---
_id: '1044'
abstract:
- lang: eng
text: Control over all internal and external degrees of freedom of molecules at
the level of single quantum states will enable a series of fundamental studies
in physics and chemistry1,2. In particular, samples of ground-state molecules
at ultralow temperatures and high number densities will facilitate new quantum-gas
studies3 and future applications in quantum information science4. However, high
phase-space densities for molecular samples are not readily attainable because
efficient cooling techniques such as laser cooling are lacking. Here we produce
an ultracold and dense sample of molecules in a single hyperfine level of the
rovibronic ground state with each molecule individually trapped in the motional
ground state of an optical lattice well. Starting from a zero-temperature atomic
Mott-insulator state with optimized double-site occupancy6, weakly bound dimer
molecules are efficiently associated on a Feshbach resonance7 and subsequently
transferred to the rovibronic ground state by a stimulated four-photon process
with >50% efficiency. The molecules are trapped in the lattice and have a lifetime
of 8 s. Our results present a crucial step towards Bose-Einstein condensation
of ground-state molecules and, when suitably generalized to polar heteronuclear
molecules, the realization of dipolar quantum-gas phases in optical lattices8-10.
acknowledgement: We thank H. Ritsch, S. Dürr, N. Bouloufa and O. Dulieu for valuable
discussions. We are indebted to R. Grimm for generous support and to H. Häffner
for the loan of a charge-coupled camera. We gratefully acknowledge financial support
by the Austrian Ministry of Science and Research (Bundesministerium für Wissenschaft
und Forschung) and the Austrian Science Fund (Fonds zur Förderung der wissenschaftlichen
Forschung) in the form of a START prize grant and by the European Science Foundation
within the framework of the EuroQUASAR collective research project QuDeGPM and within
the framework of the EuroQUAM collective research project QuDipMol. R.H. is supported
by a Marie Curie International Incoming Fellowship within the 7th European Community
Framework Programme.
article_processing_charge: No
arxiv: 1
author:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Manfred
full_name: Mark, Manfred
last_name: Mark
- first_name: Elmar
full_name: Haller, Elmar
last_name: Haller
- first_name: Mattias
full_name: Gustavsson, Mattias
last_name: Gustavsson
- first_name: Russell
full_name: Hart, Russell
last_name: Hart
- first_name: Jesus
full_name: Aldegunde, Jesus
last_name: Aldegunde
- first_name: Jeremy
full_name: Hutson, Jeremy
last_name: Hutson
- first_name: Hanns
full_name: Nägerl, Hanns
last_name: Nägerl
citation:
ama: Danzl JG, Mark M, Haller E, et al. An ultracold high-density sample of rovibronic
ground-state molecules in an optical lattice. Nature Physics. 2010;6(4):265-270.
doi:10.1038/nphys1533
apa: Danzl, J. G., Mark, M., Haller, E., Gustavsson, M., Hart, R., Aldegunde, J.,
… Nägerl, H. (2010). An ultracold high-density sample of rovibronic ground-state
molecules in an optical lattice. Nature Physics. Nature Publishing Group.
https://doi.org/10.1038/nphys1533
chicago: Danzl, Johann G, Manfred Mark, Elmar Haller, Mattias Gustavsson, Russell
Hart, Jesus Aldegunde, Jeremy Hutson, and Hanns Nägerl. “An Ultracold High-Density
Sample of Rovibronic Ground-State Molecules in an Optical Lattice.” Nature
Physics. Nature Publishing Group, 2010. https://doi.org/10.1038/nphys1533.
ieee: J. G. Danzl et al., “An ultracold high-density sample of rovibronic
ground-state molecules in an optical lattice,” Nature Physics, vol. 6,
no. 4. Nature Publishing Group, pp. 265–270, 2010.
ista: Danzl JG, Mark M, Haller E, Gustavsson M, Hart R, Aldegunde J, Hutson J, Nägerl
H. 2010. An ultracold high-density sample of rovibronic ground-state molecules
in an optical lattice. Nature Physics. 6(4), 265–270.
mla: Danzl, Johann G., et al. “An Ultracold High-Density Sample of Rovibronic Ground-State
Molecules in an Optical Lattice.” Nature Physics, vol. 6, no. 4, Nature
Publishing Group, 2010, pp. 265–70, doi:10.1038/nphys1533.
short: J.G. Danzl, M. Mark, E. Haller, M. Gustavsson, R. Hart, J. Aldegunde, J.
Hutson, H. Nägerl, Nature Physics 6 (2010) 265–270.
date_created: 2018-12-11T11:49:51Z
date_published: 2010-04-04T00:00:00Z
date_updated: 2021-01-12T06:47:53Z
day: '04'
doi: 10.1038/nphys1533
extern: '1'
external_id:
arxiv:
- '0909.4700'
fulldoi: https://doi.org/10.1038/nphys1533
intvolume: ' 6'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/0909.4700
month: '04'
oa: 1
oa_version: Preprint
page: 265 - 270
publication: Nature Physics
publication_status: published
publisher: Nature Publishing Group
publist_id: '6345'
status: public
title: An ultracold high-density sample of rovibronic ground-state molecules in an
optical lattice
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2010'
...
---
_id: '1045'
abstract:
- lang: eng
text: We report on the observation of confinement-induced resonances in strongly
interacting quantum-gas systems with tunable interactions for one- and two-dimensional
geometry. Atom-atom scattering is substantially modified when the s-wave scattering
length approaches the length scale associated with the tight transversal confinement,
leading to characteristic loss and heating signatures. Upon introducing an anisotropy
for the transversal confinement we observe a splitting of the confinement-induced
resonance. With increasing anisotropy additional resonances appear. In the limit
of a two-dimensional system we find that one resonance persists.
acknowledgement: We thank W. Zwerger for discussions and R. Grimm for generous support.
We acknowledge funding by the Austrian Science Fund and by the European Union within
the framework of the EuroQUASAR collective research project QuDeGPM. R. H. is supported
by a Marie Curie Fellowship within FP7. P. S. acknowledges financial support by
the DFG. Financial support by the Heisenberg-Landau Program is appreciated by P. S.
and V. M.
article_processing_charge: No
arxiv: 1
author:
- first_name: Elmar
full_name: Haller, Elmar
last_name: Haller
- first_name: Manfred
full_name: Mark, Manfred
last_name: Mark
- first_name: Russell
full_name: Hart, Russell
last_name: Hart
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Lukas
full_name: Reichsöllner, Lukas
last_name: Reichsöllner
- first_name: Vladimir
full_name: Melezhik, Vladimir
last_name: Melezhik
- first_name: Peter
full_name: Schmelcher, Peter
last_name: Schmelcher
- first_name: Hanns
full_name: Nägerl, Hanns
last_name: Nägerl
citation:
ama: Haller E, Mark M, Hart R, et al. Confinement-induced resonances in low-dimensional
quantum systems. Physical Review Letters. 2010;104(15). doi:10.1103/PhysRevLett.104.153203
apa: Haller, E., Mark, M., Hart, R., Danzl, J. G., Reichsöllner, L., Melezhik, V.,
… Nägerl, H. (2010). Confinement-induced resonances in low-dimensional quantum
systems. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.104.153203
chicago: Haller, Elmar, Manfred Mark, Russell Hart, Johann G Danzl, Lukas Reichsöllner,
Vladimir Melezhik, Peter Schmelcher, and Hanns Nägerl. “Confinement-Induced Resonances
in Low-Dimensional Quantum Systems.” Physical Review Letters. American
Physical Society, 2010. https://doi.org/10.1103/PhysRevLett.104.153203.
ieee: E. Haller et al., “Confinement-induced resonances in low-dimensional
quantum systems,” Physical Review Letters, vol. 104, no. 15. American Physical
Society, 2010.
ista: Haller E, Mark M, Hart R, Danzl JG, Reichsöllner L, Melezhik V, Schmelcher
P, Nägerl H. 2010. Confinement-induced resonances in low-dimensional quantum systems.
Physical Review Letters. 104(15).
mla: Haller, Elmar, et al. “Confinement-Induced Resonances in Low-Dimensional Quantum
Systems.” Physical Review Letters, vol. 104, no. 15, American Physical
Society, 2010, doi:10.1103/PhysRevLett.104.153203.
short: E. Haller, M. Mark, R. Hart, J.G. Danzl, L. Reichsöllner, V. Melezhik, P.
Schmelcher, H. Nägerl, Physical Review Letters 104 (2010).
date_created: 2018-12-11T11:49:51Z
date_published: 2010-04-14T00:00:00Z
date_updated: 2021-01-12T06:47:53Z
day: '14'
doi: 10.1103/PhysRevLett.104.153203
extern: '1'
external_id:
arxiv:
- '1002.3795'
fulldoi: https://doi.org/10.1103/PhysRevLett.104.153203
intvolume: ' 104'
issue: '15'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1002.3795
month: '04'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '6344'
status: public
title: Confinement-induced resonances in low-dimensional quantum systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 104
year: '2010'
...
---
_id: '1046'
abstract:
- lang: eng
text: The phenomenon of matter-wave interference lies at the heart of quantum physics.
It has been observed in various contexts in the limit of non-interacting particles
as a single-particle effect. Here we observe and control matter-wave interference
whose evolution is driven by interparticle interactions. In a multi-path matter-wave
interferometer, the macroscopic manybody wave function of an interacting atomic
Bose-Einstein condensate develops a regular interference pattern, allowing us
to detect and directly visualize the effect of interaction-induced phase shifts.
We demonstrate control over the phase evolution by inhibiting interaction-induced
dephasing and by refocusing a dephased macroscopic matter wave in a spin-echo-type
experiment. Our results show that interactions in a many-body system lead to a
surprisingly coherent evolution, possibly enabling narrow-band and high-brightness
matterwave interferometers based on atom lasers.
acknowledgement: We thank E Arimondo, O Morsch, W Schleich, A Smerzi, D Witthaut and
A Buchleitner and his group for helpful discussions. We also thank R Grimm for generous
support. We gratefully acknowledge funding from the Austrian Ministry of Science
and Research (Bundesministerium für Wissenschaft und Forschung) and the Austrian
Science Fund (Fonds zur Förderung der wissenschaftlichen Forschung) in the form
of a START prize grant and through SFB 15. RH is supported by a Marie Curie International
Incoming Fellowship within the 7th European Community Framework Programme.
article_processing_charge: No
author:
- first_name: Mattias
full_name: Gustavsson, Mattias
last_name: Gustavsson
- first_name: Elmar
full_name: Haller, Elmar
last_name: Haller
- first_name: Manfred
full_name: Mark, Manfred
last_name: Mark
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Russell
full_name: Hart, Russell
last_name: Hart
- first_name: Andrew
full_name: Daley, Andrew
last_name: Daley
- first_name: Hanns
full_name: Nägerl, Hanns
last_name: Nägerl
citation:
ama: Gustavsson M, Haller E, Mark M, et al. Interference of interacting matter waves.
New Journal of Physics. 2010;12. doi:10.1088/1367-2630/12/6/065029
apa: Gustavsson, M., Haller, E., Mark, M., Danzl, J. G., Hart, R., Daley, A., &
Nägerl, H. (2010). Interference of interacting matter waves. New Journal of
Physics. IOP Publishing Ltd. https://doi.org/10.1088/1367-2630/12/6/065029
chicago: Gustavsson, Mattias, Elmar Haller, Manfred Mark, Johann G Danzl, Russell
Hart, Andrew Daley, and Hanns Nägerl. “Interference of Interacting Matter Waves.”
New Journal of Physics. IOP Publishing Ltd., 2010. https://doi.org/10.1088/1367-2630/12/6/065029.
ieee: M. Gustavsson et al., “Interference of interacting matter waves,” New
Journal of Physics, vol. 12. IOP Publishing Ltd., 2010.
ista: Gustavsson M, Haller E, Mark M, Danzl JG, Hart R, Daley A, Nägerl H. 2010.
Interference of interacting matter waves. New Journal of Physics. 12.
mla: Gustavsson, Mattias, et al. “Interference of Interacting Matter Waves.” New
Journal of Physics, vol. 12, IOP Publishing Ltd., 2010, doi:10.1088/1367-2630/12/6/065029.
short: M. Gustavsson, E. Haller, M. Mark, J.G. Danzl, R. Hart, A. Daley, H. Nägerl,
New Journal of Physics 12 (2010).
date_created: 2018-12-11T11:49:51Z
date_published: 2010-06-28T00:00:00Z
date_updated: 2021-01-12T06:47:53Z
day: '28'
doi: 10.1088/1367-2630/12/6/065029
extern: '1'
fulldoi: https://doi.org/10.1088/1367-2630/12/6/065029
intvolume: ' 12'
language:
- iso: eng
month: '06'
oa_version: None
publication: New Journal of Physics
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '6342'
status: public
title: Interference of interacting matter waves
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2010'
...
---
_id: '1047'
abstract:
- lang: eng
text: Particles in a perfect lattice potential perform Bloch oscillations when subject
to a constant force, leading to localization and preventing conductivity. For
a weakly interacting Bose-Einstein condensate of Cs atoms, we observe giant center-of-mass
oscillations in position space with a displacement across hundreds of lattice
sites when we add a periodic modulation to the force near the Bloch frequency.
We study the dependence of these "super" Bloch oscillations on lattice
depth, modulation amplitude, and modulation frequency and show that they provide
a means to induce linear transport in a dissipation-free lattice.
acknowledgement: We thank A. R. Kolovsky, A. Zenesini, and A. Wacker for discussions
and R. Grimm for generous support. We acknowledge funding by the Austrian Ministry
of Science and Research and the Austrian Science Fund and by the European Union
within the framework of the EuroQUASAR collective research project QuDeGPM. R. H.
is supported by a Marie Curie Action within FP7.
article_processing_charge: No
arxiv: 1
author:
- first_name: Elmar
full_name: Haller, Elmar
last_name: Haller
- first_name: Russell
full_name: Hart, Russell
last_name: Hart
- first_name: Manfred
full_name: Mark, Manfred
last_name: Mark
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Lukas
full_name: Reichsöllner, Lukas
last_name: Reichsöllner
- first_name: Hanns
full_name: Nägerl, Hanns
last_name: Nägerl
citation:
ama: Haller E, Hart R, Mark M, Danzl JG, Reichsöllner L, Nägerl H. Inducing transport
in a dissipation-free lattice with super bloch oscillations. Physical Review
Letters. 2010;104(20). doi:10.1103/PhysRevLett.104.200403
apa: Haller, E., Hart, R., Mark, M., Danzl, J. G., Reichsöllner, L., & Nägerl,
H. (2010). Inducing transport in a dissipation-free lattice with super bloch oscillations.
Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.104.200403
chicago: Haller, Elmar, Russell Hart, Manfred Mark, Johann G Danzl, Lukas Reichsöllner,
and Hanns Nägerl. “Inducing Transport in a Dissipation-Free Lattice with Super
Bloch Oscillations.” Physical Review Letters. American Physical Society,
2010. https://doi.org/10.1103/PhysRevLett.104.200403.
ieee: E. Haller, R. Hart, M. Mark, J. G. Danzl, L. Reichsöllner, and H. Nägerl,
“Inducing transport in a dissipation-free lattice with super bloch oscillations,”
Physical Review Letters, vol. 104, no. 20. American Physical Society, 2010.
ista: Haller E, Hart R, Mark M, Danzl JG, Reichsöllner L, Nägerl H. 2010. Inducing
transport in a dissipation-free lattice with super bloch oscillations. Physical
Review Letters. 104(20).
mla: Haller, Elmar, et al. “Inducing Transport in a Dissipation-Free Lattice with
Super Bloch Oscillations.” Physical Review Letters, vol. 104, no. 20, American
Physical Society, 2010, doi:10.1103/PhysRevLett.104.200403.
short: E. Haller, R. Hart, M. Mark, J.G. Danzl, L. Reichsöllner, H. Nägerl, Physical
Review Letters 104 (2010).
date_created: 2018-12-11T11:49:52Z
date_published: 2010-05-21T00:00:00Z
date_updated: 2021-01-12T06:47:54Z
day: '21'
doi: 10.1103/PhysRevLett.104.200403
extern: '1'
external_id:
arxiv:
- '1001.1206'
fulldoi: https://doi.org/10.1103/PhysRevLett.104.200403
intvolume: ' 104'
issue: '20'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1001.1206
month: '05'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '6343'
status: public
title: Inducing transport in a dissipation-free lattice with super bloch oscillations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 104
year: '2010'
...
---
_id: '1049'
abstract:
- lang: eng
text: Quantum many-body systems can have phase transitions even at zero temperature;
fluctuations arising from Heisenbergĝ€™s uncertainty principle, as opposed to
thermal effects, drive the system from one phase to another. Typically, during
the transition the relative strength of two competing terms in the systemĝ€™s
Hamiltonian changes across a finite critical value. A well-known example is the
Mottĝ€" Hubbard quantum phase transition from a superfluid to an insulating
phase, which has been observed for weakly interacting bosonic atomic gases. However,
for strongly interacting quantum systems confined to lower-dimensional geometry,
a novel type of quantum phase transition may be induced and driven by an arbitrarily
weak perturbation to the Hamiltonian. Here we observe such an effectĝ€"the
sineĝ€"Gordon quantum phase transition from a superfluid Luttinger liquid
to a Mott insulatorĝ€ "in a one-dimensional quantum gas of bosonic caesium
atoms with tunable interactions. For sufficiently strong interactions, the transition
is induced by adding an arbitrarily weak optical lattice commensurate with the
atomic granularity, which leads to immediate pinning of the atoms. We map out
the phase diagram and find that our measurements in the strongly interacting regime
agree well with a quantum field description based on the exactly solvable sineĝ€"Gordon
model. We trace the phase boundary all the way to the weakly interacting regime,
where we find good agreement with the predictions of the one-dimensional Boseĝ€"Hubbard
model. Our results open up the experimental study of quantum phase transitions,
criticality and transport phenomena beyond Hubbard-type models in the context
of ultracold gases.
acknowledgement: We thank W. Zwerger for discussions. We are indebted to R. Grimm
for generous support. We gratefully acknowledge funding by the Austrian Ministry
of Science and Research (Bundesministerium für Wissenschaft und Forschung) and the
Austrian Science Fund (Fonds zur Förderung der wissenschaftlichen Forschung) in
the form of a START prize grant, and by the European Union through the STREP FP7-ICT-2007-C
project NAME-QUAM (Nanodesigning of Atomic and Molecular Quantum Matter) and within
the framework of the EuroQUASAR collective research project QuDeGPM. R.H. is supported
by a Marie Curie International Incoming Fellowship within the 7th European Community
Framework Programme.
article_processing_charge: No
arxiv: 1
author:
- first_name: Elmar
full_name: Haller, Elmar
last_name: Haller
- first_name: Russell
full_name: Hart, Russell
last_name: Hart
- first_name: Manfred
full_name: Mark, Manfred
last_name: Mark
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Lukas
full_name: Reichsöllner, Lukas
last_name: Reichsöllner
- first_name: Mattias
full_name: Gustavsson, Mattias
last_name: Gustavsson
- first_name: Marcello
full_name: Dalmonte, Marcello
last_name: Dalmonte
- first_name: Guido
full_name: Pupillo, Guido
last_name: Pupillo
- first_name: Hanns
full_name: Nägerl, Hanns
last_name: Nägerl
citation:
ama: Haller E, Hart R, Mark M, et al. Pinning quantum phase transition for a Luttinger
liquid of strongly interacting bosons. Nature. 2010;466(7306):597-600.
doi:10.1038/nature09259
apa: Haller, E., Hart, R., Mark, M., Danzl, J. G., Reichsöllner, L., Gustavsson,
M., … Nägerl, H. (2010). Pinning quantum phase transition for a Luttinger liquid
of strongly interacting bosons. Nature. Nature Publishing Group. https://doi.org/10.1038/nature09259
chicago: Haller, Elmar, Russell Hart, Manfred Mark, Johann G Danzl, Lukas Reichsöllner,
Mattias Gustavsson, Marcello Dalmonte, Guido Pupillo, and Hanns Nägerl. “Pinning
Quantum Phase Transition for a Luttinger Liquid of Strongly Interacting Bosons.”
Nature. Nature Publishing Group, 2010. https://doi.org/10.1038/nature09259.
ieee: E. Haller et al., “Pinning quantum phase transition for a Luttinger
liquid of strongly interacting bosons,” Nature, vol. 466, no. 7306. Nature
Publishing Group, pp. 597–600, 2010.
ista: Haller E, Hart R, Mark M, Danzl JG, Reichsöllner L, Gustavsson M, Dalmonte
M, Pupillo G, Nägerl H. 2010. Pinning quantum phase transition for a Luttinger
liquid of strongly interacting bosons. Nature. 466(7306), 597–600.
mla: Haller, Elmar, et al. “Pinning Quantum Phase Transition for a Luttinger Liquid
of Strongly Interacting Bosons.” Nature, vol. 466, no. 7306, Nature Publishing
Group, 2010, pp. 597–600, doi:10.1038/nature09259.
short: E. Haller, R. Hart, M. Mark, J.G. Danzl, L. Reichsöllner, M. Gustavsson,
M. Dalmonte, G. Pupillo, H. Nägerl, Nature 466 (2010) 597–600.
date_created: 2018-12-11T11:49:52Z
date_published: 2010-07-29T00:00:00Z
date_updated: 2021-01-12T06:47:54Z
day: '29'
doi: 10.1038/nature09259
extern: '1'
external_id:
arxiv:
- '1004.3168'
fulldoi: https://doi.org/10.1038/nature09259
intvolume: ' 466'
issue: '7306'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1004.3168
month: '07'
oa: 1
oa_version: Preprint
page: 597 - 600
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6341'
status: public
title: Pinning quantum phase transition for a Luttinger liquid of strongly interacting
bosons
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 466
year: '2010'
...
---
_id: '758'
abstract:
- lang: eng
text: Set agreement [4] is a fundamental problem in distributed computing, in which
processes collectively choose a small subset of values from a larger set of proposals.
Set agreement has been extensively studied in both synchronous and asynchronous
systems [10,11,3,5,8,9]. Real world distributed systems, however, are neither
purely synchronous nor purely asynchronous. To describe such a system, Dwork et
al. [6] introduced the idea of partial synchrony. They assume for every execution
some (unknown) time GST (global stabilization time), after which the system is
synchronous. In a recent paper [1,2], we study the complexity of set agreement
in the context of partially synchronous systems, determining the minimum-sized
window of synchrony in which set agreement can be solved. We show that at least
⌊t/k⌋ + 2 synchronous rounds are required for k-set agreement, where t < n
is the number of crashes, and k is the agreement parameter of the set agreement
task. We then introduce an algorithm that terminates in any window of synchrony
of size at least ⌊t/k⌋ + 4 rounds. Together, these results tightly bound the inherent
price of tolerating some asynchrony.
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: Seth
full_name: Gilbert, Seth
last_name: Gilbert
- first_name: Rachid
full_name: Guerraoui, Rachid
last_name: Guerraoui
- first_name: Corentin
full_name: Travers, Corentin
last_name: Travers
citation:
ama: 'Alistarh D-A, Gilbert S, Guerraoui R, Travers C. Brief announcement: New bounds
for partially synchronous set agreement. In: Vol 6343 LNCS. Springer; 2010:404-405.
doi:10.1007/978-3-642-15763-9_40'
apa: 'Alistarh, D.-A., Gilbert, S., Guerraoui, R., & Travers, C. (2010). Brief
announcement: New bounds for partially synchronous set agreement (Vol. 6343 LNCS,
pp. 404–405). Presented at the DISC: Distributed Computing, Springer. https://doi.org/10.1007/978-3-642-15763-9_40'
chicago: 'Alistarh, Dan-Adrian, Seth Gilbert, Rachid Guerraoui, and Corentin Travers.
“Brief Announcement: New Bounds for Partially Synchronous Set Agreement,” 6343
LNCS:404–5. Springer, 2010. https://doi.org/10.1007/978-3-642-15763-9_40.'
ieee: 'D.-A. Alistarh, S. Gilbert, R. Guerraoui, and C. Travers, “Brief announcement:
New bounds for partially synchronous set agreement,” presented at the DISC: Distributed
Computing, 2010, vol. 6343 LNCS, pp. 404–405.'
ista: 'Alistarh D-A, Gilbert S, Guerraoui R, Travers C. 2010. Brief announcement:
New bounds for partially synchronous set agreement. DISC: Distributed Computing,
LNCS, vol. 6343 LNCS, 404–405.'
mla: 'Alistarh, Dan-Adrian, et al. Brief Announcement: New Bounds for Partially
Synchronous Set Agreement. Vol. 6343 LNCS, Springer, 2010, pp. 404–05, doi:10.1007/978-3-642-15763-9_40.'
short: D.-A. Alistarh, S. Gilbert, R. Guerraoui, C. Travers, in:, Springer, 2010,
pp. 404–405.
conference:
name: 'DISC: Distributed Computing'
date_created: 2018-12-11T11:48:21Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2023-02-23T13:11:26Z
day: '01'
doi: 10.1007/978-3-642-15763-9_40
extern: '1'
fulldoi: https://doi.org/10.1007/978-3-642-15763-9_40
language:
- iso: eng
month: '01'
oa_version: None
page: 404 - 405
publication_status: published
publisher: Springer
publist_id: '6899'
status: public
title: 'Brief announcement: New bounds for partially synchronous set agreement'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6343 LNCS
year: '2010'
...
---
_id: '7703'
abstract:
- lang: eng
text: By combining gene expression profiling with image registration, Tomer et al.
(2010) find that the mushroom body of the segmented worm Platynereis dumerilii
shares many features with the mammalian cerebral cortex. The authors propose that
the mushroom body and cortex evolved from the same structure in the common ancestor
of vertebrates and invertebrates.
article_processing_charge: No
article_type: original
author:
- first_name: Lora Beatrice Jaeger
full_name: Sweeney, Lora Beatrice Jaeger
id: 56BE8254-C4F0-11E9-8E45-0B23E6697425
last_name: Sweeney
orcid: 0000-0001-9242-5601
- first_name: Liqun
full_name: Luo, Liqun
last_name: Luo
citation:
ama: 'Sweeney LB, Luo L. ‘Fore brain: A hint of the ancestral cortex. Cell.
2010;142(5):679-681. doi:10.1016/j.cell.2010.08.024'
apa: 'Sweeney, L. B., & Luo, L. (2010). ‘Fore brain: A hint of the ancestral
cortex. Cell. Elsevier. https://doi.org/10.1016/j.cell.2010.08.024'
chicago: 'Sweeney, Lora B., and Liqun Luo. “‘Fore Brain: A Hint of the Ancestral
Cortex.” Cell. Elsevier, 2010. https://doi.org/10.1016/j.cell.2010.08.024.'
ieee: 'L. B. Sweeney and L. Luo, “‘Fore brain: A hint of the ancestral cortex,”
Cell, vol. 142, no. 5. Elsevier, pp. 679–681, 2010.'
ista: 'Sweeney LB, Luo L. 2010. ‘Fore brain: A hint of the ancestral cortex. Cell.
142(5), 679–681.'
mla: 'Sweeney, Lora B., and Liqun Luo. “‘Fore Brain: A Hint of the Ancestral Cortex.”
Cell, vol. 142, no. 5, Elsevier, 2010, pp. 679–81, doi:10.1016/j.cell.2010.08.024.'
short: L.B. Sweeney, L. Luo, Cell 142 (2010) 679–681.
date_created: 2020-04-30T10:36:52Z
date_published: 2010-09-03T00:00:00Z
date_updated: 2024-01-31T10:14:59Z
day: '03'
doi: 10.1016/j.cell.2010.08.024
extern: '1'
fulldoi: https://doi.org/10.1016/j.cell.2010.08.024
intvolume: ' 142'
issue: '5'
language:
- iso: eng
month: '09'
oa_version: None
page: 679-681
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: '‘Fore brain: A hint of the ancestral cortex'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 142
year: '2010'
...
---
_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'
fulldoi: https://doi.org/10.1021/ja100726a
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'
fulldoi: https://doi.org/10.1074/jbc.m109.061168
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'
fulldoi: https://doi.org/10.1016/s1874-575x(10)00310-3
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'
fulldoi: https://doi.org/10.1142/9789814304634_0017
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
fulldoi: https://doi.org/10.1038/nature09105
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
fulldoi: https://doi.org/10.1038/nature08691
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
fulldoi: https://doi.org/10.1098/rstb.2009.0286
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
fulldoi: https://doi.org/10.1186/1745-6150-5-5
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'
fulldoi: https://doi.org/10.1021/am100375w
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
fulldoi: https://doi.org/10.1038/nrg2689
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
fulldoi: https://doi.org/10.1186/1745-6150-5-68
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'
fulldoi: https://doi.org/10.1103/physrevlett.104.138302
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'
fulldoi: https://doi.org/10.1103/physrevlett.105.088304
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'
...