---
_id: '3728'
abstract:
- lang: eng
text: Mechanical unfolding of single bacteriorhodopsins from a membrane bilayer
is studied using molecular dynamics simulations. The initial conformation of the
lipid membrane is determined through all-atom simulations and then its coarse-grained
representation is used in the studies of stretching. A Go-like model with a realistic
contact map and with Lennard–Jones contact interactions is applied to model the
protein–membrane system. The model qualitatively reproduces the experimentally
observed differences between force-extension patterns obtained on bacteriorhodopsin
at different temperatures and predicts a lack of symmetry in the choice of the
terminus to pull by. It also illustrates the decisive role of the interactions
of the protein with the membrane in determining the force pattern and thus the
stability of transmembrane proteins.
author:
- first_name: Marek
full_name: Cieplak, Marek
last_name: Cieplak
- first_name: Sławomir
full_name: Filipek, Sławomir
last_name: Filipek
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Krystiana
full_name: Krzysko, Krystiana A
last_name: Krzysko
citation:
ama: 'Cieplak M, Filipek S, Janovjak HL, Krzysko K. Pulling single bacteriorhodopsin
out of a membrane: Comparison of simulation and experiment. Biochimica et Biophysica
Acta (BBA) - Biomembranes. 2006;1758(4):537-544. doi:10.1016/j.bbamem.2006.03.028'
apa: 'Cieplak, M., Filipek, S., Janovjak, H. L., & Krzysko, K. (2006). Pulling
single bacteriorhodopsin out of a membrane: Comparison of simulation and experiment.
Biochimica et Biophysica Acta (BBA) - Biomembranes. Elsevier. https://doi.org/10.1016/j.bbamem.2006.03.028'
chicago: 'Cieplak, Marek, Sławomir Filipek, Harald L Janovjak, and Krystiana Krzysko.
“Pulling Single Bacteriorhodopsin out of a Membrane: Comparison of Simulation
and Experiment.” Biochimica et Biophysica Acta (BBA) - Biomembranes. Elsevier,
2006. https://doi.org/10.1016/j.bbamem.2006.03.028.'
ieee: 'M. Cieplak, S. Filipek, H. L. Janovjak, and K. Krzysko, “Pulling single bacteriorhodopsin
out of a membrane: Comparison of simulation and experiment,” Biochimica et
Biophysica Acta (BBA) - Biomembranes, vol. 1758, no. 4. Elsevier, pp. 537–544,
2006.'
ista: 'Cieplak M, Filipek S, Janovjak HL, Krzysko K. 2006. Pulling single bacteriorhodopsin
out of a membrane: Comparison of simulation and experiment. Biochimica et Biophysica
Acta (BBA) - Biomembranes. 1758(4), 537–544.'
mla: 'Cieplak, Marek, et al. “Pulling Single Bacteriorhodopsin out of a Membrane:
Comparison of Simulation and Experiment.” Biochimica et Biophysica Acta (BBA)
- Biomembranes, vol. 1758, no. 4, Elsevier, 2006, pp. 537–44, doi:10.1016/j.bbamem.2006.03.028.'
short: M. Cieplak, S. Filipek, H.L. Janovjak, K. Krzysko, Biochimica et Biophysica
Acta (BBA) - Biomembranes 1758 (2006) 537–544.
date_created: 2018-12-11T12:04:50Z
date_published: 2006-04-01T00:00:00Z
date_updated: 2021-01-12T07:51:46Z
day: '01'
doi: 10.1016/j.bbamem.2006.03.028
extern: 1
intvolume: ' 1758'
issue: '4'
month: '04'
page: 537 - 544
publication: Biochimica et Biophysica Acta (BBA) - Biomembranes
publication_status: published
publisher: Elsevier
publist_id: '2502'
quality_controlled: 0
status: public
title: 'Pulling single bacteriorhodopsin out of a membrane: Comparison of simulation
and experiment'
type: journal_article
volume: 1758
year: '2006'
...
---
_id: '3722'
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
citation:
ama: 'Janovjak HL, Mueller D. Rastersondenmikroskopie. In: Bioanalytik. Spektrum
Akademischer Verlag; 2006.'
apa: Janovjak, H. L., & Mueller, D. (2006). Rastersondenmikroskopie. In Bioanalytik.
Spektrum Akademischer Verlag.
chicago: Janovjak, Harald L, and Daniel Mueller. “Rastersondenmikroskopie.” In Bioanalytik.
Spektrum Akademischer Verlag, 2006.
ieee: H. L. Janovjak and D. Mueller, “Rastersondenmikroskopie,” in Bioanalytik,
Spektrum Akademischer Verlag, 2006.
ista: 'Janovjak HL, Mueller D. 2006.Rastersondenmikroskopie. In: Bioanalytik. .'
mla: Janovjak, Harald L., and Daniel Mueller. “Rastersondenmikroskopie.” Bioanalytik,
Spektrum Akademischer Verlag, 2006.
short: H.L. Janovjak, D. Mueller, in:, Bioanalytik, Spektrum Akademischer Verlag,
2006.
date_created: 2018-12-11T12:04:48Z
date_published: 2006-06-16T00:00:00Z
date_updated: 2021-01-12T07:51:44Z
day: '16'
extern: 1
month: '06'
publication: Bioanalytik
publication_status: published
publisher: Spektrum Akademischer Verlag
publist_id: '2508'
quality_controlled: 0
status: public
title: Rastersondenmikroskopie
type: book_chapter
year: '2006'
...
---
_id: '3755'
abstract:
- lang: eng
text: A primitive example of adaptation in gene expression is the balance between
the rate of synthesis and degradation of cellular RNA, which allows rapid responses
to environmental signals. Here, we investigate how multidrug efflux pump systems
mediate the dynamics of a simple drug-inducible system in response to a steady
level of inducer. Using fluorescence correlation spectroscopy, we measured in
real time within a single bacterium the transcription activity at the RNA level
of the acrAB-TolC multidrug efflux pump system. When cells are exposed to constant
level of anhydrotetracycline inducer and are adsorbed onto a poly-L-lysine-coated
surface, we found that the acrAB-TolC promoter is steadily active. We also monitored
the activity of the tet promoter to characterize the effect of this efflux system
on the dynamics of drug-inducible transcription. We found that the transcriptional
response of the tet promoter to a steady level of aTc rises and then falls back
to its preinduction level. The rate of RNA degradation was constant throughout
the transcriptional pulse, indicating that the modulation of intracellular inducer
concentration alone can produce this pulsating response. Single-cell experiments
together with numerical simulations suggest that such pulsating response in drug-inducible
genetic systems is a property emerging from the dependence of drug-inducible transcription
on multidrug efflux systems.
author:
- first_name: Thuc
full_name: Le,Thuc T.
last_name: Le
- first_name: Thierry
full_name: Emonet,Thierry
last_name: Emonet
- 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: Philippe
full_name: Cluzel,Philippe
last_name: Cluzel
citation:
ama: Le T, Emonet T, Harlepp S, Guet CC, Cluzel P. Dynamical determinants of drug-inducible
gene expression in a single bacterium. Biophysical Journal. 2006;90(9):3315-3321.
doi:10.1529/biophysj.105.073353
apa: Le, T., Emonet, T., Harlepp, S., Guet, C. C., & Cluzel, P. (2006). Dynamical
determinants of drug-inducible gene expression in a single bacterium. Biophysical
Journal. Biophysical Society. https://doi.org/10.1529/biophysj.105.073353
chicago: Le, Thuc, Thierry Emonet, Sébastien Harlepp, Calin C Guet, and Philippe
Cluzel. “Dynamical Determinants of Drug-Inducible Gene Expression in a Single
Bacterium.” Biophysical Journal. Biophysical Society, 2006. https://doi.org/10.1529/biophysj.105.073353.
ieee: T. Le, T. Emonet, S. Harlepp, C. C. Guet, and P. Cluzel, “Dynamical determinants
of drug-inducible gene expression in a single bacterium,” Biophysical Journal,
vol. 90, no. 9. Biophysical Society, pp. 3315–3321, 2006.
ista: Le T, Emonet T, Harlepp S, Guet CC, Cluzel P. 2006. Dynamical determinants
of drug-inducible gene expression in a single bacterium. Biophysical Journal.
90(9), 3315–3321.
mla: Le, Thuc, et al. “Dynamical Determinants of Drug-Inducible Gene Expression
in a Single Bacterium.” Biophysical Journal, vol. 90, no. 9, Biophysical
Society, 2006, pp. 3315–21, doi:10.1529/biophysj.105.073353.
short: T. Le, T. Emonet, S. Harlepp, C.C. Guet, P. Cluzel, Biophysical Journal 90
(2006) 3315–3321.
date_created: 2018-12-11T12:04:59Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:51:58Z
day: '01'
doi: 10.1529/biophysj.105.073353
extern: 1
intvolume: ' 90'
issue: '9'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1432126/
month: '01'
oa: 1
page: 3315 - 3321
publication: Biophysical Journal
publication_status: published
publisher: Biophysical Society
publist_id: '2472'
quality_controlled: 0
status: public
title: Dynamical determinants of drug-inducible gene expression in a single bacterium
type: journal_article
volume: 90
year: '2006'
...
---
_id: '3758'
abstract:
- lang: eng
text: Control of physical simulation has become a popular topic in the field of
computer graphics. Keyframe control has been applied to simulations of rigid bodies,
smoke, liquid, flocks, and finite element-based elastic bodies. In this paper,
we create a framework for controlling systems of interacting particles -- paying
special attention to simulations of cloth and flocking behavior. We introduce
a novel integrator-swapping approximation in order to apply the adjoint method
to linearized implicit schemes appropriate for cloth simulation. This allows the
control of cloth while avoiding computationally infeasible derivative calculations.
Meanwhile, flocking control using the adjoint method is significantly more efficient
than currently-used methods for constraining group behaviors, allowing the controlled
simulation of greater numbers of agents in fewer optimization iterations.
article_processing_charge: No
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: Peter
full_name: Mucha, Peter
last_name: Mucha
- first_name: Greg
full_name: Turk, Greg
last_name: Turk
citation:
ama: 'Wojtan C, Mucha P, Turk G. Keyframe control of complex particle systems using
the adjoint method. In: ACM; 2006:15-23.'
apa: 'Wojtan, C., Mucha, P., & Turk, G. (2006). Keyframe control of complex
particle systems using the adjoint method (pp. 15–23). Presented at the SCA: ACM
SIGGRAPH/Eurographics Symposium on Computer animation, ACM.'
chicago: Wojtan, Chris, Peter Mucha, and Greg Turk. “Keyframe Control of Complex
Particle Systems Using the Adjoint Method,” 15–23. ACM, 2006.
ieee: 'C. Wojtan, P. Mucha, and G. Turk, “Keyframe control of complex particle systems
using the adjoint method,” presented at the SCA: ACM SIGGRAPH/Eurographics Symposium
on Computer animation, 2006, pp. 15–23.'
ista: 'Wojtan C, Mucha P, Turk G. 2006. Keyframe control of complex particle systems
using the adjoint method. SCA: ACM SIGGRAPH/Eurographics Symposium on Computer
animation, 15–23.'
mla: Wojtan, Chris, et al. Keyframe Control of Complex Particle Systems Using
the Adjoint Method. ACM, 2006, pp. 15–23.
short: C. Wojtan, P. Mucha, G. Turk, in:, ACM, 2006, pp. 15–23.
conference:
name: 'SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation'
date_created: 2018-12-11T12:05:00Z
date_published: 2006-09-01T00:00:00Z
date_updated: 2023-02-23T11:41:22Z
day: '01'
extern: '1'
language:
- iso: eng
main_file_link:
- url: http://www.amath.unc.edu/Faculty/mucha/Reprints/SCAclothcontrolpreprint.pdf
month: '09'
oa_version: None
page: 15 - 23
publication_status: published
publisher: ACM
publist_id: '2469'
status: public
title: Keyframe control of complex particle systems using the adjoint method
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2006'
...
---
_id: '3818'
abstract:
- lang: eng
text: Rigorous analysis of synaptic transmission in the central nervous system requires
access to presynaptic terminals. However, cortical terminals have been largely
inaccessible to presynaptic patch-clamp recording, due to their small size. Using
improved patch-clamp techniques in brain slices, we recorded from mossy fiber
terminals in the CA3 region of the hippocampus, which have a diameter of 2-5 microm.
The major steps of improvement were the enhanced visibility provided by high-numerical
aperture objectives and infrared illumination, the development of vibratomes with
minimal vertical blade vibrations and the use of sucrose-based solutions for storage
and cutting. Based on these improvements, we describe a protocol that allows us
to routinely record from hippocampal mossy fiber boutons. Presynaptic recordings
can be obtained in slices from both rats and mice. Presynaptic recordings can
be also obtained in slices from transgenic mice in which terminals are labeled
with enhanced green fluorescent protein.
author:
- first_name: Josef
full_name: Bischofberger, Josef
last_name: Bischofberger
- first_name: Dominique
full_name: Engel, Dominique
last_name: Engel
- first_name: Liyi
full_name: Li, Liyi
last_name: Li
- first_name: Jörg
full_name: Geiger, Jörg R
last_name: Geiger
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Bischofberger J, Engel D, Li L, Geiger J, Jonas PM. Patch-clamp recording from
mossy fiber terminals in hippocampal slices. Nature Protocols. 2006;1(4):2075-2081.
doi:10.1038/nprot.2006.312
apa: Bischofberger, J., Engel, D., Li, L., Geiger, J., & Jonas, P. M. (2006).
Patch-clamp recording from mossy fiber terminals in hippocampal slices. Nature
Protocols. Nature Publishing Group. https://doi.org/10.1038/nprot.2006.312
chicago: Bischofberger, Josef, Dominique Engel, Liyi Li, Jörg Geiger, and Peter
M Jonas. “Patch-Clamp Recording from Mossy Fiber Terminals in Hippocampal Slices.”
Nature Protocols. Nature Publishing Group, 2006. https://doi.org/10.1038/nprot.2006.312 .
ieee: J. Bischofberger, D. Engel, L. Li, J. Geiger, and P. M. Jonas, “Patch-clamp
recording from mossy fiber terminals in hippocampal slices,” Nature Protocols,
vol. 1, no. 4. Nature Publishing Group, pp. 2075–81, 2006.
ista: Bischofberger J, Engel D, Li L, Geiger J, Jonas PM. 2006. Patch-clamp recording
from mossy fiber terminals in hippocampal slices. Nature Protocols. 1(4), 2075–81.
mla: Bischofberger, Josef, et al. “Patch-Clamp Recording from Mossy Fiber Terminals
in Hippocampal Slices.” Nature Protocols, vol. 1, no. 4, Nature Publishing
Group, 2006, pp. 2075–81, doi:10.1038/nprot.2006.312 .
short: J. Bischofberger, D. Engel, L. Li, J. Geiger, P.M. Jonas, Nature Protocols
1 (2006) 2075–81.
date_created: 2018-12-11T12:05:20Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:25Z
day: '01'
doi: '10.1038/nprot.2006.312 '
extern: 1
intvolume: ' 1'
issue: '4'
month: '01'
page: 2075 - 81
publication: Nature Protocols
publication_status: published
publisher: Nature Publishing Group
publist_id: '2392'
quality_controlled: 0
status: public
title: Patch-clamp recording from mossy fiber terminals in hippocampal slices
type: journal_article
volume: 1
year: '2006'
...
---
_id: '3890'
abstract:
- lang: eng
text: We consider two-player infinite games played on graphs. The games are concurrent,
in that at each state the players choose their moves simultaneously and independently,
and stochastic, in that the moves determine a probability distribution for the
successor state. The value of a game is the maximal probability with which a player
can guarantee the satisfaction of her objective. We show that the values of concurrent
games with w-regular objectives expressed as parity conditions can be decided
in NP boolean AND coNP. This result substantially improves the best known previous
bound of 3EXPTIME. It also shows that the full class of concurrent parity games
is no harder than the special case of turn-based stochastic reachability games,
for which NP boolean AND coNP is the best known bound. While the previous, more
restricted NP boolean AND coNP results for graph games relied on the existence
of particularly simple (pure memoryless) optimal strategies, in concurrent games
with parity objectives optimal strategies may not exist, and epsilon-optimal strategies
(which achieve the value of the game within a parameter epsilon > 0) require
in general both randomization and infinite memory. Hence our proof must rely on
a more detailed analysis of strategies and, in addition to the main result, yields
two results that are interesting on their own. First, we show that there exist
epsilon-optimal strategies that in the limit coincide with memoryless strategies;
this parallels the celebrated result of Mertens-Neyman for concurrent games with
limit-average objectives. Second, we complete the characterization of the memory
requirements for epsilon-optimal strategies for concurrent games with parity conditions,
by showing that memoryless strategies suffice for epsilon-optimality for coBachi
conditions.
acknowledgement: This research was supported in part by the AFOSR MURI grant F49620-00-1-0327
and the NSF ITR grant CCR-0225610.
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Luca
full_name: de Alfaro, Luca
last_name: De Alfaro
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Chatterjee K, De Alfaro L, Henzinger TA. The complexity of quantitative concurrent
parity games. In: SIAM; 2006:678-687. doi:10.1145/1109557.1109631'
apa: 'Chatterjee, K., De Alfaro, L., & Henzinger, T. A. (2006). The complexity
of quantitative concurrent parity games (pp. 678–687). Presented at the SODA:
Symposium on Discrete Algorithms, SIAM. https://doi.org/10.1145/1109557.1109631'
chicago: Chatterjee, Krishnendu, Luca De Alfaro, and Thomas A Henzinger. “The Complexity
of Quantitative Concurrent Parity Games,” 678–87. SIAM, 2006. https://doi.org/10.1145/1109557.1109631.
ieee: 'K. Chatterjee, L. De Alfaro, and T. A. Henzinger, “The complexity of quantitative
concurrent parity games,” presented at the SODA: Symposium on Discrete Algorithms,
2006, pp. 678–687.'
ista: 'Chatterjee K, De Alfaro L, Henzinger TA. 2006. The complexity of quantitative
concurrent parity games. SODA: Symposium on Discrete Algorithms, 678–687.'
mla: Chatterjee, Krishnendu, et al. The Complexity of Quantitative Concurrent
Parity Games. SIAM, 2006, pp. 678–87, doi:10.1145/1109557.1109631.
short: K. Chatterjee, L. De Alfaro, T.A. Henzinger, in:, SIAM, 2006, pp. 678–687.
conference:
name: 'SODA: Symposium on Discrete Algorithms'
date_created: 2018-12-11T12:05:43Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:59Z
day: '01'
doi: 10.1145/1109557.1109631
extern: 1
month: '01'
page: 678 - 687
publication_status: published
publisher: SIAM
publist_id: '2273'
quality_controlled: 0
status: public
title: The complexity of quantitative concurrent parity games
type: conference
year: '2006'
...
---
_id: '3889'
abstract:
- lang: eng
text: We study observation-based strategies for two-player turn-based games on graphs
with omega-regular objectives. An observation-based strategy relies on imperfect
information about the history of a play, namely, on the past sequence of observations.
Such games occur in the synthesis of a controller that does not see the private
state of the plant. Our main results are twofold. First, we give a fixed-point
algorithm for computing the set of states from which a player can win with a deterministic
observation-based strategy for any omega-regular objective. The fixed point is
computed in the lattice of antichains of state sets. This algorithm has the advantages
of being directed by the objective and of avoiding an explicit subset construction
on the game graph. Second, we give an algorithm for computing the set of states
from which a player can win with probability 1 with a randomized observation-based
strategy for a Buchi objective. This set is of interest because in the absence
of perfect information, randomized strategies are more powerful than deterministic
ones. We show that our algorithms are optimal by proving matching lower bounds.
acknowledgement: This research was supported in part by the NSF grants CCR-0225610
and CCR-0234690, by the SNSF under the Indo-Swiss Joint Research Programme, and
by the FRFC project “Centre Fédéré en Vérification” funded by the FNRS under grant
2.4530.02.
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: Laurent
full_name: Doyen, Laurent
last_name: Doyen
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jean
full_name: Raskin, Jean-François
last_name: Raskin
citation:
ama: 'Chatterjee K, Doyen L, Henzinger TA, Raskin J. Algorithms for omega-regular
games with imperfect information. In: Vol 4207. Springer; 2006:287-302. doi:10.1007/11874683_19'
apa: 'Chatterjee, K., Doyen, L., Henzinger, T. A., & Raskin, J. (2006). Algorithms
for omega-regular games with imperfect information (Vol. 4207, pp. 287–302). Presented
at the CSL: Computer Science Logic, Springer. https://doi.org/10.1007/11874683_19'
chicago: Chatterjee, Krishnendu, Laurent Doyen, Thomas A Henzinger, and Jean Raskin.
“Algorithms for Omega-Regular Games with Imperfect Information,” 4207:287–302.
Springer, 2006. https://doi.org/10.1007/11874683_19.
ieee: 'K. Chatterjee, L. Doyen, T. A. Henzinger, and J. Raskin, “Algorithms for
omega-regular games with imperfect information,” presented at the CSL: Computer
Science Logic, 2006, vol. 4207, pp. 287–302.'
ista: 'Chatterjee K, Doyen L, Henzinger TA, Raskin J. 2006. Algorithms for omega-regular
games with imperfect information. CSL: Computer Science Logic, LNCS, vol. 4207,
287–302.'
mla: Chatterjee, Krishnendu, et al. Algorithms for Omega-Regular Games with Imperfect
Information. Vol. 4207, Springer, 2006, pp. 287–302, doi:10.1007/11874683_19.
short: K. Chatterjee, L. Doyen, T.A. Henzinger, J. Raskin, in:, Springer, 2006,
pp. 287–302.
conference:
name: 'CSL: Computer Science Logic'
date_created: 2018-12-11T12:05:43Z
date_published: 2006-11-13T00:00:00Z
date_updated: 2021-01-12T07:52:59Z
day: '13'
doi: 10.1007/11874683_19
extern: 1
intvolume: ' 4207'
month: '11'
page: 287 - 302
publication_status: published
publisher: Springer
publist_id: '2276'
quality_controlled: 0
status: public
title: Algorithms for omega-regular games with imperfect information
type: conference
volume: 4207
year: '2006'
...
---
_id: '3891'
abstract:
- lang: eng
text: 'We study infinite stochastic games played by two-players over a finite state
space, with objectives specified by sets of infinite traces. The games are concurrent
(players make moves simultaneously and independently), stochastic (the next state
is determined by a probability distribution that depends on the current state
and chosen moves of the players) and infinite (proceeds for infinite number of
rounds). The analysis of concurrent stochastic games can be classified into: quantitative
analysis, analyzing the optimum value of the game; and qualitative analysis, analyzing
the set of states with optimum value 1. We consider concurrent games with tail
objectives, i.e., objectives that are independent of the finite-prefix of traces,
and show that the class of tail objectives are strictly richer than the omega-regular
objectives. We develop new proof techniques to extend several properties of concurrent
games with omega-regular objectives to concurrent games with tail objectives.
We prove the positive limit-one property for tail objectives, that states for
all concurrent games if the optimum value for a player is positive for a tail
objective Phi at some state, then there is a state where the optimum value is
1 for Phi, for the player. We also show that the optimum values of zero-sum (strictly
conflicting objectives) games with tail objectives can be related to equilibrium
values of nonzero-sum (not strictly conflicting objectives) games with simpler
reachability objectives. A consequence of our analysis presents a polynomial time
reduction of the quantitative analysis of tail objectives to the qualitative analysis
for the sub-class of one-player stochastic games (Markov decision processes).'
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. Concurrent games with tail objectives. In: Vol 4207. Springer;
2006:256-270. doi:10.1007/11874683_17'
apa: 'Chatterjee, K. (2006). Concurrent games with tail objectives (Vol. 4207, pp.
256–270). Presented at the CSL: Computer Science Logic, Springer. https://doi.org/10.1007/11874683_17'
chicago: Chatterjee, Krishnendu. “Concurrent Games with Tail Objectives,” 4207:256–70.
Springer, 2006. https://doi.org/10.1007/11874683_17.
ieee: 'K. Chatterjee, “Concurrent games with tail objectives,” presented at the
CSL: Computer Science Logic, 2006, vol. 4207, pp. 256–270.'
ista: 'Chatterjee K. 2006. Concurrent games with tail objectives. CSL: Computer
Science Logic, LNCS , vol. 4207, 256–270.'
mla: Chatterjee, Krishnendu. Concurrent Games with Tail Objectives. Vol.
4207, Springer, 2006, pp. 256–70, doi:10.1007/11874683_17.
short: K. Chatterjee, in:, Springer, 2006, pp. 256–270.
conference:
name: 'CSL: Computer Science Logic'
date_created: 2018-12-11T12:05:44Z
date_published: 2006-09-28T00:00:00Z
date_updated: 2021-01-12T07:53:00Z
day: '28'
doi: 10.1007/11874683_17
extern: 1
intvolume: ' 4207'
month: '09'
page: 256 - 270
publication_status: published
publisher: Springer
publist_id: '2272'
quality_controlled: 0
status: public
title: Concurrent games with tail objectives
type: conference
volume: 4207
year: '2006'
...
---
_id: '3888'
abstract:
- lang: eng
text: A stochastic graph game is played by two players on a game graph with probabilistic
transitions. We consider stochastic graph games with omega-regular winning conditions
specified as Rabin or Streett objectives. These games are NP-complete and coNP-complete,
respectively. The value of the game for a player at a state s given an objective
Phi is the maximal probability with which the player can guarantee the satisfaction
of Phi from s. We present a strategy-improvement algorithm to compute values in
stochastic Rabin games, where an improvement step involves solving Markov decision
processes (MDPs) and nonstochastic Rabin games. The algorithm also computes values
for stochastic Streett games but does not directly yield an optimal strategy for
Streett objectives. We then show how to obtain an optimal strategy for Streett
objectives by solving certain nonstochastic Streett games.
acknowledgement: This research was supported in part by the NSF grants CCR-0225610
and CCR-0234690, and by the SNSF under the Indo-Swiss Joint Research Programme.
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
citation:
ama: 'Chatterjee K, Henzinger TA. Strategy improvement for stochastic Rabin and
Streett games. In: Vol 4137. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2006:375-389. doi:10.1007/11817949_25'
apa: 'Chatterjee, K., & Henzinger, T. A. (2006). Strategy improvement for stochastic
Rabin and Streett games (Vol. 4137, pp. 375–389). Presented at the CONCUR: Concurrency
Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/11817949_25'
chicago: Chatterjee, Krishnendu, and Thomas A Henzinger. “Strategy Improvement for
Stochastic Rabin and Streett Games,” 4137:375–89. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2006. https://doi.org/10.1007/11817949_25.
ieee: 'K. Chatterjee and T. A. Henzinger, “Strategy improvement for stochastic Rabin
and Streett games,” presented at the CONCUR: Concurrency Theory, 2006, vol. 4137,
pp. 375–389.'
ista: 'Chatterjee K, Henzinger TA. 2006. Strategy improvement for stochastic Rabin
and Streett games. CONCUR: Concurrency Theory, LNCS, vol. 4137, 375–389.'
mla: Chatterjee, Krishnendu, and Thomas A. Henzinger. Strategy Improvement for
Stochastic Rabin and Streett Games. Vol. 4137, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2006, pp. 375–89, doi:10.1007/11817949_25.
short: K. Chatterjee, T.A. Henzinger, in:, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2006, pp. 375–389.
conference:
name: 'CONCUR: Concurrency Theory'
date_created: 2018-12-11T12:05:43Z
date_published: 2006-08-10T00:00:00Z
date_updated: 2021-01-12T07:52:58Z
day: '10'
doi: 10.1007/11817949_25
extern: 1
intvolume: ' 4137'
month: '08'
page: 375 - 389
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '2278'
quality_controlled: 0
status: public
title: Strategy improvement for stochastic Rabin and Streett games
type: conference
volume: 4137
year: '2006'
...
---
_id: '3908'
abstract:
- lang: eng
text: 'It is commonly believed that both the average length and the frequency of
microsatellites correlate with genome size. We have estimated the frequency and
the average length for 69 perfect dinucleotide microsatellites in an insect with
an exceptionally large genome: Chorthippus biguttulus (Orthoptera, Acrididae).
Dinucleotide microsatellites are not more frequent in C. biguttulus, but repeat
arrays are 1.4 to 2 times longer than in other insect species. The average repeat
number in C. biguttulus lies in the range of higher vertebrates. Natural populations
are highly variable. At least 30 alleles per locus were found and the expected
heterozygosity is above 0.95 at all three loci studied. In contrast, the observed
heterozygosity is much lower (≤0.51), which could be caused by long null alleles.'
author:
- first_name: Jana
full_name: Ustinova, Jana
last_name: Ustinova
- first_name: Roland
full_name: Achmann, Roland
last_name: Achmann
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Frieder
full_name: Mayer, Frieder
last_name: Mayer
citation:
ama: 'Ustinova J, Achmann R, Cremer S, Mayer F. Long repeats in a huge gemome: microsatellite
loci in the grasshopper Chorthippus biguttulus. Journal of Molecular Evolution.
2006;62(2):158-167. doi:10.1007/s00239-005-0022-6'
apa: 'Ustinova, J., Achmann, R., Cremer, S., & Mayer, F. (2006). Long repeats
in a huge gemome: microsatellite loci in the grasshopper Chorthippus biguttulus.
Journal of Molecular Evolution. Springer. https://doi.org/10.1007/s00239-005-0022-6'
chicago: 'Ustinova, Jana, Roland Achmann, Sylvia Cremer, and Frieder Mayer. “Long
Repeats in a Huge Gemome: Microsatellite Loci in the Grasshopper Chorthippus Biguttulus.”
Journal of Molecular Evolution. Springer, 2006. https://doi.org/10.1007/s00239-005-0022-6.'
ieee: 'J. Ustinova, R. Achmann, S. Cremer, and F. Mayer, “Long repeats in a huge
gemome: microsatellite loci in the grasshopper Chorthippus biguttulus,” Journal
of Molecular Evolution, vol. 62, no. 2. Springer, pp. 158–167, 2006.'
ista: 'Ustinova J, Achmann R, Cremer S, Mayer F. 2006. Long repeats in a huge gemome:
microsatellite loci in the grasshopper Chorthippus biguttulus. Journal of Molecular
Evolution. 62(2), 158–167.'
mla: 'Ustinova, Jana, et al. “Long Repeats in a Huge Gemome: Microsatellite Loci
in the Grasshopper Chorthippus Biguttulus.” Journal of Molecular Evolution,
vol. 62, no. 2, Springer, 2006, pp. 158–67, doi:10.1007/s00239-005-0022-6.'
short: J. Ustinova, R. Achmann, S. Cremer, F. Mayer, Journal of Molecular Evolution
62 (2006) 158–167.
date_created: 2018-12-11T12:05:49Z
date_published: 2006-02-01T00:00:00Z
date_updated: 2021-01-12T07:53:07Z
day: '01'
doi: 10.1007/s00239-005-0022-6
extern: '1'
intvolume: ' 62'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 158 - 167
publication: Journal of Molecular Evolution
publication_status: published
publisher: Springer
publist_id: '2242'
status: public
title: 'Long repeats in a huge gemome: microsatellite loci in the grasshopper Chorthippus
biguttulus'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 62
year: '2006'
...