---
_id: '3721'
abstract:
- lang: eng
text: Recent advances in atomic force microscopy allowed globular and membrane proteins
to be mechanically unfolded on a single-molecule level. Presented is an extension
to the existing force spectroscopy experiments. While unfolding single bacteriorhodopsins
from native purple membranes, small oscillation amplitudes (6–9nm) were supplied
to the vertical displacement of the cantilever at a frequency of 3kHz. The phase
and amplitude response of the cantilever-protein system was converted to reveal
the elastic (conservative) and viscous (dissipative) contributions to the unfolding
process. The elastic response (stiffness) of the extended parts of the protein
were in the range of a few tens pN/nm and could be well described by the derivative
of the wormlike chain model. Discrete events in the viscous response coincided
with the unfolding of single secondary structure elements and were in the range
of 1μNs/m. In addition, these force modulation spectroscopy experiments revealed
novel mechanical unfolding intermediates of bacteriorhodopsin. We found that kinks
result in a loss of unfolding cooperativity in transmembrane helices. Reconstructing
force-distance spectra by the integration of amplitude-distance spectra verified
their position, offering a novel approach to detect intermediates during the forced
unfolding of single proteins.
author:
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
- first_name: Andrew
full_name: Humphris, Andrew D
last_name: Humphris
citation:
ama: Janovjak HL, Mueller D, Humphris A. Molecular force modulation spectroscopy
revealing the dynamic response of single bacteriorhodopsins. Biophysical Journal.
2005;88(2):1423-1431. doi:10.1529/biophysj.104.052746
apa: Janovjak, H. L., Mueller, D., & Humphris, A. (2005). Molecular force modulation
spectroscopy revealing the dynamic response of single bacteriorhodopsins. Biophysical
Journal. Biophysical Society. https://doi.org/10.1529/biophysj.104.052746
chicago: Janovjak, Harald L, Daniel Mueller, and Andrew Humphris. “Molecular Force
Modulation Spectroscopy Revealing the Dynamic Response of Single Bacteriorhodopsins.”
Biophysical Journal. Biophysical Society, 2005. https://doi.org/10.1529/biophysj.104.052746.
ieee: H. L. Janovjak, D. Mueller, and A. Humphris, “Molecular force modulation spectroscopy
revealing the dynamic response of single bacteriorhodopsins,” Biophysical Journal,
vol. 88, no. 2. Biophysical Society, pp. 1423–1431, 2005.
ista: Janovjak HL, Mueller D, Humphris A. 2005. Molecular force modulation spectroscopy
revealing the dynamic response of single bacteriorhodopsins. Biophysical Journal.
88(2), 1423–1431.
mla: Janovjak, Harald L., et al. “Molecular Force Modulation Spectroscopy Revealing
the Dynamic Response of Single Bacteriorhodopsins.” Biophysical Journal,
vol. 88, no. 2, Biophysical Society, 2005, pp. 1423–31, doi:10.1529/biophysj.104.052746.
short: H.L. Janovjak, D. Mueller, A. Humphris, Biophysical Journal 88 (2005) 1423–1431.
date_created: 2018-12-11T12:04:48Z
date_published: 2005-02-01T00:00:00Z
date_updated: 2021-01-12T07:51:43Z
day: '01'
doi: 10.1529/biophysj.104.052746
extern: 1
fulldoi: https://doi.org/10.1529/biophysj.104.052746
intvolume: ' 88'
issue: '2'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1305144/
month: '02'
oa: 1
page: 1423 - 1431
publication: Biophysical Journal
publication_status: published
publisher: Biophysical Society
publist_id: '2509'
quality_controlled: 0
status: public
title: Molecular force modulation spectroscopy revealing the dynamic response of single
bacteriorhodopsins
type: journal_article
volume: 88
year: '2005'
...
---
_id: '3741'
abstract:
- lang: eng
text: In an age of increasingly large data sets, investigators in many different
disciplines have turned to clustering as a tool for data analysis and exploration.
Existing clustering methods, however, typically depend on several nontrivial assumptions
about the structure of data. Here, we reformulate the clustering problem from
an information theoretic perspective that avoids many of these assumptions. In
particular, our formulation obviates the need for defining a cluster "prototype,"
does not require an a priori similarity metric, is invariant to changes in the
representation of the data, and naturally captures nonlinear relations. We apply
this approach to different domains and find that it consistently produces clusters
that are more coherent than those extracted by existing algorithms. Finally, our
approach provides a way of clustering based on collective notions of similarity
rather than the traditional pairwise measures.
author:
- first_name: N.
full_name: Slonim,N.
last_name: Slonim
- first_name: G.
full_name: Atwal,G.
last_name: Atwal
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: William
full_name: Bialek, William S
last_name: Bialek
citation:
ama: Slonim N, Atwal G, Tkačik G, Bialek W. Information-based clustering. PNAS.
2005;102(51):18297-18302. doi:10.1073/pnas.0507432102
apa: Slonim, N., Atwal, G., Tkačik, G., & Bialek, W. (2005). Information-based
clustering. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.0507432102
chicago: Slonim, N., G. Atwal, Gašper Tkačik, and William Bialek. “Information-Based
Clustering.” PNAS. National Academy of Sciences, 2005. https://doi.org/10.1073/pnas.0507432102.
ieee: N. Slonim, G. Atwal, G. Tkačik, and W. Bialek, “Information-based clustering,”
PNAS, vol. 102, no. 51. National Academy of Sciences, pp. 18297–18302,
2005.
ista: Slonim N, Atwal G, Tkačik G, Bialek W. 2005. Information-based clustering.
PNAS. 102(51), 18297–18302.
mla: Slonim, N., et al. “Information-Based Clustering.” PNAS, vol. 102, no.
51, National Academy of Sciences, 2005, pp. 18297–302, doi:10.1073/pnas.0507432102.
short: N. Slonim, G. Atwal, G. Tkačik, W. Bialek, PNAS 102 (2005) 18297–18302.
date_created: 2018-12-11T12:04:55Z
date_published: 2005-12-20T00:00:00Z
date_updated: 2021-01-12T07:51:52Z
day: '20'
doi: 10.1073/pnas.0507432102
extern: 1
fulldoi: https://doi.org/10.1073/pnas.0507432102
intvolume: ' 102'
issue: '51'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1317937
month: '12'
oa: 1
page: 18297 - 18302
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '2490'
quality_controlled: 0
status: public
title: Information-based clustering
type: journal_article
volume: 102
year: '2005'
...
---
_id: '3746'
abstract:
- lang: eng
text: We address the practical problems of estimating the information relations
that characterize large networks. Building on methods developed for analysis of
the neural code, we show that reliable estimates of mutual information can be
obtained with manageable computational effort. The same methods allow estimation
of higher order, multi-information terms. These ideas are illustrated by analyses
of gene expression, financial markets, and consumer preferences. In each case,
information theoretic measures correlate with independent, intuitive measures
of the underlying structures in the system.
author:
- first_name: Noam
full_name: Slonim,Noam
last_name: Slonim
- first_name: Gurinder
full_name: Atwal,Gurinder S
last_name: Atwal
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: William
full_name: Bialek, William S
last_name: Bialek
citation:
ama: Slonim N, Atwal G, Tkačik G, Bialek W. Estimating mutual information and multi-information
in large networks. ArXiv. 2005:1-11.
apa: Slonim, N., Atwal, G., Tkačik, G., & Bialek, W. (2005). Estimating mutual
information and multi-information in large networks. ArXiv. ArXiv.
chicago: Slonim, Noam, Gurinder Atwal, Gašper Tkačik, and William Bialek. “Estimating
Mutual Information and Multi-Information in Large Networks.” ArXiv. ArXiv,
2005.
ieee: N. Slonim, G. Atwal, G. Tkačik, and W. Bialek, “Estimating mutual information
and multi-information in large networks,” ArXiv. ArXiv, pp. 1–11, 2005.
ista: Slonim N, Atwal G, Tkačik G, Bialek W. 2005. Estimating mutual information
and multi-information in large networks. ArXiv, 1–11, .
mla: Slonim, Noam, et al. “Estimating Mutual Information and Multi-Information in
Large Networks.” ArXiv, ArXiv, 2005, pp. 1–11.
short: N. Slonim, G. Atwal, G. Tkačik, W. Bialek, ArXiv (2005) 1–11.
date_created: 2018-12-11T12:04:56Z
date_published: 2005-02-03T00:00:00Z
date_updated: 2021-01-12T07:51:54Z
day: '03'
extern: 1
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/cs/0502017v1
month: '02'
oa: 1
page: 1 - 11
publication: ArXiv
publication_status: published
publisher: ArXiv
publist_id: '2484'
quality_controlled: 0
status: public
title: Estimating mutual information and multi-information in large networks
type: preprint
year: '2005'
...
---
_id: '3753'
abstract:
- lang: eng
text: Characterizing the dynamics of specific RNA levels requires real-time RNA
profiling in a single cell. We show that the combination of a synthetic modular
genetic system with fluorescence correlation spectroscopy allows us to directly
measure in real time the activity of any specific promoter in prokaryotes. Using
a simple inducible gene expression system, we found that induced RNA levels within
a single bacterium of Escherichia coli exhibited a pulsating profile in response
to a steady input of inducer. The genetic deletion of an efflux pump system, a
key determinant of antibiotic resistance, altered the pulsating transcriptional
dynamics and caused overexpression of induced RNA. In contrast with population
measurements, real-time RNA profiling permits identifying relationships between
genotypes and transcriptional dynamics that are accessible only at the level of
the single cell.
acknowledgement: '4237'
author:
- first_name: Thuc
full_name: Le,Thuc T.
last_name: Le
- first_name: Sébastien
full_name: Harlepp, Sébastien
last_name: Harlepp
- first_name: Calin C
full_name: Calin Guet
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Kimberly
full_name: Dittmar,Kimberly
last_name: Dittmar
- first_name: Thierry
full_name: Emonet,Thierry
last_name: Emonet
- first_name: Tao
full_name: Pan,Tao
last_name: Pan
- first_name: Philippe
full_name: Cluzel,Philippe
last_name: Cluzel
citation:
ama: Le T, Harlepp S, Guet CC, et al. Real-time RNA profiling within a single bacterium.
PNAS. 2005;102(26):9160-9164. doi:10.1073/pnas.0503311102
apa: Le, T., Harlepp, S., Guet, C. C., Dittmar, K., Emonet, T., Pan, T., & Cluzel,
P. (2005). Real-time RNA profiling within a single bacterium. PNAS. National
Academy of Sciences. https://doi.org/10.1073/pnas.0503311102
chicago: Le, Thuc, Sébastien Harlepp, Calin C Guet, Kimberly Dittmar, Thierry Emonet,
Tao Pan, and Philippe Cluzel. “Real-Time RNA Profiling within a Single Bacterium.”
PNAS. National Academy of Sciences, 2005. https://doi.org/10.1073/pnas.0503311102.
ieee: T. Le et al., “Real-time RNA profiling within a single bacterium,”
PNAS, vol. 102, no. 26. National Academy of Sciences, pp. 9160–9164, 2005.
ista: Le T, Harlepp S, Guet CC, Dittmar K, Emonet T, Pan T, Cluzel P. 2005. Real-time
RNA profiling within a single bacterium. PNAS. 102(26), 9160–9164.
mla: Le, Thuc, et al. “Real-Time RNA Profiling within a Single Bacterium.” PNAS,
vol. 102, no. 26, National Academy of Sciences, 2005, pp. 9160–64, doi:10.1073/pnas.0503311102.
short: T. Le, S. Harlepp, C.C. Guet, K. Dittmar, T. Emonet, T. Pan, P. Cluzel, PNAS
102 (2005) 9160–9164.
date_created: 2018-12-11T12:04:59Z
date_published: 2005-01-01T00:00:00Z
date_updated: 2021-01-12T07:51:57Z
day: '01'
doi: 10.1073/pnas.0503311102
extern: 1
fulldoi: https://doi.org/10.1073/pnas.0503311102
intvolume: ' 102'
issue: '26'
month: '01'
page: 9160 - 9164
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '2476'
quality_controlled: 0
status: public
title: Real-time RNA profiling within a single bacterium
type: journal_article
volume: 102
year: '2005'
...
---
_id: '3763'
abstract:
- lang: eng
text: The generation of realistic motion satisfying user-defined requirements is
one of the most important goals of computer animation. Our aim in this paper is
the synthesis of realistic, controllable motion for lightweight natural objects
in a gaseous medium. We formulate this problem as a large-scale spacetime optimization
with user controls and fluid motion equations as constraints. We have devised
novel and effective methods to make this large optimization tractable. Initial
trajectories are generated with data-driven synthesis based on stylistic motion
planning. Smoothed particle hydrodynamics (SPH) is used during optimization to
produce fluid simulations at a reasonable computational cost, while interesting
vortex-based fluid motion is generated by recording the presence of vortices in
the initial trajectories and maintaining them through optimization. Object rotations
are refined as a postprocess to enhance the visual quality of the results. We
demonstrate our techniques on a number of animations involving single or multiple
objects.
article_processing_charge: No
author:
- first_name: Lin
full_name: Shi, Lin
last_name: Shi
- first_name: Yizhou
full_name: Yu, Yizhou
last_name: Yu
- 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: Stephen
full_name: Chenney, Stephen
last_name: Chenney
citation:
ama: Shi L, Yu Y, Wojtan C, Chenney S. Controllable motion synthesis in a gaseous
medium. The Visual Computer. 2005;21(7):474-487. doi:10.1007/s00371-005-0296-0
apa: Shi, L., Yu, Y., Wojtan, C., & Chenney, S. (2005). Controllable motion
synthesis in a gaseous medium. The Visual Computer. Springer. https://doi.org/10.1007/s00371-005-0296-0
chicago: Shi, Lin, Yizhou Yu, Chris Wojtan, and Stephen Chenney. “Controllable Motion
Synthesis in a Gaseous Medium.” The Visual Computer. Springer, 2005. https://doi.org/10.1007/s00371-005-0296-0.
ieee: L. Shi, Y. Yu, C. Wojtan, and S. Chenney, “Controllable motion synthesis in
a gaseous medium,” The Visual Computer, vol. 21, no. 7. Springer, pp. 474–487,
2005.
ista: Shi L, Yu Y, Wojtan C, Chenney S. 2005. Controllable motion synthesis in a
gaseous medium. The Visual Computer. 21(7), 474–487.
mla: Shi, Lin, et al. “Controllable Motion Synthesis in a Gaseous Medium.” The
Visual Computer, vol. 21, no. 7, Springer, 2005, pp. 474–87, doi:10.1007/s00371-005-0296-0.
short: L. Shi, Y. Yu, C. Wojtan, S. Chenney, The Visual Computer 21 (2005) 474–487.
date_created: 2018-12-11T12:05:02Z
date_published: 2005-08-01T00:00:00Z
date_updated: 2023-02-23T11:41:36Z
day: '01'
doi: 10.1007/s00371-005-0296-0
extern: '1'
fulldoi: https://doi.org/10.1007/s00371-005-0296-0
intvolume: ' 21'
issue: '7'
language:
- iso: eng
month: '08'
oa_version: None
page: 474 - 487
publication: The Visual Computer
publication_status: published
publisher: Springer
publist_id: '2465'
status: public
title: Controllable motion synthesis in a gaseous medium
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2005'
...
---
_id: '3808'
abstract:
- lang: eng
text: Action potentials in central neurons are initiated near the axon initial segment,
propagate into the axon, and finally invade the presynaptic terminals, where they
trigger transmitter release. Voltage-gated Na(+) channels are key determinants
of excitability, but Na(+) channel density and properties in axons and presynaptic
terminals of cortical neurons have not been examined yet. In hippocampal mossy
fiber boutons, which emerge from parent axons en passant, Na(+) channels are very
abundant, with an estimated number of approximately 2000 channels per bouton.
Presynaptic Na(+) channels show faster inactivation kinetics than somatic channels,
suggesting differences between subcellular compartments of the same cell. Computational
analysis of action potential propagation in axon-multibouton structures reveals
that Na(+) channels in boutons preferentially amplify the presynaptic action potential
and enhance Ca(2+) inflow, whereas Na(+) channels in axons control the reliability
and speed of propagation. Thus, presynaptic and axonal Na(+) channels contribute
differentially to mossy fiber synaptic transmission.
author:
- first_name: Dominique
full_name: Engel, Dominique
last_name: Engel
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Engel D, Jonas PM. Presynaptic action potential amplification by voltage-gated
Na+ channels in hippocampal mossy fiber boutons. Neuron. 2005;45(3):405-417.
doi:10.1016/j.neuron.2004.12.048
apa: Engel, D., & Jonas, P. M. (2005). Presynaptic action potential amplification
by voltage-gated Na+ channels in hippocampal mossy fiber boutons. Neuron.
Elsevier. https://doi.org/10.1016/j.neuron.2004.12.048
chicago: Engel, Dominique, and Peter M Jonas. “Presynaptic Action Potential Amplification
by Voltage-Gated Na+ Channels in Hippocampal Mossy Fiber Boutons.” Neuron.
Elsevier, 2005. https://doi.org/10.1016/j.neuron.2004.12.048
.
ieee: D. Engel and P. M. Jonas, “Presynaptic action potential amplification by voltage-gated
Na+ channels in hippocampal mossy fiber boutons,” Neuron, vol. 45, no.
3. Elsevier, pp. 405–17, 2005.
ista: Engel D, Jonas PM. 2005. Presynaptic action potential amplification by voltage-gated
Na+ channels in hippocampal mossy fiber boutons. Neuron. 45(3), 405–17.
mla: Engel, Dominique, and Peter M. Jonas. “Presynaptic Action Potential Amplification
by Voltage-Gated Na+ Channels in Hippocampal Mossy Fiber Boutons.” Neuron,
vol. 45, no. 3, Elsevier, 2005, pp. 405–17, doi:10.1016/j.neuron.2004.12.048 .
short: D. Engel, P.M. Jonas, Neuron 45 (2005) 405–17.
date_created: 2018-12-11T12:05:17Z
date_published: 2005-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:21Z
day: '01'
doi: '10.1016/j.neuron.2004.12.048 '
extern: 1
fulldoi: 'https://doi.org/10.1016/j.neuron.2004.12.048 '
intvolume: ' 45'
issue: '3'
month: '01'
page: 405 - 17
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '2400'
quality_controlled: 0
status: public
title: Presynaptic action potential amplification by voltage-gated Na+ channels in
hippocampal mossy fiber boutons
type: journal_article
volume: 45
year: '2005'
...
---
_id: '3812'
abstract:
- lang: eng
text: Hippocampal GABAergic interneurons show diverse molecular and morphological
properties. The functional significance of this diversity for information processing
is poorly understood. Here we show that cholecystokinin (CCK)-expressing interneurons
in rat dentate gyrus release GABA in a highly asynchronous manner, in contrast
to parvalbumin (PV) interneurons. With a gamma-frequency burst of ten action potentials,
the ratio of asynchronous to synchronous release is 3:1 in CCK interneurons but
is 1:5 in parvalbumin interneurons. N-type channels trigger synchronous and asynchronous
release in CCK interneuron synapses, whereas P/Q-type Ca(2+) channels mediate
release at PV interneuron synapses. Effects of Ca(2+) chelators suggest that both
a long-lasting presynaptic Ca(2+) transient and a large distance between Ca(2+)
source and sensor of exocytosis contribute to the higher ratio of asynchronous
to synchronous release in CCK interneuron synapses. Asynchronous release occurs
at physiological temperature and with behaviorally relevant stimulation patterns,
thus generating long-lasting inhibition in the brain.
author:
- first_name: Stefan
full_name: Hefft, Stefan
last_name: Hefft
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Hefft S, Jonas PM. Asynchronous GABA release generates long-lasting inhibition
at a hippocampal interneuron-principal neuron synapse (Review). Nature Neuroscience.
2005;8(10):1319-1328. doi:10.1038/nn1542
apa: Hefft, S., & Jonas, P. M. (2005). Asynchronous GABA release generates long-lasting
inhibition at a hippocampal interneuron-principal neuron synapse (Review). Nature
Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn1542
chicago: Hefft, Stefan, and Peter M Jonas. “Asynchronous GABA Release Generates
Long-Lasting Inhibition at a Hippocampal Interneuron-Principal Neuron Synapse
(Review).” Nature Neuroscience. Nature Publishing Group, 2005. https://doi.org/10.1038/nn1542.
ieee: S. Hefft and P. M. Jonas, “Asynchronous GABA release generates long-lasting
inhibition at a hippocampal interneuron-principal neuron synapse (Review),” Nature
Neuroscience, vol. 8, no. 10. Nature Publishing Group, pp. 1319–28, 2005.
ista: Hefft S, Jonas PM. 2005. Asynchronous GABA release generates long-lasting
inhibition at a hippocampal interneuron-principal neuron synapse (Review). Nature
Neuroscience. 8(10), 1319–28.
mla: Hefft, Stefan, and Peter M. Jonas. “Asynchronous GABA Release Generates Long-Lasting
Inhibition at a Hippocampal Interneuron-Principal Neuron Synapse (Review).” Nature
Neuroscience, vol. 8, no. 10, Nature Publishing Group, 2005, pp. 1319–28,
doi:10.1038/nn1542.
short: S. Hefft, P.M. Jonas, Nature Neuroscience 8 (2005) 1319–28.
date_created: 2018-12-11T12:05:18Z
date_published: 2005-01-01T00:00:00Z
date_updated: 2019-04-26T07:22:35Z
day: '01'
doi: 10.1038/nn1542
extern: 1
fulldoi: https://doi.org/10.1038/nn1542
intvolume: ' 8'
issue: '10'
month: '01'
page: 1319 - 28
publication: Nature Neuroscience
publication_status: published
publisher: Nature Publishing Group
publist_id: '2399'
quality_controlled: 0
status: public
title: Asynchronous GABA release generates long-lasting inhibition at a hippocampal
interneuron-principal neuron synapse (Review)
type: review
volume: 8
year: '2005'
...
---
_id: '3892'
abstract:
- lang: eng
text: 'In 2-player non-zero-sum games, Nash equilibria capture the options for rational
behavior if each player attempts to maximize her payoff. In contrast to classical
game theory, we consider lexicographic objectives: first, each player tries to
maximize her own payoff, and then, the player tries to minimize the opponent''s
payoff. Such objectives arise naturally in the verification of systems with multiple
components. There, instead of proving that each component satisfies its specification
no matter how the other components behave, it often suffices to prove that each
component satisfies its specification provided that the other components satisfy
their specifications. We say that a Nash equilibrium is secure if it is an equilibrium
with respect to the lexicographic objectives of both players. We prove that in
graph games with Borel winning conditions, which include the games that arise
in verification, there may be several Nash equilibria, but there is always a unique
maximal payoff profile of a secure equilibrium. We show how this equilibrium can
be computed in the case of omega-regular winning conditions, and we characterize
the memory requirements of strategies that achieve the equilibrium.'
acknowledgement: |-
This research was supported in part by the ONR grant N00014-02-1-0671, the AFOSR MURI grant F49620-00-1-0327, and the NSF grant CCR-0225610.
This is an extended version of the paper “Games with Secure Equilibria” that appeared in the proceedings of Logic in Computer Science (LICS), 2004.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Marcin
full_name: Jurdziński, Marcin
last_name: Jurdziński
citation:
ama: 'Chatterjee K, Henzinger TA, Jurdziński M. Games with secure equilibria. In:
Vol 3657. Springer; 2005:141-161. doi:10.1007/11561163_7'
apa: 'Chatterjee, K., Henzinger, T. A., & Jurdziński, M. (2005). Games with
secure equilibria (Vol. 3657, pp. 141–161). Presented at the FMCO: Formal Methods
for Components and Objects, Springer. https://doi.org/10.1007/11561163_7'
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Marcin Jurdziński. “Games
with Secure Equilibria,” 3657:141–61. Springer, 2005. https://doi.org/10.1007/11561163_7.
ieee: 'K. Chatterjee, T. A. Henzinger, and M. Jurdziński, “Games with secure equilibria,”
presented at the FMCO: Formal Methods for Components and Objects, 2005, vol. 3657,
pp. 141–161.'
ista: 'Chatterjee K, Henzinger TA, Jurdziński M. 2005. Games with secure equilibria.
FMCO: Formal Methods for Components and Objects, LNCS, vol. 3657, 141–161.'
mla: Chatterjee, Krishnendu, et al. Games with Secure Equilibria. Vol. 3657,
Springer, 2005, pp. 141–61, doi:10.1007/11561163_7.
short: K. Chatterjee, T.A. Henzinger, M. Jurdziński, in:, Springer, 2005, pp. 141–161.
conference:
name: 'FMCO: Formal Methods for Components and Objects'
date_created: 2018-12-11T12:05:44Z
date_published: 2005-09-19T00:00:00Z
date_updated: 2021-01-12T07:53:00Z
day: '19'
doi: 10.1007/11561163_7
extern: 1
fulldoi: https://doi.org/10.1007/11561163_7
intvolume: ' 3657'
month: '09'
page: 141 - 161
publication_status: published
publisher: Springer
publist_id: '2269'
quality_controlled: 0
status: public
title: Games with secure equilibria
type: conference
volume: 3657
year: '2005'
...
---
_id: '3893'
abstract:
- lang: eng
text: 'We study infinite stochastic games played by two-players on a finite graph
with goals specified by sets of infinite traces. The games are concurrent (each
player simultaneously and independently chooses an action at each round), stochastic
(the next state is determined by a probability distribution depending on the current
state and the chosen actions), infinite (the game continues for an infinite number
of rounds), nonzero-sum (the players'' goals are not necessarily conflicting),
and undiscounted. We show that if each player has an W-regular objective expressed
as a paxity objective, then there exists an epsilon-Nash equilibrium, for every
epsilon > 0. However, exact Nash equilibria need not exist. We study the complexity
of finding values (payoff profile) of an epsilon-Nash equilibrium. We show that
the values of an epsilon-Nash equilibrium in nonzero-sum concurrent parity games
can be computed by solving the following two simpler problems: computing the values
of zero-sum (the goals of the players axe strictly conflicting) concurrent parity
games and computing epsilon-Nash equilibrium values of nonzero-sum concurrent
games with reachability objectives. As a consequence we establish that values
of an epsilon-Nash equilibrium can be computed in TFNP (total functional NP),
and hence in EXPTIME.'
alternative_title:
- 'LNCS '
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: 'Chatterjee K. Two-player nonzero-sum ω-regular games. In: Vol 3653. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik; 2005:413-427. doi:10.1007/11539452_32'
apa: 'Chatterjee, K. (2005). Two-player nonzero-sum ω-regular games (Vol. 3653,
pp. 413–427). Presented at the CONCUR: Concurrency Theory, Schloss Dagstuhl -
Leibniz-Zentrum für Informatik. https://doi.org/10.1007/11539452_32'
chicago: Chatterjee, Krishnendu. “Two-Player Nonzero-Sum ω-Regular Games,” 3653:413–27.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2005. https://doi.org/10.1007/11539452_32.
ieee: 'K. Chatterjee, “Two-player nonzero-sum ω-regular games,” presented at the
CONCUR: Concurrency Theory, 2005, vol. 3653, pp. 413–427.'
ista: 'Chatterjee K. 2005. Two-player nonzero-sum ω-regular games. CONCUR: Concurrency
Theory, LNCS , vol. 3653, 413–427.'
mla: Chatterjee, Krishnendu. Two-Player Nonzero-Sum ω-Regular Games. Vol.
3653, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2005, pp. 413–27, doi:10.1007/11539452_32.
short: K. Chatterjee, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2005,
pp. 413–427.
conference:
name: 'CONCUR: Concurrency Theory'
date_created: 2018-12-11T12:05:44Z
date_published: 2005-09-05T00:00:00Z
date_updated: 2021-01-12T07:53:00Z
day: '05'
doi: 10.1007/11539452_32
extern: 1
fulldoi: https://doi.org/10.1007/11539452_32
intvolume: ' 3653'
month: '09'
page: 413 - 427
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '2267'
quality_controlled: 0
status: public
title: Two-player nonzero-sum ω-regular games
type: conference
volume: 3653
year: '2005'
...
---
_id: '3896'
abstract:
- lang: eng
text: Temporal Logic Model Checking is one of the most potent tools for the verification
of finite state systems. Computation Tree Logic (CTL) has gained popularity because
unlike most other logics, CTL model checking of a single transition system can
be achieved in polynomial time. However, in most real-life problems, specially
in distributed and parallel systems, the system consist of a set of concurrent
processes and the verification problem translates to model check the composition
of the component processes. Since explicit composition leads to state explosion,
verifying the system without actually composing the components is attractive,
even for possibly restrictive class of systems. We show that the problem of compositional
CTL model checking is PSPACE complete for the class of systems composed of components
that are tree-like transition structure and do not interact among themselves.
For the simplest forms of existential and universal CTL formulas model checking
turns out to be NP complete and coNP complete, respectively. The results hold
for both synchronous and asynchronous composition.
acknowledgement: Pallab Dasgupta and P.P.Chakrabarti thank the Dept. of Science &
Tech., Govt. of India, for partial support of this work
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Pallab
full_name: Dasgupta, Pallab
last_name: Dasgupta
- first_name: Partha
full_name: Chakrabarti, Partha P
last_name: Chakrabarti
citation:
ama: 'Chatterjee K, Dasgupta P, Chakrabarti P. Complexity of compositional model
checking of computation tree logic on simple structures. In: Vol 3326. Springer;
2005:89-102. doi:10.1007/978-3-540-30536-1_13'
apa: 'Chatterjee, K., Dasgupta, P., & Chakrabarti, P. (2005). Complexity of
compositional model checking of computation tree logic on simple structures (Vol.
3326, pp. 89–102). Presented at the IWDC: International Workshop on Distributed
Computing , Springer. https://doi.org/10.1007/978-3-540-30536-1_13'
chicago: Chatterjee, Krishnendu, Pallab Dasgupta, and Partha Chakrabarti. “Complexity
of Compositional Model Checking of Computation Tree Logic on Simple Structures,”
3326:89–102. Springer, 2005. https://doi.org/10.1007/978-3-540-30536-1_13.
ieee: 'K. Chatterjee, P. Dasgupta, and P. Chakrabarti, “Complexity of compositional
model checking of computation tree logic on simple structures,” presented at the
IWDC: International Workshop on Distributed Computing , 2005, vol. 3326, pp. 89–102.'
ista: 'Chatterjee K, Dasgupta P, Chakrabarti P. 2005. Complexity of compositional
model checking of computation tree logic on simple structures. IWDC: International
Workshop on Distributed Computing , LNCS, vol. 3326, 89–102.'
mla: Chatterjee, Krishnendu, et al. Complexity of Compositional Model Checking
of Computation Tree Logic on Simple Structures. Vol. 3326, Springer, 2005,
pp. 89–102, doi:10.1007/978-3-540-30536-1_13.
short: K. Chatterjee, P. Dasgupta, P. Chakrabarti, in:, Springer, 2005, pp. 89–102.
conference:
name: 'IWDC: International Workshop on Distributed Computing '
date_created: 2018-12-11T12:05:45Z
date_published: 2005-02-14T00:00:00Z
date_updated: 2021-01-12T07:53:02Z
day: '14'
doi: 10.1007/978-3-540-30536-1_13
extern: 1
fulldoi: https://doi.org/10.1007/978-3-540-30536-1_13
intvolume: ' 3326'
month: '02'
page: 89 - 102
publication_status: published
publisher: Springer
publist_id: '2261'
quality_controlled: 0
status: public
title: Complexity of compositional model checking of computation tree logic on simple
structures
type: conference
volume: 3326
year: '2005'
...
---
_id: '3902'
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Jacobus
full_name: Boomsma, Jacobus
last_name: Boomsma
citation:
ama: 'Cremer S, Boomsma J. The drawback of mobility: invasive species in a globalised
world. In: Elsevier; 2005.'
apa: 'Cremer, S., & Boomsma, J. (2005). The drawback of mobility: invasive species
in a globalised world. Presented at the Marie Curie Conference, Elsevier.'
chicago: 'Cremer, Sylvia, and Jacobus Boomsma. “The Drawback of Mobility: Invasive
Species in a Globalised World.” Elsevier, 2005.'
ieee: 'S. Cremer and J. Boomsma, “The drawback of mobility: invasive species in
a globalised world,” presented at the Marie Curie Conference, 2005.'
ista: 'Cremer S, Boomsma J. 2005. The drawback of mobility: invasive species in
a globalised world. Marie Curie Conference.'
mla: 'Cremer, Sylvia, and Jacobus Boomsma. The Drawback of Mobility: Invasive
Species in a Globalised World. Elsevier, 2005.'
short: S. Cremer, J. Boomsma, in:, Elsevier, 2005.
conference:
name: Marie Curie Conference
date_created: 2018-12-11T12:05:47Z
date_published: 2005-09-01T00:00:00Z
date_updated: 2021-01-12T07:53:05Z
day: '01'
extern: '1'
language:
- iso: eng
main_file_link:
- url: http://www.docstoc.com/docs/15327566/1-The-drawback-of-mobility-invasive-species-in-a-globalised-world
month: '09'
oa_version: None
publication_status: published
publisher: Elsevier
publist_id: '2252'
status: public
title: 'The drawback of mobility: invasive species in a globalised world'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2005'
...
---
_id: '3915'
abstract:
- lang: eng
text: "In the ant Cardiocondyla obscurior, wingless males compete with nestmate
males for access to female mating\r\npartners, leading to local mate competition
(LMC). Queen number varies between colonies, resulting in\r\nvariation in the
strength of LMC. Cremer & Heinze (2002, Proceedings of the Royal Society of
London, Series B,\r\n269, 417–422) showed that colonies responded to increasing
queen number by producing a less femalebiased\r\nsex ratio, as predicted by LMC
theory. However, the proximate mechanisms responsible for this\r\nvariation in
the sex ratio could not be determined because the study was restricted to adult
sex ratios.With\r\nLMC, the primary sex ratio (proportion of haploid eggs laid
by the queen) is expected to be female biased,\r\nwhich lowers the conflict between
queens and workers over sex allocation. We compared the primary sex\r\nratios
laid by queens in monogynous and in polygynous experimental colonies of C. obscurior.
The\r\nproportion of haploid eggs laid by queens was significantly lower in single-queen
than in multiple-queen\r\ncolonies. Furthermore, queens rapidly adjusted their
primary sex ratios to changes in colony queen\r\nnumber. This is the first report
of an adaptive adjustment of the primary sex ratio in response to LMC by\r\nant
queens."
author:
- first_name: Ludivine
full_name: De Menten, Ludivine
last_name: De Menten
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
- first_name: Serge
full_name: Aron, Serge
last_name: Aron
citation:
ama: De Menten L, Cremer S, Heinze J, Aron S. Primary sex ratio adjustment by ant
queens in response to local mate competition. Animal Behaviour. 2005;69(5):1031-1035.
doi:10.1016/j.anbehav.2004.09.005
apa: De Menten, L., Cremer, S., Heinze, J., & Aron, S. (2005). Primary sex ratio
adjustment by ant queens in response to local mate competition. Animal Behaviour.
Elsevier. https://doi.org/10.1016/j.anbehav.2004.09.005
chicago: De Menten, Ludivine, Sylvia Cremer, Jürgen Heinze, and Serge Aron. “Primary
Sex Ratio Adjustment by Ant Queens in Response to Local Mate Competition.” Animal
Behaviour. Elsevier, 2005. https://doi.org/10.1016/j.anbehav.2004.09.005.
ieee: L. De Menten, S. Cremer, J. Heinze, and S. Aron, “Primary sex ratio adjustment
by ant queens in response to local mate competition,” Animal Behaviour,
vol. 69, no. 5. Elsevier, pp. 1031–1035, 2005.
ista: De Menten L, Cremer S, Heinze J, Aron S. 2005. Primary sex ratio adjustment
by ant queens in response to local mate competition. Animal Behaviour. 69(5),
1031–1035.
mla: De Menten, Ludivine, et al. “Primary Sex Ratio Adjustment by Ant Queens in
Response to Local Mate Competition.” Animal Behaviour, vol. 69, no. 5,
Elsevier, 2005, pp. 1031–35, doi:10.1016/j.anbehav.2004.09.005.
short: L. De Menten, S. Cremer, J. Heinze, S. Aron, Animal Behaviour 69 (2005) 1031–1035.
date_created: 2018-12-11T12:05:52Z
date_published: 2005-05-01T00:00:00Z
date_updated: 2021-01-12T07:53:10Z
day: '01'
doi: 10.1016/j.anbehav.2004.09.005
extern: '1'
fulldoi: https://doi.org/10.1016/j.anbehav.2004.09.005
intvolume: ' 69'
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
page: 1031 - 1035
publication: Animal Behaviour
publication_status: published
publisher: Elsevier
publist_id: '2237'
status: public
title: Primary sex ratio adjustment by ant queens in response to local mate competition
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 69
year: '2005'
...
---
_id: '3916'
abstract:
- lang: eng
text: Divergent reproductive interests of males and females often cause sexual conflict
[1] and [2]. Males of many species manipulate females by transferring seminal
fluids that boost female short-term fecundity while decreasing their life expectancy
and future reproductivity [3] and [4]. The life history of ants, however, is expected
to reduce sexual conflict; whereas most insect females show repeated phases of
mating and reproduction, antqueens mate only during a short period early in life
and undergo a lifelong commitment to their mates by storing sperm [5]. Furthermore,
sexual offspring can only be reared after a sterile worker force has been built
up [5]. Therefore, the males should also profit from a long female lifespan. In
the antCardiocondyla obscurior, mating indeed has a positive effect on the lifetime
reproductive success of queens. Queens that mated to either one fertile or one
sterilized male lived considerably longer and started laying eggs earlier than
virgin queens. Only queens that received viable sperm from fertile males showed
increased fecundity. The lack of a trade-off between fecundity and longevity is
unexpected, given evolutionary theories of aging [6]. Our data instead reveal
the existence of sexual cooperation in ants.
author:
- first_name: Alexandra
full_name: Schrempf, Alexandra
last_name: Schrempf
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: 'Schrempf A, Heinze J, Cremer S. Sexual cooperation: mating increases longevity
in ant queens. Current Biology. 2005;15(3):267-270. doi:10.1016/j.cub.2005.01.036'
apa: 'Schrempf, A., Heinze, J., & Cremer, S. (2005). Sexual cooperation: mating
increases longevity in ant queens. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2005.01.036'
chicago: 'Schrempf, Alexandra, Jürgen Heinze, and Sylvia Cremer. “Sexual Cooperation:
Mating Increases Longevity in Ant Queens.” Current Biology. Cell Press,
2005. https://doi.org/10.1016/j.cub.2005.01.036.'
ieee: 'A. Schrempf, J. Heinze, and S. Cremer, “Sexual cooperation: mating increases
longevity in ant queens,” Current Biology, vol. 15, no. 3. Cell Press,
pp. 267–270, 2005.'
ista: 'Schrempf A, Heinze J, Cremer S. 2005. Sexual cooperation: mating increases
longevity in ant queens. Current Biology. 15(3), 267–270.'
mla: 'Schrempf, Alexandra, et al. “Sexual Cooperation: Mating Increases Longevity
in Ant Queens.” Current Biology, vol. 15, no. 3, Cell Press, 2005, pp.
267–70, doi:10.1016/j.cub.2005.01.036.'
short: A. Schrempf, J. Heinze, S. Cremer, Current Biology 15 (2005) 267–270.
date_created: 2018-12-11T12:05:52Z
date_published: 2005-02-08T00:00:00Z
date_updated: 2021-01-12T07:53:10Z
day: '08'
doi: 10.1016/j.cub.2005.01.036
extern: '1'
fulldoi: https://doi.org/10.1016/j.cub.2005.01.036
intvolume: ' 15'
issue: '3'
language:
- iso: eng
month: '02'
oa_version: None
page: 267 - 270
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '2238'
status: public
title: 'Sexual cooperation: mating increases longevity in ant queens'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2005'
...
---
_id: '3933'
abstract:
- lang: eng
text: Resident dendritic cells (DC) within the T cell area of the lymph node take
up soluble antigens that enter via the afferent lymphatics before antigen carrying
DC arrive from the periphery. The reticular network within the lymph node is a
conduit system forming the infrastructure for the fast delivery of soluble substances
from the afferent lymph to the lumen of high endothelial venules (HEVs). Using
high-resolution light microscopy and 3D reconstruction, we show here that these
conduits are unique basement membrane-like structures ensheathed by fibroblastic
reticular cells with occasional resident DC embedded within this cell layer. Conduit-associated
DC are capable of taking up and processing soluble antigens transported within
the conduits, whereas immigrated mature DC occur remote from the reticular fibers.
The conduit system is, therefore, not a closed compartment that shuttles substances
through the lymph node but represents the morphological equivalent to the filtering
function of the lymph node.
author:
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Nobuo
full_name: Kanazawa, Nobuo
last_name: Kanazawa
- first_name: Manuel
full_name: Selg, Manuel
last_name: Selg
- first_name: Thomas
full_name: Samson, Thomas
last_name: Samson
- first_name: Gunnel
full_name: Roos, Gunnel
last_name: Roos
- first_name: Dieter
full_name: Reinhardt, Dieter
last_name: Reinhardt
- first_name: Reinhard
full_name: Pabst, Reinhard
last_name: Pabst
- first_name: Manfred
full_name: Lutz, Manfred
last_name: Lutz
- first_name: Lydia
full_name: Sorokin, Lydia
last_name: Sorokin
citation:
ama: Sixt MK, Kanazawa N, Selg M, et al. The conduit system transports soluble antigens
from the afferent lymph to resident dendritic cells in the T cell area of the
lymph node. Immunity. 2005;22(1):19-29. doi:10.1016/j.immuni.2004.11.013
apa: Sixt, M. K., Kanazawa, N., Selg, M., Samson, T., Roos, G., Reinhardt, D., …
Sorokin, L. (2005). The conduit system transports soluble antigens from the afferent
lymph to resident dendritic cells in the T cell area of the lymph node. Immunity.
Cell Press. https://doi.org/10.1016/j.immuni.2004.11.013
chicago: Sixt, Michael K, Nobuo Kanazawa, Manuel Selg, Thomas Samson, Gunnel Roos,
Dieter Reinhardt, Reinhard Pabst, Manfred Lutz, and Lydia Sorokin. “The Conduit
System Transports Soluble Antigens from the Afferent Lymph to Resident Dendritic
Cells in the T Cell Area of the Lymph Node.” Immunity. Cell Press, 2005.
https://doi.org/10.1016/j.immuni.2004.11.013.
ieee: M. K. Sixt et al., “The conduit system transports soluble antigens
from the afferent lymph to resident dendritic cells in the T cell area of the
lymph node,” Immunity, vol. 22, no. 1. Cell Press, pp. 19–29, 2005.
ista: Sixt MK, Kanazawa N, Selg M, Samson T, Roos G, Reinhardt D, Pabst R, Lutz
M, Sorokin L. 2005. The conduit system transports soluble antigens from the afferent
lymph to resident dendritic cells in the T cell area of the lymph node. Immunity.
22(1), 19–29.
mla: Sixt, Michael K., et al. “The Conduit System Transports Soluble Antigens from
the Afferent Lymph to Resident Dendritic Cells in the T Cell Area of the Lymph
Node.” Immunity, vol. 22, no. 1, Cell Press, 2005, pp. 19–29, doi:10.1016/j.immuni.2004.11.013.
short: M.K. Sixt, N. Kanazawa, M. Selg, T. Samson, G. Roos, D. Reinhardt, R. Pabst,
M. Lutz, L. Sorokin, Immunity 22 (2005) 19–29.
date_created: 2018-12-11T12:05:58Z
date_published: 2005-01-25T00:00:00Z
date_updated: 2021-01-12T07:53:18Z
day: '25'
doi: 10.1016/j.immuni.2004.11.013
extern: '1'
fulldoi: https://doi.org/10.1016/j.immuni.2004.11.013
intvolume: ' 22'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 19 - 29
publication: Immunity
publication_status: published
publisher: Cell Press
publist_id: '2195'
status: public
title: The conduit system transports soluble antigens from the afferent lymph to resident
dendritic cells in the T cell area of the lymph node
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2005'
...
---
OA_type: closed access
_id: '3989'
abstract:
- lang: eng
text: We introduce local and global comparison measures for a collection of k less
than or equal to d real-valued smooth functions on a common d-dimensional Riemannian
manifold. For k = d = 2 we relate the measures to the set of critical points of
one function restricted to the level sets of the other. The definition of the
measures extends to piecewise linear functions for which they ace easy to compute.
The computation of the measures forms the centerpiece of a software tool which
we use to study scientific datasets.
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
- first_name: John
full_name: Harer, John
last_name: Harer
- first_name: Vijay
full_name: Natarajan, Vijay
last_name: Natarajan
- first_name: Valerio
full_name: Pascucci, Valerio
last_name: Pascucci
citation:
ama: 'Edelsbrunner H, Harer J, Natarajan V, Pascucci V. Local and global comparison
of continuous functions. In: IEEE; 2005:275-280. doi:10.1109/VISUAL.2004.68'
apa: 'Edelsbrunner, H., Harer, J., Natarajan, V., & Pascucci, V. (2005). Local
and global comparison of continuous functions (pp. 275–280). Presented at the
VIS: IEEE Visualization, Austin, TX, United States: IEEE. https://doi.org/10.1109/VISUAL.2004.68'
chicago: Edelsbrunner, Herbert, John Harer, Vijay Natarajan, and Valerio Pascucci.
“Local and Global Comparison of Continuous Functions,” 275–80. IEEE, 2005. https://doi.org/10.1109/VISUAL.2004.68.
ieee: 'H. Edelsbrunner, J. Harer, V. Natarajan, and V. Pascucci, “Local and global
comparison of continuous functions,” presented at the VIS: IEEE Visualization,
Austin, TX, United States, 2005, pp. 275–280.'
ista: 'Edelsbrunner H, Harer J, Natarajan V, Pascucci V. 2005. Local and global
comparison of continuous functions. VIS: IEEE Visualization, 275–280.'
mla: Edelsbrunner, Herbert, et al. Local and Global Comparison of Continuous
Functions. IEEE, 2005, pp. 275–80, doi:10.1109/VISUAL.2004.68.
short: H. Edelsbrunner, J. Harer, V. Natarajan, V. Pascucci, in:, IEEE, 2005, pp.
275–280.
conference:
end_date: 2004-10-15
location: Austin, TX, United States
name: 'VIS: IEEE Visualization'
start_date: 2004-10-10
date_created: 2018-12-11T12:06:18Z
date_published: 2005-02-28T00:00:00Z
date_updated: 2026-05-29T12:06:45Z
day: '28'
doi: 10.1109/VISUAL.2004.68
extern: '1'
fulldoi: https://doi.org/10.1109/VISUAL.2004.68
language:
- iso: eng
month: '02'
oa_version: None
page: 275 - 280
publication_identifier:
isbn:
- '0780387880'
publication_status: published
publisher: IEEE
publist_id: '2137'
quality_controlled: '1'
status: public
title: Local and global comparison of continuous functions
type: conference
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2005'
...
---
_id: '17715'
abstract:
- lang: eng
text: At redshifts beyond z>6, as the mean fraction of neutral hydrogen x_HI in
the intergalactic medium (IGM) increases, the line flux of Lyman alpha (Lya) emitters
can be significantly suppressed, which can result in a decrease in the observed
number of emitters at a given Lya flux. However, cosmological HII regions surrounding
the Lya emitting galaxies alleviate these effects. We use simple models of the
Lya line suppression that incorporate the presence of HII regions to predict the
overall effect of the Lya absorption on the Lya luminosity function. We find,
in agreement with other recent studies, that unless ionizing sources are unusually
strongly clustered, a fully neutral IGM may be inconsistent with the large abundance
of confirmed z=6.5 Lya emitters. However, the presence of local HII regions prohibits
placing a tight constraint on the mean neutral fraction. We find x_HI < 0.25;
the presence of strong winds and/or the clustering of ionizing sources would further
weaken this constraint. We conclude that the evolution of the Lya LF is consistent
with reionization occurring near this redshift. Finally, we suggest that a measurement
of observed Lya line width as a function of the Lya luminosity, in a future, larger
sample of Lya emitters, may serve as a robust diagnostic of the neutral fraction
in the IGM.
article_processing_charge: No
article_type: original
author:
- first_name: Zoltán
full_name: Haiman, Zoltán
id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36
last_name: Haiman
- first_name: Renyue
full_name: Cen, Renyue
last_name: Cen
citation:
ama: Haiman Z, Cen R. Constraining reionization with the evolution of the luminosity
function of Lyα emitting galaxies. The Astrophysical Journal. 2005;623(2):627-631.
doi:10.1086/428645
apa: Haiman, Z., & Cen, R. (2005). Constraining reionization with the evolution
of the luminosity function of Lyα emitting galaxies. The Astrophysical Journal.
American Astronomical Society. https://doi.org/10.1086/428645
chicago: Haiman, Zoltán, and Renyue Cen. “Constraining Reionization with the Evolution
of the Luminosity Function of Lyα Emitting Galaxies.” The Astrophysical Journal.
American Astronomical Society, 2005. https://doi.org/10.1086/428645.
ieee: Z. Haiman and R. Cen, “Constraining reionization with the evolution of the
luminosity function of Lyα emitting galaxies,” The Astrophysical Journal,
vol. 623, no. 2. American Astronomical Society, pp. 627–631, 2005.
ista: Haiman Z, Cen R. 2005. Constraining reionization with the evolution of the
luminosity function of Lyα emitting galaxies. The Astrophysical Journal. 623(2),
627–631.
mla: Haiman, Zoltán, and Renyue Cen. “Constraining Reionization with the Evolution
of the Luminosity Function of Lyα Emitting Galaxies.” The Astrophysical Journal,
vol. 623, no. 2, American Astronomical Society, 2005, pp. 627–31, doi:10.1086/428645.
short: Z. Haiman, R. Cen, The Astrophysical Journal 623 (2005) 627–631.
date_created: 2024-09-06T08:59:08Z
date_published: 2005-04-20T00:00:00Z
date_updated: 2024-09-25T12:55:58Z
day: '20'
doi: 10.1086/428645
extern: '1'
fulldoi: https://doi.org/10.1086/428645
intvolume: ' 623'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1086/428645
month: '04'
oa: 1
oa_version: Published Version
page: 627-631
publication: The Astrophysical Journal
publication_identifier:
issn:
- 0004-637X
- 1538-4357
publication_status: published
publisher: American Astronomical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Constraining reionization with the evolution of the luminosity function of
Lyα emitting galaxies
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 623
year: '2005'
...
---
_id: '17720'
abstract:
- lang: eng
text: We revisit the possibility of detecting an extrasolar planet around a background
star as it crosses the fold caustic of a foreground binary lens. During such an
event, the planet's flux can be magnified by a factor of ~100 or more. The detectability
of the planet depends strongly on the orientation of its orbit relative to the
caustic. If the source star is inside the intercaustic region, detecting the caustic-crossing
planet is difficult against the magnified flux of its parent star. In the more
favorable configuration, when the star is outside the intercaustic region when
the planet crosses the caustic, a close-in Jupiter-like planet around a Sun-like
star at a distance of 8 kpc is detectable in 8 minute integrations with a 10 m
telescope at maximal signal-to-noise ratio (S/N) ~15 for phase angle ϕ ~ 10°.
In this example, we find further that the presence of methane, at its measured
abundance in Jupiter, and/or water, sodium, and potassium, at the abundances expected
in theoretical atmosphere models of close-in Jupiters, could be inferred from
a nondetection of the planet in strong broad absorption bands at 0.6-1.4 μm caused
by these compounds, accompanied by a S/N ~ 10 detection in adjacent bands. We
conclude that future generations of large telescopes might be able to probe the
composition of the atmospheres of distant extrasolar planets.
article_processing_charge: No
article_type: original
author:
- first_name: David S.
full_name: Spiegel, David S.
last_name: Spiegel
- first_name: Michel
full_name: Zamojski, Michel
last_name: Zamojski
- first_name: Alan
full_name: Gersch, Alan
last_name: Gersch
- first_name: Jennifer
full_name: Donovan, Jennifer
last_name: Donovan
- first_name: Zoltán
full_name: Haiman, Zoltán
id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36
last_name: Haiman
citation:
ama: Spiegel DS, Zamojski M, Gersch A, Donovan J, Haiman Z. Can we probe the atmospheric
composition of an extrasolar planet from its reflection spectrum in a high‐magnification
microlensing event? The Astrophysical Journal. 2005;628(1):478-486. doi:10.1086/430696
apa: Spiegel, D. S., Zamojski, M., Gersch, A., Donovan, J., & Haiman, Z. (2005).
Can we probe the atmospheric composition of an extrasolar planet from its reflection
spectrum in a high‐magnification microlensing event? The Astrophysical Journal.
American Astronomical Society. https://doi.org/10.1086/430696
chicago: Spiegel, David S., Michel Zamojski, Alan Gersch, Jennifer Donovan, and
Zoltán Haiman. “Can We Probe the Atmospheric Composition of an Extrasolar Planet
from Its Reflection Spectrum in a High‐magnification Microlensing Event?” The
Astrophysical Journal. American Astronomical Society, 2005. https://doi.org/10.1086/430696.
ieee: D. S. Spiegel, M. Zamojski, A. Gersch, J. Donovan, and Z. Haiman, “Can we
probe the atmospheric composition of an extrasolar planet from its reflection
spectrum in a high‐magnification microlensing event?,” The Astrophysical Journal,
vol. 628, no. 1. American Astronomical Society, pp. 478–486, 2005.
ista: Spiegel DS, Zamojski M, Gersch A, Donovan J, Haiman Z. 2005. Can we probe
the atmospheric composition of an extrasolar planet from its reflection spectrum
in a high‐magnification microlensing event? The Astrophysical Journal. 628(1),
478–486.
mla: Spiegel, David S., et al. “Can We Probe the Atmospheric Composition of an Extrasolar
Planet from Its Reflection Spectrum in a High‐magnification Microlensing Event?”
The Astrophysical Journal, vol. 628, no. 1, American Astronomical Society,
2005, pp. 478–86, doi:10.1086/430696.
short: D.S. Spiegel, M. Zamojski, A. Gersch, J. Donovan, Z. Haiman, The Astrophysical
Journal 628 (2005) 478–486.
date_created: 2024-09-06T09:05:00Z
date_published: 2005-07-20T00:00:00Z
date_updated: 2024-09-25T13:51:34Z
day: '20'
doi: 10.1086/430696
extern: '1'
fulldoi: https://doi.org/10.1086/430696
intvolume: ' 628'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1086/430696
month: '07'
oa: 1
oa_version: Published Version
page: 478-486
publication: The Astrophysical Journal
publication_identifier:
issn:
- 0004-637X
- 1538-4357
publication_status: published
publisher: American Astronomical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Can we probe the atmospheric composition of an extrasolar planet from its reflection
spectrum in a high‐magnification microlensing event?
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 628
year: '2005'
...
---
_id: '17731'
abstract:
- lang: eng
text: In cosmological structure formation models, massive non-linear objects in
the process of formation, such as galaxy clusters, are surrounded by large-scale
shocks at or around the expected virial radius. Direct observational evidence
for such virial shocks is currently lacking, but we show here that their presence
can be inferred from future, high resolution, high-sensitivity observations of
the Sunyaev-Zel'dovich (SZ) effect in galaxy clusters. We study the detectability
of virial shocks in mock SZ maps, using simple models of cluster structure (gas
density and temperature distributions) and noise (background and foreground galaxy
clusters projected along the line of sight, as well as the cosmic microwave background
anisotropies). We find that at an angular resolution of 2'' and sensitivity of
10 micro K, expected to be reached at ~ 100 GHz frequencies in a ~ 20 hr integration
with the forthcoming ALMA instrument, virial shocks associated with massive M
~ 10^15 M_Sun clusters will stand out from the noise, and can be detected at high
significance. More generally, our results imply that the projected SZ surface
brightness profile in future, high-resolution experiments will provide sensitive
constraints on the density profile of cluster gas.
article_processing_charge: No
article_type: original
author:
- first_name: Bence
full_name: Kocsis, Bence
last_name: Kocsis
- first_name: Zoltán
full_name: Haiman, Zoltán
id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36
last_name: Haiman
- first_name: Zsolt
full_name: Frei, Zsolt
last_name: Frei
citation:
ama: Kocsis B, Haiman Z, Frei Z. Can virialization shocks be detected around galaxy
clusters through the Sunyaev‐Zel’dovich effect? The Astrophysical Journal.
2005;623(2):632-649. doi:10.1086/427975
apa: Kocsis, B., Haiman, Z., & Frei, Z. (2005). Can virialization shocks be
detected around galaxy clusters through the Sunyaev‐Zel’dovich effect? The
Astrophysical Journal. American Astronomical Society. https://doi.org/10.1086/427975
chicago: Kocsis, Bence, Zoltán Haiman, and Zsolt Frei. “Can Virialization Shocks
Be Detected around Galaxy Clusters through the Sunyaev‐Zel’dovich Effect?” The
Astrophysical Journal. American Astronomical Society, 2005. https://doi.org/10.1086/427975.
ieee: B. Kocsis, Z. Haiman, and Z. Frei, “Can virialization shocks be detected around
galaxy clusters through the Sunyaev‐Zel’dovich effect?,” The Astrophysical
Journal, vol. 623, no. 2. American Astronomical Society, pp. 632–649, 2005.
ista: Kocsis B, Haiman Z, Frei Z. 2005. Can virialization shocks be detected around
galaxy clusters through the Sunyaev‐Zel’dovich effect? The Astrophysical Journal.
623(2), 632–649.
mla: Kocsis, Bence, et al. “Can Virialization Shocks Be Detected around Galaxy Clusters
through the Sunyaev‐Zel’dovich Effect?” The Astrophysical Journal, vol.
623, no. 2, American Astronomical Society, 2005, pp. 632–49, doi:10.1086/427975.
short: B. Kocsis, Z. Haiman, Z. Frei, The Astrophysical Journal 623 (2005) 632–649.
date_created: 2024-09-06T09:16:44Z
date_published: 2005-04-20T00:00:00Z
date_updated: 2024-09-26T07:37:23Z
day: '20'
doi: 10.1086/427975
extern: '1'
fulldoi: https://doi.org/10.1086/427975
intvolume: ' 623'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1086/427975
month: '04'
oa: 1
oa_version: Published Version
page: 632-649
publication: The Astrophysical Journal
publication_identifier:
issn:
- 0004-637X
- 1538-4357
publication_status: published
publisher: American Astronomical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Can virialization shocks be detected around galaxy clusters through the Sunyaev‐Zel’dovich
effect?
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 623
year: '2005'
...
---
_id: '17737'
abstract:
- lang: eng
text: Cosmological models that include suppression of the power spectrum of density
fluctuations on small scales exhibit an exponential reduction of high-redshift,
non-linear structures, including a reduction in the rate of gamma ray bursts (GRBs).
Here we quantify the constraints that the detection of distant GRBs would place
on structure formation models with reduced small-scale power. We compute the number
of GRBs that could be detectable by the Swift satellite at high redshifts (z >
6), assuming that the GRBs trace the cosmic star formation history, which itself
traces the formation of non-linear structures. We calibrate simple models of the
intrinsic luminosity function of the bursts to the number and flux distribution
of GRBs observed by the Burst And Transient Source Experiment (BATSE). We find
that a discovery of high-z GRBs would imply strong constraints on models with
reduced small-scale power. For example, a single GRB at z > 10, or 10 GRBs at
z > 5, discovered by Swift during its scheduled two-year mission, would rule out
an exponential suppression of the power spectrum on scales below R_c=0.09 Mpc
(exemplified by warm dark matter models with a particle mass of m_x=2 keV). Models
with a less sharp suppression of small-scale power, such as those with a red tilt
or a running scalar index, n_s, are more difficult to constrain, because they
are more degenerate with an increase in the power spectrum normalization, sigma_8,
and with models in which star-formation is allowed in low-mass minihalos. We find
that a tilt of \delta n_s ~ 0.1 is difficult to detect; however, an observed rate
of 1 GRB/yr at z > 12 would yield an upper limit on the running of the spectral
index, alpha = d(n_s)/d(ln k) > -0.05.
article_processing_charge: No
article_type: original
author:
- first_name: Andrei
full_name: Mesinger, Andrei
last_name: Mesinger
- first_name: Rosalba
full_name: Perna, Rosalba
last_name: Perna
- first_name: Zoltán
full_name: Haiman, Zoltán
id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36
last_name: Haiman
citation:
ama: Mesinger A, Perna R, Haiman Z. Constraints on the small‐scale power spectrum
of density fluctuations from high‐redshift gamma‐ray bursts. The Astrophysical
Journal. 2005;623(1):1-10. doi:10.1086/428770
apa: Mesinger, A., Perna, R., & Haiman, Z. (2005). Constraints on the small‐scale
power spectrum of density fluctuations from high‐redshift gamma‐ray bursts. The
Astrophysical Journal. American Astronomical Society. https://doi.org/10.1086/428770
chicago: Mesinger, Andrei, Rosalba Perna, and Zoltán Haiman. “Constraints on the
Small‐scale Power Spectrum of Density Fluctuations from High‐redshift Gamma‐ray
Bursts.” The Astrophysical Journal. American Astronomical Society, 2005.
https://doi.org/10.1086/428770.
ieee: A. Mesinger, R. Perna, and Z. Haiman, “Constraints on the small‐scale power
spectrum of density fluctuations from high‐redshift gamma‐ray bursts,” The
Astrophysical Journal, vol. 623, no. 1. American Astronomical Society, pp.
1–10, 2005.
ista: Mesinger A, Perna R, Haiman Z. 2005. Constraints on the small‐scale power
spectrum of density fluctuations from high‐redshift gamma‐ray bursts. The Astrophysical
Journal. 623(1), 1–10.
mla: Mesinger, Andrei, et al. “Constraints on the Small‐scale Power Spectrum of
Density Fluctuations from High‐redshift Gamma‐ray Bursts.” The Astrophysical
Journal, vol. 623, no. 1, American Astronomical Society, 2005, pp. 1–10, doi:10.1086/428770.
short: A. Mesinger, R. Perna, Z. Haiman, The Astrophysical Journal 623 (2005) 1–10.
date_created: 2024-09-06T09:20:42Z
date_published: 2005-04-10T00:00:00Z
date_updated: 2024-09-26T14:02:13Z
day: '10'
doi: 10.1086/428770
extern: '1'
fulldoi: https://doi.org/10.1086/428770
intvolume: ' 623'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1086/428770
month: '04'
oa: 1
oa_version: Published Version
page: 1-10
publication: The Astrophysical Journal
publication_identifier:
issn:
- 0004-637X
- 1538-4357
publication_status: published
publisher: American Astronomical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Constraints on the small‐scale power spectrum of density fluctuations from
high‐redshift gamma‐ray bursts
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 623
year: '2005'
...
---
_id: '17761'
abstract:
- lang: eng
text: We explore the possibility of resolving an image of a damped Lyα (DLA) system
in absorption against an extended, diffuse, background X-ray source. Typical columns
of neutral hydrogen in DLA systems are high enough to block out up to ~30% of
the soft X-ray flux at an observed photon energy of 0.5 keV, and we find that
~1% of the area of extended X-ray sources at z ≳ 1 have their 0.5 keV flux reduced
by at least 20% because of intervening DLA systems. We discuss the observability
of such absorption and find that ≳300 photons per angular resolution element are
required in the 0.3-8 keV band for its detection and in order to distinguish it
from intrinsic surface brightness fluctuations. For the surface brightness of
the currently known high-redshift extended X-ray sources, this requires an integration
time of a few megaseconds on Chandra, if the maps are smoothed spatially to ≈2''
resolution. The exact required integration time depends on the DLA system's column
density, metallicity, and, most strongly, its redshift. Current X-ray telescopes
are likely to detect DLA systems with N < 10^22 cm^-2 only out to z ≈ 2.3. The
availability of DLA systems with a suitably high column density for a silhouette
detection is currently poorly known. We suggest that at low redshifts archival
data of bright X-ray point sources may be useful in constraining the high-N end
of the column density distribution. We briefly discuss an alternative strategy
of searching for extended X-ray sources behind known DLA systems. Although with
current X-ray telescopes the detections are challenging, they will be within the
reach of a routine observation with a next generation X-ray telescope, such as
the X-Ray Evolving Universe Spectrometer (XEUS) or Generation-X, and will deliver
novel constraints on the nature of protogalaxies.
article_processing_charge: No
article_type: original
author:
- first_name: Mark
full_name: Dijkstra, Mark
last_name: Dijkstra
- first_name: Zoltán
full_name: Haiman, Zoltán
id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36
last_name: Haiman
- first_name: Caleb
full_name: Scharf, Caleb
last_name: Scharf
citation:
ama: Dijkstra M, Haiman Z, Scharf C. On detecting the X‐ray silhouette of a damped
Lyα system. The Astrophysical Journal. 2005;624(1):85-93. doi:10.1086/428766
apa: Dijkstra, M., Haiman, Z., & Scharf, C. (2005). On detecting the X‐ray silhouette
of a damped Lyα system. The Astrophysical Journal. American Astronomical
Society. https://doi.org/10.1086/428766
chicago: Dijkstra, Mark, Zoltán Haiman, and Caleb Scharf. “On Detecting the X‐ray
Silhouette of a Damped Lyα System.” The Astrophysical Journal. American
Astronomical Society, 2005. https://doi.org/10.1086/428766.
ieee: M. Dijkstra, Z. Haiman, and C. Scharf, “On detecting the X‐ray silhouette
of a damped Lyα system,” The Astrophysical Journal, vol. 624, no. 1. American
Astronomical Society, pp. 85–93, 2005.
ista: Dijkstra M, Haiman Z, Scharf C. 2005. On detecting the X‐ray silhouette of
a damped Lyα system. The Astrophysical Journal. 624(1), 85–93.
mla: Dijkstra, Mark, et al. “On Detecting the X‐ray Silhouette of a Damped Lyα System.”
The Astrophysical Journal, vol. 624, no. 1, American Astronomical Society,
2005, pp. 85–93, doi:10.1086/428766.
short: M. Dijkstra, Z. Haiman, C. Scharf, The Astrophysical Journal 624 (2005) 85–93.
date_created: 2024-09-06T09:48:59Z
date_published: 2005-05-01T00:00:00Z
date_updated: 2024-09-30T08:55:54Z
day: '01'
doi: 10.1086/428766
extern: '1'
fulldoi: https://doi.org/10.1086/428766
intvolume: ' 624'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1086/428766
month: '05'
oa: 1
oa_version: Published Version
page: 85-93
publication: The Astrophysical Journal
publication_identifier:
issn:
- 0004-637X
- 1538-4357
publication_status: published
publisher: American Astronomical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: On detecting the X‐ray silhouette of a damped Lyα system
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 624
year: '2005'
...