full_name: Serafeimidou, Eleni
last_name: Serafeimidou
- first_name: Marian
full_name: Fernández-Otero, Marian
last_name: Fernández-Otero
- first_name: Carmen
full_name: Streicher, Carmen
id: 36BCB99C-F248-11E8-B48F-1D18A9856A87
last_name: Streicher
- first_name: Sebastian J.
full_name: Arnold, Sebastian J.
last_name: Arnold
- first_name: Martin
full_name: Meyer, Martin
last_name: Meyer
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Miguel
full_name: Maravall, Miguel
last_name: Maravall
- first_name: Oscar
full_name: Marín, Oscar
last_name: Marín
citation:
ama: Llorca A, Ciceri G, Beattie RJ, et al. Heterogeneous progenitor cell behaviors
underlie the assembly of neocortical cytoarchitecture. bioRxiv. doi:10.1101/494088
apa: Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou,
E., … Marín, O. (n.d.). Heterogeneous progenitor cell behaviors underlie the assembly
of neocortical cytoarchitecture. bioRxiv. Cold Spring Harbor Laboratory.
https://doi.org/10.1101/494088
chicago: Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong K. Wong, Giovanni
Diana, Eleni Serafeimidou, Marian Fernández-Otero, et al. “Heterogeneous Progenitor
Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” BioRxiv.
Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/494088.
ieee: A. Llorca et al., “Heterogeneous progenitor cell behaviors underlie
the assembly of neocortical cytoarchitecture,” bioRxiv. Cold Spring Harbor
Laboratory.
ista: Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou E, Fernández-Otero
M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marín O. Heterogeneous
progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture.
bioRxiv, 10.1101/494088.
mla: Llorca, Alfredo, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the
Assembly of Neocortical Cytoarchitecture.” BioRxiv, Cold Spring Harbor
Laboratory, doi:10.1101/494088.
short: A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou,
M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall,
O. Marín, BioRxiv (n.d.).
date_created: 2020-09-21T12:01:50Z
date_published: 2018-12-13T00:00:00Z
date_updated: 2021-01-12T08:20:00Z
day: '13'
department:
- _id: SiHi
doi: 10.1101/494088
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/494088
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
- _id: 264E56E2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02416
name: Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex
publication: bioRxiv
publication_status: submitted
publisher: Cold Spring Harbor Laboratory
status: public
title: Heterogeneous progenitor cell behaviors underlie the assembly of neocortical
cytoarchitecture
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '86'
abstract:
- lang: eng
text: Responsiveness—the requirement that every request to a system be eventually
handled—is one of the fundamental liveness properties of a reactive system. Average
response time is a quantitative measure for the responsiveness requirement used
commonly in performance evaluation. We show how average response time can be computed
on state-transition graphs, on Markov chains, and on game graphs. In all three
cases, we give polynomial-time algorithms.
acknowledgement: 'This research was supported in part by the Austrian Science Fund
(FWF) under grants S11402-N23, S11407-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein
Award), ERC Start grant (279307: Graph Games), Vienna Science and Technology Fund
(WWTF) through project ICT15-003 and by the National Science Centre (NCN), Poland
under grant 2014/15/D/ST6/04543.'
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: 'Chatterjee K, Henzinger TA, Otop J. Computing average response time. In: Lohstroh
M, Derler P, Sirjani M, eds. Principles of Modeling. Vol 10760. Springer;
2018:143-161. doi:10.1007/978-3-319-95246-8_9'
apa: Chatterjee, K., Henzinger, T. A., & Otop, J. (2018). Computing average
response time. In M. Lohstroh, P. Derler, & M. Sirjani (Eds.), Principles
of Modeling (Vol. 10760, pp. 143–161). Springer. https://doi.org/10.1007/978-3-319-95246-8_9
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Computing Average
Response Time.” In Principles of Modeling, edited by Marten Lohstroh, Patricia
Derler, and Marjan Sirjani, 10760:143–61. Springer, 2018. https://doi.org/10.1007/978-3-319-95246-8_9.
ieee: K. Chatterjee, T. A. Henzinger, and J. Otop, “Computing average response time,”
in Principles of Modeling, vol. 10760, M. Lohstroh, P. Derler, and M. Sirjani,
Eds. Springer, 2018, pp. 143–161.
ista: 'Chatterjee K, Henzinger TA, Otop J. 2018.Computing average response time.
In: Principles of Modeling. LNCS, vol. 10760, 143–161.'
mla: Chatterjee, Krishnendu, et al. “Computing Average Response Time.” Principles
of Modeling, edited by Marten Lohstroh et al., vol. 10760, Springer, 2018,
pp. 143–61, doi:10.1007/978-3-319-95246-8_9.
short: K. Chatterjee, T.A. Henzinger, J. Otop, in:, M. Lohstroh, P. Derler, M. Sirjani
(Eds.), Principles of Modeling, Springer, 2018, pp. 143–161.
date_created: 2018-12-11T11:44:33Z
date_published: 2018-07-20T00:00:00Z
date_updated: 2021-01-12T08:20:14Z
day: '20'
ddc:
- '000'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/978-3-319-95246-8_9
ec_funded: 1
editor:
- first_name: Marten
full_name: Lohstroh, Marten
last_name: Lohstroh
- first_name: Patricia
full_name: Derler, Patricia
last_name: Derler
- first_name: Marjan
full_name: Sirjani, Marjan
last_name: Sirjani
file:
- access_level: open_access
checksum: 9995c6ce6957333baf616fc4f20be597
content_type: application/pdf
creator: dernst
date_created: 2019-11-19T08:22:18Z
date_updated: 2020-07-14T12:48:14Z
file_id: '7053'
file_name: 2018_PrinciplesModeling_Chatterjee.pdf
file_size: 516307
relation: main_file
file_date_updated: 2020-07-14T12:48:14Z
has_accepted_license: '1'
intvolume: ' 10760'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 143 - 161
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication: Principles of Modeling
publication_status: published
publisher: Springer
publist_id: '7968'
quality_controlled: '1'
scopus_import: 1
status: public
title: Computing average response time
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10760
year: '2018'
...
---
_id: '9062'
abstract:
- lang: eng
text: 'Self-assembly is the autonomous organization of components into patterns
or structures: an essential ingredient of biology and a desired route to complex
organization1. At equilibrium, the structure is encoded through specific interactions2,3,4,5,6,7,8,
at an unfavourable entropic cost for the system. An alternative approach, widely
used by nature, uses energy input to bypass the entropy bottleneck and develop
features otherwise impossible at equilibrium9. Dissipative building blocks that
inject energy locally were made available by recent advances in colloidal science10,11
but have not been used to control self-assembly. Here we show the targeted formation
of self-powered microgears from active particles and their autonomous synchronization
into dynamical superstructures. We use a photoactive component that consumes fuel,
haematite, to devise phototactic microswimmers that form self-spinning microgears
following spatiotemporal light patterns. The gears are coupled via their chemical
clouds by diffusiophoresis12 and constitute the elementary bricks of synchronized
superstructures, which autonomously regulate their dynamics. The results are quantitatively
rationalized on the basis of a stochastic description of diffusio-phoretic oscillators
dynamically coupled by chemical gradients. Our findings harness non-equilibrium
phoretic phenomena to program interactions and direct self-assembly with fidelity
and specificity. It lays the groundwork for the autonomous construction of dynamical
architectures and functional micro-machinery.'
article_processing_charge: No
article_type: original
author:
- first_name: Antoine
full_name: Aubret, Antoine
last_name: Aubret
- first_name: Mena
full_name: Youssef, Mena
last_name: Youssef
- first_name: Stefano
full_name: Sacanna, Stefano
last_name: Sacanna
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
citation:
ama: Aubret A, Youssef M, Sacanna S, Palacci JA. Targeted assembly and synchronization
of self-spinning microgears. Nature Physics. 2018;14(11):1114-1118. doi:10.1038/s41567-018-0227-4
apa: Aubret, A., Youssef, M., Sacanna, S., & Palacci, J. A. (2018). Targeted
assembly and synchronization of self-spinning microgears. Nature Physics.
Springer Nature. https://doi.org/10.1038/s41567-018-0227-4
chicago: Aubret, Antoine, Mena Youssef, Stefano Sacanna, and Jérémie A Palacci.
“Targeted Assembly and Synchronization of Self-Spinning Microgears.” Nature
Physics. Springer Nature, 2018. https://doi.org/10.1038/s41567-018-0227-4.
ieee: A. Aubret, M. Youssef, S. Sacanna, and J. A. Palacci, “Targeted assembly and
synchronization of self-spinning microgears,” Nature Physics, vol. 14,
no. 11. Springer Nature, pp. 1114–1118, 2018.
ista: Aubret A, Youssef M, Sacanna S, Palacci JA. 2018. Targeted assembly and synchronization
of self-spinning microgears. Nature Physics. 14(11), 1114–1118.
mla: Aubret, Antoine, et al. “Targeted Assembly and Synchronization of Self-Spinning
Microgears.” Nature Physics, vol. 14, no. 11, Springer Nature, 2018, pp.
1114–18, doi:10.1038/s41567-018-0227-4.
short: A. Aubret, M. Youssef, S. Sacanna, J.A. Palacci, Nature Physics 14 (2018)
1114–1118.
date_created: 2021-02-02T13:52:49Z
date_published: 2018-11-01T00:00:00Z
date_updated: 2023-02-23T13:48:02Z
day: '01'
doi: 10.1038/s41567-018-0227-4
extern: '1'
external_id:
arxiv:
- '1810.01033'
intvolume: ' 14'
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1810.01033
month: '11'
oa: 1
oa_version: Preprint
page: 1114-1118
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Targeted assembly and synchronization of self-spinning microgears
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 14
year: '2018'
...
---
_id: '9229'
alternative_title:
- Molecular and cellular neuroscience
article_processing_charge: No
article_type: letter_note
author:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
citation:
ama: Danzl JG. Diffraction-unlimited optical imaging for synaptic physiology. Opera
Medica et Physiologica. 2018;4(S1):11. doi:10.20388/omp2018.00s1.001
apa: Danzl, J. G. (2018). Diffraction-unlimited optical imaging for synaptic physiology.
Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod.
https://doi.org/10.20388/omp2018.00s1.001
chicago: Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.”
Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod,
2018. https://doi.org/10.20388/omp2018.00s1.001.
ieee: J. G. Danzl, “Diffraction-unlimited optical imaging for synaptic physiology,”
Opera Medica et Physiologica, vol. 4, no. S1. Lobachevsky State University
of Nizhny Novgorod, p. 11, 2018.
ista: Danzl JG. 2018. Diffraction-unlimited optical imaging for synaptic physiology.
Opera Medica et Physiologica. 4(S1), 11.
mla: Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.”
Opera Medica et Physiologica, vol. 4, no. S1, Lobachevsky State University
of Nizhny Novgorod, 2018, p. 11, doi:10.20388/omp2018.00s1.001.
short: J.G. Danzl, Opera Medica et Physiologica 4 (2018) 11.
date_created: 2021-03-07T23:01:25Z
date_published: 2018-06-30T00:00:00Z
date_updated: 2021-12-03T07:31:05Z
day: '30'
department:
- _id: JoDa
doi: 10.20388/omp2018.00s1.001
intvolume: ' 4'
issue: S1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://operamedphys.org/content/molecular-and-cellular-neuroscience
month: '06'
oa: 1
oa_version: Published Version
page: '11'
publication: Opera Medica et Physiologica
publication_identifier:
eissn:
- 2500-2295
issn:
- 2500-2287
publication_status: published
publisher: Lobachevsky State University of Nizhny Novgorod
quality_controlled: '1'
scopus_import: '1'
status: public
title: Diffraction-unlimited optical imaging for synaptic physiology
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 4
year: '2018'
...
---
_id: '6005'
abstract:
- lang: eng
text: Network games are widely used as a model for selfish resource-allocation problems.
In the classicalmodel, each player selects a path connecting her source and target
vertices. The cost of traversingan edge depends on theload; namely, number of
players that traverse it. Thus, it abstracts the factthat different users may
use a resource at different times and for different durations, which playsan important
role in determining the costs of the users in reality. For example, when transmittingpackets
in a communication network, routing traffic in a road network, or processing a
task in aproduction system, actual sharing and congestion of resources crucially
depends on time.In [13], we introducedtimed network games, which add a time component
to network games.Each vertexvin the network is associated with a cost function,
mapping the load onvto theprice that a player pays for staying invfor one time
unit with this load. Each edge in thenetwork is guarded by the time intervals
in which it can be traversed, which forces the players tospend time in the vertices.
In this work we significantly extend the way time can be referred toin timed network
games. In the model we study, the network is equipped withclocks, and, as intimed
automata, edges are guarded by constraints on the values of the clocks, and their
traversalmay involve a reset of some clocks. We argue that the stronger model
captures many realisticnetworks. The addition of clocks breaks the techniques
we developed in [13] and we developnew techniques in order to show that positive
results on classic network games carry over to thestronger timed setting.
alternative_title:
- LIPIcs
article_number: '23'
article_processing_charge: No
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Shibashis
full_name: Guha, Shibashis
last_name: Guha
- first_name: Orna
full_name: Kupferman, Orna
last_name: Kupferman
citation:
ama: 'Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 117.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPICS.MFCS.2018.23'
apa: 'Avni, G., Guha, S., & Kupferman, O. (2018). Timed network games with clocks
(Vol. 117). Presented at the MFCS: Mathematical Foundations of Computer Science,
Liverpool, United Kingdom: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPICS.MFCS.2018.23'
chicago: Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with
Clocks,” Vol. 117. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.MFCS.2018.23.
ieee: 'G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented
at the MFCS: Mathematical Foundations of Computer Science, Liverpool, United Kingdom,
2018, vol. 117.'
ista: 'Avni G, Guha S, Kupferman O. 2018. Timed network games with clocks. MFCS:
Mathematical Foundations of Computer Science, LIPIcs, vol. 117, 23.'
mla: Avni, Guy, et al. Timed Network Games with Clocks. Vol. 117, 23, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPICS.MFCS.2018.23.
short: G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2018.
conference:
end_date: 2018-08-31
location: Liverpool, United Kingdom
name: 'MFCS: Mathematical Foundations of Computer Science'
start_date: 2018-08-27
date_created: 2019-02-14T14:12:09Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2023-02-23T14:02:58Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.4230/LIPICS.MFCS.2018.23
file:
- access_level: open_access
checksum: 41ab2ae9b63f5eb49fa995250c0ba128
content_type: application/pdf
creator: dernst
date_created: 2019-02-14T14:22:04Z
date_updated: 2020-07-14T12:47:15Z
file_id: '6007'
file_name: 2018_LIPIcs_Avni.pdf
file_size: 542889
relation: main_file
file_date_updated: 2020-07-14T12:47:15Z
has_accepted_license: '1'
intvolume: ' 117'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 264B3912-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02369
name: Formal Methods meets Algorithmic Game Theory
publication_identifier:
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
related_material:
record:
- id: '963'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Timed network games with clocks
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 117
year: '2018'
...
---
_id: '9668'
abstract:
- lang: eng
text: Estimating the homogeneous ice nucleation rate from undercooled liquid water
is crucial for understanding many important physical phenomena and technological
applications, and challenging for both experiments and theory. From a theoretical
point of view, difficulties arise due to the long time scales required, as well
as the numerous nucleation pathways involved to form ice nuclei with different
stacking disorders. We computed the homogeneous ice nucleation rate at a physically
relevant undercooling for a single-site water model, taking into account the diffuse
nature of ice–water interfaces, stacking disorders in ice nuclei, and the addition
rate of particles to the critical nucleus. We disentangled and investigated the
relative importance of all the terms, including interfacial free energy, entropic
contributions and the kinetic prefactor, that contribute to the overall nucleation
rate. Breaking down the problem into pieces not only provides physical insights
into ice nucleation, but also sheds light on the long-standing discrepancy between
different theoretical predictions, as well as between theoretical and experimental
determinations of the nucleation rate. Moreover, we pinpoint the main shortcomings
and suggest strategies to systematically improve the existing simulation methods.
article_processing_charge: No
article_type: original
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Christoph
full_name: Dellago, Christoph
last_name: Dellago
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: 'Cheng B, Dellago C, Ceriotti M. Theoretical prediction of the homogeneous
ice nucleation rate: Disentangling thermodynamics and kinetics. Physical Chemistry
Chemical Physics. 2018;20(45):28732-28740. doi:10.1039/c8cp04561e'
apa: 'Cheng, B., Dellago, C., & Ceriotti, M. (2018). Theoretical prediction
of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics.
Physical Chemistry Chemical Physics. Royal Society of Chemistry. https://doi.org/10.1039/c8cp04561e'
chicago: 'Cheng, Bingqing, Christoph Dellago, and Michele Ceriotti. “Theoretical
Prediction of the Homogeneous Ice Nucleation Rate: Disentangling Thermodynamics
and Kinetics.” Physical Chemistry Chemical Physics. Royal Society of Chemistry,
2018. https://doi.org/10.1039/c8cp04561e.'
ieee: 'B. Cheng, C. Dellago, and M. Ceriotti, “Theoretical prediction of the homogeneous
ice nucleation rate: Disentangling thermodynamics and kinetics,” Physical Chemistry
Chemical Physics, vol. 20, no. 45. Royal Society of Chemistry, pp. 28732–28740,
2018.'
ista: 'Cheng B, Dellago C, Ceriotti M. 2018. Theoretical prediction of the homogeneous
ice nucleation rate: Disentangling thermodynamics and kinetics. Physical Chemistry
Chemical Physics. 20(45), 28732–28740.'
mla: 'Cheng, Bingqing, et al. “Theoretical Prediction of the Homogeneous Ice Nucleation
Rate: Disentangling Thermodynamics and Kinetics.” Physical Chemistry Chemical
Physics, vol. 20, no. 45, Royal Society of Chemistry, 2018, pp. 28732–40,
doi:10.1039/c8cp04561e.'
short: B. Cheng, C. Dellago, M. Ceriotti, Physical Chemistry Chemical Physics 20
(2018) 28732–28740.
date_created: 2021-07-15T12:51:44Z
date_published: 2018-12-07T00:00:00Z
date_updated: 2021-08-09T12:36:47Z
day: '07'
doi: 10.1039/c8cp04561e
extern: '1'
external_id:
arxiv:
- '1807.05551'
pmid:
- '30412211'
intvolume: ' 20'
issue: '45'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1807.05551
month: '12'
oa: 1
oa_version: Preprint
page: 28732-28740
pmid: 1
publication: Physical Chemistry Chemical Physics
publication_identifier:
eissn:
- 1463-9084
issn:
- 1463-9076
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Theoretical prediction of the homogeneous ice nucleation rate: Disentangling
thermodynamics and kinetics'
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 20
year: '2018'
...
---
_id: '9687'
abstract:
- lang: eng
text: The Gibbs free energy is the fundamental thermodynamic potential underlying
the relative stability of different states of matter under constant-pressure conditions.
However, computing this quantity from atomic-scale simulations is far from trivial,
so the potential energy of a system is often used as a proxy. In this paper, we
use a combination of thermodynamic integration methods to accurately evaluate
the Gibbs free energies associated with defects in crystals, including the vacancy
formation energy in bcc iron, and the stacking fault energy in fcc nickel, iron,
and cobalt. We quantify the importance of entropic and anharmonic effects in determining
the free energies of defects at high temperatures, and show that the potential
energy approximation as well as the harmonic approximation may produce inaccurate
or even qualitatively wrong results. Our calculations manifest the necessity to
employ accurate free energy methods such as thermodynamic integration to estimate
the stability of crystallographic defects at high temperatures.
article_number: '054102'
article_processing_charge: No
article_type: original
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: 'Cheng B, Ceriotti M. Computing the absolute Gibbs free energy in atomistic
simulations: Applications to defects in solids. Physical Review B. 2018;97(5).
doi:10.1103/physrevb.97.054102'
apa: 'Cheng, B., & Ceriotti, M. (2018). Computing the absolute Gibbs free energy
in atomistic simulations: Applications to defects in solids. Physical Review
B. American Physical Society. https://doi.org/10.1103/physrevb.97.054102'
chicago: 'Cheng, Bingqing, and Michele Ceriotti. “Computing the Absolute Gibbs Free
Energy in Atomistic Simulations: Applications to Defects in Solids.” Physical
Review B. American Physical Society, 2018. https://doi.org/10.1103/physrevb.97.054102.'
ieee: 'B. Cheng and M. Ceriotti, “Computing the absolute Gibbs free energy in atomistic
simulations: Applications to defects in solids,” Physical Review B, vol.
97, no. 5. American Physical Society, 2018.'
ista: 'Cheng B, Ceriotti M. 2018. Computing the absolute Gibbs free energy in atomistic
simulations: Applications to defects in solids. Physical Review B. 97(5), 054102.'
mla: 'Cheng, Bingqing, and Michele Ceriotti. “Computing the Absolute Gibbs Free
Energy in Atomistic Simulations: Applications to Defects in Solids.” Physical
Review B, vol. 97, no. 5, 054102, American Physical Society, 2018, doi:10.1103/physrevb.97.054102.'
short: B. Cheng, M. Ceriotti, Physical Review B 97 (2018).
date_created: 2021-07-19T09:39:48Z
date_published: 2018-02-01T00:00:00Z
date_updated: 2021-08-09T12:38:26Z
day: '01'
doi: 10.1103/physrevb.97.054102
extern: '1'
external_id:
arxiv:
- '1710.02815'
intvolume: ' 97'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1710.02815
month: '02'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Computing the absolute Gibbs free energy in atomistic simulations: Applications
to defects in solids'
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 97
year: '2018'
...
---
_id: '315'
abstract:
- lang: eng
text: 'More than 100 years after Grigg’s influential analysis of species’ borders,
the causes of limits to species’ ranges still represent a puzzle that has never
been understood with clarity. The topic has become especially important recently
as many scientists have become interested in the potential for species’ ranges
to shift in response to climate change—and yet nearly all of those studies fail
to recognise or incorporate evolutionary genetics in a way that relates to theoretical
developments. I show that range margins can be understood based on just two measurable
parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and
(ii) the strength of genetic drift, which reduces genetic diversity. Together,
these two parameters define an ‘expansion threshold’: adaptation fails when genetic
drift reduces genetic diversity below that required for adaptation to a heterogeneous
environment. When the key parameters drop below this expansion threshold locally,
a sharp range margin forms. When they drop below this threshold throughout the
species’ range, adaptation collapses everywhere, resulting in either extinction
or formation of a fragmented metapopulation. Because the effects of dispersal
differ fundamentally with dimension, the second parameter—the strength of genetic
drift—is qualitatively different compared to a linear habitat. In two-dimensional
habitats, genetic drift becomes effectively independent of selection. It decreases
with ‘neighbourhood size’—the number of individuals accessible by dispersal within
one generation. Moreover, in contrast to earlier predictions, which neglected
evolution of genetic variance and/or stochasticity in two dimensions, dispersal
into small marginal populations aids adaptation. This is because the reduction
of both genetic and demographic stochasticity has a stronger effect than the cost
of dispersal through increased maladaptation. The expansion threshold thus provides
a novel, theoretically justified, and testable prediction for formation of the
range margin and collapse of the species’ range.'
article_number: e2005372
author:
- first_name: Jitka
full_name: Polechova, Jitka
id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
last_name: Polechova
orcid: 0000-0003-0951-3112
citation:
ama: Polechova J. Is the sky the limit? On the expansion threshold of a species’
range. PLoS Biology. 2018;16(6). doi:10.1371/journal.pbio.2005372
apa: Polechova, J. (2018). Is the sky the limit? On the expansion threshold of a
species’ range. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005372
chicago: Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of
a Species’ Range.” PLoS Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005372.
ieee: J. Polechova, “Is the sky the limit? On the expansion threshold of a species’
range,” PLoS Biology, vol. 16, no. 6. Public Library of Science, 2018.
ista: Polechova J. 2018. Is the sky the limit? On the expansion threshold of a species’
range. PLoS Biology. 16(6), e2005372.
mla: Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’
Range.” PLoS Biology, vol. 16, no. 6, e2005372, Public Library of Science,
2018, doi:10.1371/journal.pbio.2005372.
short: J. Polechova, PLoS Biology 16 (2018).
date_created: 2018-12-11T11:45:46Z
date_published: 2018-06-15T00:00:00Z
date_updated: 2023-02-23T14:10:16Z
day: '15'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1371/journal.pbio.2005372
file:
- access_level: open_access
checksum: 908c52751bba30c55ed36789e5e4c84d
content_type: application/pdf
creator: dernst
date_created: 2019-01-22T08:30:03Z
date_updated: 2020-07-14T12:46:01Z
file_id: '5870'
file_name: 2017_PLOS_Polechova.pdf
file_size: 6968201
relation: main_file
file_date_updated: 2020-07-14T12:46:01Z
has_accepted_license: '1'
intvolume: ' 16'
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_identifier:
issn:
- '15449173'
publication_status: published
publisher: Public Library of Science
publist_id: '7550'
quality_controlled: '1'
related_material:
record:
- id: '9839'
relation: research_data
status: public
scopus_import: 1
status: public
title: Is the sky the limit? On the expansion threshold of a species’ range
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2018'
...
---
_id: '8417'
abstract:
- lang: eng
text: The restricted planar elliptic three body problem (RPETBP) describes the motion
of a massless particle (a comet or an asteroid) under the gravitational field
of two massive bodies (the primaries, say the Sun and Jupiter) revolving around
their center of mass on elliptic orbits with some positive eccentricity. The aim
of this paper is to show the existence of orbits whose angular momentum performs
arbitrary excursions in a large region. In particular, there exist diffusive orbits,
that is, with a large variation of angular momentum. The leading idea of the proof
consists in analyzing parabolic motions of the comet. By a well-known result of
McGehee, the union of future (resp. past) parabolic orbits is an analytic manifold
P+ (resp. P−). In a properly chosen coordinate system these manifolds are stable
(resp. unstable) manifolds of a manifold at infinity P∞, which we call the manifold
at parabolic infinity. On P∞ it is possible to define two scattering maps, which
contain the map structure of the homoclinic trajectories to it, i.e. orbits parabolic
both in the future and the past. Since the inner dynamics inside P∞ is trivial,
two different scattering maps are used. The combination of these two scattering
maps permits the design of the desired diffusive pseudo-orbits. Using shadowing
techniques and these pseudo orbits we show the existence of true trajectories
of the RPETBP whose angular momentum varies in any predetermined fashion.
article_processing_charge: No
article_type: original
author:
- first_name: Amadeu
full_name: Delshams, Amadeu
last_name: Delshams
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Abraham
full_name: de la Rosa, Abraham
last_name: de la Rosa
- first_name: Tere M.
full_name: Seara, Tere M.
last_name: Seara
citation:
ama: Delshams A, Kaloshin V, de la Rosa A, Seara TM. Global instability in the restricted
planar elliptic three body problem. Communications in Mathematical Physics.
2018;366(3):1173-1228. doi:10.1007/s00220-018-3248-z
apa: Delshams, A., Kaloshin, V., de la Rosa, A., & Seara, T. M. (2018). Global
instability in the restricted planar elliptic three body problem. Communications
in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-018-3248-z
chicago: Delshams, Amadeu, Vadim Kaloshin, Abraham de la Rosa, and Tere M. Seara.
“Global Instability in the Restricted Planar Elliptic Three Body Problem.” Communications
in Mathematical Physics. Springer Nature, 2018. https://doi.org/10.1007/s00220-018-3248-z.
ieee: A. Delshams, V. Kaloshin, A. de la Rosa, and T. M. Seara, “Global instability
in the restricted planar elliptic three body problem,” Communications in Mathematical
Physics, vol. 366, no. 3. Springer Nature, pp. 1173–1228, 2018.
ista: Delshams A, Kaloshin V, de la Rosa A, Seara TM. 2018. Global instability in
the restricted planar elliptic three body problem. Communications in Mathematical
Physics. 366(3), 1173–1228.
mla: Delshams, Amadeu, et al. “Global Instability in the Restricted Planar Elliptic
Three Body Problem.” Communications in Mathematical Physics, vol. 366,
no. 3, Springer Nature, 2018, pp. 1173–228, doi:10.1007/s00220-018-3248-z.
short: A. Delshams, V. Kaloshin, A. de la Rosa, T.M. Seara, Communications in Mathematical
Physics 366 (2018) 1173–1228.
date_created: 2020-09-17T10:41:43Z
date_published: 2018-09-05T00:00:00Z
date_updated: 2021-01-12T08:19:08Z
day: '05'
doi: 10.1007/s00220-018-3248-z
extern: '1'
intvolume: ' 366'
issue: '3'
keyword:
- Mathematical Physics
- Statistical and Nonlinear Physics
language:
- iso: eng
month: '09'
oa_version: None
page: 1173-1228
publication: Communications in Mathematical Physics
publication_identifier:
issn:
- 0010-3616
- 1432-0916
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Global instability in the restricted planar elliptic three body problem
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 366
year: '2018'
...
---
_id: '8422'
abstract:
- lang: eng
text: 'The Birkhoff conjecture says that the boundary of a strictly convex integrable
billiard table is necessarily an ellipse. In this article, we consider a stronger
notion of integrability, namely integrability close to the boundary, and prove
a local version of this conjecture: a small perturbation of an ellipse of small
eccentricity which preserves integrability near the boundary, is itself an ellipse.
This extends the result in Avila et al. (Ann Math 184:527–558, ADK16), where integrability
was assumed on a larger set. In particular, it shows that (local) integrability
near the boundary implies global integrability. One of the crucial ideas in the
proof consists in analyzing Taylor expansion of the corresponding action-angle
coordinates with respect to the eccentricity parameter, deriving and studying
higher order conditions for the preservation of integrable rational caustics.'
article_processing_charge: No
article_type: original
author:
- first_name: Guan
full_name: Huang, Guan
last_name: Huang
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Alfonso
full_name: Sorrentino, Alfonso
last_name: Sorrentino
citation:
ama: Huang G, Kaloshin V, Sorrentino A. Nearly circular domains which are integrable
close to the boundary are ellipses. Geometric and Functional Analysis.
2018;28(2):334-392. doi:10.1007/s00039-018-0440-4
apa: Huang, G., Kaloshin, V., & Sorrentino, A. (2018). Nearly circular domains
which are integrable close to the boundary are ellipses. Geometric and Functional
Analysis. Springer Nature. https://doi.org/10.1007/s00039-018-0440-4
chicago: Huang, Guan, Vadim Kaloshin, and Alfonso Sorrentino. “Nearly Circular Domains
Which Are Integrable Close to the Boundary Are Ellipses.” Geometric and Functional
Analysis. Springer Nature, 2018. https://doi.org/10.1007/s00039-018-0440-4.
ieee: G. Huang, V. Kaloshin, and A. Sorrentino, “Nearly circular domains which are
integrable close to the boundary are ellipses,” Geometric and Functional Analysis,
vol. 28, no. 2. Springer Nature, pp. 334–392, 2018.
ista: Huang G, Kaloshin V, Sorrentino A. 2018. Nearly circular domains which are
integrable close to the boundary are ellipses. Geometric and Functional Analysis.
28(2), 334–392.
mla: Huang, Guan, et al. “Nearly Circular Domains Which Are Integrable Close to
the Boundary Are Ellipses.” Geometric and Functional Analysis, vol. 28,
no. 2, Springer Nature, 2018, pp. 334–92, doi:10.1007/s00039-018-0440-4.
short: G. Huang, V. Kaloshin, A. Sorrentino, Geometric and Functional Analysis 28
(2018) 334–392.
date_created: 2020-09-17T10:42:30Z
date_published: 2018-03-18T00:00:00Z
date_updated: 2021-01-12T08:19:11Z
day: '18'
doi: 10.1007/s00039-018-0440-4
extern: '1'
external_id:
arxiv:
- '1705.10601'
intvolume: ' 28'
issue: '2'
keyword:
- Geometry and Topology
- Analysis
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.10601
month: '03'
oa: 1
oa_version: Preprint
page: 334-392
publication: Geometric and Functional Analysis
publication_identifier:
issn:
- 1016-443X
- 1420-8970
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Nearly circular domains which are integrable close to the boundary are ellipses
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 28
year: '2018'
...