---
_id: '9014'
abstract:
- lang: eng
text: In this Letter, we explore experimentally the phase behavior of a dense active
suspension of self-propelled colloids. In addition to a solidlike and gaslike
phase observed for high and low densities, a novel cluster phase is reported at
intermediate densities. This takes the form of a stationary assembly of dense
aggregates—resulting from a permanent dynamical merging and separation of active
colloids—whose average size grows with activity as a linear function of the self-propelling
velocity. While different possible scenarios can be considered to account for
these observations—such as a generic velocity weakening instability recently put
forward—we show that the experimental results are reproduced mathematically by
a chemotactic aggregation mechanism, originally introduced to account for bacterial
aggregation and accounting here for diffusiophoretic chemical interaction between
colloidal swimmers.
article_number: '268303'
article_processing_charge: No
article_type: letter_note
author:
- first_name: I.
full_name: Theurkauff, I.
last_name: Theurkauff
- first_name: C.
full_name: Cottin-Bizonne, C.
last_name: Cottin-Bizonne
- 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: C.
full_name: Ybert, C.
last_name: Ybert
- first_name: L.
full_name: Bocquet, L.
last_name: Bocquet
citation:
ama: Theurkauff I, Cottin-Bizonne C, Palacci JA, Ybert C, Bocquet L. Dynamic clustering
in active colloidal suspensions with chemical signaling. Physical Review Letters.
2012;108(26). doi:10.1103/physrevlett.108.268303
apa: Theurkauff, I., Cottin-Bizonne, C., Palacci, J. A., Ybert, C., & Bocquet,
L. (2012). Dynamic clustering in active colloidal suspensions with chemical signaling.
Physical Review Letters. American Physical Society . https://doi.org/10.1103/physrevlett.108.268303
chicago: Theurkauff, I., C. Cottin-Bizonne, Jérémie A Palacci, C. Ybert, and L.
Bocquet. “Dynamic Clustering in Active Colloidal Suspensions with Chemical Signaling.”
Physical Review Letters. American Physical Society , 2012. https://doi.org/10.1103/physrevlett.108.268303.
ieee: I. Theurkauff, C. Cottin-Bizonne, J. A. Palacci, C. Ybert, and L. Bocquet,
“Dynamic clustering in active colloidal suspensions with chemical signaling,”
Physical Review Letters, vol. 108, no. 26. American Physical Society ,
2012.
ista: Theurkauff I, Cottin-Bizonne C, Palacci JA, Ybert C, Bocquet L. 2012. Dynamic
clustering in active colloidal suspensions with chemical signaling. Physical Review
Letters. 108(26), 268303.
mla: Theurkauff, I., et al. “Dynamic Clustering in Active Colloidal Suspensions
with Chemical Signaling.” Physical Review Letters, vol. 108, no. 26, 268303,
American Physical Society , 2012, doi:10.1103/physrevlett.108.268303.
short: I. Theurkauff, C. Cottin-Bizonne, J.A. Palacci, C. Ybert, L. Bocquet, Physical
Review Letters 108 (2012).
date_created: 2021-01-19T10:26:59Z
date_published: 2012-06-29T00:00:00Z
date_updated: 2023-02-23T13:46:45Z
day: '29'
doi: 10.1103/physrevlett.108.268303
extern: '1'
external_id:
arxiv:
- '1202.6264'
pmid:
- '23005020'
intvolume: ' 108'
issue: '26'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1202.6264
month: '06'
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: Dynamic clustering in active colloidal suspensions with chemical signaling
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 108
year: '2012'
...
---
_id: '91'
abstract:
- lang: eng
text: 'We demonstrate how to appropriately estimate the zero-frequency (static)
hyperpolarizability of an organic molecule from its charge distribution, and we
explore applications of these estimates for identifying and evaluating new organic
nonlinear optical (NLO) materials. First, we calculate hyperpolarizabilities from
Hartree-Fock-derived charge distributions and find order-of-magnitude agreement
with experimental values. We show that these simple arithmetic calculations will
enable systematic searches for new organic NLO molecules. Second, we derive hyperpolarizabilities
from crystallographic data using a multipolar charge-density analysis and find
good agreement with empirical calculations. This demonstrates an experimental
determination of the full static hyperpolarizability tensor in a solid-state sample. '
acknowledgement: This work was supported by The Winston Churchill Foundation of the
United States (A.P.H., M.A.B.F., D.D.H.), The Royal Society via a University Research
Fellowship (J.M.C.), and the University of New Brunswick via The Vice-Chancellor’s
Research Chair (J.M.C.).
article_number: '033512'
author:
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: Jacqueline
full_name: Cole, Jacqueline
last_name: Cole
- first_name: Martin
full_name: Blood Forsythe, Martin
last_name: Blood Forsythe
- first_name: Daniel
full_name: Hickstein, Daniel
last_name: Hickstein
citation:
ama: Higginbotham AP, Cole J, Blood Forsythe M, Hickstein D. Identifying and evaluating
organic nonlinear optical materials via molecular moments. Journal of Applied
Physics. 2012;111(3). doi:10.1063/1.3678593
apa: Higginbotham, A. P., Cole, J., Blood Forsythe, M., & Hickstein, D. (2012).
Identifying and evaluating organic nonlinear optical materials via molecular moments.
Journal of Applied Physics. American Institute of Physics. https://doi.org/10.1063/1.3678593
chicago: Higginbotham, Andrew P, Jacqueline Cole, Martin Blood Forsythe, and Daniel
Hickstein. “Identifying and Evaluating Organic Nonlinear Optical Materials via
Molecular Moments.” Journal of Applied Physics. American Institute of Physics,
2012. https://doi.org/10.1063/1.3678593.
ieee: A. P. Higginbotham, J. Cole, M. Blood Forsythe, and D. Hickstein, “Identifying
and evaluating organic nonlinear optical materials via molecular moments,” Journal
of Applied Physics, vol. 111, no. 3. American Institute of Physics, 2012.
ista: Higginbotham AP, Cole J, Blood Forsythe M, Hickstein D. 2012. Identifying
and evaluating organic nonlinear optical materials via molecular moments. Journal
of Applied Physics. 111(3), 033512.
mla: Higginbotham, Andrew P., et al. “Identifying and Evaluating Organic Nonlinear
Optical Materials via Molecular Moments.” Journal of Applied Physics, vol.
111, no. 3, 033512, American Institute of Physics, 2012, doi:10.1063/1.3678593.
short: A.P. Higginbotham, J. Cole, M. Blood Forsythe, D. Hickstein, Journal of Applied
Physics 111 (2012).
date_created: 2018-12-11T11:44:35Z
date_published: 2012-02-07T00:00:00Z
date_updated: 2021-01-12T08:21:50Z
day: '07'
doi: 10.1063/1.3678593
extern: '1'
intvolume: ' 111'
issue: '3'
language:
- iso: eng
month: '02'
oa_version: None
publication: Journal of Applied Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '7963'
quality_controlled: '1'
status: public
title: Identifying and evaluating organic nonlinear optical materials via molecular
moments
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 111
year: '2012'
...
---
_id: '9142'
abstract:
- lang: eng
text: "In models of radiative–convective equilibrium it is known that convection
can spontaneously aggregate into one single localized moist region if the domain
is large enough. The large changes in the mean climate state and radiative fluxes
accompanying this self-aggregation raise questions as to what simulations at lower
resolutions with parameterized convection, in similar homogeneous geometries,
should be expected to produce to be considered successful in mimicking a cloud-resolving
model.\r\nThe authors investigate this self-aggregation in a nonrotating, three-dimensional
cloud-resolving model on a square domain without large-scale forcing. It is found
that self-aggregation is sensitive not only to the domain size, but also to the
horizontal resolution. With horizontally homogeneous initial conditions, convective
aggregation only occurs on domains larger than about 200km and with resolutions
coarser than about 2km in the model examined. The system exhibits hysteresis,
so that with aggregated initial conditions, convection remains aggregated even
at our finest resolution, 500m, as long as the domain is greater than 200–300km.\r\nThe
sensitivity of self-aggregation to resolution and domain size in this model is
due to the sensitivity of the distribution of low clouds to these two parameters.
Indeed, the mechanism responsible for the aggregation of convection is the dynamical
response to the longwave radiative cooling from low clouds. Strong longwave cooling
near cloud top in dry regions forces downward motion, which by continuity generates
inflow near cloud top and near-surface outflow from dry regions. This circulation
results in the net export of moist static energy from regions with low moist static
energy, yielding a positive feedback."
article_processing_charge: No
article_type: original
author:
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
- first_name: Isaac M.
full_name: Held, Isaac M.
last_name: Held
citation:
ama: Muller CJ, Held IM. Detailed investigation of the self-aggregation of convection
in cloud-resolving simulations. Journal of the Atmospheric Sciences. 2012;69(8):2551-2565.
doi:10.1175/jas-d-11-0257.1
apa: Muller, C. J., & Held, I. M. (2012). Detailed investigation of the self-aggregation
of convection in cloud-resolving simulations. Journal of the Atmospheric Sciences.
American Meteorological Society. https://doi.org/10.1175/jas-d-11-0257.1
chicago: Muller, Caroline J, and Isaac M. Held. “Detailed Investigation of the Self-Aggregation
of Convection in Cloud-Resolving Simulations.” Journal of the Atmospheric Sciences.
American Meteorological Society, 2012. https://doi.org/10.1175/jas-d-11-0257.1.
ieee: C. J. Muller and I. M. Held, “Detailed investigation of the self-aggregation
of convection in cloud-resolving simulations,” Journal of the Atmospheric Sciences,
vol. 69, no. 8. American Meteorological Society, pp. 2551–2565, 2012.
ista: Muller CJ, Held IM. 2012. Detailed investigation of the self-aggregation of
convection in cloud-resolving simulations. Journal of the Atmospheric Sciences.
69(8), 2551–2565.
mla: Muller, Caroline J., and Isaac M. Held. “Detailed Investigation of the Self-Aggregation
of Convection in Cloud-Resolving Simulations.” Journal of the Atmospheric Sciences,
vol. 69, no. 8, American Meteorological Society, 2012, pp. 2551–65, doi:10.1175/jas-d-11-0257.1.
short: C.J. Muller, I.M. Held, Journal of the Atmospheric Sciences 69 (2012) 2551–2565.
date_created: 2021-02-15T14:39:03Z
date_published: 2012-08-01T00:00:00Z
date_updated: 2022-01-24T13:49:41Z
day: '01'
doi: 10.1175/jas-d-11-0257.1
extern: '1'
intvolume: ' 69'
issue: '8'
keyword:
- Atmospheric Science
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1175/JAS-D-11-0257.1
month: '08'
oa: 1
oa_version: Published Version
page: 2551-2565
publication: Journal of the Atmospheric Sciences
publication_identifier:
issn:
- 0022-4928
- 1520-0469
publication_status: published
publisher: American Meteorological Society
quality_controlled: '1'
status: public
title: Detailed investigation of the self-aggregation of convection in cloud-resolving
simulations
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 69
year: '2012'
...
---
_id: '9451'
abstract:
- lang: eng
text: The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes
DNA demethylation before fertilization, but the targeting preferences, mechanism,
and biological significance of this process remain unclear. Here, we show that
active DNA demethylation mediated by the DEMETER DNA glycosylase accounts for
all of the demethylation in the central cell and preferentially targets small,
AT-rich, and nucleosome-depleted euchromatic transposable elements. The vegetative
cell, the companion cell of sperm, also undergoes DEMETER-dependent demethylation
of similar sequences, and lack of DEMETER in vegetative cells causes reduced small
RNA–directed DNA methylation of transposons in sperm. Our results demonstrate
that demethylation in companion cells reinforces transposon methylation in plant
gametes and likely contributes to stable silencing of transposable elements across
generations.
article_processing_charge: No
article_type: original
author:
- first_name: Christian A.
full_name: Ibarra, Christian A.
last_name: Ibarra
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
last_name: Feng
- first_name: Vera K.
full_name: Schoft, Vera K.
last_name: Schoft
- first_name: Tzung-Fu
full_name: Hsieh, Tzung-Fu
last_name: Hsieh
- first_name: Rie
full_name: Uzawa, Rie
last_name: Uzawa
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Assaf
full_name: Zemach, Assaf
last_name: Zemach
- first_name: Nina
full_name: Chumak, Nina
last_name: Chumak
- first_name: Adriana
full_name: Machlicova, Adriana
last_name: Machlicova
- first_name: Toshiro
full_name: Nishimura, Toshiro
last_name: Nishimura
- first_name: Denisse
full_name: Rojas, Denisse
last_name: Rojas
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Hisashi
full_name: Tamaru, Hisashi
last_name: Tamaru
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Ibarra CA, Feng X, Schoft VK, et al. Active DNA demethylation in plant companion
cells reinforces transposon methylation in gametes. Science. 2012;337(6100):1360-1364.
doi:10.1126/science.1224839
apa: Ibarra, C. A., Feng, X., Schoft, V. K., Hsieh, T.-F., Uzawa, R., Rodrigues,
J. A., … Zilberman, D. (2012). Active DNA demethylation in plant companion cells
reinforces transposon methylation in gametes. Science. American Association
for the Advancement of Science. https://doi.org/10.1126/science.1224839
chicago: Ibarra, Christian A., Xiaoqi Feng, Vera K. Schoft, Tzung-Fu Hsieh, Rie
Uzawa, Jessica A. Rodrigues, Assaf Zemach, et al. “Active DNA Demethylation in
Plant Companion Cells Reinforces Transposon Methylation in Gametes.” Science.
American Association for the Advancement of Science, 2012. https://doi.org/10.1126/science.1224839.
ieee: C. A. Ibarra et al., “Active DNA demethylation in plant companion cells
reinforces transposon methylation in gametes,” Science, vol. 337, no. 6100.
American Association for the Advancement of Science, pp. 1360–1364, 2012.
ista: Ibarra CA, Feng X, Schoft VK, Hsieh T-F, Uzawa R, Rodrigues JA, Zemach A,
Chumak N, Machlicova A, Nishimura T, Rojas D, Fischer RL, Tamaru H, Zilberman
D. 2012. Active DNA demethylation in plant companion cells reinforces transposon
methylation in gametes. Science. 337(6100), 1360–1364.
mla: Ibarra, Christian A., et al. “Active DNA Demethylation in Plant Companion Cells
Reinforces Transposon Methylation in Gametes.” Science, vol. 337, no. 6100,
American Association for the Advancement of Science, 2012, pp. 1360–64, doi:10.1126/science.1224839.
short: C.A. Ibarra, X. Feng, V.K. Schoft, T.-F. Hsieh, R. Uzawa, J.A. Rodrigues,
A. Zemach, N. Chumak, A. Machlicova, T. Nishimura, D. Rojas, R.L. Fischer, H.
Tamaru, D. Zilberman, Science 337 (2012) 1360–1364.
date_created: 2021-06-04T07:51:31Z
date_published: 2012-09-14T00:00:00Z
date_updated: 2021-12-14T08:28:51Z
day: '14'
ddc:
- '580'
department:
- _id: DaZi
doi: 10.1126/science.1224839
extern: '1'
external_id:
pmid:
- '22984074'
has_accepted_license: '1'
intvolume: ' 337'
issue: '6100'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034762/
month: '09'
oa: 1
oa_version: Published Version
page: 1360-1364
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Active DNA demethylation in plant companion cells reinforces transposon methylation
in gametes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 337
year: '2012'
...
---
_id: '9535'
abstract:
- lang: eng
text: The most well-studied function of DNA methylation in eukaryotic cells is the
transcriptional silencing of genes and transposons. More recent results showed
that many eukaryotes methylate the bodies of genes as well and that this methylation
correlates with transcriptional activity rather than repression. The purpose of
gene body methylation remains mysterious, but is potentially related to the histone
variant H2A.Z. Studies in plants and animals have shown that the genome-wide distributions
of H2A.Z and DNA methylation are strikingly anticorrelated. Furthermore, we and
other investigators have shown that this relationship is likely to be the result
of an ancient but unknown mechanism by which DNA methylation prevents the incorporation
of H2A.Z. Recently, we discovered strong correlations between the presence of
H2A.Z within gene bodies, the degree to which a gene's expression varies across
tissue types or environmental conditions, and transcriptional misregulation in
an h2a.z mutant. We propose that one basal function of gene body methylation is
the establishment of constitutive expression patterns within housekeeping genes
by excluding H2A.Z from their bodies.
article_processing_charge: No
article_type: review
author:
- first_name: D.
full_name: Coleman-Derr, D.
last_name: Coleman-Derr
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Coleman-Derr D, Zilberman D. DNA methylation, H2A.Z, and the regulation of
constitutive expression. Cold Spring Harbor Symposia on Quantitative Biology.
2012;77:147-154. doi:10.1101/sqb.2012.77.014944
apa: Coleman-Derr, D., & Zilberman, D. (2012). DNA methylation, H2A.Z, and the
regulation of constitutive expression. Cold Spring Harbor Symposia on Quantitative
Biology. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/sqb.2012.77.014944
chicago: Coleman-Derr, D., and Daniel Zilberman. “DNA Methylation, H2A.Z, and the
Regulation of Constitutive Expression.” Cold Spring Harbor Symposia on Quantitative
Biology. Cold Spring Harbor Laboratory Press, 2012. https://doi.org/10.1101/sqb.2012.77.014944.
ieee: D. Coleman-Derr and D. Zilberman, “DNA methylation, H2A.Z, and the regulation
of constitutive expression,” Cold Spring Harbor Symposia on Quantitative Biology,
vol. 77. Cold Spring Harbor Laboratory Press, pp. 147–154, 2012.
ista: Coleman-Derr D, Zilberman D. 2012. DNA methylation, H2A.Z, and the regulation
of constitutive expression. Cold Spring Harbor Symposia on Quantitative Biology.
77, 147–154.
mla: Coleman-Derr, D., and Daniel Zilberman. “DNA Methylation, H2A.Z, and the Regulation
of Constitutive Expression.” Cold Spring Harbor Symposia on Quantitative Biology,
vol. 77, Cold Spring Harbor Laboratory Press, 2012, pp. 147–54, doi:10.1101/sqb.2012.77.014944.
short: D. Coleman-Derr, D. Zilberman, Cold Spring Harbor Symposia on Quantitative
Biology 77 (2012) 147–154.
date_created: 2021-06-08T13:01:23Z
date_published: 2012-12-18T00:00:00Z
date_updated: 2021-12-14T08:33:09Z
day: '18'
department:
- _id: DaZi
doi: 10.1101/sqb.2012.77.014944
extern: '1'
external_id:
pmid:
- '23250988'
intvolume: ' 77'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/sqb.2012.77.014944
month: '12'
oa: 1
oa_version: Published Version
page: 147-154
pmid: 1
publication: Cold Spring Harbor Symposia on Quantitative Biology
publication_identifier:
eissn:
- 1943-4456
issn:
- 0091-7451
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA methylation, H2A.Z, and the regulation of constitutive expression
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 77
year: '2012'
...