---
_id: '3290'
abstract:
- lang: eng
text: 'Analysis of genomic data requires an efficient way to calculate likelihoods
across very large numbers of loci. We describe a general method for finding the
distribution of genealogies: we allow migration between demes, splitting of demes
[as in the isolation-with-migration (IM) model], and recombination between linked
loci. These processes are described by a set of linear recursions for the generating
function of branch lengths. Under the infinite-sites model, the probability of
any configuration of mutations can be found by differentiating this generating
function. Such calculations are feasible for small numbers of sampled genomes:
as an example, we show how the generating function can be derived explicitly for
three genes under the two-deme IM model. This derivation is done automatically,
using Mathematica. Given data from a large number of unlinked and nonrecombining
blocks of sequence, these results can be used to find maximum-likelihood estimates
of model parameters by tabulating the probabilities of all relevant mutational
configurations and then multiplying across loci. The feasibility of the method
is demonstrated by applying it to simulated data and to a data set previously
analyzed by Wang and Hey (2010) consisting of 26,141 loci sampled from Drosophila
simulans and D. melanogaster. Our results suggest that such likelihood calculations
are scalable to genomic data as long as the numbers of sampled individuals and
mutations per sequence block are small.'
author:
- first_name: Konrad
full_name: Lohse, Konrad
last_name: Lohse
- first_name: Richard
full_name: Harrison, Richard
last_name: Harrison
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Lohse K, Harrison R, Barton NH. A general method for calculating likelihoods
under the coalescent process. Genetics. 2011;189(3):977-987. doi:10.1534/genetics.111.129569
apa: Lohse, K., Harrison, R., & Barton, N. H. (2011). A general method for calculating
likelihoods under the coalescent process. Genetics. Genetics Society of
America. https://doi.org/10.1534/genetics.111.129569
chicago: Lohse, Konrad, Richard Harrison, and Nicholas H Barton. “A General Method
for Calculating Likelihoods under the Coalescent Process.” Genetics. Genetics
Society of America, 2011. https://doi.org/10.1534/genetics.111.129569.
ieee: K. Lohse, R. Harrison, and N. H. Barton, “A general method for calculating
likelihoods under the coalescent process,” Genetics, vol. 189, no. 3. Genetics
Society of America, pp. 977–987, 2011.
ista: Lohse K, Harrison R, Barton NH. 2011. A general method for calculating likelihoods
under the coalescent process. Genetics. 189(3), 977–987.
mla: Lohse, Konrad, et al. “A General Method for Calculating Likelihoods under the
Coalescent Process.” Genetics, vol. 189, no. 3, Genetics Society of America,
2011, pp. 977–87, doi:10.1534/genetics.111.129569.
short: K. Lohse, R. Harrison, N.H. Barton, Genetics 189 (2011) 977–987.
date_created: 2018-12-11T12:02:29Z
date_published: 2011-11-01T00:00:00Z
date_updated: 2021-01-12T07:42:26Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.111.129569
ec_funded: 1
intvolume: ' 189'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3213358/
month: '11'
oa: 1
oa_version: Submitted Version
page: 977 - 987
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '3355'
quality_controlled: '1'
scopus_import: 1
status: public
title: A general method for calculating likelihoods under the coalescent process
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 189
year: '2011'
...
---
_id: '3297'
abstract:
- lang: eng
text: "Animating detailed liquid surfaces has always been a challenge for computer
graphics researchers and visual effects artists. Over the past few years, researchers
in this field have focused on mesh-based surface tracking to synthesize extremely
detailed liquid surfaces as efficiently as possible. This course provides a solid
understanding of the steps required to create a fluid simulator with a mesh-based
liquid surface.\r\n\r\nThe course begins with an overview of several existing
liquid-surface-tracking techniques and the pros and cons of each method. Then
it explains how to embed a triangle mesh into a finite-difference-based fluid
simulator and describes several methods for allowing the liquid surface to merge
together or break apart. The final section showcases the benefits and further
applications of a mesh-based liquid surface, highlighting state-of-the-art methods
for tracking colors and textures, maintaining liquid volume, preserving small
surface features, and simulating realistic surface-tension waves."
article_number: '8'
author:
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Matthias
full_name: Müller Fischer, Matthias
last_name: Müller Fischer
- first_name: Tyson
full_name: Brochu, Tyson
last_name: Brochu
citation:
ama: 'Wojtan C, Müller Fischer M, Brochu T. Liquid simulation with mesh-based surface
tracking. In: ACM; 2011. doi:10.1145/2037636.2037644'
apa: 'Wojtan, C., Müller Fischer, M., & Brochu, T. (2011). Liquid simulation
with mesh-based surface tracking. Presented at the SIGGRAPH: Special Interest
Group on Computer Graphics and Interactive Techniques, Vancouver, BC, Canada:
ACM. https://doi.org/10.1145/2037636.2037644'
chicago: Wojtan, Chris, Matthias Müller Fischer, and Tyson Brochu. “Liquid Simulation
with Mesh-Based Surface Tracking.” ACM, 2011. https://doi.org/10.1145/2037636.2037644.
ieee: 'C. Wojtan, M. Müller Fischer, and T. Brochu, “Liquid simulation with mesh-based
surface tracking,” presented at the SIGGRAPH: Special Interest Group on Computer
Graphics and Interactive Techniques, Vancouver, BC, Canada, 2011.'
ista: 'Wojtan C, Müller Fischer M, Brochu T. 2011. Liquid simulation with mesh-based
surface tracking. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive
Techniques, 8.'
mla: Wojtan, Chris, et al. Liquid Simulation with Mesh-Based Surface Tracking.
8, ACM, 2011, doi:10.1145/2037636.2037644.
short: C. Wojtan, M. Müller Fischer, T. Brochu, in:, ACM, 2011.
conference:
end_date: 2011-08-11
location: Vancouver, BC, Canada
name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques'
start_date: 2011-08-07
date_created: 2018-12-11T12:02:31Z
date_published: 2011-08-07T00:00:00Z
date_updated: 2023-02-23T11:21:02Z
day: '07'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2037636.2037644
file:
- access_level: open_access
checksum: 8d508ad7c82f50978acbaa4170ee0a75
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:34Z
date_updated: 2020-07-14T12:46:06Z
file_id: '5018'
file_name: IST-2016-599-v1+1_meshyFluidsCourseSIGGRAPH2011.pdf
file_size: 34672096
relation: main_file
file_date_updated: 2020-07-14T12:46:06Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication_status: published
publisher: ACM
publist_id: '3344'
pubrep_id: '599'
quality_controlled: '1'
scopus_import: 1
status: public
title: Liquid simulation with mesh-based surface tracking
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3298'
abstract:
- lang: eng
text: We present a new algorithm for enforcing incompressibility for Smoothed Particle
Hydrodynamics (SPH) by preserving uniform density across the domain. We propose
a hybrid method that uses a Poisson solve on a coarse grid to enforce a divergence
free velocity field, followed by a local density correction of the particles. This
avoids typical grid artifacts and maintains the Lagrangian nature of SPH by directly
transferring pressures onto particles. Our method can be easily integrated with
existing SPH techniques such as the incompressible PCISPH method as well as weakly
compressible SPH by adding an additional force term. We show that this hybrid
method accelerates convergence towards uniform density and permits a significantly
larger time step compared to earlier approaches while producing similar results.
We demonstrate our approach in a variety of scenarios with significant pressure
gradients such as splashing liquids.
author:
- first_name: Karthik
full_name: Raveendran, Karthik
last_name: Raveendran
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Greg
full_name: Turk, Greg
last_name: Turk
citation:
ama: 'Raveendran K, Wojtan C, Turk G. Hybrid smoothed particle hydrodynamics. In:
Spencer S, ed. ACM; 2011:33-42. doi:10.1145/2019406.2019411'
apa: 'Raveendran, K., Wojtan, C., & Turk, G. (2011). Hybrid smoothed particle
hydrodynamics. In S. Spencer (Ed.) (pp. 33–42). Presented at the SCA: ACM SIGGRAPH/Eurographics
Symposium on Computer animation, Vancouver, Canada: ACM. https://doi.org/10.1145/2019406.2019411'
chicago: Raveendran, Karthik, Chris Wojtan, and Greg Turk. “Hybrid Smoothed Particle
Hydrodynamics.” edited by Stephen Spencer, 33–42. ACM, 2011. https://doi.org/10.1145/2019406.2019411.
ieee: 'K. Raveendran, C. Wojtan, and G. Turk, “Hybrid smoothed particle hydrodynamics,”
presented at the SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation,
Vancouver, Canada, 2011, pp. 33–42.'
ista: 'Raveendran K, Wojtan C, Turk G. 2011. Hybrid smoothed particle hydrodynamics.
SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, 33–42.'
mla: Raveendran, Karthik, et al. Hybrid Smoothed Particle Hydrodynamics.
Edited by Stephen Spencer, ACM, 2011, pp. 33–42, doi:10.1145/2019406.2019411.
short: K. Raveendran, C. Wojtan, G. Turk, in:, S. Spencer (Ed.), ACM, 2011, pp.
33–42.
conference:
end_date: 2011-08-07
location: Vancouver, Canada
name: 'SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation'
start_date: 2011-08-05
date_created: 2018-12-11T12:02:32Z
date_published: 2011-08-05T00:00:00Z
date_updated: 2023-02-23T11:21:05Z
day: '05'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2019406.2019411
editor:
- first_name: Stephen
full_name: Spencer, Stephen
last_name: Spencer
file:
- access_level: open_access
checksum: 6579d27709946e0eefbfa60a456b4913
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:44Z
date_updated: 2020-07-14T12:46:06Z
file_id: '4769'
file_name: IST-2016-598-v1+1_HybridSPH_Preprint.pdf
file_size: 2536216
relation: main_file
file_date_updated: 2020-07-14T12:46:06Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 33 - 42
publication_status: published
publisher: ACM
publist_id: '3343'
pubrep_id: '598'
quality_controlled: '1'
scopus_import: 1
status: public
title: Hybrid smoothed particle hydrodynamics
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3299'
abstract:
- lang: eng
text: 'We introduce propagation models, a formalism designed to support general
and efficient data structures for the transient analysis of biochemical reaction
networks. We give two use cases for propagation abstract data types: the uniformization
method and numerical integration. We also sketch an implementation of a propagation
abstract data type, which uses abstraction to approximate states.'
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Maria
full_name: Mateescu, Maria
last_name: Mateescu
citation:
ama: 'Henzinger TA, Mateescu M. Propagation models for computing biochemical reaction
networks. In: Springer; 2011:1-3. doi:10.1145/2037509.2037510'
apa: 'Henzinger, T. A., & Mateescu, M. (2011). Propagation models for computing
biochemical reaction networks (pp. 1–3). Presented at the CMSB: Computational
Methods in Systems Biology, Paris, France: Springer. https://doi.org/10.1145/2037509.2037510'
chicago: Henzinger, Thomas A, and Maria Mateescu. “Propagation Models for Computing
Biochemical Reaction Networks,” 1–3. Springer, 2011. https://doi.org/10.1145/2037509.2037510.
ieee: 'T. A. Henzinger and M. Mateescu, “Propagation models for computing biochemical
reaction networks,” presented at the CMSB: Computational Methods in Systems Biology,
Paris, France, 2011, pp. 1–3.'
ista: 'Henzinger TA, Mateescu M. 2011. Propagation models for computing biochemical
reaction networks. CMSB: Computational Methods in Systems Biology, 1–3.'
mla: Henzinger, Thomas A., and Maria Mateescu. Propagation Models for Computing
Biochemical Reaction Networks. Springer, 2011, pp. 1–3, doi:10.1145/2037509.2037510.
short: T.A. Henzinger, M. Mateescu, in:, Springer, 2011, pp. 1–3.
conference:
end_date: 2011-09-23
location: Paris, France
name: 'CMSB: Computational Methods in Systems Biology'
start_date: 2011-09-21
date_created: 2018-12-11T12:02:32Z
date_published: 2011-09-21T00:00:00Z
date_updated: 2021-01-12T07:42:29Z
day: '21'
ddc:
- '000'
- '004'
department:
- _id: ToHe
doi: 10.1145/2037509.2037510
file:
- access_level: open_access
checksum: 7f5c65509db1a9fb049abedd9663ed06
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:50Z
date_updated: 2020-07-14T12:46:06Z
file_id: '4649'
file_name: IST-2012-92-v1+1_Propagation_models_for_computing_biochemical_reaction_networks.pdf
file_size: 255780
relation: main_file
file_date_updated: 2020-07-14T12:46:06Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 1 - 3
publication_status: published
publisher: Springer
publist_id: '3341'
pubrep_id: '92'
quality_controlled: '1'
scopus_import: 1
status: public
title: Propagation models for computing biochemical reaction networks
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3301'
abstract:
- lang: eng
text: The chemical master equation is a differential equation describing the time
evolution of the probability distribution over the possible “states” of a biochemical
system. The solution of this equation is of interest within the systems biology
field ever since the importance of the molec- ular noise has been acknowledged.
Unfortunately, most of the systems do not have analytical solutions, and numerical
solutions suffer from the course of dimensionality and therefore need to be approximated.
Here, we introduce the concept of tail approximation, which retrieves an approximation
of the probabilities in the tail of a distribution from the total probability
of the tail and its conditional expectation. This approximation method can then
be used to numerically compute the solution of the chemical master equation on
a subset of the state space, thus fighting the explosion of the state space, for
which this problem is renowned.
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Maria
full_name: Mateescu, Maria
last_name: Mateescu
citation:
ama: 'Henzinger TA, Mateescu M. Tail approximation for the chemical master equation.
In: Tampere International Center for Signal Processing; 2011.'
apa: 'Henzinger, T. A., & Mateescu, M. (2011). Tail approximation for the chemical
master equation. Presented at the WCSB: Workshop on Computational Systems Biology
(TICSP), Tampere International Center for Signal Processing.'
chicago: Henzinger, Thomas A, and Maria Mateescu. “Tail Approximation for the Chemical
Master Equation.” Tampere International Center for Signal Processing, 2011.
ieee: 'T. A. Henzinger and M. Mateescu, “Tail approximation for the chemical master
equation,” presented at the WCSB: Workshop on Computational Systems Biology (TICSP),
2011.'
ista: 'Henzinger TA, Mateescu M. 2011. Tail approximation for the chemical master
equation. WCSB: Workshop on Computational Systems Biology (TICSP).'
mla: Henzinger, Thomas A., and Maria Mateescu. Tail Approximation for the Chemical
Master Equation. Tampere International Center for Signal Processing, 2011.
short: T.A. Henzinger, M. Mateescu, in:, Tampere International Center for Signal
Processing, 2011.
conference:
name: 'WCSB: Workshop on Computational Systems Biology (TICSP)'
date_created: 2018-12-11T12:02:33Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:30Z
day: '01'
ddc:
- '005'
- '570'
department:
- _id: ToHe
file:
- access_level: open_access
checksum: aa4d7a832a5419e6c0090650ebff2b9a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:12Z
date_updated: 2020-07-14T12:46:06Z
file_id: '5331'
file_name: IST-2012-91-v1+1_Tail_approximation_for_the_chemical_master_equation.pdf
file_size: 240820
relation: main_file
file_date_updated: 2020-07-14T12:46:06Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
publication_status: published
publisher: Tampere International Center for Signal Processing
publist_id: '3339'
pubrep_id: '91'
quality_controlled: '1'
status: public
title: Tail approximation for the chemical master equation
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3302'
abstract:
- lang: eng
text: Cloud computing aims to give users virtually unlimited pay-per-use computing
resources without the burden of managing the underlying infrastructure. We present
a new job execution environment Flextic that exploits scal- able static scheduling
techniques to provide the user with a flexible pricing model, such as a tradeoff
between dif- ferent degrees of execution speed and execution price, and at the
same time, reduce scheduling overhead for the cloud provider. We have evaluated
a prototype of Flextic on Amazon EC2 and compared it against Hadoop. For various
data parallel jobs from machine learning, im- age processing, and gene sequencing
that we considered, Flextic has low scheduling overhead and reduces job du- ration
by up to 15% compared to Hadoop, a dynamic cloud scheduler.
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Anmol
full_name: Singh, Anmol
id: 72A86902-E99F-11E9-9F62-915534D1B916
last_name: Singh
- first_name: Vasu
full_name: Singh, Vasu
id: 4DAE2708-F248-11E8-B48F-1D18A9856A87
last_name: Singh
- first_name: Thomas
full_name: Wies, Thomas
id: 447BFB88-F248-11E8-B48F-1D18A9856A87
last_name: Wies
- first_name: Damien
full_name: Zufferey, Damien
id: 4397AC76-F248-11E8-B48F-1D18A9856A87
last_name: Zufferey
orcid: 0000-0002-3197-8736
citation:
ama: 'Henzinger TA, Singh A, Singh V, Wies T, Zufferey D. Static scheduling in clouds.
In: USENIX; 2011:1-6.'
apa: 'Henzinger, T. A., Singh, A., Singh, V., Wies, T., & Zufferey, D. (2011).
Static scheduling in clouds (pp. 1–6). Presented at the HotCloud: Workshop on
Hot Topics in Cloud Computing, USENIX.'
chicago: Henzinger, Thomas A, Anmol Singh, Vasu Singh, Thomas Wies, and Damien Zufferey.
“Static Scheduling in Clouds,” 1–6. USENIX, 2011.
ieee: 'T. A. Henzinger, A. Singh, V. Singh, T. Wies, and D. Zufferey, “Static scheduling
in clouds,” presented at the HotCloud: Workshop on Hot Topics in Cloud Computing,
2011, pp. 1–6.'
ista: 'Henzinger TA, Singh A, Singh V, Wies T, Zufferey D. 2011. Static scheduling
in clouds. HotCloud: Workshop on Hot Topics in Cloud Computing, 1–6.'
mla: Henzinger, Thomas A., et al. Static Scheduling in Clouds. USENIX, 2011,
pp. 1–6.
short: T.A. Henzinger, A. Singh, V. Singh, T. Wies, D. Zufferey, in:, USENIX, 2011,
pp. 1–6.
conference:
end_date: 2011-06-15
name: 'HotCloud: Workshop on Hot Topics in Cloud Computing'
start_date: 2011-06-14
date_created: 2018-12-11T12:02:33Z
date_published: 2011-06-14T00:00:00Z
date_updated: 2021-01-12T07:42:31Z
day: '14'
ddc:
- '000'
- '005'
department:
- _id: ToHe
file:
- access_level: open_access
checksum: 21a461ac004bb535c83320fe79b30375
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:14Z
date_updated: 2020-07-14T12:46:06Z
file_id: '5333'
file_name: IST-2012-90-v1+1_Static_scheduling_in_clouds.pdf
file_size: 232770
relation: main_file
file_date_updated: 2020-07-14T12:46:06Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 1 - 6
publication_status: published
publisher: USENIX
publist_id: '3338'
pubrep_id: '90'
quality_controlled: '1'
status: public
title: Static scheduling in clouds
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3311'
abstract:
- lang: eng
text: Alpha shapes have been conceived in 1981 as an attempt to define the shape
of a finite set of point in the plane. Since then, connections to diverse areas
in the sciences and engineering have developed, including to pattern recognition,
digital shape sampling and processing, and structural molecular biology. This
survey begins with a historical account and discusses geometric, algorithmic,
topological, and combinatorial aspects of alpha shapes in this sequence.
article_processing_charge: No
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Edelsbrunner H. Alpha shapes - a survey. In: van de Weygaert R, Vegter G,
Ritzerveld J, Icke V, eds. Tessellations in the Sciences: Virtues, Techniques
and Applications of Geometric Tilings. Springer.'
apa: 'Edelsbrunner, H. (n.d.). Alpha shapes - a survey. In R. van de Weygaert, G.
Vegter, J. Ritzerveld, & V. Icke (Eds.), Tessellations in the Sciences:
Virtues, Techniques and Applications of Geometric Tilings. Springer.'
chicago: 'Edelsbrunner, Herbert. “Alpha Shapes - a Survey.” In Tessellations
in the Sciences: Virtues, Techniques and Applications of Geometric Tilings,
edited by R van de Weygaert, G Vegter, J Ritzerveld, and V Icke. Springer, n.d.'
ieee: 'H. Edelsbrunner, “Alpha shapes - a survey,” in Tessellations in the Sciences:
Virtues, Techniques and Applications of Geometric Tilings, R. van de Weygaert,
G. Vegter, J. Ritzerveld, and V. Icke, Eds. Springer.'
ista: 'Edelsbrunner H.Alpha shapes - a survey. In: Tessellations in the Sciences:
Virtues, Techniques and Applications of Geometric Tilings. .'
mla: 'Edelsbrunner, Herbert. “Alpha Shapes - a Survey.” Tessellations in the
Sciences: Virtues, Techniques and Applications of Geometric Tilings, edited
by R van de Weygaert et al., Springer.'
short: 'H. Edelsbrunner, in:, R. van de Weygaert, G. Vegter, J. Ritzerveld, V. Icke
(Eds.), Tessellations in the Sciences: Virtues, Techniques and Applications of
Geometric Tilings, Springer, n.d.'
date_created: 2018-12-11T12:02:36Z
date_published: 2011-12-31T00:00:00Z
date_updated: 2022-05-24T07:56:30Z
day: '31'
ddc:
- '510'
department:
- _id: HeEd
editor:
- first_name: R
full_name: van de Weygaert, R
last_name: van de Weygaert
- first_name: G
full_name: Vegter, G
last_name: Vegter
- first_name: J
full_name: Ritzerveld, J
last_name: Ritzerveld
- first_name: V
full_name: Icke, V
last_name: Icke
file:
- access_level: open_access
checksum: a592ea438351e7280eea993a7713ab8f
content_type: application/pdf
creator: dernst
date_created: 2022-05-24T07:55:05Z
date_updated: 2022-05-24T07:55:05Z
file_id: '11408'
file_name: 2010_AlphaShapes.pdf
file_size: 475254
relation: main_file
success: 1
file_date_updated: 2022-05-24T07:55:05Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Submitted Version
publication: 'Tessellations in the Sciences: Virtues, Techniques and Applications
of Geometric Tilings'
publication_status: inpress
publisher: Springer
publist_id: '3329'
quality_controlled: '1'
status: public
title: Alpha shapes - a survey
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3312'
abstract:
- lang: eng
text: We study the 3D reconstruction of plant roots from multiple 2D images. To
meet the challenge caused by the delicate nature of thin branches, we make three
innovations to cope with the sensitivity to image quality and calibration. First,
we model the background as a harmonic function to improve the segmentation of
the root in each 2D image. Second, we develop the concept of the regularized visual
hull which reduces the effect of jittering and refraction by ensuring consistency
with one 2D image. Third, we guarantee connectedness through adjustments to the
3D reconstruction that minimize global error. Our software is part of a biological
phenotype/genotype study of agricultural root systems. It has been tested on more
than 40 plant roots and results are promising in terms of reconstruction quality
and efficiency.
acknowledgement: This research is supported by the National Science Foundation (NSF)
under grant DBI-0820624.
article_number: '6126475'
article_processing_charge: No
author:
- first_name: Ying
full_name: Zheng, Ying
last_name: Zheng
- first_name: Steve
full_name: Gu, Steve
last_name: Gu
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Carlo
full_name: Tomasi, Carlo
last_name: Tomasi
- first_name: Philip
full_name: Benfey, Philip
last_name: Benfey
citation:
ama: Zheng Y, Gu S, Edelsbrunner H, Tomasi C, Benfey P. Detailed Reconstruction
of 3D Plant Root Shape. IEEE; 2011. doi:10.1109/ICCV.2011.6126475
apa: 'Zheng, Y., Gu, S., Edelsbrunner, H., Tomasi, C., & Benfey, P. (2011).
Detailed reconstruction of 3D plant root shape. Proceedings of the IEEE
International Conference on Computer Vision. Barcelona, Spain: IEEE. https://doi.org/10.1109/ICCV.2011.6126475'
chicago: Zheng, Ying, Steve Gu, Herbert Edelsbrunner, Carlo Tomasi, and Philip Benfey.
Detailed Reconstruction of 3D Plant Root Shape. Proceedings of the IEEE
International Conference on Computer Vision. IEEE, 2011. https://doi.org/10.1109/ICCV.2011.6126475.
ieee: Y. Zheng, S. Gu, H. Edelsbrunner, C. Tomasi, and P. Benfey, Detailed reconstruction
of 3D plant root shape. IEEE, 2011.
ista: Zheng Y, Gu S, Edelsbrunner H, Tomasi C, Benfey P. 2011. Detailed reconstruction
of 3D plant root shape, IEEE,p.
mla: Zheng, Ying, et al. “Detailed Reconstruction of 3D Plant Root Shape.” Proceedings
of the IEEE International Conference on Computer Vision, 6126475, IEEE, 2011,
doi:10.1109/ICCV.2011.6126475.
short: Y. Zheng, S. Gu, H. Edelsbrunner, C. Tomasi, P. Benfey, Detailed Reconstruction
of 3D Plant Root Shape, IEEE, 2011.
conference:
end_date: 2011-11-13
location: Barcelona, Spain
name: 'ICCV: International Conference on Computer Vision'
start_date: 2011-11-06
date_created: 2018-12-11T12:02:36Z
date_published: 2011-12-31T00:00:00Z
date_updated: 2020-07-14T23:03:43Z
day: '31'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1109/ICCV.2011.6126475
file:
- access_level: open_access
checksum: 30a33564b7b45a7ee31610898267fd0e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:04Z
date_updated: 2020-07-14T12:46:07Z
file_id: '4727'
file_name: IST-2016-541-v1+1_2011-P-07-RootReconstruction.pdf
file_size: 5622728
relation: main_file
file_date_updated: 2020-07-14T12:46:07Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Submitted Version
publication: Proceedings of the IEEE International Conference on Computer Vision
publication_status: published
publisher: IEEE
publist_id: '3328'
pubrep_id: '541'
quality_controlled: '1'
status: public
title: Detailed reconstruction of 3D plant root shape
type: conference_poster
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3313'
abstract:
- lang: eng
text: Interpreting an image as a function on a compact sub- set of the Euclidean
plane, we get its scale-space by diffu- sion, spreading the image over the entire
plane. This gener- ates a 1-parameter family of functions alternatively defined
as convolutions with a progressively wider Gaussian ker- nel. We prove that the
corresponding 1-parameter family of persistence diagrams have norms that go rapidly
to zero as time goes to infinity. This result rationalizes experimental observations
about scale-space. We hope this will lead to targeted improvements of related
computer vision methods.
article_number: '6126271'
author:
- first_name: Chao
full_name: Chen, Chao
id: 3E92416E-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Chen C, Edelsbrunner H. Diffusion runs low on persistence fast. In: Proceedings
of the IEEE International Conference on Computer Vision. IEEE; 2011. doi:10.1109/ICCV.2011.6126271'
apa: 'Chen, C., & Edelsbrunner, H. (2011). Diffusion runs low on persistence
fast. In Proceedings of the IEEE International Conference on Computer Vision.
Barcelona, Spain: IEEE. https://doi.org/10.1109/ICCV.2011.6126271'
chicago: Chen, Chao, and Herbert Edelsbrunner. “Diffusion Runs Low on Persistence
Fast.” In Proceedings of the IEEE International Conference on Computer Vision.
IEEE, 2011. https://doi.org/10.1109/ICCV.2011.6126271.
ieee: C. Chen and H. Edelsbrunner, “Diffusion runs low on persistence fast,” in
Proceedings of the IEEE International Conference on Computer Vision, Barcelona,
Spain, 2011.
ista: 'Chen C, Edelsbrunner H. 2011. Diffusion runs low on persistence fast. Proceedings
of the IEEE International Conference on Computer Vision. ICCV: International Conference
on Computer Vision, 6126271.'
mla: Chen, Chao, and Herbert Edelsbrunner. “Diffusion Runs Low on Persistence Fast.”
Proceedings of the IEEE International Conference on Computer Vision, 6126271,
IEEE, 2011, doi:10.1109/ICCV.2011.6126271.
short: C. Chen, H. Edelsbrunner, in:, Proceedings of the IEEE International Conference
on Computer Vision, IEEE, 2011.
conference:
end_date: 2011-11-13
location: Barcelona, Spain
name: 'ICCV: International Conference on Computer Vision'
start_date: 2011-11-06
date_created: 2018-12-11T12:02:37Z
date_published: 2011-11-06T00:00:00Z
date_updated: 2021-01-12T07:42:35Z
day: '06'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1109/ICCV.2011.6126271
file:
- access_level: open_access
checksum: 6984684081ba123808b344f9f2e64a8f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:28Z
date_updated: 2020-07-14T12:46:07Z
file_id: '5282'
file_name: IST-2016-540-v1+1_2011-P-08-RunEmpty.pdf
file_size: 614050
relation: main_file
file_date_updated: 2020-07-14T12:46:07Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
publication: Proceedings of the IEEE International Conference on Computer Vision
publication_status: published
publisher: IEEE
publist_id: '3327'
pubrep_id: '540'
quality_controlled: '1'
scopus_import: 1
status: public
title: Diffusion runs low on persistence fast
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3315'
abstract:
- lang: eng
text: We consider two-player games played in real time on game structures with clocks
where the objectives of players are described using parity conditions. The games
are concurrent in that at each turn, both players independently propose a time
delay and an action, and the action with the shorter delay is chosen. To prevent
a player from winning by blocking time, we restrict each player to play strategies
that ensure that the player cannot be responsible for causing a zeno run. First,
we present an efficient reduction of these games to turn-based (i.e., not concurrent)
finite-state (i.e., untimed) parity games. Our reduction improves the best known
complexity for solving timed parity games. Moreover, the rich class of algorithms
for classical parity games can now be applied to timed parity games. The states
of the resulting game are based on clock regions of the original game, and the
state space of the finite game is linear in the size of the region graph. Second,
we consider two restricted classes of strategies for the player that represents
the controller in a real-time synthesis problem, namely, limit-robust and bounded-robust
winning strategies. Using a limit-robust winning strategy, the controller cannot
choose an exact real-valued time delay but must allow for some nonzero jitter
in each of its actions. If there is a given lower bound on the jitter, then the
strategy is bounded-robust winning. We show that exact strategies are more powerful
than limit-robust strategies, which are more powerful than bounded-robust winning
strategies for any bound. For both kinds of robust strategies, we present efficient
reductions to standard timed automaton games. These reductions provide algorithms
for the synthesis of robust real-time controllers.
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Vinayak
full_name: Prabhu, Vinayak
last_name: Prabhu
citation:
ama: 'Chatterjee K, Henzinger TA, Prabhu V. Timed parity games: Complexity and robustness.
Logical Methods in Computer Science. 2011;7(4). doi:10.2168/LMCS-7(4:8)2011'
apa: 'Chatterjee, K., Henzinger, T. A., & Prabhu, V. (2011). Timed parity games:
Complexity and robustness. Logical Methods in Computer Science. International
Federation of Computational Logic. https://doi.org/10.2168/LMCS-7(4:8)2011'
chicago: 'Chatterjee, Krishnendu, Thomas A Henzinger, and Vinayak Prabhu. “Timed
Parity Games: Complexity and Robustness.” Logical Methods in Computer Science.
International Federation of Computational Logic, 2011. https://doi.org/10.2168/LMCS-7(4:8)2011.'
ieee: 'K. Chatterjee, T. A. Henzinger, and V. Prabhu, “Timed parity games: Complexity
and robustness,” Logical Methods in Computer Science, vol. 7, no. 4. International
Federation of Computational Logic, 2011.'
ista: 'Chatterjee K, Henzinger TA, Prabhu V. 2011. Timed parity games: Complexity
and robustness. Logical Methods in Computer Science. 7(4).'
mla: 'Chatterjee, Krishnendu, et al. “Timed Parity Games: Complexity and Robustness.”
Logical Methods in Computer Science, vol. 7, no. 4, International Federation
of Computational Logic, 2011, doi:10.2168/LMCS-7(4:8)2011.'
short: K. Chatterjee, T.A. Henzinger, V. Prabhu, Logical Methods in Computer Science
7 (2011).
date_created: 2018-12-11T12:02:37Z
date_published: 2011-12-14T00:00:00Z
date_updated: 2023-02-23T11:46:35Z
day: '14'
ddc:
- '000'
- '005'
department:
- _id: KrCh
- _id: ToHe
doi: 10.2168/LMCS-7(4:8)2011
ec_funded: 1
file:
- access_level: open_access
checksum: 3480e1594bbef25ff7462fa93a8a814e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:42Z
date_updated: 2020-07-14T12:46:07Z
file_id: '5231'
file_name: IST-2016-86-v2+1_1011.0688_3_.pdf
file_size: 588863
relation: main_file
file_date_updated: 2020-07-14T12:46:07Z
has_accepted_license: '1'
intvolume: ' 7'
issue: '4'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nd/4.0/
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 25EFB36C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '215543'
name: COMponent-Based Embedded Systems design Techniques
publication: Logical Methods in Computer Science
publication_status: published
publisher: International Federation of Computational Logic
publist_id: '3324'
pubrep_id: '506'
quality_controlled: '1'
related_material:
record:
- id: '3876'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: 'Timed parity games: Complexity and robustness'
tmp:
image: /image/cc_by_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
short: CC BY-ND (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2011'
...
---
_id: '3316'
abstract:
- lang: eng
text: In addition to being correct, a system should be robust, that is, it should
behave reasonably even after receiving unexpected inputs. In this paper, we summarize
two formal notions of robustness that we have introduced previously for reactive
systems. One of the notions is based on assigning costs for failures on a user-provided
notion of incorrect transitions in a specification. Here, we define a system to
be robust if a finite number of incorrect inputs does not lead to an infinite
number of incorrect outputs. We also give a more refined notion of robustness
that aims to minimize the ratio of output failures to input failures. The second
notion is aimed at liveness. In contrast to the previous notion, it has no concept
of recovery from an error. Instead, it compares the ratio of the number of liveness
constraints that the system violates to the number of liveness constraints that
the environment violates.
article_processing_charge: No
author:
- first_name: Roderick
full_name: Bloem, Roderick
last_name: Bloem
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Karin
full_name: Greimel, Karin
last_name: Greimel
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Barbara
full_name: Jobstmann, Barbara
last_name: Jobstmann
citation:
ama: 'Bloem R, Chatterjee K, Greimel K, Henzinger TA, Jobstmann B. Specification-centered
robustness. In: 6th IEEE International Symposium on Industrial and Embedded
Systems. IEEE; 2011:176-185. doi:10.1109/SIES.2011.5953660'
apa: 'Bloem, R., Chatterjee, K., Greimel, K., Henzinger, T. A., & Jobstmann,
B. (2011). Specification-centered robustness. In 6th IEEE International Symposium
on Industrial and Embedded Systems (pp. 176–185). Vasteras, Sweden: IEEE.
https://doi.org/10.1109/SIES.2011.5953660'
chicago: Bloem, Roderick, Krishnendu Chatterjee, Karin Greimel, Thomas A Henzinger,
and Barbara Jobstmann. “Specification-Centered Robustness.” In 6th IEEE International
Symposium on Industrial and Embedded Systems, 176–85. IEEE, 2011. https://doi.org/10.1109/SIES.2011.5953660.
ieee: R. Bloem, K. Chatterjee, K. Greimel, T. A. Henzinger, and B. Jobstmann, “Specification-centered
robustness,” in 6th IEEE International Symposium on Industrial and Embedded
Systems, Vasteras, Sweden, 2011, pp. 176–185.
ista: 'Bloem R, Chatterjee K, Greimel K, Henzinger TA, Jobstmann B. 2011. Specification-centered
robustness. 6th IEEE International Symposium on Industrial and Embedded Systems. SIES:
International Symposium on Industrial Embedded Systems, 176–185.'
mla: Bloem, Roderick, et al. “Specification-Centered Robustness.” 6th IEEE International
Symposium on Industrial and Embedded Systems, IEEE, 2011, pp. 176–85, doi:10.1109/SIES.2011.5953660.
short: R. Bloem, K. Chatterjee, K. Greimel, T.A. Henzinger, B. Jobstmann, in:, 6th
IEEE International Symposium on Industrial and Embedded Systems, IEEE, 2011, pp.
176–185.
conference:
end_date: 2011-06-17
location: Vasteras, Sweden
name: ' SIES: International Symposium on Industrial Embedded Systems'
start_date: 2011-06-15
date_created: 2018-12-11T12:02:38Z
date_published: 2011-07-14T00:00:00Z
date_updated: 2021-01-12T07:42:36Z
day: '14'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1109/SIES.2011.5953660
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://openlib.tugraz.at/download.php?id=5cb57c8a49344&location=browse
month: '07'
oa: 1
oa_version: Published Version
page: 176 - 185
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F2ACDE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Rigorous Systems Engineering
- _id: 25F1337C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '214373'
name: Design for Embedded Systems
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: 6th IEEE International Symposium on Industrial and Embedded Systems
publication_status: published
publisher: IEEE
publist_id: '3323'
quality_controlled: '1'
scopus_import: 1
status: public
title: Specification-centered robustness
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '11094'
abstract:
- lang: eng
text: Nuclear pore complexes (NPCs) assemble at the end of mitosis during nuclear
envelope (NE) reformation and into an intact NE as cells progress through interphase.
Although recent studies have shown that NPC formation occurs by two different
molecular mechanisms at two distinct cell cycle stages, little is known about
the molecular players that mediate the fusion of the outer and inner nuclear membranes
to form pores. In this paper, we provide evidence that the transmembrane nucleoporin
(Nup), POM121, but not the Nup107–160 complex, is present at new pore assembly
sites at a time that coincides with inner nuclear membrane (INM) and outer nuclear
membrane (ONM) fusion. Overexpression of POM121 resulted in juxtaposition of the
INM and ONM. Additionally, Sun1, an INM protein that is known to interact with
the cytoskeleton, was specifically required for interphase assembly and localized
with POM121 at forming pores. We propose a model in which POM121 and Sun1 interact
transiently to promote early steps of interphase NPC assembly.
article_processing_charge: No
article_type: original
author:
- first_name: Jessica A.
full_name: Talamas, Jessica A.
last_name: Talamas
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Talamas JA, Hetzer M. POM121 and Sun1 play a role in early steps of interphase
NPC assembly. Journal of Cell Biology. 2011;194(1):27-37. doi:10.1083/jcb.201012154
apa: Talamas, J. A., & Hetzer, M. (2011). POM121 and Sun1 play a role in early
steps of interphase NPC assembly. Journal of Cell Biology. Rockefeller
University Press. https://doi.org/10.1083/jcb.201012154
chicago: Talamas, Jessica A., and Martin Hetzer. “POM121 and Sun1 Play a Role in
Early Steps of Interphase NPC Assembly.” Journal of Cell Biology. Rockefeller
University Press, 2011. https://doi.org/10.1083/jcb.201012154.
ieee: J. A. Talamas and M. Hetzer, “POM121 and Sun1 play a role in early steps of
interphase NPC assembly,” Journal of Cell Biology, vol. 194, no. 1. Rockefeller
University Press, pp. 27–37, 2011.
ista: Talamas JA, Hetzer M. 2011. POM121 and Sun1 play a role in early steps of
interphase NPC assembly. Journal of Cell Biology. 194(1), 27–37.
mla: Talamas, Jessica A., and Martin Hetzer. “POM121 and Sun1 Play a Role in Early
Steps of Interphase NPC Assembly.” Journal of Cell Biology, vol. 194, no.
1, Rockefeller University Press, 2011, pp. 27–37, doi:10.1083/jcb.201012154.
short: J.A. Talamas, M. Hetzer, Journal of Cell Biology 194 (2011) 27–37.
date_created: 2022-04-07T07:52:18Z
date_published: 2011-07-04T00:00:00Z
date_updated: 2022-07-18T08:53:46Z
day: '04'
doi: 10.1083/jcb.201012154
extern: '1'
external_id:
pmid:
- '21727197'
intvolume: ' 194'
issue: '1'
keyword:
- Cell Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1083/jcb.201012154
month: '07'
oa: 1
oa_version: Published Version
page: 27-37
pmid: 1
publication: Journal of Cell Biology
publication_identifier:
eissn:
- 1540-8140
issn:
- 0021-9525
publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: POM121 and Sun1 play a role in early steps of interphase NPC assembly
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 194
year: '2011'
...
---
_id: '112'
abstract:
- lang: eng
text: Particle beams are important tools for probing atomic and molecular interactions.
Here we demonstrate that particle beams also offer a unique opportunity to investigate
interactions in macroscopic systems, such as granular media. Motivated by recent
experiments on streams of grains that exhibit liquid-like breakup into droplets,
we use molecular dynamics simulations to investigate the evolution of a dense
stream of macroscopic spheres accelerating out of an opening at the bottom of
a reservoir. We show how nanoscale details associated with energy dissipation
during collisions modify the stream\'s macroscopic behavior. We find that inelastic
collisions collimate the stream, while the presence of short-range attractive
interactions drives structure formation. Parameterizing the collision dynamics
by the coefficient of restitution (i.e., the ratio of relative velocities before
and after impact) and the strength of the cohesive interaction, we map out a spectrum
of behaviors that ranges from gaslike jets in which all grains drift apart to
liquid-like streams that break into large droplets containing hundreds of grains.
We also find a new, intermediate regime in which small aggregates form by capture
from the gas phase, similar to what can be observed in molecular beams. Our results
show that nearly all aspects of stream behavior are closely related to the velocity
gradient associated with vertical free fall. Led by this observation, we propose
a simple energy balance model to explain the droplet formation process. The qualitative
as well as many quantitative features of the simulations and the model compare
well with available experimental data and provide a first quantitative measure
of the role of attractions in freely cooling granular streams.
acknowledgement: This work was supported by the NSF through CBET-0933242. We acknowledge
use of shared facilities provided by the Keck Facility for Ultrafast Imaging at
the University of Chicago and by the Chicago MRSEC through NSF DMR-0820054. Software
support by Itasca Consulting Group, Inc., under the Itasca Educational Partnership
is gratefully acknowledged. H.G. thanks the German-American Fulbright Commission
for fellowship support during his stay at the University of Chicago.
article_number: '051302'
arxiv: 1
author:
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
- first_name: Helge
full_name: Grütjen, Helge
last_name: Grütjen
- first_name: John
full_name: Royer, John
last_name: Royer
- first_name: Heinrich
full_name: Jaeger, Heinrich
last_name: Jaeger
citation:
ama: Waitukaitis SR, Grütjen H, Royer J, Jaeger H. Droplet and cluster formation
in freely falling granular streams. Physical Review E. 2011;83(5). doi:10.1103/PhysRevE.83.051302
apa: Waitukaitis, S. R., Grütjen, H., Royer, J., & Jaeger, H. (2011). Droplet
and cluster formation in freely falling granular streams. Physical Review E.
American Physical Society. https://doi.org/10.1103/PhysRevE.83.051302
chicago: Waitukaitis, Scott R, Helge Grütjen, John Royer, and Heinrich Jaeger. “Droplet
and Cluster Formation in Freely Falling Granular Streams.” Physical Review
E. American Physical Society, 2011. https://doi.org/10.1103/PhysRevE.83.051302.
ieee: S. R. Waitukaitis, H. Grütjen, J. Royer, and H. Jaeger, “Droplet and cluster
formation in freely falling granular streams,” Physical Review E, vol.
83, no. 5. American Physical Society, 2011.
ista: Waitukaitis SR, Grütjen H, Royer J, Jaeger H. 2011. Droplet and cluster formation
in freely falling granular streams. Physical Review E. 83(5), 051302.
mla: Waitukaitis, Scott R., et al. “Droplet and Cluster Formation in Freely Falling
Granular Streams.” Physical Review E, vol. 83, no. 5, 051302, American
Physical Society, 2011, doi:10.1103/PhysRevE.83.051302.
short: S.R. Waitukaitis, H. Grütjen, J. Royer, H. Jaeger, Physical Review E 83 (2011).
date_created: 2018-12-11T11:44:41Z
date_published: 2011-05-12T00:00:00Z
date_updated: 2021-01-12T06:48:25Z
day: '12'
doi: 10.1103/PhysRevE.83.051302
extern: '1'
external_id:
arxiv:
- '1006.1371'
intvolume: ' 83'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1006.1371
month: '05'
oa: 1
oa_version: Preprint
publication: Physical Review E
publication_status: published
publisher: American Physical Society
publist_id: '7942'
quality_controlled: '1'
status: public
title: Droplet and cluster formation in freely falling granular streams
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 83
year: '2011'
...
---
_id: '3396'
abstract:
- lang: eng
text: Facial branchiomotor neurons (FBMNs) in zebrafish and mouse embryonic hindbrain
undergo a characteristic tangential migration from rhombomere (r) 4, where they
are born, to r6/7. Cohesion among neuroepithelial cells (NCs) has been suggested
to function in FBMN migration by inhibiting FBMNs positioned in the basal neuroepithelium
such that they move apically between NCs towards the midline of the neuroepithelium
instead of tangentially along the basal side of the neuroepithelium towards r6/7.
However, direct experimental evaluation of this hypothesis is still lacking. Here,
we have used a combination of biophysical cell adhesion measurements and high-resolution
time-lapse microscopy to determine the role of NC cohesion in FBMN migration.
We show that reducing NC cohesion by interfering with Cadherin 2 (Cdh2) activity
results in FBMNs positioned at the basal side of the neuroepithelium moving apically
towards the neural tube midline instead of tangentially towards r6/7. In embryos
with strongly reduced NC cohesion, ectopic apical FBMN movement frequently results
in fusion of the bilateral FBMN clusters over the apical midline of the neural
tube. By contrast, reducing cohesion among FBMNs by interfering with Contactin
2 (Cntn2) expression in these cells has little effect on apical FBMN movement,
but reduces the fusion of the bilateral FBMN clusters in embryos with strongly
diminished NC cohesion. These data provide direct experimental evidence that NC
cohesion functions in tangential FBMN migration by restricting their apical movement.
acknowledged_ssus:
- _id: Bio
- _id: PreCl
article_type: original
author:
- first_name: Petra
full_name: Stockinger, Petra
id: 261CB030-E90D-11E9-B182-F697D44B663C
last_name: Stockinger
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Jean-Léon
full_name: Maître, Jean-Léon
id: 48F1E0D8-F248-11E8-B48F-1D18A9856A87
last_name: Maître
orcid: 0000-0002-3688-1474
citation:
ama: Stockinger P, Heisenberg C-PJ, Maître J-L. Defective neuroepithelial cell cohesion
affects tangential branchiomotor neuron migration in the zebrafish neural tube.
Development. 2011;138(21):4673-4683. doi:10.1242/dev.071233
apa: Stockinger, P., Heisenberg, C.-P. J., & Maître, J.-L. (2011). Defective
neuroepithelial cell cohesion affects tangential branchiomotor neuron migration
in the zebrafish neural tube. Development. Company of Biologists. https://doi.org/10.1242/dev.071233
chicago: Stockinger, Petra, Carl-Philipp J Heisenberg, and Jean-Léon Maître. “Defective
Neuroepithelial Cell Cohesion Affects Tangential Branchiomotor Neuron Migration
in the Zebrafish Neural Tube.” Development. Company of Biologists, 2011.
https://doi.org/10.1242/dev.071233.
ieee: P. Stockinger, C.-P. J. Heisenberg, and J.-L. Maître, “Defective neuroepithelial
cell cohesion affects tangential branchiomotor neuron migration in the zebrafish
neural tube,” Development, vol. 138, no. 21. Company of Biologists, pp.
4673–4683, 2011.
ista: Stockinger P, Heisenberg C-PJ, Maître J-L. 2011. Defective neuroepithelial
cell cohesion affects tangential branchiomotor neuron migration in the zebrafish
neural tube. Development. 138(21), 4673–4683.
mla: Stockinger, Petra, et al. “Defective Neuroepithelial Cell Cohesion Affects
Tangential Branchiomotor Neuron Migration in the Zebrafish Neural Tube.” Development,
vol. 138, no. 21, Company of Biologists, 2011, pp. 4673–83, doi:10.1242/dev.071233.
short: P. Stockinger, C.-P.J. Heisenberg, J.-L. Maître, Development 138 (2011) 4673–4683.
date_created: 2018-12-11T12:03:06Z
date_published: 2011-09-28T00:00:00Z
date_updated: 2021-01-12T07:43:11Z
day: '28'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1242/dev.071233
file:
- access_level: open_access
checksum: ca12b79e01ef36c1ef1aea31cf7e7139
content_type: application/pdf
creator: dernst
date_created: 2019-10-07T14:19:42Z
date_updated: 2020-07-14T12:46:12Z
file_id: '6930'
file_name: 2011_Development_Stockinger.pdf
file_size: 4672439
relation: main_file
file_date_updated: 2020-07-14T12:46:12Z
has_accepted_license: '1'
intvolume: ' 138'
issue: '21'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 4673 - 4683
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '3210'
quality_controlled: '1'
scopus_import: 1
status: public
title: Defective neuroepithelial cell cohesion affects tangential branchiomotor neuron
migration in the zebrafish neural tube
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 138
year: '2011'
...
---
_id: '3379'
abstract:
- lang: eng
text: The process of gastrulation is highly conserved across vertebrates on both
the genetic and morphological levels, despite great variety in embryonic shape
and speed of development. This mechanism spatially separates the germ layers and
establishes the organizational foundation for future development. Mesodermal identity
is specified in a superficial layer of cells, the epiblast, where cells maintain
an epithelioid morphology. These cells involute to join the deeper hypoblast layer
where they adopt a migratory, mesenchymal morphology. Expression of a cascade
of related transcription factors orchestrates the parallel genetic transition
from primitive to mature mesoderm. Although the early and late stages of this
process are increasingly well understood, the transition between them has remained
largely mysterious. We present here the first high resolution in vivo observations
of the blebby transitional morphology of involuting mesodermal cells in a vertebrate
embryo. We further demonstrate that the zebrafish spadetail mutation creates a
reversible block in the maturation program, stalling cells in the transition state.
This mutation creates an ideal system for dissecting the specific properties of
cells undergoing the morphological transition of maturing mesoderm, as we demonstrate
with a direct measurement of cell–cell adhesion.
article_type: original
author:
- first_name: Richard
full_name: Row, Richard
last_name: Row
- first_name: Jean-Léon
full_name: Maître, Jean-Léon
id: 48F1E0D8-F248-11E8-B48F-1D18A9856A87
last_name: Maître
orcid: 0000-0002-3688-1474
- first_name: Benjamin
full_name: Martin, Benjamin
last_name: Martin
- first_name: Petra
full_name: Stockinger, Petra
id: 261CB030-E90D-11E9-B182-F697D44B663C
last_name: Stockinger
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: David
full_name: Kimelman, David
last_name: Kimelman
citation:
ama: Row R, Maître J-L, Martin B, Stockinger P, Heisenberg C-PJ, Kimelman D. Completion
of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail.
Developmental Biology. 2011;354(1):102-110. doi:10.1016/j.ydbio.2011.03.025
apa: Row, R., Maître, J.-L., Martin, B., Stockinger, P., Heisenberg, C.-P. J., &
Kimelman, D. (2011). Completion of the epithelial to mesenchymal transition in
zebrafish mesoderm requires Spadetail. Developmental Biology. Elsevier.
https://doi.org/10.1016/j.ydbio.2011.03.025
chicago: Row, Richard, Jean-Léon Maître, Benjamin Martin, Petra Stockinger, Carl-Philipp
J Heisenberg, and David Kimelman. “Completion of the Epithelial to Mesenchymal
Transition in Zebrafish Mesoderm Requires Spadetail.” Developmental Biology.
Elsevier, 2011. https://doi.org/10.1016/j.ydbio.2011.03.025.
ieee: R. Row, J.-L. Maître, B. Martin, P. Stockinger, C.-P. J. Heisenberg, and D.
Kimelman, “Completion of the epithelial to mesenchymal transition in zebrafish
mesoderm requires Spadetail,” Developmental Biology, vol. 354, no. 1. Elsevier,
pp. 102–110, 2011.
ista: Row R, Maître J-L, Martin B, Stockinger P, Heisenberg C-PJ, Kimelman D. 2011.
Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires
Spadetail. Developmental Biology. 354(1), 102–110.
mla: Row, Richard, et al. “Completion of the Epithelial to Mesenchymal Transition
in Zebrafish Mesoderm Requires Spadetail.” Developmental Biology, vol.
354, no. 1, Elsevier, 2011, pp. 102–10, doi:10.1016/j.ydbio.2011.03.025.
short: R. Row, J.-L. Maître, B. Martin, P. Stockinger, C.-P.J. Heisenberg, D. Kimelman,
Developmental Biology 354 (2011) 102–110.
date_created: 2018-12-11T12:03:00Z
date_published: 2011-06-01T00:00:00Z
date_updated: 2021-01-12T07:43:04Z
day: '01'
department:
- _id: CaHe
doi: 10.1016/j.ydbio.2011.03.025
external_id:
pmid:
- '1463614'
intvolume: ' 354'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3090540/
month: '06'
oa: 1
oa_version: Submitted Version
page: 102 - 110
pmid: 1
publication: Developmental Biology
publication_status: published
publisher: Elsevier
publist_id: '3228'
quality_controlled: '1'
scopus_import: 1
status: public
title: Completion of the epithelial to mesenchymal transition in zebrafish mesoderm
requires Spadetail
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 354
year: '2011'
...
---
_id: '12653'
abstract:
- lang: eng
text: 'Daily streamflow from stations close to five Swiss glaciers is analyzed for
trends with the Mann-Kendall test. We consider a common period of record (1974–2004)
and longer periods based on data availability. The trend statistical significance
is tested on annual and seasonal bases. We also examine changes in precipitation,
temperature, and snow cover characteristics. Highly glacierized basins show statistically
significant positive trends in annual streamflow caused by increasing streamflow
in spring and summer. Trends are more numerous and stronger at lower and mid than
at the upper quantiles. The basin characterized by lower glacier coverage, conversely,
does not exhibit consistently statistically significant trends. Changes in precipitation
are not sufficient to explain the observed streamflow trends. Air temperature
sees an increase in mean, minimum, and maximum values at all sites. Variations
in the seasonal snow accumulation and ablation process are evident. Solid precipitation
is decreasing at all sites and trends may be due to a shift from snowfall into
rainfall. Mean snow depth is also decreasing, and its duration is getting shorter
because of a decrease in solid precipitation and enhanced melting. Trend magnitude
attenuates with longer time series. Contrasting trends are detected for different
subperiods in the last 70 years: statistically significant negative trends are
observed in the periods 1944–1974 and 1954–1984 for Aletschgletscher, in contrast
with the results for the common period. These trends are explained by different
rates of ice volume changes, and the sign of trends is clearly related to phases
of positive or negative glacier mass balance.'
article_number: W10522
article_processing_charge: No
article_type: original
author:
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: A.
full_name: Bauder, A.
last_name: Bauder
- first_name: M.
full_name: Parola, M.
last_name: Parola
citation:
ama: Pellicciotti F, Bauder A, Parola M. Effect of glaciers on streamflow trends
in the Swiss Alps. Water Resources Research. 2010;46(10). doi:10.1029/2009wr009039
apa: Pellicciotti, F., Bauder, A., & Parola, M. (2010). Effect of glaciers on
streamflow trends in the Swiss Alps. Water Resources Research. American
Geophysical Union. https://doi.org/10.1029/2009wr009039
chicago: Pellicciotti, Francesca, A. Bauder, and M. Parola. “Effect of Glaciers
on Streamflow Trends in the Swiss Alps.” Water Resources Research. American
Geophysical Union, 2010. https://doi.org/10.1029/2009wr009039.
ieee: F. Pellicciotti, A. Bauder, and M. Parola, “Effect of glaciers on streamflow
trends in the Swiss Alps,” Water Resources Research, vol. 46, no. 10. American
Geophysical Union, 2010.
ista: Pellicciotti F, Bauder A, Parola M. 2010. Effect of glaciers on streamflow
trends in the Swiss Alps. Water Resources Research. 46(10), W10522.
mla: Pellicciotti, Francesca, et al. “Effect of Glaciers on Streamflow Trends in
the Swiss Alps.” Water Resources Research, vol. 46, no. 10, W10522, American
Geophysical Union, 2010, doi:10.1029/2009wr009039.
short: F. Pellicciotti, A. Bauder, M. Parola, Water Resources Research 46 (2010).
date_created: 2023-02-20T08:18:27Z
date_published: 2010-10-01T00:00:00Z
date_updated: 2023-02-20T09:39:29Z
day: '01'
doi: 10.1029/2009wr009039
extern: '1'
intvolume: ' 46'
issue: '10'
keyword:
- Water Science and Technology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1029/2009WR009039
month: '10'
oa: 1
oa_version: Published Version
publication: Water Resources Research
publication_identifier:
eissn:
- 1944-7973
issn:
- 0043-1397
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
scopus_import: '1'
status: public
title: Effect of glaciers on streamflow trends in the Swiss Alps
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 46
year: '2010'
...
---
_id: '9012'
abstract:
- lang: eng
text: In this Letter, we characterize experimentally the diffusiophoretic motion
of colloids and λ-DNA toward higher concentration of solutes, using microfluidic
technology to build spatially and temporally controlled concentration gradients.
We then demonstrate that segregation and spatial patterning of the particles can
be achieved from temporal variations of the solute concentration profile. This
segregation takes the form of a strong trapping potential, stemming from an osmotically
induced rectification mechanism of the solute time-dependent variations. Depending
on the spatial and temporal symmetry of the solute signal, localization patterns
with various shapes can be achieved. These results highlight the role of solute
contrasts in out-of-equilibrium processes occurring in soft matter.
article_number: '138302'
article_processing_charge: No
article_type: letter_note
arxiv: 1
author:
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
- first_name: Benjamin
full_name: Abécassis, Benjamin
last_name: Abécassis
- 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, Abécassis B, Cottin-Bizonne C, Ybert C, Bocquet L. Colloidal motility
and pattern formation under rectified diffusiophoresis. Physical Review Letters.
2010;104(13). doi:10.1103/physrevlett.104.138302
apa: Palacci, J. A., Abécassis, B., Cottin-Bizonne, C., Ybert, C., & Bocquet,
L. (2010). Colloidal motility and pattern formation under rectified diffusiophoresis.
Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.104.138302
chicago: Palacci, Jérémie A, Benjamin Abécassis, Cécile Cottin-Bizonne, Christophe
Ybert, and Lydéric Bocquet. “Colloidal Motility and Pattern Formation under Rectified
Diffusiophoresis.” Physical Review Letters. American Physical Society,
2010. https://doi.org/10.1103/physrevlett.104.138302.
ieee: J. A. Palacci, B. Abécassis, C. Cottin-Bizonne, C. Ybert, and L. Bocquet,
“Colloidal motility and pattern formation under rectified diffusiophoresis,” Physical
Review Letters, vol. 104, no. 13. American Physical Society, 2010.
ista: Palacci JA, Abécassis B, Cottin-Bizonne C, Ybert C, Bocquet L. 2010. Colloidal
motility and pattern formation under rectified diffusiophoresis. Physical Review
Letters. 104(13), 138302.
mla: Palacci, Jérémie A., et al. “Colloidal Motility and Pattern Formation under
Rectified Diffusiophoresis.” Physical Review Letters, vol. 104, no. 13,
138302, American Physical Society, 2010, doi:10.1103/physrevlett.104.138302.
short: J.A. Palacci, B. Abécassis, C. Cottin-Bizonne, C. Ybert, L. Bocquet, Physical
Review Letters 104 (2010).
date_created: 2021-01-19T10:25:04Z
date_published: 2010-04-02T00:00:00Z
date_updated: 2023-02-23T13:46:40Z
day: '02'
doi: 10.1103/physrevlett.104.138302
extern: '1'
external_id:
arxiv:
- '1004.1256 '
pmid:
- '20481918'
intvolume: ' 104'
issue: '13'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1004.1256
month: '04'
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: Colloidal motility and pattern formation under rectified diffusiophoresis
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 104
year: '2010'
...
---
_id: '9013'
abstract:
- lang: eng
text: In this Letter, we investigate experimentally the nonequilibrium steady state
of an active colloidal suspension under gravity field. The active particles are
made of chemically powered colloids, showing self propulsion in the presence of
an added fuel, here hydrogen peroxide. The active suspension is studied in a dedicated
microfluidic device, made of permeable gel microstructures. Both the microdynamics
of individual colloids and the global stationary state of the suspension under
gravity are measured with optical microscopy. This yields a direct measurement
of the effective temperature of the active system as a function of the particle
activity, on the basis of the fluctuation-dissipation relationship. Our work is
a first step in the experimental exploration of the out-of-equilibrium properties
of active colloidal systems.
article_number: '088304'
article_processing_charge: No
article_type: letter_note
arxiv: 1
author:
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
- first_name: Cécile
full_name: Cottin-Bizonne, Cécile
last_name: Cottin-Bizonne
- first_name: Christophe
full_name: Ybert, Christophe
last_name: Ybert
- first_name: Lydéric
full_name: Bocquet, Lydéric
last_name: Bocquet
citation:
ama: Palacci JA, Cottin-Bizonne C, Ybert C, Bocquet L. Sedimentation and effective
temperature of active colloidal suspensions. Physical Review Letters. 2010;105(8).
doi:10.1103/physrevlett.105.088304
apa: Palacci, J. A., Cottin-Bizonne, C., Ybert, C., & Bocquet, L. (2010). Sedimentation
and effective temperature of active colloidal suspensions. Physical Review
Letters. American Physical Society . https://doi.org/10.1103/physrevlett.105.088304
chicago: Palacci, Jérémie A, Cécile Cottin-Bizonne, Christophe Ybert, and Lydéric
Bocquet. “Sedimentation and Effective Temperature of Active Colloidal Suspensions.”
Physical Review Letters. American Physical Society , 2010. https://doi.org/10.1103/physrevlett.105.088304.
ieee: J. A. Palacci, C. Cottin-Bizonne, C. Ybert, and L. Bocquet, “Sedimentation
and effective temperature of active colloidal suspensions,” Physical Review
Letters, vol. 105, no. 8. American Physical Society , 2010.
ista: Palacci JA, Cottin-Bizonne C, Ybert C, Bocquet L. 2010. Sedimentation and
effective temperature of active colloidal suspensions. Physical Review Letters.
105(8), 088304.
mla: Palacci, Jérémie A., et al. “Sedimentation and Effective Temperature of Active
Colloidal Suspensions.” Physical Review Letters, vol. 105, no. 8, 088304,
American Physical Society , 2010, doi:10.1103/physrevlett.105.088304.
short: J.A. Palacci, C. Cottin-Bizonne, C. Ybert, L. Bocquet, Physical Review Letters
105 (2010).
date_created: 2021-01-19T10:26:33Z
date_published: 2010-08-20T00:00:00Z
date_updated: 2023-02-23T13:46:42Z
day: '20'
doi: 10.1103/physrevlett.105.088304
extern: '1'
external_id:
arxiv:
- '1004.4340'
pmid:
- '20868136'
intvolume: ' 105'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1004.4340
month: '08'
oa: 1
oa_version: Preprint
pmid: 1
publication: Physical Review Letters
publication_identifier:
eissn:
- '10797114'
issn:
- '00319007'
publication_status: published
publisher: 'American Physical Society '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sedimentation and effective temperature of active colloidal suspensions
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 105
year: '2010'
...
---
_id: '9146'
abstract:
- lang: eng
text: "The factors governing the rate of change in the amount of atmospheric water
vapor are analyzed in simulations of climate change. The global-mean amount of
water vapor is estimated to increase at a differential rate of 7.3% K − 1 with
respect to global-mean surface air temperature in the multi-model mean. Larger
rates of change result if the fractional change is evaluated over a finite change
in temperature (e.g., 8.2% K − 1 for a 3 K warming), and rates of change of zonal-mean
column water vapor range from 6 to 12% K − 1 depending on latitude.\r\nClausius–Clapeyron
scaling is directly evaluated using an invariant distribution of monthly-mean
relative humidity, giving a rate of 7.4% K − 1 for global-mean water vapor. There
are deviations from Clausius–Clapeyron scaling of zonal-mean column water vapor
in the tropics and mid-latitudes, but they largely cancel in the global mean.
A purely thermodynamic scaling based on a saturated troposphere gives a higher
global rate of 7.9% K − 1.\r\nSurface specific humidity increases at a rate of
5.7% K − 1, considerably lower than the rate for global-mean water vapor. Surface
specific humidity closely follows Clausius–Clapeyron scaling over ocean. But there
are widespread decreases in surface relative humidity over land (by more than
1% K − 1 in many regions), and it is argued that decreases of this magnitude could
result from the land/ocean contrast in surface warming."
article_number: '025207'
article_processing_charge: No
article_type: original
author:
- first_name: P A
full_name: O’Gorman, P A
last_name: O’Gorman
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
citation:
ama: O’Gorman PA, Muller CJ. How closely do changes in surface and column water
vapor follow Clausius–Clapeyron scaling in climate change simulations? Environmental
Research Letters. 2010;5(2). doi:10.1088/1748-9326/5/2/025207
apa: O’Gorman, P. A., & Muller, C. J. (2010). How closely do changes in surface
and column water vapor follow Clausius–Clapeyron scaling in climate change simulations?
Environmental Research Letters. IOP Publishing. https://doi.org/10.1088/1748-9326/5/2/025207
chicago: O’Gorman, P A, and Caroline J Muller. “How Closely Do Changes in Surface
and Column Water Vapor Follow Clausius–Clapeyron Scaling in Climate Change Simulations?”
Environmental Research Letters. IOP Publishing, 2010. https://doi.org/10.1088/1748-9326/5/2/025207.
ieee: P. A. O’Gorman and C. J. Muller, “How closely do changes in surface and column
water vapor follow Clausius–Clapeyron scaling in climate change simulations?,”
Environmental Research Letters, vol. 5, no. 2. IOP Publishing, 2010.
ista: O’Gorman PA, Muller CJ. 2010. How closely do changes in surface and column
water vapor follow Clausius–Clapeyron scaling in climate change simulations? Environmental
Research Letters. 5(2), 025207.
mla: O’Gorman, P. A., and Caroline J. Muller. “How Closely Do Changes in Surface
and Column Water Vapor Follow Clausius–Clapeyron Scaling in Climate Change Simulations?”
Environmental Research Letters, vol. 5, no. 2, 025207, IOP Publishing,
2010, doi:10.1088/1748-9326/5/2/025207.
short: P.A. O’Gorman, C.J. Muller, Environmental Research Letters 5 (2010).
date_created: 2021-02-15T14:40:46Z
date_published: 2010-04-09T00:00:00Z
date_updated: 2022-01-24T13:51:02Z
day: '09'
doi: 10.1088/1748-9326/5/2/025207
extern: '1'
intvolume: ' 5'
issue: '2'
keyword:
- Renewable Energy
- Sustainability and the Environment
- Public Health
- Environmental and Occupational Health
- General Environmental Science
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1088/1748-9326/5/2/025207
month: '04'
oa: 1
oa_version: Published Version
publication: Environmental Research Letters
publication_identifier:
issn:
- 1748-9326
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
status: public
title: How closely do changes in surface and column water vapor follow Clausius–Clapeyron
scaling in climate change simulations?
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 5
year: '2010'
...
---
_id: '7078'
abstract:
- lang: eng
text: We report resonant ultrasound spectroscopy (RUS), dilatometry/magnetostriction,
magnetotransport, magnetization, specific-heat, and 119Sn Mössbauer spectroscopy
measurements on SnTe and Sn0.995Cr0.005Te. Hall measurements at T=77 K indicate
that our Bridgman-grown single crystals have a p-type carrier concentration of
3.4×1019 cm−3 and that our Cr-doped crystals have an n-type concentration of 5.8×1022 cm−3.
Although our SnTe crystals are diamagnetic over the temperature range 2≤T≤1100 K,
the Cr-doped crystals are room-temperature ferromagnets with a Curie temperature
of 294 K. For each sample type, three-terminal capacitive dilatometry measurements
detect a subtle 0.5 μm distortion at Tc≈85 K. Whereas our RUS measurements on
SnTe show elastic hardening near the structural transition, pointing to co-elastic
behavior, similar measurements on Sn0.995Cr0.005Te show a pronounced softening,
pointing to ferroelastic behavior. Effective Debye temperature, θD, values of
SnTe obtained from 119Sn Mössbauer studies show a hardening of phonons in the
range 60–115 K (θD=162 K) as compared with the 100–300 K range (θD=150 K). In
addition, a precursor softening extending over approximately 100 K anticipates
this collapse at the critical temperature and quantitative analysis over three
decades of its reduced modulus finds ΔC44/C44=A|(T−T0)/T0|−κ with κ=0.50±0.02,
a value indicating a three-dimensional softening of phonon branches at a temperature
T0∼75 K, considerably below Tc. We suggest that the differences in these two types
of elastic behaviors lie in the absence of elastic domain-wall motion in the one
case and their nucleation in the other.
article_number: '184112'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: E. K. H.
full_name: Salje, E. K. H.
last_name: Salje
- first_name: D. J.
full_name: Safarik, D. J.
last_name: Safarik
- first_name: Kimberly A
full_name: Modic, Kimberly A
id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425
last_name: Modic
orcid: 0000-0001-9760-3147
- first_name: J. E.
full_name: Gubernatis, J. E.
last_name: Gubernatis
- first_name: J. C.
full_name: Cooley, J. C.
last_name: Cooley
- first_name: R. D.
full_name: Taylor, R. D.
last_name: Taylor
- first_name: B.
full_name: Mihaila, B.
last_name: Mihaila
- first_name: A.
full_name: Saxena, A.
last_name: Saxena
- first_name: T.
full_name: Lookman, T.
last_name: Lookman
- first_name: J. L.
full_name: Smith, J. L.
last_name: Smith
- first_name: R. A.
full_name: Fisher, R. A.
last_name: Fisher
- first_name: M.
full_name: Pasternak, M.
last_name: Pasternak
- first_name: C. P.
full_name: Opeil, C. P.
last_name: Opeil
- first_name: T.
full_name: Siegrist, T.
last_name: Siegrist
- first_name: P. B.
full_name: Littlewood, P. B.
last_name: Littlewood
- first_name: J. C.
full_name: Lashley, J. C.
last_name: Lashley
citation:
ama: 'Salje EKH, Safarik DJ, Modic KA, et al. Tin telluride: A weakly co-elastic
metal. Physical Review B. 2010;82(18). doi:10.1103/physrevb.82.184112'
apa: 'Salje, E. K. H., Safarik, D. J., Modic, K. A., Gubernatis, J. E., Cooley,
J. C., Taylor, R. D., … Lashley, J. C. (2010). Tin telluride: A weakly co-elastic
metal. Physical Review B. APS. https://doi.org/10.1103/physrevb.82.184112'
chicago: 'Salje, E. K. H., D. J. Safarik, Kimberly A Modic, J. E. Gubernatis, J.
C. Cooley, R. D. Taylor, B. Mihaila, et al. “Tin Telluride: A Weakly Co-Elastic
Metal.” Physical Review B. APS, 2010. https://doi.org/10.1103/physrevb.82.184112.'
ieee: 'E. K. H. Salje et al., “Tin telluride: A weakly co-elastic metal,”
Physical Review B, vol. 82, no. 18. APS, 2010.'
ista: 'Salje EKH, Safarik DJ, Modic KA, Gubernatis JE, Cooley JC, Taylor RD, Mihaila
B, Saxena A, Lookman T, Smith JL, Fisher RA, Pasternak M, Opeil CP, Siegrist T,
Littlewood PB, Lashley JC. 2010. Tin telluride: A weakly co-elastic metal. Physical
Review B. 82(18), 184112.'
mla: 'Salje, E. K. H., et al. “Tin Telluride: A Weakly Co-Elastic Metal.” Physical
Review B, vol. 82, no. 18, 184112, APS, 2010, doi:10.1103/physrevb.82.184112.'
short: E.K.H. Salje, D.J. Safarik, K.A. Modic, J.E. Gubernatis, J.C. Cooley, R.D.
Taylor, B. Mihaila, A. Saxena, T. Lookman, J.L. Smith, R.A. Fisher, M. Pasternak,
C.P. Opeil, T. Siegrist, P.B. Littlewood, J.C. Lashley, Physical Review B 82 (2010).
date_created: 2019-11-19T13:46:28Z
date_published: 2010-11-18T00:00:00Z
date_updated: 2021-01-12T08:11:44Z
day: '18'
doi: 10.1103/physrevb.82.184112
extern: '1'
external_id:
arxiv:
- '1011.1445'
intvolume: ' 82'
issue: '18'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1011.1445
month: '11'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
issn:
- 1098-0121
- 1550-235X
publication_status: published
publisher: APS
quality_controlled: '1'
status: public
title: 'Tin telluride: A weakly co-elastic metal'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 82
year: '2010'
...