---
_id: '3223'
abstract:
- lang: eng
text: |-
“Hash then encrypt” is an approach to message authentication, where first the message is hashed down using an ε-universal hash function, and then the resulting k-bit value is encrypted, say with a block-cipher. The security of this scheme is proportional to εq2, where q is the number of MACs the adversary can request. As ε is at least 2−k, the best one can hope for is O(q2/2k) security. Unfortunately, such small ε is not achieved by simple hash functions used in practice, such as the polynomial evaluation or the Merkle-Damg ̊ard construction, where ε grows with the message length L.
The main insight of this work comes from the fact that, by using ran- domized message preprocessing via a short random salt p (which must then be sent as part of the authentication tag), we can use the “hash then encrypt” paradigm with suboptimal “practical” ε-universal hash func- tions, and still improve its exact security to optimal O(q2/2k). Specif- ically, by using at most an O(logL)-bit salt p, one can always regain the optimal exact security O(q2/2k), even in situations where ε grows polynomially with L. We also give very simple preprocessing maps for popular “suboptimal” hash functions, namely polynomial evaluation and the Merkle-Damg ̊ard construction.
Our results come from a general extension of the classical Carter- Wegman paradigm, which we believe is of independent interest. On a high level, it shows that public randomization allows one to use the potentially much smaller “average-case” collision probability in place of the “worst-case” collision probability ε.
alternative_title:
- LNCS
author:
- first_name: Yevgeniy
full_name: Dodis, Yevgeniy
last_name: Dodis
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Dodis Y, Pietrzak KZ. Improving the security of MACs via randomized message
preprocessing. In: Vol 4593. Springer; 2007:414-433. doi:10.1007/978-3-540-74619-5_26'
apa: 'Dodis, Y., & Pietrzak, K. Z. (2007). Improving the security of MACs via
randomized message preprocessing (Vol. 4593, pp. 414–433). Presented at the FSE:
Fast Software Encryption, Springer. https://doi.org/10.1007/978-3-540-74619-5_26'
chicago: Dodis, Yevgeniy, and Krzysztof Z Pietrzak. “Improving the Security of MACs
via Randomized Message Preprocessing,” 4593:414–33. Springer, 2007. https://doi.org/10.1007/978-3-540-74619-5_26.
ieee: 'Y. Dodis and K. Z. Pietrzak, “Improving the security of MACs via randomized
message preprocessing,” presented at the FSE: Fast Software Encryption, 2007,
vol. 4593, pp. 414–433.'
ista: 'Dodis Y, Pietrzak KZ. 2007. Improving the security of MACs via randomized
message preprocessing. FSE: Fast Software Encryption, LNCS, vol. 4593, 414–433.'
mla: Dodis, Yevgeniy, and Krzysztof Z. Pietrzak. Improving the Security of MACs
via Randomized Message Preprocessing. Vol. 4593, Springer, 2007, pp. 414–33,
doi:10.1007/978-3-540-74619-5_26.
short: Y. Dodis, K.Z. Pietrzak, in:, Springer, 2007, pp. 414–433.
conference:
name: 'FSE: Fast Software Encryption'
date_created: 2018-12-11T12:02:06Z
date_published: 2007-10-11T00:00:00Z
date_updated: 2021-01-12T07:41:55Z
day: '11'
doi: 10.1007/978-3-540-74619-5_26
extern: 1
intvolume: ' 4593'
month: '10'
page: 414 - 433
publication_status: published
publisher: Springer
publist_id: '3458'
quality_controlled: 0
status: public
title: Improving the security of MACs via randomized message preprocessing
type: conference
volume: 4593
year: '2007'
...
---
_id: '3305'
abstract:
- lang: eng
text: The accumulation of deleterious mutations plays a major role in evolution,
and key to this are the interactions between their fitness effects, known as epistasis.
Whether mutations tend to interact synergistically (with multiple mutations being
more deleterious than would be expected from their individual fitness effects)
or antagonistically is important for a variety of evolutionary questions, particularly
the evolution of sex. Unfortunately, the experimental evidence on the prevalence
and strength of epistasis is mixed and inconclusive. Here we study theoretically
whether synergistic or antagonistic epistasis is likely to be favored by evolution
and by how much. We find that in the presence of recombination, evolution favors
less synergistic or more antagonistic epistasis whenever mutations that change
the epistasis in this direction are possible. This is because evolution favors
increased buffering against the effects of deleterious mutations. This suggests
that we should not expect synergistic epistasis to be widespread in nature and
hence that the mutational deterministic hypothesis for the advantage of sex may
not apply widely.
author:
- first_name: Michael
full_name: Desai, Michael M
last_name: Desai
- first_name: Daniel
full_name: Daniel Weissman
id: 2D0CE020-F248-11E8-B48F-1D18A9856A87
last_name: Weissman
- first_name: Marcus
full_name: Feldman, Marcus W
last_name: Feldman
citation:
ama: Desai M, Weissman D, Feldman M. Evolution can favor antagonistic epistasis.
Genetics. 2007;177(2):1001-1010. doi:10.1534/genetics.107.075812
apa: Desai, M., Weissman, D., & Feldman, M. (2007). Evolution can favor antagonistic
epistasis. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.107.075812
chicago: Desai, Michael, Daniel Weissman, and Marcus Feldman. “Evolution Can Favor
Antagonistic Epistasis.” Genetics. Genetics Society of America, 2007. https://doi.org/10.1534/genetics.107.075812.
ieee: M. Desai, D. Weissman, and M. Feldman, “Evolution can favor antagonistic epistasis,”
Genetics, vol. 177, no. 2. Genetics Society of America, pp. 1001–10, 2007.
ista: Desai M, Weissman D, Feldman M. 2007. Evolution can favor antagonistic epistasis.
Genetics. 177(2), 1001–10.
mla: Desai, Michael, et al. “Evolution Can Favor Antagonistic Epistasis.” Genetics,
vol. 177, no. 2, Genetics Society of America, 2007, pp. 1001–10, doi:10.1534/genetics.107.075812.
short: M. Desai, D. Weissman, M. Feldman, Genetics 177 (2007) 1001–10.
date_created: 2018-12-11T12:02:34Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:32Z
day: '01'
doi: 10.1534/genetics.107.075812
extern: 1
intvolume: ' 177'
issue: '2'
month: '01'
page: 1001 - 10
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '3335'
quality_controlled: 0
status: public
title: Evolution can favor antagonistic epistasis
type: journal_article
volume: 177
year: '2007'
...
---
_id: '11115'
abstract:
- lang: eng
text: The formation of the nuclear envelope (NE) around chromatin is a major membrane-remodelling
event that occurs during cell division of metazoa. It is unclear whether the nuclear
membrane reforms by the fusion of NE fragments or if it re-emerges from an intact
tubular network of the endoplasmic reticulum (ER). Here, we show that NE formation
and expansion requires a tubular ER network and occurs efficiently in the presence
of the membrane fusion inhibitor GTPγS. Chromatin recruitment of membranes, which
is initiated by tubule-end binding, followed by the formation, expansion and sealing
of flat membrane sheets, is mediated by DNA-binding proteins residing in the ER.
Thus, chromatin plays an active role in reshaping of the ER during NE formation.
article_processing_charge: No
article_type: original
author:
- first_name: Daniel J.
full_name: Anderson, Daniel J.
last_name: Anderson
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Anderson DJ, Hetzer M. Nuclear envelope formation by chromatin-mediated reorganization
of the endoplasmic reticulum. Nature Cell Biology. 2007;9(10):1160-1166.
doi:10.1038/ncb1636
apa: Anderson, D. J., & Hetzer, M. (2007). Nuclear envelope formation by chromatin-mediated
reorganization of the endoplasmic reticulum. Nature Cell Biology. Springer
Nature. https://doi.org/10.1038/ncb1636
chicago: Anderson, Daniel J., and Martin Hetzer. “Nuclear Envelope Formation by
Chromatin-Mediated Reorganization of the Endoplasmic Reticulum.” Nature Cell
Biology. Springer Nature, 2007. https://doi.org/10.1038/ncb1636.
ieee: D. J. Anderson and M. Hetzer, “Nuclear envelope formation by chromatin-mediated
reorganization of the endoplasmic reticulum,” Nature Cell Biology, vol.
9, no. 10. Springer Nature, pp. 1160–1166, 2007.
ista: Anderson DJ, Hetzer M. 2007. Nuclear envelope formation by chromatin-mediated
reorganization of the endoplasmic reticulum. Nature Cell Biology. 9(10), 1160–1166.
mla: Anderson, Daniel J., and Martin Hetzer. “Nuclear Envelope Formation by Chromatin-Mediated
Reorganization of the Endoplasmic Reticulum.” Nature Cell Biology, vol.
9, no. 10, Springer Nature, 2007, pp. 1160–66, doi:10.1038/ncb1636.
short: D.J. Anderson, M. Hetzer, Nature Cell Biology 9 (2007) 1160–1166.
date_created: 2022-04-07T07:56:04Z
date_published: 2007-09-09T00:00:00Z
date_updated: 2022-07-18T08:56:38Z
day: '09'
doi: 10.1038/ncb1636
extern: '1'
external_id:
pmid:
- '17828249'
intvolume: ' 9'
issue: '10'
keyword:
- Cell Biology
language:
- iso: eng
month: '09'
oa_version: None
page: 1160-1166
pmid: 1
publication: Nature Cell Biology
publication_identifier:
eissn:
- 1476-4679
issn:
- 1465-7392
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nuclear envelope formation by chromatin-mediated reorganization of the endoplasmic
reticulum
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 9
year: '2007'
...
---
_id: '11116'
abstract:
- lang: eng
text: The metazoan nuclear envelope (NE) breaks down and re-forms during each cell
cycle. Nuclear pore complexes (NPCs), which allow nucleocytoplasmic transport
during interphase, assemble into the re-forming NE at the end of mitosis. Using
in vitro NE assembly, we show that the vertebrate homologue of MEL-28 (maternal
effect lethal), a recently discovered NE component in Caenorhabditis elegans,
functions in postmitotic NPC assembly. MEL-28 interacts with the Nup107–160 complex
(Nup for nucleoporin), an important building block of the NPC, and is essential
for the recruitment of the Nup107–160 complex to chromatin. We suggest that MEL-28
acts as a seeding point for NPC assembly.
article_processing_charge: No
article_type: original
author:
- first_name: Cerstin
full_name: Franz, Cerstin
last_name: Franz
- first_name: Rudolf
full_name: Walczak, Rudolf
last_name: Walczak
- first_name: Sevil
full_name: Yavuz, Sevil
last_name: Yavuz
- first_name: Rachel
full_name: Santarella, Rachel
last_name: Santarella
- first_name: Marc
full_name: Gentzel, Marc
last_name: Gentzel
- first_name: Peter
full_name: Askjaer, Peter
last_name: Askjaer
- first_name: Vincent
full_name: Galy, Vincent
last_name: Galy
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
- first_name: Iain W
full_name: Mattaj, Iain W
last_name: Mattaj
- first_name: Wolfram
full_name: Antonin, Wolfram
last_name: Antonin
citation:
ama: Franz C, Walczak R, Yavuz S, et al. MEL‐28/ELYS is required for the recruitment
of nucleoporins to chromatin and postmitotic nuclear pore complex assembly. EMBO
reports. 2007;8(2):165-172. doi:10.1038/sj.embor.7400889
apa: Franz, C., Walczak, R., Yavuz, S., Santarella, R., Gentzel, M., Askjaer, P.,
… Antonin, W. (2007). MEL‐28/ELYS is required for the recruitment of nucleoporins
to chromatin and postmitotic nuclear pore complex assembly. EMBO Reports.
EMBO. https://doi.org/10.1038/sj.embor.7400889
chicago: Franz, Cerstin, Rudolf Walczak, Sevil Yavuz, Rachel Santarella, Marc Gentzel,
Peter Askjaer, Vincent Galy, Martin Hetzer, Iain W Mattaj, and Wolfram Antonin.
“MEL‐28/ELYS Is Required for the Recruitment of Nucleoporins to Chromatin and
Postmitotic Nuclear Pore Complex Assembly.” EMBO Reports. EMBO, 2007. https://doi.org/10.1038/sj.embor.7400889.
ieee: C. Franz et al., “MEL‐28/ELYS is required for the recruitment of nucleoporins
to chromatin and postmitotic nuclear pore complex assembly,” EMBO reports,
vol. 8, no. 2. EMBO, pp. 165–172, 2007.
ista: Franz C, Walczak R, Yavuz S, Santarella R, Gentzel M, Askjaer P, Galy V, Hetzer
M, Mattaj IW, Antonin W. 2007. MEL‐28/ELYS is required for the recruitment of
nucleoporins to chromatin and postmitotic nuclear pore complex assembly. EMBO
reports. 8(2), 165–172.
mla: Franz, Cerstin, et al. “MEL‐28/ELYS Is Required for the Recruitment of Nucleoporins
to Chromatin and Postmitotic Nuclear Pore Complex Assembly.” EMBO Reports,
vol. 8, no. 2, EMBO, 2007, pp. 165–72, doi:10.1038/sj.embor.7400889.
short: C. Franz, R. Walczak, S. Yavuz, R. Santarella, M. Gentzel, P. Askjaer, V.
Galy, M. Hetzer, I.W. Mattaj, W. Antonin, EMBO Reports 8 (2007) 165–172.
date_created: 2022-04-07T07:56:13Z
date_published: 2007-01-19T00:00:00Z
date_updated: 2022-07-18T08:56:40Z
day: '19'
doi: 10.1038/sj.embor.7400889
extern: '1'
external_id:
pmid:
- '17235358'
intvolume: ' 8'
issue: '2'
keyword:
- Genetics
- Molecular Biology
- Biochemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/sj.embor.7400889
month: '01'
oa: 1
oa_version: Published Version
page: 165-172
pmid: 1
publication: EMBO reports
publication_identifier:
eissn:
- 1469-3178
issn:
- 1469-221X
publication_status: published
publisher: EMBO
quality_controlled: '1'
scopus_import: '1'
status: public
title: MEL‐28/ELYS is required for the recruitment of nucleoporins to chromatin and
postmitotic nuclear pore complex assembly
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 8
year: '2007'
...
---
_id: '7780'
abstract:
- lang: eng
text: 'We used single-channel electrical recordings and Langevin molecular dynamics
simulations to explore the electrophoretic translocation of various β-hairpin
peptides across the staphylococcal α-hemolysin (αHL) protein pore at single-molecule
resolution. The β-hairpin peptides, which varied in their folding properties,
corresponded to the C terminal residues of the B1 domain of protein G. The translocation
time was strongly dependent on the electric force and was correlated with the
folding features of the β-hairpin peptides. Highly unfolded peptides entered the
pore in an extended conformation, resulting in fast single-file translocation
events. In contrast, the translocation of the folded β-hairpin peptides occurred
more slowly. In this case, the β-hairpin peptides traversed the αHL pore in a
misfolded or fully folded conformation. This study demonstrates that the interaction
between a polypeptide and a β-barrel protein pore is dependent on the folding
features of the polypeptide. '
article_processing_charge: No
article_type: original
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Serdal
full_name: Kirmizialtin, Serdal
last_name: Kirmizialtin
- first_name: Beatrice M.
full_name: Huyghues-Despointes, Beatrice M.
last_name: Huyghues-Despointes
- first_name: Aiping
full_name: Zhu, Aiping
last_name: Zhu
- first_name: J. Martin
full_name: Scholtz, J. Martin
last_name: Scholtz
- first_name: Dmitrii E.
full_name: Makarov, Dmitrii E.
last_name: Makarov
- first_name: Liviu
full_name: Movileanu, Liviu
last_name: Movileanu
citation:
ama: Goodrich CP, Kirmizialtin S, Huyghues-Despointes BM, et al. Single-molecule
electrophoresis of β-hairpin peptides by electrical recordings and Langevin dynamics
simulations. The Journal of Physical Chemistry B. 2007;111(13):3332-3335.
doi:10.1021/jp071364h
apa: Goodrich, C. P., Kirmizialtin, S., Huyghues-Despointes, B. M., Zhu, A., Scholtz,
J. M., Makarov, D. E., & Movileanu, L. (2007). Single-molecule electrophoresis
of β-hairpin peptides by electrical recordings and Langevin dynamics simulations.
The Journal of Physical Chemistry B. American Chemical Society. https://doi.org/10.1021/jp071364h
chicago: Goodrich, Carl Peter, Serdal Kirmizialtin, Beatrice M. Huyghues-Despointes,
Aiping Zhu, J. Martin Scholtz, Dmitrii E. Makarov, and Liviu Movileanu. “Single-Molecule
Electrophoresis of β-Hairpin Peptides by Electrical Recordings and Langevin Dynamics
Simulations.” The Journal of Physical Chemistry B. American Chemical Society,
2007. https://doi.org/10.1021/jp071364h.
ieee: C. P. Goodrich et al., “Single-molecule electrophoresis of β-hairpin
peptides by electrical recordings and Langevin dynamics simulations,” The Journal
of Physical Chemistry B, vol. 111, no. 13. American Chemical Society, pp.
3332–3335, 2007.
ista: Goodrich CP, Kirmizialtin S, Huyghues-Despointes BM, Zhu A, Scholtz JM, Makarov
DE, Movileanu L. 2007. Single-molecule electrophoresis of β-hairpin peptides by
electrical recordings and Langevin dynamics simulations. The Journal of Physical
Chemistry B. 111(13), 3332–3335.
mla: Goodrich, Carl Peter, et al. “Single-Molecule Electrophoresis of β-Hairpin
Peptides by Electrical Recordings and Langevin Dynamics Simulations.” The Journal
of Physical Chemistry B, vol. 111, no. 13, American Chemical Society, 2007,
pp. 3332–35, doi:10.1021/jp071364h.
short: C.P. Goodrich, S. Kirmizialtin, B.M. Huyghues-Despointes, A. Zhu, J.M. Scholtz,
D.E. Makarov, L. Movileanu, The Journal of Physical Chemistry B 111 (2007) 3332–3335.
date_created: 2020-04-30T12:19:15Z
date_published: 2007-03-13T00:00:00Z
date_updated: 2021-01-12T08:15:29Z
day: '13'
doi: 10.1021/jp071364h
extern: '1'
intvolume: ' 111'
issue: '13'
language:
- iso: eng
month: '03'
oa_version: None
page: 3332-3335
publication: The Journal of Physical Chemistry B
publication_identifier:
issn:
- 1520-6106
- 1520-5207
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: Single-molecule electrophoresis of β-hairpin peptides by electrical recordings
and Langevin dynamics simulations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 111
year: '2007'
...
---
_id: '7781'
abstract:
- lang: eng
text: Males are predicted to compete for reproductive opportunities, with sexual
selection driving the evolution of large body size and weaponry through the advantage
they confer for access to females. Few studies have explored potential trade‐offs
of investment in secondary sexual traits between different components of fitness
or tested for sexually antagonistic selection pressures. These factors may provide
explanations for observed polymorphisms in both form and quality of secondary
sexual traits. We report here an analysis of selection on horn phenotype in a
feral population of Soay sheep (Ovis aries) on the island of Hirta, St. Kilda,
Scotland. Soay sheep display a phenotypic polymorphism for horn type with males
growing either normal or reduced (scurred) horns, and females growing either normal,
scurred, or no (polled) horns; further variation in size exists within horn morphs.
We show that horn phenotype and the size of the trait displayed is subject to
different selection pressures in males and females, generating sexually antagonistic
selection. Furthermore, there was evidence of a trade‐off between breeding success
and longevity in normal‐horned males, with both the normal horn type and larger
horn size being associated with greater annual breeding success but reduced longevity.
Therefore, selection through lifetime breeding success was not found to act upon
horn phenotype in males. In females, a negative association of annual breeding
success within the normal‐horned phenotype did not result in a significant difference
in lifetime fitness when compared to scurred individuals, as no significant difference
in longevity was found. However, increased horn size within this group was negatively
associated with breeding success and longevity. Females without horns (polled)
suffered reduced longevity and thus reduced lifetime breeding success relative
the other horn morphs. Our results therefore suggest that trade‐offs between different
components of fitness and antagonistic selection between the sexes may maintain
genetic variation for secondary sexual traits within a population.
article_processing_charge: No
article_type: original
author:
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Jill G.
full_name: Pilkington, Jill G.
last_name: Pilkington
- first_name: Tim H.
full_name: Clutton-Brock, Tim H.
last_name: Clutton-Brock
- first_name: Josephine M.
full_name: Pemberton, Josephine M.
last_name: Pemberton
- first_name: Loeske E.B.
full_name: Kruuk, Loeske E.B.
last_name: Kruuk
citation:
ama: 'Robinson MR, Pilkington JG, Clutton-Brock TH, Pemberton JM, Kruuk LEB. Live
fast, die young: Trade-offs between fitness components and sexually antagonistic
selection on weaponry in soay sheep. Evolution. 2007;60(10):2168-2181.
doi:10.1111/j.0014-3820.2006.tb01854.x'
apa: 'Robinson, M. R., Pilkington, J. G., Clutton-Brock, T. H., Pemberton, J. M.,
& Kruuk, L. E. B. (2007). Live fast, die young: Trade-offs between fitness
components and sexually antagonistic selection on weaponry in soay sheep. Evolution.
Wiley. https://doi.org/10.1111/j.0014-3820.2006.tb01854.x'
chicago: 'Robinson, Matthew Richard, Jill G. Pilkington, Tim H. Clutton-Brock, Josephine
M. Pemberton, and Loeske E.B. Kruuk. “Live Fast, Die Young: Trade-Offs between
Fitness Components and Sexually Antagonistic Selection on Weaponry in Soay Sheep.”
Evolution. Wiley, 2007. https://doi.org/10.1111/j.0014-3820.2006.tb01854.x.'
ieee: 'M. R. Robinson, J. G. Pilkington, T. H. Clutton-Brock, J. M. Pemberton, and
L. E. B. Kruuk, “Live fast, die young: Trade-offs between fitness components and
sexually antagonistic selection on weaponry in soay sheep,” Evolution,
vol. 60, no. 10. Wiley, pp. 2168–2181, 2007.'
ista: 'Robinson MR, Pilkington JG, Clutton-Brock TH, Pemberton JM, Kruuk LEB. 2007.
Live fast, die young: Trade-offs between fitness components and sexually antagonistic
selection on weaponry in soay sheep. Evolution. 60(10), 2168–2181.'
mla: 'Robinson, Matthew Richard, et al. “Live Fast, Die Young: Trade-Offs between
Fitness Components and Sexually Antagonistic Selection on Weaponry in Soay Sheep.”
Evolution, vol. 60, no. 10, Wiley, 2007, pp. 2168–81, doi:10.1111/j.0014-3820.2006.tb01854.x.'
short: M.R. Robinson, J.G. Pilkington, T.H. Clutton-Brock, J.M. Pemberton, L.E.B.
Kruuk, Evolution 60 (2007) 2168–2181.
date_created: 2020-04-30T13:01:47Z
date_published: 2007-05-08T00:00:00Z
date_updated: 2021-01-12T08:15:30Z
day: '08'
doi: 10.1111/j.0014-3820.2006.tb01854.x
extern: '1'
intvolume: ' 60'
issue: '10'
language:
- iso: eng
month: '05'
oa_version: None
page: 2168-2181
publication: Evolution
publication_identifier:
issn:
- 0014-3820
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: 'Live fast, die young: Trade-offs between fitness components and sexually antagonistic
selection on weaponry in soay sheep'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 60
year: '2007'
...
---
_id: '8027'
abstract:
- lang: eng
text: Gating deficits and hallucinatory sensations are prominent symptoms of schizophrenia.
Comparing these abnormalities with the failure modes of network models is an interesting
way to explore how they arise. We present a network model that can both propagate
and gate signals. The model exhibits effects reminiscent of clinically observed
pathologies when the balance between excitation and inhibition that it requires
is not properly maintained.
article_processing_charge: No
article_type: original
author:
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: L.
full_name: Abbott, L.
last_name: Abbott
citation:
ama: 'Vogels TP, Abbott L. Gating deficits in model networks: A path to schizophrenia?
Pharmacopsychiatry. 2007;40(S 1):S73-S77. doi:10.1055/s-2007-992130'
apa: 'Vogels, T. P., & Abbott, L. (2007). Gating deficits in model networks:
A path to schizophrenia? Pharmacopsychiatry. Thieme. https://doi.org/10.1055/s-2007-992130'
chicago: 'Vogels, Tim P, and L. Abbott. “Gating Deficits in Model Networks: A Path
to Schizophrenia?” Pharmacopsychiatry. Thieme, 2007. https://doi.org/10.1055/s-2007-992130.'
ieee: 'T. P. Vogels and L. Abbott, “Gating deficits in model networks: A path to
schizophrenia?,” Pharmacopsychiatry, vol. 40, no. S 1. Thieme, pp. S73–S77,
2007.'
ista: 'Vogels TP, Abbott L. 2007. Gating deficits in model networks: A path to schizophrenia?
Pharmacopsychiatry. 40(S 1), S73–S77.'
mla: 'Vogels, Tim P., and L. Abbott. “Gating Deficits in Model Networks: A Path
to Schizophrenia?” Pharmacopsychiatry, vol. 40, no. S 1, Thieme, 2007,
pp. S73–77, doi:10.1055/s-2007-992130.'
short: T.P. Vogels, L. Abbott, Pharmacopsychiatry 40 (2007) S73–S77.
date_created: 2020-06-25T13:11:37Z
date_published: 2007-12-01T00:00:00Z
date_updated: 2021-01-12T08:16:36Z
day: '01'
doi: 10.1055/s-2007-992130
extern: '1'
external_id:
pmid:
- '18080946'
intvolume: ' 40'
issue: S 1
language:
- iso: eng
month: '12'
oa_version: None
page: S73-S77
pmid: 1
publication: Pharmacopsychiatry
publication_identifier:
issn:
- 0176-3679
- 1439-0795
publication_status: published
publisher: Thieme
quality_controlled: '1'
status: public
title: 'Gating deficits in model networks: A path to schizophrenia?'
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 40
year: '2007'
...
---
_id: '8483'
abstract:
- lang: eng
text: Atom-resolved real-time studies of kinetic processes in proteins have been
hampered in the past by the lack of experimental techniques that yield sufficient
temporal and atomic resolution. Here we present band-selective optimized flip-angle
short transient (SOFAST) real-time 2D NMR spectroscopy, a method that allows simultaneous
observation of reaction kinetics for a large number of nuclear sites along the
polypeptide chain of a protein with an unprecedented time resolution of a few
seconds. SOFAST real-time 2D NMR spectroscopy combines fast NMR data acquisition
techniques with rapid sample mixing inside the NMR magnet to initiate the kinetic
event. We demonstrate the use of SOFAST real-time 2D NMR to monitor the conformational
transition of α-lactalbumin from a molten globular to the native state for a large
number of amide sites along the polypeptide chain. The kinetic behavior observed
for the disappearance of the molten globule and the appearance of the native state
is monoexponential and uniform along the polypeptide chain. This observation confirms
previous findings that a single transition state ensemble controls folding of
α-lactalbumin from the molten globule to the native state. In a second application,
the spontaneous unfolding of native ubiquitin under nondenaturing conditions is
characterized by amide hydrogen exchange rate constants measured at high pH by
using SOFAST real-time 2D NMR. Our data reveal that ubiquitin unfolds in a gradual
manner with distinct unfolding regimes.
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: V.
full_name: Forge, V.
last_name: Forge
- first_name: B.
full_name: Brutscher, B.
last_name: Brutscher
citation:
ama: Schanda P, Forge V, Brutscher B. Protein folding and unfolding studied at atomic
resolution by fast two-dimensional NMR spectroscopy. Proceedings of the National
Academy of Sciences. 2007;104(27):11257-11262. doi:10.1073/pnas.0702069104
apa: Schanda, P., Forge, V., & Brutscher, B. (2007). Protein folding and unfolding
studied at atomic resolution by fast two-dimensional NMR spectroscopy. Proceedings
of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.0702069104
chicago: Schanda, Paul, V. Forge, and B. Brutscher. “Protein Folding and Unfolding
Studied at Atomic Resolution by Fast Two-Dimensional NMR Spectroscopy.” Proceedings
of the National Academy of Sciences. National Academy of Sciences, 2007. https://doi.org/10.1073/pnas.0702069104.
ieee: P. Schanda, V. Forge, and B. Brutscher, “Protein folding and unfolding studied
at atomic resolution by fast two-dimensional NMR spectroscopy,” Proceedings
of the National Academy of Sciences, vol. 104, no. 27. National Academy of
Sciences, pp. 11257–11262, 2007.
ista: Schanda P, Forge V, Brutscher B. 2007. Protein folding and unfolding studied
at atomic resolution by fast two-dimensional NMR spectroscopy. Proceedings of
the National Academy of Sciences. 104(27), 11257–11262.
mla: Schanda, Paul, et al. “Protein Folding and Unfolding Studied at Atomic Resolution
by Fast Two-Dimensional NMR Spectroscopy.” Proceedings of the National Academy
of Sciences, vol. 104, no. 27, National Academy of Sciences, 2007, pp. 11257–62,
doi:10.1073/pnas.0702069104.
short: P. Schanda, V. Forge, B. Brutscher, Proceedings of the National Academy of
Sciences 104 (2007) 11257–11262.
date_created: 2020-09-18T10:12:54Z
date_published: 2007-07-03T00:00:00Z
date_updated: 2021-01-12T08:19:35Z
day: '03'
doi: 10.1073/pnas.0702069104
extern: '1'
intvolume: ' 104'
issue: '27'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '07'
oa_version: None
page: 11257-11262
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
status: public
title: Protein folding and unfolding studied at atomic resolution by fast two-dimensional
NMR spectroscopy
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 104
year: '2007'
...
---
_id: '8484'
abstract:
- lang: eng
text: A series of sequential, intra-residue, and bi-directional BEST H–N–CA, H–N–CO,
and H–N–CB pulse sequences is presented that extends the BEST concept introduced
recently for fast multidimensional protein NMR [Schanda et al., J. Am. Chem. Soc.
128 (2006) 9042] to the complete set of experiments required for sequential resonance
assignment. We demonstrate for the protein ubiquitin that 3D BEST H–N–C correlation
spectra can be recorded on a 600 MHz NMR spectrometer equipped with a cryogenic
probe in only a few minutes of acquisition time with sufficient sensitivity to
detect all expected cross peaks.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Ewen
full_name: Lescop, Ewen
last_name: Lescop
- 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: Lescop E, Schanda P, Brutscher B. A set of BEST triple-resonance experiments
for time-optimized protein resonance assignment. Journal of Magnetic Resonance.
2007;187(1):163-169. doi:10.1016/j.jmr.2007.04.002
apa: Lescop, E., Schanda, P., & Brutscher, B. (2007). A set of BEST triple-resonance
experiments for time-optimized protein resonance assignment. Journal of Magnetic
Resonance. Elsevier. https://doi.org/10.1016/j.jmr.2007.04.002
chicago: Lescop, Ewen, Paul Schanda, and Bernhard Brutscher. “A Set of BEST Triple-Resonance
Experiments for Time-Optimized Protein Resonance Assignment.” Journal of Magnetic
Resonance. Elsevier, 2007. https://doi.org/10.1016/j.jmr.2007.04.002.
ieee: E. Lescop, P. Schanda, and B. Brutscher, “A set of BEST triple-resonance experiments
for time-optimized protein resonance assignment,” Journal of Magnetic Resonance,
vol. 187, no. 1. Elsevier, pp. 163–169, 2007.
ista: Lescop E, Schanda P, Brutscher B. 2007. A set of BEST triple-resonance experiments
for time-optimized protein resonance assignment. Journal of Magnetic Resonance.
187(1), 163–169.
mla: Lescop, Ewen, et al. “A Set of BEST Triple-Resonance Experiments for Time-Optimized
Protein Resonance Assignment.” Journal of Magnetic Resonance, vol. 187,
no. 1, Elsevier, 2007, pp. 163–69, doi:10.1016/j.jmr.2007.04.002.
short: E. Lescop, P. Schanda, B. Brutscher, Journal of Magnetic Resonance 187 (2007)
163–169.
date_created: 2020-09-18T10:13:02Z
date_published: 2007-07-01T00:00:00Z
date_updated: 2021-01-12T08:19:35Z
day: '01'
doi: 10.1016/j.jmr.2007.04.002
extern: '1'
intvolume: ' 187'
issue: '1'
language:
- iso: eng
month: '07'
oa_version: None
page: 163-169
publication: Journal of Magnetic Resonance
publication_identifier:
issn:
- 1090-7807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: A set of BEST triple-resonance experiments for time-optimized protein resonance
assignment
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 187
year: '2007'
...
---
_id: '8485'
abstract:
- lang: eng
text: High signal to noise is a necessity for the quantification of NMR spectral
parameters to be translated into accurate and precise restraints on protein structure
and dynamics. An important source of long-range structural information is obtained
from 1H–1H residual dipolar couplings (RDCs) measured for weakly aligned molecules.
For sensitivity reasons, such measurements are generally performed on highly deuterated
protein samples. Here we show that high sensitivity is also obtained for protonated
protein samples if the pulse schemes are optimized in terms of longitudinal relaxation
efficiency and J-mismatch compensated coherence transfer. The new sensitivity-optimized
quantitative J-correlation experiment yields important signal gains reaching factors
of 1.5 to 8 for individual correlation peaks when compared to previously proposed
pulse schemes.
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: Ewen
full_name: Lescop, Ewen
last_name: Lescop
- first_name: Mirjam
full_name: Falge, Mirjam
last_name: Falge
- first_name: Rémy
full_name: Sounier, Rémy
last_name: Sounier
- first_name: Jérôme
full_name: Boisbouvier, Jérôme
last_name: Boisbouvier
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
citation:
ama: Schanda P, Lescop E, Falge M, Sounier R, Boisbouvier J, Brutscher B. Sensitivity-optimized
experiment for the measurement of residual dipolar couplings between amide protons.
Journal of Biomolecular NMR. 2007;38:47-55. doi:10.1007/s10858-006-9138-2
apa: Schanda, P., Lescop, E., Falge, M., Sounier, R., Boisbouvier, J., & Brutscher,
B. (2007). Sensitivity-optimized experiment for the measurement of residual dipolar
couplings between amide protons. Journal of Biomolecular NMR. Springer
Nature. https://doi.org/10.1007/s10858-006-9138-2
chicago: Schanda, Paul, Ewen Lescop, Mirjam Falge, Rémy Sounier, Jérôme Boisbouvier,
and Bernhard Brutscher. “Sensitivity-Optimized Experiment for the Measurement
of Residual Dipolar Couplings between Amide Protons.” Journal of Biomolecular
NMR. Springer Nature, 2007. https://doi.org/10.1007/s10858-006-9138-2.
ieee: P. Schanda, E. Lescop, M. Falge, R. Sounier, J. Boisbouvier, and B. Brutscher,
“Sensitivity-optimized experiment for the measurement of residual dipolar couplings
between amide protons,” Journal of Biomolecular NMR, vol. 38. Springer
Nature, pp. 47–55, 2007.
ista: Schanda P, Lescop E, Falge M, Sounier R, Boisbouvier J, Brutscher B. 2007.
Sensitivity-optimized experiment for the measurement of residual dipolar couplings
between amide protons. Journal of Biomolecular NMR. 38, 47–55.
mla: Schanda, Paul, et al. “Sensitivity-Optimized Experiment for the Measurement
of Residual Dipolar Couplings between Amide Protons.” Journal of Biomolecular
NMR, vol. 38, Springer Nature, 2007, pp. 47–55, doi:10.1007/s10858-006-9138-2.
short: P. Schanda, E. Lescop, M. Falge, R. Sounier, J. Boisbouvier, B. Brutscher,
Journal of Biomolecular NMR 38 (2007) 47–55.
date_created: 2020-09-18T10:13:12Z
date_published: 2007-03-08T00:00:00Z
date_updated: 2021-01-12T08:19:36Z
day: '08'
doi: 10.1007/s10858-006-9138-2
extern: '1'
intvolume: ' 38'
keyword:
- Spectroscopy
- Biochemistry
language:
- iso: eng
month: '03'
oa_version: None
page: 47-55
publication: Journal of Biomolecular NMR
publication_identifier:
issn:
- 0925-2738
- 1573-5001
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Sensitivity-optimized experiment for the measurement of residual dipolar couplings
between amide protons
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 38
year: '2007'
...
---
_id: '8486'
abstract:
- lang: eng
text: A technique is described that allows reducing acquisition times of multidimensional
NMR experiments by extensive spectral folding. The method is simple and has many
interesting applications for NMR studies of molecular structure, dynamics, and
kinetics.
article_processing_charge: No
article_type: original
author:
- first_name: Ewen
full_name: Lescop, Ewen
last_name: Lescop
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Rodolfo
full_name: Rasia, Rodolfo
last_name: Rasia
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
citation:
ama: Lescop E, Schanda P, Rasia R, Brutscher B. Automated spectral compression for
fast multidimensional NMR and increased time resolution in real-time NMR spectroscopy.
Journal of the American Chemical Society. 2007;129(10):2756-2757. doi:10.1021/ja068949u
apa: Lescop, E., Schanda, P., Rasia, R., & Brutscher, B. (2007). Automated spectral
compression for fast multidimensional NMR and increased time resolution in real-time
NMR spectroscopy. Journal of the American Chemical Society. American Chemical
Society. https://doi.org/10.1021/ja068949u
chicago: Lescop, Ewen, Paul Schanda, Rodolfo Rasia, and Bernhard Brutscher. “Automated
Spectral Compression for Fast Multidimensional NMR and Increased Time Resolution
in Real-Time NMR Spectroscopy.” Journal of the American Chemical Society.
American Chemical Society, 2007. https://doi.org/10.1021/ja068949u.
ieee: E. Lescop, P. Schanda, R. Rasia, and B. Brutscher, “Automated spectral compression
for fast multidimensional NMR and increased time resolution in real-time NMR spectroscopy,”
Journal of the American Chemical Society, vol. 129, no. 10. American Chemical
Society, pp. 2756–2757, 2007.
ista: Lescop E, Schanda P, Rasia R, Brutscher B. 2007. Automated spectral compression
for fast multidimensional NMR and increased time resolution in real-time NMR spectroscopy.
Journal of the American Chemical Society. 129(10), 2756–2757.
mla: Lescop, Ewen, et al. “Automated Spectral Compression for Fast Multidimensional
NMR and Increased Time Resolution in Real-Time NMR Spectroscopy.” Journal of
the American Chemical Society, vol. 129, no. 10, American Chemical Society,
2007, pp. 2756–57, doi:10.1021/ja068949u.
short: E. Lescop, P. Schanda, R. Rasia, B. Brutscher, Journal of the American Chemical
Society 129 (2007) 2756–2757.
date_created: 2020-09-18T10:13:21Z
date_published: 2007-02-17T00:00:00Z
date_updated: 2021-01-12T08:19:36Z
day: '17'
doi: 10.1021/ja068949u
extern: '1'
intvolume: ' 129'
issue: '10'
keyword:
- Colloid and Surface Chemistry
- Biochemistry
- General Chemistry
- Catalysis
language:
- iso: eng
month: '02'
oa_version: None
page: 2756-2757
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: Automated spectral compression for fast multidimensional NMR and increased
time resolution in real-time NMR spectroscopy
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 129
year: '2007'
...
---
_id: '8487'
abstract:
- lang: eng
text: Following unidirectional biophysical events such as the folding of proteins
or the equilibration of binding interactions, requires experimental methods that
yield information at both atomic-level resolution and at high repetition rates.
Toward this end a number of different approaches enabling the rapid acquisition
of 2D NMR spectra have been recently introduced, including spatially encoded “ultrafast”
2D NMR spectroscopy and SOFAST HMQC NMR. Whereas the former accelerates acquisitions
by reducing the number of scans that are necessary for completing arbitrary 2D
NMR experiments, the latter operates by reducing the delay between consecutive
scans while preserving sensitivity. Given the complementarities between these
two approaches it seems natural to combine them into a single tool, enabling the
acquisition of full 2D protein NMR spectra at high repetition rates. We demonstrate
here this capability with the introduction of “ultraSOFAST” HMQC NMR, a spatially
encoded and relaxation-optimized approach that can provide 2D protein correlation
spectra at ∼1 s repetition rates for samples in the ∼2 mM concentration range.
The principles, relative advantages, and current limitations of this new approach
are discussed, and its application is exemplified with a study of the fast hydrogen−deuterium
exchange characterizing amide sites in Ubiquitin.
article_processing_charge: No
article_type: original
author:
- first_name: Maayan
full_name: Gal, Maayan
last_name: Gal
- 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
- first_name: Lucio
full_name: Frydman, Lucio
last_name: Frydman
citation:
ama: Gal M, Schanda P, Brutscher B, Frydman L. UltraSOFAST HMQC NMR and the repetitive
acquisition of 2D protein spectra at Hz rates. Journal of the American Chemical
Society. 2007;129(5):1372-1377. doi:10.1021/ja066915g
apa: Gal, M., Schanda, P., Brutscher, B., & Frydman, L. (2007). UltraSOFAST
HMQC NMR and the repetitive acquisition of 2D protein spectra at Hz rates. Journal
of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja066915g
chicago: Gal, Maayan, Paul Schanda, Bernhard Brutscher, and Lucio Frydman. “UltraSOFAST
HMQC NMR and the Repetitive Acquisition of 2D Protein Spectra at Hz Rates.” Journal
of the American Chemical Society. American Chemical Society, 2007. https://doi.org/10.1021/ja066915g.
ieee: M. Gal, P. Schanda, B. Brutscher, and L. Frydman, “UltraSOFAST HMQC NMR and
the repetitive acquisition of 2D protein spectra at Hz rates,” Journal of the
American Chemical Society, vol. 129, no. 5. American Chemical Society, pp.
1372–1377, 2007.
ista: Gal M, Schanda P, Brutscher B, Frydman L. 2007. UltraSOFAST HMQC NMR and the
repetitive acquisition of 2D protein spectra at Hz rates. Journal of the American
Chemical Society. 129(5), 1372–1377.
mla: Gal, Maayan, et al. “UltraSOFAST HMQC NMR and the Repetitive Acquisition of
2D Protein Spectra at Hz Rates.” Journal of the American Chemical Society,
vol. 129, no. 5, American Chemical Society, 2007, pp. 1372–77, doi:10.1021/ja066915g.
short: M. Gal, P. Schanda, B. Brutscher, L. Frydman, Journal of the American Chemical
Society 129 (2007) 1372–1377.
date_created: 2020-09-18T10:13:27Z
date_published: 2007-01-10T00:00:00Z
date_updated: 2021-01-12T08:19:37Z
day: '10'
doi: 10.1021/ja066915g
extern: '1'
intvolume: ' 129'
issue: '5'
keyword:
- Colloid and Surface Chemistry
- Biochemistry
- General Chemistry
- Catalysis
language:
- iso: eng
month: '01'
oa_version: None
page: 1372-1377
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: UltraSOFAST HMQC NMR and the repetitive acquisition of 2D protein spectra at
Hz rates
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 129
year: '2007'
...
---
_id: '8511'
abstract:
- lang: eng
text: "Here we study an amazing phenomenon discovered by Newhouse [S. Newhouse,
Non-density of Axiom A(a) on S2, in: Proc. Sympos. Pure Math., vol. 14, Amer.
Math. Soc., 1970, pp. 191–202; S. Newhouse,\r\nDiffeomorphisms with infinitely
many sinks, Topology 13 (1974) 9–18; S. Newhouse, The abundance of\r\nwild hyperbolic
sets and nonsmooth stable sets of diffeomorphisms, Publ. Math. Inst. Hautes Études
Sci.\r\n50 (1979) 101–151]. It turns out that in the space of Cr smooth diffeomorphisms
Diffr(M) of a compact\r\nsurface M there is an open set U such that a Baire generic
diffeomorphism f ∈ U has infinitely many coexisting sinks. In this paper we make
a step towards understanding “how often does a surface diffeomorphism\r\nhave
infinitely many sinks.” Our main result roughly says that with probability one
for any positive D a\r\nsurface diffeomorphism has only finitely many localized
sinks either of cyclicity bounded by D or those\r\nwhose period is relatively
large compared to its cyclicity. It verifies a particular case of Palis’ Conjecture\r\nsaying
that even though diffeomorphisms with infinitely many coexisting sinks are Baire
generic, they have\r\nprobability zero.\r\nOne of the key points of the proof
is an application of Newton Interpolation Polynomials to study the dynamics initiated
in [V. Kaloshin, B. Hunt, A stretched exponential bound on the rate of growth
of the number\r\nof periodic points for prevalent diffeomorphisms I, Ann. of Math.,
in press, 92 pp.; V. Kaloshin, A stretched\r\nexponential bound on the rate of
growth of the number of periodic points for prevalent diffeomorphisms II,\r\npreprint,
85 pp.]."
article_processing_charge: No
article_type: original
author:
- first_name: A.
full_name: Gorodetski, A.
last_name: Gorodetski
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
citation:
ama: Gorodetski A, Kaloshin V. How often surface diffeomorphisms have infinitely
many sinks and hyperbolicity of periodic points near a homoclinic tangency. Advances
in Mathematics. 2007;208(2):710-797. doi:10.1016/j.aim.2006.03.012
apa: Gorodetski, A., & Kaloshin, V. (2007). How often surface diffeomorphisms
have infinitely many sinks and hyperbolicity of periodic points near a homoclinic
tangency. Advances in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2006.03.012
chicago: Gorodetski, A., and Vadim Kaloshin. “How Often Surface Diffeomorphisms
Have Infinitely Many Sinks and Hyperbolicity of Periodic Points near a Homoclinic
Tangency.” Advances in Mathematics. Elsevier, 2007. https://doi.org/10.1016/j.aim.2006.03.012.
ieee: A. Gorodetski and V. Kaloshin, “How often surface diffeomorphisms have infinitely
many sinks and hyperbolicity of periodic points near a homoclinic tangency,” Advances
in Mathematics, vol. 208, no. 2. Elsevier, pp. 710–797, 2007.
ista: Gorodetski A, Kaloshin V. 2007. How often surface diffeomorphisms have infinitely
many sinks and hyperbolicity of periodic points near a homoclinic tangency. Advances
in Mathematics. 208(2), 710–797.
mla: Gorodetski, A., and Vadim Kaloshin. “How Often Surface Diffeomorphisms Have
Infinitely Many Sinks and Hyperbolicity of Periodic Points near a Homoclinic Tangency.”
Advances in Mathematics, vol. 208, no. 2, Elsevier, 2007, pp. 710–97, doi:10.1016/j.aim.2006.03.012.
short: A. Gorodetski, V. Kaloshin, Advances in Mathematics 208 (2007) 710–797.
date_created: 2020-09-18T10:48:27Z
date_published: 2007-01-30T00:00:00Z
date_updated: 2021-01-12T08:19:47Z
day: '30'
doi: 10.1016/j.aim.2006.03.012
extern: '1'
intvolume: ' 208'
issue: '2'
keyword:
- General Mathematics
language:
- iso: eng
month: '01'
oa_version: None
page: 710-797
publication: Advances in Mathematics
publication_identifier:
issn:
- 0001-8708
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: How often surface diffeomorphisms have infinitely many sinks and hyperbolicity
of periodic points near a homoclinic tangency
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 208
year: '2007'
...
---
_id: '8512'
abstract:
- lang: eng
text: "For diffeomorphisms of smooth compact finite-dimensional manifolds, we consider
the problem of how fast the number of periodic points with period n grows as a
function of n. In many familiar cases (e.g., Anosov systems) the growth is exponential,
but arbitrarily fast growth is possible; in fact, the first author has shown that
arbitrarily fast growth is topologically (Baire) generic for C2 or smoother diffeomorphisms.
In the present work we show that, by contrast, for a measure-theoretic notion
of genericity we call “prevalence”, the growth is not much faster than exponential.
Specifically, we show that for each ρ,δ>0, there is a prevalent set of C1+ρ (or
smoother) diffeomorphisms for which the number of periodic n points is bounded
above by exp(Cn1+δ) for some C independent of n. We also obtain a related bound
on the decay of hyperbolicity of the periodic points as a function of n, and obtain
the same results for 1-dimensional endomorphisms. The contrast between topologically
generic and measure-theoretically generic behavior for the growth of the number
of periodic points and the decay of their hyperbolicity show this to be a subtle
and complex phenomenon, reminiscent of KAM theory. Here in Part I we state our
results and describe the methods we use. We complete most of the proof in the
1-dimensional C2-smooth case and outline the remaining steps, deferred to Part
II, that are needed to establish the general case.\r\n\r\nThe novel feature of
the approach we develop in this paper is the introduction of Newton Interpolation
Polynomials as a tool for perturbing trajectories of iterated maps."
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: Brian
full_name: Hunt, Brian
last_name: Hunt
citation:
ama: Kaloshin V, Hunt B. Stretched exponential estimates on growth of the number
of periodic points for prevalent diffeomorphisms I. Annals of Mathematics.
2007;165(1):89-170. doi:10.4007/annals.2007.165.89
apa: Kaloshin, V., & Hunt, B. (2007). Stretched exponential estimates on growth
of the number of periodic points for prevalent diffeomorphisms I. Annals of
Mathematics. Princeton University Press. https://doi.org/10.4007/annals.2007.165.89
chicago: Kaloshin, Vadim, and Brian Hunt. “Stretched Exponential Estimates on Growth
of the Number of Periodic Points for Prevalent Diffeomorphisms I.” Annals of
Mathematics. Princeton University Press, 2007. https://doi.org/10.4007/annals.2007.165.89.
ieee: V. Kaloshin and B. Hunt, “Stretched exponential estimates on growth of the
number of periodic points for prevalent diffeomorphisms I,” Annals of Mathematics,
vol. 165, no. 1. Princeton University Press, pp. 89–170, 2007.
ista: Kaloshin V, Hunt B. 2007. Stretched exponential estimates on growth of the
number of periodic points for prevalent diffeomorphisms I. Annals of Mathematics.
165(1), 89–170.
mla: Kaloshin, Vadim, and Brian Hunt. “Stretched Exponential Estimates on Growth
of the Number of Periodic Points for Prevalent Diffeomorphisms I.” Annals of
Mathematics, vol. 165, no. 1, Princeton University Press, 2007, pp. 89–170,
doi:10.4007/annals.2007.165.89.
short: V. Kaloshin, B. Hunt, Annals of Mathematics 165 (2007) 89–170.
date_created: 2020-09-18T10:48:33Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T08:19:48Z
day: '01'
doi: 10.4007/annals.2007.165.89
extern: '1'
intvolume: ' 165'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 89-170
publication: Annals of Mathematics
publication_identifier:
issn:
- 0003-486X
publication_status: published
publisher: Princeton University Press
quality_controlled: '1'
status: public
title: Stretched exponential estimates on growth of the number of periodic points
for prevalent diffeomorphisms I
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 165
year: '2007'
...
---
_id: '860'
abstract:
- lang: eng
text: We identified a mutation in the CRYGD gene (P23S) of the γ-crystallin gene
cluster that is associated with a polymorphic congenital cataract that occurs
with frequency of ∼0.3% in a human population. To gain insight into the molecular
mechanism of the pathogenesis of γ-crystallin isoforms, we undertook an evolutionary
analysis of the available mammalian and newly obtained primate sequences of the
γ-crystallin genes. The cataract-associated serine at site 23 corresponds to the
ancestral state, since it was found in CRYGD of a lower primate and all the surveyed
nonprimate mammals. Crystallin proteins include two structurally similar domains,
and substitutions in mammalian CRYGD protein at site 23 of the first domain were
always associated with substitutions in the structurally reciprocal sites 109
and 136 of the second domain. These data suggest that the cataractogenic effect
of serine at site 23 in the N-terminal domain of CRYGD may be compensated indirectly
by amino acid changes in a distal domain. We also found that gene conversion was
a factor in the evolution of the γ-crystallin gene cluster throughout different
mammalian clades. The high rate of gene conversion observed between the functional
CRYGD gene and two primate γ-crystallin pseudogenes (CRYGEP1 and CRYGFP1) coupled
with a surprising finding of apparent negative selection in primate pseudogenes
suggest a deleterious impact of recently derived pseudogenes involved in gene
conversion in the γ-crystallin gene cluster.
acknowledgement: This study was supported by the Biodiversity and Dynamics of Gene
Pools program of the Presidium of the Russian Academy of Sciences (support to E.I.R.).
E.I.R. is also supported in part by the National Institute of Diabetes and Digestive
and Kidney Diseases and National Institute of Neurological Disorders and Stroke
(National Institutes of Health), and F.A.K. is supported by a National Science Foundation
graduate research fellowship.
author:
- first_name: Olga
full_name: Plotnikova, Olga V
last_name: Plotnikova
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Peter
full_name: Vlasov, Peter K
last_name: Vlasov
- first_name: Anastasia
full_name: Grigorenko, Anastasia P
last_name: Grigorenko
- first_name: Evgeny
full_name: Ginter, Evgeny K
last_name: Ginter
- first_name: Evgeny
full_name: Rogaev, Evgeny I
last_name: Rogaev
citation:
ama: Plotnikova O, Kondrashov F, Vlasov P, Grigorenko A, Ginter E, Rogaev E. Conversion
and compensatory evolution of the γ-crystallin genes and identification of a cataractogenic
mutation that reverses the sequence of the human CRYGD gene to an ancestral state.
American Journal of Human Genetics. 2007;81(1):32-43. doi:10.1086/518616
apa: Plotnikova, O., Kondrashov, F., Vlasov, P., Grigorenko, A., Ginter, E., &
Rogaev, E. (2007). Conversion and compensatory evolution of the γ-crystallin genes
and identification of a cataractogenic mutation that reverses the sequence of
the human CRYGD gene to an ancestral state. American Journal of Human Genetics.
Cell Press. https://doi.org/10.1086/518616
chicago: Plotnikova, Olga, Fyodor Kondrashov, Peter Vlasov, Anastasia Grigorenko,
Evgeny Ginter, and Evgeny Rogaev. “Conversion and Compensatory Evolution of the
γ-Crystallin Genes and Identification of a Cataractogenic Mutation That Reverses
the Sequence of the Human CRYGD Gene to an Ancestral State.” American Journal
of Human Genetics. Cell Press, 2007. https://doi.org/10.1086/518616.
ieee: O. Plotnikova, F. Kondrashov, P. Vlasov, A. Grigorenko, E. Ginter, and E.
Rogaev, “Conversion and compensatory evolution of the γ-crystallin genes and identification
of a cataractogenic mutation that reverses the sequence of the human CRYGD gene
to an ancestral state,” American Journal of Human Genetics, vol. 81, no.
1. Cell Press, pp. 32–43, 2007.
ista: Plotnikova O, Kondrashov F, Vlasov P, Grigorenko A, Ginter E, Rogaev E. 2007.
Conversion and compensatory evolution of the γ-crystallin genes and identification
of a cataractogenic mutation that reverses the sequence of the human CRYGD gene
to an ancestral state. American Journal of Human Genetics. 81(1), 32–43.
mla: Plotnikova, Olga, et al. “Conversion and Compensatory Evolution of the γ-Crystallin
Genes and Identification of a Cataractogenic Mutation That Reverses the Sequence
of the Human CRYGD Gene to an Ancestral State.” American Journal of Human Genetics,
vol. 81, no. 1, Cell Press, 2007, pp. 32–43, doi:10.1086/518616.
short: O. Plotnikova, F. Kondrashov, P. Vlasov, A. Grigorenko, E. Ginter, E. Rogaev,
American Journal of Human Genetics 81 (2007) 32–43.
date_created: 2018-12-11T11:48:53Z
date_published: 2007-07-01T00:00:00Z
date_updated: 2021-01-12T08:20:14Z
day: '01'
doi: 10.1086/518616
extern: 1
intvolume: ' 81'
issue: '1'
month: '07'
page: 32 - 43
publication: American Journal of Human Genetics
publication_status: published
publisher: Cell Press
publist_id: '6788'
quality_controlled: 0
status: public
title: Conversion and compensatory evolution of the γ-crystallin genes and identification
of a cataractogenic mutation that reverses the sequence of the human CRYGD gene
to an ancestral state
type: journal_article
volume: 81
year: '2007'
...
---
_id: '861'
abstract:
- lang: eng
text: 'Background: Mitochondrial tRNAs have been the subject of study for structural
biologists interested in their secondary structure characteristics, evolutionary
biologists have researched patterns of compensatory and structural evolution and
medical studies have been directed towards understanding the basis of human disease.
However, an up to date, manually curated database of mitochondrially encoded tRNAs
from higher animals is currently not available. Description: We obtained the complete
mitochondrial sequence for 277 tetrapod species from GenBank and re-annotated
all of the tRNAs based on a multiple alignment of each tRNA gene and secondary
structure prediction made independently for each tRNA. The mitochondrial (mt)
tRNA sequences and the secondary structure based multiple alignments are freely
available as Supplemental Information online. Conclusion: We compiled a manually
curated database of mitochondrially encoded tRNAs from tetrapods with completely
sequenced genomes. In the course of our work, we reannotated more than 10% of
all tetrapod mt-tRNAs and subsequently predicted the secondary structures of 6060
mitochondrial tRNAs. This carefully constructed database can be utilized to enhance
our knowledge in several different fields including the evolution of mt-tRNA secondary
structure and prediction of pathogenic mt-tRNA mutations. In addition, researchers
reporting novel mitochondrial genome sequences should check their tRNA gene annotations
against our database to ensure a higher level of fidelity of their annotation.'
acknowledgement: KYuP and LAM were supported by the Molecular and Cellular Biology
Program of the Russian Academy of Science. KYuP was supported by the Russian Fund
of Basic Research (grant 04-04-49623). LAM was partially supported by grants from
the Howard Hughes Medical Institute (55005610), INTAS (05-1000008-8028). FAK is
a National Science Foundation Graduate Research Fellow.
author:
- first_name: Konstantin
full_name: Popadin, Konstantin Yu
last_name: Popadin
- first_name: Leila
full_name: Mamirova, Leila A
last_name: Mamirova
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Popadin K, Mamirova L, Kondrashov F. A manually curated database of tetrapod
mitochondrially encoded tRNA sequences and secondary structures. BMC Bioinformatics.
2007;8. doi:10.1186/1471-2105-8-441
apa: Popadin, K., Mamirova, L., & Kondrashov, F. (2007). A manually curated
database of tetrapod mitochondrially encoded tRNA sequences and secondary structures.
BMC Bioinformatics. BioMed Central. https://doi.org/10.1186/1471-2105-8-441
chicago: Popadin, Konstantin, Leila Mamirova, and Fyodor Kondrashov. “A Manually
Curated Database of Tetrapod Mitochondrially Encoded TRNA Sequences and Secondary
Structures.” BMC Bioinformatics. BioMed Central, 2007. https://doi.org/10.1186/1471-2105-8-441.
ieee: K. Popadin, L. Mamirova, and F. Kondrashov, “A manually curated database of
tetrapod mitochondrially encoded tRNA sequences and secondary structures,” BMC
Bioinformatics, vol. 8. BioMed Central, 2007.
ista: Popadin K, Mamirova L, Kondrashov F. 2007. A manually curated database of
tetrapod mitochondrially encoded tRNA sequences and secondary structures. BMC
Bioinformatics. 8.
mla: Popadin, Konstantin, et al. “A Manually Curated Database of Tetrapod Mitochondrially
Encoded TRNA Sequences and Secondary Structures.” BMC Bioinformatics, vol.
8, BioMed Central, 2007, doi:10.1186/1471-2105-8-441.
short: K. Popadin, L. Mamirova, F. Kondrashov, BMC Bioinformatics 8 (2007).
date_created: 2018-12-11T11:48:54Z
date_published: 2007-11-14T00:00:00Z
date_updated: 2021-01-12T08:20:18Z
day: '14'
doi: 10.1186/1471-2105-8-441
extern: 1
intvolume: ' 8'
month: '11'
publication: BMC Bioinformatics
publication_status: published
publisher: BioMed Central
publist_id: '6789'
quality_controlled: 0
status: public
title: A manually curated database of tetrapod mitochondrially encoded tRNA sequences
and secondary structures
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: 8
year: '2007'
...
---
_id: '879'
abstract:
- lang: eng
text: Having an extra copy of a gene is thought to provide some functional redundancy,
which results in a higher rate of evolution in duplicated genes. In this article,
we estimate the impact of gene duplication on the selection of tuf paralogs, and
we find that in the absence of gene conversion, tuf paralogs have evolved significantly
slower than when gene conversion has been a factor in their evolution. Thus, tuf
gene copies evolve under a selective pressure that ensures their functional uniformity,
and gene conversion reduces selection against amino acid substitutions that affect
the function of the encoded protein, EF-Tu.
acknowledgement: We thank Peter Andolfatto, Doris Bachtrog, Robert Cutler, Hideki
Innan, Eugene Koonin, Alexey Kondrashov and Martin Lercher for comments on the manuscript
and for discussions on the interplay between gene conversion and selection. This
work was supported by a National Science Foundation Graduate Research Fellowship
(F.A.K.) and a Molecular and Cellular Biology RAS (Program No 10) grant (P.K.V.).
author:
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Tatiana
full_name: Gurbich, Tatiana A
last_name: Gurbich
- first_name: Peter
full_name: Vlasov, Peter K
last_name: Vlasov
citation:
ama: Kondrashov F, Gurbich T, Vlasov P. Selection for functional uniformity of tuf
duplicates in γ-proteobacteria. Trends in Genetics. 2007;23(5):215-218.
doi:10.1016/j.tig.2007.03.002
apa: Kondrashov, F., Gurbich, T., & Vlasov, P. (2007). Selection for functional
uniformity of tuf duplicates in γ-proteobacteria. Trends in Genetics. Elsevier.
https://doi.org/10.1016/j.tig.2007.03.002
chicago: Kondrashov, Fyodor, Tatiana Gurbich, and Peter Vlasov. “Selection for Functional
Uniformity of Tuf Duplicates in γ-Proteobacteria.” Trends in Genetics.
Elsevier, 2007. https://doi.org/10.1016/j.tig.2007.03.002.
ieee: F. Kondrashov, T. Gurbich, and P. Vlasov, “Selection for functional uniformity
of tuf duplicates in γ-proteobacteria,” Trends in Genetics, vol. 23, no.
5. Elsevier, pp. 215–218, 2007.
ista: Kondrashov F, Gurbich T, Vlasov P. 2007. Selection for functional uniformity
of tuf duplicates in γ-proteobacteria. Trends in Genetics. 23(5), 215–218.
mla: Kondrashov, Fyodor, et al. “Selection for Functional Uniformity of Tuf Duplicates
in γ-Proteobacteria.” Trends in Genetics, vol. 23, no. 5, Elsevier, 2007,
pp. 215–18, doi:10.1016/j.tig.2007.03.002.
short: F. Kondrashov, T. Gurbich, P. Vlasov, Trends in Genetics 23 (2007) 215–218.
date_created: 2018-12-11T11:48:59Z
date_published: 2007-05-01T00:00:00Z
date_updated: 2021-01-12T08:21:04Z
day: '01'
doi: 10.1016/j.tig.2007.03.002
extern: 1
intvolume: ' 23'
issue: '5'
month: '05'
page: 215 - 218
publication: Trends in Genetics
publication_status: published
publisher: Elsevier
publist_id: '6771'
quality_controlled: 0
status: public
title: Selection for functional uniformity of tuf duplicates in γ-proteobacteria
type: journal_article
volume: 23
year: '2007'
...
---
_id: '167'
abstract:
- lang: eng
text: This book contains research articles on Diophantine Geometry, written by participants
of a research program held at the Ennio De Giorgi Mathematical Research Center
in Pisa, Italy, during the period April – July 2005. The authors are eminent experts
in the field. Several subfields of the main topic are presented; the volume thus
is particularly useful to get a broad overview of recent research developments.
alternative_title:
- CRM Series
article_processing_charge: No
arxiv: 1
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Roger
full_name: Heath Brown, Roger
last_name: Heath Brown
citation:
ama: 'Browning TD, Heath Brown R. Simultaneous equal sums of three powers. In: Zannier
U, ed. Diophantine Geometry. Vol 4. Edizioni della Normale; 2007:93-100.'
apa: Browning, T. D., & Heath Brown, R. (2007). Simultaneous equal sums of three
powers. In U. Zannier (Ed.), Diophantine Geometry (Vol. 4, pp. 93–100).
Edizioni della Normale.
chicago: Browning, Timothy D, and Roger Heath Brown. “Simultaneous Equal Sums of
Three Powers.” In Diophantine Geometry, edited by Umberto Zannier, 4:93–100.
Edizioni della Normale, 2007.
ieee: T. D. Browning and R. Heath Brown, “Simultaneous equal sums of three powers,”
in Diophantine Geometry, vol. 4, U. Zannier, Ed. Edizioni della Normale,
2007, pp. 93–100.
ista: 'Browning TD, Heath Brown R. 2007.Simultaneous equal sums of three powers.
In: Diophantine Geometry. CRM Series, vol. 4, 93–100.'
mla: Browning, Timothy D., and Roger Heath Brown. “Simultaneous Equal Sums of Three
Powers.” Diophantine Geometry, edited by Umberto Zannier, vol. 4, Edizioni
della Normale, 2007, pp. 93–100.
short: T.D. Browning, R. Heath Brown, in:, U. Zannier (Ed.), Diophantine Geometry,
Edizioni della Normale, 2007, pp. 93–100.
date_created: 2018-12-11T11:44:59Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T06:52:24Z
day: '01'
editor:
- first_name: Umberto
full_name: Zannier, Umberto
last_name: Zannier
extern: '1'
external_id:
arxiv:
- '0509152'
intvolume: ' 4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/math/0509152
month: '01'
oa: 1
oa_version: Preprint
page: 93 - 100
publication: Diophantine Geometry
publication_status: published
publisher: Edizioni della Normale
publist_id: '7754'
quality_controlled: '1'
status: public
title: Simultaneous equal sums of three powers
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2007'
...
---
_id: '1750'
abstract:
- lang: eng
text: The authors investigate the composition profile of SiGe islands after capping
with Si to form quantum dots, using a two step etching procedure and atomic force
microscopy. Initially, the Si capping layers are removed by etching selectively
Si over Ge and then the composition of the disclosed islands is addressed by selectively
etching Ge over Si. For samples grown at 580 °C the authors show that even when
overgrowth leads to a flat Si surface and the islands undergo strong morphological
changes, a Ge-rich core region is still preserved in the dot. At high growth and
overgrowth temperatures (740 °C), the experiments show that the newly formed base
of the buried islands is more Si rich than their top. Furthermore, the authors
find that for the growth conditions used, no lateral motion takes place during
capping.
author:
- first_name: Georgios
full_name: Georgios Katsaros
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
- first_name: Mathieu
full_name: Stoffel, Mathieu
last_name: Stoffel
- first_name: Armando
full_name: Rastelli, Armando
last_name: Rastelli
- first_name: Oliver
full_name: Schmidt, Oliver G
last_name: Schmidt
- first_name: Klaus
full_name: Kern, Klaus
last_name: Kern
- first_name: Jerry
full_name: Tersoff, Jerry
last_name: Tersoff
citation:
ama: Katsaros G, Stoffel M, Rastelli A, Schmidt O, Kern K, Tersoff J. Three-dimensional
isocompositional profiles of buried SiGeSi (001) islands. Applied Physics Letters.
2007;91(1). doi:10.1063/1.2752730
apa: Katsaros, G., Stoffel, M., Rastelli, A., Schmidt, O., Kern, K., & Tersoff,
J. (2007). Three-dimensional isocompositional profiles of buried SiGeSi (001)
islands. Applied Physics Letters. American Institute of Physics. https://doi.org/10.1063/1.2752730
chicago: Katsaros, Georgios, Mathieu Stoffel, Armando Rastelli, Oliver Schmidt,
Klaus Kern, and Jerry Tersoff. “Three-Dimensional Isocompositional Profiles of
Buried SiGeSi (001) Islands.” Applied Physics Letters. American Institute
of Physics, 2007. https://doi.org/10.1063/1.2752730.
ieee: G. Katsaros, M. Stoffel, A. Rastelli, O. Schmidt, K. Kern, and J. Tersoff,
“Three-dimensional isocompositional profiles of buried SiGeSi (001) islands,”
Applied Physics Letters, vol. 91, no. 1. American Institute of Physics,
2007.
ista: Katsaros G, Stoffel M, Rastelli A, Schmidt O, Kern K, Tersoff J. 2007. Three-dimensional
isocompositional profiles of buried SiGeSi (001) islands. Applied Physics Letters.
91(1).
mla: Katsaros, Georgios, et al. “Three-Dimensional Isocompositional Profiles of
Buried SiGeSi (001) Islands.” Applied Physics Letters, vol. 91, no. 1,
American Institute of Physics, 2007, doi:10.1063/1.2752730.
short: G. Katsaros, M. Stoffel, A. Rastelli, O. Schmidt, K. Kern, J. Tersoff, Applied
Physics Letters 91 (2007).
date_created: 2018-12-11T11:53:48Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T06:52:58Z
day: '01'
doi: 10.1063/1.2752730
extern: 1
intvolume: ' 91'
issue: '1'
month: '01'
publication: Applied Physics Letters
publication_status: published
publisher: American Institute of Physics
publist_id: '5375'
quality_controlled: 0
status: public
title: Three-dimensional isocompositional profiles of buried SiGeSi (001) islands
type: journal_article
volume: 91
year: '2007'
...
---
_id: '1762'
abstract:
- lang: eng
text: In quantum information science, the phase of a wave function plays an important
role in encoding information. Although most experiments in this field rely on
dynamic effects to manipulate this information, an alternative approach is to
use geometric phase, which has been argued to have potential fault tolerance.
We demonstrated the controlled accumulation of a geometric phase, Berry's phase,
in a superconducting qubit; we manipulated the qubit geometrically by means of
microwave radiation and observed the accumulated phase in an interference experiment.
We found excellent agreement with Berry's predictions and also observed a geometry-dependent
contribution to dephasing.
acknowledgement: Supported by the EC via an Intra-European Marie Curie Fellowship
(P.J.L.), the Natural Sciences and Engineering Research Council of Canada, Canadian
Institute for Advanced Research, and Fonds Québécois de la Recherche sur la Nature
et les Technologies (A.B.), the National Security Agency under the Army Research
Office, NSF, and Yale University (D.I.S., L.F., and R.J.S.), Consiglio Nazionale
delle Ricerche–Istituto di Cibernetica, Pozzuoli, Italy (L.F.), the Ontario Research
Development Challenge Fund and Mathematics of Information Technology and Complex
Systems (J.M.G.), the Swiss National Science Foundation, and ETH Zürich
author:
- first_name: Peter
full_name: Leek, Peter J
last_name: Leek
- first_name: Johannes M
full_name: Johannes Fink
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: Alexandre
full_name: Blais, Alexandre
last_name: Blais
- first_name: R
full_name: Bianchetti, R
last_name: Bianchetti
- first_name: M
full_name: Göppl, M
last_name: Göppl
- first_name: Jay
full_name: Gambetta, Jay M
last_name: Gambetta
- first_name: David
full_name: Schuster, David I
last_name: Schuster
- first_name: Luigi
full_name: Frunzio, Luigi
last_name: Frunzio
- first_name: Robert
full_name: Schoelkopf, Robert J
last_name: Schoelkopf
- first_name: Andreas
full_name: Wallraff, Andreas
last_name: Wallraff
citation:
ama: Leek P, Fink JM, Blais A, et al. Observation of Berry’s phase in a solid-state
qubit. Science. 2007;318(5858):1889-1892. doi:10.1126/science.1149858
apa: Leek, P., Fink, J. M., Blais, A., Bianchetti, R., Göppl, M., Gambetta, J.,
… Wallraff, A. (2007). Observation of Berry’s phase in a solid-state qubit. Science.
American Association for the Advancement of Science. https://doi.org/10.1126/science.1149858
chicago: Leek, Peter, Johannes M Fink, Alexandre Blais, R Bianchetti, M Göppl, Jay
Gambetta, David Schuster, Luigi Frunzio, Robert Schoelkopf, and Andreas Wallraff.
“Observation of Berry’s Phase in a Solid-State Qubit.” Science. American
Association for the Advancement of Science, 2007. https://doi.org/10.1126/science.1149858.
ieee: P. Leek et al., “Observation of Berry’s phase in a solid-state qubit,”
Science, vol. 318, no. 5858. American Association for the Advancement of
Science, pp. 1889–1892, 2007.
ista: Leek P, Fink JM, Blais A, Bianchetti R, Göppl M, Gambetta J, Schuster D, Frunzio
L, Schoelkopf R, Wallraff A. 2007. Observation of Berry’s phase in a solid-state
qubit. Science. 318(5858), 1889–1892.
mla: Leek, Peter, et al. “Observation of Berry’s Phase in a Solid-State Qubit.”
Science, vol. 318, no. 5858, American Association for the Advancement of
Science, 2007, pp. 1889–92, doi:10.1126/science.1149858.
short: P. Leek, J.M. Fink, A. Blais, R. Bianchetti, M. Göppl, J. Gambetta, D. Schuster,
L. Frunzio, R. Schoelkopf, A. Wallraff, Science 318 (2007) 1889–1892.
date_created: 2018-12-11T11:53:52Z
date_published: 2007-12-27T00:00:00Z
date_updated: 2021-01-12T06:53:02Z
day: '27'
doi: 10.1126/science.1149858
extern: 1
intvolume: ' 318'
issue: '5858'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/0711.0218
month: '12'
oa: 1
page: 1889 - 1892
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '5360'
quality_controlled: 0
status: public
title: Observation of Berry's phase in a solid-state qubit
type: journal_article
volume: 318
year: '2007'
...