---
_id: '8472'
abstract:
- lang: eng
text: Characterization of protein dynamics by solid-state NMR spectroscopy requires
robust and accurate measurement protocols, which are not yet fully developed.
In this study, we investigate the backbone dynamics of microcrystalline ubiquitin
using different approaches. A rotational-echo double-resonance type (REDOR-type)
methodology allows one to accurately measure 1H−15N order parameters in highly
deuterated samples. We show that the systematic errors in the REDOR experiment
are as low as 1% or even less, giving access to accurate data for the amplitudes
of backbone mobility. Combining such dipolar-coupling-derived order parameters
with autocorrelated and cross-correlated 15N relaxation rates, we are able to
quantitate amplitudes and correlation times of backbone dynamics on picosecond
and nanosecond time scales in a residue-resolved manner. While the mobility on
picosecond time scales appears to have rather uniform amplitude throughout the
protein, we unambiguously identify and quantitate nanosecond mobility with order
parameters S2 as low as 0.8 in some regions of the protein, where nanosecond dynamics
has also been revealed in solution state. The methodology used here, a combination
of accurate dipolar-coupling measurements and different relaxation parameters,
yields details about dynamics on different time scales and can be applied to solid
protein samples such as amyloid fibrils or membrane proteins.
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: Beat H.
full_name: Meier, Beat H.
last_name: Meier
- first_name: Matthias
full_name: Ernst, Matthias
last_name: Ernst
citation:
ama: Schanda P, Meier BH, Ernst M. Quantitative analysis of protein backbone dynamics
in microcrystalline ubiquitin by solid-state NMR spectroscopy. Journal of the
American Chemical Society. 2010;132(45):15957-15967. doi:10.1021/ja100726a
apa: Schanda, P., Meier, B. H., & Ernst, M. (2010). Quantitative analysis of
protein backbone dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy.
Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja100726a
chicago: Schanda, Paul, Beat H. Meier, and Matthias Ernst. “Quantitative Analysis
of Protein Backbone Dynamics in Microcrystalline Ubiquitin by Solid-State NMR
Spectroscopy.” Journal of the American Chemical Society. American Chemical
Society, 2010. https://doi.org/10.1021/ja100726a.
ieee: P. Schanda, B. H. Meier, and M. Ernst, “Quantitative analysis of protein backbone
dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy,” Journal
of the American Chemical Society, vol. 132, no. 45. American Chemical Society,
pp. 15957–15967, 2010.
ista: Schanda P, Meier BH, Ernst M. 2010. Quantitative analysis of protein backbone
dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy. Journal
of the American Chemical Society. 132(45), 15957–15967.
mla: Schanda, Paul, et al. “Quantitative Analysis of Protein Backbone Dynamics in
Microcrystalline Ubiquitin by Solid-State NMR Spectroscopy.” Journal of the
American Chemical Society, vol. 132, no. 45, American Chemical Society, 2010,
pp. 15957–67, doi:10.1021/ja100726a.
short: P. Schanda, B.H. Meier, M. Ernst, Journal of the American Chemical Society
132 (2010) 15957–15967.
date_created: 2020-09-18T10:11:13Z
date_published: 2010-10-26T00:00:00Z
date_updated: 2021-01-12T08:19:30Z
day: '26'
doi: 10.1021/ja100726a
extern: '1'
intvolume: ' 132'
issue: '45'
language:
- iso: eng
month: '10'
oa_version: None
page: 15957-15967
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: Quantitative analysis of protein backbone dynamics in microcrystalline ubiquitin
by solid-state NMR spectroscopy
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 132
year: '2010'
...
---
_id: '8473'
abstract:
- lang: eng
text: β2-microglobulin (β2m), the light chain of class I major histocompatibility
complex, is responsible for the dialysis-related amyloidosis and, in patients
undergoing long term dialysis, the full-length and chemically unmodified β2m converts
into amyloid fibrils. The protein, belonging to the immunoglobulin superfamily,
in common to other members of this family, experiences during its folding a long-lived
intermediate associated to the trans-to-cis isomerization of Pro-32 that has been
addressed as the precursor of the amyloid fibril formation. In this respect, previous
studies on the W60G β2m mutant, showing that the lack of Trp-60 prevents fibril
formation in mild aggregating condition, prompted us to reinvestigate the refolding
kinetics of wild type and W60G β2m at atomic resolution by real-time NMR. The
analysis, conducted at ambient temperature by the band selective flip angle short
transient real-time two-dimensional NMR techniques and probing the β2m states
every 15 s, revealed a more complex folding energy landscape than previously reported
for wild type β2m, involving more than a single intermediate species, and shedding
new light into the fibrillogenic pathway. Moreover, a significant difference in
the kinetic scheme previously characterized by optical spectroscopic methods was
discovered for the W60G β2m mutant.
article_processing_charge: No
article_type: original
author:
- first_name: Alessandra
full_name: Corazza, Alessandra
last_name: Corazza
- first_name: Enrico
full_name: Rennella, Enrico
last_name: Rennella
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Maria Chiara
full_name: Mimmi, Maria Chiara
last_name: Mimmi
- first_name: Thomas
full_name: Cutuil, Thomas
last_name: Cutuil
- first_name: Sara
full_name: Raimondi, Sara
last_name: Raimondi
- first_name: Sofia
full_name: Giorgetti, Sofia
last_name: Giorgetti
- first_name: Federico
full_name: Fogolari, Federico
last_name: Fogolari
- first_name: Paolo
full_name: Viglino, Paolo
last_name: Viglino
- first_name: Lucio
full_name: Frydman, Lucio
last_name: Frydman
- first_name: Maayan
full_name: Gal, Maayan
last_name: Gal
- first_name: Vittorio
full_name: Bellotti, Vittorio
last_name: Bellotti
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
- first_name: Gennaro
full_name: Esposito, Gennaro
last_name: Esposito
citation:
ama: Corazza A, Rennella E, Schanda P, et al. Native-unlike long-lived intermediates
along the folding pathway of the amyloidogenic protein β2-Microglobulin revealed
by real-time two-dimensional NMR. Journal of Biological Chemistry. 2010;285(8):5827-5835.
doi:10.1074/jbc.m109.061168
apa: Corazza, A., Rennella, E., Schanda, P., Mimmi, M. C., Cutuil, T., Raimondi,
S., … Esposito, G. (2010). Native-unlike long-lived intermediates along the folding
pathway of the amyloidogenic protein β2-Microglobulin revealed by real-time two-dimensional
NMR. Journal of Biological Chemistry. American Society for Biochemistry
& Molecular Biology. https://doi.org/10.1074/jbc.m109.061168
chicago: Corazza, Alessandra, Enrico Rennella, Paul Schanda, Maria Chiara Mimmi,
Thomas Cutuil, Sara Raimondi, Sofia Giorgetti, et al. “Native-Unlike Long-Lived
Intermediates along the Folding Pathway of the Amyloidogenic Protein Β2-Microglobulin
Revealed by Real-Time Two-Dimensional NMR.” Journal of Biological Chemistry.
American Society for Biochemistry & Molecular Biology, 2010. https://doi.org/10.1074/jbc.m109.061168.
ieee: A. Corazza et al., “Native-unlike long-lived intermediates along the
folding pathway of the amyloidogenic protein β2-Microglobulin revealed by real-time
two-dimensional NMR,” Journal of Biological Chemistry, vol. 285, no. 8.
American Society for Biochemistry & Molecular Biology, pp. 5827–5835, 2010.
ista: Corazza A, Rennella E, Schanda P, Mimmi MC, Cutuil T, Raimondi S, Giorgetti
S, Fogolari F, Viglino P, Frydman L, Gal M, Bellotti V, Brutscher B, Esposito
G. 2010. Native-unlike long-lived intermediates along the folding pathway of the
amyloidogenic protein β2-Microglobulin revealed by real-time two-dimensional NMR.
Journal of Biological Chemistry. 285(8), 5827–5835.
mla: Corazza, Alessandra, et al. “Native-Unlike Long-Lived Intermediates along the
Folding Pathway of the Amyloidogenic Protein Β2-Microglobulin Revealed by Real-Time
Two-Dimensional NMR.” Journal of Biological Chemistry, vol. 285, no. 8,
American Society for Biochemistry & Molecular Biology, 2010, pp. 5827–35,
doi:10.1074/jbc.m109.061168.
short: A. Corazza, E. Rennella, P. Schanda, M.C. Mimmi, T. Cutuil, S. Raimondi,
S. Giorgetti, F. Fogolari, P. Viglino, L. Frydman, M. Gal, V. Bellotti, B. Brutscher,
G. Esposito, Journal of Biological Chemistry 285 (2010) 5827–5835.
date_created: 2020-09-18T10:11:23Z
date_published: 2010-02-19T00:00:00Z
date_updated: 2021-01-12T08:19:31Z
day: '19'
doi: 10.1074/jbc.m109.061168
extern: '1'
intvolume: ' 285'
issue: '8'
keyword:
- Cell Biology
- Biochemistry
- Molecular Biology
language:
- iso: eng
month: '02'
oa_version: None
page: 5827-5835
publication: Journal of Biological Chemistry
publication_identifier:
issn:
- 0021-9258
- 1083-351X
publication_status: published
publisher: American Society for Biochemistry & Molecular Biology
quality_controlled: '1'
status: public
title: Native-unlike long-lived intermediates along the folding pathway of the amyloidogenic
protein β2-Microglobulin revealed by real-time two-dimensional NMR
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 285
year: '2010'
...
---
_id: '8506'
article_processing_charge: No
author:
- first_name: Brian R.
full_name: Hunt, Brian R.
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: 'Hunt BR, Kaloshin V. Prevalence. In: Handbook of Dynamical Systems.
Vol 3. Elsevier; 2010:43-87. doi:10.1016/s1874-575x(10)00310-3'
apa: Hunt, B. R., & Kaloshin, V. (2010). Prevalence. In Handbook of Dynamical
Systems (Vol. 3, pp. 43–87). Elsevier. https://doi.org/10.1016/s1874-575x(10)00310-3
chicago: Hunt, Brian R., and Vadim Kaloshin. “Prevalence.” In Handbook of Dynamical
Systems, 3:43–87. Elsevier, 2010. https://doi.org/10.1016/s1874-575x(10)00310-3.
ieee: B. R. Hunt and V. Kaloshin, “Prevalence,” in Handbook of Dynamical Systems,
vol. 3, Elsevier, 2010, pp. 43–87.
ista: 'Hunt BR, Kaloshin V. 2010.Prevalence. In: Handbook of Dynamical Systems.
vol. 3, 43–87.'
mla: Hunt, Brian R., and Vadim Kaloshin. “Prevalence.” Handbook of Dynamical
Systems, vol. 3, Elsevier, 2010, pp. 43–87, doi:10.1016/s1874-575x(10)00310-3.
short: B.R. Hunt, V. Kaloshin, in:, Handbook of Dynamical Systems, Elsevier, 2010,
pp. 43–87.
date_created: 2020-09-18T10:47:48Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2021-01-12T08:19:45Z
day: '01'
doi: 10.1016/s1874-575x(10)00310-3
extern: '1'
intvolume: ' 3'
language:
- iso: eng
month: '01'
oa_version: None
page: 43-87
publication: Handbook of Dynamical Systems
publication_identifier:
isbn:
- '9780444531414'
issn:
- 1874-575X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Prevalence
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2010'
...
---
_id: '8507'
abstract:
- lang: eng
text: "We study a Cr nearly integrable Hamiltonian system defined on \U0001D54B3
× ℝ3. Let and µΣ1 be the restriction of Lebesgue measure on \U0001D54B3 × ℝ3
to ∑. We prove there is a perturbation , and an orbit (q(t), p(t)): ℝ → \U0001D54B3
× ℝ3 of the Hamiltonian equation such that ."
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: KE
full_name: ZHANG, KE
last_name: ZHANG
- first_name: YONG
full_name: ZHENG, YONG
last_name: ZHENG
citation:
ama: 'Kaloshin V, ZHANG K, ZHENG Y. Almost dense orbit on energy surface. In: XVIth
International Congress on Mathematical Physics. World Scientific; 2010:314-322.
doi:10.1142/9789814304634_0017'
apa: 'Kaloshin, V., ZHANG, K., & ZHENG, Y. (2010). Almost dense orbit on energy
surface. In XVIth International Congress on Mathematical Physics (pp. 314–322).
Prague, Czech Republic: World Scientific. https://doi.org/10.1142/9789814304634_0017'
chicago: Kaloshin, Vadim, KE ZHANG, and YONG ZHENG. “Almost Dense Orbit on Energy
Surface.” In XVIth International Congress on Mathematical Physics, 314–22.
World Scientific, 2010. https://doi.org/10.1142/9789814304634_0017.
ieee: V. Kaloshin, K. ZHANG, and Y. ZHENG, “Almost dense orbit on energy surface,”
in XVIth International Congress on Mathematical Physics, Prague, Czech
Republic, 2010, pp. 314–322.
ista: Kaloshin V, ZHANG K, ZHENG Y. 2010. Almost dense orbit on energy surface.
XVIth International Congress on Mathematical Physics. International Congress on
Mathematical Physics, 314–322.
mla: Kaloshin, Vadim, et al. “Almost Dense Orbit on Energy Surface.” XVIth International
Congress on Mathematical Physics, World Scientific, 2010, pp. 314–22, doi:10.1142/9789814304634_0017.
short: V. Kaloshin, K. ZHANG, Y. ZHENG, in:, XVIth International Congress on Mathematical
Physics, World Scientific, 2010, pp. 314–322.
conference:
end_date: 2009-08-08
location: Prague, Czech Republic
name: International Congress on Mathematical Physics
start_date: 2009-08-03
date_created: 2020-09-18T10:47:56Z
date_published: 2010-03-01T00:00:00Z
date_updated: 2021-01-12T08:19:46Z
day: '01'
doi: 10.1142/9789814304634_0017
extern: '1'
language:
- iso: eng
month: '03'
oa_version: None
page: 314-322
publication: XVIth International Congress on Mathematical Physics
publication_identifier:
isbn:
- '9789814304627'
- '9789814304634'
publication_status: published
publisher: World Scientific
quality_controlled: '1'
status: public
title: Almost dense orbit on energy surface
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '857'
abstract:
- lang: eng
text: 'The need to maintain the structural and functional integrity of an evolving
protein severely restricts the repertoire of acceptable amino-acid substitutions.
However, it is not known whether these restrictions impose a global limit on how
far homologous protein sequences can diverge from each other. Here we explore
the limits of protein evolution using sequence divergence data. We formulate a
computational approach to study the rate of divergence of distant protein sequences
and measure this rate for ancient proteins, those that were present in the last
universal common ancestor. We show that ancient proteins are still diverging from
each other, indicating an ongoing expansion of the protein sequence universe.
The slow rate of this divergence is imposed by the sparseness of functional protein
sequences in sequence space and the ruggedness of the protein fitness landscape:
98 per cent of sites cannot accept an amino-acid substitution at any given moment
but a vast majority of all sites may eventually be permitted to evolve when other,
compensatory, changes occur. Thus, 3.5 × 10 9 yr has not been enough to reach
the limit of divergent evolution of proteins, and for most proteins the limit
of sequence similarity imposed by common function may not exceed that of random
sequences.'
acknowledgement: |
We thank E. Koonin, Y. Wolf, A. Lobkovsky, D. Petrov, D. Ivankov, J. Sharpe, B. Lehner, Y. Jaeger, P. Vlasov, M. Ptitsyn and M. Roytberg for discussions and A. Kondrashov for extensive feedback on our manuscript. We thank D. Tawfik for inspiring us to start the investigation of the functional limits in sequence space.
author:
- first_name: Inna
full_name: Povolotskaya, Inna
last_name: Povolotskaya
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Povolotskaya I, Kondrashov F. Sequence space and the ongoing expansion of the
protein universe. Nature. 2010;465(7300):922-926. doi:10.1038/nature09105
apa: Povolotskaya, I., & Kondrashov, F. (2010). Sequence space and the ongoing
expansion of the protein universe. Nature. Nature Publishing Group. https://doi.org/10.1038/nature09105
chicago: Povolotskaya, Inna, and Fyodor Kondrashov. “Sequence Space and the Ongoing
Expansion of the Protein Universe.” Nature. Nature Publishing Group, 2010.
https://doi.org/10.1038/nature09105.
ieee: I. Povolotskaya and F. Kondrashov, “Sequence space and the ongoing expansion
of the protein universe,” Nature, vol. 465, no. 7300. Nature Publishing
Group, pp. 922–926, 2010.
ista: Povolotskaya I, Kondrashov F. 2010. Sequence space and the ongoing expansion
of the protein universe. Nature. 465(7300), 922–926.
mla: Povolotskaya, Inna, and Fyodor Kondrashov. “Sequence Space and the Ongoing
Expansion of the Protein Universe.” Nature, vol. 465, no. 7300, Nature
Publishing Group, 2010, pp. 922–26, doi:10.1038/nature09105.
short: I. Povolotskaya, F. Kondrashov, Nature 465 (2010) 922–926.
date_created: 2018-12-11T11:48:52Z
date_published: 2010-06-17T00:00:00Z
date_updated: 2021-01-12T08:20:05Z
day: '17'
doi: 10.1038/nature09105
extern: 1
intvolume: ' 465'
issue: '7300'
month: '06'
page: 922 - 926
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6791'
quality_controlled: 0
status: public
title: Sequence space and the ongoing expansion of the protein universe
type: journal_article
volume: 465
year: '2010'
...
---
_id: '862'
abstract:
- lang: eng
text: A long-standing controversy in evolutionary biology is whether or not evolving
lineages can cross valleys on the fitness landscape that correspond to low-fitness
genotypes, which can eventually enable them to reach isolated fitness peaks1-9.
Here we study the fitness landscapes traversed by switches between different AU
and GC Watson-Crick nucleotide pairs at complementary sites of mitochondrial transfer
RNA stem regions in 83 mammalian species. We find that such Watson-Crick switches
occur 30-40 times more slowly than pairs of neutral substitutions, and that alleles
corresponding to GU and AC non-Watson-Crick intermediate states segregate within
human populations at low frequencies, similar to those of non-synonymous alleles.
Substitutions leading to a Watson-Crick switch are strongly correlated, especially
in mitochondrial tRNAs encoded on the GT-nucleotide-rich strand of the mitochondrial
genome. Using these data we estimate that a typical Watson-Crick switch involves
crossing a fitness valley of a depth of about 10-3 or even about 10-2, with AC
intermediates being slightly more deleterious than GU intermediates. This compensatory
evolution must proceed through rare intermediate variants that never reach fixation.
The ubiquitous nature of compensatory evolution in mammalian mitochondrial tRNAs
and other molecules implies that simultaneous fixation of two alleles that are
individually deleterious may be a common phenomenon at the molecular level.
acknowledgement: We thank H. Innan, M. Laessig, R. Guigo, I. Povolotskaya, D. Ivankov
and M. Breen for thoughtful discussions and critical reading of the manuscript.
author:
- first_name: Margarita
full_name: Meer, Margarita V
last_name: Meer
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
- first_name: Yael
full_name: Artzy-Randrup, Yael
last_name: Artzy Randrup
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Meer M, Kondrashov A, Artzy Randrup Y, Kondrashov F. Compensatory evolution
in mitochondrial tRNAs navigates valleys of low fitness. Nature. 2010;464(7286):279-282.
doi:10.1038/nature08691
apa: Meer, M., Kondrashov, A., Artzy Randrup, Y., & Kondrashov, F. (2010). Compensatory
evolution in mitochondrial tRNAs navigates valleys of low fitness. Nature.
Nature Publishing Group. https://doi.org/10.1038/nature08691
chicago: Meer, Margarita, Alexey Kondrashov, Yael Artzy Randrup, and Fyodor Kondrashov.
“Compensatory Evolution in Mitochondrial TRNAs Navigates Valleys of Low Fitness.”
Nature. Nature Publishing Group, 2010. https://doi.org/10.1038/nature08691.
ieee: M. Meer, A. Kondrashov, Y. Artzy Randrup, and F. Kondrashov, “Compensatory
evolution in mitochondrial tRNAs navigates valleys of low fitness,” Nature,
vol. 464, no. 7286. Nature Publishing Group, pp. 279–282, 2010.
ista: Meer M, Kondrashov A, Artzy Randrup Y, Kondrashov F. 2010. Compensatory evolution
in mitochondrial tRNAs navigates valleys of low fitness. Nature. 464(7286), 279–282.
mla: Meer, Margarita, et al. “Compensatory Evolution in Mitochondrial TRNAs Navigates
Valleys of Low Fitness.” Nature, vol. 464, no. 7286, Nature Publishing
Group, 2010, pp. 279–82, doi:10.1038/nature08691.
short: M. Meer, A. Kondrashov, Y. Artzy Randrup, F. Kondrashov, Nature 464 (2010)
279–282.
date_created: 2018-12-11T11:48:54Z
date_published: 2010-03-11T00:00:00Z
date_updated: 2021-01-12T08:20:20Z
day: '11'
doi: 10.1038/nature08691
extern: 1
intvolume: ' 464'
issue: '7286'
month: '03'
page: 279 - 282
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6784'
quality_controlled: 0
status: public
title: Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness
type: journal_article
volume: 464
year: '2010'
...
---
_id: '872'
abstract:
- lang: eng
text: The rate of spontaneous mutation in natural populations is a fundamental parameter
for many evolutionary phenomena. Because the rate of mutation is generally low,
most of what is currently known about mutation has been obtained through indirect,
complex and imprecise methodological approaches. However, in the past few years
genome-wide sequencing of closely related individuals has made it possible to
estimate the rates of mutation directly at the level of the DNA, avoiding most
of the problems associated with using indirect methods. Here, we review the methods
used in the past with an emphasis on next generation sequencing, which may soon
make the accurate measurement of spontaneous mutation rates a matter of routine.
author:
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
citation:
ama: Kondrashov F, Kondrashov A. Measurements of spontaneous rates of mutations
in the recent past and the near future. Philosophical Transactions of the Royal
Society of London Series B, Biological Sciences. 2010;365(1544):1169-1176.
doi:10.1098/rstb.2009.0286
apa: Kondrashov, F., & Kondrashov, A. (2010). Measurements of spontaneous rates
of mutations in the recent past and the near future. Philosophical Transactions
of the Royal Society of London. Series B, Biological Sciences. Royal Society,
The. https://doi.org/10.1098/rstb.2009.0286
chicago: Kondrashov, Fyodor, and Alexey Kondrashov. “Measurements of Spontaneous
Rates of Mutations in the Recent Past and the near Future.” Philosophical Transactions
of the Royal Society of London. Series B, Biological Sciences. Royal Society,
The, 2010. https://doi.org/10.1098/rstb.2009.0286.
ieee: F. Kondrashov and A. Kondrashov, “Measurements of spontaneous rates of mutations
in the recent past and the near future,” Philosophical Transactions of the
Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1544.
Royal Society, The, pp. 1169–1176, 2010.
ista: Kondrashov F, Kondrashov A. 2010. Measurements of spontaneous rates of mutations
in the recent past and the near future. Philosophical Transactions of the Royal
Society of London. Series B, Biological Sciences. 365(1544), 1169–1176.
mla: Kondrashov, Fyodor, and Alexey Kondrashov. “Measurements of Spontaneous Rates
of Mutations in the Recent Past and the near Future.” Philosophical Transactions
of the Royal Society of London. Series B, Biological Sciences, vol. 365, no.
1544, Royal Society, The, 2010, pp. 1169–76, doi:10.1098/rstb.2009.0286.
short: F. Kondrashov, A. Kondrashov, Philosophical Transactions of the Royal Society
of London. Series B, Biological Sciences 365 (2010) 1169–1176.
date_created: 2018-12-11T11:48:57Z
date_published: 2010-04-27T00:00:00Z
date_updated: 2021-01-12T08:20:43Z
day: '27'
doi: 10.1098/rstb.2009.0286
extern: 1
intvolume: ' 365'
issue: '1544'
month: '04'
page: 1169 - 1176
publication: Philosophical Transactions of the Royal Society of London. Series B,
Biological Sciences
publication_status: published
publisher: Royal Society, The
publist_id: '6772'
quality_controlled: 0
status: public
title: Measurements of spontaneous rates of mutations in the recent past and the near
future
type: journal_article
volume: 365
year: '2010'
...
---
_id: '884'
abstract:
- lang: eng
text: 'Background: Divergence of two independently evolving sequences that originated
from a common ancestor can be described by two parameters, the asymptotic level
of divergence E and the rate r at which this level of divergence is approached.
Constant negative selection impedes allele replacements and, therefore, is routinely
assumed to decelerate sequence divergence. However, its impact on E and on r has
not been formally investigated.Results: Strong selection that favors only one
allele can make E arbitrarily small and r arbitrarily large. In contrast, in the
case of 4 possible alleles and equal mutation rates, the lowest value of r, attained
when two alleles confer equal fitnesses and the other two are strongly deleterious,
is only two times lower than its value under selective neutrality.Conclusions:
Constant selection can strongly constrain the level of sequence divergence, but
cannot reduce substantially the rate at which this level is approached. In particular,
under any constant selection the divergence of sequences that accumulated one
substitution per neutral site since their origin from the common ancestor must
already constitute at least one half of the asymptotic divergence at sites under
such selection.Reviewers: This article was reviewed by Drs. Nicolas Galtier, Sergei
Maslov, and Nick Grishin.'
author:
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
- first_name: Inna
full_name: Povolotskaya, Inna
last_name: Povolotskaya
- first_name: Dmitry
full_name: Ivankov, Dmitry N
last_name: Ivankov
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Kondrashov A, Povolotskaya I, Ivankov D, Kondrashov F. Rate of sequence divergence
under constant selection. Biology Direct. 2010;5. doi:10.1186/1745-6150-5-5
apa: Kondrashov, A., Povolotskaya, I., Ivankov, D., & Kondrashov, F. (2010).
Rate of sequence divergence under constant selection. Biology Direct. BioMed
Central. https://doi.org/10.1186/1745-6150-5-5
chicago: Kondrashov, Alexey, Inna Povolotskaya, Dmitry Ivankov, and Fyodor Kondrashov.
“Rate of Sequence Divergence under Constant Selection.” Biology Direct.
BioMed Central, 2010. https://doi.org/10.1186/1745-6150-5-5.
ieee: A. Kondrashov, I. Povolotskaya, D. Ivankov, and F. Kondrashov, “Rate of sequence
divergence under constant selection,” Biology Direct, vol. 5. BioMed Central,
2010.
ista: Kondrashov A, Povolotskaya I, Ivankov D, Kondrashov F. 2010. Rate of sequence
divergence under constant selection. Biology Direct. 5.
mla: Kondrashov, Alexey, et al. “Rate of Sequence Divergence under Constant Selection.”
Biology Direct, vol. 5, BioMed Central, 2010, doi:10.1186/1745-6150-5-5.
short: A. Kondrashov, I. Povolotskaya, D. Ivankov, F. Kondrashov, Biology Direct
5 (2010).
date_created: 2018-12-11T11:49:00Z
date_published: 2010-01-21T00:00:00Z
date_updated: 2021-01-12T08:21:15Z
day: '21'
doi: 10.1186/1745-6150-5-5
extern: 1
intvolume: ' 5'
month: '01'
publication: Biology Direct
publication_status: published
publisher: BioMed Central
publist_id: '6762'
quality_controlled: 0
status: public
title: Rate of sequence divergence under constant selection
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: 5
year: '2010'
...
---
_id: '89'
abstract:
- lang: eng
text: We demonstrate the operation of a device that can produce chitosan nanoparticles
in a tunable size range from 50-300 nm with small size dispersion. A piezoelectric
oscillator operated at megahertz frequencies is used to aerosolize a solution
containing dissolved chitosan. The solvent is then evaporated from the aerosolized
droplets in a heat pipe, leaving monodisperse nanoparticles to be collected. The
nanoparticle size is controlled both by the concentration of the dissolved polymer
and by the size of the aerosol droplets that are created. Our device can be used
with any polymer or polymer/therapeutic combination that can be prepared in a
homogeneous solution and vaporized.
acknowledgement: This work was supported by the National Science Foundation under
Grants PHY-0456898 and PHY-0757989, and acknowledgment is made to the Donors of
the Petroleum Research Fund administered by the American Chemical Society for partial
support of this research.
author:
- first_name: Ian
full_name: Wright, Ian
last_name: Wright
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: Shenda
full_name: Baker, Shenda
last_name: Baker
- first_name: Tom
full_name: Donnelly, Tom
last_name: Donnelly
citation:
ama: Wright I, Higginbotham AP, Baker S, Donnelly T. Generation of nanoparticles
of controlled size using ultrasonic piezoelectric oscillators in solution. ACS
Applied Materials and Interfaces. 2010;2(8):2360-2364. doi:10.1021/am100375w
apa: Wright, I., Higginbotham, A. P., Baker, S., & Donnelly, T. (2010). Generation
of nanoparticles of controlled size using ultrasonic piezoelectric oscillators
in solution. ACS Applied Materials and Interfaces. American Chemical Society.
https://doi.org/10.1021/am100375w
chicago: Wright, Ian, Andrew P Higginbotham, Shenda Baker, and Tom Donnelly. “Generation
of Nanoparticles of Controlled Size Using Ultrasonic Piezoelectric Oscillators
in Solution.” ACS Applied Materials and Interfaces. American Chemical Society,
2010. https://doi.org/10.1021/am100375w.
ieee: I. Wright, A. P. Higginbotham, S. Baker, and T. Donnelly, “Generation of nanoparticles
of controlled size using ultrasonic piezoelectric oscillators in solution,” ACS
Applied Materials and Interfaces, vol. 2, no. 8. American Chemical Society,
pp. 2360–2364, 2010.
ista: Wright I, Higginbotham AP, Baker S, Donnelly T. 2010. Generation of nanoparticles
of controlled size using ultrasonic piezoelectric oscillators in solution. ACS
Applied Materials and Interfaces. 2(8), 2360–2364.
mla: Wright, Ian, et al. “Generation of Nanoparticles of Controlled Size Using Ultrasonic
Piezoelectric Oscillators in Solution.” ACS Applied Materials and Interfaces,
vol. 2, no. 8, American Chemical Society, 2010, pp. 2360–64, doi:10.1021/am100375w.
short: I. Wright, A.P. Higginbotham, S. Baker, T. Donnelly, ACS Applied Materials
and Interfaces 2 (2010) 2360–2364.
date_created: 2018-12-11T11:44:34Z
date_published: 2010-07-20T00:00:00Z
date_updated: 2021-01-12T08:21:17Z
day: '20'
doi: 10.1021/am100375w
extern: '1'
external_id:
pmid:
- ' 20735108'
intvolume: ' 2'
issue: '8'
language:
- iso: eng
month: '07'
oa_version: None
page: 2360 - 2364
pmid: 1
publication: ACS Applied Materials and Interfaces
publication_status: published
publisher: American Chemical Society
publist_id: '7965'
quality_controlled: '1'
status: public
title: Generation of nanoparticles of controlled size using ultrasonic piezoelectric
oscillators in solution
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2010'
...
---
_id: '891'
abstract:
- lang: eng
text: Gene duplications and their subsequent divergence play an important part in
the evolution of novel gene functions. Several models for the emergence, maintenance
and evolution of gene copies have been proposed. However, a clear consensus on
how gene duplications are fixed and maintained in genomes is lacking. Here, we
present a comprehensive classification of the models that are relevant to all
stages of the evolution of gene duplications. Each model predicts a unique combination
of evolutionary dynamics and functional properties. Setting out these predictions
is an important step towards identifying the main mechanisms that are involved
in the evolution of gene duplications.
acknowledgement: |
We thank M. Lynch for insightful comments on the manuscript.
author:
- first_name: Hideki
full_name: Innan, Hideki
last_name: Innan
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: 'Innan H, Kondrashov F. The evolution of gene duplications: Classifying and
distinguishing between models. Nature Reviews Genetics. 2010;11(2):97-108.
doi:10.1038/nrg2689'
apa: 'Innan, H., & Kondrashov, F. (2010). The evolution of gene duplications:
Classifying and distinguishing between models. Nature Reviews Genetics.
Nature Publishing Group. https://doi.org/10.1038/nrg2689'
chicago: 'Innan, Hideki, and Fyodor Kondrashov. “The Evolution of Gene Duplications:
Classifying and Distinguishing between Models.” Nature Reviews Genetics.
Nature Publishing Group, 2010. https://doi.org/10.1038/nrg2689.'
ieee: 'H. Innan and F. Kondrashov, “The evolution of gene duplications: Classifying
and distinguishing between models,” Nature Reviews Genetics, vol. 11, no.
2. Nature Publishing Group, pp. 97–108, 2010.'
ista: 'Innan H, Kondrashov F. 2010. The evolution of gene duplications: Classifying
and distinguishing between models. Nature Reviews Genetics. 11(2), 97–108.'
mla: 'Innan, Hideki, and Fyodor Kondrashov. “The Evolution of Gene Duplications:
Classifying and Distinguishing between Models.” Nature Reviews Genetics,
vol. 11, no. 2, Nature Publishing Group, 2010, pp. 97–108, doi:10.1038/nrg2689.'
short: H. Innan, F. Kondrashov, Nature Reviews Genetics 11 (2010) 97–108.
date_created: 2018-12-11T11:49:03Z
date_published: 2010-02-01T00:00:00Z
date_updated: 2021-01-12T08:21:19Z
day: '01'
doi: 10.1038/nrg2689
extern: 1
intvolume: ' 11'
issue: '2'
month: '02'
page: 97 - 108
publication: Nature Reviews Genetics
publication_status: published
publisher: Nature Publishing Group
publist_id: '6755'
quality_controlled: 0
status: public
title: 'The evolution of gene duplications: Classifying and distinguishing between
models'
type: journal_article
volume: 11
year: '2010'
...
---
_id: '901'
abstract:
- lang: eng
text: 'Background: Surveying deleterious variation in human populations is crucial
for our understanding, diagnosis and potential treatment of human genetic pathologies.
A number of recent genome-wide analyses focused on the prevalence of segregating
deleterious alleles in the nuclear genome. However, such studies have not been
conducted for the mitochondrial genome.Results: We present a systematic survey
of polymorphisms in the human mitochondrial genome, including those predicted
to be deleterious and those that correspond to known pathogenic mutations. Analyzing
4458 completely sequenced mitochondrial genomes we characterize the genetic diversity
of different types of single nucleotide polymorphisms (SNPs) in African (L haplotypes)
and non-African (M and N haplotypes) populations. We find that the overall level
of polymorphism is higher in the mitochondrial compared to the nuclear genome,
although the mitochondrial genome appears to be under stronger selection as indicated
by proportionally fewer nonsynonymous than synonymous substitutions. The African
mitochondrial genomes show higher heterozygosity, a greater number of polymorphic
sites and higher frequencies of polymorphisms for synonymous, benign and damaging
polymorphism than non-African genomes. However, African genomes carry significantly
fewer SNPs that have been previously characterized as pathogenic compared to non-African
genomes.Conclusions: Finding SNPs classified as pathogenic to be the only category
of polymorphisms that are more abundant in non-African genomes is best explained
by a systematic ascertainment bias that favours the discovery of pathogenic polymorphisms
segregating in non-African populations. This further suggests that, contrary to
the common disease-common variant hypothesis, pathogenic mutations are largely
population-specific and different SNPs may be associated with the same disease
in different populations. Therefore, to obtain a comprehensive picture of the
deleterious variability in the human population, as well as to improve the diagnostics
of individuals carrying African mitochondrial haplotypes, it is necessary to survey
different populations independently.Reviewers: This article was reviewed by Dr
Mikhail Gelfand, Dr Vasily Ramensky (nominated by Dr Eugene Koonin) and Dr David
Rand (nominated by Dr Laurence Hurst).'
acknowledgement: We thank Ivan Adzhubei and Shamil Sunyaev for extensive assistance
with PolyPhen 2 and insightful discussion. We thank the Spanish Ministry of Science
and Innovation, Plan Nacional Program grant BFU2009-09271 for funding.
author:
- first_name: Michael
full_name: Breen, Michael S
last_name: Breen
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Breen M, Kondrashov F. Mitochondrial pathogenic mutations are population-specific.
Biology Direct. 2010;5. doi:10.1186/1745-6150-5-68
apa: Breen, M., & Kondrashov, F. (2010). Mitochondrial pathogenic mutations
are population-specific. Biology Direct. BioMed Central. https://doi.org/10.1186/1745-6150-5-68
chicago: Breen, Michael, and Fyodor Kondrashov. “Mitochondrial Pathogenic Mutations
Are Population-Specific.” Biology Direct. BioMed Central, 2010. https://doi.org/10.1186/1745-6150-5-68.
ieee: M. Breen and F. Kondrashov, “Mitochondrial pathogenic mutations are population-specific,”
Biology Direct, vol. 5. BioMed Central, 2010.
ista: Breen M, Kondrashov F. 2010. Mitochondrial pathogenic mutations are population-specific.
Biology Direct. 5.
mla: Breen, Michael, and Fyodor Kondrashov. “Mitochondrial Pathogenic Mutations
Are Population-Specific.” Biology Direct, vol. 5, BioMed Central, 2010,
doi:10.1186/1745-6150-5-68.
short: M. Breen, F. Kondrashov, Biology Direct 5 (2010).
date_created: 2018-12-11T11:49:06Z
date_published: 2010-12-31T00:00:00Z
date_updated: 2021-01-12T08:21:46Z
day: '31'
doi: 10.1186/1745-6150-5-68
extern: 1
intvolume: ' 5'
month: '12'
publication: Biology Direct
publication_status: published
publisher: BioMed Central
publist_id: '6749'
quality_controlled: 0
status: public
title: Mitochondrial pathogenic mutations are population-specific
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: 5
year: '2010'
...
---
_id: '9012'
abstract:
- lang: eng
text: In this Letter, we characterize experimentally the diffusiophoretic motion
of colloids and λ-DNA toward higher concentration of solutes, using microfluidic
technology to build spatially and temporally controlled concentration gradients.
We then demonstrate that segregation and spatial patterning of the particles can
be achieved from temporal variations of the solute concentration profile. This
segregation takes the form of a strong trapping potential, stemming from an osmotically
induced rectification mechanism of the solute time-dependent variations. Depending
on the spatial and temporal symmetry of the solute signal, localization patterns
with various shapes can be achieved. These results highlight the role of solute
contrasts in out-of-equilibrium processes occurring in soft matter.
article_number: '138302'
article_processing_charge: No
article_type: letter_note
arxiv: 1
author:
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
- first_name: Benjamin
full_name: Abécassis, Benjamin
last_name: Abécassis
- first_name: Cécile
full_name: Cottin-Bizonne, Cécile
last_name: Cottin-Bizonne
- first_name: Christophe
full_name: Ybert, Christophe
last_name: Ybert
- first_name: Lydéric
full_name: Bocquet, Lydéric
last_name: Bocquet
citation:
ama: Palacci JA, Abécassis B, Cottin-Bizonne C, Ybert C, Bocquet L. Colloidal motility
and pattern formation under rectified diffusiophoresis. Physical Review Letters.
2010;104(13). doi:10.1103/physrevlett.104.138302
apa: Palacci, J. A., Abécassis, B., Cottin-Bizonne, C., Ybert, C., & Bocquet,
L. (2010). Colloidal motility and pattern formation under rectified diffusiophoresis.
Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.104.138302
chicago: Palacci, Jérémie A, Benjamin Abécassis, Cécile Cottin-Bizonne, Christophe
Ybert, and Lydéric Bocquet. “Colloidal Motility and Pattern Formation under Rectified
Diffusiophoresis.” Physical Review Letters. American Physical Society,
2010. https://doi.org/10.1103/physrevlett.104.138302.
ieee: J. A. Palacci, B. Abécassis, C. Cottin-Bizonne, C. Ybert, and L. Bocquet,
“Colloidal motility and pattern formation under rectified diffusiophoresis,” Physical
Review Letters, vol. 104, no. 13. American Physical Society, 2010.
ista: Palacci JA, Abécassis B, Cottin-Bizonne C, Ybert C, Bocquet L. 2010. Colloidal
motility and pattern formation under rectified diffusiophoresis. Physical Review
Letters. 104(13), 138302.
mla: Palacci, Jérémie A., et al. “Colloidal Motility and Pattern Formation under
Rectified Diffusiophoresis.” Physical Review Letters, vol. 104, no. 13,
138302, American Physical Society, 2010, doi:10.1103/physrevlett.104.138302.
short: J.A. Palacci, B. Abécassis, C. Cottin-Bizonne, C. Ybert, L. Bocquet, Physical
Review Letters 104 (2010).
date_created: 2021-01-19T10:25:04Z
date_published: 2010-04-02T00:00:00Z
date_updated: 2023-02-23T13:46:40Z
day: '02'
doi: 10.1103/physrevlett.104.138302
extern: '1'
external_id:
arxiv:
- '1004.1256 '
pmid:
- '20481918'
intvolume: ' 104'
issue: '13'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1004.1256
month: '04'
oa: 1
oa_version: Preprint
pmid: 1
publication: Physical Review Letters
publication_identifier:
eissn:
- '10797114'
issn:
- '00319007'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Colloidal motility and pattern formation under rectified diffusiophoresis
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 104
year: '2010'
...
---
_id: '9013'
abstract:
- lang: eng
text: In this Letter, we investigate experimentally the nonequilibrium steady state
of an active colloidal suspension under gravity field. The active particles are
made of chemically powered colloids, showing self propulsion in the presence of
an added fuel, here hydrogen peroxide. The active suspension is studied in a dedicated
microfluidic device, made of permeable gel microstructures. Both the microdynamics
of individual colloids and the global stationary state of the suspension under
gravity are measured with optical microscopy. This yields a direct measurement
of the effective temperature of the active system as a function of the particle
activity, on the basis of the fluctuation-dissipation relationship. Our work is
a first step in the experimental exploration of the out-of-equilibrium properties
of active colloidal systems.
article_number: '088304'
article_processing_charge: No
article_type: letter_note
arxiv: 1
author:
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
- first_name: Cécile
full_name: Cottin-Bizonne, Cécile
last_name: Cottin-Bizonne
- first_name: Christophe
full_name: Ybert, Christophe
last_name: Ybert
- first_name: Lydéric
full_name: Bocquet, Lydéric
last_name: Bocquet
citation:
ama: Palacci JA, Cottin-Bizonne C, Ybert C, Bocquet L. Sedimentation and effective
temperature of active colloidal suspensions. Physical Review Letters. 2010;105(8).
doi:10.1103/physrevlett.105.088304
apa: Palacci, J. A., Cottin-Bizonne, C., Ybert, C., & Bocquet, L. (2010). Sedimentation
and effective temperature of active colloidal suspensions. Physical Review
Letters. American Physical Society . https://doi.org/10.1103/physrevlett.105.088304
chicago: Palacci, Jérémie A, Cécile Cottin-Bizonne, Christophe Ybert, and Lydéric
Bocquet. “Sedimentation and Effective Temperature of Active Colloidal Suspensions.”
Physical Review Letters. American Physical Society , 2010. https://doi.org/10.1103/physrevlett.105.088304.
ieee: J. A. Palacci, C. Cottin-Bizonne, C. Ybert, and L. Bocquet, “Sedimentation
and effective temperature of active colloidal suspensions,” Physical Review
Letters, vol. 105, no. 8. American Physical Society , 2010.
ista: Palacci JA, Cottin-Bizonne C, Ybert C, Bocquet L. 2010. Sedimentation and
effective temperature of active colloidal suspensions. Physical Review Letters.
105(8), 088304.
mla: Palacci, Jérémie A., et al. “Sedimentation and Effective Temperature of Active
Colloidal Suspensions.” Physical Review Letters, vol. 105, no. 8, 088304,
American Physical Society , 2010, doi:10.1103/physrevlett.105.088304.
short: J.A. Palacci, C. Cottin-Bizonne, C. Ybert, L. Bocquet, Physical Review Letters
105 (2010).
date_created: 2021-01-19T10:26:33Z
date_published: 2010-08-20T00:00:00Z
date_updated: 2023-02-23T13:46:42Z
day: '20'
doi: 10.1103/physrevlett.105.088304
extern: '1'
external_id:
arxiv:
- '1004.4340'
pmid:
- '20868136'
intvolume: ' 105'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1004.4340
month: '08'
oa: 1
oa_version: Preprint
pmid: 1
publication: Physical Review Letters
publication_identifier:
eissn:
- '10797114'
issn:
- '00319007'
publication_status: published
publisher: 'American Physical Society '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sedimentation and effective temperature of active colloidal suspensions
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 105
year: '2010'
...
---
_id: '9145'
abstract:
- lang: eng
text: "We have found a new way to express the solutions of the RSM (Reynolds Stress
Model) equations that allows us to present the turbulent diffusivities for heat,
salt and momentum in a way that is considerably simpler and thus easier to implement
than in previous work. The RSM provides the dimensionless mixing efficiencies
Γα (α stands for heat, salt and momentum). However, to compute the diffusivities,
one needs additional information, specifically, the dissipation ε. Since a dynamic
equation for the latter that includes the physical processes relevant to the ocean
is still not available, one must resort to different sources of information outside
the RSM to obtain a complete Mixing Scheme usable in OGCMs.\r\nAs for the RSM
results, we show that the Γα’s are functions of both Ri and Rρ (Richardson number
and density ratio representing double diffusion, DD); the Γα are different for
heat, salt and momentum; in the case of heat, the traditional value Γh = 0.2 is
valid only in the presence of strong shear (when DD is inoperative) while when
shear subsides, NATRE data show that Γh can be three times as large, a result
that we reproduce. The salt Γs is given in terms of Γh. The momentum Γm has thus
far been guessed with different prescriptions while the RSM provides a well defined
expression for Γm(Ri, Rρ). Having tested Γh, we then test the momentum Γm by showing
that the turbulent Prandtl number Γm/Γh vs. Ri reproduces the available data quite
well.\r\n\r\nAs for the dissipation ε, we use different representations, one for
the mixed layer (ML), one for the thermocline and one for the ocean’s bottom.
For the ML, we adopt a procedure analogous to the one successfully used in PB
(planetary boundary layer) studies; for the thermocline, we employ an expression
for the variable εN−2 from studies of the internal gravity waves spectra which
includes a latitude dependence; for the ocean bottom, we adopt the enhanced bottom
diffusivity expression used by previous authors but with a state of the art internal
tidal energy formulation and replace the fixed Γα = 0.2 with the RSM result that
brings into the problem the Ri, Rρ dependence of the Γα; the unresolved bottom
drag, which has thus far been either ignored or modeled with heuristic relations,
is modeled using a formalism we previously developed and tested in PBL studies.\r\nWe
carried out several tests without an OGCM. Prandtl and flux Richardson numbers
vs. Ri. The RSM model reproduces both types of data satisfactorily. DD and Mixing
efficiency Γh(Ri, Rρ). The RSM model reproduces well the NATRE data. Bimodal ε-distribution.
NATRE data show that ε(Ri < 1) ≈ 10ε(Ri > 1), which our model reproduces. Heat
to salt flux ratio. In the Ri ≫ 1 regime, the RSM predictions reproduce the data
satisfactorily. NATRE mass diffusivity. The z-profile of the mass diffusivity
reproduces well the measurements at NATRE. The local form of the mixing scheme
is algebraic with one cubic equation to solve."
article_processing_charge: No
article_type: original
author:
- first_name: V.M.
full_name: Canuto, V.M.
last_name: Canuto
- first_name: A.M.
full_name: Howard, A.M.
last_name: Howard
- first_name: Y.
full_name: Cheng, Y.
last_name: Cheng
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
- first_name: A.
full_name: Leboissetier, A.
last_name: Leboissetier
- first_name: S.R.
full_name: Jayne, S.R.
last_name: Jayne
citation:
ama: 'Canuto VM, Howard AM, Cheng Y, Muller CJ, Leboissetier A, Jayne SR. Ocean
turbulence, III: New GISS vertical mixing scheme. Ocean Modelling. 2010;34(3-4):70-91.
doi:10.1016/j.ocemod.2010.04.006'
apa: 'Canuto, V. M., Howard, A. M., Cheng, Y., Muller, C. J., Leboissetier, A.,
& Jayne, S. R. (2010). Ocean turbulence, III: New GISS vertical mixing scheme.
Ocean Modelling. Elsevier. https://doi.org/10.1016/j.ocemod.2010.04.006'
chicago: 'Canuto, V.M., A.M. Howard, Y. Cheng, Caroline J Muller, A. Leboissetier,
and S.R. Jayne. “Ocean Turbulence, III: New GISS Vertical Mixing Scheme.” Ocean
Modelling. Elsevier, 2010. https://doi.org/10.1016/j.ocemod.2010.04.006.'
ieee: 'V. M. Canuto, A. M. Howard, Y. Cheng, C. J. Muller, A. Leboissetier, and
S. R. Jayne, “Ocean turbulence, III: New GISS vertical mixing scheme,” Ocean
Modelling, vol. 34, no. 3–4. Elsevier, pp. 70–91, 2010.'
ista: 'Canuto VM, Howard AM, Cheng Y, Muller CJ, Leboissetier A, Jayne SR. 2010.
Ocean turbulence, III: New GISS vertical mixing scheme. Ocean Modelling. 34(3–4),
70–91.'
mla: 'Canuto, V. M., et al. “Ocean Turbulence, III: New GISS Vertical Mixing Scheme.”
Ocean Modelling, vol. 34, no. 3–4, Elsevier, 2010, pp. 70–91, doi:10.1016/j.ocemod.2010.04.006.'
short: V.M. Canuto, A.M. Howard, Y. Cheng, C.J. Muller, A. Leboissetier, S.R. Jayne,
Ocean Modelling 34 (2010) 70–91.
date_created: 2021-02-15T14:40:19Z
date_published: 2010-05-12T00:00:00Z
date_updated: 2022-01-24T13:51:35Z
day: '12'
doi: 10.1016/j.ocemod.2010.04.006
extern: '1'
intvolume: ' 34'
issue: 3-4
keyword:
- Computer Science (miscellaneous)
- Geotechnical Engineering and Engineering Geology
- Atmospheric Science
- Oceanography
language:
- iso: eng
month: '05'
oa_version: None
page: 70-91
publication: Ocean Modelling
publication_identifier:
issn:
- 1463-5003
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'Ocean turbulence, III: New GISS vertical mixing scheme'
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 34
year: '2010'
...
---
_id: '9146'
abstract:
- lang: eng
text: "The factors governing the rate of change in the amount of atmospheric water
vapor are analyzed in simulations of climate change. The global-mean amount of
water vapor is estimated to increase at a differential rate of 7.3% K − 1 with
respect to global-mean surface air temperature in the multi-model mean. Larger
rates of change result if the fractional change is evaluated over a finite change
in temperature (e.g., 8.2% K − 1 for a 3 K warming), and rates of change of zonal-mean
column water vapor range from 6 to 12% K − 1 depending on latitude.\r\nClausius–Clapeyron
scaling is directly evaluated using an invariant distribution of monthly-mean
relative humidity, giving a rate of 7.4% K − 1 for global-mean water vapor. There
are deviations from Clausius–Clapeyron scaling of zonal-mean column water vapor
in the tropics and mid-latitudes, but they largely cancel in the global mean.
A purely thermodynamic scaling based on a saturated troposphere gives a higher
global rate of 7.9% K − 1.\r\nSurface specific humidity increases at a rate of
5.7% K − 1, considerably lower than the rate for global-mean water vapor. Surface
specific humidity closely follows Clausius–Clapeyron scaling over ocean. But there
are widespread decreases in surface relative humidity over land (by more than
1% K − 1 in many regions), and it is argued that decreases of this magnitude could
result from the land/ocean contrast in surface warming."
article_number: '025207'
article_processing_charge: No
article_type: original
author:
- first_name: P A
full_name: O’Gorman, P A
last_name: O’Gorman
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
citation:
ama: O’Gorman PA, Muller CJ. How closely do changes in surface and column water
vapor follow Clausius–Clapeyron scaling in climate change simulations? Environmental
Research Letters. 2010;5(2). doi:10.1088/1748-9326/5/2/025207
apa: O’Gorman, P. A., & Muller, C. J. (2010). How closely do changes in surface
and column water vapor follow Clausius–Clapeyron scaling in climate change simulations?
Environmental Research Letters. IOP Publishing. https://doi.org/10.1088/1748-9326/5/2/025207
chicago: O’Gorman, P A, and Caroline J Muller. “How Closely Do Changes in Surface
and Column Water Vapor Follow Clausius–Clapeyron Scaling in Climate Change Simulations?”
Environmental Research Letters. IOP Publishing, 2010. https://doi.org/10.1088/1748-9326/5/2/025207.
ieee: P. A. O’Gorman and C. J. Muller, “How closely do changes in surface and column
water vapor follow Clausius–Clapeyron scaling in climate change simulations?,”
Environmental Research Letters, vol. 5, no. 2. IOP Publishing, 2010.
ista: O’Gorman PA, Muller CJ. 2010. How closely do changes in surface and column
water vapor follow Clausius–Clapeyron scaling in climate change simulations? Environmental
Research Letters. 5(2), 025207.
mla: O’Gorman, P. A., and Caroline J. Muller. “How Closely Do Changes in Surface
and Column Water Vapor Follow Clausius–Clapeyron Scaling in Climate Change Simulations?”
Environmental Research Letters, vol. 5, no. 2, 025207, IOP Publishing,
2010, doi:10.1088/1748-9326/5/2/025207.
short: P.A. O’Gorman, C.J. Muller, Environmental Research Letters 5 (2010).
date_created: 2021-02-15T14:40:46Z
date_published: 2010-04-09T00:00:00Z
date_updated: 2022-01-24T13:51:02Z
day: '09'
doi: 10.1088/1748-9326/5/2/025207
extern: '1'
intvolume: ' 5'
issue: '2'
keyword:
- Renewable Energy
- Sustainability and the Environment
- Public Health
- Environmental and Occupational Health
- General Environmental Science
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1088/1748-9326/5/2/025207
month: '04'
oa: 1
oa_version: Published Version
publication: Environmental Research Letters
publication_identifier:
issn:
- 1748-9326
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
status: public
title: How closely do changes in surface and column water vapor follow Clausius–Clapeyron
scaling in climate change simulations?
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 5
year: '2010'
...
---
_id: '920'
abstract:
- lang: eng
text: Most eukaryotic cells sense and respond to the mechanical properties of their
surroundings. This can strongly influence their collective behavior in embryonic
development, tissue function, and wound healing. We use a deformable substrate
to measure collective behavior in cell motion due to substrate mediated cell-cell
interactions. We quantify spatial and temporal correlations in migration velocity
and substrate deformation, and show that cooperative cell-driven patterns of substrate
deformation mediate long-distance mechanical coupling between cells and control
collective cell migration.
acknowledgement: "This work was supported by the NSF (DMR-0602684) and the Harvard
MRSEC (DMR-0820484).\r\nWe would like to thank Dr. James Butler for helpful conversations."
article_processing_charge: No
author:
- first_name: Thomas
full_name: Angelini, Thomas
last_name: Angelini
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Xavier
full_name: Trepat, Xavier
last_name: Trepat
- first_name: Jeffrey
full_name: Fredberg, Jeffrey
last_name: Fredberg
- first_name: David
full_name: Weitz, David
last_name: Weitz
citation:
ama: Angelini T, Hannezo EB, Trepat X, Fredberg J, Weitz D. Cell migration driven
by cooperative substrate deformation patterns. Physical Review Letters.
2010;104(16). doi:10.1103/PhysRevLett.104.168104
apa: Angelini, T., Hannezo, E. B., Trepat, X., Fredberg, J., & Weitz, D. (2010).
Cell migration driven by cooperative substrate deformation patterns. Physical
Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.104.168104
chicago: Angelini, Thomas, Edouard B Hannezo, Xavier Trepat, Jeffrey Fredberg, and
David Weitz. “Cell Migration Driven by Cooperative Substrate Deformation Patterns.”
Physical Review Letters. American Physical Society, 2010. https://doi.org/10.1103/PhysRevLett.104.168104.
ieee: T. Angelini, E. B. Hannezo, X. Trepat, J. Fredberg, and D. Weitz, “Cell migration
driven by cooperative substrate deformation patterns,” Physical Review Letters,
vol. 104, no. 16. American Physical Society, 2010.
ista: Angelini T, Hannezo EB, Trepat X, Fredberg J, Weitz D. 2010. Cell migration
driven by cooperative substrate deformation patterns. Physical Review Letters.
104(16).
mla: Angelini, Thomas, et al. “Cell Migration Driven by Cooperative Substrate Deformation
Patterns.” Physical Review Letters, vol. 104, no. 16, American Physical
Society, 2010, doi:10.1103/PhysRevLett.104.168104.
short: T. Angelini, E.B. Hannezo, X. Trepat, J. Fredberg, D. Weitz, Physical Review
Letters 104 (2010).
date_created: 2018-12-11T11:49:12Z
date_published: 2010-04-23T00:00:00Z
date_updated: 2021-01-12T08:21:55Z
day: '23'
doi: 10.1103/PhysRevLett.104.168104
extern: '1'
intvolume: ' 104'
issue: '16'
language:
- iso: eng
month: '04'
oa_version: None
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '6523'
status: public
title: Cell migration driven by cooperative substrate deformation patterns
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 104
year: '2010'
...
---
_id: '7078'
abstract:
- lang: eng
text: We report resonant ultrasound spectroscopy (RUS), dilatometry/magnetostriction,
magnetotransport, magnetization, specific-heat, and 119Sn Mössbauer spectroscopy
measurements on SnTe and Sn0.995Cr0.005Te. Hall measurements at T=77 K indicate
that our Bridgman-grown single crystals have a p-type carrier concentration of
3.4×1019 cm−3 and that our Cr-doped crystals have an n-type concentration of 5.8×1022 cm−3.
Although our SnTe crystals are diamagnetic over the temperature range 2≤T≤1100 K,
the Cr-doped crystals are room-temperature ferromagnets with a Curie temperature
of 294 K. For each sample type, three-terminal capacitive dilatometry measurements
detect a subtle 0.5 μm distortion at Tc≈85 K. Whereas our RUS measurements on
SnTe show elastic hardening near the structural transition, pointing to co-elastic
behavior, similar measurements on Sn0.995Cr0.005Te show a pronounced softening,
pointing to ferroelastic behavior. Effective Debye temperature, θD, values of
SnTe obtained from 119Sn Mössbauer studies show a hardening of phonons in the
range 60–115 K (θD=162 K) as compared with the 100–300 K range (θD=150 K). In
addition, a precursor softening extending over approximately 100 K anticipates
this collapse at the critical temperature and quantitative analysis over three
decades of its reduced modulus finds ΔC44/C44=A|(T−T0)/T0|−κ with κ=0.50±0.02,
a value indicating a three-dimensional softening of phonon branches at a temperature
T0∼75 K, considerably below Tc. We suggest that the differences in these two types
of elastic behaviors lie in the absence of elastic domain-wall motion in the one
case and their nucleation in the other.
article_number: '184112'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: E. K. H.
full_name: Salje, E. K. H.
last_name: Salje
- first_name: D. J.
full_name: Safarik, D. J.
last_name: Safarik
- first_name: Kimberly A
full_name: Modic, Kimberly A
id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425
last_name: Modic
orcid: 0000-0001-9760-3147
- first_name: J. E.
full_name: Gubernatis, J. E.
last_name: Gubernatis
- first_name: J. C.
full_name: Cooley, J. C.
last_name: Cooley
- first_name: R. D.
full_name: Taylor, R. D.
last_name: Taylor
- first_name: B.
full_name: Mihaila, B.
last_name: Mihaila
- first_name: A.
full_name: Saxena, A.
last_name: Saxena
- first_name: T.
full_name: Lookman, T.
last_name: Lookman
- first_name: J. L.
full_name: Smith, J. L.
last_name: Smith
- first_name: R. A.
full_name: Fisher, R. A.
last_name: Fisher
- first_name: M.
full_name: Pasternak, M.
last_name: Pasternak
- first_name: C. P.
full_name: Opeil, C. P.
last_name: Opeil
- first_name: T.
full_name: Siegrist, T.
last_name: Siegrist
- first_name: P. B.
full_name: Littlewood, P. B.
last_name: Littlewood
- first_name: J. C.
full_name: Lashley, J. C.
last_name: Lashley
citation:
ama: 'Salje EKH, Safarik DJ, Modic KA, et al. Tin telluride: A weakly co-elastic
metal. Physical Review B. 2010;82(18). doi:10.1103/physrevb.82.184112'
apa: 'Salje, E. K. H., Safarik, D. J., Modic, K. A., Gubernatis, J. E., Cooley,
J. C., Taylor, R. D., … Lashley, J. C. (2010). Tin telluride: A weakly co-elastic
metal. Physical Review B. APS. https://doi.org/10.1103/physrevb.82.184112'
chicago: 'Salje, E. K. H., D. J. Safarik, Kimberly A Modic, J. E. Gubernatis, J.
C. Cooley, R. D. Taylor, B. Mihaila, et al. “Tin Telluride: A Weakly Co-Elastic
Metal.” Physical Review B. APS, 2010. https://doi.org/10.1103/physrevb.82.184112.'
ieee: 'E. K. H. Salje et al., “Tin telluride: A weakly co-elastic metal,”
Physical Review B, vol. 82, no. 18. APS, 2010.'
ista: 'Salje EKH, Safarik DJ, Modic KA, Gubernatis JE, Cooley JC, Taylor RD, Mihaila
B, Saxena A, Lookman T, Smith JL, Fisher RA, Pasternak M, Opeil CP, Siegrist T,
Littlewood PB, Lashley JC. 2010. Tin telluride: A weakly co-elastic metal. Physical
Review B. 82(18), 184112.'
mla: 'Salje, E. K. H., et al. “Tin Telluride: A Weakly Co-Elastic Metal.” Physical
Review B, vol. 82, no. 18, 184112, APS, 2010, doi:10.1103/physrevb.82.184112.'
short: E.K.H. Salje, D.J. Safarik, K.A. Modic, J.E. Gubernatis, J.C. Cooley, R.D.
Taylor, B. Mihaila, A. Saxena, T. Lookman, J.L. Smith, R.A. Fisher, M. Pasternak,
C.P. Opeil, T. Siegrist, P.B. Littlewood, J.C. Lashley, Physical Review B 82 (2010).
date_created: 2019-11-19T13:46:28Z
date_published: 2010-11-18T00:00:00Z
date_updated: 2021-01-12T08:11:44Z
day: '18'
doi: 10.1103/physrevb.82.184112
extern: '1'
external_id:
arxiv:
- '1011.1445'
intvolume: ' 82'
issue: '18'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1011.1445
month: '11'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
issn:
- 1098-0121
- 1550-235X
publication_status: published
publisher: APS
quality_controlled: '1'
status: public
title: 'Tin telluride: A weakly co-elastic metal'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 82
year: '2010'
...
---
_id: '7079'
abstract:
- lang: eng
text: We have observed that reacting Pb:Te:Ag:Se in a 1:1:1.9:1 molar ratio gives
rise to what appears to be a predominantly single-phase alloy, which crystallizes
in the PbSe cF8 fcc structure. However, further investigation of the structure
using energy dispersive x-ray analysis reveals the presence of two phases, PbSe
and β-Ag2Te, with identical lattice parameters. The total thermal conductivity
of the formed alloy is remarkably low for a crystalline material, κT<0.6W∕mK at
675K, it is reproducible, and in addition, the compound has good mechanical properties.
article_number: '033519'
article_processing_charge: No
article_type: original
author:
- first_name: Fivos R.
full_name: Drymiotis, Fivos R.
last_name: Drymiotis
- first_name: Tyler B.
full_name: Drye, Tyler B.
last_name: Drye
- first_name: Yisha
full_name: Wang, Yisha
last_name: Wang
- first_name: Jian
full_name: He, Jian
last_name: He
- first_name: Daniel
full_name: Rhodes, Daniel
last_name: Rhodes
- first_name: Kimberly A
full_name: Modic, Kimberly A
id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425
last_name: Modic
orcid: 0000-0001-9760-3147
- first_name: Samantha
full_name: Cawthorne, Samantha
last_name: Cawthorne
- first_name: Qiu Run
full_name: Zhang, Qiu Run
last_name: Zhang
citation:
ama: Drymiotis FR, Drye TB, Wang Y, et al. Structure formation and very low thermal
conductivity in Pb:Te:Ag:Se mixtures. Journal of Applied Physics. 2010;107(3).
doi:10.1063/1.3284946
apa: Drymiotis, F. R., Drye, T. B., Wang, Y., He, J., Rhodes, D., Modic, K. A.,
… Zhang, Q. R. (2010). Structure formation and very low thermal conductivity in
Pb:Te:Ag:Se mixtures. Journal of Applied Physics. AIP. https://doi.org/10.1063/1.3284946
chicago: Drymiotis, Fivos R., Tyler B. Drye, Yisha Wang, Jian He, Daniel Rhodes,
Kimberly A Modic, Samantha Cawthorne, and Qiu Run Zhang. “Structure Formation
and Very Low Thermal Conductivity in Pb:Te:Ag:Se Mixtures.” Journal of Applied
Physics. AIP, 2010. https://doi.org/10.1063/1.3284946.
ieee: F. R. Drymiotis et al., “Structure formation and very low thermal conductivity
in Pb:Te:Ag:Se mixtures,” Journal of Applied Physics, vol. 107, no. 3.
AIP, 2010.
ista: Drymiotis FR, Drye TB, Wang Y, He J, Rhodes D, Modic KA, Cawthorne S, Zhang
QR. 2010. Structure formation and very low thermal conductivity in Pb:Te:Ag:Se
mixtures. Journal of Applied Physics. 107(3), 033519.
mla: Drymiotis, Fivos R., et al. “Structure Formation and Very Low Thermal Conductivity
in Pb:Te:Ag:Se Mixtures.” Journal of Applied Physics, vol. 107, no. 3,
033519, AIP, 2010, doi:10.1063/1.3284946.
short: F.R. Drymiotis, T.B. Drye, Y. Wang, J. He, D. Rhodes, K.A. Modic, S. Cawthorne,
Q.R. Zhang, Journal of Applied Physics 107 (2010).
date_created: 2019-11-19T13:47:24Z
date_published: 2010-02-09T00:00:00Z
date_updated: 2021-01-12T08:11:44Z
day: '09'
doi: 10.1063/1.3284946
extern: '1'
intvolume: ' 107'
issue: '3'
language:
- iso: eng
month: '02'
oa_version: None
publication: Journal of Applied Physics
publication_identifier:
issn:
- 0021-8979
- 1089-7550
publication_status: published
publisher: AIP
quality_controlled: '1'
status: public
title: Structure formation and very low thermal conductivity in Pb:Te:Ag:Se mixtures
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 107
year: '2010'
...
---
_id: '7318'
abstract:
- lang: eng
text: The decomposition reaction of H2O2 aqueous solutions (H2O2 - H2O + 1/2O2)
catalyzed by transition metal oxide powders has been compared with the charging
voltage of nonaqueous Li-O2 cells containing the same catalyst. An inverse linear
relationship between Ln k (rate constant for the H2O2 decomposition) and the charging
voltage has been found, despite differences in media and possible mechanistic
differences. The results suggest that the decomposition may be a reliable, useful,
and fast screening tool for materials that promote the charging process of the
Li-O2 battery and may ultimately give insight into the charging mechanism.
article_number: A180
article_processing_charge: No
article_type: letter_note
author:
- first_name: V.
full_name: Giordani, V.
last_name: Giordani
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: P. G.
full_name: Bruce, P. G.
last_name: Bruce
- first_name: J.-M.
full_name: Tarascon, J.-M.
last_name: Tarascon
- first_name: D.
full_name: Larcher, D.
last_name: Larcher
citation:
ama: Giordani V, Freunberger SA, Bruce PG, Tarascon J-M, Larcher D. H2O2 decomposition
reaction as selecting tool for catalysts in Li–O2 cells. Electrochemical and
Solid-State Letters. 2010;13(12). doi:10.1149/1.3494045
apa: Giordani, V., Freunberger, S. A., Bruce, P. G., Tarascon, J.-M., & Larcher,
D. (2010). H2O2 decomposition reaction as selecting tool for catalysts in Li–O2
cells. Electrochemical and Solid-State Letters. The Electrochemical Society.
https://doi.org/10.1149/1.3494045
chicago: Giordani, V., Stefan Alexander Freunberger, P. G. Bruce, J.-M. Tarascon,
and D. Larcher. “H2O2 Decomposition Reaction as Selecting Tool for Catalysts in
Li–O2 Cells.” Electrochemical and Solid-State Letters. The Electrochemical
Society, 2010. https://doi.org/10.1149/1.3494045.
ieee: V. Giordani, S. A. Freunberger, P. G. Bruce, J.-M. Tarascon, and D. Larcher,
“H2O2 decomposition reaction as selecting tool for catalysts in Li–O2 cells,”
Electrochemical and Solid-State Letters, vol. 13, no. 12. The Electrochemical
Society, 2010.
ista: Giordani V, Freunberger SA, Bruce PG, Tarascon J-M, Larcher D. 2010. H2O2
decomposition reaction as selecting tool for catalysts in Li–O2 cells. Electrochemical
and Solid-State Letters. 13(12), A180.
mla: Giordani, V., et al. “H2O2 Decomposition Reaction as Selecting Tool for Catalysts
in Li–O2 Cells.” Electrochemical and Solid-State Letters, vol. 13, no.
12, A180, The Electrochemical Society, 2010, doi:10.1149/1.3494045.
short: V. Giordani, S.A. Freunberger, P.G. Bruce, J.-M. Tarascon, D. Larcher, Electrochemical
and Solid-State Letters 13 (2010).
date_created: 2020-01-15T12:21:06Z
date_published: 2010-10-04T00:00:00Z
date_updated: 2021-01-12T08:13:01Z
day: '04'
doi: 10.1149/1.3494045
extern: '1'
intvolume: ' 13'
issue: '12'
language:
- iso: eng
month: '10'
oa_version: None
publication: Electrochemical and Solid-State Letters
publication_identifier:
issn:
- 1099-0062
publication_status: published
publisher: The Electrochemical Society
quality_controlled: '1'
status: public
title: H2O2 decomposition reaction as selecting tool for catalysts in Li–O2 cells
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2010'
...
---
_id: '754'
abstract:
- lang: eng
text: 'Most people believe that renaming is easy: simply choose a name at random;
if more than one process selects the same name, then try again. We highlight the
issues that occur when trying to implement such a scheme and shed new light on
the read-write complexity of randomized renaming in an asynchronous environment.
At the heart of our new perspective stands an adaptive implementation of a randomized
test-and-set object, that has poly-logarithmic step complexity per operation,
with high probability. Interestingly, our implementation is anonymous, as it does
not require process identifiers. Based on this implementation, we present two
new randomized renaming algorithms. The first ensures a tight namespace of n names
using O( n log4 n) total steps, with high probability. This significantly improves
on the complexity of the best previously known namespace-optimal algorithms. The
second algorithm achieves a namespace of size k (1 + ε) using O( k log4 k / log2
(1 + ε) ) total steps, both with high probability, where k is the total contention
in the execution. It is the first adaptive randomized renaming algorithm, and
it improves on existing deterministic solutions by providing a smaller namespace,
and by lowering step complexity.'
acknowledgement: The work of Dan Alistarh is supported by the Swiss NCCR MICS project.
The work of Hagit Attiya is supported in part by the Israel Science Foundation (grant
number 953/06).
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Hagit
full_name: Attiya, Hagit
last_name: Attiya
- first_name: Seth
full_name: Gilbert, Seth
last_name: Gilbert
- first_name: Andrei
full_name: Giurgiu, Andrei
last_name: Giurgiu
- first_name: Rachid
full_name: Guerraoui, Rachid
last_name: Guerraoui
citation:
ama: 'Alistarh D-A, Attiya H, Gilbert S, Giurgiu A, Guerraoui R. Fast randomized
test-and-set and renaming. In: Vol 6343 LNCS. Springer; 2010:94-108. doi:10.1007/978-3-642-15763-9_9'
apa: 'Alistarh, D.-A., Attiya, H., Gilbert, S., Giurgiu, A., & Guerraoui, R.
(2010). Fast randomized test-and-set and renaming (Vol. 6343 LNCS, pp. 94–108).
Presented at the DISC: Distributed Computing, Springer. https://doi.org/10.1007/978-3-642-15763-9_9'
chicago: Alistarh, Dan-Adrian, Hagit Attiya, Seth Gilbert, Andrei Giurgiu, and Rachid
Guerraoui. “Fast Randomized Test-and-Set and Renaming,” 6343 LNCS:94–108. Springer,
2010. https://doi.org/10.1007/978-3-642-15763-9_9.
ieee: 'D.-A. Alistarh, H. Attiya, S. Gilbert, A. Giurgiu, and R. Guerraoui, “Fast
randomized test-and-set and renaming,” presented at the DISC: Distributed Computing,
2010, vol. 6343 LNCS, pp. 94–108.'
ista: 'Alistarh D-A, Attiya H, Gilbert S, Giurgiu A, Guerraoui R. 2010. Fast randomized
test-and-set and renaming. DISC: Distributed Computing, LNCS, vol. 6343 LNCS,
94–108.'
mla: Alistarh, Dan-Adrian, et al. Fast Randomized Test-and-Set and Renaming.
Vol. 6343 LNCS, Springer, 2010, pp. 94–108, doi:10.1007/978-3-642-15763-9_9.
short: D.-A. Alistarh, H. Attiya, S. Gilbert, A. Giurgiu, R. Guerraoui, in:, Springer,
2010, pp. 94–108.
conference:
name: 'DISC: Distributed Computing'
date_created: 2018-12-11T11:48:19Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2023-02-23T13:10:21Z
day: '01'
doi: 10.1007/978-3-642-15763-9_9
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 94 - 108
publication_status: published
publisher: Springer
publist_id: '6900'
status: public
title: Fast randomized test-and-set and renaming
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6343 LNCS
year: '2010'
...