---
_id: '8570'
abstract:
- lang: eng
text: 'This report presents the results of a friendly competition for formal verification
of continuous and hybrid systems with linear continuous dynamics. The friendly
competition took place as part of the workshop Applied Verification for Continuous
and Hybrid Systems (ARCH) in 2019. In its third edition, seven tools have been
applied to solve six different benchmark problems in the category for linear continuous
dynamics (in alphabetical order): CORA, CORA/SX, HyDRA, Hylaa, JuliaReach, SpaceEx,
and XSpeed. This report is a snapshot of the current landscape of tools and the
types of benchmarks they are particularly suited for. Due to the diversity of
problems, we are not ranking tools, yet the presented results provide one of the
most complete assessments of tools for the safety verification of continuous and
hybrid systems with linear continuous dynamics up to this date.'
article_processing_charge: No
author:
- first_name: Matthias
full_name: Althoff, Matthias
last_name: Althoff
- first_name: Stanley
full_name: Bak, Stanley
last_name: Bak
- first_name: Marcelo
full_name: Forets, Marcelo
last_name: Forets
- first_name: Goran
full_name: Frehse, Goran
last_name: Frehse
- first_name: Niklas
full_name: Kochdumper, Niklas
last_name: Kochdumper
- first_name: Rajarshi
full_name: Ray, Rajarshi
last_name: Ray
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
- first_name: Stefan
full_name: Schupp, Stefan
last_name: Schupp
citation:
ama: 'Althoff M, Bak S, Forets M, et al. ARCH-COMP19 Category Report: Continuous
and hybrid systems with linear continuous dynamics. In: EPiC Series in Computing.
Vol 61. EasyChair; 2019:14-40. doi:10.29007/bj1w'
apa: 'Althoff, M., Bak, S., Forets, M., Frehse, G., Kochdumper, N., Ray, R., … Schupp,
S. (2019). ARCH-COMP19 Category Report: Continuous and hybrid systems with linear
continuous dynamics. In EPiC Series in Computing (Vol. 61, pp. 14–40).
Montreal, Canada: EasyChair. https://doi.org/10.29007/bj1w'
chicago: 'Althoff, Matthias, Stanley Bak, Marcelo Forets, Goran Frehse, Niklas Kochdumper,
Rajarshi Ray, Christian Schilling, and Stefan Schupp. “ARCH-COMP19 Category Report:
Continuous and Hybrid Systems with Linear Continuous Dynamics.” In EPiC Series
in Computing, 61:14–40. EasyChair, 2019. https://doi.org/10.29007/bj1w.'
ieee: 'M. Althoff et al., “ARCH-COMP19 Category Report: Continuous and hybrid
systems with linear continuous dynamics,” in EPiC Series in Computing,
Montreal, Canada, 2019, vol. 61, pp. 14–40.'
ista: 'Althoff M, Bak S, Forets M, Frehse G, Kochdumper N, Ray R, Schilling C, Schupp
S. 2019. ARCH-COMP19 Category Report: Continuous and hybrid systems with linear
continuous dynamics. EPiC Series in Computing. ARCH: International Workshop on
Applied Verification on Continuous and Hybrid Systems vol. 61, 14–40.'
mla: 'Althoff, Matthias, et al. “ARCH-COMP19 Category Report: Continuous and Hybrid
Systems with Linear Continuous Dynamics.” EPiC Series in Computing, vol.
61, EasyChair, 2019, pp. 14–40, doi:10.29007/bj1w.'
short: M. Althoff, S. Bak, M. Forets, G. Frehse, N. Kochdumper, R. Ray, C. Schilling,
S. Schupp, in:, EPiC Series in Computing, EasyChair, 2019, pp. 14–40.
conference:
end_date: 2019-04-15
location: Montreal, Canada
name: 'ARCH: International Workshop on Applied Verification on Continuous and Hybrid
Systems'
start_date: 2019-04-15
date_created: 2020-09-26T14:23:54Z
date_published: 2019-05-25T00:00:00Z
date_updated: 2021-01-12T08:20:05Z
day: '25'
department:
- _id: ToHe
doi: 10.29007/bj1w
intvolume: ' 61'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://easychair.org/publications/open/1gbP
month: '05'
oa: 1
oa_version: Published Version
page: 14-40
publication: EPiC Series in Computing
publication_identifier:
eissn:
- '23987340'
publication_status: published
publisher: EasyChair
quality_controlled: '1'
status: public
title: 'ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous
dynamics'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 61
year: '2019'
...
---
_id: '9016'
abstract:
- lang: eng
text: Inhibiting the histone H3–ASF1 (anti‐silencing function 1) protein–protein
interaction (PPI) represents a potential approach for treating numerous cancers.
As an α‐helix‐mediated PPI, constraining the key histone H3 helix (residues 118–135)
is a strategy through which chemical probes might be elaborated to test this hypothesis.
In this work, variant H3118–135 peptides bearing pentenylglycine residues at the
i and i+4 positions were constrained by olefin metathesis. Biophysical analyses
revealed that promotion of a bioactive helical conformation depends on the position
at which the constraint is introduced, but that the potency of binding towards
ASF1 is unaffected by the constraint and instead that enthalpy–entropy compensation
occurs.
article_processing_charge: No
article_type: original
author:
- first_name: May M
full_name: Bakail, May M
id: FB3C3F8E-522F-11EA-B186-22963DDC885E
last_name: Bakail
orcid: 0000-0002-9592-1587
- first_name: Silvia
full_name: Rodriguez‐Marin, Silvia
last_name: Rodriguez‐Marin
- first_name: Zsófia
full_name: Hegedüs, Zsófia
last_name: Hegedüs
- first_name: Marie E.
full_name: Perrin, Marie E.
last_name: Perrin
- first_name: Françoise
full_name: Ochsenbein, Françoise
last_name: Ochsenbein
- first_name: Andrew J.
full_name: Wilson, Andrew J.
last_name: Wilson
citation:
ama: Bakail MM, Rodriguez‐Marin S, Hegedüs Z, Perrin ME, Ochsenbein F, Wilson AJ.
Recognition of ASF1 by using hydrocarbon‐constrained peptides. ChemBioChem.
2019;20(7):891-895. doi:10.1002/cbic.201800633
apa: Bakail, M. M., Rodriguez‐Marin, S., Hegedüs, Z., Perrin, M. E., Ochsenbein,
F., & Wilson, A. J. (2019). Recognition of ASF1 by using hydrocarbon‐constrained
peptides. ChemBioChem. Wiley. https://doi.org/10.1002/cbic.201800633
chicago: Bakail, May M, Silvia Rodriguez‐Marin, Zsófia Hegedüs, Marie E. Perrin,
Françoise Ochsenbein, and Andrew J. Wilson. “Recognition of ASF1 by Using Hydrocarbon‐constrained
Peptides.” ChemBioChem. Wiley, 2019. https://doi.org/10.1002/cbic.201800633.
ieee: M. M. Bakail, S. Rodriguez‐Marin, Z. Hegedüs, M. E. Perrin, F. Ochsenbein,
and A. J. Wilson, “Recognition of ASF1 by using hydrocarbon‐constrained peptides,”
ChemBioChem, vol. 20, no. 7. Wiley, pp. 891–895, 2019.
ista: Bakail MM, Rodriguez‐Marin S, Hegedüs Z, Perrin ME, Ochsenbein F, Wilson AJ.
2019. Recognition of ASF1 by using hydrocarbon‐constrained peptides. ChemBioChem.
20(7), 891–895.
mla: Bakail, May M., et al. “Recognition of ASF1 by Using Hydrocarbon‐constrained
Peptides.” ChemBioChem, vol. 20, no. 7, Wiley, 2019, pp. 891–95, doi:10.1002/cbic.201800633.
short: M.M. Bakail, S. Rodriguez‐Marin, Z. Hegedüs, M.E. Perrin, F. Ochsenbein,
A.J. Wilson, ChemBioChem 20 (2019) 891–895.
date_created: 2021-01-19T10:59:14Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2023-02-23T13:46:48Z
day: '01'
doi: 10.1002/cbic.201800633
extern: '1'
intvolume: ' 20'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.1002/cbic.201800633'
month: '04'
oa: 1
oa_version: Published Version
page: 891-895
publication: ChemBioChem
publication_identifier:
issn:
- 1439-4227
- 1439-7633
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Recognition of ASF1 by using hydrocarbon‐constrained peptides
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2019'
...
---
_id: '9060'
abstract:
- lang: eng
text: Molecular motors are essential to the living, generating fluctuations that
boost transport and assist assembly. Active colloids, that consume energy to move,
hold similar potential for man-made materials controlled by forces generated from
within. Yet, their use as a powerhouse in materials science lacks. Here we show
a massive acceleration of the annealing of a monolayer of passive beads by moderate
addition of self-propelled microparticles. We rationalize our observations with
a model of collisions that drive active fluctuations and activate the annealing.
The experiment is quantitatively compared with Brownian dynamic simulations that
further unveil a dynamical transition in the mechanism of annealing. Active dopants
travel uniformly in the system or co-localize at the grain boundaries as a result
of the persistence of their motion. Our findings uncover the potential of internal
activity to control materials and lay the groundwork for the rise of materials
science beyond equilibrium.
article_number: '3380'
article_processing_charge: No
article_type: original
author:
- first_name: Sophie
full_name: Ramananarivo, Sophie
last_name: Ramananarivo
- first_name: Etienne
full_name: Ducrot, Etienne
last_name: Ducrot
- 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: Ramananarivo S, Ducrot E, Palacci JA. Activity-controlled annealing of colloidal
monolayers. Nature Communications. 2019;10(1). doi:10.1038/s41467-019-11362-y
apa: Ramananarivo, S., Ducrot, E., & Palacci, J. A. (2019). Activity-controlled
annealing of colloidal monolayers. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-019-11362-y
chicago: Ramananarivo, Sophie, Etienne Ducrot, and Jérémie A Palacci. “Activity-Controlled
Annealing of Colloidal Monolayers.” Nature Communications. Springer Nature,
2019. https://doi.org/10.1038/s41467-019-11362-y.
ieee: S. Ramananarivo, E. Ducrot, and J. A. Palacci, “Activity-controlled annealing
of colloidal monolayers,” Nature Communications, vol. 10, no. 1. Springer
Nature, 2019.
ista: Ramananarivo S, Ducrot E, Palacci JA. 2019. Activity-controlled annealing
of colloidal monolayers. Nature Communications. 10(1), 3380.
mla: Ramananarivo, Sophie, et al. “Activity-Controlled Annealing of Colloidal Monolayers.”
Nature Communications, vol. 10, no. 1, 3380, Springer Nature, 2019, doi:10.1038/s41467-019-11362-y.
short: S. Ramananarivo, E. Ducrot, J.A. Palacci, Nature Communications 10 (2019).
date_created: 2021-02-02T13:43:36Z
date_published: 2019-07-29T00:00:00Z
date_updated: 2023-02-23T13:47:59Z
day: '29'
ddc:
- '530'
doi: 10.1038/s41467-019-11362-y
extern: '1'
external_id:
arxiv:
- '1909.07382'
pmid:
- '31358762'
file:
- access_level: open_access
checksum: 70c6e5d6fbea0932b0669505ab6633ec
content_type: application/pdf
creator: cziletti
date_created: 2021-02-02T13:47:21Z
date_updated: 2021-02-02T13:47:21Z
file_id: '9061'
file_name: 2019_NatureComm_Ramananarivo.pdf
file_size: 2820337
relation: main_file
success: 1
file_date_updated: 2021-02-02T13:47:21Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '1'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Physics and Astronomy
- General Chemistry
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Activity-controlled annealing of colloidal monolayers
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: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 10
year: '2019'
...
---
_id: '9460'
abstract:
- lang: eng
text: Epigenetic reprogramming is required for proper regulation of gene expression
in eukaryotic organisms. In Arabidopsis, active DNA demethylation is crucial for
seed viability, pollen function, and successful reproduction. The DEMETER (DME)
DNA glycosylase initiates localized DNA demethylation in vegetative and central
cells, so-called companion cells that are adjacent to sperm and egg gametes, respectively.
In rice, the central cell genome displays local DNA hypomethylation, suggesting
that active DNA demethylation also occurs in rice; however, the enzyme responsible
for this process is unknown. One candidate is the rice REPRESSOR OF SILENCING
1a (ROS1a) gene, which is related to DME and is essential for rice seed viability
and pollen function. Here, we report genome-wide analyses of DNA methylation in
wild-type and ros1a mutant sperm and vegetative cells. We find that the rice vegetative
cell genome is locally hypomethylated compared with sperm by a process that requires
ROS1a activity. We show that many ROS1a target sequences in the vegetative cell
are hypomethylated in the rice central cell, suggesting that ROS1a also demethylates
the central cell genome. Similar to Arabidopsis, we show that sperm non-CG methylation
is indirectly promoted by DNA demethylation in the vegetative cell. These results
reveal that DNA glycosylase-mediated DNA demethylation processes are conserved
in Arabidopsis and rice, plant species that diverged 150 million years ago. Finally,
although global non-CG methylation levels of sperm and egg differ, the maternal
and paternal embryo genomes show similar non-CG methylation levels, suggesting
that rice gamete genomes undergo dynamic DNA methylation reprogramming after cell
fusion.
article_processing_charge: No
article_type: original
author:
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Akemi
full_name: Ono, Akemi
last_name: Ono
- first_name: Stefan
full_name: Scholten, Stefan
last_name: Scholten
- first_name: Tetsu
full_name: Kinoshita, Tetsu
last_name: Kinoshita
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Takashi
full_name: Okamoto, Takashi
last_name: Okamoto
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
citation:
ama: Kim MY, Ono A, Scholten S, et al. DNA demethylation by ROS1a in rice vegetative
cells promotes methylation in sperm. Proceedings of the National Academy of
Sciences. 2019;116(19):9652-9657. doi:10.1073/pnas.1821435116
apa: Kim, M. Y., Ono, A., Scholten, S., Kinoshita, T., Zilberman, D., Okamoto, T.,
& Fischer, R. L. (2019). DNA demethylation by ROS1a in rice vegetative cells
promotes methylation in sperm. Proceedings of the National Academy of Sciences.
National Academy of Sciences. https://doi.org/10.1073/pnas.1821435116
chicago: Kim, M. Yvonne, Akemi Ono, Stefan Scholten, Tetsu Kinoshita, Daniel Zilberman,
Takashi Okamoto, and Robert L. Fischer. “DNA Demethylation by ROS1a in Rice Vegetative
Cells Promotes Methylation in Sperm.” Proceedings of the National Academy of
Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1821435116.
ieee: M. Y. Kim et al., “DNA demethylation by ROS1a in rice vegetative cells
promotes methylation in sperm,” Proceedings of the National Academy of Sciences,
vol. 116, no. 19. National Academy of Sciences, pp. 9652–9657, 2019.
ista: Kim MY, Ono A, Scholten S, Kinoshita T, Zilberman D, Okamoto T, Fischer RL.
2019. DNA demethylation by ROS1a in rice vegetative cells promotes methylation
in sperm. Proceedings of the National Academy of Sciences. 116(19), 9652–9657.
mla: Kim, M. Yvonne, et al. “DNA Demethylation by ROS1a in Rice Vegetative Cells
Promotes Methylation in Sperm.” Proceedings of the National Academy of Sciences,
vol. 116, no. 19, National Academy of Sciences, 2019, pp. 9652–57, doi:10.1073/pnas.1821435116.
short: M.Y. Kim, A. Ono, S. Scholten, T. Kinoshita, D. Zilberman, T. Okamoto, R.L.
Fischer, Proceedings of the National Academy of Sciences 116 (2019) 9652–9657.
date_created: 2021-06-04T12:38:20Z
date_published: 2019-05-07T00:00:00Z
date_updated: 2021-12-14T07:52:30Z
day: '07'
ddc:
- '580'
department:
- _id: DaZi
doi: 10.1073/pnas.1821435116
extern: '1'
external_id:
pmid:
- '31000601'
file:
- access_level: open_access
checksum: 5b0ae3779b8b21b5223bd2d3cceede3a
content_type: application/pdf
creator: asandaue
date_created: 2021-06-04T12:50:47Z
date_updated: 2021-06-04T12:50:47Z
file_id: '9461'
file_name: 2019_PNAS_Kim.pdf
file_size: 1142540
relation: main_file
success: 1
file_date_updated: 2021-06-04T12:50:47Z
has_accepted_license: '1'
intvolume: ' 116'
issue: '19'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 9652-9657
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA demethylation by ROS1a in rice vegetative cells promotes methylation in
sperm
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 116
year: '2019'
...
---
_id: '9689'
abstract:
- lang: eng
text: A central goal of computational physics and chemistry is to predict material
properties by using first-principles methods based on the fundamental laws of
quantum mechanics. However, the high computational costs of these methods typically
prevent rigorous predictions of macroscopic quantities at finite temperatures,
such as heat capacity, density, and chemical potential. Here, we enable such predictions
by marrying advanced free-energy methods with data-driven machine-learning interatomic
potentials. We show that, for the ubiquitous and technologically essential system
of water, a first-principles thermodynamic description not only leads to excellent
agreement with experiments, but also reveals the crucial role of nuclear quantum
fluctuations in modulating the thermodynamic stabilities of different phases of
water.
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: Edgar A.
full_name: Engel, Edgar A.
last_name: Engel
- first_name: Jörg
full_name: Behler, Jörg
last_name: Behler
- first_name: Christoph
full_name: Dellago, Christoph
last_name: Dellago
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: Cheng B, Engel EA, Behler J, Dellago C, Ceriotti M. Ab initio thermodynamics
of liquid and solid water. Proceedings of the National Academy of Sciences.
2019;116(4):1110-1115. doi:10.1073/pnas.1815117116
apa: Cheng, B., Engel, E. A., Behler, J., Dellago, C., & Ceriotti, M. (2019).
Ab initio thermodynamics of liquid and solid water. Proceedings of the National
Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1815117116
chicago: Cheng, Bingqing, Edgar A. Engel, Jörg Behler, Christoph Dellago, and Michele
Ceriotti. “Ab Initio Thermodynamics of Liquid and Solid Water.” Proceedings
of the National Academy of Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1815117116.
ieee: B. Cheng, E. A. Engel, J. Behler, C. Dellago, and M. Ceriotti, “Ab initio
thermodynamics of liquid and solid water,” Proceedings of the National Academy
of Sciences, vol. 116, no. 4. National Academy of Sciences, pp. 1110–1115,
2019.
ista: Cheng B, Engel EA, Behler J, Dellago C, Ceriotti M. 2019. Ab initio thermodynamics
of liquid and solid water. Proceedings of the National Academy of Sciences. 116(4),
1110–1115.
mla: Cheng, Bingqing, et al. “Ab Initio Thermodynamics of Liquid and Solid Water.”
Proceedings of the National Academy of Sciences, vol. 116, no. 4, National
Academy of Sciences, 2019, pp. 1110–15, doi:10.1073/pnas.1815117116.
short: B. Cheng, E.A. Engel, J. Behler, C. Dellago, M. Ceriotti, Proceedings of
the National Academy of Sciences 116 (2019) 1110–1115.
date_created: 2021-07-19T10:17:09Z
date_published: 2019-01-22T00:00:00Z
date_updated: 2023-02-23T14:05:08Z
day: '22'
doi: 10.1073/pnas.1815117116
extern: '1'
external_id:
arxiv:
- '1811.08630'
pmid:
- '30610171'
intvolume: ' 116'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1815117116
month: '01'
oa: 1
oa_version: Published Version
page: 1110-1115
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ab initio thermodynamics of liquid and solid water
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 116
year: '2019'
...
---
_id: '6819'
abstract:
- lang: eng
text: Glyphosate (N-phosphonomethyl glycine) and its commercial herbicide formulations
have been shown to exert toxicity via various mechanisms. It has been asserted
that glyphosate substitutes for glycine in polypeptide chains leading to protein
misfolding and toxicity. However, as no direct evidence exists for glycine to
glyphosate substitution in proteins, including in mammalian organisms, we tested
this claim by conducting a proteomics analysis of MDA-MB-231 human breast cancer
cells grown in the presence of 100 mg/L glyphosate for 6 days. Protein extracts
from three treated and three untreated cell cultures were analysed as one TMT-6plex
labelled sample, to highlight a specific pattern (+/+/+/−/−/−) of reporter intensities
for peptides bearing true glyphosate treatment induced-post translational modifications
as well as allowing an investigation of the total proteome.
article_number: '494'
article_processing_charge: No
author:
- first_name: Michael N.
full_name: Antoniou, Michael N.
last_name: Antoniou
- first_name: Armel
full_name: Nicolas, Armel
id: 2A103192-F248-11E8-B48F-1D18A9856A87
last_name: Nicolas
- first_name: Robin
full_name: Mesnage, Robin
last_name: Mesnage
- first_name: Martina
full_name: Biserni, Martina
last_name: Biserni
- first_name: Francesco V.
full_name: Rao, Francesco V.
last_name: Rao
- first_name: Cristina Vazquez
full_name: Martin, Cristina Vazquez
last_name: Martin
citation:
ama: Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. Glyphosate
does not substitute for glycine in proteins of actively dividing mammalian cells.
BMC Research Notes. 2019;12. doi:10.1186/s13104-019-4534-3
apa: Antoniou, M. N., Nicolas, A., Mesnage, R., Biserni, M., Rao, F. V., & Martin,
C. V. (2019). Glyphosate does not substitute for glycine in proteins of actively
dividing mammalian cells. BMC Research Notes. BioMed Central. https://doi.org/10.1186/s13104-019-4534-3
chicago: Antoniou, Michael N., Armel Nicolas, Robin Mesnage, Martina Biserni, Francesco
V. Rao, and Cristina Vazquez Martin. “Glyphosate Does Not Substitute for Glycine
in Proteins of Actively Dividing Mammalian Cells.” BMC Research Notes.
BioMed Central, 2019. https://doi.org/10.1186/s13104-019-4534-3.
ieee: M. N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F. V. Rao, and C. V. Martin,
“Glyphosate does not substitute for glycine in proteins of actively dividing mammalian
cells,” BMC Research Notes, vol. 12. BioMed Central, 2019.
ista: Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. 2019. Glyphosate
does not substitute for glycine in proteins of actively dividing mammalian cells.
BMC Research Notes. 12, 494.
mla: Antoniou, Michael N., et al. “Glyphosate Does Not Substitute for Glycine in
Proteins of Actively Dividing Mammalian Cells.” BMC Research Notes, vol.
12, 494, BioMed Central, 2019, doi:10.1186/s13104-019-4534-3.
short: M.N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F.V. Rao, C.V. Martin,
BMC Research Notes 12 (2019).
date_created: 2019-08-18T22:00:39Z
date_published: 2019-08-08T00:00:00Z
date_updated: 2023-02-23T14:08:14Z
day: '08'
ddc:
- '570'
department:
- _id: LifeSc
doi: 10.1186/s13104-019-4534-3
external_id:
pmid:
- '31395095'
file:
- access_level: open_access
checksum: 4a2bb7994b7f2c432bf44f5127ea3102
content_type: application/pdf
creator: dernst
date_created: 2019-08-23T11:10:35Z
date_updated: 2020-07-14T12:47:40Z
file_id: '6829'
file_name: 2019_BMC_Antoniou.pdf
file_size: 1177482
relation: main_file
file_date_updated: 2020-07-14T12:47:40Z
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intvolume: ' 12'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: BMC Research Notes
publication_identifier:
eissn:
- 1756-0500
publication_status: published
publisher: BioMed Central
quality_controlled: '1'
related_material:
record:
- id: '9784'
relation: research_data
status: public
scopus_import: 1
status: public
title: Glyphosate does not substitute for glycine in proteins of actively dividing
mammalian cells
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2019'
...
---
_id: '9784'
abstract:
- lang: eng
text: 'Additional file 1: Table S1. Kinetics of MDA-MB-231 cell growth in either
the presence or absence of 100Â mg/L glyphosate. Cell counts are given at day-1
of seeding flasks and following 6-days of continuous culture. Note: no differences
in cell numbers were observed between negative control and glyphosate treated
cultures.'
article_processing_charge: No
author:
- first_name: Michael N.
full_name: Antoniou, Michael N.
last_name: Antoniou
- first_name: Armel
full_name: Nicolas, Armel
id: 2A103192-F248-11E8-B48F-1D18A9856A87
last_name: Nicolas
- first_name: Robin
full_name: Mesnage, Robin
last_name: Mesnage
- first_name: Martina
full_name: Biserni, Martina
last_name: Biserni
- first_name: Francesco V.
full_name: Rao, Francesco V.
last_name: Rao
- first_name: Cristina Vazquez
full_name: Martin, Cristina Vazquez
last_name: Martin
citation:
ama: Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. MOESM1 of
Glyphosate does not substitute for glycine in proteins of actively dividing mammalian
cells. 2019. doi:10.6084/m9.figshare.9411761.v1
apa: Antoniou, M. N., Nicolas, A., Mesnage, R., Biserni, M., Rao, F. V., & Martin,
C. V. (2019). MOESM1 of Glyphosate does not substitute for glycine in proteins
of actively dividing mammalian cells. Springer Nature. https://doi.org/10.6084/m9.figshare.9411761.v1
chicago: Antoniou, Michael N., Armel Nicolas, Robin Mesnage, Martina Biserni, Francesco
V. Rao, and Cristina Vazquez Martin. “MOESM1 of Glyphosate Does Not Substitute
for Glycine in Proteins of Actively Dividing Mammalian Cells.” Springer Nature,
2019. https://doi.org/10.6084/m9.figshare.9411761.v1.
ieee: M. N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F. V. Rao, and C. V. Martin,
“MOESM1 of Glyphosate does not substitute for glycine in proteins of actively
dividing mammalian cells.” Springer Nature, 2019.
ista: Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. 2019. MOESM1
of Glyphosate does not substitute for glycine in proteins of actively dividing
mammalian cells, Springer Nature, 10.6084/m9.figshare.9411761.v1.
mla: Antoniou, Michael N., et al. MOESM1 of Glyphosate Does Not Substitute for
Glycine in Proteins of Actively Dividing Mammalian Cells. Springer Nature,
2019, doi:10.6084/m9.figshare.9411761.v1.
short: M.N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F.V. Rao, C.V. Martin,
(2019).
date_created: 2021-08-06T08:14:05Z
date_published: 2019-08-09T00:00:00Z
date_updated: 2023-02-23T12:52:29Z
day: '09'
department:
- _id: LifeSc
doi: 10.6084/m9.figshare.9411761.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.9411761.v1
month: '08'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '6819'
relation: used_in_publication
status: public
status: public
title: MOESM1 of Glyphosate does not substitute for glycine in proteins of actively
dividing mammalian cells
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9839'
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_processing_charge: No
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. Data from: Is the sky the limit? On the expansion threshold of
a species’ range. 2019. doi:10.5061/dryad.5vv37'
apa: 'Polechova, J. (2019). Data from: Is the sky the limit? On the expansion threshold
of a species’ range. Dryad. https://doi.org/10.5061/dryad.5vv37'
chicago: 'Polechova, Jitka. “Data from: Is the Sky the Limit? On the Expansion Threshold
of a Species’ Range.” Dryad, 2019. https://doi.org/10.5061/dryad.5vv37.'
ieee: 'J. Polechova, “Data from: Is the sky the limit? On the expansion threshold
of a species’ range.” Dryad, 2019.'
ista: 'Polechova J. 2019. Data from: Is the sky the limit? On the expansion threshold
of a species’ range, Dryad, 10.5061/dryad.5vv37.'
mla: 'Polechova, Jitka. Data from: Is the Sky the Limit? On the Expansion Threshold
of a Species’ Range. Dryad, 2019, doi:10.5061/dryad.5vv37.'
short: J. Polechova, (2019).
date_created: 2021-08-09T13:07:28Z
date_published: 2019-06-22T00:00:00Z
date_updated: 2023-02-23T11:14:30Z
day: '22'
department:
- _id: NiBa
doi: 10.5061/dryad.5vv37
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.5vv37
month: '06'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '315'
relation: used_in_publication
status: public
status: public
title: 'Data from: Is the sky the limit? On the expansion threshold of a species''
range'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '8418'
abstract:
- lang: eng
text: For the Restricted Circular Planar 3 Body Problem, we show that there exists
an open set U in phase space of fixed measure, where the set of initial points
which lead to collision is O(μ120) dense as μ→0.
article_processing_charge: No
article_type: original
author:
- first_name: Marcel
full_name: Guardia, Marcel
last_name: Guardia
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Jianlu
full_name: Zhang, Jianlu
last_name: Zhang
citation:
ama: Guardia M, Kaloshin V, Zhang J. Asymptotic density of collision orbits in the
Restricted Circular Planar 3 Body Problem. Archive for Rational Mechanics and
Analysis. 2019;233(2):799-836. doi:10.1007/s00205-019-01368-7
apa: Guardia, M., Kaloshin, V., & Zhang, J. (2019). Asymptotic density of collision
orbits in the Restricted Circular Planar 3 Body Problem. Archive for Rational
Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-019-01368-7
chicago: Guardia, Marcel, Vadim Kaloshin, and Jianlu Zhang. “Asymptotic Density
of Collision Orbits in the Restricted Circular Planar 3 Body Problem.” Archive
for Rational Mechanics and Analysis. Springer Nature, 2019. https://doi.org/10.1007/s00205-019-01368-7.
ieee: M. Guardia, V. Kaloshin, and J. Zhang, “Asymptotic density of collision orbits
in the Restricted Circular Planar 3 Body Problem,” Archive for Rational Mechanics
and Analysis, vol. 233, no. 2. Springer Nature, pp. 799–836, 2019.
ista: Guardia M, Kaloshin V, Zhang J. 2019. Asymptotic density of collision orbits
in the Restricted Circular Planar 3 Body Problem. Archive for Rational Mechanics
and Analysis. 233(2), 799–836.
mla: Guardia, Marcel, et al. “Asymptotic Density of Collision Orbits in the Restricted
Circular Planar 3 Body Problem.” Archive for Rational Mechanics and Analysis,
vol. 233, no. 2, Springer Nature, 2019, pp. 799–836, doi:10.1007/s00205-019-01368-7.
short: M. Guardia, V. Kaloshin, J. Zhang, Archive for Rational Mechanics and Analysis
233 (2019) 799–836.
date_created: 2020-09-17T10:41:51Z
date_published: 2019-03-12T00:00:00Z
date_updated: 2021-01-12T08:19:09Z
day: '12'
doi: 10.1007/s00205-019-01368-7
extern: '1'
intvolume: ' 233'
issue: '2'
keyword:
- Mechanical Engineering
- Mathematics (miscellaneous)
- Analysis
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/s00205-019-01368-7
month: '03'
oa: 1
oa_version: Published Version
page: 799-836
publication: Archive for Rational Mechanics and Analysis
publication_identifier:
issn:
- 0003-9527
- 1432-0673
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Asymptotic density of collision orbits in the Restricted Circular Planar 3
Body Problem
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 233
year: '2019'
...
---
_id: '8416'
abstract:
- lang: eng
text: In this paper, we show that any smooth one-parameter deformations of a strictly
convex integrable billiard table Ω0 preserving the integrability near the boundary
have to be tangent to a finite dimensional space passing through Ω0.
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
citation:
ama: Huang G, Kaloshin V. On the finite dimensionality of integrable deformations
of strictly convex integrable billiard tables. Moscow Mathematical Journal.
2019;19(2):307-327. doi:10.17323/1609-4514-2019-19-2-307-327
apa: Huang, G., & Kaloshin, V. (2019). On the finite dimensionality of integrable
deformations of strictly convex integrable billiard tables. Moscow Mathematical
Journal. American Mathematical Society. https://doi.org/10.17323/1609-4514-2019-19-2-307-327
chicago: Huang, Guan, and Vadim Kaloshin. “On the Finite Dimensionality of Integrable
Deformations of Strictly Convex Integrable Billiard Tables.” Moscow Mathematical
Journal. American Mathematical Society, 2019. https://doi.org/10.17323/1609-4514-2019-19-2-307-327.
ieee: G. Huang and V. Kaloshin, “On the finite dimensionality of integrable deformations
of strictly convex integrable billiard tables,” Moscow Mathematical Journal,
vol. 19, no. 2. American Mathematical Society, pp. 307–327, 2019.
ista: Huang G, Kaloshin V. 2019. On the finite dimensionality of integrable deformations
of strictly convex integrable billiard tables. Moscow Mathematical Journal. 19(2),
307–327.
mla: Huang, Guan, and Vadim Kaloshin. “On the Finite Dimensionality of Integrable
Deformations of Strictly Convex Integrable Billiard Tables.” Moscow Mathematical
Journal, vol. 19, no. 2, American Mathematical Society, 2019, pp. 307–27,
doi:10.17323/1609-4514-2019-19-2-307-327.
short: G. Huang, V. Kaloshin, Moscow Mathematical Journal 19 (2019) 307–327.
date_created: 2020-09-17T10:41:36Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2021-01-12T08:19:08Z
day: '01'
doi: 10.17323/1609-4514-2019-19-2-307-327
extern: '1'
external_id:
arxiv:
- '1809.09341'
intvolume: ' 19'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1809.09341
month: '04'
oa: 1
oa_version: Preprint
page: 307-327
publication: Moscow Mathematical Journal
publication_identifier:
issn:
- 1609-4514
publication_status: published
publisher: American Mathematical Society
quality_controlled: '1'
status: public
title: On the finite dimensionality of integrable deformations of strictly convex
integrable billiard tables
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2019'
...
---
_id: '8693'
abstract:
- lang: eng
text: We review V. I. Arnold’s 1963 celebrated paper [1] Proof of A. N. Kolmogorov’s
Theorem on the Conservation of Conditionally Periodic Motions with a Small Variation
in the Hamiltonian, and prove that, optimising Arnold’s scheme, one can get “sharp”
asymptotic quantitative conditions (as ε → 0, ε being the strength of the perturbation).
All constants involved are explicitly computed.
article_processing_charge: No
article_type: original
author:
- first_name: Luigi
full_name: Chierchia, Luigi
last_name: Chierchia
- first_name: Edmond
full_name: Koudjinan, Edmond
id: 52DF3E68-AEFA-11EA-95A4-124A3DDC885E
last_name: Koudjinan
orcid: 0000-0003-2640-4049
citation:
ama: Chierchia L, Koudjinan E. V. I. Arnold’s “pointwise” KAM theorem. Regular
and Chaotic Dynamics. 2019;24:583–606. doi:10.1134/S1560354719060017
apa: Chierchia, L., & Koudjinan, E. (2019). V. I. Arnold’s “pointwise” KAM theorem.
Regular and Chaotic Dynamics. Springer. https://doi.org/10.1134/S1560354719060017
chicago: Chierchia, Luigi, and Edmond Koudjinan. “V. I. Arnold’s ‘Pointwise’ KAM
Theorem.” Regular and Chaotic Dynamics. Springer, 2019. https://doi.org/10.1134/S1560354719060017.
ieee: L. Chierchia and E. Koudjinan, “V. I. Arnold’s ‘pointwise’ KAM theorem,” Regular
and Chaotic Dynamics, vol. 24. Springer, pp. 583–606, 2019.
ista: Chierchia L, Koudjinan E. 2019. V. I. Arnold’s “pointwise” KAM theorem. Regular
and Chaotic Dynamics. 24, 583–606.
mla: Chierchia, Luigi, and Edmond Koudjinan. “V. I. Arnold’s ‘Pointwise’ KAM Theorem.”
Regular and Chaotic Dynamics, vol. 24, Springer, 2019, pp. 583–606, doi:10.1134/S1560354719060017.
short: L. Chierchia, E. Koudjinan, Regular and Chaotic Dynamics 24 (2019) 583–606.
date_created: 2020-10-21T15:25:45Z
date_published: 2019-12-10T00:00:00Z
date_updated: 2021-01-12T08:20:34Z
day: '10'
doi: 10.1134/S1560354719060017
extern: '1'
external_id:
arxiv:
- '1908.02523'
intvolume: ' 24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1908.02523
month: '12'
oa: 1
oa_version: Preprint
page: 583–606
publication: Regular and Chaotic Dynamics
publication_status: published
publisher: Springer
quality_controlled: '1'
status: public
title: V. I. Arnold’s “pointwise” KAM theorem
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2019'
...
---
_id: '9018'
abstract:
- lang: eng
text: Anti-silencing function 1 (ASF1) is a conserved H3-H4 histone chaperone involved
in histone dynamics during replication, transcription, and DNA repair. Overexpressed
in proliferating tissues including many tumors, ASF1 has emerged as a promising
therapeutic target. Here, we combine structural, computational, and biochemical
approaches to design peptides that inhibit the ASF1-histone interaction. Starting
from the structure of the human ASF1-histone complex, we developed a rational
design strategy combining epitope tethering and optimization of interface contacts
to identify a potent peptide inhibitor with a dissociation constant of 3 nM. When
introduced into cultured cells, the inhibitors impair cell proliferation, perturb
cell-cycle progression, and reduce cell migration and invasion in a manner commensurate
with their affinity for ASF1. Finally, we find that direct injection of the most
potent ASF1 peptide inhibitor in mouse allografts reduces tumor growth. Our results
open new avenues to use ASF1 inhibitors as promising leads for cancer therapy.
article_processing_charge: No
article_type: original
author:
- first_name: May M
full_name: Bakail, May M
id: FB3C3F8E-522F-11EA-B186-22963DDC885E
last_name: Bakail
orcid: 0000-0002-9592-1587
- first_name: Albane
full_name: Gaubert, Albane
last_name: Gaubert
- first_name: Jessica
full_name: Andreani, Jessica
last_name: Andreani
- first_name: Gwenaëlle
full_name: Moal, Gwenaëlle
last_name: Moal
- first_name: Guillaume
full_name: Pinna, Guillaume
last_name: Pinna
- first_name: Ekaterina
full_name: Boyarchuk, Ekaterina
last_name: Boyarchuk
- first_name: Marie-Cécile
full_name: Gaillard, Marie-Cécile
last_name: Gaillard
- first_name: Regis
full_name: Courbeyrette, Regis
last_name: Courbeyrette
- first_name: Carl
full_name: Mann, Carl
last_name: Mann
- first_name: Jean-Yves
full_name: Thuret, Jean-Yves
last_name: Thuret
- first_name: Bérengère
full_name: Guichard, Bérengère
last_name: Guichard
- first_name: Brice
full_name: Murciano, Brice
last_name: Murciano
- first_name: Nicolas
full_name: Richet, Nicolas
last_name: Richet
- first_name: Adeline
full_name: Poitou, Adeline
last_name: Poitou
- first_name: Claire
full_name: Frederic, Claire
last_name: Frederic
- first_name: Marie-Hélène
full_name: Le Du, Marie-Hélène
last_name: Le Du
- first_name: Morgane
full_name: Agez, Morgane
last_name: Agez
- first_name: Caroline
full_name: Roelants, Caroline
last_name: Roelants
- first_name: Zachary A.
full_name: Gurard-Levin, Zachary A.
last_name: Gurard-Levin
- first_name: Geneviève
full_name: Almouzni, Geneviève
last_name: Almouzni
- first_name: Nadia
full_name: Cherradi, Nadia
last_name: Cherradi
- first_name: Raphael
full_name: Guerois, Raphael
last_name: Guerois
- first_name: Françoise
full_name: Ochsenbein, Françoise
last_name: Ochsenbein
citation:
ama: Bakail MM, Gaubert A, Andreani J, et al. Design on a rational basis of high-affinity
peptides inhibiting the histone chaperone ASF1. Cell Chemical Biology.
2019;26(11):1573-1585.e10. doi:10.1016/j.chembiol.2019.09.002
apa: Bakail, M. M., Gaubert, A., Andreani, J., Moal, G., Pinna, G., Boyarchuk, E.,
… Ochsenbein, F. (2019). Design on a rational basis of high-affinity peptides
inhibiting the histone chaperone ASF1. Cell Chemical Biology. Elsevier.
https://doi.org/10.1016/j.chembiol.2019.09.002
chicago: Bakail, May M, Albane Gaubert, Jessica Andreani, Gwenaëlle Moal, Guillaume
Pinna, Ekaterina Boyarchuk, Marie-Cécile Gaillard, et al. “Design on a Rational
Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1.” Cell
Chemical Biology. Elsevier, 2019. https://doi.org/10.1016/j.chembiol.2019.09.002.
ieee: M. M. Bakail et al., “Design on a rational basis of high-affinity peptides
inhibiting the histone chaperone ASF1,” Cell Chemical Biology, vol. 26,
no. 11. Elsevier, p. 1573–1585.e10, 2019.
ista: Bakail MM, Gaubert A, Andreani J, Moal G, Pinna G, Boyarchuk E, Gaillard M-C,
Courbeyrette R, Mann C, Thuret J-Y, Guichard B, Murciano B, Richet N, Poitou A,
Frederic C, Le Du M-H, Agez M, Roelants C, Gurard-Levin ZA, Almouzni G, Cherradi
N, Guerois R, Ochsenbein F. 2019. Design on a rational basis of high-affinity
peptides inhibiting the histone chaperone ASF1. Cell Chemical Biology. 26(11),
1573–1585.e10.
mla: Bakail, May M., et al. “Design on a Rational Basis of High-Affinity Peptides
Inhibiting the Histone Chaperone ASF1.” Cell Chemical Biology, vol. 26,
no. 11, Elsevier, 2019, p. 1573–1585.e10, doi:10.1016/j.chembiol.2019.09.002.
short: M.M. Bakail, A. Gaubert, J. Andreani, G. Moal, G. Pinna, E. Boyarchuk, M.-C.
Gaillard, R. Courbeyrette, C. Mann, J.-Y. Thuret, B. Guichard, B. Murciano, N.
Richet, A. Poitou, C. Frederic, M.-H. Le Du, M. Agez, C. Roelants, Z.A. Gurard-Levin,
G. Almouzni, N. Cherradi, R. Guerois, F. Ochsenbein, Cell Chemical Biology 26
(2019) 1573–1585.e10.
date_created: 2021-01-19T11:04:50Z
date_published: 2019-11-21T00:00:00Z
date_updated: 2023-02-23T13:46:53Z
day: '21'
doi: 10.1016/j.chembiol.2019.09.002
extern: '1'
external_id:
pmid:
- '31543461'
intvolume: ' 26'
issue: '11'
keyword:
- Clinical Biochemistry
- Molecular Medicine
- Biochemistry
- Molecular Biology
- Pharmacology
- Drug Discovery
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.chembiol.2019.09.002
month: '11'
oa: 1
oa_version: Published Version
page: 1573-1585.e10
pmid: 1
publication: Cell Chemical Biology
publication_identifier:
issn:
- 2451-9456
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Design on a rational basis of high-affinity peptides inhibiting the histone
chaperone ASF1
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2019'
...
---
_id: '9530'
abstract:
- lang: eng
text: "Background\r\nDNA methylation of active genes, also known as gene body methylation,
is found in many animal and plant genomes. Despite this, the transcriptional and
developmental role of such methylation remains poorly understood. Here, we explore
the dynamic range of DNA methylation in honey bee, a model organism for gene body
methylation.\r\n\r\nResults\r\nOur data show that CG methylation in gene bodies
globally fluctuates during honey bee development. However, these changes cause
no gene expression alterations. Intriguingly, despite the global alterations,
tissue-specific CG methylation patterns of complete genes or exons are rare, implying
robust maintenance of genic methylation during development. Additionally, we show
that CG methylation maintenance fluctuates in somatic cells, while reaching maximum
fidelity in sperm cells. Finally, unlike universally present CG methylation, we
discovered non-CG methylation specifically in bee heads that resembles such methylation
in mammalian brain tissue.\r\n\r\nConclusions\r\nBased on these results, we propose
that gene body CG methylation can oscillate during development if it is kept to
a level adequate to preserve function. Additionally, our data suggest that heightened
non-CG methylation is a conserved regulator of animal nervous systems."
article_number: '62'
article_processing_charge: No
article_type: original
author:
- first_name: Keith D.
full_name: Harris, Keith D.
last_name: Harris
- first_name: James P. B.
full_name: Lloyd, James P. B.
last_name: Lloyd
- first_name: Katherine
full_name: Domb, Katherine
last_name: Domb
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Assaf
full_name: Zemach, Assaf
last_name: Zemach
citation:
ama: Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. DNA methylation is maintained
with high fidelity in the honey bee germline and exhibits global non-functional
fluctuations during somatic development. Epigenetics and Chromatin. 2019;12.
doi:10.1186/s13072-019-0307-4
apa: Harris, K. D., Lloyd, J. P. B., Domb, K., Zilberman, D., & Zemach, A. (2019).
DNA methylation is maintained with high fidelity in the honey bee germline and
exhibits global non-functional fluctuations during somatic development. Epigenetics
and Chromatin. Springer Nature. https://doi.org/10.1186/s13072-019-0307-4
chicago: Harris, Keith D., James P. B. Lloyd, Katherine Domb, Daniel Zilberman,
and Assaf Zemach. “DNA Methylation Is Maintained with High Fidelity in the Honey
Bee Germline and Exhibits Global Non-Functional Fluctuations during Somatic Development.”
Epigenetics and Chromatin. Springer Nature, 2019. https://doi.org/10.1186/s13072-019-0307-4.
ieee: K. D. Harris, J. P. B. Lloyd, K. Domb, D. Zilberman, and A. Zemach, “DNA methylation
is maintained with high fidelity in the honey bee germline and exhibits global
non-functional fluctuations during somatic development,” Epigenetics and Chromatin,
vol. 12. Springer Nature, 2019.
ista: Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. 2019. DNA methylation
is maintained with high fidelity in the honey bee germline and exhibits global
non-functional fluctuations during somatic development. Epigenetics and Chromatin.
12, 62.
mla: Harris, Keith D., et al. “DNA Methylation Is Maintained with High Fidelity
in the Honey Bee Germline and Exhibits Global Non-Functional Fluctuations during
Somatic Development.” Epigenetics and Chromatin, vol. 12, 62, Springer
Nature, 2019, doi:10.1186/s13072-019-0307-4.
short: K.D. Harris, J.P.B. Lloyd, K. Domb, D. Zilberman, A. Zemach, Epigenetics
and Chromatin 12 (2019).
date_created: 2021-06-08T09:21:51Z
date_published: 2019-10-10T00:00:00Z
date_updated: 2021-12-14T07:53:00Z
day: '10'
ddc:
- '570'
department:
- _id: DaZi
doi: 10.1186/s13072-019-0307-4
extern: '1'
external_id:
pmid:
- '31601251'
file:
- access_level: open_access
checksum: 86ff50a7517891511af2733c76c81b67
content_type: application/pdf
creator: asandaue
date_created: 2021-06-08T09:29:19Z
date_updated: 2021-06-08T09:29:19Z
file_id: '9531'
file_name: 2019_EpigeneticsAndChromatin_Harris.pdf
file_size: 3221067
relation: main_file
success: 1
file_date_updated: 2021-06-08T09:29:19Z
has_accepted_license: '1'
intvolume: ' 12'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Epigenetics and Chromatin
publication_identifier:
eissn:
- 1756-8935
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA methylation is maintained with high fidelity in the honey bee germline
and exhibits global non-functional fluctuations during somatic development
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 12
year: '2019'
...
---
_id: '9586'
abstract:
- lang: eng
text: "Consider integers \U0001D458,ℓ such that 0⩽ℓ⩽(\U0001D4582) . Given a large
graph \U0001D43A , what is the fraction of \U0001D458 -vertex subsets of \U0001D43A
\ which span exactly ℓ edges? When \U0001D43A is empty or complete, and ℓ
\ is zero or (\U0001D4582) , this fraction can be exactly 1. On the other hand,
if ℓ is far from these extreme values, one might expect that this fraction is
substantially smaller than 1. This was recently proved by Alon, Hefetz, Krivelevich,
and Tyomkyn who initiated the systematic study of this question and proposed several
natural conjectures.\r\nLet ℓ∗=min{ℓ,(\U0001D4582)−ℓ} . Our main result is that
for any \U0001D458 and ℓ , the fraction of \U0001D458 -vertex subsets that
span ℓ edges is at most log\U0001D442(1)(ℓ∗/\U0001D458)√ \U0001D458/ℓ∗, which
is best-possible up to the logarithmic factor. This improves on multiple results
of Alon, Hefetz, Krivelevich, and Tyomkyn, and resolves one of their conjectures.
In addition, we also make some first steps towards some analogous questions for
hypergraphs.\r\nOur proofs involve some Ramsey-type arguments, and a number of
different probabilistic tools, such as polynomial anticoncentration inequalities,
hypercontractivity, and a coupling trick for random variables defined on a ‘slice’
of the Boolean hypercube."
article_processing_charge: No
article_type: original
author:
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Benny
full_name: Sudakov, Benny
last_name: Sudakov
- first_name: Tuan
full_name: Tran, Tuan
last_name: Tran
citation:
ama: Kwan MA, Sudakov B, Tran T. Anticoncentration for subgraph statistics. Journal
of the London Mathematical Society. 2019;99(3):757-777. doi:10.1112/jlms.12192
apa: Kwan, M. A., Sudakov, B., & Tran, T. (2019). Anticoncentration for subgraph
statistics. Journal of the London Mathematical Society. Wiley. https://doi.org/10.1112/jlms.12192
chicago: Kwan, Matthew Alan, Benny Sudakov, and Tuan Tran. “Anticoncentration for
Subgraph Statistics.” Journal of the London Mathematical Society. Wiley,
2019. https://doi.org/10.1112/jlms.12192.
ieee: M. A. Kwan, B. Sudakov, and T. Tran, “Anticoncentration for subgraph statistics,”
Journal of the London Mathematical Society, vol. 99, no. 3. Wiley, pp.
757–777, 2019.
ista: Kwan MA, Sudakov B, Tran T. 2019. Anticoncentration for subgraph statistics.
Journal of the London Mathematical Society. 99(3), 757–777.
mla: Kwan, Matthew Alan, et al. “Anticoncentration for Subgraph Statistics.” Journal
of the London Mathematical Society, vol. 99, no. 3, Wiley, 2019, pp. 757–77,
doi:10.1112/jlms.12192.
short: M.A. Kwan, B. Sudakov, T. Tran, Journal of the London Mathematical Society
99 (2019) 757–777.
date_created: 2021-06-22T09:46:03Z
date_published: 2019-05-03T00:00:00Z
date_updated: 2023-02-23T14:01:53Z
day: '03'
doi: 10.1112/jlms.12192
extern: '1'
external_id:
arxiv:
- '1807.05202'
intvolume: ' 99'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1807.05202
month: '05'
oa: 1
oa_version: Preprint
page: 757-777
publication: Journal of the London Mathematical Society
publication_identifier:
eissn:
- 1469-7750
issn:
- 0024-6107
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Anticoncentration for subgraph statistics
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 99
year: '2019'
...
---
_id: '9580'
abstract:
- lang: eng
text: An r-cut of a k-uniform hypergraph H is a partition of the vertex set of H
into r parts and the size of the cut is the number of edges which have a vertex
in each part. A classical result of Edwards says that every m-edge graph has a
2-cut of size m/2+Ω)(m−−√) and this is best possible. That is, there exist cuts
which exceed the expected size of a random cut by some multiple of the standard
deviation. We study analogues of this and related results in hypergraphs. First,
we observe that similarly to graphs, every m-edge k-uniform hypergraph has an
r-cut whose size is Ω(m−−√) larger than the expected size of a random r-cut. Moreover,
in the case where k = 3 and r = 2 this bound is best possible and is attained
by Steiner triple systems. Surprisingly, for all other cases (that is, if k ≥
4 or r ≥ 3), we show that every m-edge k-uniform hypergraph has an r-cut whose
size is Ω(m5/9) larger than the expected size of a random r-cut. This is a significant
difference in behaviour, since the amount by which the size of the largest cut
exceeds the expected size of a random cut is now considerably larger than the
standard deviation.
article_processing_charge: No
article_type: original
author:
- first_name: David
full_name: Conlon, David
last_name: Conlon
- first_name: Jacob
full_name: Fox, Jacob
last_name: Fox
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Benny
full_name: Sudakov, Benny
last_name: Sudakov
citation:
ama: Conlon D, Fox J, Kwan MA, Sudakov B. Hypergraph cuts above the average. Israel
Journal of Mathematics. 2019;233(1):67-111. doi:10.1007/s11856-019-1897-z
apa: Conlon, D., Fox, J., Kwan, M. A., & Sudakov, B. (2019). Hypergraph cuts
above the average. Israel Journal of Mathematics. Springer. https://doi.org/10.1007/s11856-019-1897-z
chicago: Conlon, David, Jacob Fox, Matthew Alan Kwan, and Benny Sudakov. “Hypergraph
Cuts above the Average.” Israel Journal of Mathematics. Springer, 2019.
https://doi.org/10.1007/s11856-019-1897-z.
ieee: D. Conlon, J. Fox, M. A. Kwan, and B. Sudakov, “Hypergraph cuts above the
average,” Israel Journal of Mathematics, vol. 233, no. 1. Springer, pp.
67–111, 2019.
ista: Conlon D, Fox J, Kwan MA, Sudakov B. 2019. Hypergraph cuts above the average.
Israel Journal of Mathematics. 233(1), 67–111.
mla: Conlon, David, et al. “Hypergraph Cuts above the Average.” Israel Journal
of Mathematics, vol. 233, no. 1, Springer, 2019, pp. 67–111, doi:10.1007/s11856-019-1897-z.
short: D. Conlon, J. Fox, M.A. Kwan, B. Sudakov, Israel Journal of Mathematics 233
(2019) 67–111.
date_created: 2021-06-21T13:36:02Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2023-02-23T14:01:41Z
day: '01'
doi: 10.1007/s11856-019-1897-z
extern: '1'
external_id:
arxiv:
- '1803.08462'
intvolume: ' 233'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1803.08462
month: '08'
oa: 1
oa_version: Preprint
page: 67-111
publication: Israel Journal of Mathematics
publication_identifier:
eissn:
- 1565-8511
issn:
- 0021-2172
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: Hypergraph cuts above the average
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 233
year: '2019'
...
---
_id: '9585'
abstract:
- lang: eng
text: An n-vertex graph is called C-Ramsey if it has no clique or independent set
of size C log n. All known constructions of Ramsey graphs involve randomness in
an essential way, and there is an ongoing line of research towards showing that
in fact all Ramsey graphs must obey certain “richness” properties characteristic
of random graphs. More than 25 years ago, Erdős, Faudree and Sós conjectured that
in any C-Ramsey graph there are Ω(n^5/2) induced subgraphs, no pair of which have
the same numbers of vertices and edges. Improving on earlier results of Alon,
Balogh, Kostochka and Samotij, in this paper we prove this conjecture.
article_processing_charge: No
article_type: original
author:
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Benny
full_name: Sudakov, Benny
last_name: Sudakov
citation:
ama: Kwan MA, Sudakov B. Proof of a conjecture on induced subgraphs of Ramsey graphs.
Transactions of the American Mathematical Society. 2019;372(8):5571-5594.
doi:10.1090/tran/7729
apa: Kwan, M. A., & Sudakov, B. (2019). Proof of a conjecture on induced subgraphs
of Ramsey graphs. Transactions of the American Mathematical Society. American
Mathematical Society. https://doi.org/10.1090/tran/7729
chicago: Kwan, Matthew Alan, and Benny Sudakov. “Proof of a Conjecture on Induced
Subgraphs of Ramsey Graphs.” Transactions of the American Mathematical Society.
American Mathematical Society, 2019. https://doi.org/10.1090/tran/7729.
ieee: M. A. Kwan and B. Sudakov, “Proof of a conjecture on induced subgraphs of
Ramsey graphs,” Transactions of the American Mathematical Society, vol.
372, no. 8. American Mathematical Society, pp. 5571–5594, 2019.
ista: Kwan MA, Sudakov B. 2019. Proof of a conjecture on induced subgraphs of Ramsey
graphs. Transactions of the American Mathematical Society. 372(8), 5571–5594.
mla: Kwan, Matthew Alan, and Benny Sudakov. “Proof of a Conjecture on Induced Subgraphs
of Ramsey Graphs.” Transactions of the American Mathematical Society, vol.
372, no. 8, American Mathematical Society, 2019, pp. 5571–94, doi:10.1090/tran/7729.
short: M.A. Kwan, B. Sudakov, Transactions of the American Mathematical Society
372 (2019) 5571–5594.
date_created: 2021-06-22T09:31:45Z
date_published: 2019-10-15T00:00:00Z
date_updated: 2023-02-23T14:01:50Z
day: '15'
doi: 10.1090/tran/7729
extern: '1'
external_id:
arxiv:
- '1712.05656'
intvolume: ' 372'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1090/tran/7729
month: '10'
oa: 1
oa_version: Submitted Version
page: 5571-5594
publication: Transactions of the American Mathematical Society
publication_identifier:
eissn:
- 1088-6850
issn:
- 0002-9947
publication_status: published
publisher: American Mathematical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Proof of a conjecture on induced subgraphs of Ramsey graphs
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 372
year: '2019'
...
---
_id: '9677'
abstract:
- lang: eng
text: Progress in the atomic-scale modeling of matter over the past decade has been
tremendous. This progress has been brought about by improvements in methods for
evaluating interatomic forces that work by either solving the electronic structure
problem explicitly, or by computing accurate approximations of the solution and
by the development of techniques that use the Born–Oppenheimer (BO) forces to
move the atoms on the BO potential energy surface. As a consequence of these developments
it is now possible to identify stable or metastable states, to sample configurations
consistent with the appropriate thermodynamic ensemble, and to estimate the kinetics
of reactions and phase transitions. All too often, however, progress is slowed
down by the bottleneck associated with implementing new optimization algorithms
and/or sampling techniques into the many existing electronic-structure and empirical-potential
codes. To address this problem, we are thus releasing a new version of the i-PI
software. This piece of software is an easily extensible framework for implementing
advanced atomistic simulation techniques using interatomic potentials and forces
calculated by an external driver code. While the original version of the code
(Ceriotti et al., 2014) was developed with a focus on path integral molecular
dynamics techniques, this second release of i-PI not only includes several new
advanced path integral methods, but also offers other classes of algorithms. In
other words, i-PI is moving towards becoming a universal force engine that is
both modular and tightly coupled to the driver codes that evaluate the potential
energy surface and its derivatives.
article_processing_charge: No
article_type: original
author:
- first_name: Venkat
full_name: Kapil, Venkat
last_name: Kapil
- first_name: Mariana
full_name: Rossi, Mariana
last_name: Rossi
- first_name: Ondrej
full_name: Marsalek, Ondrej
last_name: Marsalek
- first_name: Riccardo
full_name: Petraglia, Riccardo
last_name: Petraglia
- first_name: Yair
full_name: Litman, Yair
last_name: Litman
- first_name: Thomas
full_name: Spura, Thomas
last_name: Spura
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Alice
full_name: Cuzzocrea, Alice
last_name: Cuzzocrea
- first_name: Robert H.
full_name: Meißner, Robert H.
last_name: Meißner
- first_name: David M.
full_name: Wilkins, David M.
last_name: Wilkins
- first_name: Benjamin A.
full_name: Helfrecht, Benjamin A.
last_name: Helfrecht
- first_name: Przemysław
full_name: Juda, Przemysław
last_name: Juda
- first_name: Sébastien P.
full_name: Bienvenue, Sébastien P.
last_name: Bienvenue
- first_name: Wei
full_name: Fang, Wei
last_name: Fang
- first_name: Jan
full_name: Kessler, Jan
last_name: Kessler
- first_name: Igor
full_name: Poltavsky, Igor
last_name: Poltavsky
- first_name: Steven
full_name: Vandenbrande, Steven
last_name: Vandenbrande
- first_name: Jelle
full_name: Wieme, Jelle
last_name: Wieme
- first_name: Clemence
full_name: Corminboeuf, Clemence
last_name: Corminboeuf
- first_name: Thomas D.
full_name: Kühne, Thomas D.
last_name: Kühne
- first_name: David E.
full_name: Manolopoulos, David E.
last_name: Manolopoulos
- first_name: Thomas E.
full_name: Markland, Thomas E.
last_name: Markland
- first_name: Jeremy O.
full_name: Richardson, Jeremy O.
last_name: Richardson
- first_name: Alexandre
full_name: Tkatchenko, Alexandre
last_name: Tkatchenko
- first_name: Gareth A.
full_name: Tribello, Gareth A.
last_name: Tribello
- first_name: Veronique
full_name: Van Speybroeck, Veronique
last_name: Van Speybroeck
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: 'Kapil V, Rossi M, Marsalek O, et al. i-PI 2.0: A universal force engine for
advanced molecular simulations. Computer Physics Communications. 2019;236:214-223.
doi:10.1016/j.cpc.2018.09.020'
apa: 'Kapil, V., Rossi, M., Marsalek, O., Petraglia, R., Litman, Y., Spura, T.,
… Ceriotti, M. (2019). i-PI 2.0: A universal force engine for advanced molecular
simulations. Computer Physics Communications. Elsevier. https://doi.org/10.1016/j.cpc.2018.09.020'
chicago: 'Kapil, Venkat, Mariana Rossi, Ondrej Marsalek, Riccardo Petraglia, Yair
Litman, Thomas Spura, Bingqing Cheng, et al. “I-PI 2.0: A Universal Force Engine
for Advanced Molecular Simulations.” Computer Physics Communications. Elsevier,
2019. https://doi.org/10.1016/j.cpc.2018.09.020.'
ieee: 'V. Kapil et al., “i-PI 2.0: A universal force engine for advanced
molecular simulations,” Computer Physics Communications, vol. 236. Elsevier,
pp. 214–223, 2019.'
ista: 'Kapil V, Rossi M, Marsalek O, Petraglia R, Litman Y, Spura T, Cheng B, Cuzzocrea
A, Meißner RH, Wilkins DM, Helfrecht BA, Juda P, Bienvenue SP, Fang W, Kessler
J, Poltavsky I, Vandenbrande S, Wieme J, Corminboeuf C, Kühne TD, Manolopoulos
DE, Markland TE, Richardson JO, Tkatchenko A, Tribello GA, Van Speybroeck V, Ceriotti
M. 2019. i-PI 2.0: A universal force engine for advanced molecular simulations.
Computer Physics Communications. 236, 214–223.'
mla: 'Kapil, Venkat, et al. “I-PI 2.0: A Universal Force Engine for Advanced Molecular
Simulations.” Computer Physics Communications, vol. 236, Elsevier, 2019,
pp. 214–23, doi:10.1016/j.cpc.2018.09.020.'
short: V. Kapil, M. Rossi, O. Marsalek, R. Petraglia, Y. Litman, T. Spura, B. Cheng,
A. Cuzzocrea, R.H. Meißner, D.M. Wilkins, B.A. Helfrecht, P. Juda, S.P. Bienvenue,
W. Fang, J. Kessler, I. Poltavsky, S. Vandenbrande, J. Wieme, C. Corminboeuf,
T.D. Kühne, D.E. Manolopoulos, T.E. Markland, J.O. Richardson, A. Tkatchenko,
G.A. Tribello, V. Van Speybroeck, M. Ceriotti, Computer Physics Communications
236 (2019) 214–223.
date_created: 2021-07-16T08:53:01Z
date_published: 2019-03-01T00:00:00Z
date_updated: 2021-08-09T12:37:16Z
day: '01'
doi: 10.1016/j.cpc.2018.09.020
extern: '1'
external_id:
arxiv:
- '1808.03824'
intvolume: ' 236'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1808.03824
month: '03'
oa: 1
oa_version: Preprint
page: 214-223
publication: Computer Physics Communications
publication_identifier:
issn:
- 0010-4655
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'i-PI 2.0: A universal force engine for advanced molecular simulations'
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 236
year: '2019'
...
---
_id: '9680'
abstract:
- lang: eng
text: Atomistic modeling of phase transitions, chemical reactions, or other rare
events that involve overcoming high free energy barriers usually entails prohibitively
long simulation times. Introducing a bias potential as a function of an appropriately
chosen set of collective variables can significantly accelerate the exploration
of phase space, albeit at the price of distorting the distribution of microstates.
Efficient reweighting to recover the unbiased distribution can be nontrivial when
employing adaptive sampling techniques such as metadynamics, variationally enhanced
sampling, or parallel bias metadynamics, in which the system evolves in a quasi-equilibrium
manner under a time-dependent bias. We introduce an iterative unbiasing scheme
that makes efficient use of all the trajectory data and that does not require
the distribution to be evaluated on a grid. The method can thus be used even when
the bias has a high dimensionality. We benchmark this approach against some of
the existing schemes on model systems with different complexity and dimensionality.
article_processing_charge: No
article_type: original
author:
- first_name: F.
full_name: Giberti, F.
last_name: Giberti
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: G. A.
full_name: Tribello, G. A.
last_name: Tribello
- first_name: M.
full_name: Ceriotti, M.
last_name: Ceriotti
citation:
ama: Giberti F, Cheng B, Tribello GA, Ceriotti M. Iterative unbiasing of quasi-equilibrium
sampling. Journal of Chemical Theory and Computation. 2019;16(1):100-107.
doi:10.1021/acs.jctc.9b00907
apa: Giberti, F., Cheng, B., Tribello, G. A., & Ceriotti, M. (2019). Iterative
unbiasing of quasi-equilibrium sampling. Journal of Chemical Theory and Computation.
American Chemical Society. https://doi.org/10.1021/acs.jctc.9b00907
chicago: Giberti, F., Bingqing Cheng, G. A. Tribello, and M. Ceriotti. “Iterative
Unbiasing of Quasi-Equilibrium Sampling.” Journal of Chemical Theory and Computation.
American Chemical Society, 2019. https://doi.org/10.1021/acs.jctc.9b00907.
ieee: F. Giberti, B. Cheng, G. A. Tribello, and M. Ceriotti, “Iterative unbiasing
of quasi-equilibrium sampling,” Journal of Chemical Theory and Computation,
vol. 16, no. 1. American Chemical Society, pp. 100–107, 2019.
ista: Giberti F, Cheng B, Tribello GA, Ceriotti M. 2019. Iterative unbiasing of
quasi-equilibrium sampling. Journal of Chemical Theory and Computation. 16(1),
100–107.
mla: Giberti, F., et al. “Iterative Unbiasing of Quasi-Equilibrium Sampling.” Journal
of Chemical Theory and Computation, vol. 16, no. 1, American Chemical Society,
2019, pp. 100–07, doi:10.1021/acs.jctc.9b00907.
short: F. Giberti, B. Cheng, G.A. Tribello, M. Ceriotti, Journal of Chemical Theory
and Computation 16 (2019) 100–107.
date_created: 2021-07-19T06:56:45Z
date_published: 2019-01-14T00:00:00Z
date_updated: 2021-08-09T12:37:37Z
day: '14'
doi: 10.1021/acs.jctc.9b00907
extern: '1'
external_id:
arxiv:
- '1911.01140'
pmid:
- '31743021'
intvolume: ' 16'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1911.01140
month: '01'
oa: 1
oa_version: Preprint
page: 100-107
pmid: 1
publication: Journal of Chemical Theory and Computation
publication_identifier:
eissn:
- 1549-9626
issn:
- 1549-9618
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Iterative unbiasing of quasi-equilibrium sampling
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 16
year: '2019'
...
---
_id: '12600'
abstract:
- lang: eng
text: The snow cover dynamics of High Mountain Asia are usually assessed at spatial
resolutions of 250 m or greater, but this scale is too coarse to clearly represent
the rugged topography common to the region. Higher-resolution measurement of snow-covered
area often results in biased sampling due to cloud cover and deep shadows. We
therefore develop a Normalized Difference Snow Index-based workflow to delineate
snow lines from Landsat Thematic Mapper/Enhanced Thematic Mapper+ imagery and
apply it to the upper Langtang Valley in Nepal, processing 194 scenes spanning
1999 to 2013. For each scene, we determine the spatial distribution of snow line
altitudes (SLAs) with respect to aspect and across six subcatchments. Our results
show that the mean SLA exhibits distinct seasonal behavior based on aspect and
subcatchment position. We find that SLA dynamics respond to spatial and seasonal
trade-offs in precipitation, temperature, and solar radiation, which act as primary
controls. We identify two SLA spatial gradients, which we attribute to the effect
of spatially variable precipitation. Our results also reveal that aspect-related
SLA differences vary seasonally and are influenced by solar radiation. In terms
of seasonal dominant controls, we demonstrate that the snow line is controlled
by snow precipitation in winter, melt in premonsoon, a combination of both in
postmonsoon, and temperature in monsoon, explaining to a large extent the spatial
and seasonal variability of the SLA in the upper Langtang Valley. We conclude
that while SLA and snow-covered area are complementary metrics, the SLA has a
strong potential for understanding local-scale snow cover dynamics and their controlling
mechanisms.
article_processing_charge: No
article_type: original
author:
- first_name: Marc
full_name: Girona‐Mata, Marc
last_name: Girona‐Mata
- first_name: Evan S.
full_name: Miles, Evan S.
last_name: Miles
- first_name: Silvan
full_name: Ragettli, Silvan
last_name: Ragettli
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
citation:
ama: Girona‐Mata M, Miles ES, Ragettli S, Pellicciotti F. High‐resolution snowline
delineation from Landsat imagery to infer snow cover controls in a Himalayan catchment.
Water Resources Research. 2019;55(8):6754-6772. doi:10.1029/2019wr024935
apa: Girona‐Mata, M., Miles, E. S., Ragettli, S., & Pellicciotti, F. (2019).
High‐resolution snowline delineation from Landsat imagery to infer snow cover
controls in a Himalayan catchment. Water Resources Research. American Geophysical
Union. https://doi.org/10.1029/2019wr024935
chicago: Girona‐Mata, Marc, Evan S. Miles, Silvan Ragettli, and Francesca Pellicciotti.
“High‐resolution Snowline Delineation from Landsat Imagery to Infer Snow Cover
Controls in a Himalayan Catchment.” Water Resources Research. American
Geophysical Union, 2019. https://doi.org/10.1029/2019wr024935.
ieee: M. Girona‐Mata, E. S. Miles, S. Ragettli, and F. Pellicciotti, “High‐resolution
snowline delineation from Landsat imagery to infer snow cover controls in a Himalayan
catchment,” Water Resources Research, vol. 55, no. 8. American Geophysical
Union, pp. 6754–6772, 2019.
ista: Girona‐Mata M, Miles ES, Ragettli S, Pellicciotti F. 2019. High‐resolution
snowline delineation from Landsat imagery to infer snow cover controls in a Himalayan
catchment. Water Resources Research. 55(8), 6754–6772.
mla: Girona‐Mata, Marc, et al. “High‐resolution Snowline Delineation from Landsat
Imagery to Infer Snow Cover Controls in a Himalayan Catchment.” Water Resources
Research, vol. 55, no. 8, American Geophysical Union, 2019, pp. 6754–72, doi:10.1029/2019wr024935.
short: M. Girona‐Mata, E.S. Miles, S. Ragettli, F. Pellicciotti, Water Resources
Research 55 (2019) 6754–6772.
date_created: 2023-02-20T08:12:59Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2023-02-28T12:14:18Z
day: '01'
doi: 10.1029/2019wr024935
extern: '1'
intvolume: ' 55'
issue: '8'
keyword:
- Water Science and Technology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1029/2019WR024935
month: '08'
oa: 1
oa_version: Published Version
page: 6754-6772
publication: Water Resources Research
publication_identifier:
eissn:
- 1944-7973
issn:
- 0043-1397
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
scopus_import: '1'
status: public
title: High‐resolution snowline delineation from Landsat imagery to infer snow cover
controls in a Himalayan catchment
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2019'
...
---
_id: '12602'
abstract:
- lang: eng
text: 'This study aims at developing and applying a spatially-distributed coupled
glacier mass balance and ice-flow model to attribute the response of glaciers
to natural and anthropogenic climate change. We focus on two glaciers with contrasting
surface characteristics: a debris-covered glacier (Langtang Glacier in Nepal)
and a clean-ice glacier (Hintereisferner in Austria). The model is applied from
the end of the Little Ice Age (1850) to the present-day (2016) and is forced with
four bias-corrected General Circulation Models (GCMs) from the historical experiment
of the CMIP5 archive. The selected GCMs represent region-specific warm-dry, warm-wet,
cold-dry, and cold-wet climate conditions. To isolate the effects of anthropogenic
climate change on glacier mass balance and flow runs from these GCMs with and
without further anthropogenic forcing after 1970 until 2016 are selected. The
outcomes indicate that both glaciers experience the largest reduction in area
and volume under warm climate conditions, whereas area and volume reductions are
smaller under cold climate conditions. Simultaneously with changes in glacier
area and volume, surface velocities generally decrease over time. Without further
anthropogenic forcing the results reveal a 3% (9%) smaller decline in glacier
area (volume) for the debris-covered glacier and a 18% (39%) smaller decline in
glacier area (volume) for the clean-ice glacier. The difference in the magnitude
between the two glaciers can mainly be attributed to differences in the response
time of the glaciers, where the clean-ice glacier shows a much faster response
to climate change. We conclude that the response of the two glaciers can mainly
be attributed to anthropogenic climate change and that the impact is larger on
the clean-ice glacier. The outcomes show that the model performs well under different
climate conditions and that the developed approach can be used for regional-scale
glacio-hydrological modeling.'
article_number: '143'
article_processing_charge: No
article_type: original
author:
- first_name: René R.
full_name: Wijngaard, René R.
last_name: Wijngaard
- first_name: Jakob F.
full_name: Steiner, Jakob F.
last_name: Steiner
- first_name: Philip D. A.
full_name: Kraaijenbrink, Philip D. A.
last_name: Kraaijenbrink
- first_name: Christoph
full_name: Klug, Christoph
last_name: Klug
- first_name: Surendra
full_name: Adhikari, Surendra
last_name: Adhikari
- first_name: Argha
full_name: Banerjee, Argha
last_name: Banerjee
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: Ludovicus P. H.
full_name: van Beek, Ludovicus P. H.
last_name: van Beek
- first_name: Marc F. P.
full_name: Bierkens, Marc F. P.
last_name: Bierkens
- first_name: Arthur F.
full_name: Lutz, Arthur F.
last_name: Lutz
- first_name: Walter W.
full_name: Immerzeel, Walter W.
last_name: Immerzeel
citation:
ama: Wijngaard RR, Steiner JF, Kraaijenbrink PDA, et al. Modeling the response of
the Langtang Glacier and the Hintereisferner to a changing climate since the Little
Ice Age. Frontiers in Earth Science. 2019;7. doi:10.3389/feart.2019.00143
apa: Wijngaard, R. R., Steiner, J. F., Kraaijenbrink, P. D. A., Klug, C., Adhikari,
S., Banerjee, A., … Immerzeel, W. W. (2019). Modeling the response of the Langtang
Glacier and the Hintereisferner to a changing climate since the Little Ice Age.
Frontiers in Earth Science. Frontiers Media. https://doi.org/10.3389/feart.2019.00143
chicago: Wijngaard, René R., Jakob F. Steiner, Philip D. A. Kraaijenbrink, Christoph
Klug, Surendra Adhikari, Argha Banerjee, Francesca Pellicciotti, et al. “Modeling
the Response of the Langtang Glacier and the Hintereisferner to a Changing Climate
since the Little Ice Age.” Frontiers in Earth Science. Frontiers Media,
2019. https://doi.org/10.3389/feart.2019.00143.
ieee: R. R. Wijngaard et al., “Modeling the response of the Langtang Glacier
and the Hintereisferner to a changing climate since the Little Ice Age,” Frontiers
in Earth Science, vol. 7. Frontiers Media, 2019.
ista: Wijngaard RR, Steiner JF, Kraaijenbrink PDA, Klug C, Adhikari S, Banerjee
A, Pellicciotti F, van Beek LPH, Bierkens MFP, Lutz AF, Immerzeel WW. 2019. Modeling
the response of the Langtang Glacier and the Hintereisferner to a changing climate
since the Little Ice Age. Frontiers in Earth Science. 7, 143.
mla: Wijngaard, René R., et al. “Modeling the Response of the Langtang Glacier and
the Hintereisferner to a Changing Climate since the Little Ice Age.” Frontiers
in Earth Science, vol. 7, 143, Frontiers Media, 2019, doi:10.3389/feart.2019.00143.
short: R.R. Wijngaard, J.F. Steiner, P.D.A. Kraaijenbrink, C. Klug, S. Adhikari,
A. Banerjee, F. Pellicciotti, L.P.H. van Beek, M.F.P. Bierkens, A.F. Lutz, W.W.
Immerzeel, Frontiers in Earth Science 7 (2019).
date_created: 2023-02-20T08:13:08Z
date_published: 2019-06-04T00:00:00Z
date_updated: 2023-02-28T12:04:48Z
day: '04'
doi: 10.3389/feart.2019.00143
extern: '1'
intvolume: ' 7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.3389/feart.2019.00143
month: '06'
oa: 1
oa_version: Published Version
publication: Frontiers in Earth Science
publication_identifier:
issn:
- 2296-6463
publication_status: published
publisher: Frontiers Media
quality_controlled: '1'
scopus_import: '1'
status: public
title: Modeling the response of the Langtang Glacier and the Hintereisferner to a
changing climate since the Little Ice Age
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2019'
...