---
_id: '9013'
abstract:
- lang: eng
text: In this Letter, we investigate experimentally the nonequilibrium steady state
of an active colloidal suspension under gravity field. The active particles are
made of chemically powered colloids, showing self propulsion in the presence of
an added fuel, here hydrogen peroxide. The active suspension is studied in a dedicated
microfluidic device, made of permeable gel microstructures. Both the microdynamics
of individual colloids and the global stationary state of the suspension under
gravity are measured with optical microscopy. This yields a direct measurement
of the effective temperature of the active system as a function of the particle
activity, on the basis of the fluctuation-dissipation relationship. Our work is
a first step in the experimental exploration of the out-of-equilibrium properties
of active colloidal systems.
article_number: '088304'
article_processing_charge: No
article_type: letter_note
arxiv: 1
author:
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
- first_name: Cécile
full_name: Cottin-Bizonne, Cécile
last_name: Cottin-Bizonne
- first_name: Christophe
full_name: Ybert, Christophe
last_name: Ybert
- first_name: Lydéric
full_name: Bocquet, Lydéric
last_name: Bocquet
citation:
ama: Palacci JA, Cottin-Bizonne C, Ybert C, Bocquet L. Sedimentation and effective
temperature of active colloidal suspensions. Physical Review Letters. 2010;105(8).
doi:10.1103/physrevlett.105.088304
apa: Palacci, J. A., Cottin-Bizonne, C., Ybert, C., & Bocquet, L. (2010). Sedimentation
and effective temperature of active colloidal suspensions. Physical Review
Letters. American Physical Society . https://doi.org/10.1103/physrevlett.105.088304
chicago: Palacci, Jérémie A, Cécile Cottin-Bizonne, Christophe Ybert, and Lydéric
Bocquet. “Sedimentation and Effective Temperature of Active Colloidal Suspensions.”
Physical Review Letters. American Physical Society , 2010. https://doi.org/10.1103/physrevlett.105.088304.
ieee: J. A. Palacci, C. Cottin-Bizonne, C. Ybert, and L. Bocquet, “Sedimentation
and effective temperature of active colloidal suspensions,” Physical Review
Letters, vol. 105, no. 8. American Physical Society , 2010.
ista: Palacci JA, Cottin-Bizonne C, Ybert C, Bocquet L. 2010. Sedimentation and
effective temperature of active colloidal suspensions. Physical Review Letters.
105(8), 088304.
mla: Palacci, Jérémie A., et al. “Sedimentation and Effective Temperature of Active
Colloidal Suspensions.” Physical Review Letters, vol. 105, no. 8, 088304,
American Physical Society , 2010, doi:10.1103/physrevlett.105.088304.
short: J.A. Palacci, C. Cottin-Bizonne, C. Ybert, L. Bocquet, Physical Review Letters
105 (2010).
date_created: 2021-01-19T10:26:33Z
date_published: 2010-08-20T00:00:00Z
date_updated: 2023-02-23T13:46:42Z
day: '20'
doi: 10.1103/physrevlett.105.088304
extern: '1'
external_id:
arxiv:
- '1004.4340'
pmid:
- '20868136'
intvolume: ' 105'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1004.4340
month: '08'
oa: 1
oa_version: Preprint
pmid: 1
publication: Physical Review Letters
publication_identifier:
eissn:
- '10797114'
issn:
- '00319007'
publication_status: published
publisher: 'American Physical Society '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sedimentation and effective temperature of active colloidal suspensions
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 105
year: '2010'
...
---
_id: '9146'
abstract:
- lang: eng
text: "The factors governing the rate of change in the amount of atmospheric water
vapor are analyzed in simulations of climate change. The global-mean amount of
water vapor is estimated to increase at a differential rate of 7.3% K − 1 with
respect to global-mean surface air temperature in the multi-model mean. Larger
rates of change result if the fractional change is evaluated over a finite change
in temperature (e.g., 8.2% K − 1 for a 3 K warming), and rates of change of zonal-mean
column water vapor range from 6 to 12% K − 1 depending on latitude.\r\nClausius–Clapeyron
scaling is directly evaluated using an invariant distribution of monthly-mean
relative humidity, giving a rate of 7.4% K − 1 for global-mean water vapor. There
are deviations from Clausius–Clapeyron scaling of zonal-mean column water vapor
in the tropics and mid-latitudes, but they largely cancel in the global mean.
A purely thermodynamic scaling based on a saturated troposphere gives a higher
global rate of 7.9% K − 1.\r\nSurface specific humidity increases at a rate of
5.7% K − 1, considerably lower than the rate for global-mean water vapor. Surface
specific humidity closely follows Clausius–Clapeyron scaling over ocean. But there
are widespread decreases in surface relative humidity over land (by more than
1% K − 1 in many regions), and it is argued that decreases of this magnitude could
result from the land/ocean contrast in surface warming."
article_number: '025207'
article_processing_charge: No
article_type: original
author:
- first_name: P A
full_name: O’Gorman, P A
last_name: O’Gorman
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
citation:
ama: O’Gorman PA, Muller CJ. How closely do changes in surface and column water
vapor follow Clausius–Clapeyron scaling in climate change simulations? Environmental
Research Letters. 2010;5(2). doi:10.1088/1748-9326/5/2/025207
apa: O’Gorman, P. A., & Muller, C. J. (2010). How closely do changes in surface
and column water vapor follow Clausius–Clapeyron scaling in climate change simulations?
Environmental Research Letters. IOP Publishing. https://doi.org/10.1088/1748-9326/5/2/025207
chicago: O’Gorman, P A, and Caroline J Muller. “How Closely Do Changes in Surface
and Column Water Vapor Follow Clausius–Clapeyron Scaling in Climate Change Simulations?”
Environmental Research Letters. IOP Publishing, 2010. https://doi.org/10.1088/1748-9326/5/2/025207.
ieee: P. A. O’Gorman and C. J. Muller, “How closely do changes in surface and column
water vapor follow Clausius–Clapeyron scaling in climate change simulations?,”
Environmental Research Letters, vol. 5, no. 2. IOP Publishing, 2010.
ista: O’Gorman PA, Muller CJ. 2010. How closely do changes in surface and column
water vapor follow Clausius–Clapeyron scaling in climate change simulations? Environmental
Research Letters. 5(2), 025207.
mla: O’Gorman, P. A., and Caroline J. Muller. “How Closely Do Changes in Surface
and Column Water Vapor Follow Clausius–Clapeyron Scaling in Climate Change Simulations?”
Environmental Research Letters, vol. 5, no. 2, 025207, IOP Publishing,
2010, doi:10.1088/1748-9326/5/2/025207.
short: P.A. O’Gorman, C.J. Muller, Environmental Research Letters 5 (2010).
date_created: 2021-02-15T14:40:46Z
date_published: 2010-04-09T00:00:00Z
date_updated: 2022-01-24T13:51:02Z
day: '09'
doi: 10.1088/1748-9326/5/2/025207
extern: '1'
intvolume: ' 5'
issue: '2'
keyword:
- Renewable Energy
- Sustainability and the Environment
- Public Health
- Environmental and Occupational Health
- General Environmental Science
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1088/1748-9326/5/2/025207
month: '04'
oa: 1
oa_version: Published Version
publication: Environmental Research Letters
publication_identifier:
issn:
- 1748-9326
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
status: public
title: How closely do changes in surface and column water vapor follow Clausius–Clapeyron
scaling in climate change simulations?
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 5
year: '2010'
...
---
_id: '9485'
abstract:
- lang: eng
text: 'Cytosine methylation silences transposable elements in plants, vertebrates,
and fungi but also regulates gene expression. Plant methylation is catalyzed by
three families of enzymes, each with a preferred sequence context: CG, CHG (H
= A, C, or T), and CHH, with CHH methylation targeted by the RNAi pathway. Arabidopsis
thaliana endosperm, a placenta-like tissue that nourishes the embryo, is globally
hypomethylated in the CG context while retaining high non-CG methylation. Global
methylation dynamics in seeds of cereal crops that provide the bulk of human nutrition
remain unknown. Here, we show that rice endosperm DNA is hypomethylated in all
sequence contexts. Non-CG methylation is reduced evenly across the genome, whereas
CG hypomethylation is localized. CHH methylation of small transposable elements
is increased in embryos, suggesting that endosperm demethylation enhances transposon
silencing. Genes preferentially expressed in endosperm, including those coding
for major storage proteins and starch synthesizing enzymes, are frequently hypomethylated
in endosperm, indicating that DNA methylation is a crucial regulator of rice endosperm
biogenesis. Our data show that genome-wide reshaping of seed DNA methylation is
conserved among angiosperms and has a profound effect on gene expression in cereal
crops.'
article_processing_charge: No
article_type: original
author:
- first_name: Assaf
full_name: Zemach, Assaf
last_name: Zemach
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Pedro
full_name: Silva, Pedro
last_name: Silva
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Bradley
full_name: Dotson, Bradley
last_name: Dotson
- first_name: Matthew D.
full_name: Brooks, Matthew D.
last_name: Brooks
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Zemach A, Kim MY, Silva P, et al. Local DNA hypomethylation activates genes
in rice endosperm. Proceedings of the National Academy of Sciences. 2010;107(43):18729-18734.
doi:10.1073/pnas.1009695107
apa: Zemach, A., Kim, M. Y., Silva, P., Rodrigues, J. A., Dotson, B., Brooks, M.
D., & Zilberman, D. (2010). Local DNA hypomethylation activates genes in rice
endosperm. Proceedings of the National Academy of Sciences. National Academy
of Sciences. https://doi.org/10.1073/pnas.1009695107
chicago: Zemach, Assaf, M. Yvonne Kim, Pedro Silva, Jessica A. Rodrigues, Bradley
Dotson, Matthew D. Brooks, and Daniel Zilberman. “Local DNA Hypomethylation Activates
Genes in Rice Endosperm.” Proceedings of the National Academy of Sciences.
National Academy of Sciences, 2010. https://doi.org/10.1073/pnas.1009695107.
ieee: A. Zemach et al., “Local DNA hypomethylation activates genes in rice
endosperm,” Proceedings of the National Academy of Sciences, vol. 107,
no. 43. National Academy of Sciences, pp. 18729–18734, 2010.
ista: Zemach A, Kim MY, Silva P, Rodrigues JA, Dotson B, Brooks MD, Zilberman D.
2010. Local DNA hypomethylation activates genes in rice endosperm. Proceedings
of the National Academy of Sciences. 107(43), 18729–18734.
mla: Zemach, Assaf, et al. “Local DNA Hypomethylation Activates Genes in Rice Endosperm.”
Proceedings of the National Academy of Sciences, vol. 107, no. 43, National
Academy of Sciences, 2010, pp. 18729–34, doi:10.1073/pnas.1009695107.
short: A. Zemach, M.Y. Kim, P. Silva, J.A. Rodrigues, B. Dotson, M.D. Brooks, D.
Zilberman, Proceedings of the National Academy of Sciences 107 (2010) 18729–18734.
date_created: 2021-06-07T09:31:01Z
date_published: 2010-10-26T00:00:00Z
date_updated: 2021-12-14T08:40:02Z
day: '26'
department:
- _id: DaZi
doi: 10.1073/pnas.1009695107
extern: '1'
external_id:
pmid:
- '20937895'
intvolume: ' 107'
issue: '43'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1009695107
month: '10'
oa: 1
oa_version: Published Version
page: 18729-18734
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: Local DNA hypomethylation activates genes in rice endosperm
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 107
year: '2010'
...
---
_id: '9489'
abstract:
- lang: eng
text: Cytosine methylation is an ancient process with conserved enzymology but diverse
biological functions that include defense against transposable elements and regulation
of gene expression. Here we will discuss the evolution and biological significance
of eukaryotic DNA methylation, the likely drivers of that evolution, and major
remaining mysteries.
article_processing_charge: No
article_type: review
author:
- first_name: Assaf
full_name: Zemach, Assaf
last_name: Zemach
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Zemach A, Zilberman D. Evolution of eukaryotic DNA methylation and the pursuit
of safer sex. Current Biology. 2010;20(17):R780-R785. doi:10.1016/j.cub.2010.07.007
apa: Zemach, A., & Zilberman, D. (2010). Evolution of eukaryotic DNA methylation
and the pursuit of safer sex. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2010.07.007
chicago: Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation
and the Pursuit of Safer Sex.” Current Biology. Elsevier, 2010. https://doi.org/10.1016/j.cub.2010.07.007.
ieee: A. Zemach and D. Zilberman, “Evolution of eukaryotic DNA methylation and the
pursuit of safer sex,” Current Biology, vol. 20, no. 17. Elsevier, pp.
R780–R785, 2010.
ista: Zemach A, Zilberman D. 2010. Evolution of eukaryotic DNA methylation and the
pursuit of safer sex. Current Biology. 20(17), R780–R785.
mla: Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation
and the Pursuit of Safer Sex.” Current Biology, vol. 20, no. 17, Elsevier,
2010, pp. R780–85, doi:10.1016/j.cub.2010.07.007.
short: A. Zemach, D. Zilberman, Current Biology 20 (2010) R780–R785.
date_created: 2021-06-07T09:45:27Z
date_published: 2010-09-14T00:00:00Z
date_updated: 2021-12-14T08:52:34Z
day: '14'
department:
- _id: DaZi
doi: 10.1016/j.cub.2010.07.007
extern: '1'
external_id:
pmid:
- '20833323'
intvolume: ' 20'
issue: '17'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cub.2010.07.007
month: '09'
oa: 1
oa_version: Published Version
page: R780-R785
pmid: 1
publication: Current Biology
publication_identifier:
eissn:
- 1879-0445
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolution of eukaryotic DNA methylation and the pursuit of safer sex
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 20
year: '2010'
...
---
_id: '10127'
abstract:
- lang: eng
text: We use numerical simulations to show how noninteracting hard particles binding
to a deformable elastic shell may self-assemble into a variety of linear patterns.
This is a result of the nontrivial elastic response to deformations of shells.
The morphology of the patterns can be controlled by the mechanical properties
of the surface, and can be fine-tuned by varying the binding energy of the particles.
We also repeat our calculations for a fully flexible chain and find that the chain
conformations follow patterns similar to those formed by the nanoparticles under
analogous conditions. We propose a simple way of understanding and sorting the
different structures and relate it to the underlying shape transition of the shell.
Finally, we discuss the implications of our results.
acknowledgement: This work was supported by the National Science Foundation under
Career Grant No. DMR-0846426. We thank Josep C. Pàmies for helpful discussions.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Angelo
full_name: Cacciuto, Angelo
last_name: Cacciuto
citation:
ama: Šarić A, Cacciuto A. Particle self-assembly on soft elastic shells. Soft
Matter. 2010;7(5):1874-1878. doi:10.1039/c0sm01143f
apa: Šarić, A., & Cacciuto, A. (2010). Particle self-assembly on soft elastic
shells. Soft Matter. Royal Society of Chemistry (RSC). https://doi.org/10.1039/c0sm01143f
chicago: Šarić, Anđela, and Angelo Cacciuto. “Particle Self-Assembly on Soft Elastic
Shells.” Soft Matter. Royal Society of Chemistry (RSC), 2010. https://doi.org/10.1039/c0sm01143f.
ieee: A. Šarić and A. Cacciuto, “Particle self-assembly on soft elastic shells,”
Soft Matter, vol. 7, no. 5. Royal Society of Chemistry (RSC), pp. 1874–1878,
2010.
ista: Šarić A, Cacciuto A. 2010. Particle self-assembly on soft elastic shells.
Soft Matter. 7(5), 1874–1878.
mla: Šarić, Anđela, and Angelo Cacciuto. “Particle Self-Assembly on Soft Elastic
Shells.” Soft Matter, vol. 7, no. 5, Royal Society of Chemistry (RSC),
2010, pp. 1874–78, doi:10.1039/c0sm01143f.
short: A. Šarić, A. Cacciuto, Soft Matter 7 (2010) 1874–1878.
date_created: 2021-10-12T08:34:23Z
date_published: 2010-12-23T00:00:00Z
date_updated: 2021-10-12T09:49:27Z
day: '23'
doi: 10.1039/c0sm01143f
extern: '1'
external_id:
arxiv:
- '1010.2453'
intvolume: ' 7'
issue: '5'
keyword:
- condensed matter physics
- general chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1010.2453
month: '12'
oa: 1
oa_version: Preprint
page: 1874-1878
publication: Soft Matter
publication_identifier:
issn:
- 1744-683X
- 1744-6848
publication_status: published
publisher: Royal Society of Chemistry (RSC)
quality_controlled: '1'
status: public
title: Particle self-assembly on soft elastic shells
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 7
year: '2010'
...
---
_id: '10390'
abstract:
- lang: eng
text: 'We use numerical simulations to study the phase behavior of a system of purely
repulsive soft dumbbells as a function of size ratio of the two components and
their relative degree of deformability. We find a plethora of different phases,
which includes most of the mesophases observed in self-assembly of block copolymers
but also crystalline structures formed by asymmetric, hard binary mixtures. Our
results detail the phenomenological behavior of these systems when softness is
introduced in terms of two different classes of interparticle interactions: (a)
the elastic Hertz potential, which has a finite energy cost for complete overlap
of any two components, and (b) a generic power-law repulsion with tunable exponent.
We discuss how simple geometric arguments can be used to account for the large
structural variety observed in these systems and detail the similarities and differences
in the phase behavior for the two classes of potentials under consideration.'
acknowledgement: This work was supported by the National Science Foundation under
CAREER Grant No. DMR-0846426 and partly by Columbia University.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Behnaz
full_name: Bozorgui, Behnaz
last_name: Bozorgui
- first_name: Angelo
full_name: Cacciuto, Angelo
last_name: Cacciuto
citation:
ama: Šarić A, Bozorgui B, Cacciuto A. Packing of soft asymmetric dumbbells. The
Journal of Physical Chemistry B. 2010;115(22):7182-7189. doi:10.1021/jp107545w
apa: Šarić, A., Bozorgui, B., & Cacciuto, A. (2010). Packing of soft asymmetric
dumbbells. The Journal of Physical Chemistry B. American Chemical Society.
https://doi.org/10.1021/jp107545w
chicago: Šarić, Anđela, Behnaz Bozorgui, and Angelo Cacciuto. “Packing of Soft Asymmetric
Dumbbells.” The Journal of Physical Chemistry B. American Chemical Society,
2010. https://doi.org/10.1021/jp107545w.
ieee: A. Šarić, B. Bozorgui, and A. Cacciuto, “Packing of soft asymmetric dumbbells,”
The Journal of Physical Chemistry B, vol. 115, no. 22. American Chemical
Society, pp. 7182–7189, 2010.
ista: Šarić A, Bozorgui B, Cacciuto A. 2010. Packing of soft asymmetric dumbbells.
The Journal of Physical Chemistry B. 115(22), 7182–7189.
mla: Šarić, Anđela, et al. “Packing of Soft Asymmetric Dumbbells.” The Journal
of Physical Chemistry B, vol. 115, no. 22, American Chemical Society, 2010,
pp. 7182–89, doi:10.1021/jp107545w.
short: A. Šarić, B. Bozorgui, A. Cacciuto, The Journal of Physical Chemistry B 115
(2010) 7182–7189.
date_created: 2021-11-29T15:13:17Z
date_published: 2010-10-15T00:00:00Z
date_updated: 2021-11-29T16:20:29Z
day: '15'
doi: 10.1021/jp107545w
extern: '1'
external_id:
arxiv:
- '1010.2458'
pmid:
- '20949934'
intvolume: ' 115'
issue: '22'
keyword:
- materials chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1010.2458
month: '10'
oa: 1
oa_version: Preprint
page: 7182-7189
pmid: 1
publication: The Journal of Physical Chemistry B
publication_identifier:
eissn:
- 1520-5207
issn:
- 1520-6106
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Packing of soft asymmetric dumbbells
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 115
year: '2010'
...
---
_id: '10391'
abstract:
- lang: eng
text: We use numerical simulations to show how a fully flexible filament binding
to a deformable cylindrical surface may acquire a macroscopic persistence length
and a helical conformation. This is a result of the nontrivial elastic response
to deformations of elastic sheets. We find that the filament’s helical pitch is
completely determined by the mechanical properties of the surface, and can be
easily tuned by varying the surface stretching rigidity. We propose simple scaling
arguments to understand the physical mechanism behind this phenomenon and present
a phase diagram indicating under what conditions one should expect a fully flexible
chain to behave as a helical semiflexible filament. Finally, we discuss the implications
of our results.
acknowledgement: This work was supported by the National Science Foundation under
Career Grant No. DMR-0846426.
article_number: '226101'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Josep C.
full_name: Pàmies, Josep C.
last_name: Pàmies
- first_name: Angelo
full_name: Cacciuto, Angelo
last_name: Cacciuto
citation:
ama: Šarić A, Pàmies JC, Cacciuto A. Effective elasticity of a flexible filament
bound to a deformable cylindrical surface. Physical Review Letters. 2010;104(22).
doi:10.1103/physrevlett.104.226101
apa: Šarić, A., Pàmies, J. C., & Cacciuto, A. (2010). Effective elasticity of
a flexible filament bound to a deformable cylindrical surface. Physical Review
Letters. American Physical Society. https://doi.org/10.1103/physrevlett.104.226101
chicago: Šarić, Anđela, Josep C. Pàmies, and Angelo Cacciuto. “Effective Elasticity
of a Flexible Filament Bound to a Deformable Cylindrical Surface.” Physical
Review Letters. American Physical Society, 2010. https://doi.org/10.1103/physrevlett.104.226101.
ieee: A. Šarić, J. C. Pàmies, and A. Cacciuto, “Effective elasticity of a flexible
filament bound to a deformable cylindrical surface,” Physical Review Letters,
vol. 104, no. 22. American Physical Society, 2010.
ista: Šarić A, Pàmies JC, Cacciuto A. 2010. Effective elasticity of a flexible filament
bound to a deformable cylindrical surface. Physical Review Letters. 104(22), 226101.
mla: Šarić, Anđela, et al. “Effective Elasticity of a Flexible Filament Bound to
a Deformable Cylindrical Surface.” Physical Review Letters, vol. 104, no.
22, 226101, American Physical Society, 2010, doi:10.1103/physrevlett.104.226101.
short: A. Šarić, J.C. Pàmies, A. Cacciuto, Physical Review Letters 104 (2010).
date_created: 2021-11-29T15:14:33Z
date_published: 2010-06-03T00:00:00Z
date_updated: 2021-11-30T08:11:19Z
day: '03'
doi: 10.1103/physrevlett.104.226101
extern: '1'
external_id:
arxiv:
- '1005.2429'
pmid:
- '20867183'
intvolume: ' 104'
issue: '22'
keyword:
- general physics and astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1005.2429
month: '06'
oa: 1
oa_version: Preprint
pmid: 1
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Effective elasticity of a flexible filament bound to a deformable cylindrical
surface
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 104
year: '2010'
...
---
_id: '1044'
abstract:
- lang: eng
text: Control over all internal and external degrees of freedom of molecules at
the level of single quantum states will enable a series of fundamental studies
in physics and chemistry1,2. In particular, samples of ground-state molecules
at ultralow temperatures and high number densities will facilitate new quantum-gas
studies3 and future applications in quantum information science4. However, high
phase-space densities for molecular samples are not readily attainable because
efficient cooling techniques such as laser cooling are lacking. Here we produce
an ultracold and dense sample of molecules in a single hyperfine level of the
rovibronic ground state with each molecule individually trapped in the motional
ground state of an optical lattice well. Starting from a zero-temperature atomic
Mott-insulator state with optimized double-site occupancy6, weakly bound dimer
molecules are efficiently associated on a Feshbach resonance7 and subsequently
transferred to the rovibronic ground state by a stimulated four-photon process
with >50% efficiency. The molecules are trapped in the lattice and have a lifetime
of 8 s. Our results present a crucial step towards Bose-Einstein condensation
of ground-state molecules and, when suitably generalized to polar heteronuclear
molecules, the realization of dipolar quantum-gas phases in optical lattices8-10.
acknowledgement: We thank H. Ritsch, S. Dürr, N. Bouloufa and O. Dulieu for valuable
discussions. We are indebted to R. Grimm for generous support and to H. Häffner
for the loan of a charge-coupled camera. We gratefully acknowledge financial support
by the Austrian Ministry of Science and Research (Bundesministerium für Wissenschaft
und Forschung) and the Austrian Science Fund (Fonds zur Förderung der wissenschaftlichen
Forschung) in the form of a START prize grant and by the European Science Foundation
within the framework of the EuroQUASAR collective research project QuDeGPM and within
the framework of the EuroQUAM collective research project QuDipMol. R.H. is supported
by a Marie Curie International Incoming Fellowship within the 7th European Community
Framework Programme.
article_processing_charge: No
arxiv: 1
author:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Manfred
full_name: Mark, Manfred
last_name: Mark
- first_name: Elmar
full_name: Haller, Elmar
last_name: Haller
- first_name: Mattias
full_name: Gustavsson, Mattias
last_name: Gustavsson
- first_name: Russell
full_name: Hart, Russell
last_name: Hart
- first_name: Jesus
full_name: Aldegunde, Jesus
last_name: Aldegunde
- first_name: Jeremy
full_name: Hutson, Jeremy
last_name: Hutson
- first_name: Hanns
full_name: Nägerl, Hanns
last_name: Nägerl
citation:
ama: Danzl JG, Mark M, Haller E, et al. An ultracold high-density sample of rovibronic
ground-state molecules in an optical lattice. Nature Physics. 2010;6(4):265-270.
doi:10.1038/nphys1533
apa: Danzl, J. G., Mark, M., Haller, E., Gustavsson, M., Hart, R., Aldegunde, J.,
… Nägerl, H. (2010). An ultracold high-density sample of rovibronic ground-state
molecules in an optical lattice. Nature Physics. Nature Publishing Group.
https://doi.org/10.1038/nphys1533
chicago: Danzl, Johann G, Manfred Mark, Elmar Haller, Mattias Gustavsson, Russell
Hart, Jesus Aldegunde, Jeremy Hutson, and Hanns Nägerl. “An Ultracold High-Density
Sample of Rovibronic Ground-State Molecules in an Optical Lattice.” Nature
Physics. Nature Publishing Group, 2010. https://doi.org/10.1038/nphys1533.
ieee: J. G. Danzl et al., “An ultracold high-density sample of rovibronic
ground-state molecules in an optical lattice,” Nature Physics, vol. 6,
no. 4. Nature Publishing Group, pp. 265–270, 2010.
ista: Danzl JG, Mark M, Haller E, Gustavsson M, Hart R, Aldegunde J, Hutson J, Nägerl
H. 2010. An ultracold high-density sample of rovibronic ground-state molecules
in an optical lattice. Nature Physics. 6(4), 265–270.
mla: Danzl, Johann G., et al. “An Ultracold High-Density Sample of Rovibronic Ground-State
Molecules in an Optical Lattice.” Nature Physics, vol. 6, no. 4, Nature
Publishing Group, 2010, pp. 265–70, doi:10.1038/nphys1533.
short: J.G. Danzl, M. Mark, E. Haller, M. Gustavsson, R. Hart, J. Aldegunde, J.
Hutson, H. Nägerl, Nature Physics 6 (2010) 265–270.
date_created: 2018-12-11T11:49:51Z
date_published: 2010-04-04T00:00:00Z
date_updated: 2021-01-12T06:47:53Z
day: '04'
doi: 10.1038/nphys1533
extern: '1'
external_id:
arxiv:
- '0909.4700'
intvolume: ' 6'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/0909.4700
month: '04'
oa: 1
oa_version: Preprint
page: 265 - 270
publication: Nature Physics
publication_status: published
publisher: Nature Publishing Group
publist_id: '6345'
status: public
title: An ultracold high-density sample of rovibronic ground-state molecules in an
optical lattice
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2010'
...
---
_id: '1045'
abstract:
- lang: eng
text: We report on the observation of confinement-induced resonances in strongly
interacting quantum-gas systems with tunable interactions for one- and two-dimensional
geometry. Atom-atom scattering is substantially modified when the s-wave scattering
length approaches the length scale associated with the tight transversal confinement,
leading to characteristic loss and heating signatures. Upon introducing an anisotropy
for the transversal confinement we observe a splitting of the confinement-induced
resonance. With increasing anisotropy additional resonances appear. In the limit
of a two-dimensional system we find that one resonance persists.
acknowledgement: We thank W. Zwerger for discussions and R. Grimm for generous support.
We acknowledge funding by the Austrian Science Fund and by the European Union within
the framework of the EuroQUASAR collective research project QuDeGPM. R. H. is supported
by a Marie Curie Fellowship within FP7. P. S. acknowledges financial support by
the DFG. Financial support by the Heisenberg-Landau Program is appreciated by P. S.
and V. M.
article_processing_charge: No
arxiv: 1
author:
- first_name: Elmar
full_name: Haller, Elmar
last_name: Haller
- first_name: Manfred
full_name: Mark, Manfred
last_name: Mark
- first_name: Russell
full_name: Hart, Russell
last_name: Hart
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Lukas
full_name: Reichsöllner, Lukas
last_name: Reichsöllner
- first_name: Vladimir
full_name: Melezhik, Vladimir
last_name: Melezhik
- first_name: Peter
full_name: Schmelcher, Peter
last_name: Schmelcher
- first_name: Hanns
full_name: Nägerl, Hanns
last_name: Nägerl
citation:
ama: Haller E, Mark M, Hart R, et al. Confinement-induced resonances in low-dimensional
quantum systems. Physical Review Letters. 2010;104(15). doi:10.1103/PhysRevLett.104.153203
apa: Haller, E., Mark, M., Hart, R., Danzl, J. G., Reichsöllner, L., Melezhik, V.,
… Nägerl, H. (2010). Confinement-induced resonances in low-dimensional quantum
systems. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.104.153203
chicago: Haller, Elmar, Manfred Mark, Russell Hart, Johann G Danzl, Lukas Reichsöllner,
Vladimir Melezhik, Peter Schmelcher, and Hanns Nägerl. “Confinement-Induced Resonances
in Low-Dimensional Quantum Systems.” Physical Review Letters. American
Physical Society, 2010. https://doi.org/10.1103/PhysRevLett.104.153203.
ieee: E. Haller et al., “Confinement-induced resonances in low-dimensional
quantum systems,” Physical Review Letters, vol. 104, no. 15. American Physical
Society, 2010.
ista: Haller E, Mark M, Hart R, Danzl JG, Reichsöllner L, Melezhik V, Schmelcher
P, Nägerl H. 2010. Confinement-induced resonances in low-dimensional quantum systems.
Physical Review Letters. 104(15).
mla: Haller, Elmar, et al. “Confinement-Induced Resonances in Low-Dimensional Quantum
Systems.” Physical Review Letters, vol. 104, no. 15, American Physical
Society, 2010, doi:10.1103/PhysRevLett.104.153203.
short: E. Haller, M. Mark, R. Hart, J.G. Danzl, L. Reichsöllner, V. Melezhik, P.
Schmelcher, H. Nägerl, Physical Review Letters 104 (2010).
date_created: 2018-12-11T11:49:51Z
date_published: 2010-04-14T00:00:00Z
date_updated: 2021-01-12T06:47:53Z
day: '14'
doi: 10.1103/PhysRevLett.104.153203
extern: '1'
external_id:
arxiv:
- '1002.3795'
intvolume: ' 104'
issue: '15'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1002.3795
month: '04'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '6344'
status: public
title: Confinement-induced resonances in low-dimensional quantum systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 104
year: '2010'
...
---
_id: '1047'
abstract:
- lang: eng
text: Particles in a perfect lattice potential perform Bloch oscillations when subject
to a constant force, leading to localization and preventing conductivity. For
a weakly interacting Bose-Einstein condensate of Cs atoms, we observe giant center-of-mass
oscillations in position space with a displacement across hundreds of lattice
sites when we add a periodic modulation to the force near the Bloch frequency.
We study the dependence of these "super" Bloch oscillations on lattice
depth, modulation amplitude, and modulation frequency and show that they provide
a means to induce linear transport in a dissipation-free lattice.
acknowledgement: We thank A. R. Kolovsky, A. Zenesini, and A. Wacker for discussions
and R. Grimm for generous support. We acknowledge funding by the Austrian Ministry
of Science and Research and the Austrian Science Fund and by the European Union
within the framework of the EuroQUASAR collective research project QuDeGPM. R. H.
is supported by a Marie Curie Action within FP7.
article_processing_charge: No
arxiv: 1
author:
- first_name: Elmar
full_name: Haller, Elmar
last_name: Haller
- first_name: Russell
full_name: Hart, Russell
last_name: Hart
- first_name: Manfred
full_name: Mark, Manfred
last_name: Mark
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Lukas
full_name: Reichsöllner, Lukas
last_name: Reichsöllner
- first_name: Hanns
full_name: Nägerl, Hanns
last_name: Nägerl
citation:
ama: Haller E, Hart R, Mark M, Danzl JG, Reichsöllner L, Nägerl H. Inducing transport
in a dissipation-free lattice with super bloch oscillations. Physical Review
Letters. 2010;104(20). doi:10.1103/PhysRevLett.104.200403
apa: Haller, E., Hart, R., Mark, M., Danzl, J. G., Reichsöllner, L., & Nägerl,
H. (2010). Inducing transport in a dissipation-free lattice with super bloch oscillations.
Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.104.200403
chicago: Haller, Elmar, Russell Hart, Manfred Mark, Johann G Danzl, Lukas Reichsöllner,
and Hanns Nägerl. “Inducing Transport in a Dissipation-Free Lattice with Super
Bloch Oscillations.” Physical Review Letters. American Physical Society,
2010. https://doi.org/10.1103/PhysRevLett.104.200403.
ieee: E. Haller, R. Hart, M. Mark, J. G. Danzl, L. Reichsöllner, and H. Nägerl,
“Inducing transport in a dissipation-free lattice with super bloch oscillations,”
Physical Review Letters, vol. 104, no. 20. American Physical Society, 2010.
ista: Haller E, Hart R, Mark M, Danzl JG, Reichsöllner L, Nägerl H. 2010. Inducing
transport in a dissipation-free lattice with super bloch oscillations. Physical
Review Letters. 104(20).
mla: Haller, Elmar, et al. “Inducing Transport in a Dissipation-Free Lattice with
Super Bloch Oscillations.” Physical Review Letters, vol. 104, no. 20, American
Physical Society, 2010, doi:10.1103/PhysRevLett.104.200403.
short: E. Haller, R. Hart, M. Mark, J.G. Danzl, L. Reichsöllner, H. Nägerl, Physical
Review Letters 104 (2010).
date_created: 2018-12-11T11:49:52Z
date_published: 2010-05-21T00:00:00Z
date_updated: 2021-01-12T06:47:54Z
day: '21'
doi: 10.1103/PhysRevLett.104.200403
extern: '1'
external_id:
arxiv:
- '1001.1206'
intvolume: ' 104'
issue: '20'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1001.1206
month: '05'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '6343'
status: public
title: Inducing transport in a dissipation-free lattice with super bloch oscillations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 104
year: '2010'
...
---
_id: '1049'
abstract:
- lang: eng
text: Quantum many-body systems can have phase transitions even at zero temperature;
fluctuations arising from Heisenbergĝ€™s uncertainty principle, as opposed to
thermal effects, drive the system from one phase to another. Typically, during
the transition the relative strength of two competing terms in the systemĝ€™s
Hamiltonian changes across a finite critical value. A well-known example is the
Mottĝ€" Hubbard quantum phase transition from a superfluid to an insulating
phase, which has been observed for weakly interacting bosonic atomic gases. However,
for strongly interacting quantum systems confined to lower-dimensional geometry,
a novel type of quantum phase transition may be induced and driven by an arbitrarily
weak perturbation to the Hamiltonian. Here we observe such an effectĝ€"the
sineĝ€"Gordon quantum phase transition from a superfluid Luttinger liquid
to a Mott insulatorĝ€ "in a one-dimensional quantum gas of bosonic caesium
atoms with tunable interactions. For sufficiently strong interactions, the transition
is induced by adding an arbitrarily weak optical lattice commensurate with the
atomic granularity, which leads to immediate pinning of the atoms. We map out
the phase diagram and find that our measurements in the strongly interacting regime
agree well with a quantum field description based on the exactly solvable sineĝ€"Gordon
model. We trace the phase boundary all the way to the weakly interacting regime,
where we find good agreement with the predictions of the one-dimensional Boseĝ€"Hubbard
model. Our results open up the experimental study of quantum phase transitions,
criticality and transport phenomena beyond Hubbard-type models in the context
of ultracold gases.
acknowledgement: We thank W. Zwerger for discussions. We are indebted to R. Grimm
for generous support. We gratefully acknowledge funding by the Austrian Ministry
of Science and Research (Bundesministerium für Wissenschaft und Forschung) and the
Austrian Science Fund (Fonds zur Förderung der wissenschaftlichen Forschung) in
the form of a START prize grant, and by the European Union through the STREP FP7-ICT-2007-C
project NAME-QUAM (Nanodesigning of Atomic and Molecular Quantum Matter) and within
the framework of the EuroQUASAR collective research project QuDeGPM. R.H. is supported
by a Marie Curie International Incoming Fellowship within the 7th European Community
Framework Programme.
article_processing_charge: No
arxiv: 1
author:
- first_name: Elmar
full_name: Haller, Elmar
last_name: Haller
- first_name: Russell
full_name: Hart, Russell
last_name: Hart
- first_name: Manfred
full_name: Mark, Manfred
last_name: Mark
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Lukas
full_name: Reichsöllner, Lukas
last_name: Reichsöllner
- first_name: Mattias
full_name: Gustavsson, Mattias
last_name: Gustavsson
- first_name: Marcello
full_name: Dalmonte, Marcello
last_name: Dalmonte
- first_name: Guido
full_name: Pupillo, Guido
last_name: Pupillo
- first_name: Hanns
full_name: Nägerl, Hanns
last_name: Nägerl
citation:
ama: Haller E, Hart R, Mark M, et al. Pinning quantum phase transition for a Luttinger
liquid of strongly interacting bosons. Nature. 2010;466(7306):597-600.
doi:10.1038/nature09259
apa: Haller, E., Hart, R., Mark, M., Danzl, J. G., Reichsöllner, L., Gustavsson,
M., … Nägerl, H. (2010). Pinning quantum phase transition for a Luttinger liquid
of strongly interacting bosons. Nature. Nature Publishing Group. https://doi.org/10.1038/nature09259
chicago: Haller, Elmar, Russell Hart, Manfred Mark, Johann G Danzl, Lukas Reichsöllner,
Mattias Gustavsson, Marcello Dalmonte, Guido Pupillo, and Hanns Nägerl. “Pinning
Quantum Phase Transition for a Luttinger Liquid of Strongly Interacting Bosons.”
Nature. Nature Publishing Group, 2010. https://doi.org/10.1038/nature09259.
ieee: E. Haller et al., “Pinning quantum phase transition for a Luttinger
liquid of strongly interacting bosons,” Nature, vol. 466, no. 7306. Nature
Publishing Group, pp. 597–600, 2010.
ista: Haller E, Hart R, Mark M, Danzl JG, Reichsöllner L, Gustavsson M, Dalmonte
M, Pupillo G, Nägerl H. 2010. Pinning quantum phase transition for a Luttinger
liquid of strongly interacting bosons. Nature. 466(7306), 597–600.
mla: Haller, Elmar, et al. “Pinning Quantum Phase Transition for a Luttinger Liquid
of Strongly Interacting Bosons.” Nature, vol. 466, no. 7306, Nature Publishing
Group, 2010, pp. 597–600, doi:10.1038/nature09259.
short: E. Haller, R. Hart, M. Mark, J.G. Danzl, L. Reichsöllner, M. Gustavsson,
M. Dalmonte, G. Pupillo, H. Nägerl, Nature 466 (2010) 597–600.
date_created: 2018-12-11T11:49:52Z
date_published: 2010-07-29T00:00:00Z
date_updated: 2021-01-12T06:47:54Z
day: '29'
doi: 10.1038/nature09259
extern: '1'
external_id:
arxiv:
- '1004.3168'
intvolume: ' 466'
issue: '7306'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1004.3168
month: '07'
oa: 1
oa_version: Preprint
page: 597 - 600
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6341'
status: public
title: Pinning quantum phase transition for a Luttinger liquid of strongly interacting
bosons
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 466
year: '2010'
...
---
_id: '11797'
abstract:
- lang: eng
text: "Inspired by online ad allocation, we study online stochastic packing integer
programs from theoretical and practical standpoints. We first present a near-optimal
online algorithm for a general class of packing integer programs which model various
online resource allocation problems including online variants of routing, ad allocations,
generalized assignment, and combinatorial auctions. As our main theoretical result,
we prove that a simple dual training-based algorithm achieves a (1 − o(1))-approximation
guarantee in the random order stochastic model. This is a significant improvement
over logarithmic or constant-factor approximations for the adversarial variants
of the same problems (e.g. factor 1−1\U0001D452 for online ad allocation, and
log(m) for online routing). We then focus on the online display ad allocation
problem and study the efficiency and fairness of various training-based and online
allocation algorithms on data sets collected from real-life display ad allocation
system. Our experimental evaluation confirms the effectiveness of training-based
algorithms on real data sets, and also indicates an intrinsic trade-off between
fairness and efficiency."
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Jon
full_name: Feldman, Jon
last_name: Feldman
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Nitish
full_name: Korula, Nitish
last_name: Korula
- first_name: Vahab S.
full_name: Mirrokni, Vahab S.
last_name: Mirrokni
- first_name: Cliff
full_name: Stein, Cliff
last_name: Stein
citation:
ama: 'Feldman J, Henzinger MH, Korula N, Mirrokni VS, Stein C. Online stochastic
packing applied to display ad allocation. In: 18th Annual European Symposium
on Algorithms. Vol 6346. Springer Nature; 2010:182–194. doi:10.1007/978-3-642-15775-2_16'
apa: 'Feldman, J., Henzinger, M. H., Korula, N., Mirrokni, V. S., & Stein, C.
(2010). Online stochastic packing applied to display ad allocation. In 18th
Annual European Symposium on Algorithms (Vol. 6346, pp. 182–194). Liverpool,
United Kingdom: Springer Nature. https://doi.org/10.1007/978-3-642-15775-2_16'
chicago: Feldman, Jon, Monika H Henzinger, Nitish Korula, Vahab S. Mirrokni, and
Cliff Stein. “Online Stochastic Packing Applied to Display Ad Allocation.” In
18th Annual European Symposium on Algorithms, 6346:182–194. Springer Nature,
2010. https://doi.org/10.1007/978-3-642-15775-2_16.
ieee: J. Feldman, M. H. Henzinger, N. Korula, V. S. Mirrokni, and C. Stein, “Online
stochastic packing applied to display ad allocation,” in 18th Annual European
Symposium on Algorithms, Liverpool, United Kingdom, 2010, vol. 6346, pp. 182–194.
ista: 'Feldman J, Henzinger MH, Korula N, Mirrokni VS, Stein C. 2010. Online stochastic
packing applied to display ad allocation. 18th Annual European Symposium on Algorithms.
ESA: European Symposium on Algorithms, LNCS, vol. 6346, 182–194.'
mla: Feldman, Jon, et al. “Online Stochastic Packing Applied to Display Ad Allocation.”
18th Annual European Symposium on Algorithms, vol. 6346, Springer Nature,
2010, pp. 182–194, doi:10.1007/978-3-642-15775-2_16.
short: J. Feldman, M.H. Henzinger, N. Korula, V.S. Mirrokni, C. Stein, in:, 18th
Annual European Symposium on Algorithms, Springer Nature, 2010, pp. 182–194.
conference:
end_date: 2010-09-08
location: Liverpool, United Kingdom
name: 'ESA: European Symposium on Algorithms'
start_date: 2010-09-06
date_created: 2022-08-11T12:14:20Z
date_published: 2010-09-01T00:00:00Z
date_updated: 2023-02-13T11:36:46Z
day: '01'
doi: 10.1007/978-3-642-15775-2_16
extern: '1'
external_id:
arxiv:
- '1001.5076'
intvolume: ' 6346'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1001.5076
month: '09'
oa: 1
oa_version: Preprint
page: 182–194
publication: 18th Annual European Symposium on Algorithms
publication_identifier:
isbn:
- '3642157742'
issn:
- 1611-3349
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Online stochastic packing applied to display ad allocation
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6346
year: '2010'
...
---
_id: '11838'
abstract:
- lang: eng
text: Two-sided matching markets play a prominent role in economic theory. A prime
example of such a market is the sponsored search market where $n$ advertisers
compete for the assignment of one of $k$ sponsored search results, also known
as ``slots'', for certain keywords they are interested in. Here, as in other markets
of that kind, market equilibria correspond to stable matchings. In this paper,
we show how to modify Kuhn's Hungarian Method (Kuhn, 1955) so that it finds an
optimal stable matching between advertisers and advertising slots in settings
with generalized linear utilities, per-bidder-item reserve prices, and per-bidder-item
maximum prices. The only algorithm for this problem presented so far (Aggarwal
et al., 2009) requires the market to be in ''general position''. We do not make
this assumption.
alternative_title:
- LIPIcs
article_processing_charge: No
arxiv: 1
author:
- first_name: Paul
full_name: Dütting, Paul
last_name: Dütting
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Ingmar
full_name: Weber, Ingmar
last_name: Weber
citation:
ama: 'Dütting P, Henzinger MH, Weber I. Sponsored search, market equilibria, and
the Hungarian Method. In: 27th International Symposium on Theoretical Aspects
of Computer Science. Vol 5. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2010:287-298. doi:10.4230/LIPICS.STACS.2010.2463'
apa: 'Dütting, P., Henzinger, M. H., & Weber, I. (2010). Sponsored search, market
equilibria, and the Hungarian Method. In 27th International Symposium on Theoretical
Aspects of Computer Science (Vol. 5, pp. 287–298). Nancy, France: Schloss
Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.STACS.2010.2463'
chicago: Dütting, Paul, Monika H Henzinger, and Ingmar Weber. “Sponsored Search,
Market Equilibria, and the Hungarian Method.” In 27th International Symposium
on Theoretical Aspects of Computer Science, 5:287–98. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2010. https://doi.org/10.4230/LIPICS.STACS.2010.2463.
ieee: P. Dütting, M. H. Henzinger, and I. Weber, “Sponsored search, market equilibria,
and the Hungarian Method,” in 27th International Symposium on Theoretical Aspects
of Computer Science, Nancy, France, 2010, vol. 5, pp. 287–298.
ista: 'Dütting P, Henzinger MH, Weber I. 2010. Sponsored search, market equilibria,
and the Hungarian Method. 27th International Symposium on Theoretical Aspects
of Computer Science. STACS: Symposium on Theoretical Aspects of Computer Science,
LIPIcs, vol. 5, 287–298.'
mla: Dütting, Paul, et al. “Sponsored Search, Market Equilibria, and the Hungarian
Method.” 27th International Symposium on Theoretical Aspects of Computer Science,
vol. 5, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 287–98, doi:10.4230/LIPICS.STACS.2010.2463.
short: P. Dütting, M.H. Henzinger, I. Weber, in:, 27th International Symposium on
Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2010, pp. 287–298.
conference:
end_date: 2010-03-06
location: Nancy, France
name: 'STACS: Symposium on Theoretical Aspects of Computer Science'
start_date: 2010-03-04
date_created: 2022-08-12T11:45:49Z
date_published: 2010-03-09T00:00:00Z
date_updated: 2023-02-21T16:30:02Z
day: '09'
doi: 10.4230/LIPICS.STACS.2010.2463
extern: '1'
external_id:
arxiv:
- '0912.1934'
intvolume: ' 5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.4230/LIPIcs.STACS.2010.2463
month: '03'
oa: 1
oa_version: Published Version
page: 287-298
publication: 27th International Symposium on Theoretical Aspects of Computer Science
publication_identifier:
isbn:
- 978-3-939897-16-3
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
related_material:
record:
- id: '11838'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Sponsored search, market equilibria, and the Hungarian Method
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2010'
...
---
_id: '12653'
abstract:
- lang: eng
text: 'Daily streamflow from stations close to five Swiss glaciers is analyzed for
trends with the Mann-Kendall test. We consider a common period of record (1974–2004)
and longer periods based on data availability. The trend statistical significance
is tested on annual and seasonal bases. We also examine changes in precipitation,
temperature, and snow cover characteristics. Highly glacierized basins show statistically
significant positive trends in annual streamflow caused by increasing streamflow
in spring and summer. Trends are more numerous and stronger at lower and mid than
at the upper quantiles. The basin characterized by lower glacier coverage, conversely,
does not exhibit consistently statistically significant trends. Changes in precipitation
are not sufficient to explain the observed streamflow trends. Air temperature
sees an increase in mean, minimum, and maximum values at all sites. Variations
in the seasonal snow accumulation and ablation process are evident. Solid precipitation
is decreasing at all sites and trends may be due to a shift from snowfall into
rainfall. Mean snow depth is also decreasing, and its duration is getting shorter
because of a decrease in solid precipitation and enhanced melting. Trend magnitude
attenuates with longer time series. Contrasting trends are detected for different
subperiods in the last 70 years: statistically significant negative trends are
observed in the periods 1944–1974 and 1954–1984 for Aletschgletscher, in contrast
with the results for the common period. These trends are explained by different
rates of ice volume changes, and the sign of trends is clearly related to phases
of positive or negative glacier mass balance.'
article_number: W10522
article_processing_charge: No
article_type: original
author:
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: A.
full_name: Bauder, A.
last_name: Bauder
- first_name: M.
full_name: Parola, M.
last_name: Parola
citation:
ama: Pellicciotti F, Bauder A, Parola M. Effect of glaciers on streamflow trends
in the Swiss Alps. Water Resources Research. 2010;46(10). doi:10.1029/2009wr009039
apa: Pellicciotti, F., Bauder, A., & Parola, M. (2010). Effect of glaciers on
streamflow trends in the Swiss Alps. Water Resources Research. American
Geophysical Union. https://doi.org/10.1029/2009wr009039
chicago: Pellicciotti, Francesca, A. Bauder, and M. Parola. “Effect of Glaciers
on Streamflow Trends in the Swiss Alps.” Water Resources Research. American
Geophysical Union, 2010. https://doi.org/10.1029/2009wr009039.
ieee: F. Pellicciotti, A. Bauder, and M. Parola, “Effect of glaciers on streamflow
trends in the Swiss Alps,” Water Resources Research, vol. 46, no. 10. American
Geophysical Union, 2010.
ista: Pellicciotti F, Bauder A, Parola M. 2010. Effect of glaciers on streamflow
trends in the Swiss Alps. Water Resources Research. 46(10), W10522.
mla: Pellicciotti, Francesca, et al. “Effect of Glaciers on Streamflow Trends in
the Swiss Alps.” Water Resources Research, vol. 46, no. 10, W10522, American
Geophysical Union, 2010, doi:10.1029/2009wr009039.
short: F. Pellicciotti, A. Bauder, M. Parola, Water Resources Research 46 (2010).
date_created: 2023-02-20T08:18:27Z
date_published: 2010-10-01T00:00:00Z
date_updated: 2023-02-20T09:39:29Z
day: '01'
doi: 10.1029/2009wr009039
extern: '1'
intvolume: ' 46'
issue: '10'
keyword:
- Water Science and Technology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1029/2009WR009039
month: '10'
oa: 1
oa_version: Published Version
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: Effect of glaciers on streamflow trends in the Swiss Alps
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 46
year: '2010'
...
---
_id: '3430'
abstract:
- lang: eng
text: These are notes for a set of 7 two-hour lectures given at the 2010 Summer
School on Quantitative Evolutionary and Comparative Genomics at OIST, Okinawa,
Japan. The emphasis is on understanding how biological systems process information.
We take a physicist's approach of looking for simple phenomenological descriptions
that can address the questions of biological function without necessarily modeling
all (mostly unknown) microscopic details; the example that is developed throughout
the notes is transcriptional regulation in genetic regulatory networks. We present
tools from information theory and statistical physics that can be used to analyze
noisy nonlinear biological networks, and build generative and predictive models
of regulatory processes.
author:
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: 'Tkačik G. Lecture notes for 2010 summer school on Quantitative Evolutionary
and Comparative Genomics. In: Elsevier; 2010.'
apa: Tkačik, G. (2010). Lecture notes for 2010 summer school on Quantitative Evolutionary
and Comparative Genomics. Presented at the Summer School on Quantitative Evolutionary
and Comparative Genomics, Elsevier.
chicago: Tkačik, Gašper. “Lecture Notes for 2010 Summer School on Quantitative Evolutionary
and Comparative Genomics.” Elsevier, 2010.
ieee: G. Tkačik, “Lecture notes for 2010 summer school on Quantitative Evolutionary
and Comparative Genomics,” presented at the Summer School on Quantitative Evolutionary
and Comparative Genomics, 2010.
ista: Tkačik G. 2010. Lecture notes for 2010 summer school on Quantitative Evolutionary
and Comparative Genomics. Summer School on Quantitative Evolutionary and Comparative
Genomics.
mla: Tkačik, Gašper. Lecture Notes for 2010 Summer School on Quantitative Evolutionary
and Comparative Genomics. Elsevier, 2010.
short: G. Tkačik, in:, Elsevier, 2010.
conference:
name: Summer School on Quantitative Evolutionary and Comparative Genomics
date_created: 2018-12-11T12:03:17Z
date_published: 2010-06-22T00:00:00Z
date_updated: 2021-01-12T07:43:25Z
day: '22'
extern: 1
main_file_link:
- open_access: '1'
url: http://arxiv.org/pdf/1006.4291
month: '06'
oa: 1
publication_status: published
publisher: Elsevier
publist_id: '2970'
quality_controlled: 0
status: public
title: Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative
Genomics
type: conference
year: '2010'
...
---
_id: '3538'
abstract:
- lang: eng
text: How seizures start is a major question in epilepsy research. Preictal EEG
changes occur in both human patients and animal models, but their underlying mechanisms
and relationship with seizure initiation remain unknown. Here we demonstrate the
existence, in the hippocampal CA1 region, of a preictal state characterized by
the progressive and global increase in neuronal activity associated with a widespread
buildup of low-amplitude high-frequency activity (HFA) (> 100 Hz) and reduction
in system complexity. HFA is generated by the firing of neurons, mainly pyramidal
cells, at much lower frequencies. Individual cycles of HFA are generated by the
near-synchronous (within similar to 5 ms) firing of small numbers of pyramidal
cells. The presence of HFA in the low-calcium model implicates nonsynaptic synchronization;
the presence of very similar HFA in the high-potassium model shows that it does
not depend on an absence of synaptic transmission. Immediately before seizure
onset, CA1 is in a state of high sensitivity in which weak depolarizing or synchronizing
perturbations can trigger seizures. Transition to seizure is characterized by
a rapid expansion and fusion of the neuronal populations responsible for HFA,
associated with a progressive slowing of HFA, leading to a single, massive, hypersynchronous
cluster generating the high-amplitude low-frequency activity of the seizure.
author:
- first_name: Premysl
full_name: Jiruska, Premysl
last_name: Jiruska
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: Andrew
full_name: Powell, Andrew
last_name: Powell
- first_name: John
full_name: Fox, John
last_name: Fox
- first_name: Wei
full_name: Chang, Wei
last_name: Chang
- first_name: Martin
full_name: Vreugdenhil, Martin
last_name: Vreugdenhil
- first_name: Xiaoli
full_name: Li, Xiaoli
last_name: Li
- first_name: Milan
full_name: Palus, Milan
last_name: Palus
- first_name: Alejandro
full_name: Bujan, Alejandro
last_name: Bujan
- first_name: Richard
full_name: Dearden, Richard
last_name: Dearden
- first_name: John
full_name: Jefferys, John
last_name: Jefferys
citation:
ama: Jiruska P, Csicsvari JL, Powell A, et al. High-frequency network activity,
global increase in neuronal activity, and synchrony expansion precede epileptic
seizures in vitro. Journal of Neuroscience. 2010;30(16):5690-5701. doi:10.1523/JNEUROSCI.0535-10.2010
apa: Jiruska, P., Csicsvari, J. L., Powell, A., Fox, J., Chang, W., Vreugdenhil,
M., … Jefferys, J. (2010). High-frequency network activity, global increase in
neuronal activity, and synchrony expansion precede epileptic seizures in vitro.
Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0535-10.2010
chicago: Jiruska, Premysl, Jozsef L Csicsvari, Andrew Powell, John Fox, Wei Chang,
Martin Vreugdenhil, Xiaoli Li, et al. “High-Frequency Network Activity, Global
Increase in Neuronal Activity, and Synchrony Expansion Precede Epileptic Seizures
in Vitro.” Journal of Neuroscience. Society for Neuroscience, 2010. https://doi.org/10.1523/JNEUROSCI.0535-10.2010.
ieee: P. Jiruska et al., “High-frequency network activity, global increase
in neuronal activity, and synchrony expansion precede epileptic seizures in vitro,”
Journal of Neuroscience, vol. 30, no. 16. Society for Neuroscience, pp.
5690–5701, 2010.
ista: Jiruska P, Csicsvari JL, Powell A, Fox J, Chang W, Vreugdenhil M, Li X, Palus
M, Bujan A, Dearden R, Jefferys J. 2010. High-frequency network activity, global
increase in neuronal activity, and synchrony expansion precede epileptic seizures
in vitro. Journal of Neuroscience. 30(16), 5690–5701.
mla: Jiruska, Premysl, et al. “High-Frequency Network Activity, Global Increase
in Neuronal Activity, and Synchrony Expansion Precede Epileptic Seizures in Vitro.”
Journal of Neuroscience, vol. 30, no. 16, Society for Neuroscience, 2010,
pp. 5690–701, doi:10.1523/JNEUROSCI.0535-10.2010.
short: P. Jiruska, J.L. Csicsvari, A. Powell, J. Fox, W. Chang, M. Vreugdenhil,
X. Li, M. Palus, A. Bujan, R. Dearden, J. Jefferys, Journal of Neuroscience 30
(2010) 5690–5701.
date_created: 2018-12-11T12:03:51Z
date_published: 2010-04-21T00:00:00Z
date_updated: 2021-01-12T07:44:10Z
day: '21'
doi: 10.1523/JNEUROSCI.0535-10.2010
extern: '1'
intvolume: ' 30'
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.jneurosci.org/content/30/16/5690
month: '04'
oa: 1
oa_version: None
page: 5690 - 5701
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '2848'
quality_controlled: '1'
status: public
title: High-frequency network activity, global increase in neuronal activity, and
synchrony expansion precede epileptic seizures in vitro
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2010'
...
---
_id: '3719'
abstract:
- lang: eng
text: The induction of a signaling pathway is characterized by transient complex
formation and mutual posttranslational modification of proteins. To faithfully
capture this combinatorial process in a math- ematical model is an important challenge
in systems biology. Exploiting the limited context on which most binding and modification
events are conditioned, attempts have been made to reduce the com- binatorial
complexity by quotienting the reachable set of molecular species, into species
aggregates while preserving the deterministic semantics of the thermodynamic limit.
Recently we proposed a quotienting that also preserves the stochastic semantics
and that is complete in the sense that the semantics of individual species can
be recovered from the aggregate semantics. In this paper we prove that this quotienting
yields a sufficient condition for weak lumpability and that it gives rise to a
backward Markov bisimulation between the original and aggregated transition system.
We illustrate the framework on a case study of the EGF/insulin receptor crosstalk.
acknowledgement: Jérôme Feret’s contribution was partially supported by the ABSTRACTCELL
ANR-Chair of Excellence. Heinz Koeppl acknowledges the support from the Swiss National
Science Foundation, grant no. 200020-117975/1. Tatjana Petrov acknowledges the support
from SystemsX.ch, the Swiss Initiative in Systems Biology.
alternative_title:
- EPTCS
arxiv: 1
author:
- first_name: Jérôme
full_name: Feret, Jérôme
last_name: Feret
- 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: Heinz
full_name: Koeppl, Heinz
last_name: Koeppl
- first_name: Tatjana
full_name: Petrov, Tatjana
id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
last_name: Petrov
orcid: 0000-0002-9041-0905
citation:
ama: 'Feret J, Henzinger TA, Koeppl H, Petrov T. Lumpability abstractions of rule-based
systems. In: Vol 40. Open Publishing Association; 2010:142-161.'
apa: 'Feret, J., Henzinger, T. A., Koeppl, H., & Petrov, T. (2010). Lumpability
abstractions of rule-based systems (Vol. 40, pp. 142–161). Presented at the MECBIC:
Membrane Computing and Biologically Inspired Process Calculi, Jena, Germany: Open
Publishing Association.'
chicago: Feret, Jérôme, Thomas A Henzinger, Heinz Koeppl, and Tatjana Petrov. “Lumpability
Abstractions of Rule-Based Systems,” 40:142–61. Open Publishing Association, 2010.
ieee: 'J. Feret, T. A. Henzinger, H. Koeppl, and T. Petrov, “Lumpability abstractions
of rule-based systems,” presented at the MECBIC: Membrane Computing and Biologically
Inspired Process Calculi, Jena, Germany, 2010, vol. 40, pp. 142–161.'
ista: 'Feret J, Henzinger TA, Koeppl H, Petrov T. 2010. Lumpability abstractions
of rule-based systems. MECBIC: Membrane Computing and Biologically Inspired Process
Calculi, EPTCS, vol. 40, 142–161.'
mla: Feret, Jérôme, et al. Lumpability Abstractions of Rule-Based Systems.
Vol. 40, Open Publishing Association, 2010, pp. 142–61.
short: J. Feret, T.A. Henzinger, H. Koeppl, T. Petrov, in:, Open Publishing Association,
2010, pp. 142–161.
conference:
end_date: 2010-08-23
location: Jena, Germany
name: 'MECBIC: Membrane Computing and Biologically Inspired Process Calculi'
start_date: 2010-08-23
date_created: 2018-12-11T12:04:47Z
date_published: 2010-10-30T00:00:00Z
date_updated: 2023-02-23T11:15:19Z
day: '30'
ddc:
- '570'
department:
- _id: ToHe
- _id: CaGu
external_id:
arxiv:
- '1011.0496'
file:
- access_level: open_access
checksum: eaaba991a86fff37606b0eb5196878e8
content_type: application/pdf
creator: kschuh
date_created: 2019-01-31T12:09:09Z
date_updated: 2020-07-14T12:46:14Z
file_id: '5904'
file_name: Lumpability_abstractions_of_rule-based_systems.pdf
file_size: 907155
relation: main_file
file_date_updated: 2020-07-14T12:46:14Z
has_accepted_license: '1'
intvolume: ' 40'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 142-161
publication_status: published
publisher: Open Publishing Association
publist_id: '2511'
quality_controlled: '1'
related_material:
record:
- id: '3168'
relation: later_version
status: public
scopus_import: 1
status: public
title: Lumpability abstractions of rule-based systems
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 40
year: '2010'
...
---
_id: '3743'
abstract:
- lang: eng
text: These are notes for a set of 7 two-hour lectures given at the 2010 Summer
School on Quantitative Evolutionary and Comparative Genomics at OIST, Okinawa,
Japan. The emphasis is on understanding how biological systems process information.
We take a physicist's approach of looking for simple phenomenological descriptions
that can address the questions of biological function without necessarily modeling
all (mostly unknown) microscopic details; the example that is developed throughout
the notes is transcriptional regulation in genetic regulatory networks. We present
tools from information theory and statistical physics that can be used to analyze
noisy nonlinear biological networks, and build generative and predictive models
of regulatory processes.
author:
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: 'Tkačik G. From statistical mechanics to information theory: understanding
biophysical information-processing systems. ArXiv. 2010;q-MN:1-52.'
apa: 'Tkačik, G. (2010). From statistical mechanics to information theory: understanding
biophysical information-processing systems. ArXiv. ArXiv.'
chicago: 'Tkačik, Gašper. “From Statistical Mechanics to Information Theory: Understanding
Biophysical Information-Processing Systems.” ArXiv. ArXiv, 2010.'
ieee: 'G. Tkačik, “From statistical mechanics to information theory: understanding
biophysical information-processing systems,” ArXiv, vol. q-MN. ArXiv, pp.
1–52, 2010.'
ista: 'Tkačik G. 2010. From statistical mechanics to information theory: understanding
biophysical information-processing systems. ArXiv, q-MN, 1–52, .'
mla: 'Tkačik, Gašper. “From Statistical Mechanics to Information Theory: Understanding
Biophysical Information-Processing Systems.” ArXiv, vol. q-MN, ArXiv, 2010,
pp. 1–52.'
short: G. Tkačik, ArXiv q-MN (2010) 1–52.
date_created: 2018-12-11T12:04:55Z
date_published: 2010-06-22T00:00:00Z
date_updated: 2021-01-12T07:51:53Z
day: '22'
extern: 1
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1006.4291v1
month: '06'
oa: 1
page: 1 - 52
publication: ArXiv
publication_status: published
publisher: ArXiv
publist_id: '2487'
quality_controlled: 0
status: public
title: 'From statistical mechanics to information theory: understanding biophysical
information-processing systems'
type: preprint
volume: q-bio.MN
year: '2010'
...
---
_id: '3748'
abstract:
- lang: eng
text: The chemotaxis signalling network in Escherichia coli that controls the locomotion
of bacteria is a classic model system for signal transduction1, 2. This pathway
modulates the behaviour of flagellar motors to propel bacteria towards sources
of chemical attractants. Although this system relaxes to a steady state in response
to environmental changes, the signalling events within the chemotaxis network
are noisy and cause large temporal variations of the motor behaviour even in the
absence of stimulus3. That the same signalling network governs both behavioural
variability and cellular response raises the question of whether these two traits
are independent. Here, we experimentally establish a fluctuation–response relationship
in the chemotaxis system of living bacteria. Using this relationship, we demonstrate
the possibility of inferring the cellular response from the behavioural variability
measured before stimulus. In monitoring the pre- and post-stimulus switching behaviour
of individual bacterial motors, we found that variability scales linearly with
the response time for different functioning states of the cell. This study highlights
that the fundamental relationship between fluctuation and response is not constrained
to physical systems at thermodynamic equilibrium4 but is extensible to living
cells5. Such a relationship not only implies that behavioural variability and
cellular response can be coupled traits, but it also provides a general framework
within which we can examine how the selection of a network design shapes this
interdependence
author:
- first_name: Heungwon
full_name: Park, Heungwon
last_name: Park
- first_name: William
full_name: Pontius, William
last_name: Pontius
- first_name: Calin C
full_name: Calin Guet
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: John
full_name: Marko, John F
last_name: Marko
- first_name: Thierry
full_name: Emonet,Thierry
last_name: Emonet
- first_name: Philippe
full_name: Cluzel,Philippe
last_name: Cluzel
citation:
ama: Park H, Pontius W, Guet CC, Marko J, Emonet T, Cluzel P. Interdependence of
behavioural variability and response to small stimuli in bacteria. Nature.
2010;468:819-823. doi:10.1038/nature09551
apa: Park, H., Pontius, W., Guet, C. C., Marko, J., Emonet, T., & Cluzel, P.
(2010). Interdependence of behavioural variability and response to small stimuli
in bacteria. Nature. Nature Publishing Group. https://doi.org/10.1038/nature09551
chicago: Park, Heungwon, William Pontius, Calin C Guet, John Marko, Thierry Emonet,
and Philippe Cluzel. “Interdependence of Behavioural Variability and Response
to Small Stimuli in Bacteria.” Nature. Nature Publishing Group, 2010. https://doi.org/10.1038/nature09551.
ieee: H. Park, W. Pontius, C. C. Guet, J. Marko, T. Emonet, and P. Cluzel, “Interdependence
of behavioural variability and response to small stimuli in bacteria,” Nature,
vol. 468. Nature Publishing Group, pp. 819–823, 2010.
ista: Park H, Pontius W, Guet CC, Marko J, Emonet T, Cluzel P. 2010. Interdependence
of behavioural variability and response to small stimuli in bacteria. Nature.
468, 819–823.
mla: Park, Heungwon, et al. “Interdependence of Behavioural Variability and Response
to Small Stimuli in Bacteria.” Nature, vol. 468, Nature Publishing Group,
2010, pp. 819–23, doi:10.1038/nature09551.
short: H. Park, W. Pontius, C.C. Guet, J. Marko, T. Emonet, P. Cluzel, Nature 468
(2010) 819–823.
date_created: 2018-12-11T12:04:57Z
date_published: 2010-12-09T00:00:00Z
date_updated: 2021-01-12T07:51:55Z
day: '09'
doi: 10.1038/nature09551
extern: 1
intvolume: ' 468'
main_file_link:
- open_access: '1'
url: http://europepmc.org/articles/pmc3230254
month: '12'
oa: 1
page: 819 - 823
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '2480'
quality_controlled: 0
status: public
title: Interdependence of behavioural variability and response to small stimuli in
bacteria
type: journal_article
volume: 468
year: '2010'
...
---
_id: '3749'
abstract:
- lang: eng
text: 'In E. coli, chemotactic behavior exhibits perfect adaptation that is robust
to changes in the intracellular concentration of the chemotactic proteins, such
as CheR and CheB. However, the robustness of the perfect adaptation does not explicitly
imply a robust chemotactic response. Previous studies on the robustness of the
chemotactic response relied on swarming assays, which can be confounded by processes
besides chemotaxis, such as cellular growth and depletion of nutrients. Here,
using a high-throughput capillary assay that eliminates the effects of growth,
we experimentally studied how the chemotactic response depends on the relative
concentration of the chemotactic proteins. We simultaneously measured both the
chemotactic response of E. coli cells to L: -aspartate and the concentrations
of YFP-CheR and CheB-CFP fusion proteins. We found that the chemotactic response
is fine-tuned to a specific ratio of [CheR]/[CheB] with a maximum response comparable
to the chemotactic response of wild-type behavior. In contrast to adaptation in
chemotaxis, that is robust and exact, capillary assays revealed that the chemotactic
response in swimming bacteria is fined-tuned to wild-type level of the [CheR]/[CheB]
ratio.'
acknowledgement: "P50 GM081892-04/GM/NIGMS NIH HHS/United States\nR01 AI059195-01A1/AI/NIAID
NIH HHS/United States\nR01 AI059195-02/AI/NIAID NIH HHS/United States\nR01 AI059195-03/AI/NIAID
NIH HHS/United States\nR01AI059195-03/AI/NIAID NIH HHS/United States\n\n\nPMCID:
PMC3230253 "
author:
- first_name: Heungwon
full_name: Park, Heungwon
last_name: Park
- first_name: Calin C
full_name: Calin Guet
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Thierry
full_name: Emonet,Thierry
last_name: Emonet
- first_name: Philippe
full_name: Cluzel,Philippe
last_name: Cluzel
citation:
ama: Park H, Guet CC, Emonet T, Cluzel P. Fine-tuning of chemotactic response in
E. coli determined by high-throughput capillary assay. Current Microbiology.
2010;62(3):764-769. doi:10.1007/s00284-010-9778-z
apa: Park, H., Guet, C. C., Emonet, T., & Cluzel, P. (2010). Fine-tuning of
chemotactic response in E. coli determined by high-throughput capillary assay.
Current Microbiology. Springer. https://doi.org/10.1007/s00284-010-9778-z
chicago: Park, Heungwon, Calin C Guet, Thierry Emonet, and Philippe Cluzel. “Fine-Tuning
of Chemotactic Response in E. Coli Determined by High-Throughput Capillary Assay.”
Current Microbiology. Springer, 2010. https://doi.org/10.1007/s00284-010-9778-z.
ieee: H. Park, C. C. Guet, T. Emonet, and P. Cluzel, “Fine-tuning of chemotactic
response in E. coli determined by high-throughput capillary assay,” Current
Microbiology, vol. 62, no. 3. Springer, pp. 764–769, 2010.
ista: Park H, Guet CC, Emonet T, Cluzel P. 2010. Fine-tuning of chemotactic response
in E. coli determined by high-throughput capillary assay. Current Microbiology.
62(3), 764–769.
mla: Park, Heungwon, et al. “Fine-Tuning of Chemotactic Response in E. Coli Determined
by High-Throughput Capillary Assay.” Current Microbiology, vol. 62, no.
3, Springer, 2010, pp. 764–69, doi:10.1007/s00284-010-9778-z.
short: H. Park, C.C. Guet, T. Emonet, P. Cluzel, Current Microbiology 62 (2010)
764–769.
date_created: 2018-12-11T12:04:57Z
date_published: 2010-10-23T00:00:00Z
date_updated: 2021-01-12T07:51:55Z
day: '23'
doi: 10.1007/s00284-010-9778-z
extern: 1
intvolume: ' 62'
issue: '3'
main_file_link:
- open_access: '1'
url: http://europepmc.org/articles/pmc3230253
month: '10'
oa: 1
page: 764 - 769
publication: Current Microbiology
publication_status: published
publisher: Springer
publist_id: '2479'
quality_controlled: 0
status: public
title: Fine-tuning of chemotactic response in E. coli determined by high-throughput
capillary assay
type: journal_article
volume: 62
year: '2010'
...