---
_id: '4237'
abstract:
- lang: eng
text: The growth function of populations is central in biomathematics. The main
dogma is the existence of density-dependence mechanisms, which can be modelled
with distinct functional forms that depend on the size of the Population. One
important class of regulatory functions is the theta-logistic, which generalizes
the logistic equation. Using this model as a motivation, this paper introduces
a simple dynamical reformulation that generalizes many growth functions. The reformulation
consists of two equations, one for population size, and one for the growth rate.
Furthermore, the model shows that although population is density-dependent, the
dynamics of the growth rate does not depend either on population size, nor on
the carrying capacity. Actually, the growth equation is uncoupled from the population
size equation, and the model has only two parameters, a Malthusian parameter rho
and a competition coefficient theta. Distinct sign combinations of these parameters
reproduce not only the family of theta-logistics, but also the van Bertalanffy,
Gompertz and Potential Growth equations, among other possibilities. It is also
shown that, except for two critical points, there is a general size-scaling relation
that includes those appearing in the most important allometric theories, including
the recently proposed Metabolic Theory of Ecology. With this model, several issues
of general interest are discussed such as the growth of animal population, extinctions,
cell growth and allometry, and the effect of environment over a population. (c)
2005 Elsevier Ltd. All rights reserved.
article_processing_charge: No
author:
- first_name: Harold
full_name: de Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: de Vladar
orcid: 0000-0002-5985-7653
citation:
ama: de Vladar H. Density-dependence as a size-independent regulatory mechanism.
Journal of Theoretical Biology. 2006;238(2):245-256. doi:3802
apa: de Vladar, H. (2006). Density-dependence as a size-independent regulatory mechanism.
Journal of Theoretical Biology. Elsevier. https://doi.org/3802
chicago: Vladar, Harold de. “Density-Dependence as a Size-Independent Regulatory
Mechanism.” Journal of Theoretical Biology. Elsevier, 2006. https://doi.org/3802.
ieee: H. de Vladar, “Density-dependence as a size-independent regulatory mechanism,”
Journal of Theoretical Biology, vol. 238, no. 2. Elsevier, pp. 245–256,
2006.
ista: de Vladar H. 2006. Density-dependence as a size-independent regulatory mechanism.
Journal of Theoretical Biology. 238(2), 245–256.
mla: de Vladar, Harold. “Density-Dependence as a Size-Independent Regulatory Mechanism.”
Journal of Theoretical Biology, vol. 238, no. 2, Elsevier, 2006, pp. 245–56,
doi:3802.
short: H. de Vladar, Journal of Theoretical Biology 238 (2006) 245–256.
date_created: 2018-12-11T12:07:46Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:55:31Z
day: '01'
doi: '3802'
extern: '1'
intvolume: ' 238'
issue: '2'
language:
- iso: eng
month: '01'
oa_version: None
page: 245 - 256
publication: Journal of Theoretical Biology
publication_status: published
publisher: Elsevier
publist_id: '1878'
status: public
title: Density-dependence as a size-independent regulatory mechanism
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 238
year: '2006'
...
---
_id: '4235'
author:
- first_name: Harold
full_name: Harold Vladar
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: Vladar
orcid: 0000-0002-5985-7653
- first_name: J.
full_name: González,J. A
last_name: González
citation:
ama: de Vladar H, González J. Dynamic response of cancer under the influence of
immunological activity and therapy. Journal of Theoretical Biology. 2006:91-109.
apa: de Vladar, H., & González, J. (2006). Dynamic response of cancer under
the influence of immunological activity and therapy. Journal of Theoretical
Biology. Elsevier.
chicago: Vladar, Harold de, and J. González. “Dynamic Response of Cancer under the
Influence of Immunological Activity and Therapy.” Journal of Theoretical Biology.
Elsevier, 2006.
ieee: H. de Vladar and J. González, “Dynamic response of cancer under the influence
of immunological activity and therapy,” Journal of Theoretical Biology.
Elsevier, pp. 91–109, 2006.
ista: de Vladar H, González J. 2006. Dynamic response of cancer under the influence
of immunological activity and therapy. Journal of Theoretical Biology., 91–109.
mla: de Vladar, Harold, and J. González. “Dynamic Response of Cancer under the Influence
of Immunological Activity and Therapy.” Journal of Theoretical Biology,
Elsevier, 2006, pp. 91–109.
short: H. de Vladar, J. González, Journal of Theoretical Biology (2006) 91–109.
date_created: 2018-12-11T12:07:45Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:55:30Z
day: '01'
extern: 1
month: '01'
page: 91 - 109
publication: Journal of Theoretical Biology
publication_status: published
publisher: Elsevier
publist_id: '1879'
quality_controlled: 0
status: public
title: Dynamic response of cancer under the influence of immunological activity and
therapy
type: journal_article
year: '2006'
...
---
_id: '4248'
abstract:
- lang: eng
text: 'In finite populations, genetic drift generates interference between selected
loci, causing advantageous alleles to be found more often on different chromosomes
than on the same chromosome, which reduces the rate of adaptation. This “Hill–Robertson
effect” generates indirect selection to increase recombination rates. We present
a new method to quantify the strength of this selection. Our model represents
a new beneficial allele (A) entering a population as a single copy, while another
beneficial allele (B) is sweeping at another locus. A third locus affects the
recombination rate between selected loci. Using a branching process model, we
calculate the probability distribution of the number of copies of A on the different
genetic backgrounds, after it is established but while it is still rare. Then,
we use a deterministic model to express the change in frequency of the recombination
modifier, due to hitchhiking, as A goes to fixation. We show that this method
can give good estimates of selection for recombination. Moreover, it shows that
recombination is selected through two different effects: it increases the fixation
probability of new alleles, and it accelerates selective sweeps. The relative
importance of these two effects depends on the relative times of occurrence of
the beneficial alleles.'
author:
- first_name: Denis
full_name: Roze, Denis
last_name: Roze
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Roze D, Barton NH. The Hill-Robertson effect and the evolution of recombination.
Genetics. 2006;173(3):1793-1811. doi:10.1534/genetics.106.058586
apa: Roze, D., & Barton, N. H. (2006). The Hill-Robertson effect and the evolution
of recombination. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.106.058586
chicago: Roze, Denis, and Nicholas H Barton. “The Hill-Robertson Effect and the
Evolution of Recombination.” Genetics. Genetics Society of America, 2006.
https://doi.org/10.1534/genetics.106.058586
.
ieee: D. Roze and N. H. Barton, “The Hill-Robertson effect and the evolution of
recombination,” Genetics, vol. 173, no. 3. Genetics Society of America,
pp. 1793–1811, 2006.
ista: Roze D, Barton NH. 2006. The Hill-Robertson effect and the evolution of recombination.
Genetics. 173(3), 1793–1811.
mla: Roze, Denis, and Nicholas H. Barton. “The Hill-Robertson Effect and the Evolution
of Recombination.” Genetics, vol. 173, no. 3, Genetics Society of America,
2006, pp. 1793–811, doi:10.1534/genetics.106.058586
.
short: D. Roze, N.H. Barton, Genetics 173 (2006) 1793–1811.
date_created: 2018-12-11T12:07:50Z
date_published: 2006-07-01T00:00:00Z
date_updated: 2021-01-12T07:55:36Z
day: '01'
doi: '10.1534/genetics.106.058586 '
extern: 1
intvolume: ' 173'
issue: '3'
month: '07'
page: 1793 - 1811
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '1854'
quality_controlled: 0
status: public
title: The Hill-Robertson effect and the evolution of recombination
type: journal_article
volume: 173
year: '2006'
...
---
_id: '4250'
abstract:
- lang: eng
text: A recent analysis has shown that divergence between human and chimpanzee varies
greatly across the genome. Although this is consistent with ‘hybridisation’ between
the diverging human and chimp lineages, such observations can be explained more
simply by the null model of allopatric speciation.
author:
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Barton NH. Evolutionary Biology: How did the human species form? Current
Biology. 2006;16(16):647-650. doi:10.1016/j.cub.2006.07.032'
apa: 'Barton, N. H. (2006). Evolutionary Biology: How did the human species form?
Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2006.07.032'
chicago: 'Barton, Nicholas H. “Evolutionary Biology: How Did the Human Species Form?”
Current Biology. Cell Press, 2006. https://doi.org/10.1016/j.cub.2006.07.032.'
ieee: 'N. H. Barton, “Evolutionary Biology: How did the human species form?,” Current
Biology, vol. 16, no. 16. Cell Press, pp. 647–650, 2006.'
ista: 'Barton NH. 2006. Evolutionary Biology: How did the human species form? Current
Biology. 16(16), 647–650.'
mla: 'Barton, Nicholas H. “Evolutionary Biology: How Did the Human Species Form?”
Current Biology, vol. 16, no. 16, Cell Press, 2006, pp. 647–50, doi:10.1016/j.cub.2006.07.032.'
short: N.H. Barton, Current Biology 16 (2006) 647–650.
date_created: 2018-12-11T12:07:51Z
date_published: 2006-08-22T00:00:00Z
date_updated: 2019-04-26T07:22:41Z
day: '22'
doi: 10.1016/j.cub.2006.07.032
extern: 1
intvolume: ' 16'
issue: '16'
month: '08'
page: 647 - 650
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '1850'
quality_controlled: 0
status: public
title: 'Evolutionary Biology: How did the human species form?'
type: review
volume: 16
year: '2006'
...
---
_id: '4359'
alternative_title:
- LNCS 3855
author:
- first_name: Thomas
full_name: Thomas Wies
id: 447BFB88-F248-11E8-B48F-1D18A9856A87
last_name: Wies
- first_name: Viktor
full_name: Kuncak, Viktor
last_name: Kuncak
- first_name: Patrick
full_name: Lam,Patrick
last_name: Lam
- first_name: Andreas
full_name: Podelski,Andreas
last_name: Podelski
- first_name: Martin
full_name: Rinard,Martin
last_name: Rinard
citation:
ama: 'Wies T, Kuncak V, Lam P, Podelski A, Rinard M. Field Constraint Analysis.
In: Springer; 2006:157-173. doi:1551'
apa: 'Wies, T., Kuncak, V., Lam, P., Podelski, A., & Rinard, M. (2006). Field
Constraint Analysis (pp. 157–173). Presented at the VMCAI: Verification, Model
Checking and Abstract Interpretation, Springer. https://doi.org/1551'
chicago: Wies, Thomas, Viktor Kuncak, Patrick Lam, Andreas Podelski, and Martin
Rinard. “Field Constraint Analysis,” 157–73. Springer, 2006. https://doi.org/1551.
ieee: 'T. Wies, V. Kuncak, P. Lam, A. Podelski, and M. Rinard, “Field Constraint
Analysis,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation,
2006, pp. 157–173.'
ista: 'Wies T, Kuncak V, Lam P, Podelski A, Rinard M. 2006. Field Constraint Analysis.
VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS 3855, ,
157–173.'
mla: Wies, Thomas, et al. Field Constraint Analysis. Springer, 2006, pp.
157–73, doi:1551.
short: T. Wies, V. Kuncak, P. Lam, A. Podelski, M. Rinard, in:, Springer, 2006,
pp. 157–173.
conference:
name: 'VMCAI: Verification, Model Checking and Abstract Interpretation'
date_created: 2018-12-11T12:08:27Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:56:23Z
day: '01'
doi: '1551'
extern: 1
month: '01'
page: 157 - 173
publication_status: published
publisher: Springer
publist_id: '1097'
quality_controlled: 0
status: public
title: Field Constraint Analysis
type: conference
year: '2006'
...
---
_id: '4373'
alternative_title:
- LNCS
author:
- first_name: Oded
full_name: Maler, Oded
last_name: Maler
- first_name: Dejan
full_name: Dejan Nickovic
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
- first_name: Amir
full_name: Pnueli,Amir
last_name: Pnueli
citation:
ama: 'Maler O, Nickovic D, Pnueli A. Real Time Temporal Logic: Past, Present, Future.
In: Springer; 2006:2-16. doi:1571'
apa: 'Maler, O., Nickovic, D., & Pnueli, A. (2006). Real Time Temporal Logic:
Past, Present, Future (pp. 2–16). Presented at the FORMATS: Formal Modeling and
Analysis of Timed Systems, Springer. https://doi.org/1571'
chicago: 'Maler, Oded, Dejan Nickovic, and Amir Pnueli. “Real Time Temporal Logic:
Past, Present, Future,” 2–16. Springer, 2006. https://doi.org/1571.'
ieee: 'O. Maler, D. Nickovic, and A. Pnueli, “Real Time Temporal Logic: Past, Present,
Future,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems,
2006, pp. 2–16.'
ista: 'Maler O, Nickovic D, Pnueli A. 2006. Real Time Temporal Logic: Past, Present,
Future. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, , 2–16.'
mla: 'Maler, Oded, et al. Real Time Temporal Logic: Past, Present, Future.
Springer, 2006, pp. 2–16, doi:1571.'
short: O. Maler, D. Nickovic, A. Pnueli, in:, Springer, 2006, pp. 2–16.
conference:
name: 'FORMATS: Formal Modeling and Analysis of Timed Systems'
date_created: 2018-12-11T12:08:31Z
date_published: 2006-01-23T00:00:00Z
date_updated: 2021-01-12T07:56:29Z
day: '23'
doi: '1571'
extern: 1
month: '01'
page: 2 - 16
publication_status: published
publisher: Springer
publist_id: '1084'
quality_controlled: 0
status: public
title: 'Real Time Temporal Logic: Past, Present, Future'
type: conference
year: '2006'
...
---
_id: '4374'
alternative_title:
- LNCS
author:
- first_name: Oded
full_name: Maler, Oded
last_name: Maler
- first_name: Dejan
full_name: Dejan Nickovic
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
- first_name: Amir
full_name: Pnueli,Amir
last_name: Pnueli
citation:
ama: 'Maler O, Nickovic D, Pnueli A. From MITL to Timed Automata. In: Springer;
2006:274-289. doi:1570'
apa: 'Maler, O., Nickovic, D., & Pnueli, A. (2006). From MITL to Timed Automata
(pp. 274–289). Presented at the FORMATS: Formal Modeling and Analysis of Timed
Systems, Springer. https://doi.org/1570'
chicago: Maler, Oded, Dejan Nickovic, and Amir Pnueli. “From MITL to Timed Automata,”
274–89. Springer, 2006. https://doi.org/1570.
ieee: 'O. Maler, D. Nickovic, and A. Pnueli, “From MITL to Timed Automata,” presented
at the FORMATS: Formal Modeling and Analysis of Timed Systems, 2006, pp. 274–289.'
ista: 'Maler O, Nickovic D, Pnueli A. 2006. From MITL to Timed Automata. FORMATS:
Formal Modeling and Analysis of Timed Systems, LNCS, , 274–289.'
mla: Maler, Oded, et al. From MITL to Timed Automata. Springer, 2006, pp.
274–89, doi:1570.
short: O. Maler, D. Nickovic, A. Pnueli, in:, Springer, 2006, pp. 274–289.
conference:
name: 'FORMATS: Formal Modeling and Analysis of Timed Systems'
date_created: 2018-12-11T12:08:31Z
date_published: 2006-10-19T00:00:00Z
date_updated: 2021-01-12T07:56:30Z
day: '19'
doi: '1570'
extern: 1
month: '10'
page: 274 - 289
publication_status: published
publisher: Springer
publist_id: '1085'
quality_controlled: 0
status: public
title: From MITL to Timed Automata
type: conference
year: '2006'
...
---
_id: '4406'
abstract:
- lang: eng
text: We propose and evaluate a new algorithm for checking the universality of nondeterministic
finite automata. In contrast to the standard algorithm, which uses the subset
construction to explicitly determinize the automaton, we keep the determinization
step implicit. Our algorithm computes the least fixed point of a monotone function
on the lattice of antichains of state sets. We evaluate the performance of our
algorithm experimentally using the random automaton model recently proposed by
Tabakov and Vardi. We show that on the difficult instances of this probabilistic
model, the antichain algorithm outperforms the standard one by several orders
of magnitude. We also show how variations of the antichain method can be used
for solving the language-inclusion problem for nondeterministic finite automata,
and the emptiness problem for alternating finite automata.
acknowledgement: This research was supported in part by the NSF grants CCR-0234690
and CCR-0225610, and the Belgian FNRS grant 2.4530.02 of the FRFC project “Centre
Fédéré en Vérification.”
alternative_title:
- LNCS
author:
- first_name: Martin
full_name: De Wulf, Martin
last_name: De Wulf
- 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: 'De Wulf M, Doyen L, Henzinger TA, Raskin J. Antichains: A new algorithm for
checking universality of finite automata. In: Vol 4144. Springer; 2006:17-30.
doi:10.1007/11817963_5'
apa: 'De Wulf, M., Doyen, L., Henzinger, T. A., & Raskin, J. (2006). Antichains:
A new algorithm for checking universality of finite automata (Vol. 4144, pp. 17–30).
Presented at the CAV: Computer Aided Verification, Springer. https://doi.org/10.1007/11817963_5'
chicago: 'De Wulf, Martin, Laurent Doyen, Thomas A Henzinger, and Jean Raskin. “Antichains:
A New Algorithm for Checking Universality of Finite Automata,” 4144:17–30. Springer,
2006. https://doi.org/10.1007/11817963_5.'
ieee: 'M. De Wulf, L. Doyen, T. A. Henzinger, and J. Raskin, “Antichains: A new
algorithm for checking universality of finite automata,” presented at the CAV:
Computer Aided Verification, 2006, vol. 4144, pp. 17–30.'
ista: 'De Wulf M, Doyen L, Henzinger TA, Raskin J. 2006. Antichains: A new algorithm
for checking universality of finite automata. CAV: Computer Aided Verification,
LNCS, vol. 4144, 17–30.'
mla: 'De Wulf, Martin, et al. Antichains: A New Algorithm for Checking Universality
of Finite Automata. Vol. 4144, Springer, 2006, pp. 17–30, doi:10.1007/11817963_5.'
short: M. De Wulf, L. Doyen, T.A. Henzinger, J. Raskin, in:, Springer, 2006, pp.
17–30.
conference:
name: 'CAV: Computer Aided Verification'
date_created: 2018-12-11T12:08:41Z
date_published: 2006-08-08T00:00:00Z
date_updated: 2021-01-12T07:56:45Z
day: '08'
doi: 10.1007/11817963_5
extern: 1
intvolume: ' 4144'
month: '08'
page: 17 - 30
publication_status: published
publisher: Springer
publist_id: '326'
quality_controlled: 0
status: public
title: 'Antichains: A new algorithm for checking universality of finite automata'
type: conference
volume: 4144
year: '2006'
...
---
_id: '4401'
alternative_title:
- LNCS
author:
- first_name: Rajeev
full_name: Alur, Rajeev
last_name: Alur
- first_name: Pavol
full_name: Pavol Cerny
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- first_name: Steve
full_name: Zdancewic,Steve
last_name: Zdancewic
citation:
ama: 'Alur R, Cerny P, Zdancewic S. Preserving Secrecy Under Refinement. In: Springer;
2006:107-118. doi:1543'
apa: 'Alur, R., Cerny, P., & Zdancewic, S. (2006). Preserving Secrecy Under
Refinement (pp. 107–118). Presented at the ICALP: Automata, Languages and Programming,
Springer. https://doi.org/1543'
chicago: Alur, Rajeev, Pavol Cerny, and Steve Zdancewic. “Preserving Secrecy Under
Refinement,” 107–18. Springer, 2006. https://doi.org/1543.
ieee: 'R. Alur, P. Cerny, and S. Zdancewic, “Preserving Secrecy Under Refinement,”
presented at the ICALP: Automata, Languages and Programming, 2006, pp. 107–118.'
ista: 'Alur R, Cerny P, Zdancewic S. 2006. Preserving Secrecy Under Refinement.
ICALP: Automata, Languages and Programming, LNCS, , 107–118.'
mla: Alur, Rajeev, et al. Preserving Secrecy Under Refinement. Springer,
2006, pp. 107–18, doi:1543.
short: R. Alur, P. Cerny, S. Zdancewic, in:, Springer, 2006, pp. 107–118.
conference:
name: 'ICALP: Automata, Languages and Programming'
date_created: 2018-12-11T12:08:40Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:56:42Z
day: '01'
doi: '1543'
extern: 1
month: '01'
page: 107 - 118
publication_status: published
publisher: Springer
publist_id: '1054'
quality_controlled: 0
status: public
title: Preserving Secrecy Under Refinement
type: conference
year: '2006'
...
---
_id: '4437'
abstract:
- lang: eng
text: The synthesis of reactive systems requires the solution of two-player games
on graphs with ω-regular objectives. When the objective is specified by a linear
temporal logic formula or nondeterministic Büchi automaton, then previous algorithms
for solving the game require the construction of an equivalent deterministic automaton.
However, determinization for automata on infinite words is extremely complicated,
and current implementations fail to produce deterministic automata even for relatively
small inputs. We show how to construct, from a given nondeterministic Büchi automaton,
an equivalent nondeterministic parity automaton that is good for solving games
with objective . The main insight is that a nondeterministic automaton is good
for solving games if it fairly simulates the equivalent deterministic automaton.
In this way, we omit the determinization step in game solving and reactive synthesis.
The fact that our automata are nondeterministic makes them surprisingly simple,
amenable to symbolic implementation, and allows an incremental search for winning
strategies.
acknowledgement: This research was supported in part by the Swiss National Science
Foundation.
alternative_title:
- LNCS
author:
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Nir
full_name: Piterman, Nir
last_name: Piterman
citation:
ama: 'Henzinger TA, Piterman N. Solving games without determinization. In: Vol 4207.
Springer; 2006:395-410. doi:10.1007/11874683_26'
apa: 'Henzinger, T. A., & Piterman, N. (2006). Solving games without determinization
(Vol. 4207, pp. 395–410). Presented at the CSL: Computer Science Logic, Springer.
https://doi.org/10.1007/11874683_26'
chicago: Henzinger, Thomas A, and Nir Piterman. “Solving Games without Determinization,”
4207:395–410. Springer, 2006. https://doi.org/10.1007/11874683_26.
ieee: 'T. A. Henzinger and N. Piterman, “Solving games without determinization,”
presented at the CSL: Computer Science Logic, 2006, vol. 4207, pp. 395–410.'
ista: 'Henzinger TA, Piterman N. 2006. Solving games without determinization. CSL:
Computer Science Logic, LNCS, vol. 4207, 395–410.'
mla: Henzinger, Thomas A., and Nir Piterman. Solving Games without Determinization.
Vol. 4207, Springer, 2006, pp. 395–410, doi:10.1007/11874683_26.
short: T.A. Henzinger, N. Piterman, in:, Springer, 2006, pp. 395–410.
conference:
name: 'CSL: Computer Science Logic'
date_created: 2018-12-11T12:08:51Z
date_published: 2006-09-20T00:00:00Z
date_updated: 2021-01-12T07:56:58Z
day: '20'
doi: 10.1007/11874683_26
extern: 1
intvolume: ' 4207'
month: '09'
page: 395 - 410
publication_status: published
publisher: Springer
publist_id: '295'
quality_controlled: 0
status: public
title: Solving games without determinization
type: conference
volume: 4207
year: '2006'
...
---
_id: '4436'
abstract:
- lang: eng
text: We present an assume-guarantee interface algebra for real-time components.
In our formalism a component implements a set of task sequences that share a resource.
A component interface consists of an arrival rate function and a latency for each
task sequence, and a capacity function for the shared resource. The interface
specifies that the component guarantees certain task latencies depending on assumptions
about task arrival rates and allocated resource capacities. Our algebra defines
compatibility and refinement relations on interfaces. Interface compatibility
can be checked on partial designs, even when some component interfaces are yet
unknown. In this case interface composition computes as new assumptions the weakest
constraints on the unknown components that are necessary to satisfy the specified
guarantees. Interface refinement is defined in a way that ensures that compatible
interfaces can be refined and implemented independently. Our algebra thus formalizes
an interface-based design methodology that supports both the incremental addition
of new components and the independent stepwise refinement of existing components.
We demonstrate the flexibility and efficiency of the framework through simulation
experiments.
author:
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Slobodan
full_name: Matic, Slobodan
last_name: Matic
citation:
ama: 'Henzinger TA, Matic S. An interface algebra for real-time components. In:
IEEE; 2006:253-266. doi:10.1109/RTAS.2006.11'
apa: 'Henzinger, T. A., & Matic, S. (2006). An interface algebra for real-time
components (pp. 253–266). Presented at the RTAS: Real-time and Embedded Technology
and Applications Symposium, IEEE. https://doi.org/10.1109/RTAS.2006.11'
chicago: Henzinger, Thomas A, and Slobodan Matic. “An Interface Algebra for Real-Time
Components,” 253–66. IEEE, 2006. https://doi.org/10.1109/RTAS.2006.11.
ieee: 'T. A. Henzinger and S. Matic, “An interface algebra for real-time components,”
presented at the RTAS: Real-time and Embedded Technology and Applications Symposium,
2006, pp. 253–266.'
ista: 'Henzinger TA, Matic S. 2006. An interface algebra for real-time components.
RTAS: Real-time and Embedded Technology and Applications Symposium, 253–266.'
mla: Henzinger, Thomas A., and Slobodan Matic. An Interface Algebra for Real-Time
Components. IEEE, 2006, pp. 253–66, doi:10.1109/RTAS.2006.11.
short: T.A. Henzinger, S. Matic, in:, IEEE, 2006, pp. 253–266.
conference:
name: 'RTAS: Real-time and Embedded Technology and Applications Symposium'
date_created: 2018-12-11T12:08:50Z
date_published: 2006-04-24T00:00:00Z
date_updated: 2021-01-12T07:56:57Z
day: '24'
doi: 10.1109/RTAS.2006.11
extern: 1
month: '04'
page: 253 - 266
publication_status: published
publisher: IEEE
publist_id: '294'
quality_controlled: 0
status: public
title: An interface algebra for real-time components
type: conference
year: '2006'
...
---
_id: '4432'
abstract:
- lang: eng
text: We add freeze quantifiers to the game logic ATL in order to specify real-time
objectives for games played on timed structures. We define the semantics of the
resulting logic TATL by restricting the players to physically meaningful strategies,
which do not prevent time from diverging. We show that TATL can be model checked
over timed automaton games. We also specify timed optimization problems for physically
meaningful strategies, and we show that for timed automaton games, the optimal
answers can be approximated to within any degree of precision.
acknowledgement: This research was supported in part by the NSF grants CCR-0208875,
CCR-0225610, and CCR-0234690.
alternative_title:
- LNCS
author:
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Vinayak
full_name: Prabhu, Vinayak S
last_name: Prabhu
citation:
ama: 'Henzinger TA, Prabhu V. Timed alternating-time temporal logic. In: Vol 4202.
Springer; 2006:1-17. doi:10.1007/11867340_1'
apa: 'Henzinger, T. A., & Prabhu, V. (2006). Timed alternating-time temporal
logic (Vol. 4202, pp. 1–17). Presented at the FORMATS: Formal Modeling and Analysis
of Timed Systems, Springer. https://doi.org/10.1007/11867340_1'
chicago: Henzinger, Thomas A, and Vinayak Prabhu. “Timed Alternating-Time Temporal
Logic,” 4202:1–17. Springer, 2006. https://doi.org/10.1007/11867340_1.
ieee: 'T. A. Henzinger and V. Prabhu, “Timed alternating-time temporal logic,” presented
at the FORMATS: Formal Modeling and Analysis of Timed Systems, 2006, vol. 4202,
pp. 1–17.'
ista: 'Henzinger TA, Prabhu V. 2006. Timed alternating-time temporal logic. FORMATS:
Formal Modeling and Analysis of Timed Systems, LNCS, vol. 4202, 1–17.'
mla: Henzinger, Thomas A., and Vinayak Prabhu. Timed Alternating-Time Temporal
Logic. Vol. 4202, Springer, 2006, pp. 1–17, doi:10.1007/11867340_1.
short: T.A. Henzinger, V. Prabhu, in:, Springer, 2006, pp. 1–17.
conference:
name: 'FORMATS: Formal Modeling and Analysis of Timed Systems'
date_created: 2018-12-11T12:08:49Z
date_published: 2006-09-19T00:00:00Z
date_updated: 2021-01-12T07:56:56Z
day: '19'
doi: 10.1007/11867340_1
extern: 1
intvolume: ' 4202'
month: '09'
page: 1 - 17
publication_status: published
publisher: Springer
publist_id: '296'
quality_controlled: 0
status: public
title: Timed alternating-time temporal logic
type: conference
volume: 4202
year: '2006'
...
---
_id: '4431'
abstract:
- lang: eng
text: 'We summarize some current trends in embedded systems design and point out
some of their characteristics, such as the chasm between analytical and computational
models, and the gap between safety-critical and best-effort engineering practices.
We call for a coherent scientific foundation for embedded systems design, and
we discuss a few key demands on such a foundation: the need for encompassing several
manifestations of heterogeneity, and the need for constructivity in design. We
believe that the development of a satisfactory Embedded Systems Design Science
provides a timely challenge and opportunity for reinvigorating computer science.'
acknowledgement: Supported in part by the ARTIST2 European Network of Excellence on
Embedded Systems Design, by the NSF ITR Center on Hybrid and Embedded Software Systems
(CHESS), and by the SNSF NCCR on Mobile Information and Communication Systems (MICS).
alternative_title:
- LNCS
author:
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Joseph
full_name: Sifakis, Joseph
last_name: Sifakis
citation:
ama: 'Henzinger TA, Sifakis J. The embedded systems design challenge. In: Vol 4085.
Springer; 2006:1-15. doi:10.1007/11813040_1'
apa: 'Henzinger, T. A., & Sifakis, J. (2006). The embedded systems design challenge
(Vol. 4085, pp. 1–15). Presented at the FM: Formal Methods, Springer. https://doi.org/10.1007/11813040_1'
chicago: Henzinger, Thomas A, and Joseph Sifakis. “The Embedded Systems Design Challenge,”
4085:1–15. Springer, 2006. https://doi.org/10.1007/11813040_1.
ieee: 'T. A. Henzinger and J. Sifakis, “The embedded systems design challenge,”
presented at the FM: Formal Methods, 2006, vol. 4085, pp. 1–15.'
ista: 'Henzinger TA, Sifakis J. 2006. The embedded systems design challenge. FM:
Formal Methods, LNCS, vol. 4085, 1–15.'
mla: Henzinger, Thomas A., and Joseph Sifakis. The Embedded Systems Design Challenge.
Vol. 4085, Springer, 2006, pp. 1–15, doi:10.1007/11813040_1.
short: T.A. Henzinger, J. Sifakis, in:, Springer, 2006, pp. 1–15.
conference:
name: 'FM: Formal Methods'
date_created: 2018-12-11T12:08:49Z
date_published: 2006-08-10T00:00:00Z
date_updated: 2021-01-12T07:56:55Z
day: '10'
doi: 10.1007/11813040_1
extern: 1
intvolume: ' 4085'
month: '08'
page: 1 - 15
publication_status: published
publisher: Springer
publist_id: '301'
quality_controlled: 0
status: public
title: The embedded systems design challenge
type: conference
volume: 4085
year: '2006'
...
---
_id: '4451'
abstract:
- lang: eng
text: One source of complexity in the μ-calculus is its ability to specify an unbounded
number of switches between universal (AX) and existential (EX) branching modes.
We therefore study the problems of satisfiability, validity, model checking, and
implication for the universal and existential fragments of the μ-calculus, in
which only one branching mode is allowed. The universal fragment is rich enough
to express most specifications of interest, and therefore improved algorithms
are of practical importance. We show that while the satisfiability and validity
problems become indeed simpler for the existential and universal fragments, this
is, unfortunately, not the case for model checking and implication. We also show
the corresponding results for the alternation-free fragment of the μ-calculus,
where no alternations between least and greatest fixed points are allowed. Our
results imply that efforts to find a polynomial-time model-checking algorithm
for the μ-calculus can be replaced by efforts to find such an algorithm for the
universal or existential fragment.
author:
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Orna
full_name: Kupferman, Orna
last_name: Kupferman
- first_name: Ritankar
full_name: Majumdar, Ritankar S
last_name: Majumdar
citation:
ama: Henzinger TA, Kupferman O, Majumdar R. On the universal and existential fragments
of the mu-calculus. Theoretical Computer Science. 2006;354(2):173-186.
doi:10.1016/j.tcs.2005.11.015
apa: Henzinger, T. A., Kupferman, O., & Majumdar, R. (2006). On the universal
and existential fragments of the mu-calculus. Theoretical Computer Science.
Elsevier. https://doi.org/10.1016/j.tcs.2005.11.015
chicago: Henzinger, Thomas A, Orna Kupferman, and Ritankar Majumdar. “On the Universal
and Existential Fragments of the Mu-Calculus.” Theoretical Computer Science.
Elsevier, 2006. https://doi.org/10.1016/j.tcs.2005.11.015.
ieee: T. A. Henzinger, O. Kupferman, and R. Majumdar, “On the universal and existential
fragments of the mu-calculus,” Theoretical Computer Science, vol. 354,
no. 2. Elsevier, pp. 173–186, 2006.
ista: Henzinger TA, Kupferman O, Majumdar R. 2006. On the universal and existential
fragments of the mu-calculus. Theoretical Computer Science. 354(2), 173–186.
mla: Henzinger, Thomas A., et al. “On the Universal and Existential Fragments of
the Mu-Calculus.” Theoretical Computer Science, vol. 354, no. 2, Elsevier,
2006, pp. 173–86, doi:10.1016/j.tcs.2005.11.015.
short: T.A. Henzinger, O. Kupferman, R. Majumdar, Theoretical Computer Science 354
(2006) 173–186.
date_created: 2018-12-11T12:08:55Z
date_published: 2006-03-28T00:00:00Z
date_updated: 2021-01-12T07:57:04Z
day: '28'
doi: 10.1016/j.tcs.2005.11.015
extern: 1
intvolume: ' 354'
issue: '2'
month: '03'
page: 173 - 186
publication: Theoretical Computer Science
publication_status: published
publisher: Elsevier
publist_id: '276'
quality_controlled: 0
status: public
title: On the universal and existential fragments of the mu-calculus
type: journal_article
volume: 354
year: '2006'
...
---
_id: '4523'
abstract:
- lang: eng
text: We consider the problem if a given program satisfies a specified safety property.
Interesting programs have infinite state spaces, with inputs ranging over infinite
domains, and for these programs the property checking problem is undecidable.
Two broad approaches to property checking are testing and verification. Testing
tries to find inputs and executions which demonstrate violations of the property.
Verification tries to construct a formal proof which shows that all executions
of the program satisfy the property. Testing works best when errors are easy to
find, but it is often difficult to achieve sufficient coverage for correct programs.
On the other hand, verification methods are most successful when proofs are easy
to find, but they are often inefficient at discovering errors. We propose a new
algorithm, Synergy, which combines testing and verification. Synergy unifies several
ideas from the literature, including counterexample-guided model checking, directed
testing, and partition refinement.This paper presents a description of the Synergy
algorithm, its theoretical properties, a comparison with related algorithms, and
a prototype implementation called Yogi.
author:
- first_name: Bhargav
full_name: Gulavani, Bhargav S
last_name: Gulavani
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Yamini
full_name: Kannan, Yamini
last_name: Kannan
- first_name: Aditya
full_name: Nori, Aditya V
last_name: Nori
- first_name: Sriram
full_name: Rajamani, Sriram K
last_name: Rajamani
citation:
ama: 'Gulavani B, Henzinger TA, Kannan Y, Nori A, Rajamani S. Synergy: A new algorithm
for property checking. In: ACM; 2006:117-127. doi:10.1145/1181775.1181790'
apa: 'Gulavani, B., Henzinger, T. A., Kannan, Y., Nori, A., & Rajamani, S. (2006).
Synergy: A new algorithm for property checking (pp. 117–127). Presented at the
FSE: Foundations of Software Engineering, ACM. https://doi.org/10.1145/1181775.1181790'
chicago: 'Gulavani, Bhargav, Thomas A Henzinger, Yamini Kannan, Aditya Nori, and
Sriram Rajamani. “Synergy: A New Algorithm for Property Checking,” 117–27. ACM,
2006. https://doi.org/10.1145/1181775.1181790.'
ieee: 'B. Gulavani, T. A. Henzinger, Y. Kannan, A. Nori, and S. Rajamani, “Synergy:
A new algorithm for property checking,” presented at the FSE: Foundations of Software
Engineering, 2006, pp. 117–127.'
ista: 'Gulavani B, Henzinger TA, Kannan Y, Nori A, Rajamani S. 2006. Synergy: A
new algorithm for property checking. FSE: Foundations of Software Engineering,
117–127.'
mla: 'Gulavani, Bhargav, et al. Synergy: A New Algorithm for Property Checking.
ACM, 2006, pp. 117–27, doi:10.1145/1181775.1181790.'
short: B. Gulavani, T.A. Henzinger, Y. Kannan, A. Nori, S. Rajamani, in:, ACM, 2006,
pp. 117–127.
conference:
name: 'FSE: Foundations of Software Engineering'
date_created: 2018-12-11T12:09:18Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:59:26Z
day: '01'
doi: 10.1145/1181775.1181790
extern: 1
month: '01'
page: 117 - 127
publication_status: published
publisher: ACM
publist_id: '206'
quality_controlled: 0
status: public
title: 'Synergy: A new algorithm for property checking'
type: conference
year: '2006'
...
---
_id: '4526'
abstract:
- lang: eng
text: 'We designed and implemented a new programming language called Hierarchical
Timing Language (HTL) for hard realtime systems. Critical timing constraints are
specified within the language,and ensured by the compiler. Programs in HTL are
extensible in two dimensions without changing their timing behavior: new program
modules can be added, and individual program tasks can be refined. The mechanism
supporting time invariance under parallel composition is that different program
modules communicate at specified instances of time. Time invariance under refinement
is achieved by conservative scheduling of the top level. HTL is a coordination
language, in that individual tasks can be implemented in "foreign" languages.
As a case study, we present a distributed HTL implementation of an automotive
steer-by-wire controller.'
author:
- first_name: Arkadeb
full_name: Ghosal, Arkadeb
last_name: Ghosal
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Daniel
full_name: Iercan, Daniel
last_name: Iercan
- first_name: Christoph
full_name: Kirsch, Christoph M
last_name: Kirsch
- first_name: Alberto
full_name: Sangiovanni-Vincentelli, Alberto
last_name: Sangiovanni Vincentelli
citation:
ama: 'Ghosal A, Henzinger TA, Iercan D, Kirsch C, Sangiovanni Vincentelli A. A hierarchical
coordination language for interacting real-time tasks. In: ACM; 2006:132-141.
doi:10.1145/1176887.1176907'
apa: 'Ghosal, A., Henzinger, T. A., Iercan, D., Kirsch, C., & Sangiovanni Vincentelli,
A. (2006). A hierarchical coordination language for interacting real-time tasks
(pp. 132–141). Presented at the EMSOFT: Embedded Software , ACM. https://doi.org/10.1145/1176887.1176907'
chicago: Ghosal, Arkadeb, Thomas A Henzinger, Daniel Iercan, Christoph Kirsch, and
Alberto Sangiovanni Vincentelli. “A Hierarchical Coordination Language for Interacting
Real-Time Tasks,” 132–41. ACM, 2006. https://doi.org/10.1145/1176887.1176907.
ieee: 'A. Ghosal, T. A. Henzinger, D. Iercan, C. Kirsch, and A. Sangiovanni Vincentelli,
“A hierarchical coordination language for interacting real-time tasks,” presented
at the EMSOFT: Embedded Software , 2006, pp. 132–141.'
ista: 'Ghosal A, Henzinger TA, Iercan D, Kirsch C, Sangiovanni Vincentelli A. 2006.
A hierarchical coordination language for interacting real-time tasks. EMSOFT:
Embedded Software , 132–141.'
mla: Ghosal, Arkadeb, et al. A Hierarchical Coordination Language for Interacting
Real-Time Tasks. ACM, 2006, pp. 132–41, doi:10.1145/1176887.1176907.
short: A. Ghosal, T.A. Henzinger, D. Iercan, C. Kirsch, A. Sangiovanni Vincentelli,
in:, ACM, 2006, pp. 132–141.
conference:
name: 'EMSOFT: Embedded Software '
date_created: 2018-12-11T12:09:18Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:59:27Z
day: '01'
doi: 10.1145/1176887.1176907
extern: 1
month: '01'
page: 132 - 141
publication_status: published
publisher: ACM
publist_id: '201'
quality_controlled: 0
status: public
title: A hierarchical coordination language for interacting real-time tasks
type: conference
year: '2006'
...
---
_id: '4528'
abstract:
- lang: eng
text: Computational modeling of biological systems is becoming increasingly common
as scientists attempt to understand biological phenomena in their full complexity.
Here we distinguish between two types of biological models mathematical and computational
- according to their different representations of biological phenomena and their
diverse potential. We call the approach of constructing computational models of
biological systems executable biology, as it focuses on the design of executable
computer algorithms that mimic biological phenomena. We give an overview of the
main modeling efforts in this direction, and discuss some of the new challenges
that executable biology poses for computer science and biology. We argue that
for executable biology to reach its full potential as a mainstream biological
technique, formal and algorithmic approaches must be integrated into biological
research, driving biology towards a more precise engineering discipline.
author:
- first_name: Jasmin
full_name: Fisher, Jasmin
last_name: Fisher
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Fisher J, Henzinger TA. Executable biology. In: IEEE; 2006:1675-1682. doi:10.1109/WSC.2006.322942'
apa: 'Fisher, J., & Henzinger, T. A. (2006). Executable biology (pp. 1675–1682).
Presented at the WSC: Winter Simulation Conference, IEEE. https://doi.org/10.1109/WSC.2006.322942'
chicago: Fisher, Jasmin, and Thomas A Henzinger. “Executable Biology,” 1675–82.
IEEE, 2006. https://doi.org/10.1109/WSC.2006.322942.
ieee: 'J. Fisher and T. A. Henzinger, “Executable biology,” presented at the WSC:
Winter Simulation Conference, 2006, pp. 1675–1682.'
ista: 'Fisher J, Henzinger TA. 2006. Executable biology. WSC: Winter Simulation
Conference, 1675–1682.'
mla: Fisher, Jasmin, and Thomas A. Henzinger. Executable Biology. IEEE, 2006,
pp. 1675–82, doi:10.1109/WSC.2006.322942.
short: J. Fisher, T.A. Henzinger, in:, IEEE, 2006, pp. 1675–1682.
conference:
name: 'WSC: Winter Simulation Conference'
date_created: 2018-12-11T12:09:19Z
date_published: 2006-12-03T00:00:00Z
date_updated: 2021-01-12T07:59:28Z
day: '03'
doi: 10.1109/WSC.2006.322942
extern: 1
month: '12'
page: 1675 - 1682
publication_status: published
publisher: IEEE
publist_id: '197'
quality_controlled: 0
status: public
title: Executable biology
type: conference
year: '2006'
...
---
_id: '4539'
abstract:
- lang: eng
text: Games on graphs with ω-regular objectives provide a model for the control
and synthesis of reactive systems. Every ω-regular objective can be decomposed
into a safety part and a liveness part. The liveness part ensures that something
good happens “eventually.” Two main strengths of the classical, infinite-limit
formulation of liveness are robustness (independence from the granularity of transitions)
and simplicity (abstraction of complicated time bounds). However, the classical
liveness formulation suffers from the drawback that the time until something good
happens may be unbounded. A stronger formulation of liveness, so-called finitary
liveness, overcomes this drawback, while still retaining robustness and simplicity.
Finitary liveness requires that there exists an unknown, fixed bound b such that
something good happens within b transitions. While for one-shot liveness (reachability)
objectives, classical and finitary liveness coincide, for repeated liveness (Büchi)
objectives, the finitary formulation is strictly stronger. In this work we study
games with finitary parity and Streett (fairness) objectives. We prove the determinacy
of these games, present algorithms for solving these games, and characterize the
memory requirements of winning strategies. Our algorithms can be used, for example,
for synthesizing controllers that do not let the response time of a system increase
without bound.
acknowledgement: This research was supported in part by the AFOSR MURI grant F49620-00-1-0327
and the NSF ITR grant CCR-0225610.
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. Finitary winning in omega-regular games. In: Vol
3920. Springer; 2006:257-271. doi:10.1007/11691372_17'
apa: 'Chatterjee, K., & Henzinger, T. A. (2006). Finitary winning in omega-regular
games (Vol. 3920, pp. 257–271). Presented at the TACAS: Tools and Algorithms for
the Construction and Analysis of Systems, Springer. https://doi.org/10.1007/11691372_17'
chicago: Chatterjee, Krishnendu, and Thomas A Henzinger. “Finitary Winning in Omega-Regular
Games,” 3920:257–71. Springer, 2006. https://doi.org/10.1007/11691372_17.
ieee: 'K. Chatterjee and T. A. Henzinger, “Finitary winning in omega-regular games,”
presented at the TACAS: Tools and Algorithms for the Construction and Analysis
of Systems, 2006, vol. 3920, pp. 257–271.'
ista: 'Chatterjee K, Henzinger TA. 2006. Finitary winning in omega-regular games.
TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS,
vol. 3920, 257–271.'
mla: Chatterjee, Krishnendu, and Thomas A. Henzinger. Finitary Winning in Omega-Regular
Games. Vol. 3920, Springer, 2006, pp. 257–71, doi:10.1007/11691372_17.
short: K. Chatterjee, T.A. Henzinger, in:, Springer, 2006, pp. 257–271.
conference:
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
date_created: 2018-12-11T12:09:22Z
date_published: 2006-03-15T00:00:00Z
date_updated: 2021-01-12T07:59:32Z
day: '15'
doi: 10.1007/11691372_17
extern: 1
intvolume: ' 3920'
month: '03'
page: 257 - 271
publication_status: published
publisher: Springer
publist_id: '183'
quality_controlled: 0
status: public
title: Finitary winning in omega-regular games
type: conference
volume: 3920
year: '2006'
...
---
_id: '4538'
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 ω-regular winning conditions
specified as parity objectives. These games lie in NP ∩ coNP. We present a strategy
improvement algorithm for stochastic parity games; this is the first non-brute-force
algorithm for solving these games. From the strategy improvement algorithm we
obtain a randomized subexponential-time algorithm to solve such games.
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 and randomized subexponential
algorithms for stochastic parity games. In: Vol 3884. Springer; 2006:512-523.
doi:10.1007/11672142_42'
apa: 'Chatterjee, K., & Henzinger, T. A. (2006). Strategy improvement and randomized
subexponential algorithms for stochastic parity games (Vol. 3884, pp. 512–523).
Presented at the STACS: Theoretical Aspects of Computer Science, Springer. https://doi.org/10.1007/11672142_42'
chicago: Chatterjee, Krishnendu, and Thomas A Henzinger. “Strategy Improvement and
Randomized Subexponential Algorithms for Stochastic Parity Games,” 3884:512–23.
Springer, 2006. https://doi.org/10.1007/11672142_42.
ieee: 'K. Chatterjee and T. A. Henzinger, “Strategy improvement and randomized subexponential
algorithms for stochastic parity games,” presented at the STACS: Theoretical Aspects
of Computer Science, 2006, vol. 3884, pp. 512–523.'
ista: 'Chatterjee K, Henzinger TA. 2006. Strategy improvement and randomized subexponential
algorithms for stochastic parity games. STACS: Theoretical Aspects of Computer
Science, LNCS, vol. 3884, 512–523.'
mla: Chatterjee, Krishnendu, and Thomas A. Henzinger. Strategy Improvement and
Randomized Subexponential Algorithms for Stochastic Parity Games. Vol. 3884,
Springer, 2006, pp. 512–23, doi:10.1007/11672142_42.
short: K. Chatterjee, T.A. Henzinger, in:, Springer, 2006, pp. 512–523.
conference:
name: 'STACS: Theoretical Aspects of Computer Science'
date_created: 2018-12-11T12:09:22Z
date_published: 2006-02-14T00:00:00Z
date_updated: 2021-01-12T07:59:32Z
day: '14'
doi: 10.1007/11672142_42
extern: 1
intvolume: ' 3884'
month: '02'
page: 512 - 523
publication_status: published
publisher: Springer
publist_id: '184'
quality_controlled: 0
status: public
title: Strategy improvement and randomized subexponential algorithms for stochastic
parity games
type: conference
volume: 3884
year: '2006'
...
---
_id: '4551'
abstract:
- lang: eng
text: "We consider Markov decision processes (MDPs) with multiple discounted reward
objectives. Such MDPs occur in design problems where one wishes to simultaneously
optimize several criteria, for example, latency and power. The possible trade-offs
between the different objectives are characterized by the Pareto curve. We show
that every Pareto-optimal point can be achieved by a memoryless strategy; however,
unlike in the single-objective case, the memoryless strategy may require randomization.
Moreover, we show that the Pareto curve can be approximated in polynomial time
in the size of the MDP. Additionally, we study the problem if a given value vector
is realizable by any strategy, and show that it can be decided in polynomial time;
but the question whether it is realizable by a deterministic memoryless strategy
is NP-complete. These results provide efficient algorithms for design exploration
in MDP models with multiple objectives.\nThis research was supported in part by
the AFOSR MURI grant F49620-00-1-0327, and the NSF grants CCR-0225610, CCR-0234690,
and CCR-0427202. "
acknowledgement: This research was supported in part by the AFOSR MURI grant F49620-00-1-0327,
and the NSF grants CCR-0225610, CCR-0234690, and CCR-0427202.
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: Ritankar
full_name: Majumdar, Ritankar S
last_name: Majumdar
- 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, Majumdar R, Henzinger TA. Markov decision processes with multiple
objectives. In: Vol 3884. Springer; 2006:325-336. doi:10.1007/11672142_26'
apa: 'Chatterjee, K., Majumdar, R., & Henzinger, T. A. (2006). Markov decision
processes with multiple objectives (Vol. 3884, pp. 325–336). Presented at the
STACS: Theoretical Aspects of Computer Science, Springer. https://doi.org/10.1007/11672142_26'
chicago: Chatterjee, Krishnendu, Ritankar Majumdar, and Thomas A Henzinger. “Markov
Decision Processes with Multiple Objectives,” 3884:325–36. Springer, 2006. https://doi.org/10.1007/11672142_26.
ieee: 'K. Chatterjee, R. Majumdar, and T. A. Henzinger, “Markov decision processes
with multiple objectives,” presented at the STACS: Theoretical Aspects of Computer
Science, 2006, vol. 3884, pp. 325–336.'
ista: 'Chatterjee K, Majumdar R, Henzinger TA. 2006. Markov decision processes with
multiple objectives. STACS: Theoretical Aspects of Computer Science, LNCS, vol.
3884, 325–336.'
mla: Chatterjee, Krishnendu, et al. Markov Decision Processes with Multiple Objectives.
Vol. 3884, Springer, 2006, pp. 325–36, doi:10.1007/11672142_26.
short: K. Chatterjee, R. Majumdar, T.A. Henzinger, in:, Springer, 2006, pp. 325–336.
conference:
name: 'STACS: Theoretical Aspects of Computer Science'
date_created: 2018-12-11T12:09:26Z
date_published: 2006-02-14T00:00:00Z
date_updated: 2021-01-12T07:59:38Z
day: '14'
doi: 10.1007/11672142_26
extern: 1
intvolume: ' 3884'
month: '02'
page: 325 - 336
publication_status: published
publisher: Springer
publist_id: '161'
quality_controlled: 0
status: public
title: Markov decision processes with multiple objectives
type: conference
volume: 3884
year: '2006'
...
---
_id: '4550'
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 sometimes 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 ω-regular winning conditions, and we
characterize the memory requirements of strategies that achieve the equilibrium.'
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. Theoretical
Computer Science. 2006;365(1-2):67-82. doi:10.1016/j.tcs.2006.07.032
apa: Chatterjee, K., Henzinger, T. A., & Jurdziński, M. (2006). Games with secure
equilibria. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2006.07.032
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Marcin Jurdziński. “Games
with Secure Equilibria.” Theoretical Computer Science. Elsevier, 2006.
https://doi.org/10.1016/j.tcs.2006.07.032.
ieee: K. Chatterjee, T. A. Henzinger, and M. Jurdziński, “Games with secure equilibria,”
Theoretical Computer Science, vol. 365, no. 1–2. Elsevier, pp. 67–82, 2006.
ista: Chatterjee K, Henzinger TA, Jurdziński M. 2006. Games with secure equilibria.
Theoretical Computer Science. 365(1–2), 67–82.
mla: Chatterjee, Krishnendu, et al. “Games with Secure Equilibria.” Theoretical
Computer Science, vol. 365, no. 1–2, Elsevier, 2006, pp. 67–82, doi:10.1016/j.tcs.2006.07.032.
short: K. Chatterjee, T.A. Henzinger, M. Jurdziński, Theoretical Computer Science
365 (2006) 67–82.
date_created: 2018-12-11T12:09:26Z
date_published: 2006-08-07T00:00:00Z
date_updated: 2021-01-12T07:59:38Z
day: '07'
doi: 10.1016/j.tcs.2006.07.032
extern: 1
intvolume: ' 365'
issue: 1-2
month: '08'
page: 67 - 82
publication: Theoretical Computer Science
publication_status: published
publisher: Elsevier
publist_id: '164'
quality_controlled: 0
status: public
title: Games with secure equilibria
type: journal_article
volume: 365
year: '2006'
...
---
_id: '4549'
abstract:
- lang: eng
text: We present a compositional theory of system verification, where specifications
assign real-numbered costs to systems. These costs can express a wide variety
of quantitative system properties, such as resource consumption, price, or a measure
of how well a system satisfies its specification. The theory supports the composition
of systems and specifications, and the hiding of variables. Boolean refinement
relations are replaced by real-numbered distances between descriptions of a system
at different levels of detail. We show that the classical Boolean rules for compositional
reasoning have quantitative counterparts in our setting. While our general theory
allows costs to be specified by arbitrary cost functions, we also consider a class
of linear cost functions, which give rise to an instance of our framework where
all operations are computable in polynomial time.
acknowledgement: Supported in part by the NSF grants CCR-0234690, CCR-0208875, and
CCR-0225610; by the NSF grant CCR-0132780 and ARP grant SC20051123.
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: Marco
full_name: Faella, Marco
last_name: Faella
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Ritankar
full_name: Majumdar, Ritankar S
last_name: Majumdar
- first_name: Mariëlle
full_name: Stoelinga, Mariëlle
last_name: Stoelinga
citation:
ama: 'Chatterjee K, De Alfaro L, Faella M, Henzinger TA, Majumdar R, Stoelinga M.
Compositional quantitative reasoning. In: IEEE; 2006:179-188. doi:10.1109/QEST.2006.11'
apa: 'Chatterjee, K., De Alfaro, L., Faella, M., Henzinger, T. A., Majumdar, R.,
& Stoelinga, M. (2006). Compositional quantitative reasoning (pp. 179–188).
Presented at the QEST: Quantitative Evaluation of Systems, IEEE. https://doi.org/10.1109/QEST.2006.11'
chicago: Chatterjee, Krishnendu, Luca De Alfaro, Marco Faella, Thomas A Henzinger,
Ritankar Majumdar, and Mariëlle Stoelinga. “Compositional Quantitative Reasoning,”
179–88. IEEE, 2006. https://doi.org/10.1109/QEST.2006.11.
ieee: 'K. Chatterjee, L. De Alfaro, M. Faella, T. A. Henzinger, R. Majumdar, and
M. Stoelinga, “Compositional quantitative reasoning,” presented at the QEST: Quantitative
Evaluation of Systems, 2006, pp. 179–188.'
ista: 'Chatterjee K, De Alfaro L, Faella M, Henzinger TA, Majumdar R, Stoelinga
M. 2006. Compositional quantitative reasoning. QEST: Quantitative Evaluation of
Systems, 179–188.'
mla: Chatterjee, Krishnendu, et al. Compositional Quantitative Reasoning.
IEEE, 2006, pp. 179–88, doi:10.1109/QEST.2006.11.
short: K. Chatterjee, L. De Alfaro, M. Faella, T.A. Henzinger, R. Majumdar, M. Stoelinga,
in:, IEEE, 2006, pp. 179–188.
conference:
name: 'QEST: Quantitative Evaluation of Systems'
date_created: 2018-12-11T12:09:26Z
date_published: 2006-09-01T00:00:00Z
date_updated: 2021-01-12T07:59:37Z
day: '01'
doi: 10.1109/QEST.2006.11
extern: 1
month: '09'
page: 179 - 188
publication_status: published
publisher: IEEE
publist_id: '163'
quality_controlled: 0
status: public
title: Compositional quantitative reasoning
type: conference
year: '2006'
...
---
_id: '4552'
abstract:
- lang: eng
text: 'A concurrent reachability game is a two-player game played on a graph: at
each state, the players simultaneously and independently select moves; the two
moves determine jointly a probability distribution over the successor states.
The objective for player 1 consists in reaching a set of target states; the objective
for player 2 is to prevent this, so that the game is zero-sum. Our contributions
are two-fold. First, we present a simple proof of the fact that in concurrent
reachability games, for all epsilon > 0, memoryless epsilon-optimal strategies
exist. A memoryless strategy is independent of the history of plays, and an epsilon-optimal
strategy achieves the objective with probability within epsilon of the value of
the game. In contrast to previous proofs of this fact, which rely on the limit
behavior of discounted games using advanced Puisieux series analysis, our proof
is elementary and combinatorial. Second, we present a strategy-improvement (a.k.a.
policy-iteration) algorithm for concurrent games with reachability objectives.'
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. Strategy improvement for concurrent
reachability games. In: IEEE; 2006:291-300. doi:10.1109/QEST.2006.48'
apa: 'Chatterjee, K., De Alfaro, L., & Henzinger, T. A. (2006). Strategy improvement
for concurrent reachability games (pp. 291–300). Presented at the QEST: Quantitative
Evaluation of Systems, IEEE. https://doi.org/10.1109/QEST.2006.48'
chicago: Chatterjee, Krishnendu, Luca De Alfaro, and Thomas A Henzinger. “Strategy
Improvement for Concurrent Reachability Games,” 291–300. IEEE, 2006. https://doi.org/10.1109/QEST.2006.48.
ieee: 'K. Chatterjee, L. De Alfaro, and T. A. Henzinger, “Strategy improvement for
concurrent reachability games,” presented at the QEST: Quantitative Evaluation
of Systems, 2006, pp. 291–300.'
ista: 'Chatterjee K, De Alfaro L, Henzinger TA. 2006. Strategy improvement for concurrent
reachability games. QEST: Quantitative Evaluation of Systems, 291–300.'
mla: Chatterjee, Krishnendu, et al. Strategy Improvement for Concurrent Reachability
Games. IEEE, 2006, pp. 291–300, doi:10.1109/QEST.2006.48.
short: K. Chatterjee, L. De Alfaro, T.A. Henzinger, in:, IEEE, 2006, pp. 291–300.
conference:
name: 'QEST: Quantitative Evaluation of Systems'
date_created: 2018-12-11T12:09:26Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:59:39Z
day: '01'
doi: 10.1109/QEST.2006.48
extern: 1
month: '01'
page: 291 - 300
publication_status: published
publisher: IEEE
publist_id: '162'
quality_controlled: 0
status: public
title: Strategy improvement for concurrent reachability games
type: conference
year: '2006'
...
---
_id: '4574'
abstract:
- lang: eng
text: Many software model checkers are based on predicate abstraction. If the verification
goal depends on pointer structures, the approach does not work well, because it
is difficult to find adequate predicate abstractions for the heap. In contrast,
shape analysis, which uses graph-based heap abstractions, can provide a compact
representation of recursive data structures. We integrate shape analysis into
the software model checker Blast. Because shape analysis is expensive, we do not
apply it globally. Instead, we ensure that, like predicates, shape graphs are
computed and stored locally, only where necessary for proving the verification
goal. To achieve this, we extend lazy abstraction refinement, which so far has
been used only for predicate abstractions, to three-valued logical structures.
This approach does not only increase the precision of model checking, but it also
increases the efficiency of shape analysis. We implemented the technique by extending
Blast with calls to Tvla.
alternative_title:
- LNCS
author:
- first_name: Dirk
full_name: Beyer, Dirk
last_name: Beyer
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Grégory
full_name: Théoduloz, Grégory
last_name: Théoduloz
citation:
ama: 'Beyer D, Henzinger TA, Théoduloz G. Lazy shape analysis. In: Vol 4144. Springer;
2006:532-546. doi:10.1007/11817963_48'
apa: 'Beyer, D., Henzinger, T. A., & Théoduloz, G. (2006). Lazy shape analysis
(Vol. 4144, pp. 532–546). Presented at the CAV: Computer Aided Verification, Springer.
https://doi.org/10.1007/11817963_48'
chicago: Beyer, Dirk, Thomas A Henzinger, and Grégory Théoduloz. “Lazy Shape Analysis,”
4144:532–46. Springer, 2006. https://doi.org/10.1007/11817963_48.
ieee: 'D. Beyer, T. A. Henzinger, and G. Théoduloz, “Lazy shape analysis,” presented
at the CAV: Computer Aided Verification, 2006, vol. 4144, pp. 532–546.'
ista: 'Beyer D, Henzinger TA, Théoduloz G. 2006. Lazy shape analysis. CAV: Computer
Aided Verification, LNCS, vol. 4144, 532–546.'
mla: Beyer, Dirk, et al. Lazy Shape Analysis. Vol. 4144, Springer, 2006,
pp. 532–46, doi:10.1007/11817963_48.
short: D. Beyer, T.A. Henzinger, G. Théoduloz, in:, Springer, 2006, pp. 532–546.
conference:
name: 'CAV: Computer Aided Verification'
date_created: 2018-12-11T12:09:33Z
date_published: 2006-08-08T00:00:00Z
date_updated: 2021-01-12T07:59:49Z
day: '08'
doi: 10.1007/11817963_48
extern: 1
intvolume: ' 4144'
month: '08'
page: 532 - 546
publication_status: published
publisher: Springer
publist_id: '133'
quality_controlled: 0
status: public
title: Lazy shape analysis
type: conference
volume: 4144
year: '2006'
...
---
_id: '573'
abstract:
- lang: eng
text: 'Mitchison and Jozsa recently suggested that the "chained-Zeno"
counterfactual computation protocol recently proposed by Hosten et al. is counterfactual
for only one output of the computer. This claim was based on the existing abstract
algebraic definition of counterfactual computation, and indeed according to this
definition, their argument is correct. However, a more general definition (physically
adequate) for counterfactual computation is implicitly assumed by Hosten et. al.
Here we explain in detail why the protocol is counterfactual and how the "history
tracking" method of the existing description inadequately represents the
physics underlying the protocol. Consequently, we propose a modified definition
of counterfactual computation. Finally, we comment on one of the most interesting
aspects of the error-correcting protocol. '
article_processing_charge: No
author:
- first_name: Onur
full_name: Hosten, Onur
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Matthew
full_name: Rakher, Matthew
last_name: Rakher
- first_name: Julio
full_name: Barreiro, Julio
last_name: Barreiro
- first_name: Nicholas
full_name: Peters, Nicholas
last_name: Peters
- first_name: Paul
full_name: Kwiat, Paul
last_name: Kwiat
citation:
ama: Hosten O, Rakher M, Barreiro J, Peters N, Kwiat P. Counterfactual computation
revisited. 2006.
apa: Hosten, O., Rakher, M., Barreiro, J., Peters, N., & Kwiat, P. (2006). Counterfactual
computation revisited. ArXiv.
chicago: Hosten, Onur, Matthew Rakher, Julio Barreiro, Nicholas Peters, and Paul
Kwiat. “Counterfactual Computation Revisited.” ArXiv, 2006.
ieee: O. Hosten, M. Rakher, J. Barreiro, N. Peters, and P. Kwiat, “Counterfactual
computation revisited.” ArXiv, 2006.
ista: Hosten O, Rakher M, Barreiro J, Peters N, Kwiat P. 2006. Counterfactual computation
revisited.
mla: Hosten, Onur, et al. Counterfactual Computation Revisited. ArXiv, 2006.
short: O. Hosten, M. Rakher, J. Barreiro, N. Peters, P. Kwiat, (2006).
date_created: 2018-12-11T11:47:16Z
date_published: 2006-08-06T00:00:00Z
date_updated: 2020-05-12T08:23:52Z
day: '06'
extern: '1'
external_id:
arxiv:
- '0607101'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/quant-ph/0607101
month: '08'
oa: 1
oa_version: Preprint
page: '12'
publication_status: published
publisher: ArXiv
publist_id: '7241'
status: public
title: Counterfactual computation revisited
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2006'
...
---
_id: '574'
abstract:
- lang: eng
text: 'Vaidman, in a recent article adopts the method of ''quantum weak measurements
in pre- and postselected ensembles'' to ascertain whether or not the chained-Zeno
counterfactual computation scheme proposed by Hosten et al. is counterfactual;
which has been the topic of a debate on the definition of counterfactuality. We
disagree with his conclusion, which brings up some interesting aspects of quantum
weak measurements and some concerns about the way they are interpreted. '
article_processing_charge: No
author:
- first_name: Onur
full_name: Hosten, Onur
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Paul
full_name: Kwiat, Paul
last_name: Kwiat
citation:
ama: Hosten O, Kwiat P. Weak measurements and counterfactual computation. 2006.
apa: Hosten, O., & Kwiat, P. (2006). Weak measurements and counterfactual computation.
ArXiv.
chicago: Hosten, Onur, and Paul Kwiat. “Weak Measurements and Counterfactual Computation.”
ArXiv, 2006.
ieee: O. Hosten and P. Kwiat, “Weak measurements and counterfactual computation.”
ArXiv, 2006.
ista: Hosten O, Kwiat P. 2006. Weak measurements and counterfactual computation.
mla: Hosten, Onur, and Paul Kwiat. Weak Measurements and Counterfactual Computation.
ArXiv, 2006.
short: O. Hosten, P. Kwiat, (2006).
date_created: 2018-12-11T11:47:16Z
date_published: 2006-12-19T00:00:00Z
date_updated: 2020-05-12T08:18:01Z
day: '19'
extern: '1'
external_id:
arxiv:
- '0612159'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/quant-ph/0612159
month: '12'
oa: 1
oa_version: Preprint
page: '2'
publication_status: published
publisher: ArXiv
publist_id: '7240'
status: public
title: Weak measurements and counterfactual computation
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2006'
...
---
_id: '578'
abstract:
- lang: eng
text: A source of single photons allows secure quantum key distribution, in addition,
to being a critical resource for linear optics quantum computing. We describe
our progress on deterministically creating single photons from spontaneous parametric
downconversion, an extension of the Pittman, Jacobs and Franson scheme [Phys.
Rev A, v66, 042303 (2002)]. Their idea was to conditionally prepare single photons
by measuring one member of a spontaneously emitted photon pair and storing the
remaining conditionally prepared photon until a predetermined time, when it would
be "deterministically" released from storage. Our approach attempts
to improve upon this by recycling the pump pulse in order to decrease the possibility
of multiple-pair generation, while maintaining a high probability of producing
a single pair. Many of the challenges we discuss are central to other quantum
information technologies, including the need for low-loss optical storage, switching
and detection, and fast feed-forward control.
alternative_title:
- Proc. SPIE
author:
- first_name: Nicholas
full_name: Peters, Nicholas A
last_name: Peters
- first_name: Keith
full_name: Arnold, Keith J
last_name: Arnold
- first_name: Aaron
full_name: VanDevender, Aaron P
last_name: Vandevender
- first_name: Evan
full_name: Jeffrey, Evan R
last_name: Jeffrey
- first_name: Radhika
full_name: Rangarajan, Radhika
last_name: Rangarajan
- first_name: Onur
full_name: Onur Hosten
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Julio
full_name: Barreiro, Julio T
last_name: Barreiro
- first_name: Joseph
full_name: Altepeter, Joseph B
last_name: Altepeter
- first_name: Paul
full_name: Kwiat, Paul G
last_name: Kwiat
citation:
ama: 'Peters N, Arnold K, Vandevender A, et al. Towards a quasi-deterministic single-photon
source. In: Vol 6305. SPIE; 2006. doi:10.1117/12.684702'
apa: Peters, N., Arnold, K., Vandevender, A., Jeffrey, E., Rangarajan, R., Hosten,
O., … Kwiat, P. (2006). Towards a quasi-deterministic single-photon source (Vol.
6305). Presented at the Quantum Communications and Quantum Imaging, SPIE. https://doi.org/10.1117/12.684702
chicago: Peters, Nicholas, Keith Arnold, Aaron Vandevender, Evan Jeffrey, Radhika
Rangarajan, Onur Hosten, Julio Barreiro, Joseph Altepeter, and Paul Kwiat. “Towards
a Quasi-Deterministic Single-Photon Source,” Vol. 6305. SPIE, 2006. https://doi.org/10.1117/12.684702.
ieee: N. Peters et al., “Towards a quasi-deterministic single-photon source,”
presented at the Quantum Communications and Quantum Imaging, 2006, vol. 6305.
ista: Peters N, Arnold K, Vandevender A, Jeffrey E, Rangarajan R, Hosten O, Barreiro
J, Altepeter J, Kwiat P. 2006. Towards a quasi-deterministic single-photon source.
Quantum Communications and Quantum Imaging, Proc. SPIE, vol. 6305.
mla: Peters, Nicholas, et al. Towards a Quasi-Deterministic Single-Photon Source.
Vol. 6305, SPIE, 2006, doi:10.1117/12.684702.
short: N. Peters, K. Arnold, A. Vandevender, E. Jeffrey, R. Rangarajan, O. Hosten,
J. Barreiro, J. Altepeter, P. Kwiat, in:, SPIE, 2006.
conference:
name: Quantum Communications and Quantum Imaging
date_created: 2018-12-11T11:47:17Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2020-07-14T12:47:11Z
day: '01'
doi: 10.1117/12.684702
extern: 1
intvolume: ' 6305'
month: '01'
publication_status: published
publisher: SPIE
publist_id: '7234'
quality_controlled: 0
status: public
title: Towards a quasi-deterministic single-photon source
type: conference
volume: 6305
year: '2006'
...
---
_id: '577'
abstract:
- lang: eng
text: Visible light photon counters (VLPCs) and solid-state photomultipliers (SSPMs)
are high-efficiency single-photon detectors which have multi-photon counting capability.
While both the VLPCs and the SSPMs have inferred internal quantum efficiencies
above 93%, the actual measured values for both the detectors were in fact limited
to less than 88%, attributed to in-coupling losses. We are currently improving
this overall detection efficiency via a) custom anti-reflection coating the detectors
and the in-coupling fibers, b) implementing a novel cryogenic design to reduce
transmission losses and, c) using low-noise electronics to obtain a better signal-to-noise
ratio.
alternative_title:
- Proceedings of SPIE
author:
- first_name: Radhika
full_name: Rangarajan, Radhika
last_name: Rangarajan
- first_name: Joseph
full_name: Altepeter, Joseph B
last_name: Altepeter
- first_name: Evan
full_name: Jeffrey, Evan R
last_name: Jeffrey
- first_name: Micah
full_name: Stoutimore, Micah J
last_name: Stoutimore
- first_name: Nicholas
full_name: Peters, Nicholas A
last_name: Peters
- first_name: Onur
full_name: Onur Hosten
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Paul
full_name: Kwiat, Paul G
last_name: Kwiat
citation:
ama: 'Rangarajan R, Altepeter J, Jeffrey E, et al. High-efficiency single-photon
detectors. In: Vol 6372. SPIE; 2006. doi:10.1117/12.686117'
apa: Rangarajan, R., Altepeter, J., Jeffrey, E., Stoutimore, M., Peters, N., Hosten,
O., & Kwiat, P. (2006). High-efficiency single-photon detectors (Vol. 6372).
Presented at the Unknown (978-081946470-5), SPIE. https://doi.org/10.1117/12.686117
chicago: Rangarajan, Radhika, Joseph Altepeter, Evan Jeffrey, Micah Stoutimore,
Nicholas Peters, Onur Hosten, and Paul Kwiat. “High-Efficiency Single-Photon Detectors,”
Vol. 6372. SPIE, 2006. https://doi.org/10.1117/12.686117.
ieee: R. Rangarajan et al., “High-efficiency single-photon detectors,” presented
at the Unknown (978-081946470-5), 2006, vol. 6372.
ista: Rangarajan R, Altepeter J, Jeffrey E, Stoutimore M, Peters N, Hosten O, Kwiat
P. 2006. High-efficiency single-photon detectors. Unknown (978-081946470-5), Proceedings
of SPIE, vol. 6372.
mla: Rangarajan, Radhika, et al. High-Efficiency Single-Photon Detectors.
Vol. 6372, SPIE, 2006, doi:10.1117/12.686117.
short: R. Rangarajan, J. Altepeter, E. Jeffrey, M. Stoutimore, N. Peters, O. Hosten,
P. Kwiat, in:, SPIE, 2006.
conference:
name: Unknown (978-081946470-5)
date_created: 2018-12-11T11:47:17Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2020-07-14T12:47:11Z
day: '01'
doi: 10.1117/12.686117
extern: 1
intvolume: ' 6372'
month: '01'
publication_status: published
publisher: SPIE
publist_id: '7233'
quality_controlled: 0
status: public
title: High-efficiency single-photon detectors
type: conference
volume: 6372
year: '2006'
...
---
_id: '579'
abstract:
- lang: eng
text: 'The logic underlying the coherent nature of quantum information processing
often deviates from intuitive reasoning, leading to surprising effects. Counterfactual
computation constitutes a striking example: the potential outcome of a quantum
computation can be inferred, even if the computer is not run 1. Relying on similar
arguments to interaction-free measurements 2 (or quantum interrogation3), counterfactual
computation is accomplished by putting the computer in a superposition of ''running''
and ''not running'' states, and then interfering the two histories. Conditional
on the as-yet-unknown outcome of the computation, it is sometimes possible to
counterfactually infer information about the solution. Here we demonstrate counterfactual
computation, implementing Grover''s search algorithm with an all-optical approach4.
It was believed that the overall probability of such counterfactual inference
is intrinsically limited1,5, so that it could not perform better on average than
random guesses. However, using a novel ''chained'' version of the quantum Zeno
effect6, we show how to boost the counterfactual inference probability to unity,
thereby beating the random guessing limit. Our methods are general and apply to
any physical system, as illustrated by a discussion of trapped-ion systems. Finally,
we briefly show that, in certain circumstances, counterfactual computation can
eliminate errors induced by decoherence. '
author:
- first_name: Onur
full_name: Onur Hosten
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Matthew
full_name: Rakher, Matthew T
last_name: Rakher
- first_name: Julio
full_name: Barreiro, Julio T
last_name: Barreiro
- first_name: Nicholas
full_name: Peters, Nicholas A
last_name: Peters
- first_name: Paul
full_name: Kwiat, Paul G
last_name: Kwiat
citation:
ama: Hosten O, Rakher M, Barreiro J, Peters N, Kwiat P. Counterfactual quantum computation
through quantum interrogation. Nature. 2006;439(7079):949-952. doi:10.1038/nature04523
apa: Hosten, O., Rakher, M., Barreiro, J., Peters, N., & Kwiat, P. (2006). Counterfactual
quantum computation through quantum interrogation. Nature. Nature Publishing
Group. https://doi.org/10.1038/nature04523
chicago: Hosten, Onur, Matthew Rakher, Julio Barreiro, Nicholas Peters, and Paul
Kwiat. “Counterfactual Quantum Computation through Quantum Interrogation.” Nature.
Nature Publishing Group, 2006. https://doi.org/10.1038/nature04523.
ieee: O. Hosten, M. Rakher, J. Barreiro, N. Peters, and P. Kwiat, “Counterfactual
quantum computation through quantum interrogation,” Nature, vol. 439, no.
7079. Nature Publishing Group, pp. 949–952, 2006.
ista: Hosten O, Rakher M, Barreiro J, Peters N, Kwiat P. 2006. Counterfactual quantum
computation through quantum interrogation. Nature. 439(7079), 949–952.
mla: Hosten, Onur, et al. “Counterfactual Quantum Computation through Quantum Interrogation.”
Nature, vol. 439, no. 7079, Nature Publishing Group, 2006, pp. 949–52,
doi:10.1038/nature04523.
short: O. Hosten, M. Rakher, J. Barreiro, N. Peters, P. Kwiat, Nature 439 (2006)
949–952.
date_created: 2018-12-11T11:47:18Z
date_published: 2006-02-23T00:00:00Z
date_updated: 2021-01-12T08:03:29Z
day: '23'
doi: 10.1038/nature04523
extern: 1
intvolume: ' 439'
issue: '7079'
month: '02'
page: 949 - 952
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '7235'
quality_controlled: 0
status: public
title: Counterfactual quantum computation through quantum interrogation
type: journal_article
volume: 439
year: '2006'
...
---
_id: '583'
abstract:
- lang: eng
text: Visible light photon counters (VLPCs) and solid-state photomultipliers (SSPMs)
facilitate efficient single-photon detection. We are attempting to improve their
efficiency, previously limited to < 88% by coupling losses, via anti-reflection
coatings, better electronics and cryogenics.
author:
- first_name: Radhika
full_name: Rangarajan, Radhika
last_name: Rangarajan
- first_name: Nicholas
full_name: Peters, Nicholas A
last_name: Peters
- first_name: Onur
full_name: Onur Hosten
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Joseph
full_name: Altepeter, Joseph B
last_name: Altepeter
- first_name: Evan
full_name: Jeffrey, Evan R
last_name: Jeffrey
- first_name: Paul
full_name: Kwiat, Paul G
last_name: Kwiat
citation:
ama: 'Rangarajan R, Peters N, Hosten O, Altepeter J, Jeffrey E, Kwiat P. Improved
single-photon detection. In: IEEE; 2006. doi:10.1109/CLEO.2006.4628641'
apa: 'Rangarajan, R., Peters, N., Hosten, O., Altepeter, J., Jeffrey, E., &
Kwiat, P. (2006). Improved single-photon detection. Presented at the CLEO/QELS:
Conference on Lasers and Electro-Optics / Quantum Electronics and Laser Science
Conference, IEEE. https://doi.org/10.1109/CLEO.2006.4628641'
chicago: Rangarajan, Radhika, Nicholas Peters, Onur Hosten, Joseph Altepeter, Evan
Jeffrey, and Paul Kwiat. “Improved Single-Photon Detection.” IEEE, 2006. https://doi.org/10.1109/CLEO.2006.4628641.
ieee: 'R. Rangarajan, N. Peters, O. Hosten, J. Altepeter, E. Jeffrey, and P. Kwiat,
“Improved single-photon detection,” presented at the CLEO/QELS: Conference on
Lasers and Electro-Optics / Quantum Electronics and Laser Science Conference,
2006.'
ista: 'Rangarajan R, Peters N, Hosten O, Altepeter J, Jeffrey E, Kwiat P. 2006.
Improved single-photon detection. CLEO/QELS: Conference on Lasers and Electro-Optics
/ Quantum Electronics and Laser Science Conference.'
mla: Rangarajan, Radhika, et al. Improved Single-Photon Detection. IEEE,
2006, doi:10.1109/CLEO.2006.4628641.
short: R. Rangarajan, N. Peters, O. Hosten, J. Altepeter, E. Jeffrey, P. Kwiat,
in:, IEEE, 2006.
conference:
name: 'CLEO/QELS: Conference on Lasers and Electro-Optics / Quantum Electronics
and Laser Science Conference'
date_created: 2018-12-11T11:47:19Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T08:03:43Z
day: '01'
doi: 10.1109/CLEO.2006.4628641
extern: 1
month: '01'
publication_status: published
publisher: IEEE
publist_id: '7232'
quality_controlled: 0
status: public
title: Improved single-photon detection
type: conference
year: '2006'
...
---
_id: '6151'
author:
- first_name: Iris
full_name: Salecker, Iris
last_name: Salecker
- first_name: Michael
full_name: Häusser, Michael
last_name: Häusser
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: 'Salecker I, Häusser M, de Bono M. On the axonal road to circuit function and
behaviour: Workshop on the assembly and function of neuronal circuits. EMBO
reports. 2006;7(6):585-589. doi:10.1038/sj.embor.7400713'
apa: 'Salecker, I., Häusser, M., & de Bono, M. (2006). On the axonal road to
circuit function and behaviour: Workshop on the assembly and function of neuronal
circuits. EMBO Reports. Wiley. https://doi.org/10.1038/sj.embor.7400713'
chicago: 'Salecker, Iris, Michael Häusser, and Mario de Bono. “On the Axonal Road
to Circuit Function and Behaviour: Workshop on the Assembly and Function of Neuronal
Circuits.” EMBO Reports. Wiley, 2006. https://doi.org/10.1038/sj.embor.7400713.'
ieee: 'I. Salecker, M. Häusser, and M. de Bono, “On the axonal road to circuit function
and behaviour: Workshop on the assembly and function of neuronal circuits,” EMBO
reports, vol. 7, no. 6. Wiley, pp. 585–589, 2006.'
ista: 'Salecker I, Häusser M, de Bono M. 2006. On the axonal road to circuit function
and behaviour: Workshop on the assembly and function of neuronal circuits. EMBO
reports. 7(6), 585–589.'
mla: 'Salecker, Iris, et al. “On the Axonal Road to Circuit Function and Behaviour:
Workshop on the Assembly and Function of Neuronal Circuits.” EMBO Reports,
vol. 7, no. 6, Wiley, 2006, pp. 585–89, doi:10.1038/sj.embor.7400713.'
short: I. Salecker, M. Häusser, M. de Bono, EMBO Reports 7 (2006) 585–589.
date_created: 2019-03-21T08:50:43Z
date_published: 2006-06-01T00:00:00Z
date_updated: 2021-01-12T08:06:23Z
day: '01'
doi: 10.1038/sj.embor.7400713
extern: '1'
external_id:
pmid:
- '16729018'
intvolume: ' 7'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://europepmc.org/articles/pmc1479602
month: '06'
oa: 1
oa_version: Published Version
page: 585-589
pmid: 1
publication: EMBO reports
publication_identifier:
issn:
- 1469-221X
- 1469-3178
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: 'On the axonal road to circuit function and behaviour: Workshop on the assembly
and function of neuronal circuits'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2006'
...
---
_id: '6152'
author:
- first_name: Candida
full_name: Rogers, Candida
last_name: Rogers
- first_name: Annelie
full_name: Persson, Annelie
last_name: Persson
- first_name: Benny
full_name: Cheung, Benny
last_name: Cheung
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Rogers C, Persson A, Cheung B, de Bono M. Behavioral motifs and neural pathways
coordinating O2 responses and aggregation in C. elegans. Current Biology.
2006;16(7):649-659. doi:10.1016/j.cub.2006.03.023
apa: Rogers, C., Persson, A., Cheung, B., & de Bono, M. (2006). Behavioral motifs
and neural pathways coordinating O2 responses and aggregation in C. elegans. Current
Biology. Elsevier. https://doi.org/10.1016/j.cub.2006.03.023
chicago: Rogers, Candida, Annelie Persson, Benny Cheung, and Mario de Bono. “Behavioral
Motifs and Neural Pathways Coordinating O2 Responses and Aggregation in C. Elegans.”
Current Biology. Elsevier, 2006. https://doi.org/10.1016/j.cub.2006.03.023.
ieee: C. Rogers, A. Persson, B. Cheung, and M. de Bono, “Behavioral motifs and neural
pathways coordinating O2 responses and aggregation in C. elegans,” Current
Biology, vol. 16, no. 7. Elsevier, pp. 649–659, 2006.
ista: Rogers C, Persson A, Cheung B, de Bono M. 2006. Behavioral motifs and neural
pathways coordinating O2 responses and aggregation in C. elegans. Current Biology.
16(7), 649–659.
mla: Rogers, Candida, et al. “Behavioral Motifs and Neural Pathways Coordinating
O2 Responses and Aggregation in C. Elegans.” Current Biology, vol. 16,
no. 7, Elsevier, 2006, pp. 649–59, doi:10.1016/j.cub.2006.03.023.
short: C. Rogers, A. Persson, B. Cheung, M. de Bono, Current Biology 16 (2006) 649–659.
date_created: 2019-03-21T09:15:27Z
date_published: 2006-04-04T00:00:00Z
date_updated: 2021-01-12T08:06:23Z
day: '04'
doi: 10.1016/j.cub.2006.03.023
extern: '1'
external_id:
pmid:
- '16581509'
intvolume: ' 16'
issue: '7'
language:
- iso: eng
month: '04'
oa_version: None
page: 649-659
pmid: 1
publication: Current Biology
publication_identifier:
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Behavioral motifs and neural pathways coordinating O2 responses and aggregation
in C. elegans
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2006'
...
---
_id: '7328'
abstract:
- lang: eng
text: An experimental technique for measuring the current density distribution with
a resolution smaller than the channel/rib scale of the flow field in polymer electrolyte
fuel cells (PEFCs) is presented. The electron conductors in a plane perpendicular
to the channel direction are considered as two-dimensional resistors. Hence, the
current density is obtained from the solution of Laplace's equation with the potentials
at current collector and reaction layer as boundary conditions. Using ohmic drop
for calculating the local current, detailed knowledge of all resistances involved
is of prime importance. In particular, the contact resistance between the gas
diffusion layer (GDL) and flow field rib, as well as GDL bulk conductivity, are
strongly dependent on clamping pressure. They represent a substantial amount of
the total ohmic drop and therefore require careful consideration. The detailed
experimental setup as well as the concise procedure for quantitative data evaluation
is described. Finally, the method is applied successfully to a cell operated on
pure oxygen and air up to high current densities. The results show that electrical
and ionic resistances seem to govern the current distribution at low current regimes,
whereas mass transport limitations locally hamper the current production at high
loads.
article_number: A2158
article_processing_charge: No
article_type: original
author:
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Mathias
full_name: Reum, Mathias
last_name: Reum
- first_name: Jörg
full_name: Evertz, Jörg
last_name: Evertz
- first_name: Alexander
full_name: Wokaun, Alexander
last_name: Wokaun
- first_name: Felix N.
full_name: Büchi, Felix N.
last_name: Büchi
citation:
ama: Freunberger SA, Reum M, Evertz J, Wokaun A, Büchi FN. Measuring the current
distribution in PEFCs with sub-millimeter resolution. Journal of The Electrochemical
Society. 2006;153(11). doi:10.1149/1.2345591
apa: Freunberger, S. A., Reum, M., Evertz, J., Wokaun, A., & Büchi, F. N. (2006).
Measuring the current distribution in PEFCs with sub-millimeter resolution. Journal
of The Electrochemical Society. The Electrochemical Society. https://doi.org/10.1149/1.2345591
chicago: Freunberger, Stefan Alexander, Mathias Reum, Jörg Evertz, Alexander Wokaun,
and Felix N. Büchi. “Measuring the Current Distribution in PEFCs with Sub-Millimeter
Resolution.” Journal of The Electrochemical Society. The Electrochemical
Society, 2006. https://doi.org/10.1149/1.2345591.
ieee: S. A. Freunberger, M. Reum, J. Evertz, A. Wokaun, and F. N. Büchi, “Measuring
the current distribution in PEFCs with sub-millimeter resolution,” Journal
of The Electrochemical Society, vol. 153, no. 11. The Electrochemical Society,
2006.
ista: Freunberger SA, Reum M, Evertz J, Wokaun A, Büchi FN. 2006. Measuring the
current distribution in PEFCs with sub-millimeter resolution. Journal of The Electrochemical
Society. 153(11), A2158.
mla: Freunberger, Stefan Alexander, et al. “Measuring the Current Distribution in
PEFCs with Sub-Millimeter Resolution.” Journal of The Electrochemical Society,
vol. 153, no. 11, A2158, The Electrochemical Society, 2006, doi:10.1149/1.2345591.
short: S.A. Freunberger, M. Reum, J. Evertz, A. Wokaun, F.N. Büchi, Journal of
The Electrochemical Society 153 (2006).
date_created: 2020-01-15T12:23:12Z
date_published: 2006-09-20T00:00:00Z
date_updated: 2021-01-12T08:13:06Z
day: '20'
doi: 10.1149/1.2345591
extern: '1'
intvolume: ' 153'
issue: '11'
language:
- iso: eng
month: '09'
oa_version: None
publication: Journal of The Electrochemical Society
publication_identifier:
issn:
- 0013-4651
publication_status: published
publisher: The Electrochemical Society
quality_controlled: '1'
status: public
title: Measuring the current distribution in PEFCs with sub-millimeter resolution
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 153
year: '2006'
...
---
_id: '7327'
abstract:
- lang: eng
text: "Propagation of performance changes to adjacent cells in polymer electrolyte
fuel cell stacks is studied by means of voltage monitoring and local current density
measurements in peripheral cells of the stack. A technical fuel cell stack has
been modified by implementing two independent reactant and coolant supplies in
order to deliberately change the performance of one cell (anomalous cell) and
study the coupling phenomena to adjacent cells (coupling cells), while keeping
the working conditions of the later cell-group unaltered.\r\nTwo anomalies are
studied: (i) air starvation and (ii) thermal anomaly, in a single anomalous cell
in the stack and their coupling to adjacent cells. The results have shown that
anomalies inducing considerable changes in the local current density of the anomalous
cell (such as air starvation) propagate to adjacent cells affecting their performance.
The propagation of local current density changes takes place via the common bipolar
plate due to its finite thickness and in-plane conductivity. Consequently, anomalies
which do not strongly influence the local current density distribution (such as
a thermal anomaly under the studied working conditions) do not propagate to adjacent
cells."
article_processing_charge: No
article_type: original
author:
- first_name: Marco
full_name: Santis, Marco
last_name: Santis
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Matthias
full_name: Papra, Matthias
last_name: Papra
- first_name: Alexander
full_name: Wokaun, Alexander
last_name: Wokaun
- first_name: Felix N.
full_name: Büchi, Felix N.
last_name: Büchi
citation:
ama: Santis M, Freunberger SA, Papra M, Wokaun A, Büchi FN. Experimental investigation
of coupling phenomena in polymer electrolyte fuel cell stacks. Journal of Power
Sources. 2006;161(2):1076-1083. doi:10.1016/j.jpowsour.2006.06.007
apa: Santis, M., Freunberger, S. A., Papra, M., Wokaun, A., & Büchi, F. N. (2006).
Experimental investigation of coupling phenomena in polymer electrolyte fuel cell
stacks. Journal of Power Sources. Elsevier. https://doi.org/10.1016/j.jpowsour.2006.06.007
chicago: Santis, Marco, Stefan Alexander Freunberger, Matthias Papra, Alexander
Wokaun, and Felix N. Büchi. “Experimental Investigation of Coupling Phenomena
in Polymer Electrolyte Fuel Cell Stacks.” Journal of Power Sources. Elsevier,
2006. https://doi.org/10.1016/j.jpowsour.2006.06.007.
ieee: M. Santis, S. A. Freunberger, M. Papra, A. Wokaun, and F. N. Büchi, “Experimental
investigation of coupling phenomena in polymer electrolyte fuel cell stacks,”
Journal of Power Sources, vol. 161, no. 2. Elsevier, pp. 1076–1083, 2006.
ista: Santis M, Freunberger SA, Papra M, Wokaun A, Büchi FN. 2006. Experimental
investigation of coupling phenomena in polymer electrolyte fuel cell stacks. Journal
of Power Sources. 161(2), 1076–1083.
mla: Santis, Marco, et al. “Experimental Investigation of Coupling Phenomena in
Polymer Electrolyte Fuel Cell Stacks.” Journal of Power Sources, vol. 161,
no. 2, Elsevier, 2006, pp. 1076–83, doi:10.1016/j.jpowsour.2006.06.007.
short: M. Santis, S.A. Freunberger, M. Papra, A. Wokaun, F.N. Büchi, Journal of
Power Sources 161 (2006) 1076–1083.
date_created: 2020-01-15T12:22:56Z
date_published: 2006-10-27T00:00:00Z
date_updated: 2021-01-12T08:13:06Z
day: '27'
doi: 10.1016/j.jpowsour.2006.06.007
extern: '1'
intvolume: ' 161'
issue: '2'
language:
- iso: eng
month: '10'
oa_version: None
page: 1076-1083
publication: Journal of Power Sources
publication_identifier:
issn:
- 0378-7753
publication_status: published
publisher: Elsevier
status: public
title: Experimental investigation of coupling phenomena in polymer electrolyte fuel
cell stacks
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 161
year: '2006'
...
---
_id: '7326'
abstract:
- lang: eng
text: 'Often the properties of a single cell are considered as representative for
a complete polymer electrolyte fuel cell stack or even a fuel cell system. In
some cases this comes close, however, in many real cases differences on several
scales become important. Cell interaction phenomena in fuel cell stacks that arise
from inequalities between adjacent cells are investigated in detail experimentally.
For that, a specialized 2-cell stack with advanced localized diagnostics was developed.
The results show that inequalities propagate by electrical coupling, inhomogeneous
cell polarization and inducing in-plane current in the common bipolar plate. The
effects of the different loss-mechanisms are analyzed and quantified. '
article_processing_charge: No
author:
- first_name: Felix N.
full_name: Büchi, Felix N.
last_name: Büchi
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Marco
full_name: Santis, Marco
last_name: Santis
citation:
ama: 'Büchi FN, Freunberger SA, Santis M. What is learned beyond the scale of single
cells? In: ECS Transactions. Vol 3. ECS; 2006:963-968. doi:10.1149/1.2356215'
apa: 'Büchi, F. N., Freunberger, S. A., & Santis, M. (2006). What is learned
beyond the scale of single cells? In ECS Transactions (Vol. 3, pp. 963–968).
Cancun, Mexico: ECS. https://doi.org/10.1149/1.2356215'
chicago: Büchi, Felix N., Stefan Alexander Freunberger, and Marco Santis. “What
Is Learned beyond the Scale of Single Cells?” In ECS Transactions, 3:963–68.
ECS, 2006. https://doi.org/10.1149/1.2356215.
ieee: F. N. Büchi, S. A. Freunberger, and M. Santis, “What is learned beyond the
scale of single cells?,” in ECS Transactions, Cancun, Mexico, 2006, vol.
3, no. 1, pp. 963–968.
ista: Büchi FN, Freunberger SA, Santis M. 2006. What is learned beyond the scale
of single cells? ECS Transactions. ECS Meeting vol. 3, 963–968.
mla: Büchi, Felix N., et al. “What Is Learned beyond the Scale of Single Cells?”
ECS Transactions, vol. 3, no. 1, ECS, 2006, pp. 963–68, doi:10.1149/1.2356215.
short: F.N. Büchi, S.A. Freunberger, M. Santis, in:, ECS Transactions, ECS, 2006,
pp. 963–968.
conference:
end_date: 2006-11-03
location: Cancun, Mexico
name: ECS Meeting
start_date: 2006-10-29
date_created: 2020-01-15T12:22:44Z
date_published: 2006-11-03T00:00:00Z
date_updated: 2021-01-12T08:13:05Z
day: '03'
doi: 10.1149/1.2356215
extern: '1'
intvolume: ' 3'
issue: '1'
language:
- iso: eng
month: '11'
oa_version: None
page: 963-968
publication: ECS Transactions
publication_status: published
publisher: ECS
quality_controlled: '1'
status: public
title: What is learned beyond the scale of single cells?
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2006'
...
---
_id: '7329'
abstract:
- lang: eng
text: A novel measurement principle for measuring the current distribution in polymer
electrolyte fuel cells (PEFCs) is introduced. It allows, in contrast to all other
known techniques, for the first time for a resolution smaller than the channel/rib
scale of the flow field in PEFCs. The current density is obtained by considering
the electron conductors in the cell as a two-dimensional resistor with the voltage
drop caused by the current. The method was applied to a cell operated on oxygen
up to high current densities. The results show that the ohmic resistances govern
the current distribution in the low current regime, whereas mass transport limitations
hamper the current production under the land at high loads.
article_processing_charge: No
article_type: original
author:
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Mathias
full_name: Reum, Mathias
last_name: Reum
- first_name: Alexander
full_name: Wokaun, Alexander
last_name: Wokaun
- first_name: Felix N.
full_name: Büchi, Felix N.
last_name: Büchi
citation:
ama: Freunberger SA, Reum M, Wokaun A, Büchi FN. Expanding current distribution
measurement in PEFCs to sub-millimeter resolution. Electrochemistry Communications.
2006;8(9):1435-1438. doi:10.1016/j.elecom.2006.05.032
apa: Freunberger, S. A., Reum, M., Wokaun, A., & Büchi, F. N. (2006). Expanding
current distribution measurement in PEFCs to sub-millimeter resolution. Electrochemistry
Communications. Elsevier. https://doi.org/10.1016/j.elecom.2006.05.032
chicago: Freunberger, Stefan Alexander, Mathias Reum, Alexander Wokaun, and Felix
N. Büchi. “Expanding Current Distribution Measurement in PEFCs to Sub-Millimeter
Resolution.” Electrochemistry Communications. Elsevier, 2006. https://doi.org/10.1016/j.elecom.2006.05.032.
ieee: S. A. Freunberger, M. Reum, A. Wokaun, and F. N. Büchi, “Expanding current
distribution measurement in PEFCs to sub-millimeter resolution,” Electrochemistry
Communications, vol. 8, no. 9. Elsevier, pp. 1435–1438, 2006.
ista: Freunberger SA, Reum M, Wokaun A, Büchi FN. 2006. Expanding current distribution
measurement in PEFCs to sub-millimeter resolution. Electrochemistry Communications.
8(9), 1435–1438.
mla: Freunberger, Stefan Alexander, et al. “Expanding Current Distribution Measurement
in PEFCs to Sub-Millimeter Resolution.” Electrochemistry Communications,
vol. 8, no. 9, Elsevier, 2006, pp. 1435–38, doi:10.1016/j.elecom.2006.05.032.
short: S.A. Freunberger, M. Reum, A. Wokaun, F.N. Büchi, Electrochemistry Communications
8 (2006) 1435–1438.
date_created: 2020-01-15T12:23:22Z
date_published: 2006-09-01T00:00:00Z
date_updated: 2021-01-12T08:13:06Z
day: '01'
doi: 10.1016/j.elecom.2006.05.032
extern: '1'
intvolume: ' 8'
issue: '9'
language:
- iso: eng
month: '09'
oa_version: None
page: 1435-1438
publication: Electrochemistry Communications
publication_identifier:
issn:
- 1388-2481
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Expanding current distribution measurement in PEFCs to sub-millimeter resolution
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2006'
...
---
_id: '7330'
abstract:
- lang: eng
text: Polymer electrolyte fuel cells (PE fuel cells) working with air at low stoichiometries
(<2.0) and standard electrochemical components show a high degree of inhomogeneity
in the current density distribution over the active area. An inhomogeneous current
density distribution leads to a non-uniform utilization of the active area, which
could negatively affect the time of life of the cells. Furthermore, it is also
believed to lower cell performance. In this work, the homogenization of the current
density, realized by means of tailored cathodes with along-the-air-channel redistributed
catalyst loadings, is investigated. The air stoichiometry range for which a homogenization
of the current density is achieved depends upon the gradient with which the catalyst
is redistributed along the air channel. A gentle increasing catalyst loading profile
homogenizes the current density at relatively higher air stoichiometries, while
a steeper profile is suited better for lower air stoichiometries. The results
show that a homogenization of the current density by means of redistributed catalyst
loading has negative effects on cell performance. Model calculations corroborate
the experimental findings on homogenization of the current density and deliver
an explanation for the decrease in cell performance.
article_processing_charge: No
article_type: original
author:
- first_name: M.
full_name: Santis, M.
last_name: Santis
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: A.
full_name: Reiner, A.
last_name: Reiner
- first_name: F.N.
full_name: Büchi, F.N.
last_name: Büchi
citation:
ama: Santis M, Freunberger SA, Reiner A, Büchi FN. Homogenization of the current
density in polymer electrolyte fuel cells by in-plane cathode catalyst gradients.
Electrochimica Acta. 2006;51(25):5383-5393. doi:10.1016/j.electacta.2006.02.008
apa: Santis, M., Freunberger, S. A., Reiner, A., & Büchi, F. N. (2006). Homogenization
of the current density in polymer electrolyte fuel cells by in-plane cathode catalyst
gradients. Electrochimica Acta. Elsevier. https://doi.org/10.1016/j.electacta.2006.02.008
chicago: Santis, M., Stefan Alexander Freunberger, A. Reiner, and F.N. Büchi. “Homogenization
of the Current Density in Polymer Electrolyte Fuel Cells by In-Plane Cathode Catalyst
Gradients.” Electrochimica Acta. Elsevier, 2006. https://doi.org/10.1016/j.electacta.2006.02.008.
ieee: M. Santis, S. A. Freunberger, A. Reiner, and F. N. Büchi, “Homogenization
of the current density in polymer electrolyte fuel cells by in-plane cathode catalyst
gradients,” Electrochimica Acta, vol. 51, no. 25. Elsevier, pp. 5383–5393,
2006.
ista: Santis M, Freunberger SA, Reiner A, Büchi FN. 2006. Homogenization of the
current density in polymer electrolyte fuel cells by in-plane cathode catalyst
gradients. Electrochimica Acta. 51(25), 5383–5393.
mla: Santis, M., et al. “Homogenization of the Current Density in Polymer Electrolyte
Fuel Cells by In-Plane Cathode Catalyst Gradients.” Electrochimica Acta,
vol. 51, no. 25, Elsevier, 2006, pp. 5383–93, doi:10.1016/j.electacta.2006.02.008.
short: M. Santis, S.A. Freunberger, A. Reiner, F.N. Büchi, Electrochimica Acta 51
(2006) 5383–5393.
date_created: 2020-01-15T12:23:34Z
date_published: 2006-07-01T00:00:00Z
date_updated: 2021-01-12T08:13:07Z
day: '01'
doi: 10.1016/j.electacta.2006.02.008
extern: '1'
intvolume: ' 51'
issue: '25'
language:
- iso: eng
month: '07'
oa_version: None
page: 5383-5393
publication: Electrochimica Acta
publication_identifier:
issn:
- 0013-4686
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Homogenization of the current density in polymer electrolyte fuel cells by
in-plane cathode catalyst gradients
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 51
year: '2006'
...
---
_id: '7332'
abstract:
- lang: eng
text: A quasi-two-dimensional, along-the-channel mass and heat-transfer model for
a proton exchange membrane fuel cell (PEFC) is described and validated against
experimental current distribution data. The model is formulated in a dimensional
manner, i.e., local transport phenomena are treated one-dimensional in through-plane
direction and coupled in-plane by convective transport in the gas and coolant
channels. Thus, a two-dimensional slice running through the repetitive unit of
a cell from the anode channel via membrane-electrode assembly (MEA) and cathode
channel to the coolant channel and from inlet to outlet is modeled. The aim of
the work is to elucidate the influence of operating conditions such as feed gas
humidities and stoichiometric ratios on the along-the-channel current density
distribution and to identify the distinct underlying voltage loss mechanisms.
Furthermore, a complicated technical flow field is modeled by a combination of
co- and counterflow subdomains and compared with experimental current densities.
article_number: A396
article_processing_charge: No
article_type: original
author:
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Marco
full_name: Santis, Marco
last_name: Santis
- first_name: Ingo A.
full_name: Schneider, Ingo A.
last_name: Schneider
- first_name: Alexander
full_name: Wokaun, Alexander
last_name: Wokaun
- first_name: Felix N.
full_name: Büchi, Felix N.
last_name: Büchi
citation:
ama: Freunberger SA, Santis M, Schneider IA, Wokaun A, Büchi FN. In-plane effects
in large-scale PEMFCs. Journal of The Electrochemical Society. 2006;153(2).
doi:10.1149/1.2150150
apa: Freunberger, S. A., Santis, M., Schneider, I. A., Wokaun, A., & Büchi,
F. N. (2006). In-plane effects in large-scale PEMFCs. Journal of The Electrochemical
Society. The Electrochemical Society. https://doi.org/10.1149/1.2150150
chicago: Freunberger, Stefan Alexander, Marco Santis, Ingo A. Schneider, Alexander
Wokaun, and Felix N. Büchi. “In-Plane Effects in Large-Scale PEMFCs.” Journal
of The Electrochemical Society. The Electrochemical Society, 2006. https://doi.org/10.1149/1.2150150.
ieee: S. A. Freunberger, M. Santis, I. A. Schneider, A. Wokaun, and F. N. Büchi,
“In-plane effects in large-scale PEMFCs,” Journal of The Electrochemical Society,
vol. 153, no. 2. The Electrochemical Society, 2006.
ista: Freunberger SA, Santis M, Schneider IA, Wokaun A, Büchi FN. 2006. In-plane
effects in large-scale PEMFCs. Journal of The Electrochemical Society. 153(2),
A396.
mla: Freunberger, Stefan Alexander, et al. “In-Plane Effects in Large-Scale PEMFCs.”
Journal of The Electrochemical Society, vol. 153, no. 2, A396, The Electrochemical
Society, 2006, doi:10.1149/1.2150150.
short: S.A. Freunberger, M. Santis, I.A. Schneider, A. Wokaun, F.N. Büchi, Journal
of The Electrochemical Society 153 (2006).
date_created: 2020-01-15T12:24:00Z
date_published: 2006-01-04T00:00:00Z
date_updated: 2021-01-12T08:13:08Z
day: '04'
doi: 10.1149/1.2150150
extern: '1'
intvolume: ' 153'
issue: '2'
language:
- iso: eng
month: '01'
oa_version: None
publication: Journal of The Electrochemical Society
publication_identifier:
issn:
- 0013-4651
publication_status: published
publisher: The Electrochemical Society
quality_controlled: '1'
status: public
title: In-plane effects in large-scale PEMFCs
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 153
year: '2006'
...
---
_id: '7331'
abstract:
- lang: eng
text: A previously developed mathematical model for water management and current
density distribution in a polymer electrolyte fuel cell (PEFCs) is employed to
investigate the effects of cooling strategies on cell performance. The model describes
a two-dimensional slice through the cell along the channels and through the entire
cell sandwich including the coolant channels and the bipolar plate. Arbitrary
flow arrangements of fuel, oxidant, and coolant stream directions can be described.
Due to the serious impact of temperature on all processes in the PEFC, both the
relative direction of the coolant stream to the gas streams and its mass flow
turns out to significantly affect the cell performance. Besides influencing the
electrochemical reaction and all kinds of mass transfer temperature, variations
predominantly alter the local membrane hydration distribution and subseqently
its conductivity.
article_number: A909
article_processing_charge: No
article_type: original
author:
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Alexander
full_name: Wokaun, Alexander
last_name: Wokaun
- first_name: Felix N.
full_name: Büchi, Felix N.
last_name: Büchi
citation:
ama: 'Freunberger SA, Wokaun A, Büchi FN. In-plane effects in large-scale PEFCs:
II. The influence of cooling strategy on cell performance. Journal of The Electrochemical
Society. 2006;153(5). doi:10.1149/1.2185282'
apa: 'Freunberger, S. A., Wokaun, A., & Büchi, F. N. (2006). In-plane effects
in large-scale PEFCs: II. The influence of cooling strategy on cell performance.
Journal of The Electrochemical Society. The Electrochemical Society. https://doi.org/10.1149/1.2185282'
chicago: 'Freunberger, Stefan Alexander, Alexander Wokaun, and Felix N. Büchi.
“In-Plane Effects in Large-Scale PEFCs: II. The Influence of Cooling Strategy
on Cell Performance.” Journal of The Electrochemical Society. The Electrochemical
Society, 2006. https://doi.org/10.1149/1.2185282.'
ieee: 'S. A. Freunberger, A. Wokaun, and F. N. Büchi, “In-plane effects in large-scale
PEFCs: II. The influence of cooling strategy on cell performance,” Journal
of The Electrochemical Society, vol. 153, no. 5. The Electrochemical Society,
2006.'
ista: 'Freunberger SA, Wokaun A, Büchi FN. 2006. In-plane effects in large-scale
PEFCs: II. The influence of cooling strategy on cell performance. Journal of The
Electrochemical Society. 153(5), A909.'
mla: 'Freunberger, Stefan Alexander, et al. “In-Plane Effects in Large-Scale PEFCs:
II. The Influence of Cooling Strategy on Cell Performance.” Journal of The
Electrochemical Society, vol. 153, no. 5, A909, The Electrochemical Society,
2006, doi:10.1149/1.2185282.'
short: S.A. Freunberger, A. Wokaun, F.N. Büchi, Journal of The Electrochemical
Society 153 (2006).
date_created: 2020-01-15T12:23:46Z
date_published: 2006-03-27T00:00:00Z
date_updated: 2021-01-12T08:13:08Z
day: '27'
doi: 10.1149/1.2185282
extern: '1'
intvolume: ' 153'
issue: '5'
language:
- iso: eng
month: '03'
oa_version: None
publication: Journal of The Electrochemical Society
publication_identifier:
issn:
- 0013-4651
publication_status: published
publisher: The Electrochemical Society
quality_controlled: '1'
status: public
title: 'In-plane effects in large-scale PEFCs: II. The influence of cooling strategy
on cell performance'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 153
year: '2006'
...
---
_id: '854'
abstract:
- lang: eng
text: Phylogenetic relationships between the extinct woolly mammoth (Mammuthus primigenius),
and the Asian (Elephas maximus) and African savanna (Loxodonta africana) elephants
remain unresolved. Here, we report the sequence of the complete mitochondrial
genome (16,842 base pairs) of a woolly mammoth extracted from permafrost-preserved
remains from the Pleistocene epoch - the oldest mitochondrial genome sequence
determined to date. We demonstrate that well-preserved mitochondrial genome fragments,
as long as ∼1,600-1700 base pairs, can be retrieved from pre-Holocene remains
of an extinct species. Phylogenetic reconstruction of the Elephantinae clade suggests
that M. primigenius and E. maximus are sister species that diverged soon after
their common ancestor split from the L. africana lineage. Low nucleotide diversity
found between independently determined mitochondrial genomic sequences of woolly
mammoths separated geographically and in time suggests that north-eastern Siberia
was occupied by a relatively homogeneous population of M. primigenius throughout
the late Pleistocene.
acknowledgement: |-
FAK is supported by the NSF Graduate Research Fellowship.
We thank the Natural History Museum, North-Eastern Research Center, Far Eastern Branch of the Russian Academy of Sciences for photographic material ofM. primigenius leg, V. A. Nikishina for artwork and technical support, Y.B. Yurov, G. Dvoryanchikov, N. Riazanskaya and T. Kolesnikova for technical support, K. Mehren and C. Gray for elephant specimens, and V. Y. Solovyev for help with artwork of animal images.
author:
- first_name: Evgeny
full_name: Rogaev, Evgeny I
last_name: Rogaev
- first_name: Yuri
full_name: Moliaka, Yuri K
last_name: Moliaka
- first_name: Boris
full_name: Malyarchuk, Boris A
last_name: Malyarchuk
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Miroslava
full_name: Derenko, Miroslava V
last_name: Derenko
- first_name: Ilya
full_name: Chumakov, Ilya M
last_name: Chumakov
- first_name: Anastasia
full_name: Grigorenko, Anastasia P
last_name: Grigorenko
citation:
ama: Rogaev E, Moliaka Y, Malyarchuk B, et al. Complete mitochondrial genome and
phylogeny of pleistocene mammoth Mammuthus primigenius. PLoS Biology. 2006;4(3):0403-0410.
doi:10.1371/journal.pbio.0040073
apa: Rogaev, E., Moliaka, Y., Malyarchuk, B., Kondrashov, F., Derenko, M., Chumakov,
I., & Grigorenko, A. (2006). Complete mitochondrial genome and phylogeny of
pleistocene mammoth Mammuthus primigenius. PLoS Biology. Public Library
of Science. https://doi.org/10.1371/journal.pbio.0040073
chicago: Rogaev, Evgeny, Yuri Moliaka, Boris Malyarchuk, Fyodor Kondrashov, Miroslava
Derenko, Ilya Chumakov, and Anastasia Grigorenko. “Complete Mitochondrial Genome
and Phylogeny of Pleistocene Mammoth Mammuthus Primigenius.” PLoS Biology.
Public Library of Science, 2006. https://doi.org/10.1371/journal.pbio.0040073.
ieee: E. Rogaev et al., “Complete mitochondrial genome and phylogeny of pleistocene
mammoth Mammuthus primigenius,” PLoS Biology, vol. 4, no. 3. Public Library
of Science, pp. 0403–0410, 2006.
ista: Rogaev E, Moliaka Y, Malyarchuk B, Kondrashov F, Derenko M, Chumakov I, Grigorenko
A. 2006. Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus
primigenius. PLoS Biology. 4(3), 0403–0410.
mla: Rogaev, Evgeny, et al. “Complete Mitochondrial Genome and Phylogeny of Pleistocene
Mammoth Mammuthus Primigenius.” PLoS Biology, vol. 4, no. 3, Public Library
of Science, 2006, pp. 0403–10, doi:10.1371/journal.pbio.0040073.
short: E. Rogaev, Y. Moliaka, B. Malyarchuk, F. Kondrashov, M. Derenko, I. Chumakov,
A. Grigorenko, PLoS Biology 4 (2006) 0403–0410.
date_created: 2018-12-11T11:48:51Z
date_published: 2006-03-01T00:00:00Z
date_updated: 2021-01-12T08:19:58Z
day: '01'
doi: 10.1371/journal.pbio.0040073
extern: 1
intvolume: ' 4'
issue: '3'
month: '03'
page: 0403 - 0410
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '6794'
quality_controlled: 0
status: public
title: Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus
primigenius
type: journal_article
volume: 4
year: '2006'
...
---
_id: '868'
abstract:
- lang: eng
text: 'Background: The glyoxylate cycle is thought to be present in bacteria, protists,
plants, fungi, and nematodes, but not in other Metazoa. However, activity of the
glyoxylate cycle enzymes, malate synthase (MS) and isocitrate lyase (ICL), in
animal tissues has been reported. In order to clarify the status of the MS and
ICL genes in animals and get an insight into their evolution, we undertook a comparative-genomic
study. Results: Using sequence similarity searches, we identified MS genes in
arthropods, echinoderms, and vertebrates, including platypus and opossum, but
not in the numerous sequenced genomes of placental mammals. The regions of the
placental mammals'' genomes expected to code for malate synthase, as determined
by comparison of the gene orders in vertebrate genomes, show clear similarity
to the opossum MS sequence but contain stop codons, indicating that the MS gene
became a pseudogene in placental mammals. By contrast, the ICL gene is undetectable
in animals other than the nematodes that possess a bifunctional, fused ICL-MS
gene. Examination of phylogenetic trees of MS and ICL suggests multiple horizontal
gene transfer events that probably went in both directions between several bacterial
and eukaryotic lineages. The strongest evidence was obtained for the acquisition
of the bifunctional ICL-MS gene from an as yet unknown bacterial source with the
corresponding operonic organization by the common ancestor of the nematodes. Conclusion:
The distribution of the MS and ICL genes in animals suggests that either they
encode alternative enzymes of the glyoxylate cycle that are not orthologous to
the known MS and ICL or the animal MS acquired a new function that remains to
be characterized. Regardless of the ultimate solution to this conundrum, the genes
for the glyoxylate cycle enzymes present a remarkable variety of evolutionary
events including unusual horizontal gene transfer from bacteria to animals.'
acknowledgement: The authors thank Alexey Kondrashov for suggesting the possibility
of non- orthologous gene displacement in glyoxylate cycle specific enzymes and for
critical reading of this manuscript. FAK is a National Science Foundation Graduate
Fellow.
author:
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Eugene
full_name: Koonin, Eugene V
last_name: Koonin
- first_name: Igor
full_name: Morgunov, Igor G
last_name: Morgunov
- first_name: Tatiana
full_name: Finogenova, Tatiana V
last_name: Finogenova
- first_name: Marie
full_name: Kondrashova, Marie N
last_name: Kondrashova
citation:
ama: Kondrashov F, Koonin E, Morgunov I, Finogenova T, Kondrashova M. Evolution
of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal transfer
events and pseudogene formation. Biology Direct. 2006;1. doi:10.1186/1745-6150-1-31
apa: Kondrashov, F., Koonin, E., Morgunov, I., Finogenova, T., & Kondrashova,
M. (2006). Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple
horizontal transfer events and pseudogene formation. Biology Direct. BioMed
Central. https://doi.org/10.1186/1745-6150-1-31
chicago: Kondrashov, Fyodor, Eugene Koonin, Igor Morgunov, Tatiana Finogenova, and
Marie Kondrashova. “Evolution of Glyoxylate Cycle Enzymes in Metazoa Evidence
of Multiple Horizontal Transfer Events and Pseudogene Formation.” Biology Direct.
BioMed Central, 2006. https://doi.org/10.1186/1745-6150-1-31.
ieee: F. Kondrashov, E. Koonin, I. Morgunov, T. Finogenova, and M. Kondrashova,
“Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal
transfer events and pseudogene formation,” Biology Direct, vol. 1. BioMed
Central, 2006.
ista: Kondrashov F, Koonin E, Morgunov I, Finogenova T, Kondrashova M. 2006. Evolution
of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal transfer
events and pseudogene formation. Biology Direct. 1.
mla: Kondrashov, Fyodor, et al. “Evolution of Glyoxylate Cycle Enzymes in Metazoa
Evidence of Multiple Horizontal Transfer Events and Pseudogene Formation.” Biology
Direct, vol. 1, BioMed Central, 2006, doi:10.1186/1745-6150-1-31.
short: F. Kondrashov, E. Koonin, I. Morgunov, T. Finogenova, M. Kondrashova, Biology
Direct 1 (2006).
date_created: 2018-12-11T11:48:56Z
date_published: 2006-10-23T00:00:00Z
date_updated: 2021-01-12T08:20:31Z
day: '23'
doi: 10.1186/1745-6150-1-31
extern: 1
intvolume: ' 1'
month: '10'
publication: Biology Direct
publication_status: published
publisher: BioMed Central
publist_id: '6778'
quality_controlled: 0
status: public
title: Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal
transfer events and pseudogene formation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 1
year: '2006'
...
---
_id: '873'
abstract:
- lang: eng
text: New genes commonly appear through complete or partial duplications of pre-existing
genes. Duplications of long DNA segments are constantly produced by rare mutations,
may become fixed in a population by selection or random drift, and are subject
to divergent evolution of the paralogous sequences after fixation, although gene
conversion can impede this process. New data shed some light on each of these
processes. Mutations which involve duplications can occur through at least two
different mechanisms, backward strand slippage during DNA replication and unequal
crossing-over. The background rate of duplication of a complete gene in humans
is 10-9-10-10 per generation, although many genes located within hot-spots of
large-scale mutation are duplicated much more often. Many gene duplications affect
fitness strongly, and are responsible, through gene dosage effects, for a number
of genetic diseases. However, high levels of intrapopulation polymorphism caused
by presence or absence of long, gene-containing DNA segments imply that some duplications
are not under strong selection. The polymorphism to fixation ratios appear to
be approximately the same for gene duplications and for presumably selectively
neutral nucleotide substitutions, which, according to the McDonald-Kreitman test,
is consistent with selective neutrality of duplications. However, this pattern
can also be due to negative selection against most of segregating duplications
and positive selection for at least some duplications which become fixed. Patterns
in post-fixation evolution of duplicated genes do not easily reveal the causes
of fixations. Many gene duplications which became fixed recently in a variety
of organisms were positively selected because the increased expression of the
corresponding genes was beneficial. The effects of gene dosage provide a unified
framework for studying all phases of the life history of a gene duplication. Application
of well-known methods of evolutionary genetics to accumulating data on new, polymorphic,
and fixed duplication will enhance our understanding of the role of natural selection
in the evolution by gene duplication.
author:
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
citation:
ama: Kondrashov F, Kondrashov A. Role of selection in fixation of gene duplications.
Journal of Theoretical Biology. 2006;239(2):141-151. doi:10.1016/j.jtbi.2005.08.033
apa: Kondrashov, F., & Kondrashov, A. (2006). Role of selection in fixation
of gene duplications. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2005.08.033
chicago: Kondrashov, Fyodor, and Alexey Kondrashov. “Role of Selection in Fixation
of Gene Duplications.” Journal of Theoretical Biology. Elsevier, 2006.
https://doi.org/10.1016/j.jtbi.2005.08.033.
ieee: F. Kondrashov and A. Kondrashov, “Role of selection in fixation of gene duplications,”
Journal of Theoretical Biology, vol. 239, no. 2. Elsevier, pp. 141–151,
2006.
ista: Kondrashov F, Kondrashov A. 2006. Role of selection in fixation of gene duplications.
Journal of Theoretical Biology. 239(2), 141–151.
mla: Kondrashov, Fyodor, and Alexey Kondrashov. “Role of Selection in Fixation of
Gene Duplications.” Journal of Theoretical Biology, vol. 239, no. 2, Elsevier,
2006, pp. 141–51, doi:10.1016/j.jtbi.2005.08.033.
short: F. Kondrashov, A. Kondrashov, Journal of Theoretical Biology 239 (2006) 141–151.
date_created: 2018-12-11T11:48:57Z
date_published: 2006-03-21T00:00:00Z
date_updated: 2021-01-12T08:20:47Z
day: '21'
doi: 10.1016/j.jtbi.2005.08.033
extern: 1
intvolume: ' 239'
issue: '2'
month: '03'
page: 141 - 151
publication: Journal of Theoretical Biology
publication_status: published
publisher: Elsevier
publist_id: '6773'
quality_controlled: 0
status: public
title: Role of selection in fixation of gene duplications
type: journal_article
volume: 239
year: '2006'
...
---
_id: '8489'
abstract:
- lang: eng
text: Structure elucidation of proteins by either NMR or X‐ray crystallography often
requires the screening of a large number of samples for promising protein constructs
and optimum solution conditions. For large‐scale screening of protein samples
in solution, robust methods are needed that allow a rapid assessment of the folding
of a polypeptide under diverse sample conditions. Here we present HET‐SOFAST NMR,
a highly sensitive new method for semi‐quantitative characterization of the structural
compactness and heterogeneity of polypeptide chains in solution. On the basis
of one‐dimensional 1H HET‐SOFAST NMR data, obtained on well‐folded, molten globular,
partially‐ and completely unfolded proteins, we define empirical thresholds that
can be used as quantitative benchmarks for protein compactness. For 15N‐enriched
protein samples, two‐dimensional 1H‐15N HET‐SOFAST correlation spectra provide
site‐specific information about the structural heterogeneity along the polypeptide
chain.
article_processing_charge: No
article_type: original
author:
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Vincent
full_name: Forge, Vincent
last_name: Forge
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
citation:
ama: Schanda P, Forge V, Brutscher B. HET-SOFAST NMR for fast detection of structural
compactness and heterogeneity along polypeptide chains. Magnetic Resonance
in Chemistry. 2006;44(S1):S177-S184. doi:10.1002/mrc.1825
apa: Schanda, P., Forge, V., & Brutscher, B. (2006). HET-SOFAST NMR for fast
detection of structural compactness and heterogeneity along polypeptide chains.
Magnetic Resonance in Chemistry. Wiley. https://doi.org/10.1002/mrc.1825
chicago: Schanda, Paul, Vincent Forge, and Bernhard Brutscher. “HET-SOFAST NMR for
Fast Detection of Structural Compactness and Heterogeneity along Polypeptide Chains.”
Magnetic Resonance in Chemistry. Wiley, 2006. https://doi.org/10.1002/mrc.1825.
ieee: P. Schanda, V. Forge, and B. Brutscher, “HET-SOFAST NMR for fast detection
of structural compactness and heterogeneity along polypeptide chains,” Magnetic
Resonance in Chemistry, vol. 44, no. S1. Wiley, pp. S177–S184, 2006.
ista: Schanda P, Forge V, Brutscher B. 2006. HET-SOFAST NMR for fast detection of
structural compactness and heterogeneity along polypeptide chains. Magnetic Resonance
in Chemistry. 44(S1), S177–S184.
mla: Schanda, Paul, et al. “HET-SOFAST NMR for Fast Detection of Structural Compactness
and Heterogeneity along Polypeptide Chains.” Magnetic Resonance in Chemistry,
vol. 44, no. S1, Wiley, 2006, pp. S177–84, doi:10.1002/mrc.1825.
short: P. Schanda, V. Forge, B. Brutscher, Magnetic Resonance in Chemistry 44 (2006)
S177–S184.
date_created: 2020-09-18T10:13:42Z
date_published: 2006-07-06T00:00:00Z
date_updated: 2021-01-12T08:19:37Z
day: '06'
doi: 10.1002/mrc.1825
extern: '1'
intvolume: ' 44'
issue: S1
language:
- iso: eng
month: '07'
oa_version: None
page: S177-S184
publication: Magnetic Resonance in Chemistry
publication_identifier:
issn:
- 0749-1581
- 1097-458X
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: HET-SOFAST NMR for fast detection of structural compactness and heterogeneity
along polypeptide chains
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 44
year: '2006'
...
---
_id: '8488'
abstract:
- lang: eng
text: We demonstrate for different protein samples that three-dimensional HNCO and
HNCA correlation spectra may be recorded in a few minutes acquisition time using
the band-selective excitation short-transient sequences presented here. This opens
new perspectives for the NMR structural investigation of unstable protein samples
and real-time site-resolved studies of protein kinetics.
article_processing_charge: No
article_type: original
author:
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Hélène
full_name: Van Melckebeke, Hélène
last_name: Van Melckebeke
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
citation:
ama: Schanda P, Van Melckebeke H, Brutscher B. Speeding up three-dimensional protein
NMR experiments to a few minutes. Journal of the American Chemical Society.
2006;128(28):9042-9043. doi:10.1021/ja062025p
apa: Schanda, P., Van Melckebeke, H., & Brutscher, B. (2006). Speeding up three-dimensional
protein NMR experiments to a few minutes. Journal of the American Chemical
Society. American Chemical Society. https://doi.org/10.1021/ja062025p
chicago: Schanda, Paul, Hélène Van Melckebeke, and Bernhard Brutscher. “Speeding
up Three-Dimensional Protein NMR Experiments to a Few Minutes.” Journal of
the American Chemical Society. American Chemical Society, 2006. https://doi.org/10.1021/ja062025p.
ieee: P. Schanda, H. Van Melckebeke, and B. Brutscher, “Speeding up three-dimensional
protein NMR experiments to a few minutes,” Journal of the American Chemical
Society, vol. 128, no. 28. American Chemical Society, pp. 9042–9043, 2006.
ista: Schanda P, Van Melckebeke H, Brutscher B. 2006. Speeding up three-dimensional
protein NMR experiments to a few minutes. Journal of the American Chemical Society.
128(28), 9042–9043.
mla: Schanda, Paul, et al. “Speeding up Three-Dimensional Protein NMR Experiments
to a Few Minutes.” Journal of the American Chemical Society, vol. 128,
no. 28, American Chemical Society, 2006, pp. 9042–43, doi:10.1021/ja062025p.
short: P. Schanda, H. Van Melckebeke, B. Brutscher, Journal of the American Chemical
Society 128 (2006) 9042–9043.
date_created: 2020-09-18T10:13:36Z
date_published: 2006-06-21T00:00:00Z
date_updated: 2021-01-12T08:19:37Z
day: '21'
doi: 10.1021/ja062025p
extern: '1'
intvolume: ' 128'
issue: '28'
keyword:
- Colloid and Surface Chemistry
- Biochemistry
- General Chemistry
- Catalysis
language:
- iso: eng
month: '06'
oa_version: None
page: 9042-9043
publication: Journal of the American Chemical Society
publication_identifier:
issn:
- 0002-7863
- 1520-5126
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: Speeding up three-dimensional protein NMR experiments to a few minutes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 128
year: '2006'
...
---
_id: '8490'
abstract:
- lang: eng
text: We demonstrate the feasibility of recording 1H–15N correlation spectra of
proteins in only one second of acquisition time. The experiment combines recently
proposed SOFAST-HMQC with Hadamard-type 15N frequency encoding. This allows site-resolved
real-time NMR studies of kinetic processes in proteins with an increased time
resolution. The sensitivity of the experiment is sufficient to be applicable to
a wide range of molecular systems available at millimolar concentration on a high
magnetic field spectrometer.
article_processing_charge: No
article_type: original
author:
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
citation:
ama: Schanda P, Brutscher B. Hadamard frequency-encoded SOFAST-HMQC for ultrafast
two-dimensional protein NMR. Journal of Magnetic Resonance. 2006;178(2):334-339.
doi:10.1016/j.jmr.2005.10.007
apa: Schanda, P., & Brutscher, B. (2006). Hadamard frequency-encoded SOFAST-HMQC
for ultrafast two-dimensional protein NMR. Journal of Magnetic Resonance.
Elsevier. https://doi.org/10.1016/j.jmr.2005.10.007
chicago: Schanda, Paul, and Bernhard Brutscher. “Hadamard Frequency-Encoded SOFAST-HMQC
for Ultrafast Two-Dimensional Protein NMR.” Journal of Magnetic Resonance.
Elsevier, 2006. https://doi.org/10.1016/j.jmr.2005.10.007.
ieee: P. Schanda and B. Brutscher, “Hadamard frequency-encoded SOFAST-HMQC for ultrafast
two-dimensional protein NMR,” Journal of Magnetic Resonance, vol. 178,
no. 2. Elsevier, pp. 334–339, 2006.
ista: Schanda P, Brutscher B. 2006. Hadamard frequency-encoded SOFAST-HMQC for ultrafast
two-dimensional protein NMR. Journal of Magnetic Resonance. 178(2), 334–339.
mla: Schanda, Paul, and Bernhard Brutscher. “Hadamard Frequency-Encoded SOFAST-HMQC
for Ultrafast Two-Dimensional Protein NMR.” Journal of Magnetic Resonance,
vol. 178, no. 2, Elsevier, 2006, pp. 334–39, doi:10.1016/j.jmr.2005.10.007.
short: P. Schanda, B. Brutscher, Journal of Magnetic Resonance 178 (2006) 334–339.
date_created: 2020-09-18T10:13:51Z
date_published: 2006-02-01T00:00:00Z
date_updated: 2021-01-12T08:19:38Z
day: '01'
doi: 10.1016/j.jmr.2005.10.007
extern: '1'
intvolume: ' 178'
issue: '2'
keyword:
- Nuclear and High Energy Physics
- Biophysics
- Biochemistry
- Condensed Matter Physics
language:
- iso: eng
month: '02'
oa_version: None
page: 334-339
publication: Journal of Magnetic Resonance
publication_identifier:
issn:
- 1090-7807
publication_status: published
publisher: Elsevier
status: public
title: Hadamard frequency-encoded SOFAST-HMQC for ultrafast two-dimensional protein
NMR
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 178
year: '2006'
...
---
_id: '8514'
abstract:
- lang: eng
text: We study the extent to which the Hausdorff dimension of a compact subset of
an infinite-dimensional Banach space is affected by a typical mapping into a finite-dimensional
space. It is possible that the dimension drops under all such mappings, but the
amount by which it typically drops is controlled by the ‘thickness exponent’ of
the set, which was defined by Hunt and Kaloshin (Nonlinearity12 (1999), 1263–1275).
More precisely, let $X$ be a compact subset of a Banach space $B$ with thickness
exponent $\tau$ and Hausdorff dimension $d$. Let $M$ be any subspace of the (locally)
Lipschitz functions from $B$ to $\mathbb{R}^{m}$ that contains the space of bounded
linear functions. We prove that for almost every (in the sense of prevalence)
function $f \in M$, the Hausdorff dimension of $f(X)$ is at least $\min\{ m, d
/ (1 + \tau) \}$. We also prove an analogous result for a certain part of the
dimension spectra of Borel probability measures supported on $X$. The factor $1
/ (1 + \tau)$ can be improved to $1 / (1 + \tau / 2)$ if $B$ is a Hilbert space.
Since dimension cannot increase under a (locally) Lipschitz function, these theorems
become dimension preservation results when $\tau = 0$. We conjecture that many
of the attractors associated with the evolution equations of mathematical physics
have thickness exponent zero. We also discuss the sharpness of our results in
the case $\tau > 0$.
article_processing_charge: No
article_type: original
author:
- first_name: WILLIAM
full_name: OTT, WILLIAM
last_name: OTT
- first_name: BRIAN
full_name: HUNT, BRIAN
last_name: HUNT
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
citation:
ama: OTT W, HUNT B, Kaloshin V. The effect of projections on fractal sets and measures
in Banach spaces. Ergodic Theory and Dynamical Systems. 2006;26(3):869-891.
doi:10.1017/s0143385705000714
apa: OTT, W., HUNT, B., & Kaloshin, V. (2006). The effect of projections on
fractal sets and measures in Banach spaces. Ergodic Theory and Dynamical Systems.
Cambridge University Press. https://doi.org/10.1017/s0143385705000714
chicago: OTT, WILLIAM, BRIAN HUNT, and Vadim Kaloshin. “The Effect of Projections
on Fractal Sets and Measures in Banach Spaces.” Ergodic Theory and Dynamical
Systems. Cambridge University Press, 2006. https://doi.org/10.1017/s0143385705000714.
ieee: W. OTT, B. HUNT, and V. Kaloshin, “The effect of projections on fractal sets
and measures in Banach spaces,” Ergodic Theory and Dynamical Systems, vol.
26, no. 3. Cambridge University Press, pp. 869–891, 2006.
ista: OTT W, HUNT B, Kaloshin V. 2006. The effect of projections on fractal sets
and measures in Banach spaces. Ergodic Theory and Dynamical Systems. 26(3), 869–891.
mla: OTT, WILLIAM, et al. “The Effect of Projections on Fractal Sets and Measures
in Banach Spaces.” Ergodic Theory and Dynamical Systems, vol. 26, no. 3,
Cambridge University Press, 2006, pp. 869–91, doi:10.1017/s0143385705000714.
short: W. OTT, B. HUNT, V. Kaloshin, Ergodic Theory and Dynamical Systems 26 (2006)
869–891.
date_created: 2020-09-18T10:48:52Z
date_published: 2006-06-01T00:00:00Z
date_updated: 2021-01-12T08:19:48Z
day: '01'
doi: 10.1017/s0143385705000714
extern: '1'
intvolume: ' 26'
issue: '3'
language:
- iso: eng
month: '06'
oa_version: None
page: 869-891
publication: Ergodic Theory and Dynamical Systems
publication_identifier:
issn:
- 0143-3857
- 1469-4417
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
status: public
title: The effect of projections on fractal sets and measures in Banach spaces
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2006'
...
---
_id: '8515'
abstract:
- lang: eng
text: "We consider the evolution of a set carried by a space periodic incompressible
stochastic flow in a Euclidean space. We\r\nreport on three main results obtained
in [8, 9, 10] concerning long time behaviour for a typical realization of the
stochastic flow. First, at time t most of the particles are at a distance of order
√t away from the origin. Moreover, we prove a Central Limit Theorem for the evolution
of a measure carried by the flow, which holds for almost every realization of
the flow. Second, we show the existence of a zero measure full Hausdorff dimension
set of points, which\r\nescape to infinity at a linear rate. Third, in the 2-dimensional
case, we study the set of points visited by the original set by time t. Such a
set, when scaled down by the factor of t, has a limiting non random shape."
article_processing_charge: No
author:
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: D.
full_name: DOLGOPYAT, D.
last_name: DOLGOPYAT
- first_name: L.
full_name: KORALOV, L.
last_name: KORALOV
citation:
ama: 'Kaloshin V, DOLGOPYAT D, KORALOV L. Long time behaviour of periodic stochastic
flows. In: XIVth International Congress on Mathematical Physics. World
Scientific; 2006:290-295. doi:10.1142/9789812704016_0026'
apa: 'Kaloshin, V., DOLGOPYAT, D., & KORALOV, L. (2006). Long time behaviour
of periodic stochastic flows. In XIVth International Congress on Mathematical
Physics (pp. 290–295). Lisbon, Portugal: World Scientific. https://doi.org/10.1142/9789812704016_0026'
chicago: Kaloshin, Vadim, D. DOLGOPYAT, and L. KORALOV. “Long Time Behaviour of
Periodic Stochastic Flows.” In XIVth International Congress on Mathematical
Physics, 290–95. World Scientific, 2006. https://doi.org/10.1142/9789812704016_0026.
ieee: V. Kaloshin, D. DOLGOPYAT, and L. KORALOV, “Long time behaviour of periodic
stochastic flows,” in XIVth International Congress on Mathematical Physics,
Lisbon, Portugal, 2006, pp. 290–295.
ista: Kaloshin V, DOLGOPYAT D, KORALOV L. 2006. Long time behaviour of periodic
stochastic flows. XIVth International Congress on Mathematical Physics. International
Congress on Mathematical Physics, 290–295.
mla: Kaloshin, Vadim, et al. “Long Time Behaviour of Periodic Stochastic Flows.”
XIVth International Congress on Mathematical Physics, World Scientific,
2006, pp. 290–95, doi:10.1142/9789812704016_0026.
short: V. Kaloshin, D. DOLGOPYAT, L. KORALOV, in:, XIVth International Congress
on Mathematical Physics, World Scientific, 2006, pp. 290–295.
conference:
end_date: 2003-08-02
location: Lisbon, Portugal
name: International Congress on Mathematical Physics
start_date: 2003-07-28
date_created: 2020-09-18T10:48:59Z
date_published: 2006-03-01T00:00:00Z
date_updated: 2021-01-12T08:19:49Z
day: '01'
doi: 10.1142/9789812704016_0026
extern: '1'
language:
- iso: eng
month: '03'
oa_version: None
page: 290-295
publication: XIVth International Congress on Mathematical Physics
publication_identifier:
isbn:
- '9789812562012'
- '9789812704016'
publication_status: published
publisher: World Scientific
quality_controlled: '1'
status: public
title: Long time behaviour of periodic stochastic flows
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2006'
...
---
_id: '8513'
article_processing_charge: No
article_type: original
author:
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Maria
full_name: Saprykina, Maria
last_name: Saprykina
citation:
ama: Kaloshin V, Saprykina M. Generic 3-dimensional volume-preserving diffeomorphisms
with superexponential growth of number of periodic orbits. Discrete & Continuous
Dynamical Systems - A. 2006;15(2):611-640. doi:10.3934/dcds.2006.15.611
apa: Kaloshin, V., & Saprykina, M. (2006). Generic 3-dimensional volume-preserving
diffeomorphisms with superexponential growth of number of periodic orbits. Discrete
& Continuous Dynamical Systems - A. American Institute of Mathematical
Sciences (AIMS). https://doi.org/10.3934/dcds.2006.15.611
chicago: Kaloshin, Vadim, and Maria Saprykina. “Generic 3-Dimensional Volume-Preserving
Diffeomorphisms with Superexponential Growth of Number of Periodic Orbits.” Discrete
& Continuous Dynamical Systems - A. American Institute of Mathematical
Sciences (AIMS), 2006. https://doi.org/10.3934/dcds.2006.15.611.
ieee: V. Kaloshin and M. Saprykina, “Generic 3-dimensional volume-preserving diffeomorphisms
with superexponential growth of number of periodic orbits,” Discrete &
Continuous Dynamical Systems - A, vol. 15, no. 2. American Institute of Mathematical
Sciences (AIMS), pp. 611–640, 2006.
ista: Kaloshin V, Saprykina M. 2006. Generic 3-dimensional volume-preserving diffeomorphisms
with superexponential growth of number of periodic orbits. Discrete & Continuous
Dynamical Systems - A. 15(2), 611–640.
mla: Kaloshin, Vadim, and Maria Saprykina. “Generic 3-Dimensional Volume-Preserving
Diffeomorphisms with Superexponential Growth of Number of Periodic Orbits.” Discrete
& Continuous Dynamical Systems - A, vol. 15, no. 2, American Institute
of Mathematical Sciences (AIMS), 2006, pp. 611–40, doi:10.3934/dcds.2006.15.611.
short: V. Kaloshin, M. Saprykina, Discrete & Continuous Dynamical Systems -
A 15 (2006) 611–640.
date_created: 2020-09-18T10:48:43Z
date_published: 2006-05-01T00:00:00Z
date_updated: 2021-01-12T08:19:48Z
day: '01'
doi: 10.3934/dcds.2006.15.611
extern: '1'
intvolume: ' 15'
issue: '2'
language:
- iso: eng
month: '05'
oa_version: None
page: 611-640
publication: Discrete & Continuous Dynamical Systems - A
publication_identifier:
issn:
- 1553-5231
publication_status: published
publisher: American Institute of Mathematical Sciences (AIMS)
quality_controlled: '1'
status: public
title: Generic 3-dimensional volume-preserving diffeomorphisms with superexponential
growth of number of periodic orbits
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2006'
...
---
_id: '869'
abstract:
- lang: eng
text: The impact of synonymous nucleotide substitutions on fitness in mammals remains
controversial. Despite some indications of selective constraint, synonymous sites
are often assumed to be neutral, and the rate of their evolution is used as a
proxy for mutation rate. We subdivide all sites into four classes in terms of
the mutable CpG context, nonCpG, postC, preG, and postCpreG, and compare four-fold
synonymous sites and intron sites residing outside transposable elements. The
distribution of the rate of evolution across all synonymous sites is trimodal.
Rate of evolution at nonCpG synonymous sites, not preceded by C and not followed
by G, is ∼10% below that at such intron sites. In contrast, rate of evolution
at postCpreG synonymous sites is ∼30% above that at such intron sites. Finally,
synonymous and intron postC and preG sites evolve at similar rates. The relationship
between the levels of polymorphism at the corresponding synonymous and intron
sites is very similar to that between their rates of evolution. Within every class,
synonymous sites are occupied by G or C much more often than intron sites, whose
nucleotide composition is consistent with neutral mutation-drift equilibrium.
These patterns suggest that synonymous sites are under weak selection in favor
of G and C, with the average coefficient s∼0.25/Ne∼10-5, where Ne is the effective
population size. Such selection decelerates evolution and reduces variability
at sites with symmetric mutation, but has the opposite effects at sites where
the favored nucleotides are more mutable. The amino-acid composition of proteins
dictates that many synonymous sites are CpGprone, which causes them, on average,
to evolve faster and to be more polymorphic than intron sites. An average genotype
carries ∼107 suboptimal nucleotides at synonymous sites, implying synergistic
epistasis in selection against them.
acknowledgement: This research was supported in part by the Intramural Research Program
of the NIH, National Library of Medicine.
author:
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Aleksey
full_name: Ogurtsov, Aleksey Yu
last_name: Ogurtsov
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
citation:
ama: Kondrashov F, Ogurtsov A, Kondrashov A. Selection in favor of nucleotides G
and C diversifies evolution rates and levels of polymorphism at mammalian synonymous
sites. Journal of Theoretical Biology. 2006;240(4):616-626. doi:10.1016/j.jtbi.2005.10.020
apa: Kondrashov, F., Ogurtsov, A., & Kondrashov, A. (2006). Selection in favor
of nucleotides G and C diversifies evolution rates and levels of polymorphism
at mammalian synonymous sites. Journal of Theoretical Biology. Elsevier.
https://doi.org/10.1016/j.jtbi.2005.10.020
chicago: Kondrashov, Fyodor, Aleksey Ogurtsov, and Alexey Kondrashov. “Selection
in Favor of Nucleotides G and C Diversifies Evolution Rates and Levels of Polymorphism
at Mammalian Synonymous Sites.” Journal of Theoretical Biology. Elsevier,
2006. https://doi.org/10.1016/j.jtbi.2005.10.020.
ieee: F. Kondrashov, A. Ogurtsov, and A. Kondrashov, “Selection in favor of nucleotides
G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous
sites,” Journal of Theoretical Biology, vol. 240, no. 4. Elsevier, pp.
616–626, 2006.
ista: Kondrashov F, Ogurtsov A, Kondrashov A. 2006. Selection in favor of nucleotides
G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous
sites. Journal of Theoretical Biology. 240(4), 616–626.
mla: Kondrashov, Fyodor, et al. “Selection in Favor of Nucleotides G and C Diversifies
Evolution Rates and Levels of Polymorphism at Mammalian Synonymous Sites.” Journal
of Theoretical Biology, vol. 240, no. 4, Elsevier, 2006, pp. 616–26, doi:10.1016/j.jtbi.2005.10.020.
short: F. Kondrashov, A. Ogurtsov, A. Kondrashov, Journal of Theoretical Biology
240 (2006) 616–626.
date_created: 2018-12-11T11:48:56Z
date_published: 2006-06-21T00:00:00Z
date_updated: 2021-01-12T08:20:33Z
day: '21'
doi: 10.1016/j.jtbi.2005.10.020
extern: 1
intvolume: ' 240'
issue: '4'
month: '06'
page: 616 - 626
publication: Journal of Theoretical Biology
publication_status: published
publisher: Elsevier
publist_id: '6779'
quality_controlled: 0
status: public
title: Selection in favor of nucleotides G and C diversifies evolution rates and levels
of polymorphism at mammalian synonymous sites
type: journal_article
volume: 240
year: '2006'
...
---
_id: '903'
abstract:
- lang: eng
text: 'Background: Carcinogenesis typically involves multiple somatic mutations
in caretaker (DNA repair) and gatekeeper (tumor suppressors and oncogenes) genes.
Analysis of mutation spectra of the tumor suppressor that is most commonly mutated
in human cancers, p53, unexpectedly suggested that somatic evolution of the p53
gene during tumorigenesis is dominated by positive selection for gain of function.
This conclusion is supported by accumulating experimental evidence of evolution
of new functions of p53 in tumors. These findings prompted a genome-wide analysis
of possible positive selection during tumor evolution. Methods: A comprehensive
analysis of probable somatic mutations in the sequences of Expressed Sequence
Tags (ESTs) from malignant tumors and normal tissues was performed in order to
access the prevalence of positive selection in cancer evolution. For each EST,
the numbers of synonymous and non-synonymous substitutions were calculated. In
order to identify genes with a signature of positive selection in cancers, these
numbers were compared to: i) expected numbers and ii) the numbers for the respective
genes in the ESTs from normal tissues. Results: We identified 112 genes with a
signature of positive selection in cancers, i.e., a significantly elevated ratio
of non-synonymous to synonymous substitutions, in tumors as compared to 37 such
genes in an approximately equal-sized EST collection from normal tissues. A substantial
fraction of the tumor-specific positive-selection candidates have experimentally
demonstrated or strongly predicted links to cancer. Conclusion: The results of
EST analysis should be interpreted with extreme caution given the noise introduced
by sequencing errors and undetected polymorphisms. Furthermore, an inherent limitation
of EST analysis is that multiple mutations amenable to statistical analysis can
be detected only in relatively highly expressed genes. Nevertheless, the present
results suggest that positive selection might affect a substantial number of genes
during tumorigenic somatic evolution.'
acknowledgement: This work was supported by the Intramural Research Program of the
National Library of Medicine at the National Institutes of Health/DHHS. FAK is an
NSF Graduate Fellow. We thank Yuri Pavlov for helpful discussions.
author:
- first_name: Vladimir
full_name: Babenko, Vladimir N
last_name: Babenko
- first_name: Malay
full_name: Basu, Malay K
last_name: Basu
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Igor
full_name: Rogozin, Igor B
last_name: Rogozin
- first_name: Eugene
full_name: Koonin, Eugene V
last_name: Koonin
citation:
ama: Babenko V, Basu M, Kondrashov F, Rogozin I, Koonin E. Signs of positive selection
of somatic mutations in human cancers detected by EST sequence analysis. BMC
Cancer. 2006;6. doi:10.1186/1471-2407-6-36
apa: Babenko, V., Basu, M., Kondrashov, F., Rogozin, I., & Koonin, E. (2006).
Signs of positive selection of somatic mutations in human cancers detected by
EST sequence analysis. BMC Cancer. BioMed Central. https://doi.org/10.1186/1471-2407-6-36
chicago: Babenko, Vladimir, Malay Basu, Fyodor Kondrashov, Igor Rogozin, and Eugene
Koonin. “Signs of Positive Selection of Somatic Mutations in Human Cancers Detected
by EST Sequence Analysis.” BMC Cancer. BioMed Central, 2006. https://doi.org/10.1186/1471-2407-6-36.
ieee: V. Babenko, M. Basu, F. Kondrashov, I. Rogozin, and E. Koonin, “Signs of positive
selection of somatic mutations in human cancers detected by EST sequence analysis,”
BMC Cancer, vol. 6. BioMed Central, 2006.
ista: Babenko V, Basu M, Kondrashov F, Rogozin I, Koonin E. 2006. Signs of positive
selection of somatic mutations in human cancers detected by EST sequence analysis.
BMC Cancer. 6.
mla: Babenko, Vladimir, et al. “Signs of Positive Selection of Somatic Mutations
in Human Cancers Detected by EST Sequence Analysis.” BMC Cancer, vol. 6,
BioMed Central, 2006, doi:10.1186/1471-2407-6-36.
short: V. Babenko, M. Basu, F. Kondrashov, I. Rogozin, E. Koonin, BMC Cancer 6 (2006).
date_created: 2018-12-11T11:49:07Z
date_published: 2006-02-09T00:00:00Z
date_updated: 2021-01-12T08:21:47Z
day: '09'
doi: 10.1186/1471-2407-6-36
extern: 1
intvolume: ' 6'
month: '02'
publication: BMC Cancer
publication_status: published
publisher: BioMed Central
publist_id: '6744'
quality_controlled: 0
status: public
title: Signs of positive selection of somatic mutations in human cancers detected
by EST sequence analysis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 6
year: '2006'
...
---
_id: '9505'
abstract:
- lang: eng
text: 'Cytosine methylation, a common form of DNA modification that antagonizes
transcription, is found at transposons and repeats in vertebrates, plants and
fungi. Here we have mapped DNA methylation in the entire Arabidopsis thaliana
genome at high resolution. DNA methylation covers transposons and is present within
a large fraction of A. thaliana genes. Methylation within genes is conspicuously
biased away from gene ends, suggesting a dependence on RNA polymerase transit.
Genic methylation is strongly influenced by transcription: moderately transcribed
genes are most likely to be methylated, whereas genes at either extreme are least
likely. In turn, transcription is influenced by methylation: short methylated
genes are poorly expressed, and loss of methylation in the body of a gene leads
to enhanced transcription. Our results indicate that genic transcription and DNA
methylation are closely interwoven processes.'
article_processing_charge: No
article_type: original
author:
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Mary
full_name: Gehring, Mary
last_name: Gehring
- first_name: Robert K.
full_name: Tran, Robert K.
last_name: Tran
- first_name: Tracy
full_name: Ballinger, Tracy
last_name: Ballinger
- first_name: Steven
full_name: Henikoff, Steven
last_name: Henikoff
citation:
ama: Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. Genome-wide analysis
of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation
and transcription. Nature Genetics. 2006;39(1):61-69. doi:10.1038/ng1929
apa: Zilberman, D., Gehring, M., Tran, R. K., Ballinger, T., & Henikoff, S.
(2006). Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers
an interdependence between methylation and transcription. Nature Genetics.
Nature Publishing Group. https://doi.org/10.1038/ng1929
chicago: Zilberman, Daniel, Mary Gehring, Robert K. Tran, Tracy Ballinger, and Steven
Henikoff. “Genome-Wide Analysis of Arabidopsis Thaliana DNA Methylation Uncovers
an Interdependence between Methylation and Transcription.” Nature Genetics.
Nature Publishing Group, 2006. https://doi.org/10.1038/ng1929.
ieee: D. Zilberman, M. Gehring, R. K. Tran, T. Ballinger, and S. Henikoff, “Genome-wide
analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between
methylation and transcription,” Nature Genetics, vol. 39, no. 1. Nature
Publishing Group, pp. 61–69, 2006.
ista: Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. 2006. Genome-wide
analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between
methylation and transcription. Nature Genetics. 39(1), 61–69.
mla: Zilberman, Daniel, et al. “Genome-Wide Analysis of Arabidopsis Thaliana DNA
Methylation Uncovers an Interdependence between Methylation and Transcription.”
Nature Genetics, vol. 39, no. 1, Nature Publishing Group, 2006, pp. 61–69,
doi:10.1038/ng1929.
short: D. Zilberman, M. Gehring, R.K. Tran, T. Ballinger, S. Henikoff, Nature Genetics
39 (2006) 61–69.
date_created: 2021-06-07T12:19:31Z
date_published: 2006-11-26T00:00:00Z
date_updated: 2021-12-14T09:02:51Z
day: '26'
department:
- _id: DaZi
doi: 10.1038/ng1929
extern: '1'
external_id:
pmid:
- '17128275'
intvolume: ' 39'
issue: '1'
language:
- iso: eng
month: '11'
oa_version: None
page: 61-69
pmid: 1
publication: Nature Genetics
publication_identifier:
eissn:
- 1546-1718
issn:
- 1061-4036
publication_status: published
publisher: Nature Publishing Group
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence
between methylation and transcription
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 39
year: '2006'
...
---
_id: '13430'
abstract:
- lang: eng
text: Dynamic self-assembly (DySA) processes occurring outside of thermodynamic
equilibrium underlie many forms of adaptive and intellligent behaviors in natural
systems. Relatively little, however, is known about the principles that govern
DySA and the ways in which it can be extended to artificial ensembles. This article
discusses recent advances in both the theory and the practice of nonequilibrium
self-assembly. It is argued that a union of ideas from thermodynamics and dynamic
systems' theory can provide a general description of DySA. In parallel, heuristic
design rules can be used to construct DySA systems of increasing complexities
based on a variety of suitable interactions/potentials on length scales from nanoscopic
to macroscopic. Applications of these rules to magnetohydrodynamic DySA are also
discussed.
article_processing_charge: No
article_type: original
author:
- first_name: Marcin
full_name: Fialkowski, Marcin
last_name: Fialkowski
- first_name: Kyle J. M.
full_name: Bishop, Kyle J. M.
last_name: Bishop
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
- first_name: Stoyan K.
full_name: Smoukov, Stoyan K.
last_name: Smoukov
- first_name: Christopher J.
full_name: Campbell, Christopher J.
last_name: Campbell
- first_name: Bartosz A.
full_name: Grzybowski, Bartosz A.
last_name: Grzybowski
citation:
ama: Fialkowski M, Bishop KJM, Klajn R, Smoukov SK, Campbell CJ, Grzybowski BA.
Principles and implementations of dissipative (dynamic) self-assembly. The
Journal of Physical Chemistry B. 2006;110(6):2482-2496. doi:10.1021/jp054153q
apa: Fialkowski, M., Bishop, K. J. M., Klajn, R., Smoukov, S. K., Campbell, C. J.,
& Grzybowski, B. A. (2006). Principles and implementations of dissipative
(dynamic) self-assembly. The Journal of Physical Chemistry B. American
Chemical Society. https://doi.org/10.1021/jp054153q
chicago: Fialkowski, Marcin, Kyle J. M. Bishop, Rafal Klajn, Stoyan K. Smoukov,
Christopher J. Campbell, and Bartosz A. Grzybowski. “Principles and Implementations
of Dissipative (Dynamic) Self-Assembly.” The Journal of Physical Chemistry
B. American Chemical Society, 2006. https://doi.org/10.1021/jp054153q.
ieee: M. Fialkowski, K. J. M. Bishop, R. Klajn, S. K. Smoukov, C. J. Campbell, and
B. A. Grzybowski, “Principles and implementations of dissipative (dynamic) self-assembly,”
The Journal of Physical Chemistry B, vol. 110, no. 6. American Chemical
Society, pp. 2482–2496, 2006.
ista: Fialkowski M, Bishop KJM, Klajn R, Smoukov SK, Campbell CJ, Grzybowski BA.
2006. Principles and implementations of dissipative (dynamic) self-assembly. The
Journal of Physical Chemistry B. 110(6), 2482–2496.
mla: Fialkowski, Marcin, et al. “Principles and Implementations of Dissipative (Dynamic)
Self-Assembly.” The Journal of Physical Chemistry B, vol. 110, no. 6, American
Chemical Society, 2006, pp. 2482–96, doi:10.1021/jp054153q.
short: M. Fialkowski, K.J.M. Bishop, R. Klajn, S.K. Smoukov, C.J. Campbell, B.A.
Grzybowski, The Journal of Physical Chemistry B 110 (2006) 2482–2496.
date_created: 2023-08-01T10:37:35Z
date_published: 2006-01-25T00:00:00Z
date_updated: 2023-08-08T11:33:08Z
day: '25'
doi: 10.1021/jp054153q
extern: '1'
external_id:
pmid:
- '16471845'
intvolume: ' 110'
issue: '6'
keyword:
- Materials Chemistry
- Surfaces
- Coatings and Films
- Physical and Theoretical Chemistry
language:
- iso: eng
month: '01'
oa_version: None
page: 2482-2496
pmid: 1
publication: The Journal of Physical Chemistry B
publication_identifier:
issn:
- 1520-6106
- 1520-5207
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Principles and implementations of dissipative (dynamic) self-assembly
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2006'
...
---
_id: '13428'
abstract:
- lang: eng
text: Mixtures of oppositely charged nanoparticles of various sizes and charge ratios
precipitate only at the point of electroneutrality. This phenomenonspecific to
the nanoscale and reminiscent of threshold precipitation of ionsis a consequence
of the formation of core-and-shell nanoparticle aggregates, in which the shells
are composed of like-charged particles and are stabilized by efficient electrostatic
screening.
article_processing_charge: No
article_type: original
author:
- first_name: Alexander M.
full_name: Kalsin, Alexander M.
last_name: Kalsin
- first_name: Bartlomiej
full_name: Kowalczyk, Bartlomiej
last_name: Kowalczyk
- first_name: Stoyan K.
full_name: Smoukov, Stoyan K.
last_name: Smoukov
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
- first_name: Bartosz A.
full_name: Grzybowski, Bartosz A.
last_name: Grzybowski
citation:
ama: Kalsin AM, Kowalczyk B, Smoukov SK, Klajn R, Grzybowski BA. Ionic-like behavior
of oppositely charged nanoparticles. Journal of the American Chemical Society.
2006;128(47):15046-15047. doi:10.1021/ja0642966
apa: Kalsin, A. M., Kowalczyk, B., Smoukov, S. K., Klajn, R., & Grzybowski,
B. A. (2006). Ionic-like behavior of oppositely charged nanoparticles. Journal
of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja0642966
chicago: Kalsin, Alexander M., Bartlomiej Kowalczyk, Stoyan K. Smoukov, Rafal Klajn,
and Bartosz A. Grzybowski. “Ionic-like Behavior of Oppositely Charged Nanoparticles.”
Journal of the American Chemical Society. American Chemical Society, 2006.
https://doi.org/10.1021/ja0642966.
ieee: A. M. Kalsin, B. Kowalczyk, S. K. Smoukov, R. Klajn, and B. A. Grzybowski,
“Ionic-like behavior of oppositely charged nanoparticles,” Journal of the American
Chemical Society, vol. 128, no. 47. American Chemical Society, pp. 15046–15047,
2006.
ista: Kalsin AM, Kowalczyk B, Smoukov SK, Klajn R, Grzybowski BA. 2006. Ionic-like
behavior of oppositely charged nanoparticles. Journal of the American Chemical
Society. 128(47), 15046–15047.
mla: Kalsin, Alexander M., et al. “Ionic-like Behavior of Oppositely Charged Nanoparticles.”
Journal of the American Chemical Society, vol. 128, no. 47, American Chemical
Society, 2006, pp. 15046–47, doi:10.1021/ja0642966.
short: A.M. Kalsin, B. Kowalczyk, S.K. Smoukov, R. Klajn, B.A. Grzybowski, Journal
of the American Chemical Society 128 (2006) 15046–15047.
date_created: 2023-08-01T10:36:27Z
date_published: 2006-11-29T00:00:00Z
date_updated: 2023-08-08T11:30:06Z
day: '29'
doi: 10.1021/ja0642966
extern: '1'
external_id:
pmid:
- '17117829'
intvolume: ' 128'
issue: '47'
keyword:
- Colloid and Surface Chemistry
- Biochemistry
- General Chemistry
- Catalysis
language:
- iso: eng
month: '11'
oa_version: None
page: 15046-15047
pmid: 1
publication: Journal of the American Chemical Society
publication_identifier:
eissn:
- 1520-5126
issn:
- 0002-7863
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ionic-like behavior of oppositely charged nanoparticles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 128
year: '2006'
...
---
_id: '13429'
abstract:
- lang: eng
text: 'The fruitful core: Organic syntheses reported in the literature from 1850
to 2004 are analyzed with mathematical tools from network theory and statistical
physics. There is a set of substances (the core) from which the majority of other
organic compounds can be made (see picture; red: core, blue: periphery, green:
islands). Search algorithms are used to identify small optimal sets of maximally
useful chemicals.'
article_processing_charge: No
article_type: original
author:
- first_name: Kyle J. M.
full_name: Bishop, Kyle J. M.
last_name: Bishop
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
- first_name: Bartosz A.
full_name: Grzybowski, Bartosz A.
last_name: Grzybowski
citation:
ama: Bishop KJM, Klajn R, Grzybowski BA. The core and most useful molecules in organic
chemistry. Angewandte Chemie International Edition. 2006;45(32):5348-5354.
doi:10.1002/anie.200600881
apa: Bishop, K. J. M., Klajn, R., & Grzybowski, B. A. (2006). The core and most
useful molecules in organic chemistry. Angewandte Chemie International Edition.
Wiley. https://doi.org/10.1002/anie.200600881
chicago: Bishop, Kyle J. M., Rafal Klajn, and Bartosz A. Grzybowski. “The Core and
Most Useful Molecules in Organic Chemistry.” Angewandte Chemie International
Edition. Wiley, 2006. https://doi.org/10.1002/anie.200600881.
ieee: K. J. M. Bishop, R. Klajn, and B. A. Grzybowski, “The core and most useful
molecules in organic chemistry,” Angewandte Chemie International Edition,
vol. 45, no. 32. Wiley, pp. 5348–5354, 2006.
ista: Bishop KJM, Klajn R, Grzybowski BA. 2006. The core and most useful molecules
in organic chemistry. Angewandte Chemie International Edition. 45(32), 5348–5354.
mla: Bishop, Kyle J. M., et al. “The Core and Most Useful Molecules in Organic Chemistry.”
Angewandte Chemie International Edition, vol. 45, no. 32, Wiley, 2006,
pp. 5348–54, doi:10.1002/anie.200600881.
short: K.J.M. Bishop, R. Klajn, B.A. Grzybowski, Angewandte Chemie International
Edition 45 (2006) 5348–5354.
date_created: 2023-08-01T10:37:16Z
date_published: 2006-08-11T00:00:00Z
date_updated: 2023-08-08T11:31:27Z
day: '11'
doi: 10.1002/anie.200600881
extern: '1'
external_id:
pmid:
- '16835857'
intvolume: ' 45'
issue: '32'
keyword:
- General Chemistry
- Catalysis
language:
- iso: eng
month: '08'
oa_version: None
page: 5348-5354
pmid: 1
publication: Angewandte Chemie International Edition
publication_identifier:
eissn:
- 1521-3773
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: The core and most useful molecules in organic chemistry
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 45
year: '2006'
...