---
_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
arxiv: 1
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: '9049'
abstract:
- lang: eng
text: 'Diffusiophoretic motion of colloids and macromolecules under salt gradients
exhibits a logarithmic-sensing, i.e. the particle velocity is proportional to
the spatial gradient of the logarithm of the salt concentration, as VDP = DDP∇logc.
Here we explore experimentally the implications of this log-sensing behavior,
on the basis of a hydrogel microfluidic device allowing to build spatially and
temporally controlled gradients. We first demonstrate that the non-linearity of
the salt-taxis leads to a trapping of particles under concentration gradient oscillations
via a rectification of the motion. As an alternative, we make use of the high
sensitivity of diffusiophoretic migration to vanishing salt concentration due
to the log-sensing: in a counter-intuitive way, a vanishing gradient can lead
to measurable velocity provided that the solute concentration is low enough, thus
keeping ∇c/c finite. We show that this leads to a strong segregation of particles
in osmotic shock configuration, resulting from a step change of the salt concentration
at the boundaries. These various phenomena are rationalized on the basis of a
theoretical description for the time-dependent Smoluchowski equation for the colloidal
density.'
article_processing_charge: No
article_type: original
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. Osmotic traps for colloids
and macromolecules based on logarithmic sensing in salt taxis. Soft Matter.
2012;8(4):980-994. doi:10.1039/c1sm06395b
apa: Palacci, J. A., Cottin-Bizonne, C., Ybert, C., & Bocquet, L. (2012). Osmotic
traps for colloids and macromolecules based on logarithmic sensing in salt taxis.
Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c1sm06395b
chicago: Palacci, Jérémie A, Cécile Cottin-Bizonne, Christophe Ybert, and Lydéric
Bocquet. “Osmotic Traps for Colloids and Macromolecules Based on Logarithmic Sensing
in Salt Taxis.” Soft Matter. Royal Society of Chemistry, 2012. https://doi.org/10.1039/c1sm06395b.
ieee: J. A. Palacci, C. Cottin-Bizonne, C. Ybert, and L. Bocquet, “Osmotic traps
for colloids and macromolecules based on logarithmic sensing in salt taxis,” Soft
Matter, vol. 8, no. 4. Royal Society of Chemistry, pp. 980–994, 2012.
ista: Palacci JA, Cottin-Bizonne C, Ybert C, Bocquet L. 2012. Osmotic traps for
colloids and macromolecules based on logarithmic sensing in salt taxis. Soft Matter.
8(4), 980–994.
mla: Palacci, Jérémie A., et al. “Osmotic Traps for Colloids and Macromolecules
Based on Logarithmic Sensing in Salt Taxis.” Soft Matter, vol. 8, no. 4,
Royal Society of Chemistry, 2012, pp. 980–94, doi:10.1039/c1sm06395b.
short: J.A. Palacci, C. Cottin-Bizonne, C. Ybert, L. Bocquet, Soft Matter 8 (2012)
980–994.
date_created: 2021-02-01T13:43:10Z
date_published: 2012-01-28T00:00:00Z
date_updated: 2023-02-23T13:47:31Z
day: '28'
doi: 10.1039/c1sm06395b
extern: '1'
intvolume: ' 8'
issue: '4'
language:
- iso: eng
month: '01'
oa_version: None
page: 980-994
publication: Soft Matter
publication_identifier:
eissn:
- 1744-6848
issn:
- 1744-683X
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Osmotic traps for colloids and macromolecules based on logarithmic sensing
in salt taxis
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 8
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: '922'
abstract:
- lang: eng
text: 'We study theoretically the morphologies of biological tubes affected by various
pathologies. When epithelial cells grow, the negative tension produced by their
division provokes a buckling instability. Several shapes are investigated: varicose,
dilated, sinuous, or sausagelike. They are all found in pathologies of tracheal,
renal tubes, or arteries. The final shape depends crucially on the mechanical
parameters of the tissues: Young''s modulus, wall-to-lumen ratio, homeostatic
pressure. We argue that since tissues must be in quasistatic mechanical equilibrium,
abnormal shapes convey information as to what causes the pathology. We calculate
a phase diagram of tubular instabilities which could be a helpful guide for investigating
the underlying genetic regulation.'
article_processing_charge: No
arxiv: 1
author:
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Jacques
full_name: Prost, Jacques
last_name: Prost
- first_name: Jean
full_name: Joanny, Jean
last_name: Joanny
citation:
ama: Hannezo EB, Prost J, Joanny J. Mechanical instabilities of biological tubes.
Physical Review Letters. 2012;109(1). doi:10.1103/PhysRevLett.109.018101
apa: Hannezo, E. B., Prost, J., & Joanny, J. (2012). Mechanical instabilities
of biological tubes. Physical Review Letters. American Physical Society.
https://doi.org/10.1103/PhysRevLett.109.018101
chicago: Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Mechanical Instabilities
of Biological Tubes.” Physical Review Letters. American Physical Society,
2012. https://doi.org/10.1103/PhysRevLett.109.018101.
ieee: E. B. Hannezo, J. Prost, and J. Joanny, “Mechanical instabilities of biological
tubes,” Physical Review Letters, vol. 109, no. 1. American Physical Society,
2012.
ista: Hannezo EB, Prost J, Joanny J. 2012. Mechanical instabilities of biological
tubes. Physical Review Letters. 109(1).
mla: Hannezo, Edouard B., et al. “Mechanical Instabilities of Biological Tubes.”
Physical Review Letters, vol. 109, no. 1, American Physical Society, 2012,
doi:10.1103/PhysRevLett.109.018101.
short: E.B. Hannezo, J. Prost, J. Joanny, Physical Review Letters 109 (2012).
date_created: 2018-12-11T11:49:13Z
date_published: 2012-07-03T00:00:00Z
date_updated: 2021-01-12T08:21:56Z
day: '03'
doi: 10.1103/PhysRevLett.109.018101
extern: '1'
external_id:
arxiv:
- '1207.1516'
intvolume: ' 109'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1207.1516
month: '07'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '6519'
status: public
title: Mechanical instabilities of biological tubes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 109
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: '9497'
abstract:
- lang: eng
text: The regulation of eukaryotic chromatin relies on interactions between many
epigenetic factors, including histone modifications, DNA methylation, and the
incorporation of histone variants. H2A.Z, one of the most conserved but enigmatic
histone variants that is enriched at the transcriptional start sites of genes,
has been implicated in a variety of chromosomal processes. Recently, we reported
a genome-wide anticorrelation between H2A.Z and DNA methylation, an epigenetic
hallmark of heterochromatin that has also been found in the bodies of active genes
in plants and animals. Here, we investigate the basis of this anticorrelation
using a novel h2a.z loss-of-function line in Arabidopsis thaliana. Through genome-wide
bisulfite sequencing, we demonstrate that loss of H2A.Z in Arabidopsis has only
a minor effect on the level or profile of DNA methylation in genes, and we propose
that the global anticorrelation between DNA methylation and H2A.Z is primarily
caused by the exclusion of H2A.Z from methylated DNA. RNA sequencing and genomic
mapping of H2A.Z show that H2A.Z enrichment across gene bodies, rather than at
the TSS, is correlated with lower transcription levels and higher measures of
gene responsiveness. Loss of H2A.Z causes misregulation of many genes that are
disproportionately associated with response to environmental and developmental
stimuli. We propose that H2A.Z deposition in gene bodies promotes variability
in levels and patterns of gene expression, and that a major function of genic
DNA methylation is to exclude H2A.Z from constitutively expressed genes.
article_number: e1002988
article_processing_charge: No
article_type: original
author:
- first_name: Devin
full_name: Coleman-Derr, Devin
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. Deposition of histone variant H2A.Z within gene
bodies regulates responsive genes. PLoS Genetics. 2012;8(10). doi:10.1371/journal.pgen.1002988
apa: Coleman-Derr, D., & Zilberman, D. (2012). Deposition of histone variant
H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. Public
Library of Science. https://doi.org/10.1371/journal.pgen.1002988
chicago: Coleman-Derr, Devin, and Daniel Zilberman. “Deposition of Histone Variant
H2A.Z within Gene Bodies Regulates Responsive Genes.” PLoS Genetics. Public
Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002988.
ieee: D. Coleman-Derr and D. Zilberman, “Deposition of histone variant H2A.Z within
gene bodies regulates responsive genes,” PLoS Genetics, vol. 8, no. 10.
Public Library of Science, 2012.
ista: Coleman-Derr D, Zilberman D. 2012. Deposition of histone variant H2A.Z within
gene bodies regulates responsive genes. PLoS Genetics. 8(10), e1002988.
mla: Coleman-Derr, Devin, and Daniel Zilberman. “Deposition of Histone Variant H2A.Z
within Gene Bodies Regulates Responsive Genes.” PLoS Genetics, vol. 8,
no. 10, e1002988, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002988.
short: D. Coleman-Derr, D. Zilberman, PLoS Genetics 8 (2012).
date_created: 2021-06-07T10:55:27Z
date_published: 2012-10-11T00:00:00Z
date_updated: 2021-12-14T08:29:57Z
day: '11'
department:
- _id: DaZi
doi: 10.1371/journal.pgen.1002988
extern: '1'
external_id:
pmid:
- '23071449'
intvolume: ' 8'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1371/journal.pgen.1002988
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Genetics
publication_identifier:
eissn:
- 1553-7404
issn:
- 1553-7390
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Deposition of histone variant H2A.Z within gene bodies regulates responsive
genes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 8
year: '2012'
...
---
_id: '9499'
abstract:
- lang: eng
text: EMBRYONIC FLOWER1 (EMF1) is a plant-specific gene crucial to Arabidopsis vegetative
development. Loss of function mutants in the EMF1 gene mimic the phenotype caused
by mutations in Polycomb Group protein (PcG) genes, which encode epigenetic repressors
that regulate many aspects of eukaryotic development. In Arabidopsis, Polycomb
Repressor Complex 2 (PRC2), made of PcG proteins, catalyzes trimethylation of
lysine 27 on histone H3 (H3K27me3) and PRC1-like proteins catalyze H2AK119 ubiquitination.
Despite functional similarity to PcG proteins, EMF1 lacks sequence homology with
known PcG proteins; thus, its role in the PcG mechanism is unclear. To study the
EMF1 functions and its mechanism of action, we performed genome-wide mapping of
EMF1 binding and H3K27me3 modification sites in Arabidopsis seedlings. The EMF1
binding pattern is similar to that of H3K27me3 modification on the chromosomal
and genic level. ChIPOTLe peak finding and clustering analyses both show that
the highly trimethylated genes also have high enrichment levels of EMF1 binding,
termed EMF1_K27 genes. EMF1 interacts with regulatory genes, which are silenced
to allow vegetative growth, and with genes specifying cell fates during growth
and differentiation. H3K27me3 marks not only these genes but also some genes that
are involved in endosperm development and maternal effects. Transcriptome analysis,
coupled with the H3K27me3 pattern, of EMF1_K27 genes in emf1 and PRC2 mutants
showed that EMF1 represses gene activities via diverse mechanisms and plays a
novel role in the PcG mechanism.
article_number: e1002512
article_processing_charge: No
article_type: original
author:
- first_name: Sang Yeol
full_name: Kim, Sang Yeol
last_name: Kim
- first_name: Jungeun
full_name: Lee, Jungeun
last_name: Lee
- first_name: Leor
full_name: Eshed-Williams, Leor
last_name: Eshed-Williams
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Z. Renee
full_name: Sung, Z. Renee
last_name: Sung
citation:
ama: Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR. EMF1 and PRC2 cooperate
to repress key regulators of Arabidopsis development. PLoS Genetics. 2012;8(3).
doi:10.1371/journal.pgen.1002512
apa: Kim, S. Y., Lee, J., Eshed-Williams, L., Zilberman, D., & Sung, Z. R. (2012).
EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development.
PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002512
chicago: Kim, Sang Yeol, Jungeun Lee, Leor Eshed-Williams, Daniel Zilberman, and
Z. Renee Sung. “EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis
Development.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002512.
ieee: S. Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, and Z. R. Sung, “EMF1
and PRC2 cooperate to repress key regulators of Arabidopsis development,” PLoS
Genetics, vol. 8, no. 3. Public Library of Science, 2012.
ista: Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR. 2012. EMF1 and PRC2
cooperate to repress key regulators of Arabidopsis development. PLoS Genetics.
8(3), e1002512.
mla: Kim, Sang Yeol, et al. “EMF1 and PRC2 Cooperate to Repress Key Regulators of
Arabidopsis Development.” PLoS Genetics, vol. 8, no. 3, e1002512, Public
Library of Science, 2012, doi:10.1371/journal.pgen.1002512.
short: S.Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, Z.R. Sung, PLoS Genetics
8 (2012).
date_created: 2021-06-07T11:07:56Z
date_published: 2012-03-22T00:00:00Z
date_updated: 2021-12-14T08:31:14Z
day: '22'
department:
- _id: DaZi
doi: 10.1371/journal.pgen.1002512
extern: '1'
external_id:
pmid:
- '22457632'
intvolume: ' 8'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1371/journal.pgen.1002512
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Genetics
publication_identifier:
eissn:
- 1553-7404
issn:
- 1553-7390
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 8
year: '2012'
...
---
_id: '9528'
abstract:
- lang: eng
text: Accumulating evidence points toward diverse functions for plant chromatin.
Remarkable progress has been made over the last few years in elucidating the mechanisms
for a number of these functions. Activity of the histone demethylase IBM1 accurately
targets DNA methylation to silent repeats and transposable elements, not to genes.
A genetic screen uncovered the surprising role of H2A.Z-containing nucleosomes
in sensing precise differences in ambient temperature and consequent gene regulation.
Precise maintenance of chromosome number is assured by a histone modification
that suppresses inappropriate DNA replication and by centromeric histone H3 regulation
of chromosome segregation. Histones and noncoding RNAs regulate FLOWERING LOCUS
C, the expression of which quantitatively measures the duration of cold exposure,
functioning as memory of winter. These findings are a testament to the power of
using plants to research chromatin organization, and demonstrate examples of how
chromatin functions to achieve biological accuracy, precision, and memory.
article_processing_charge: No
article_type: review
author:
- first_name: Jason T.
full_name: Huff, Jason T.
last_name: Huff
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Huff JT, Zilberman D. Regulation of biological accuracy, precision, and memory
by plant chromatin organization. Current Opinion in Genetics and Development.
2012;22(2):132-138. doi:10.1016/j.gde.2012.01.007
apa: Huff, J. T., & Zilberman, D. (2012). Regulation of biological accuracy,
precision, and memory by plant chromatin organization. Current Opinion in Genetics
and Development. Elsevier. https://doi.org/10.1016/j.gde.2012.01.007
chicago: Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy,
Precision, and Memory by Plant Chromatin Organization.” Current Opinion in
Genetics and Development. Elsevier, 2012. https://doi.org/10.1016/j.gde.2012.01.007.
ieee: J. T. Huff and D. Zilberman, “Regulation of biological accuracy, precision,
and memory by plant chromatin organization,” Current Opinion in Genetics and
Development, vol. 22, no. 2. Elsevier, pp. 132–138, 2012.
ista: Huff JT, Zilberman D. 2012. Regulation of biological accuracy, precision,
and memory by plant chromatin organization. Current Opinion in Genetics and Development.
22(2), 132–138.
mla: Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy, Precision,
and Memory by Plant Chromatin Organization.” Current Opinion in Genetics and
Development, vol. 22, no. 2, Elsevier, 2012, pp. 132–38, doi:10.1016/j.gde.2012.01.007.
short: J.T. Huff, D. Zilberman, Current Opinion in Genetics and Development 22 (2012)
132–138.
date_created: 2021-06-08T08:58:52Z
date_published: 2012-04-01T00:00:00Z
date_updated: 2021-12-14T08:32:38Z
department:
- _id: DaZi
doi: 10.1016/j.gde.2012.01.007
extern: '1'
external_id:
pmid:
- '22336527'
intvolume: ' 22'
issue: '2'
language:
- iso: eng
month: '04'
oa_version: None
page: 132-138
pmid: 1
publication: Current Opinion in Genetics and Development
publication_identifier:
issn:
- 0959-437X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Regulation of biological accuracy, precision, and memory by plant chromatin
organization
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 22
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'
...
---
_id: '966'
abstract:
- lang: eng
text: Motivated by recent experiments on Ba3NiSb2O 9, we investigate possible quantum
spin liquid ground states for spin S=1 Heisenberg models on the triangular lattice.
We use variational Monte Carlo techniques to calculate the energies of microscopic
spin liquid wave functions where spin is represented by three flavors of fermionic
spinon operators. These energies are compared with the energies of various competing
three-sublattice ordered states. Our approach shows that the antiferromagnetic
Heisenberg model with biquadratic term and single-ion anisotropy does not have
a low-temperature spin liquid phase. However, for an SU(3)-invariant model with
sufficiently strong ring-exchange terms, we find a paired chiral quantum spin
liquid with a Fermi surface of deconfined spinons that is stable against all types
of ordering patterns we considered. We discuss the physics of this exotic spin
liquid state in relation to the recent experiment and suggest new ways to test
this scenario.
acknowledgement: We thank Kuang-Ting Chen, Rebecca Flint, Dmitri Ivanov, Z.-X. Liu,
Tai-Kai Ng, Lara Thompson, Tamás Tóth, and Fa Wang for helpful discussions. T.S.
is supported by NSF DMR 1005434. P.A.L. is supported by NSF DMR 1104498. S.B. acknowledges
support from the Swiss National Science Foundation (SNSF).
author:
- first_name: Samuel
full_name: Bieri, Samuel
last_name: Bieri
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Todadri
full_name: Senthil, Todadri S
last_name: Senthil
- first_name: Patrick
full_name: Lee, Patrick
last_name: Lee
citation:
ama: Bieri S, Serbyn M, Senthil T, Lee P. Paired chiral spin liquid with a Fermi
surface in S=1 model on the triangular lattice. Physical Review B - Condensed
Matter and Materials Physics. 2012;86(22). doi:10.1103/PhysRevB.86.224409
apa: Bieri, S., Serbyn, M., Senthil, T., & Lee, P. (2012). Paired chiral spin
liquid with a Fermi surface in S=1 model on the triangular lattice. Physical
Review B - Condensed Matter and Materials Physics. American Physical Society.
https://doi.org/10.1103/PhysRevB.86.224409
chicago: Bieri, Samuel, Maksym Serbyn, Todadri Senthil, and Patrick Lee. “Paired
Chiral Spin Liquid with a Fermi Surface in S=1 Model on the Triangular Lattice.”
Physical Review B - Condensed Matter and Materials Physics. American Physical
Society, 2012. https://doi.org/10.1103/PhysRevB.86.224409.
ieee: S. Bieri, M. Serbyn, T. Senthil, and P. Lee, “Paired chiral spin liquid with
a Fermi surface in S=1 model on the triangular lattice,” Physical Review B
- Condensed Matter and Materials Physics, vol. 86, no. 22. American Physical
Society, 2012.
ista: Bieri S, Serbyn M, Senthil T, Lee P. 2012. Paired chiral spin liquid with
a Fermi surface in S=1 model on the triangular lattice. Physical Review B - Condensed
Matter and Materials Physics. 86(22).
mla: Bieri, Samuel, et al. “Paired Chiral Spin Liquid with a Fermi Surface in S=1
Model on the Triangular Lattice.” Physical Review B - Condensed Matter and
Materials Physics, vol. 86, no. 22, American Physical Society, 2012, doi:10.1103/PhysRevB.86.224409.
short: S. Bieri, M. Serbyn, T. Senthil, P. Lee, Physical Review B - Condensed Matter
and Materials Physics 86 (2012).
date_created: 2018-12-11T11:49:27Z
date_published: 2012-12-13T00:00:00Z
date_updated: 2021-01-12T08:22:18Z
day: '13'
doi: 10.1103/PhysRevB.86.224409
extern: 1
intvolume: ' 86'
issue: '22'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1208.3231
month: '12'
oa: 1
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
publist_id: '6431'
quality_controlled: 0
status: public
title: Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular
lattice
type: journal_article
volume: 86
year: '2012'
...
---
_id: '10387'
abstract:
- lang: eng
text: We report numerical simulations of membrane tubulation driven by large colloidal
particles. Using Monte Carlo simulations we study how the process depends on particle
size and binding strength, and present accurate free energy calculations to sort
out how tube formation compares with the competing budding process. We find that
tube formation is a result of the collective behavior of the particles adhering
on the surface, and it occurs for binding strengths that are smaller than those
required for budding. We also find that long linear aggregates of particles forming
on the membrane surface act as nucleation seeds for tubulation by lowering the
free energy barrier associated to the process.
article_number: '188101'
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. Mechanism of membrane tube formation induced by adhesive
nanocomponents. Physical Review Letters. 2012;109(18). doi:10.1103/physrevlett.109.188101
apa: Šarić, A., & Cacciuto, A. (2012). Mechanism of membrane tube formation
induced by adhesive nanocomponents. Physical Review Letters. American Physical
Society. https://doi.org/10.1103/physrevlett.109.188101
chicago: Šarić, Anđela, and Angelo Cacciuto. “Mechanism of Membrane Tube Formation
Induced by Adhesive Nanocomponents.” Physical Review Letters. American
Physical Society, 2012. https://doi.org/10.1103/physrevlett.109.188101.
ieee: A. Šarić and A. Cacciuto, “Mechanism of membrane tube formation induced by
adhesive nanocomponents,” Physical Review Letters, vol. 109, no. 18. American
Physical Society, 2012.
ista: Šarić A, Cacciuto A. 2012. Mechanism of membrane tube formation induced by
adhesive nanocomponents. Physical Review Letters. 109(18), 188101.
mla: Šarić, Anđela, and Angelo Cacciuto. “Mechanism of Membrane Tube Formation Induced
by Adhesive Nanocomponents.” Physical Review Letters, vol. 109, no. 18,
188101, American Physical Society, 2012, doi:10.1103/physrevlett.109.188101.
short: A. Šarić, A. Cacciuto, Physical Review Letters 109 (2012).
date_created: 2021-11-29T14:08:00Z
date_published: 2012-10-31T00:00:00Z
date_updated: 2021-11-29T14:29:25Z
day: '31'
doi: 10.1103/physrevlett.109.188101
extern: '1'
external_id:
arxiv:
- '1206.3528'
pmid:
- '23215334'
intvolume: ' 109'
issue: '18'
keyword:
- general physics and astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1206.3528
month: '10'
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: Mechanism of membrane tube formation induced by adhesive nanocomponents
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 109
year: '2012'
...
---
_id: '10388'
abstract:
- lang: eng
text: Using computer simulations, we show that lipid membranes can mediate linear
aggregation of spherical nanoparticles binding to it for a wide range of biologically
relevant bending rigidities. This result is in net contrast with the isotropic
aggregation of nanoparticles on fluid interfaces or the expected clustering of
isotropic insertions in biological membranes. We present a phase diagram indicating
where linear aggregation is expected and compute explicitly the free-energy barriers
associated with linear and isotropic aggregation. Finally, we provide simple scaling
arguments to explain this phenomenology.
acknowledgement: "This work was supported by the National Science Foundation under
Career Grant No. DMR-0846426.\r\n"
article_number: '118101'
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. Fluid membranes can drive linear aggregation of adsorbed
spherical nanoparticles. Physical Review Letters. 2012;108(11). doi:10.1103/physrevlett.108.118101
apa: Šarić, A., & Cacciuto, A. (2012). Fluid membranes can drive linear aggregation
of adsorbed spherical nanoparticles. Physical Review Letters. American
Physical Society. https://doi.org/10.1103/physrevlett.108.118101
chicago: Šarić, Anđela, and Angelo Cacciuto. “Fluid Membranes Can Drive Linear Aggregation
of Adsorbed Spherical Nanoparticles.” Physical Review Letters. American
Physical Society, 2012. https://doi.org/10.1103/physrevlett.108.118101.
ieee: A. Šarić and A. Cacciuto, “Fluid membranes can drive linear aggregation of
adsorbed spherical nanoparticles,” Physical Review Letters, vol. 108, no.
11. American Physical Society, 2012.
ista: Šarić A, Cacciuto A. 2012. Fluid membranes can drive linear aggregation of
adsorbed spherical nanoparticles. Physical Review Letters. 108(11), 118101.
mla: Šarić, Anđela, and Angelo Cacciuto. “Fluid Membranes Can Drive Linear Aggregation
of Adsorbed Spherical Nanoparticles.” Physical Review Letters, vol. 108,
no. 11, 118101, American Physical Society, 2012, doi:10.1103/physrevlett.108.118101.
short: A. Šarić, A. Cacciuto, Physical Review Letters 108 (2012).
date_created: 2021-11-29T14:30:05Z
date_published: 2012-03-14T00:00:00Z
date_updated: 2021-11-29T15:12:13Z
day: '14'
doi: 10.1103/physrevlett.108.118101
extern: '1'
external_id:
arxiv:
- '1201.0036'
pmid:
- '22540513'
intvolume: ' 108'
issue: '11'
keyword:
- general physics and astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1201.0036
month: '03'
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: Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 108
year: '2012'
...
---
_id: '1055'
abstract:
- lang: eng
text: In July, 2011, a 32-year-old man presented with thoracic pain radiating to
the left arm and upper dorsum, shortness of breath, and palpitations. He had had
upper back tension for 6 months. Medical history was unremarkable apart from moderate
nicotine use (two pack-years). Echocardiography, electrocardiography, and laboratory
tests were unremarkable, excluding a cardiac event. CT of the chest after chest
radiography showed a large bulla of 16 cm diameter in the right hemithorax (figure
A). We did not detect radiological evidence of underlying pulmonary disease. The
bulla wall was unremarkable and no structures were seen within the bulla.
acknowledgement: We thank the interdisciplinary team at the ELK Berlin Chest Hospital.
article_processing_charge: No
author:
- first_name: Barbara
full_name: Erne, Barbara
last_name: Erne
- first_name: Mareike
full_name: Graff, Mareike
last_name: Graff
- first_name: Wolfram
full_name: Klemm, Wolfram
last_name: Klemm
- 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: Gunda
full_name: Leschber, Gunda
last_name: Leschber
citation:
ama: Erne B, Graff M, Klemm W, Danzl JG, Leschber G. Bulla in the lung. The Lancet.
2012;380(9849). doi:10.1016/S0140-6736(12)60690-4
apa: Erne, B., Graff, M., Klemm, W., Danzl, J. G., & Leschber, G. (2012). Bulla
in the lung. The Lancet. Elsevier. https://doi.org/10.1016/S0140-6736(12)60690-4
chicago: Erne, Barbara, Mareike Graff, Wolfram Klemm, Johann G Danzl, and Gunda
Leschber. “Bulla in the Lung.” The Lancet. Elsevier, 2012. https://doi.org/10.1016/S0140-6736(12)60690-4.
ieee: B. Erne, M. Graff, W. Klemm, J. G. Danzl, and G. Leschber, “Bulla in the lung,”
The Lancet, vol. 380, no. 9849. Elsevier, 2012.
ista: Erne B, Graff M, Klemm W, Danzl JG, Leschber G. 2012. Bulla in the lung. The
Lancet. 380(9849).
mla: Erne, Barbara, et al. “Bulla in the Lung.” The Lancet, vol. 380, no.
9849, Elsevier, 2012, doi:10.1016/S0140-6736(12)60690-4.
short: B. Erne, M. Graff, W. Klemm, J.G. Danzl, G. Leschber, The Lancet 380 (2012).
date_created: 2018-12-11T11:49:54Z
date_published: 2012-10-01T00:00:00Z
date_updated: 2021-01-12T06:47:57Z
day: '01'
doi: 10.1016/S0140-6736(12)60690-4
extern: '1'
intvolume: ' 380'
issue: '9849'
language:
- iso: eng
month: '10'
oa_version: None
publication: The Lancet
publication_status: published
publisher: Elsevier
publist_id: '6333'
status: public
title: Bulla in the lung
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 380
year: '2012'
...
---
_id: '1056'
abstract:
- lang: eng
text: We prepare and study a metastable attractive Mott-insulator state formed with
bosonic atoms in a three-dimensional optical lattice. Starting from a Mott insulator
with Cs atoms at weak repulsive interactions, we use a magnetic Feshbach resonance
to tune the interactions to large attractive values and produce a metastable state
pinned by attractive interactions with a lifetime on the order of 10 s. We probe
the (de)excitation spectrum via lattice modulation spectroscopy, measuring the
interaction dependence of two- and three-body bound-state energies. As a result
of increased on-site three-body loss we observe resonance broadening and suppression
of tunneling processes that produce three-body occupation.
acknowledgement: We are indebted to R. Grimm for generous support. We thank J. von
Stecher, P. Johnson, and E. Tiesinga for fruitful discussions. We gratefully acknowledge
funding by the Austrian Science Fund (FWF) within Project No. I153-N16 and within
the framework of the European Science Foundation (ESF) EuroQUASAR collective research
project QuDeGPM, and by the European Research Council (ERC) under Project No. 278417.
article_processing_charge: No
arxiv: 1
author:
- first_name: Manfred
full_name: Mark, Manfred
last_name: Mark
- first_name: Elmar
full_name: Haller, Elmar
last_name: Haller
- first_name: Katharina
full_name: Lauber, Katharina
last_name: Lauber
- 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: Alexander
full_name: Janisch, Alexander
last_name: Janisch
- first_name: Hans
full_name: Büchler, Hans
last_name: Büchler
- first_name: Andrew
full_name: Daley, Andrew
last_name: Daley
- first_name: Hanns
full_name: Nägerl, Hanns
last_name: Nägerl
citation:
ama: Mark M, Haller E, Lauber K, et al. Preparation and spectroscopy of a metastable
mott-insulator state with attractive interactions. Physical Review Letters.
2012;108(21). doi:10.1103/PhysRevLett.108.215302
apa: Mark, M., Haller, E., Lauber, K., Danzl, J. G., Janisch, A., Büchler, H., …
Nägerl, H. (2012). Preparation and spectroscopy of a metastable mott-insulator
state with attractive interactions. Physical Review Letters. American Physical
Society. https://doi.org/10.1103/PhysRevLett.108.215302
chicago: Mark, Manfred, Elmar Haller, Katharina Lauber, Johann G Danzl, Alexander
Janisch, Hans Büchler, Andrew Daley, and Hanns Nägerl. “Preparation and Spectroscopy
of a Metastable Mott-Insulator State with Attractive Interactions.” Physical
Review Letters. American Physical Society, 2012. https://doi.org/10.1103/PhysRevLett.108.215302.
ieee: M. Mark et al., “Preparation and spectroscopy of a metastable mott-insulator
state with attractive interactions,” Physical Review Letters, vol. 108,
no. 21. American Physical Society, 2012.
ista: Mark M, Haller E, Lauber K, Danzl JG, Janisch A, Büchler H, Daley A, Nägerl
H. 2012. Preparation and spectroscopy of a metastable mott-insulator state with
attractive interactions. Physical Review Letters. 108(21).
mla: Mark, Manfred, et al. “Preparation and Spectroscopy of a Metastable Mott-Insulator
State with Attractive Interactions.” Physical Review Letters, vol. 108,
no. 21, American Physical Society, 2012, doi:10.1103/PhysRevLett.108.215302.
short: M. Mark, E. Haller, K. Lauber, J.G. Danzl, A. Janisch, H. Büchler, A. Daley,
H. Nägerl, Physical Review Letters 108 (2012).
date_created: 2018-12-11T11:49:55Z
date_published: 2012-05-25T00:00:00Z
date_updated: 2021-01-12T06:47:58Z
day: '25'
doi: 10.1103/PhysRevLett.108.215302
extern: '1'
external_id:
arxiv:
- '1201.1008'
intvolume: ' 108'
issue: '21'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1201.1008
month: '05'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '6334'
status: public
title: Preparation and spectroscopy of a metastable mott-insulator state with attractive
interactions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2012'
...
---
_id: '11963'
abstract:
- lang: eng
text: 'Peroxides and ethers in flow: 2-Carbonyl-substituted phenols and β-ketoesters
react safely with ethers in a microreactor environment using a copper catalyst
and an organic peroxide (TBHP). This protocol results in unsymmetrical acetal
scaffolds not easily available otherwise (see scheme).'
article_processing_charge: No
article_type: letter_note
author:
- first_name: G. Sathish
full_name: Kumar, G. Sathish
last_name: Kumar
- first_name: Bartholomäus
full_name: Pieber, Bartholomäus
id: 93e5e5b2-0da6-11ed-8a41-af589a024726
last_name: Pieber
orcid: 0000-0001-8689-388X
- first_name: K. Rajender
full_name: Reddy, K. Rajender
last_name: Reddy
- first_name: C. Oliver
full_name: Kappe, C. Oliver
last_name: Kappe
citation:
ama: Kumar GS, Pieber B, Reddy KR, Kappe CO. Copper-catalyzed formation of C-O bonds
by direct α-C-H bond activation of ethers using stoichiometric amounts of peroxide
in batch and continuous-flow formats. Chemistry - A European Journal. 2012;18(20):6124-6128.
doi:10.1002/chem.201200815
apa: Kumar, G. S., Pieber, B., Reddy, K. R., & Kappe, C. O. (2012). Copper-catalyzed
formation of C-O bonds by direct α-C-H bond activation of ethers using stoichiometric
amounts of peroxide in batch and continuous-flow formats. Chemistry - A European
Journal. Wiley. https://doi.org/10.1002/chem.201200815
chicago: Kumar, G. Sathish, Bartholomäus Pieber, K. Rajender Reddy, and C. Oliver
Kappe. “Copper-Catalyzed Formation of C-O Bonds by Direct α-C-H Bond Activation
of Ethers Using Stoichiometric Amounts of Peroxide in Batch and Continuous-Flow
Formats.” Chemistry - A European Journal. Wiley, 2012. https://doi.org/10.1002/chem.201200815.
ieee: G. S. Kumar, B. Pieber, K. R. Reddy, and C. O. Kappe, “Copper-catalyzed formation
of C-O bonds by direct α-C-H bond activation of ethers using stoichiometric amounts
of peroxide in batch and continuous-flow formats,” Chemistry - A European Journal,
vol. 18, no. 20. Wiley, pp. 6124–6128, 2012.
ista: Kumar GS, Pieber B, Reddy KR, Kappe CO. 2012. Copper-catalyzed formation of
C-O bonds by direct α-C-H bond activation of ethers using stoichiometric amounts
of peroxide in batch and continuous-flow formats. Chemistry - A European Journal.
18(20), 6124–6128.
mla: Kumar, G. Sathish, et al. “Copper-Catalyzed Formation of C-O Bonds by Direct
α-C-H Bond Activation of Ethers Using Stoichiometric Amounts of Peroxide in Batch
and Continuous-Flow Formats.” Chemistry - A European Journal, vol. 18,
no. 20, Wiley, 2012, pp. 6124–28, doi:10.1002/chem.201200815.
short: G.S. Kumar, B. Pieber, K.R. Reddy, C.O. Kappe, Chemistry - A European Journal
18 (2012) 6124–6128.
date_created: 2022-08-24T12:33:05Z
date_published: 2012-05-14T00:00:00Z
date_updated: 2023-02-21T10:09:33Z
day: '14'
doi: 10.1002/chem.201200815
extern: '1'
external_id:
pmid:
- '22492535'
intvolume: ' 18'
issue: '20'
language:
- iso: eng
month: '05'
oa_version: None
page: 6124-6128
pmid: 1
publication: Chemistry - A European Journal
publication_identifier:
eissn:
- 1521-3765
issn:
- 0947-6539
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Copper-catalyzed formation of C-O bonds by direct α-C-H bond activation of
ethers using stoichiometric amounts of peroxide in batch and continuous-flow formats
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2012'
...
---
_id: '11964'
abstract:
- lang: eng
text: A detailed investigation on the direct arylation of benzene with aryl bromides
by using first-row transition metals under high-temperature/high-pressure (high-T/p)
conditions is described. By employing a parallel reactor platform for rapid reaction
screening and discovery at elevated temperatures, various metal/ligand/base combinations
were evaluated for their ability to enable biaryl formation through C-H activation.
The combination of cobalt(III) acetylacetonate and lithium bis(trimethylsilyl)amide
was subjected to further process intensification at 200 °C (15 bar), allowing
a significant reduction of the catalyst/base loading and a dramatic increase in
catalytic efficiency (turnover frequency) by a factor of 1000 compared to traditional
protocols. The high-throughput screening additionally identified novel nickel-
and copper-based metal/ligand combinations that favored an amination pathway competing
with C-H activation, with the addition of ligands, such as 1,10-phenanthroline,
having a profound influence on the selectivity. In addition to metal-based catalysts,
high-T/p process windows were also successfully applied to transition-metal-free
systems, utilizing 1,10-phenanthroline as organocatalyst.
article_processing_charge: No
article_type: original
author:
- first_name: Bartholomäus
full_name: Pieber, Bartholomäus
id: 93e5e5b2-0da6-11ed-8a41-af589a024726
last_name: Pieber
orcid: 0000-0001-8689-388X
- first_name: David
full_name: Cantillo, David
last_name: Cantillo
- first_name: C. Oliver
full_name: Kappe, C. Oliver
last_name: Kappe
citation:
ama: 'Pieber B, Cantillo D, Kappe CO. Direct arylation of benzene with aryl bromides
using high‐temperature/high‐pressure process windows: Expanding the scope of C-H
activation chemistry. Chemistry – A European Journal. 2012;18(16):5047-5055.
doi:10.1002/chem.201103748'
apa: 'Pieber, B., Cantillo, D., & Kappe, C. O. (2012). Direct arylation of benzene
with aryl bromides using high‐temperature/high‐pressure process windows: Expanding
the scope of C-H activation chemistry. Chemistry – A European Journal.
Wiley. https://doi.org/10.1002/chem.201103748'
chicago: 'Pieber, Bartholomäus, David Cantillo, and C. Oliver Kappe. “Direct Arylation
of Benzene with Aryl Bromides Using High‐temperature/High‐pressure Process Windows:
Expanding the Scope of C-H Activation Chemistry.” Chemistry – A European Journal.
Wiley, 2012. https://doi.org/10.1002/chem.201103748.'
ieee: 'B. Pieber, D. Cantillo, and C. O. Kappe, “Direct arylation of benzene with
aryl bromides using high‐temperature/high‐pressure process windows: Expanding
the scope of C-H activation chemistry,” Chemistry – A European Journal,
vol. 18, no. 16. Wiley, pp. 5047–5055, 2012.'
ista: 'Pieber B, Cantillo D, Kappe CO. 2012. Direct arylation of benzene with aryl
bromides using high‐temperature/high‐pressure process windows: Expanding the scope
of C-H activation chemistry. Chemistry – A European Journal. 18(16), 5047–5055.'
mla: 'Pieber, Bartholomäus, et al. “Direct Arylation of Benzene with Aryl Bromides
Using High‐temperature/High‐pressure Process Windows: Expanding the Scope of C-H
Activation Chemistry.” Chemistry – A European Journal, vol. 18, no. 16,
Wiley, 2012, pp. 5047–55, doi:10.1002/chem.201103748.'
short: B. Pieber, D. Cantillo, C.O. Kappe, Chemistry – A European Journal 18 (2012)
5047–5055.
date_created: 2022-08-24T12:48:28Z
date_published: 2012-04-16T00:00:00Z
date_updated: 2023-02-21T10:09:35Z
day: '16'
doi: 10.1002/chem.201103748
extern: '1'
external_id:
pmid:
- '22396386'
intvolume: ' 18'
issue: '16'
language:
- iso: eng
month: '04'
oa_version: None
page: 5047-5055
pmid: 1
publication: Chemistry – A European Journal
publication_identifier:
eissn:
- 1521-3765
issn:
- 0947-6539
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Direct arylation of benzene with aryl bromides using high‐temperature/high‐pressure
process windows: Expanding the scope of C-H activation chemistry'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2012'
...
---
_id: '12198'
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.
acknowledgement: We thank S. Harmer for assistance with the analysis of histone modifications,
the BioOptics team at the Vienna Biocenter Campus for sorting sperm and vegetative
cell nuclei, K. Slotkin for the LAT52p-amiRNA=GFP plasmid, and G. Drews for the
DD45p-GFP transgenic line. This work was partially funded by an NIH grant (GM69415)
to R.L.F., NSF grants (MCB-0918821 and IOS-1025890) to R.L.F. and D.Z., a Young
Investigator Grant from the Arnold and Mabel Beckman Foundation to D.Z., an Austrian
Science Fund (FWF) grant P21389-B03 to H.T., a Ruth L. Kirschstein NIH Predoctoral
Fellowship (GM093633) to C.A.I., a Fulbright Scholarship to J.A.R., a fellowship
from the Jane Coffin Childs Memorial Fund to A.Z., and a Robert and Colleen Haas
Scholarship to D.R. Sequencing data are deposited in GEO (GSE38935).
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
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- 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
last_name: Zilberman
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: 2023-01-16T09:21:24Z
date_published: 2012-09-14T00:00:00Z
date_updated: 2023-10-16T09:27:26Z
day: '14'
department:
- _id: XiFe
doi: 10.1126/science.1224839
external_id:
pmid:
- '22984074'
intvolume: ' 337'
issue: '6100'
keyword:
- Multidisciplinary
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 337
year: '2012'
...
---
_id: '12644'
abstract:
- lang: eng
text: In the Dry Andes of central Chile, summer water resources originate mostly
from snowmelt and ice melt. We use the physically based, spatially distributed
hydrological model TOPKAPI to study the exchange between glaciers and climate
in the upper Aconcagua River Basin during the summer season and identify the model
parameters that are robust and transferable and those that are more dependent
on calibration. TOPKAPI has recently been adapted to incorporate an enhanced temperature
index approach for snow and ice melting. We suggest a calibration procedure that
allows calibration of parameters in three steps by separating parameters governing
distinct processes. We evaluate the parameters' transferability in time and in
space by applying the model at two spatial scales. TOPKAPI's ability to simulate
the relevant processes is tested against meteorological, ablation, and glacier
runoff data measured on Juncal Norte Glacier during two glacier ablation seasons.
The model was applied successfully to the climatic setting of the Dry Andes once
its parameters were recalibrated. We found a clear distinction between parameters
that are stable in time and those that need recalibration. The parameters of the
melt model are transferable from one season to the other, while the parameters
governing the extrapolation of meteorological input data and the routing of glacier
meltwater need recalibration from one season to the other. Sensitivity analysis
revealed that the model is most sensitive to the temperature lapse rate governing
the extrapolation of air temperature from point measurements to the glacier scale
and to the melt parameter that multiplies the shortwave radiation balance.
article_number: W03509
article_processing_charge: No
article_type: original
author:
- first_name: S.
full_name: Ragettli, S.
last_name: Ragettli
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
citation:
ama: 'Ragettli S, Pellicciotti F. Calibration of a physically based, spatially distributed
hydrological model in a glacierized basin: On the use of knowledge from glaciometeorological
processes to constrain model parameters. Water Resources Research. 2012;48(3).
doi:10.1029/2011wr010559'
apa: 'Ragettli, S., & Pellicciotti, F. (2012). Calibration of a physically based,
spatially distributed hydrological model in a glacierized basin: On the use of
knowledge from glaciometeorological processes to constrain model parameters. Water
Resources Research. American Geophysical Union. https://doi.org/10.1029/2011wr010559'
chicago: 'Ragettli, S., and Francesca Pellicciotti. “Calibration of a Physically
Based, Spatially Distributed Hydrological Model in a Glacierized Basin: On the
Use of Knowledge from Glaciometeorological Processes to Constrain Model Parameters.”
Water Resources Research. American Geophysical Union, 2012. https://doi.org/10.1029/2011wr010559.'
ieee: 'S. Ragettli and F. Pellicciotti, “Calibration of a physically based, spatially
distributed hydrological model in a glacierized basin: On the use of knowledge
from glaciometeorological processes to constrain model parameters,” Water Resources
Research, vol. 48, no. 3. American Geophysical Union, 2012.'
ista: 'Ragettli S, Pellicciotti F. 2012. Calibration of a physically based, spatially
distributed hydrological model in a glacierized basin: On the use of knowledge
from glaciometeorological processes to constrain model parameters. Water Resources
Research. 48(3), W03509.'
mla: 'Ragettli, S., and Francesca Pellicciotti. “Calibration of a Physically Based,
Spatially Distributed Hydrological Model in a Glacierized Basin: On the Use of
Knowledge from Glaciometeorological Processes to Constrain Model Parameters.”
Water Resources Research, vol. 48, no. 3, W03509, American Geophysical
Union, 2012, doi:10.1029/2011wr010559.'
short: S. Ragettli, F. Pellicciotti, Water Resources Research 48 (2012).
date_created: 2023-02-20T08:17:39Z
date_published: 2012-03-01T00:00:00Z
date_updated: 2023-02-21T09:38:36Z
day: '01'
doi: 10.1029/2011wr010559
extern: '1'
intvolume: ' 48'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1029/2011WR010559
month: '03'
oa: 1
oa_version: Published Version
publication: Water Resources Research
publication_identifier:
issn:
- 0043-1397
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Calibration of a physically based, spatially distributed hydrological model
in a glacierized basin: On the use of knowledge from glaciometeorological processes
to constrain model parameters'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 48
year: '2012'
...
---
_id: '12646'
abstract:
- lang: eng
text: Assessment of water resources from remote mountainous catchments plays a crucial
role for the development of rural areas in or in the vicinity of mountain ranges.
The scarcity of data, however, prevents the application of standard approaches
that are based on data-driven models. The Hindu Kush–Karakoram–Himalaya mountain
range is a crucial area in terms of water resources, but our understanding of
the response of its high-elevation catchments to a changing climate is hindered
by lack of hydro-meteorological and cryospheric data. Hydrological modeling is
challenging here because internal inconsistencies—such as an underestimation of
precipitation input that can be compensated for by an overestimation of meltwater—might
be hidden due to the complexity of feedback mechanisms that govern melt and runoff
generation in such basins. Data scarcity adds to this difficulty by preventing
the application of systematic calibration procedures that would allow identification
of the parameter set that could guarantee internal consistency in the simulation
of the single hydrological components. In this work, we use simulations from the
Hunza River Basin in the Karakoram region obtained with the hydrological model
TOPKAPI to quantify the predictive power of discharge and snow-cover data sets,
as well as the combination of both. We also show that short-term measurements
of meteorological variables such as radiative fluxes, wind speed, relative humidity,
and air temperature from glacio-meteorological experiments are crucial for a correct
parameterization of surface melt processes. They enable detailed simulations of
the energy fluxes governing glacier–atmosphere interaction and the resulting ablation
through energy-balance modeling. These simulations are used to derive calibrated
parameters for the simplified snow and glacier routines in TOPKAPI. We demonstrate
that such parameters are stable in space and time in similar climatic regions,
thus reducing the number of parameters requiring calibration.
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: Cyrill
full_name: Buergi, Cyrill
last_name: Buergi
- first_name: Walter Willem
full_name: Immerzeel, Walter Willem
last_name: Immerzeel
- first_name: Markus
full_name: Konz, Markus
last_name: Konz
- first_name: Arun B.
full_name: Shrestha, Arun B.
last_name: Shrestha
citation:
ama: 'Pellicciotti F, Buergi C, Immerzeel WW, Konz M, Shrestha AB. Challenges and
uncertainties in hydrological modeling of remote Hindu Kush–Karakoram–Himalayan
(HKH) basins: Suggestions for calibration strategies. Mountain Research and
Development. 2012;32(1):39-50. doi:10.1659/mrd-journal-d-11-00092.1'
apa: 'Pellicciotti, F., Buergi, C., Immerzeel, W. W., Konz, M., & Shrestha,
A. B. (2012). Challenges and uncertainties in hydrological modeling of remote
Hindu Kush–Karakoram–Himalayan (HKH) basins: Suggestions for calibration strategies.
Mountain Research and Development. International Mountain Society. https://doi.org/10.1659/mrd-journal-d-11-00092.1'
chicago: 'Pellicciotti, Francesca, Cyrill Buergi, Walter Willem Immerzeel, Markus
Konz, and Arun B. Shrestha. “Challenges and Uncertainties in Hydrological Modeling
of Remote Hindu Kush–Karakoram–Himalayan (HKH) Basins: Suggestions for Calibration
Strategies.” Mountain Research and Development. International Mountain
Society, 2012. https://doi.org/10.1659/mrd-journal-d-11-00092.1.'
ieee: 'F. Pellicciotti, C. Buergi, W. W. Immerzeel, M. Konz, and A. B. Shrestha,
“Challenges and uncertainties in hydrological modeling of remote Hindu Kush–Karakoram–Himalayan
(HKH) basins: Suggestions for calibration strategies,” Mountain Research and
Development, vol. 32, no. 1. International Mountain Society, pp. 39–50, 2012.'
ista: 'Pellicciotti F, Buergi C, Immerzeel WW, Konz M, Shrestha AB. 2012. Challenges
and uncertainties in hydrological modeling of remote Hindu Kush–Karakoram–Himalayan
(HKH) basins: Suggestions for calibration strategies. Mountain Research and Development.
32(1), 39–50.'
mla: 'Pellicciotti, Francesca, et al. “Challenges and Uncertainties in Hydrological
Modeling of Remote Hindu Kush–Karakoram–Himalayan (HKH) Basins: Suggestions for
Calibration Strategies.” Mountain Research and Development, vol. 32, no.
1, International Mountain Society, 2012, pp. 39–50, doi:10.1659/mrd-journal-d-11-00092.1.'
short: F. Pellicciotti, C. Buergi, W.W. Immerzeel, M. Konz, A.B. Shrestha, Mountain
Research and Development 32 (2012) 39–50.
date_created: 2023-02-20T08:17:47Z
date_published: 2012-02-01T00:00:00Z
date_updated: 2023-02-21T09:31:54Z
day: '01'
doi: 10.1659/mrd-journal-d-11-00092.1
extern: '1'
intvolume: ' 32'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1659/MRD-JOURNAL-D-11-00092.1
month: '02'
oa: 1
oa_version: Published Version
page: 39-50
publication: Mountain Research and Development
publication_identifier:
eissn:
- 1994-7151
issn:
- 0276-4741
publication_status: published
publisher: International Mountain Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Challenges and uncertainties in hydrological modeling of remote Hindu Kush–Karakoram–Himalayan
(HKH) basins: Suggestions for calibration strategies'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2012'
...