---
OA_place: repository
OA_type: green
_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
arxiv: 1
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. doi:10.48550/arXiv.quant-ph/0612159
apa: Hosten, O., & Kwiat, P. (n.d.). Weak measurements and counterfactual computation.
ArXiv. https://doi.org/10.48550/arXiv.quant-ph/0612159
chicago: Hosten, Onur, and Paul Kwiat. “Weak Measurements and Counterfactual Computation.”
ArXiv, n.d. https://doi.org/10.48550/arXiv.quant-ph/0612159.
ieee: O. Hosten and P. Kwiat, “Weak measurements and counterfactual computation.”
ArXiv.
ista: Hosten O, Kwiat P. Weak measurements and counterfactual computation. 10.48550/arXiv.quant-ph/0612159.
mla: Hosten, Onur, and Paul Kwiat. Weak Measurements and Counterfactual Computation.
ArXiv, doi:10.48550/arXiv.quant-ph/0612159.
short: O. Hosten, P. Kwiat, (n.d.).
date_created: 2018-12-11T11:47:16Z
date_published: 2006-12-19T00:00:00Z
date_updated: 2026-05-08T11:47:32Z
day: '19'
doi: 10.48550/arXiv.quant-ph/0612159
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: submitted
publisher: ArXiv
publist_id: '7240'
status: public
title: Weak measurements and counterfactual computation
type: preprint
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2006'
...
---
OA_type: closed access
_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:
- Advanced Photon Counting Techniques
article_number: '6372'
article_processing_charge: No
author:
- first_name: Radhika
full_name: Rangarajan, Radhika
last_name: Rangarajan
- first_name: Joseph
full_name: Altepeter, Joseph
last_name: Altepeter
- first_name: Evan
full_name: Jeffrey, Evan
last_name: Jeffrey
- first_name: Micah
full_name: Stoutimore, Micah
last_name: Stoutimore
- first_name: Nicholas
full_name: Peters, Nicholas
last_name: Peters
- 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: 'Rangarajan R, Altepeter J, Jeffrey E, et al. High-efficiency single-photon
detectors. In: Optics East. 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. In Optics
East. Boston, Massachusetts, United States: 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.”
In Optics East. SPIE, 2006. https://doi.org/10.1117/12.686117.
ieee: R. Rangarajan et al., “High-efficiency single-photon detectors,” in
Optics East, Boston, Massachusetts, United States, 2006.
ista: Rangarajan R, Altepeter J, Jeffrey E, Stoutimore M, Peters N, Hosten O, Kwiat
P. 2006. High-efficiency single-photon detectors. Optics East. OPTICS EAST, Advanced
Photon Counting Techniques, , 6372.
mla: Rangarajan, Radhika, et al. “High-Efficiency Single-Photon Detectors.” Optics
East, 6372, SPIE, 2006, doi:10.1117/12.686117.
short: R. Rangarajan, J. Altepeter, E. Jeffrey, M. Stoutimore, N. Peters, O. Hosten,
P. Kwiat, in:, Optics East, SPIE, 2006.
conference:
end_date: 2006-10 04
location: Boston, Massachusetts, United States
name: OPTICS EAST
start_date: 2006-10 01
date_created: 2018-12-11T11:47:17Z
date_published: 2006-10-25T00:00:00Z
date_updated: 2026-05-08T10:31:26Z
day: '25'
doi: 10.1117/12.686117
extern: '1'
language:
- iso: eng
month: '10'
oa_version: None
publication: Optics East
publication_identifier:
eissn:
- 0277-786X
publication_status: published
publisher: SPIE
publist_id: '7233'
quality_controlled: '1'
scopus_import: '1'
status: public
title: High-efficiency single-photon detectors
type: conference
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2006'
...
---
OA_type: closed access
_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.
article_number: '630507'
article_processing_charge: No
author:
- first_name: Nicholas
full_name: Peters, Nicholas
last_name: Peters
- first_name: Keith
full_name: Arnold, Keith
last_name: Arnold
- first_name: Aaron
full_name: Vandevender, Aaron
last_name: Vandevender
- first_name: Evan
full_name: Jeffrey, Evan
last_name: Jeffrey
- first_name: Radhika
full_name: Rangarajan, Radhika
last_name: Rangarajan
- first_name: Onur
full_name: Hosten, Onur
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Julio
full_name: Barreiro, Julio
last_name: Barreiro
- first_name: Joseph
full_name: Altepeter, Joseph
last_name: Altepeter
- first_name: Paul
full_name: Kwiat, Paul
last_name: Kwiat
citation:
ama: 'Peters N, Arnold K, Vandevender A, et al. Towards a quasi-deterministic single-photon
source. In: Quantum Communications and Quantum Imaging IV. 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. In
Quantum Communications and Quantum Imaging IV (Vol. 6305). San DIego, CA,
United States: 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.” In Quantum Communications and
Quantum Imaging IV, Vol. 6305. SPIE, 2006. https://doi.org/10.1117/12.684702.
ieee: N. Peters et al., “Towards a quasi-deterministic single-photon source,”
in Quantum Communications and Quantum Imaging IV, San DIego, CA, United
States, 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 IV. SPIE OPTICS+PHOTONICS vol. 6305,
630507.
mla: Peters, Nicholas, et al. “Towards a Quasi-Deterministic Single-Photon Source.”
Quantum Communications and Quantum Imaging IV, vol. 6305, 630507, 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:, Quantum Communications and Quantum Imaging
IV, SPIE, 2006.
conference:
end_date: 2006-08-17
location: San DIego, CA, United States
name: SPIE OPTICS+PHOTONICS
start_date: 2006-08-13
date_created: 2018-12-11T11:47:17Z
date_published: 2006-09-01T00:00:00Z
date_updated: 2026-05-08T11:35:31Z
day: '01'
doi: 10.1117/12.684702
extern: '1'
intvolume: ' 6305'
language:
- iso: eng
month: '09'
oa_version: None
publication: Quantum Communications and Quantum Imaging IV
publication_status: published
publisher: SPIE
publist_id: '7234'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Towards a quasi-deterministic single-photon source
type: conference
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 6305
year: '2006'
...
---
OA_type: closed access
_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. '
article_processing_charge: No
article_type: letter_note
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 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: 2026-05-08T11:42:23Z
day: '23'
doi: 10.1038/nature04523
extern: '1'
external_id:
pmid:
- '16495993'
intvolume: ' 439'
issue: '7079'
language:
- iso: eng
month: '02'
oa_version: None
page: 949 - 952
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Nature Publishing Group
publist_id: '7235'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Counterfactual quantum computation through quantum interrogation
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 439
year: '2006'
...
---
OA_type: closed access
_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.
article_processing_charge: No
author:
- first_name: Radhika
full_name: Rangarajan, Radhika
last_name: Rangarajan
- first_name: Nicholas
full_name: Peters, Nicholas
last_name: Peters
- first_name: Onur
full_name: Hosten, Onur
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Joseph
full_name: Altepeter, Joseph
last_name: Altepeter
- first_name: Evan
full_name: Jeffrey, Evan
last_name: Jeffrey
- first_name: Paul
full_name: Kwiat, Paul
last_name: Kwiat
citation:
ama: 'Rangarajan R, Peters N, Hosten O, Altepeter J, Jeffrey E, Kwiat P. Improved
single-photon detection. In: Conference on Lasers and Electro-Optics. 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. In Conference on Lasers
and Electro-Optics. Long Beach, CA, United States: 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.” In Conference
on Lasers and Electro-Optics. 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,” in Conference on Lasers and Electro-Optics,
Long Beach, CA, United States, 2006.
ista: 'Rangarajan R, Peters N, Hosten O, Altepeter J, Jeffrey E, Kwiat P. 2006.
Improved single-photon detection. Conference on Lasers and Electro-Optics. CLEO/QELS:
Conference on Lasers and Electro-Optics / Quantum Electronics and Laser Science
Conference.'
mla: Rangarajan, Radhika, et al. “Improved Single-Photon Detection.” Conference
on Lasers and Electro-Optics, IEEE, 2006, doi:10.1109/CLEO.2006.4628641.
short: R. Rangarajan, N. Peters, O. Hosten, J. Altepeter, E. Jeffrey, P. Kwiat,
in:, Conference on Lasers and Electro-Optics, IEEE, 2006.
conference:
end_date: 2006-05-26
location: Long Beach, CA, United States
name: 'CLEO/QELS: Conference on Lasers and Electro-Optics / Quantum Electronics
and Laser Science Conference'
start_date: 2006-05-21
date_created: 2018-12-11T11:47:19Z
date_published: 2006-06-01T00:00:00Z
date_updated: 2026-05-08T10:24:12Z
day: '01'
doi: 10.1109/CLEO.2006.4628641
extern: '1'
language:
- iso: eng
month: '06'
oa_version: None
publication: Conference on Lasers and Electro-Optics
publication_identifier:
eisbn:
- '9781557528131'
eissn:
- 2160-9004
publication_status: published
publisher: IEEE
publist_id: '7232'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Improved single-photon detection
type: conference
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
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: '2066'
abstract:
- lang: eng
text: Although the X chromosome is usually similar to the autosomes in size and
cytogenetic appearance, theoretical models predict that its hemizygosity in males
may cause unusual patterns of evolution. The sequencing of several genomes has
indeed revealed differences between the X chromosome and the autosomes in the
rates of gene divergence, patterns of gene expression and rates of gene movement
between chromosomes. A better understanding of these patterns should provide valuable
information on the evolution of genes located on the X chromosome. It could also
suggest solutions to more general problems in molecular evolution, such as detecting
selection and estimating mutational effects on fitness
acknowledgement: B.V. is supported by a postgraduate fellowship from the Fundação
de Ciência e Tecnologia of Portugal, and B.C. by the Royal Society (UK)
author:
- first_name: Beatriz
full_name: Beatriz Vicoso
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Brian
full_name: Charlesworth, Brian
last_name: Charlesworth
citation:
ama: 'Vicoso B, Charlesworth B. Evolution on the X chromosome: Unusual patterns
and processes. Nature Reviews Genetics. 2006;7(8):645-653. doi:10.1038/nrg1914'
apa: 'Vicoso, B., & Charlesworth, B. (2006). Evolution on the X chromosome:
Unusual patterns and processes. Nature Reviews Genetics. Nature Publishing
Group. https://doi.org/10.1038/nrg1914'
chicago: 'Vicoso, Beatriz, and Brian Charlesworth. “Evolution on the X Chromosome:
Unusual Patterns and Processes.” Nature Reviews Genetics. Nature Publishing
Group, 2006. https://doi.org/10.1038/nrg1914.'
ieee: 'B. Vicoso and B. Charlesworth, “Evolution on the X chromosome: Unusual patterns
and processes,” Nature Reviews Genetics, vol. 7, no. 8. Nature Publishing
Group, pp. 645–653, 2006.'
ista: 'Vicoso B, Charlesworth B. 2006. Evolution on the X chromosome: Unusual patterns
and processes. Nature Reviews Genetics. 7(8), 645–653.'
mla: 'Vicoso, Beatriz, and Brian Charlesworth. “Evolution on the X Chromosome: Unusual
Patterns and Processes.” Nature Reviews Genetics, vol. 7, no. 8, Nature
Publishing Group, 2006, pp. 645–53, doi:10.1038/nrg1914.'
short: B. Vicoso, B. Charlesworth, Nature Reviews Genetics 7 (2006) 645–653.
date_created: 2018-12-11T11:55:31Z
date_published: 2006-08-01T00:00:00Z
date_updated: 2021-01-12T06:55:05Z
day: '01'
doi: 10.1038/nrg1914
extern: 1
intvolume: ' 7'
issue: '8'
month: '08'
page: 645 - 653
publication: Nature Reviews Genetics
publication_status: published
publisher: Nature Publishing Group
publist_id: '4973'
quality_controlled: 0
status: public
title: 'Evolution on the X chromosome: Unusual patterns and processes'
type: journal_article
volume: 7
year: '2006'
...
---
_id: '2077'
abstract:
- lang: eng
text: |-
We present an adaptive animation method for electrical discharges. Electrical discharges can be simulated using the dielectric breakdown model. Regular discretization of the governing Laplace equation leads to huge equation systems, and the computational cost of solving the equations quickly becomes prohibitive at high resolutions, especially for simulations in 3D. In contrast, our method discretizes the Laplace equation on an adaptive octree, reducing the size of the problem significantly, and making simulations of high resolution 3D datasets and even 3D animations feasible. In order to enhance realism for lightning animations, we propose a particle simulation that animates the residual positive charge. Thus, interaction of electrical discharges with their surroundings
can be simulated.
author:
- first_name: Bernd
full_name: Bernd Bickel
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Martin
full_name: Wicke, Martin
last_name: Wicke
- first_name: Markus
full_name: Gross, Markus
last_name: Gross
citation:
ama: 'Bickel B, Wicke M, Gross M. Adaptive simulation of electrical discharges.
In: IOS Press; 2006.'
apa: 'Bickel, B., Wicke, M., & Gross, M. (2006). Adaptive simulation of electrical
discharges. Presented at the VMV: Vision, Modeling, and Visualization, IOS Press.'
chicago: Bickel, Bernd, Martin Wicke, and Markus Gross. “Adaptive Simulation of
Electrical Discharges.” IOS Press, 2006.
ieee: 'B. Bickel, M. Wicke, and M. Gross, “Adaptive simulation of electrical discharges,”
presented at the VMV: Vision, Modeling, and Visualization, 2006.'
ista: 'Bickel B, Wicke M, Gross M. 2006. Adaptive simulation of electrical discharges.
VMV: Vision, Modeling, and Visualization.'
mla: Bickel, Bernd, et al. Adaptive Simulation of Electrical Discharges.
IOS Press, 2006.
short: B. Bickel, M. Wicke, M. Gross, in:, IOS Press, 2006.
conference:
name: 'VMV: Vision, Modeling, and Visualization'
date_created: 2018-12-11T11:55:34Z
date_published: 2006-11-01T00:00:00Z
date_updated: 2021-01-12T06:55:09Z
day: '01'
extern: 1
month: '11'
publication_status: published
publisher: IOS Press
publist_id: '4961'
quality_controlled: 0
status: public
title: Adaptive simulation of electrical discharges
type: conference
year: '2006'
...
---
_id: '1033'
abstract:
- lang: eng
text: Systems of three interacting particles are notorious for their complex physical
behaviour. A landmark theoretical result in few-body quantum physics is Efimov\'s
prediction1,2 of a universal set of bound trimer states appearing for three identical
bosons with a resonant two-body interaction. Counterintuitively, these states
even exist in the absence of a corresponding two-body bound state. Since the formulation
of Efimov\'s problem in the context of nuclear physics 35 years ago, it has attracted
great interest in many areas of physics3-8. However, the observation of Efimov
quantum states has remained an elusive goal3,5. Here we report the observation
of an Efimov resonance in an ultracold gas of caesium atoms. The resonance occurs
in the range of large negative two-body scattering lengths, arising from the coupling
of three free atoms to an Efimov trimer. Experimentally, we observe its signature
as a giant three-body recombination loss9,10 when the strength of the two-body
interaction is varied. We also detect a minimum 9,11,12 in the recombination loss
for positive scattering lengths, indicating destructive interference of decay
pathways. Our results confirm central theoretical predictions of Efimov physics
and represent a starting point with which to explore the universal properties
of resonantly interacting few-body systems7. While Feshbach resonances13,14 have
provided the key to control quantum-mechanical interactions on the two-body level,
Efimov resonances connect ultracold matter15 to the world of few-body quantum
phenomena.
acknowledgement: "We thank E. Braaten, C. Greene, B. Esry, H. Hammer and T. Ko ̈hler
for many discussions and E. Kneringer for support regarding the data analysis. We
acknowledge support by the Austrian Science Fund (FWF) within Spezialforschungsbereich
15 and within the Lise Meitner programme, and by the\r\nEuropean Union in the frame
of the TMR networks ‘Cold Molecules’ and ‘FASTNet’. M.M. is supported within the
Doktorandenprogramm of the Austrian\r\nAcademy of Sciences."
article_processing_charge: No
author:
- first_name: Tobias
full_name: Kraemer, Tobias
last_name: Kraemer
- first_name: Michael
full_name: Mark, Michael
last_name: Mark
- first_name: Philipp
full_name: Waldburger, Philipp
last_name: Waldburger
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Cheng
full_name: Chin, Cheng
last_name: Chin
- first_name: Bastian
full_name: Engeser, Bastian
last_name: Engeser
- first_name: Adam
full_name: Lange, Adam
last_name: Lange
- first_name: Karl
full_name: Pilch, Karl
last_name: Pilch
- first_name: Antti
full_name: Jaakkola, Antti
last_name: Jaakkola
- first_name: Hanns
full_name: Nägerl, Hanns
last_name: Nägerl
- first_name: Rudolf
full_name: Grimm, Rudolf
last_name: Grimm
citation:
ama: Kraemer T, Mark M, Waldburger P, et al. Evidence for Efimov quantum states
in an ultracold gas of caesium atoms. Nature. 2006;440(7082):315-318. doi:10.1038/nature04626
apa: Kraemer, T., Mark, M., Waldburger, P., Danzl, J. G., Chin, C., Engeser, B.,
… Grimm, R. (2006). Evidence for Efimov quantum states in an ultracold gas of
caesium atoms. Nature. Nature Publishing Group. https://doi.org/10.1038/nature04626
chicago: Kraemer, Tobias, Michael Mark, Philipp Waldburger, Johann G Danzl, Cheng
Chin, Bastian Engeser, Adam Lange, et al. “Evidence for Efimov Quantum States
in an Ultracold Gas of Caesium Atoms.” Nature. Nature Publishing Group,
2006. https://doi.org/10.1038/nature04626.
ieee: T. Kraemer et al., “Evidence for Efimov quantum states in an ultracold
gas of caesium atoms,” Nature, vol. 440, no. 7082. Nature Publishing Group,
pp. 315–318, 2006.
ista: Kraemer T, Mark M, Waldburger P, Danzl JG, Chin C, Engeser B, Lange A, Pilch
K, Jaakkola A, Nägerl H, Grimm R. 2006. Evidence for Efimov quantum states in
an ultracold gas of caesium atoms. Nature. 440(7082), 315–318.
mla: Kraemer, Tobias, et al. “Evidence for Efimov Quantum States in an Ultracold
Gas of Caesium Atoms.” Nature, vol. 440, no. 7082, Nature Publishing Group,
2006, pp. 315–18, doi:10.1038/nature04626.
short: T. Kraemer, M. Mark, P. Waldburger, J.G. Danzl, C. Chin, B. Engeser, A. Lange,
K. Pilch, A. Jaakkola, H. Nägerl, R. Grimm, Nature 440 (2006) 315–318.
date_created: 2018-12-11T11:49:47Z
date_published: 2006-03-16T00:00:00Z
date_updated: 2021-01-12T06:47:48Z
day: '16'
doi: 10.1038/nature04626
extern: '1'
intvolume: ' 440'
issue: '7082'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/cond-mat/0512394
month: '03'
oa: 1
oa_version: None
page: 315 - 318
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6356'
status: public
title: Evidence for Efimov quantum states in an ultracold gas of caesium atoms
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 440
year: '2006'
...
---
_id: '1034'
abstract:
- lang: eng
text: Three interacting particles form a system which is well known for its complex
physical behavior. A landmark theoretical result in few-body quantum physics is
Efimov\'s prediction of a universal set of weakly bound trimer states appearing
for three identical bosons with a resonant two-body interaction [1, 2]. Surprisingly,
these states even exist in the absence of a corresponding two-body bound state
and their precise nature is largely independent of the particular type of the
two-body interaction potential. Efimov\'s scenario has attracted great interest
in many areas of physics; an experimental test however has not been achieved.
We report the observation of an Efimov resonance in an ultracold thermal gas of
cesium atoms [3]. The resonance occurs in the range of large negative two-body
scattering lengths and arises from the coupling of three free atoms to an Efimov
trimer. We observe its signature as a giant three-body recombination loss when
the strength of the two-body interaction is varied near a Feshbach resonance.
This resonance develops into a continuum resonance at non-zero collision energies,
and we observe a shift of the resonance position as a function of temperature.
We also report on a minimum in the recombination loss for positive scattering
lengths, indicating destructive interference of decay pathways. Our results confirm
central theoretical predictions of Efimov physics and represent a starting point
from which to explore the universal properties of resonantly interacting few-body
systems.
acknowledgement: "We thank E. Braaten, C. Greene, B. Esry, H. Hammer, and T. Köhl\r\ner
for many stimulat-\r\ning and fruitful discussions and E. Kneringer for support
re\r\ngarding the data analysis. We\r\nacknowledge support by the Austrian Science
Fund (FWF) with\r\nin Spezialforschungs-\r\nbereich 15 and within the Lise Meitner
program, and by the Eur\r\nopean Union in the frame\r\nof the TMR networks “Cold
Molecules” and “FASTNet”. M.M. is s\r\nupported within the\r\nDoktorandenprogramm
of the Austrian Academy of Sciences."
article_processing_charge: No
author:
- first_name: Hanns
full_name: Nägerl, Hanns
last_name: Nägerl
- first_name: Tobias
full_name: Kraemer, Tobias
last_name: Kraemer
- first_name: Michael
full_name: Mark, Michael
last_name: Mark
- first_name: Philipp
full_name: Waldburger, Philipp
last_name: Waldburger
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Bastian
full_name: Engeser, Bastian
last_name: Engeser
- first_name: Adam
full_name: Lange, Adam
last_name: Lange
- first_name: Karl
full_name: Pilch, Karl
last_name: Pilch
- first_name: Antti
full_name: Jaakkola, Antti
last_name: Jaakkola
- first_name: Cheng
full_name: Chin, Cheng
last_name: Chin
- first_name: Rudolf
full_name: Grimm, Rudolf
last_name: Grimm
citation:
ama: 'Nägerl H, Kraemer T, Mark M, et al. Experimental evidence for Efimov quantum
states. In: Vol 869. AIP; 2006:269-277. doi:10.1063/1.2400657'
apa: 'Nägerl, H., Kraemer, T., Mark, M., Waldburger, P., Danzl, J. G., Engeser,
B., … Grimm, R. (2006). Experimental evidence for Efimov quantum states (Vol.
869, pp. 269–277). Presented at the ICAP: International Conference on Atomic Physics,
AIP. https://doi.org/10.1063/1.2400657'
chicago: Nägerl, Hanns, Tobias Kraemer, Michael Mark, Philipp Waldburger, Johann
G Danzl, Bastian Engeser, Adam Lange, et al. “Experimental Evidence for Efimov
Quantum States,” 869:269–77. AIP, 2006. https://doi.org/10.1063/1.2400657.
ieee: 'H. Nägerl et al., “Experimental evidence for Efimov quantum states,”
presented at the ICAP: International Conference on Atomic Physics, 2006, vol.
869, pp. 269–277.'
ista: 'Nägerl H, Kraemer T, Mark M, Waldburger P, Danzl JG, Engeser B, Lange A,
Pilch K, Jaakkola A, Chin C, Grimm R. 2006. Experimental evidence for Efimov quantum
states. ICAP: International Conference on Atomic Physics vol. 869, 269–277.'
mla: Nägerl, Hanns, et al. Experimental Evidence for Efimov Quantum States.
Vol. 869, AIP, 2006, pp. 269–77, doi:10.1063/1.2400657.
short: H. Nägerl, T. Kraemer, M. Mark, P. Waldburger, J.G. Danzl, B. Engeser, A.
Lange, K. Pilch, A. Jaakkola, C. Chin, R. Grimm, in:, AIP, 2006, pp. 269–277.
conference:
name: 'ICAP: International Conference on Atomic Physics'
date_created: 2018-12-11T11:49:48Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T06:47:49Z
day: '01'
doi: 10.1063/1.2400657
extern: '1'
intvolume: ' 869'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/cond-mat/0611629
month: '01'
oa: 1
oa_version: None
page: 269 - 277
publication_status: published
publisher: AIP
publist_id: '6355'
status: public
title: Experimental evidence for Efimov quantum states
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 869
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: '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: '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: '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: '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'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_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.\r\nWe
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."
article_processing_charge: No
article_type: original
author:
- first_name: Evgeny
full_name: Rogaev, Evgeny
last_name: Rogaev
- first_name: Yuri
full_name: Moliaka, Yuri
last_name: Moliaka
- first_name: Boris
full_name: Malyarchuk, Boris
last_name: Malyarchuk
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Miroslava
full_name: Derenko, Miroslava
last_name: Derenko
- first_name: Ilya
full_name: Chumakov, Ilya
last_name: Chumakov
- first_name: Anastasia
full_name: Grigorenko, Anastasia
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: 2006-02-07T00:00:00Z
date_updated: 2026-05-08T10:07:52Z
day: '07'
ddc:
- '570'
doi: 10.1371/journal.pbio.0040073
extern: '1'
external_id:
pmid:
- '16448217'
intvolume: ' 4'
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/publicdomain/zero/1.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.1371/journal.pbio.0040073
month: '02'
oa: 1
oa_version: Published Version
page: 0403 - 0410
pmid: 1
publication: PLoS Biology
publication_identifier:
eissn:
- 1545-7885
issn:
- 1544-9173
publication_status: published
publisher: Public Library of Science
publist_id: '6794'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus
primigenius
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
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'
...
---
OA_type: closed access
_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.
article_processing_charge: No
article_type: original
author:
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Aleksey
full_name: Ogurtsov, Aleksey
last_name: Ogurtsov
- first_name: Alexey
full_name: Kondrashov, Alexey
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: 2026-05-08T10:18:03Z
day: '21'
doi: 10.1016/j.jtbi.2005.10.020
extern: '1'
external_id:
pmid:
- '16343547'
intvolume: ' 240'
issue: '4'
keyword:
- Mutation
- Selection
- Synonymous site
- Evolution
- Genetic drift
language:
- iso: eng
month: '06'
oa_version: None
page: 616 - 626
pmid: 1
publication: Journal of Theoretical Biology
publication_identifier:
issn:
- 1095-8541
publication_status: published
publisher: Elsevier
publist_id: '6779'
quality_controlled: '1'
scopus_import: '1'
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
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 240
year: '2006'
...