---
_id: '14013'
abstract:
- lang: eng
text: The ultrafast motion of electrons and holes after light-matter interaction
is fundamental to a broad range of chemical and biophysical processes. We advanced
high-harmonic spectroscopy to resolve spatially and temporally the migration of
an electron hole immediately after ionization of iodoacetylene while simultaneously
demonstrating extensive control over the process. A multidimensional approach,
based on the measurement and accurate theoretical description of both even and
odd harmonic orders, enabled us to reconstruct both quantum amplitudes and phases
of the electronic states with a resolution of ~100 attoseconds. We separately
reconstructed quasi-field-free and laser-controlled charge migration as a function
of the spatial orientation of the molecule and determined the shape of the hole
created by ionization. Our technique opens the prospect of laser control over
electronic primary processes.
article_processing_charge: No
article_type: original
author:
- first_name: P. M.
full_name: Kraus, P. M.
last_name: Kraus
- first_name: B.
full_name: Mignolet, B.
last_name: Mignolet
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: A.
full_name: Rupenyan, A.
last_name: Rupenyan
- first_name: L.
full_name: Horný, L.
last_name: Horný
- first_name: E. F.
full_name: Penka, E. F.
last_name: Penka
- first_name: G.
full_name: Grassi, G.
last_name: Grassi
- first_name: O. I.
full_name: Tolstikhin, O. I.
last_name: Tolstikhin
- first_name: J.
full_name: Schneider, J.
last_name: Schneider
- first_name: F.
full_name: Jensen, F.
last_name: Jensen
- first_name: L. B.
full_name: Madsen, L. B.
last_name: Madsen
- first_name: A. D.
full_name: Bandrauk, A. D.
last_name: Bandrauk
- first_name: F.
full_name: Remacle, F.
last_name: Remacle
- first_name: H. J.
full_name: Wörner, H. J.
last_name: Wörner
citation:
ama: Kraus PM, Mignolet B, Baykusheva DR, et al. Measurement and laser control of
attosecond charge migration in ionized iodoacetylene. Science. 2015;350(6262):790-795.
doi:10.1126/science.aab2160
apa: Kraus, P. M., Mignolet, B., Baykusheva, D. R., Rupenyan, A., Horný, L., Penka,
E. F., … Wörner, H. J. (2015). Measurement and laser control of attosecond charge
migration in ionized iodoacetylene. Science. American Association for the
Advancement of Science. https://doi.org/10.1126/science.aab2160
chicago: Kraus, P. M., B. Mignolet, Denitsa Rangelova Baykusheva, A. Rupenyan, L.
Horný, E. F. Penka, G. Grassi, et al. “Measurement and Laser Control of Attosecond
Charge Migration in Ionized Iodoacetylene.” Science. American Association
for the Advancement of Science, 2015. https://doi.org/10.1126/science.aab2160.
ieee: P. M. Kraus et al., “Measurement and laser control of attosecond charge
migration in ionized iodoacetylene,” Science, vol. 350, no. 6262. American
Association for the Advancement of Science, pp. 790–795, 2015.
ista: Kraus PM, Mignolet B, Baykusheva DR, Rupenyan A, Horný L, Penka EF, Grassi
G, Tolstikhin OI, Schneider J, Jensen F, Madsen LB, Bandrauk AD, Remacle F, Wörner
HJ. 2015. Measurement and laser control of attosecond charge migration in ionized
iodoacetylene. Science. 350(6262), 790–795.
mla: Kraus, P. M., et al. “Measurement and Laser Control of Attosecond Charge Migration
in Ionized Iodoacetylene.” Science, vol. 350, no. 6262, American Association
for the Advancement of Science, 2015, pp. 790–95, doi:10.1126/science.aab2160.
short: P.M. Kraus, B. Mignolet, D.R. Baykusheva, A. Rupenyan, L. Horný, E.F. Penka,
G. Grassi, O.I. Tolstikhin, J. Schneider, F. Jensen, L.B. Madsen, A.D. Bandrauk,
F. Remacle, H.J. Wörner, Science 350 (2015) 790–795.
date_created: 2023-08-10T06:37:35Z
date_published: 2015-10-22T00:00:00Z
date_updated: 2023-08-22T08:47:39Z
day: '22'
doi: 10.1126/science.aab2160
extern: '1'
external_id:
pmid:
- '26494175'
intvolume: ' 350'
issue: '6262'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '10'
oa_version: None
page: 790-795
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Measurement and laser control of attosecond charge migration in ionized iodoacetylene
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 350
year: '2015'
...
---
_id: '14014'
abstract:
- lang: eng
text: We have studied a coupled electronic-nuclear wave packet in nitric oxide using
time-resolved strong-field photoelectron holography and rescattering. We show
that the electronic dynamics mainly appears in the holographic structures whereas
nuclear motion strongly modulates the angular distribution of the rescattered
photoelectrons.
article_number: '112135'
article_processing_charge: No
article_type: original
author:
- first_name: Samuel G
full_name: Walt, Samuel G
last_name: Walt
- first_name: N Bhargava
full_name: Ram, N Bhargava
last_name: Ram
- first_name: Aaron
full_name: von Conta, Aaron
last_name: von Conta
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: Marcos
full_name: Atala, Marcos
last_name: Atala
- first_name: Hans Jakob
full_name: Wörner, Hans Jakob
last_name: Wörner
citation:
ama: 'Walt SG, Ram NB, von Conta A, Baykusheva DR, Atala M, Wörner HJ. Resolving
the dynamics of valence-shell electrons and nuclei through laser-induced diffraction
and holography. Journal of Physics: Conference Series. 2015;635(11). doi:10.1088/1742-6596/635/11/112135'
apa: 'Walt, S. G., Ram, N. B., von Conta, A., Baykusheva, D. R., Atala, M., &
Wörner, H. J. (2015). Resolving the dynamics of valence-shell electrons and nuclei
through laser-induced diffraction and holography. Journal of Physics: Conference
Series. IOP Publishing. https://doi.org/10.1088/1742-6596/635/11/112135'
chicago: 'Walt, Samuel G, N Bhargava Ram, Aaron von Conta, Denitsa Rangelova Baykusheva,
Marcos Atala, and Hans Jakob Wörner. “Resolving the Dynamics of Valence-Shell
Electrons and Nuclei through Laser-Induced Diffraction and Holography.” Journal
of Physics: Conference Series. IOP Publishing, 2015. https://doi.org/10.1088/1742-6596/635/11/112135.'
ieee: 'S. G. Walt, N. B. Ram, A. von Conta, D. R. Baykusheva, M. Atala, and H. J.
Wörner, “Resolving the dynamics of valence-shell electrons and nuclei through
laser-induced diffraction and holography,” Journal of Physics: Conference Series,
vol. 635, no. 11. IOP Publishing, 2015.'
ista: 'Walt SG, Ram NB, von Conta A, Baykusheva DR, Atala M, Wörner HJ. 2015. Resolving
the dynamics of valence-shell electrons and nuclei through laser-induced diffraction
and holography. Journal of Physics: Conference Series. 635(11), 112135.'
mla: 'Walt, Samuel G., et al. “Resolving the Dynamics of Valence-Shell Electrons
and Nuclei through Laser-Induced Diffraction and Holography.” Journal of Physics:
Conference Series, vol. 635, no. 11, 112135, IOP Publishing, 2015, doi:10.1088/1742-6596/635/11/112135.'
short: 'S.G. Walt, N.B. Ram, A. von Conta, D.R. Baykusheva, M. Atala, H.J. Wörner,
Journal of Physics: Conference Series 635 (2015).'
date_created: 2023-08-10T06:37:44Z
date_published: 2015-11-01T00:00:00Z
date_updated: 2023-08-22T08:51:33Z
day: '01'
doi: 10.1088/1742-6596/635/11/112135
extern: '1'
intvolume: ' 635'
issue: '11'
keyword:
- General Physics and Astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1088/1742-6596/635/11/112135
month: '11'
oa: 1
oa_version: Published Version
publication: 'Journal of Physics: Conference Series'
publication_identifier:
eissn:
- 1742-6596
issn:
- 1742-6588
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Resolving the dynamics of valence-shell electrons and nuclei through laser-induced
diffraction and holography
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 635
year: '2015'
...
---
_id: '14015'
abstract:
- lang: eng
text: We advance high-harmonic spectroscopy to resolve molecular charge migration
in time and space and simultaneously demonstrate extensive control over the process.
A multidimensional approach enables us to reconstruct both quantum amplitudes
and phases with a resolution of better than 100 attoseconds and to separately
reconstruct field-free and laser- driven charge migration. Our techniques make
charge migration in molecules measurable on the attosecond time scale and open
new avenues for laser control of electronic primary processes.
article_number: '112136'
article_processing_charge: No
article_type: original
author:
- first_name: P M
full_name: Kraus, P M
last_name: Kraus
- first_name: B
full_name: Mignolet, B
last_name: Mignolet
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: A
full_name: Rupenyan, A
last_name: Rupenyan
- first_name: L
full_name: Horný, L
last_name: Horný
- first_name: E F
full_name: Penka, E F
last_name: Penka
- first_name: O I
full_name: Tolstikhin, O I
last_name: Tolstikhin
- first_name: J
full_name: Schneider, J
last_name: Schneider
- first_name: F
full_name: Jensen, F
last_name: Jensen
- first_name: L B
full_name: Madsen, L B
last_name: Madsen
- first_name: A D
full_name: Bandrauk, A D
last_name: Bandrauk
- first_name: F
full_name: Remacle, F
last_name: Remacle
- first_name: H J
full_name: Wörner, H J
last_name: Wörner
citation:
ama: 'Kraus PM, Mignolet B, Baykusheva DR, et al. Attosecond charge migration and
its laser control. Journal of Physics: Conference Series. 2015;635(11).
doi:10.1088/1742-6596/635/11/112136'
apa: 'Kraus, P. M., Mignolet, B., Baykusheva, D. R., Rupenyan, A., Horný, L., Penka,
E. F., … Wörner, H. J. (2015). Attosecond charge migration and its laser control.
Journal of Physics: Conference Series. IOP Publishing. https://doi.org/10.1088/1742-6596/635/11/112136'
chicago: 'Kraus, P M, B Mignolet, Denitsa Rangelova Baykusheva, A Rupenyan, L Horný,
E F Penka, O I Tolstikhin, et al. “Attosecond Charge Migration and Its Laser Control.”
Journal of Physics: Conference Series. IOP Publishing, 2015. https://doi.org/10.1088/1742-6596/635/11/112136.'
ieee: 'P. M. Kraus et al., “Attosecond charge migration and its laser control,”
Journal of Physics: Conference Series, vol. 635, no. 11. IOP Publishing,
2015.'
ista: 'Kraus PM, Mignolet B, Baykusheva DR, Rupenyan A, Horný L, Penka EF, Tolstikhin
OI, Schneider J, Jensen F, Madsen LB, Bandrauk AD, Remacle F, Wörner HJ. 2015.
Attosecond charge migration and its laser control. Journal of Physics: Conference
Series. 635(11), 112136.'
mla: 'Kraus, P. M., et al. “Attosecond Charge Migration and Its Laser Control.”
Journal of Physics: Conference Series, vol. 635, no. 11, 112136, IOP Publishing,
2015, doi:10.1088/1742-6596/635/11/112136.'
short: 'P.M. Kraus, B. Mignolet, D.R. Baykusheva, A. Rupenyan, L. Horný, E.F. Penka,
O.I. Tolstikhin, J. Schneider, F. Jensen, L.B. Madsen, A.D. Bandrauk, F. Remacle,
H.J. Wörner, Journal of Physics: Conference Series 635 (2015).'
date_created: 2023-08-10T06:37:53Z
date_published: 2015-07-01T00:00:00Z
date_updated: 2023-08-22T08:49:14Z
day: '01'
doi: 10.1088/1742-6596/635/11/112136
extern: '1'
intvolume: ' 635'
issue: '11'
keyword:
- General Physics and Astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1088/1742-6596/635/11/112136
month: '07'
oa: 1
oa_version: Published Version
publication: 'Journal of Physics: Conference Series'
publication_identifier:
eissn:
- 1742-6596
issn:
- 1742-6588
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Attosecond charge migration and its laser control
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 635
year: '2015'
...
---
_id: '14016'
abstract:
- lang: eng
text: All attosecond time-resolved measurements have so far relied on the use of
intense near-infrared laser pulses. In particular, attosecond streaking, laser-induced
electron diffraction and high-harmonic generation all make use of non-perturbative
light–matter interactions. Remarkably, the effect of the strong laser field on
the studied sample has often been neglected in previous studies. Here we use high-harmonic
spectroscopy to measure laser-induced modifications of the electronic structure
of molecules. We study high-harmonic spectra of spatially oriented CH3F and CH3Br
as generic examples of polar polyatomic molecules. We accurately measure intensity
ratios of even and odd-harmonic orders, and of the emission from aligned and unaligned
molecules. We show that these robust observables reveal a substantial modification
of the molecular electronic structure by the external laser field. Our insights
offer new challenges and opportunities for a range of emerging strong-field attosecond
spectroscopies.
article_number: '7039'
article_processing_charge: No
article_type: original
author:
- first_name: P. M.
full_name: Kraus, P. M.
last_name: Kraus
- first_name: O. I.
full_name: Tolstikhin, O. I.
last_name: Tolstikhin
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: A.
full_name: Rupenyan, A.
last_name: Rupenyan
- first_name: J.
full_name: Schneider, J.
last_name: Schneider
- first_name: C. Z.
full_name: Bisgaard, C. Z.
last_name: Bisgaard
- first_name: T.
full_name: Morishita, T.
last_name: Morishita
- first_name: F.
full_name: Jensen, F.
last_name: Jensen
- first_name: L. B.
full_name: Madsen, L. B.
last_name: Madsen
- first_name: H. J.
full_name: Wörner, H. J.
last_name: Wörner
citation:
ama: Kraus PM, Tolstikhin OI, Baykusheva DR, et al. Observation of laser-induced
electronic structure in oriented polyatomic molecules. Nature Communications.
2015;6. doi:10.1038/ncomms8039
apa: Kraus, P. M., Tolstikhin, O. I., Baykusheva, D. R., Rupenyan, A., Schneider,
J., Bisgaard, C. Z., … Wörner, H. J. (2015). Observation of laser-induced electronic
structure in oriented polyatomic molecules. Nature Communications. Springer
Nature. https://doi.org/10.1038/ncomms8039
chicago: Kraus, P. M., O. I. Tolstikhin, Denitsa Rangelova Baykusheva, A. Rupenyan,
J. Schneider, C. Z. Bisgaard, T. Morishita, F. Jensen, L. B. Madsen, and H. J.
Wörner. “Observation of Laser-Induced Electronic Structure in Oriented Polyatomic
Molecules.” Nature Communications. Springer Nature, 2015. https://doi.org/10.1038/ncomms8039.
ieee: P. M. Kraus et al., “Observation of laser-induced electronic structure
in oriented polyatomic molecules,” Nature Communications, vol. 6. Springer
Nature, 2015.
ista: Kraus PM, Tolstikhin OI, Baykusheva DR, Rupenyan A, Schneider J, Bisgaard
CZ, Morishita T, Jensen F, Madsen LB, Wörner HJ. 2015. Observation of laser-induced
electronic structure in oriented polyatomic molecules. Nature Communications.
6, 7039.
mla: Kraus, P. M., et al. “Observation of Laser-Induced Electronic Structure in
Oriented Polyatomic Molecules.” Nature Communications, vol. 6, 7039, Springer
Nature, 2015, doi:10.1038/ncomms8039.
short: P.M. Kraus, O.I. Tolstikhin, D.R. Baykusheva, A. Rupenyan, J. Schneider,
C.Z. Bisgaard, T. Morishita, F. Jensen, L.B. Madsen, H.J. Wörner, Nature Communications
6 (2015).
date_created: 2023-08-10T06:38:01Z
date_published: 2015-05-05T00:00:00Z
date_updated: 2023-08-22T08:52:56Z
day: '05'
doi: 10.1038/ncomms8039
extern: '1'
external_id:
pmid:
- '25940229'
intvolume: ' 6'
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/ncomms8039
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Observation of laser-induced electronic structure in oriented polyatomic molecules
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2015'
...
---
_id: '14017'
abstract:
- lang: eng
text: The detection of electron motion and electronic wave-packet dynamics is one
of the core goals of attosecond science. Recently, choosing the nitric oxide molecule
as an example, we have introduced and demonstrated an experimental approach to
measure coupled valence electronic and rotational wave packets using high-order-harmonic-generation
(HHG) spectroscopy [Kraus et al., Phys. Rev. Lett. 111, 243005 (2013)]. A short
outline of the theory to describe the combination of the pump and HHG probe process
was published together with an extensive discussion of experimental results [Baykusheva
et al., Faraday Discuss. 171, 113 (2014)]. The comparison of theory and experiment
showed good agreement on a quantitative level. Here, we present the theory in
detail, which is based on a generalized density-matrix approach that describes
the pump process and the subsequent probing of the wave packets by a semiclassical
quantitative rescattering approach. An in-depth analysis of the different Raman
scattering contributions to the creation of the coupled rotational and electronic
spin-orbit wave packets is made. We present results for parallel and perpendicular
linear polarizations of the pump and probe laser pulses. Furthermore, an analysis
of the combined rotational-electronic density matrix in terms of irreducible components
is presented that facilitates interpretation of the results.
article_number: '023421'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Song Bin
full_name: Zhang, Song Bin
last_name: Zhang
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: Peter M.
full_name: Kraus, Peter M.
last_name: Kraus
- first_name: Hans Jakob
full_name: Wörner, Hans Jakob
last_name: Wörner
- first_name: Nina
full_name: Rohringer, Nina
last_name: Rohringer
citation:
ama: Zhang SB, Baykusheva DR, Kraus PM, Wörner HJ, Rohringer N. Theoretical study
of molecular electronic and rotational coherences by high-order-harmonic generation.
Physical Review A. 2015;91(2). doi:10.1103/physreva.91.023421
apa: Zhang, S. B., Baykusheva, D. R., Kraus, P. M., Wörner, H. J., & Rohringer,
N. (2015). Theoretical study of molecular electronic and rotational coherences
by high-order-harmonic generation. Physical Review A. American Physical
Society. https://doi.org/10.1103/physreva.91.023421
chicago: Zhang, Song Bin, Denitsa Rangelova Baykusheva, Peter M. Kraus, Hans Jakob
Wörner, and Nina Rohringer. “Theoretical Study of Molecular Electronic and Rotational
Coherences by High-Order-Harmonic Generation.” Physical Review A. American
Physical Society, 2015. https://doi.org/10.1103/physreva.91.023421.
ieee: S. B. Zhang, D. R. Baykusheva, P. M. Kraus, H. J. Wörner, and N. Rohringer,
“Theoretical study of molecular electronic and rotational coherences by high-order-harmonic
generation,” Physical Review A, vol. 91, no. 2. American Physical Society,
2015.
ista: Zhang SB, Baykusheva DR, Kraus PM, Wörner HJ, Rohringer N. 2015. Theoretical
study of molecular electronic and rotational coherences by high-order-harmonic
generation. Physical Review A. 91(2), 023421.
mla: Zhang, Song Bin, et al. “Theoretical Study of Molecular Electronic and Rotational
Coherences by High-Order-Harmonic Generation.” Physical Review A, vol.
91, no. 2, 023421, American Physical Society, 2015, doi:10.1103/physreva.91.023421.
short: S.B. Zhang, D.R. Baykusheva, P.M. Kraus, H.J. Wörner, N. Rohringer, Physical
Review A 91 (2015).
date_created: 2023-08-10T06:38:10Z
date_published: 2015-02-19T00:00:00Z
date_updated: 2023-08-22T08:56:34Z
day: '19'
doi: 10.1103/physreva.91.023421
extern: '1'
external_id:
arxiv:
- '1504.03933'
intvolume: ' 91'
issue: '2'
keyword:
- Atomic and Molecular Physics
- and Optics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1504.03933
month: '02'
oa: 1
oa_version: Preprint
publication: Physical Review A
publication_identifier:
eissn:
- 1094-1622
issn:
- 1050-2947
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Theoretical study of molecular electronic and rotational coherences by high-order-harmonic
generation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 91
year: '2015'
...
---
_id: '1424'
abstract:
- lang: eng
text: We consider the problem of statistical computations with persistence diagrams,
a summary representation of topological features in data. These diagrams encode
persistent homology, a widely used invariant in topological data analysis. While
several avenues towards a statistical treatment of the diagrams have been explored
recently, we follow an alternative route that is motivated by the success of methods
based on the embedding of probability measures into reproducing kernel Hilbert
spaces. In fact, a positive definite kernel on persistence diagrams has recently
been proposed, connecting persistent homology to popular kernel-based learning
techniques such as support vector machines. However, important properties of that
kernel enabling a principled use in the context of probability measure embeddings
remain to be explored. Our contribution is to close this gap by proving universality
of a variant of the original kernel, and to demonstrate its effective use in twosample
hypothesis testing on synthetic as well as real-world data.
acknowledgement: This work was partially supported by the Austrian Science FUnd, project
no. KLI 00012.
alternative_title:
- Advances in Neural Information Processing Systems
author:
- first_name: Roland
full_name: Kwitt, Roland
last_name: Kwitt
- first_name: Stefan
full_name: Huber, Stefan
id: 4700A070-F248-11E8-B48F-1D18A9856A87
last_name: Huber
orcid: 0000-0002-8871-5814
- first_name: Marc
full_name: Niethammer, Marc
last_name: Niethammer
- first_name: Weili
full_name: Lin, Weili
last_name: Lin
- first_name: Ulrich
full_name: Bauer, Ulrich
id: 2ADD483A-F248-11E8-B48F-1D18A9856A87
last_name: Bauer
orcid: 0000-0002-9683-0724
citation:
ama: 'Kwitt R, Huber S, Niethammer M, Lin W, Bauer U. Statistical topological data
analysis-A kernel perspective. In: Vol 28. Neural Information Processing Systems;
2015:3070-3078.'
apa: 'Kwitt, R., Huber, S., Niethammer, M., Lin, W., & Bauer, U. (2015). Statistical
topological data analysis-A kernel perspective (Vol. 28, pp. 3070–3078). Presented
at the NIPS: Neural Information Processing Systems, Montreal, Canada: Neural Information
Processing Systems.'
chicago: Kwitt, Roland, Stefan Huber, Marc Niethammer, Weili Lin, and Ulrich Bauer.
“Statistical Topological Data Analysis-A Kernel Perspective,” 28:3070–78. Neural
Information Processing Systems, 2015.
ieee: 'R. Kwitt, S. Huber, M. Niethammer, W. Lin, and U. Bauer, “Statistical topological
data analysis-A kernel perspective,” presented at the NIPS: Neural Information
Processing Systems, Montreal, Canada, 2015, vol. 28, pp. 3070–3078.'
ista: 'Kwitt R, Huber S, Niethammer M, Lin W, Bauer U. 2015. Statistical topological
data analysis-A kernel perspective. NIPS: Neural Information Processing Systems,
Advances in Neural Information Processing Systems, vol. 28, 3070–3078.'
mla: Kwitt, Roland, et al. Statistical Topological Data Analysis-A Kernel Perspective.
Vol. 28, Neural Information Processing Systems, 2015, pp. 3070–78.
short: R. Kwitt, S. Huber, M. Niethammer, W. Lin, U. Bauer, in:, Neural Information
Processing Systems, 2015, pp. 3070–3078.
conference:
end_date: 2015-12-12
location: Montreal, Canada
name: 'NIPS: Neural Information Processing Systems'
start_date: 2015-12-07
date_created: 2018-12-11T11:51:56Z
date_published: 2015-12-01T00:00:00Z
date_updated: 2021-01-12T06:50:38Z
day: '01'
department:
- _id: HeEd
intvolume: ' 28'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://papers.nips.cc/paper/5887-statistical-topological-data-analysis-a-kernel-perspective
month: '12'
oa: 1
oa_version: Submitted Version
page: 3070 - 3078
publication_status: published
publisher: Neural Information Processing Systems
publist_id: '5782'
quality_controlled: '1'
status: public
title: Statistical topological data analysis-A kernel perspective
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 28
year: '2015'
...
---
_id: '1425'
abstract:
- lang: eng
text: 'In this work we aim at extending the theoretical foundations of lifelong
learning. Previous work analyzing this scenario is based on the assumption that
learning tasks are sampled i.i.d. from a task environment or limited to strongly
constrained data distributions. Instead, we study two scenarios when lifelong
learning is possible, even though the observed tasks do not form an i.i.d. sample:
first, when they are sampled from the same environment, but possibly with dependencies,
and second, when the task environment is allowed to change over time in a consistent
way. In the first case we prove a PAC-Bayesian theorem that can be seen as a direct
generalization of the analogous previous result for the i.i.d. case. For the second
scenario we propose to learn an inductive bias in form of a transfer procedure.
We present a generalization bound and show on a toy example how it can be used
to identify a beneficial transfer algorithm.'
alternative_title:
- Advances in Neural Information Processing Systems
author:
- first_name: Anastasia
full_name: Pentina, Anastasia
id: 42E87FC6-F248-11E8-B48F-1D18A9856A87
last_name: Pentina
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Pentina A, Lampert C. Lifelong learning with non-i.i.d. tasks. In: Vol 2015.
Neural Information Processing Systems; 2015:1540-1548.'
apa: 'Pentina, A., & Lampert, C. (2015). Lifelong learning with non-i.i.d. tasks
(Vol. 2015, pp. 1540–1548). Presented at the NIPS: Neural Information Processing
Systems, Montreal, Canada: Neural Information Processing Systems.'
chicago: Pentina, Anastasia, and Christoph Lampert. “Lifelong Learning with Non-i.i.d.
Tasks,” 2015:1540–48. Neural Information Processing Systems, 2015.
ieee: 'A. Pentina and C. Lampert, “Lifelong learning with non-i.i.d. tasks,” presented
at the NIPS: Neural Information Processing Systems, Montreal, Canada, 2015, vol.
2015, pp. 1540–1548.'
ista: 'Pentina A, Lampert C. 2015. Lifelong learning with non-i.i.d. tasks. NIPS:
Neural Information Processing Systems, Advances in Neural Information Processing
Systems, vol. 2015, 1540–1548.'
mla: Pentina, Anastasia, and Christoph Lampert. Lifelong Learning with Non-i.i.d.
Tasks. Vol. 2015, Neural Information Processing Systems, 2015, pp. 1540–48.
short: A. Pentina, C. Lampert, in:, Neural Information Processing Systems, 2015,
pp. 1540–1548.
conference:
end_date: 2015-12-12
location: Montreal, Canada
name: 'NIPS: Neural Information Processing Systems'
start_date: 2015-12-07
date_created: 2018-12-11T11:51:57Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:50:39Z
day: '01'
department:
- _id: ChLa
ec_funded: 1
intvolume: ' 2015'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://papers.nips.cc/paper/6007-lifelong-learning-with-non-iid-tasks
month: '01'
oa: 1
oa_version: None
page: 1540 - 1548
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication_status: published
publisher: Neural Information Processing Systems
publist_id: '5781'
quality_controlled: '1'
scopus_import: 1
status: public
title: Lifelong learning with non-i.i.d. tasks
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2015
year: '2015'
...
---
_id: '1430'
abstract:
- lang: eng
text: Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired
by natural evolution. In recent years the field of evolutionary computation has
developed a rigorous analytical theory to analyse their runtime on many illustrative
problems. Here we apply this theory to a simple model of natural evolution. In
the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between
occurrence of new mutations is much longer than the time it takes for a new beneficial
mutation to take over the population. In this situation, the population only contains
copies of one genotype and evolution can be modelled as a (1+1)-type process where
the probability of accepting a new genotype (improvements or worsenings) depends
on the change in fitness. We present an initial runtime analysis of SSWM, quantifying
its performance for various parameters and investigating differences to the (1+1)
EA. We show that SSWM can have a moderate advantage over the (1+1) EA at crossing
fitness valleys and study an example where SSWM outperforms the (1+1) EA by taking
advantage of information on the fitness gradient.
author:
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Dirk
full_name: Sudholt, Dirk
last_name: Sudholt
- first_name: Jorge
full_name: Heredia, Jorge
last_name: Heredia
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
citation:
ama: 'Paixao T, Sudholt D, Heredia J, Trubenova B. First steps towards a runtime
comparison of natural and artificial evolution. In: Proceedings of the 2015
Annual Conference on Genetic and Evolutionary Computation. ACM; 2015:1455-1462.
doi:10.1145/2739480.2754758'
apa: 'Paixao, T., Sudholt, D., Heredia, J., & Trubenova, B. (2015). First steps
towards a runtime comparison of natural and artificial evolution. In Proceedings
of the 2015 Annual Conference on Genetic and Evolutionary Computation (pp.
1455–1462). Madrid, Spain: ACM. https://doi.org/10.1145/2739480.2754758'
chicago: Paixao, Tiago, Dirk Sudholt, Jorge Heredia, and Barbora Trubenova. “First
Steps towards a Runtime Comparison of Natural and Artificial Evolution.” In Proceedings
of the 2015 Annual Conference on Genetic and Evolutionary Computation, 1455–62.
ACM, 2015. https://doi.org/10.1145/2739480.2754758.
ieee: T. Paixao, D. Sudholt, J. Heredia, and B. Trubenova, “First steps towards
a runtime comparison of natural and artificial evolution,” in Proceedings of
the 2015 Annual Conference on Genetic and Evolutionary Computation, Madrid,
Spain, 2015, pp. 1455–1462.
ista: 'Paixao T, Sudholt D, Heredia J, Trubenova B. 2015. First steps towards a
runtime comparison of natural and artificial evolution. Proceedings of the 2015
Annual Conference on Genetic and Evolutionary Computation. GECCO: Genetic and
evolutionary computation conference, 1455–1462.'
mla: Paixao, Tiago, et al. “First Steps towards a Runtime Comparison of Natural
and Artificial Evolution.” Proceedings of the 2015 Annual Conference on Genetic
and Evolutionary Computation, ACM, 2015, pp. 1455–62, doi:10.1145/2739480.2754758.
short: T. Paixao, D. Sudholt, J. Heredia, B. Trubenova, in:, Proceedings of the
2015 Annual Conference on Genetic and Evolutionary Computation, ACM, 2015, pp.
1455–1462.
conference:
end_date: 2015-07-15
location: Madrid, Spain
name: 'GECCO: Genetic and evolutionary computation conference'
start_date: 2015-07-11
date_created: 2018-12-11T11:51:58Z
date_published: 2015-07-11T00:00:00Z
date_updated: 2021-01-12T06:50:41Z
day: '11'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1145/2739480.2754758
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1504.06260
month: '07'
oa: 1
oa_version: Preprint
page: 1455 - 1462
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: Proceedings of the 2015 Annual Conference on Genetic and Evolutionary
Computation
publication_status: published
publisher: ACM
publist_id: '5768'
quality_controlled: '1'
scopus_import: 1
status: public
title: First steps towards a runtime comparison of natural and artificial evolution
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '14303'
abstract:
- lang: eng
text: Scaffolded DNA origami enables the fabrication of a variety of complex nanostructures
that promise utility in diverse fields of application, ranging from biosensing
over advanced therapeutics to metamaterials. The broad applicability of DNA origami
as a material beyond the level of proof-of-concept studies critically depends,
among other factors, on the availability of large amounts of pure single-stranded
scaffold DNA. Here, we present a method for the efficient production of M13 bacteriophage-derived
genomic DNA using high-cell-density fermentation of Escherichia coli in stirred-tank
bioreactors. We achieve phage titers of up to 1.6 × 1014 plaque-forming units
per mL. Downstream processing yields up to 410 mg of high-quality single-stranded
DNA per one liter reaction volume, thus upgrading DNA origami-based nanotechnology
from the milligram to the gram scale.
article_processing_charge: No
article_type: letter_note
author:
- first_name: B
full_name: Kick, B
last_name: Kick
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: H
full_name: Dietz, H
last_name: Dietz
- first_name: D
full_name: Weuster-Botz, D
last_name: Weuster-Botz
citation:
ama: Kick B, Praetorius FM, Dietz H, Weuster-Botz D. Efficient production of single-stranded
phage DNA as scaffolds for DNA origami. Nano Letters. 2015;15(7):4672-4676.
doi:10.1021/acs.nanolett.5b01461
apa: Kick, B., Praetorius, F. M., Dietz, H., & Weuster-Botz, D. (2015). Efficient
production of single-stranded phage DNA as scaffolds for DNA origami. Nano
Letters. ACS Publications. https://doi.org/10.1021/acs.nanolett.5b01461
chicago: Kick, B, Florian M Praetorius, H Dietz, and D Weuster-Botz. “Efficient
Production of Single-Stranded Phage DNA as Scaffolds for DNA Origami.” Nano
Letters. ACS Publications, 2015. https://doi.org/10.1021/acs.nanolett.5b01461.
ieee: B. Kick, F. M. Praetorius, H. Dietz, and D. Weuster-Botz, “Efficient production
of single-stranded phage DNA as scaffolds for DNA origami,” Nano Letters,
vol. 15, no. 7. ACS Publications, pp. 4672–4676, 2015.
ista: Kick B, Praetorius FM, Dietz H, Weuster-Botz D. 2015. Efficient production
of single-stranded phage DNA as scaffolds for DNA origami. Nano Letters. 15(7),
4672–4676.
mla: Kick, B., et al. “Efficient Production of Single-Stranded Phage DNA as Scaffolds
for DNA Origami.” Nano Letters, vol. 15, no. 7, ACS Publications, 2015,
pp. 4672–76, doi:10.1021/acs.nanolett.5b01461.
short: B. Kick, F.M. Praetorius, H. Dietz, D. Weuster-Botz, Nano Letters 15 (2015)
4672–4676.
date_created: 2023-09-06T12:52:47Z
date_published: 2015-06-01T00:00:00Z
date_updated: 2023-11-07T11:56:32Z
day: '01'
doi: 10.1021/acs.nanolett.5b01461
extern: '1'
external_id:
pmid:
- '26028443'
intvolume: ' 15'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1021/acs.nanolett.5b01461
month: '06'
oa: 1
oa_version: Published Version
page: 4672-4676
pmid: 1
publication: Nano Letters
publication_identifier:
eissn:
- 1530-6992
issn:
- 1530-6984
publication_status: published
publisher: ACS Publications
quality_controlled: '1'
status: public
title: Efficient production of single-stranded phage DNA as scaffolds for DNA origami
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2015'
...
---
_id: '9017'
abstract:
- lang: eng
text: MCM2 is a subunit of the replicative helicase machinery shown to interact
with histones H3 and H4 during the replication process through its N-terminal
domain. During replication, this interaction has been proposed to assist disassembly
and assembly of nucleosomes on DNA. However, how this interaction participates
in crosstalk with histone chaperones at the replication fork remains to be elucidated.
Here, we solved the crystal structure of the ternary complex between the histone-binding
domain of Mcm2 and the histones H3-H4 at 2.9 Å resolution. Histones H3 and H4
assemble as a tetramer in the crystal structure, but MCM2 interacts only with
a single molecule of H3-H4. The latter interaction exploits binding surfaces that
contact either DNA or H2B when H3-H4 dimers are incorporated in the nucleosome
core particle. Upon binding of the ternary complex with the histone chaperone
ASF1, the histone tetramer dissociates and both MCM2 and ASF1 interact simultaneously
with the histones forming a 1:1:1:1 heteromeric complex. Thermodynamic analysis
of the quaternary complex together with structural modeling support that ASF1
and MCM2 could form a chaperoning module for histones H3 and H4 protecting them
from promiscuous interactions. This suggests an additional function for MCM2 outside
its helicase function as a proper histone chaperone connected to the replication
pathway.
article_processing_charge: No
article_type: original
author:
- first_name: Nicolas
full_name: Richet, Nicolas
last_name: Richet
- first_name: Danni
full_name: Liu, Danni
last_name: Liu
- first_name: Pierre
full_name: Legrand, Pierre
last_name: Legrand
- first_name: Christophe
full_name: Velours, Christophe
last_name: Velours
- first_name: Armelle
full_name: Corpet, Armelle
last_name: Corpet
- first_name: Albane
full_name: Gaubert, Albane
last_name: Gaubert
- first_name: May M
full_name: Bakail, May M
id: FB3C3F8E-522F-11EA-B186-22963DDC885E
last_name: Bakail
orcid: 0000-0002-9592-1587
- first_name: Gwenaelle
full_name: Moal-Raisin, Gwenaelle
last_name: Moal-Raisin
- first_name: Raphael
full_name: Guerois, Raphael
last_name: Guerois
- first_name: Christel
full_name: Compper, Christel
last_name: Compper
- first_name: Arthur
full_name: Besle, Arthur
last_name: Besle
- first_name: Berengère
full_name: Guichard, Berengère
last_name: Guichard
- first_name: Genevieve
full_name: Almouzni, Genevieve
last_name: Almouzni
- first_name: Françoise
full_name: Ochsenbein, Françoise
last_name: Ochsenbein
citation:
ama: Richet N, Liu D, Legrand P, et al. Structural insight into how the human helicase
subunit MCM2 may act as a histone chaperone together with ASF1 at the replication
fork. Nucleic Acids Research. 2015;43(3):1905-1917. doi:10.1093/nar/gkv021
apa: Richet, N., Liu, D., Legrand, P., Velours, C., Corpet, A., Gaubert, A., … Ochsenbein,
F. (2015). Structural insight into how the human helicase subunit MCM2 may act
as a histone chaperone together with ASF1 at the replication fork. Nucleic
Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkv021
chicago: Richet, Nicolas, Danni Liu, Pierre Legrand, Christophe Velours, Armelle
Corpet, Albane Gaubert, May M Bakail, et al. “Structural Insight into How the
Human Helicase Subunit MCM2 May Act as a Histone Chaperone Together with ASF1
at the Replication Fork.” Nucleic Acids Research. Oxford University Press,
2015. https://doi.org/10.1093/nar/gkv021.
ieee: N. Richet et al., “Structural insight into how the human helicase subunit
MCM2 may act as a histone chaperone together with ASF1 at the replication fork,”
Nucleic Acids Research, vol. 43, no. 3. Oxford University Press, pp. 1905–1917,
2015.
ista: Richet N, Liu D, Legrand P, Velours C, Corpet A, Gaubert A, Bakail MM, Moal-Raisin
G, Guerois R, Compper C, Besle A, Guichard B, Almouzni G, Ochsenbein F. 2015.
Structural insight into how the human helicase subunit MCM2 may act as a histone
chaperone together with ASF1 at the replication fork. Nucleic Acids Research.
43(3), 1905–1917.
mla: Richet, Nicolas, et al. “Structural Insight into How the Human Helicase Subunit
MCM2 May Act as a Histone Chaperone Together with ASF1 at the Replication Fork.”
Nucleic Acids Research, vol. 43, no. 3, Oxford University Press, 2015,
pp. 1905–17, doi:10.1093/nar/gkv021.
short: N. Richet, D. Liu, P. Legrand, C. Velours, A. Corpet, A. Gaubert, M.M. Bakail,
G. Moal-Raisin, R. Guerois, C. Compper, A. Besle, B. Guichard, G. Almouzni, F.
Ochsenbein, Nucleic Acids Research 43 (2015) 1905–1917.
date_created: 2021-01-19T11:01:01Z
date_published: 2015-02-18T00:00:00Z
date_updated: 2023-02-23T13:46:50Z
day: '18'
doi: 10.1093/nar/gkv021
extern: '1'
external_id:
pmid:
- '25618846'
intvolume: ' 43'
issue: '3'
language:
- iso: eng
month: '02'
oa_version: Published Version
page: 1905-1917
pmid: 1
publication: Nucleic Acids Research
publication_identifier:
issn:
- 1362-4962
- 0305-1048
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
status: public
title: Structural insight into how the human helicase subunit MCM2 may act as a histone
chaperone together with ASF1 at the replication fork
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 43
year: '2015'
...
---
_id: '9057'
abstract:
- lang: eng
text: Motility is a basic feature of living microorganisms, and how it works is
often determined by environmental cues. Recent efforts have focused on developing
artificial systems that can mimic microorganisms, in particular their self-propulsion.
We report on the design and characterization of synthetic self-propelled particles
that migrate upstream, known as positive rheotaxis. This phenomenon results from
a purely physical mechanism involving the interplay between the polarity of the
particles and their alignment by a viscous torque. We show quantitative agreement
between experimental data and a simple model of an overdamped Brownian pendulum.
The model notably predicts the existence of a stagnation point in a diverging
flow. We take advantage of this property to demonstrate that our active particles
can sense and predictably organize in an imposed flow. Our colloidal system represents
an important step toward the realization of biomimetic microsystems with the ability
to sense and respond to environmental changes.
article_number: e1400214
article_processing_charge: No
article_type: original
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: Stefano
full_name: Sacanna, Stefano
last_name: Sacanna
- first_name: Anaïs
full_name: Abramian, Anaïs
last_name: Abramian
- first_name: Jérémie
full_name: Barral, Jérémie
last_name: Barral
- first_name: Kasey
full_name: Hanson, Kasey
last_name: Hanson
- first_name: Alexander Y.
full_name: Grosberg, Alexander Y.
last_name: Grosberg
- first_name: David J.
full_name: Pine, David J.
last_name: Pine
- first_name: Paul M.
full_name: Chaikin, Paul M.
last_name: Chaikin
citation:
ama: Palacci JA, Sacanna S, Abramian A, et al. Artificial rheotaxis. Science
Advances. 2015;1(4). doi:10.1126/sciadv.1400214
apa: Palacci, J. A., Sacanna, S., Abramian, A., Barral, J., Hanson, K., Grosberg,
A. Y., … Chaikin, P. M. (2015). Artificial rheotaxis. Science Advances.
American Association for the Advancement of Science . https://doi.org/10.1126/sciadv.1400214
chicago: Palacci, Jérémie A, Stefano Sacanna, Anaïs Abramian, Jérémie Barral, Kasey
Hanson, Alexander Y. Grosberg, David J. Pine, and Paul M. Chaikin. “Artificial
Rheotaxis.” Science Advances. American Association for the Advancement
of Science , 2015. https://doi.org/10.1126/sciadv.1400214.
ieee: J. A. Palacci et al., “Artificial rheotaxis,” Science Advances,
vol. 1, no. 4. American Association for the Advancement of Science , 2015.
ista: Palacci JA, Sacanna S, Abramian A, Barral J, Hanson K, Grosberg AY, Pine DJ,
Chaikin PM. 2015. Artificial rheotaxis. Science Advances. 1(4), e1400214.
mla: Palacci, Jérémie A., et al. “Artificial Rheotaxis.” Science Advances,
vol. 1, no. 4, e1400214, American Association for the Advancement of Science ,
2015, doi:10.1126/sciadv.1400214.
short: J.A. Palacci, S. Sacanna, A. Abramian, J. Barral, K. Hanson, A.Y. Grosberg,
D.J. Pine, P.M. Chaikin, Science Advances 1 (2015).
date_created: 2021-02-02T13:15:02Z
date_published: 2015-05-01T00:00:00Z
date_updated: 2023-02-23T13:47:52Z
day: '01'
ddc:
- '530'
doi: 10.1126/sciadv.1400214
extern: '1'
external_id:
arxiv:
- '1505.05111'
pmid:
- '26601175'
file:
- access_level: open_access
checksum: b97d62433581875c1b85210c5f6ae370
content_type: application/pdf
creator: cziletti
date_created: 2021-02-02T13:22:19Z
date_updated: 2021-02-02T13:22:19Z
file_id: '9058'
file_name: 2015_ScienceAdvances_Palacci.pdf
file_size: 2416780
relation: main_file
success: 1
file_date_updated: 2021-02-02T13:22:19Z
has_accepted_license: '1'
intvolume: ' 1'
issue: '4'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Science Advances
publication_identifier:
issn:
- 2375-2548
publication_status: published
publisher: 'American Association for the Advancement of Science '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Artificial rheotaxis
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 1
year: '2015'
...
---
_id: '906'
abstract:
- lang: eng
text: The origin and evolution of novel biochemical functions remains one of the
key questions in molecular evolution. We study recently emerged methacrylate reductase
function that is thought to have emerged in the last century and reported in Geobacter
sulfurreducens strain AM-1. We report the sequence and study the evolution of
the operon coding for the flavin-containing methacrylate reductase (Mrd) and tetraheme
cytochrome (Mcc) in the genome of G. sulfurreducens AM-1. Different types of signal
peptides in functionally interlinked proteins Mrd and Mcc suggest a possible complex
mechanism of biogenesis for chromoproteids of the methacrylate redox system. The
homologs of the Mrd and Mcc sequence found in δ-Proteobacteria and Deferribacteres
are also organized into an operon and their phylogenetic distribution suggested
that these two genes tend to be horizontally transferred together. Specifically,
the mrd and mcc genes from G. sulfurreducens AM-1 are not monophyletic with any
of the homologs found in other Geobacter genomes. The acquisition of methacrylate
reductase function by G. sulfurreducens AM-1 appears linked to a horizontal gene
transfer event. However, the new function of the products of mrd and mcc may have
evolved either prior or subsequent to their acquisition by G. sulfurreducens AM-1.
acknowledgement: 'Funding: The work has been supported by a grant of the HHMI International
Early Career Scientist Program (55007424), the Spanish Ministry of Economy and Competitiveness
(EUI-EURYIP-2011-4320) as part of the EMBO YIP program, two grants from the Spanish
Ministry of Economy and Competitiveness, "Centro de Excelencia Severo Ochoa 2013–2017
(Sev-2012-0208)" and (BFU2012-31329), the European Union and the European Research
Council under grant agreement 335980_EinME. The funders had no role in study design,
data collection and analysis, decision to publish, or preparation of the manuscript.Our
author Dr., Prof. Akimenko Vasilii K. (1942–2013) passed away during work on the
article. Prof. Akimenko was a leading biochemist in IBPM RAS and active researcher
until last days. A number of his work remains unfinished. We mourn premature care
of Prof. Akimenko Vasilii. We thank Heinz Himmelbauer and the CRG Genomic Unit for
the sequencing.'
author:
- first_name: Oksana
full_name: Arkhipova, Oksana V
last_name: Arkhipova
- first_name: Margarita
full_name: Meer, Margarita V
last_name: Meer
- first_name: Galina
full_name: Mikoulinskaia, Galina V
last_name: Mikoulinskaia
- first_name: Marina
full_name: Zakharova, Marina V
last_name: Zakharova
- first_name: Alexander
full_name: Galushko, Alexander S
last_name: Galushko
- first_name: Vasilii
full_name: Akimenko, Vasilii K
last_name: Akimenko
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Arkhipova O, Meer M, Mikoulinskaia G, et al. Recent origin of the methacrylate
redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer.
PLoS One. 2015;10(5). doi:10.1371/journal.pone.0125888
apa: Arkhipova, O., Meer, M., Mikoulinskaia, G., Zakharova, M., Galushko, A., Akimenko,
V., & Kondrashov, F. (2015). Recent origin of the methacrylate redox system
in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One.
Public Library of Science. https://doi.org/10.1371/journal.pone.0125888
chicago: Arkhipova, Oksana, Margarita Meer, Galina Mikoulinskaia, Marina Zakharova,
Alexander Galushko, Vasilii Akimenko, and Fyodor Kondrashov. “Recent Origin of
the Methacrylate Redox System in Geobacter Sulfurreducens AM-1 through Horizontal
Gene Transfer.” PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0125888.
ieee: O. Arkhipova et al., “Recent origin of the methacrylate redox system
in Geobacter sulfurreducens AM-1 through horizontal gene transfer,” PLoS One,
vol. 10, no. 5. Public Library of Science, 2015.
ista: Arkhipova O, Meer M, Mikoulinskaia G, Zakharova M, Galushko A, Akimenko V,
Kondrashov F. 2015. Recent origin of the methacrylate redox system in Geobacter
sulfurreducens AM-1 through horizontal gene transfer. PLoS One. 10(5).
mla: Arkhipova, Oksana, et al. “Recent Origin of the Methacrylate Redox System in
Geobacter Sulfurreducens AM-1 through Horizontal Gene Transfer.” PLoS One,
vol. 10, no. 5, Public Library of Science, 2015, doi:10.1371/journal.pone.0125888.
short: O. Arkhipova, M. Meer, G. Mikoulinskaia, M. Zakharova, A. Galushko, V. Akimenko,
F. Kondrashov, PLoS One 10 (2015).
date_created: 2018-12-11T11:49:08Z
date_published: 2015-05-11T00:00:00Z
date_updated: 2021-01-12T08:21:48Z
day: '11'
doi: 10.1371/journal.pone.0125888
extern: 1
intvolume: ' 10'
issue: '5'
month: '05'
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '6742'
quality_controlled: 0
status: public
title: Recent origin of the methacrylate redox system in Geobacter sulfurreducens
AM-1 through horizontal gene transfer
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: 10
year: '2015'
...
---
_id: '9141'
abstract:
- lang: eng
text: The breaking of internal tides is believed to provide a large part of the
power needed to mix the abyssal ocean and sustain the meridional overturning circulation.
Both the fraction of internal tide energy that is dissipated locally and the resulting
vertical mixing distribution are crucial for the ocean state, but remain poorly
quantified. Here we present a first worldwide estimate of mixing due to internal
tides generated at small‐scale abyssal hills. Our estimate is based on linear
wave theory, a nonlinear parameterization for wave breaking and uses quasi‐global
small‐scale abyssal hill bathymetry, stratification, and tidal data. We show that
a large fraction of abyssal‐hill generated internal tide energy is locally dissipated
over mid‐ocean ridges in the Southern Hemisphere. Significant dissipation occurs
above ridge crests, and, upon rescaling by the local stratification, follows a
monotonic exponential decay with height off the bottom, with a nonuniform decay
scale. We however show that a substantial part of the dissipation occurs over
the smoother flanks of mid‐ocean ridges, and exhibits a middepth maximum due to
the interplay of wave amplitude with stratification. We link the three‐dimensional
map of dissipation to abyssal hills characteristics, ocean stratification, and
tidal forcing, and discuss its potential implementation in time‐evolving parameterizations
for global climate models. Current tidal parameterizations only account for waves
generated at large‐scale satellite‐resolved bathymetry. Our results suggest that
the presence of small‐scale, mostly unresolved abyssal hills could significantly
enhance the spatial inhomogeneity of tidal mixing, particularly above mid‐ocean
ridges in the Southern Hemisphere.
article_processing_charge: No
article_type: original
author:
- first_name: Adrien
full_name: Lefauve, Adrien
last_name: Lefauve
- 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: Angélique
full_name: Melet, Angélique
last_name: Melet
citation:
ama: 'Lefauve A, Muller CJ, Melet A. A three-dimensional map of tidal dissipation
over abyssal hills. Journal of Geophysical Research: Oceans. 2015;120(7):4760-4777.
doi:10.1002/2014jc010598'
apa: 'Lefauve, A., Muller, C. J., & Melet, A. (2015). A three-dimensional map
of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans.
American Geophysical Union. https://doi.org/10.1002/2014jc010598'
chicago: 'Lefauve, Adrien, Caroline J Muller, and Angélique Melet. “A Three-Dimensional
Map of Tidal Dissipation over Abyssal Hills.” Journal of Geophysical Research:
Oceans. American Geophysical Union, 2015. https://doi.org/10.1002/2014jc010598.'
ieee: 'A. Lefauve, C. J. Muller, and A. Melet, “A three-dimensional map of tidal
dissipation over abyssal hills,” Journal of Geophysical Research: Oceans,
vol. 120, no. 7. American Geophysical Union, pp. 4760–4777, 2015.'
ista: 'Lefauve A, Muller CJ, Melet A. 2015. A three-dimensional map of tidal dissipation
over abyssal hills. Journal of Geophysical Research: Oceans. 120(7), 4760–4777.'
mla: 'Lefauve, Adrien, et al. “A Three-Dimensional Map of Tidal Dissipation over
Abyssal Hills.” Journal of Geophysical Research: Oceans, vol. 120, no.
7, American Geophysical Union, 2015, pp. 4760–77, doi:10.1002/2014jc010598.'
short: 'A. Lefauve, C.J. Muller, A. Melet, Journal of Geophysical Research: Oceans
120 (2015) 4760–4777.'
date_created: 2021-02-15T14:21:49Z
date_published: 2015-06-08T00:00:00Z
date_updated: 2022-01-24T13:45:41Z
day: '08'
doi: 10.1002/2014jc010598
extern: '1'
intvolume: ' 120'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/2014JC010598
month: '06'
oa: 1
oa_version: Published Version
page: 4760-4777
publication: 'Journal of Geophysical Research: Oceans'
publication_identifier:
issn:
- 2169-9275
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
status: public
title: A three-dimensional map of tidal dissipation over abyssal hills
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 120
year: '2015'
...
---
_id: '924'
abstract:
- lang: eng
text: This paper presents a numerical study of a Capillary Pumped Loop evaporator.
A two-dimensional unsteady mathematical model of a flat evaporator is developed
to simulate heat and mass transfer in unsaturated porous wick with phase change.
The liquid-vapor phase change inside the porous wick is described by Langmuir's
law. The governing equations are solved by the Finite Element Method. The results
are presented then for a sintered nickel wick and methanol as a working fluid.
The heat flux required to the transition from the all-liquid wick to the vapor-liquid
wick is calculated. The dynamic and thermodynamic behavior of the working fluid
in the capillary structure are discussed in this paper.
acknowledgement: The work presented in this paper is supported by Alstom Transport,
site de Tarbes (Contract number is 11099).
article_processing_charge: No
author:
- first_name: Riadh
full_name: Boubaker, Riadh
last_name: Boubaker
- first_name: Vincent
full_name: Platel, Vincent
last_name: Platel
- first_name: Alexis
full_name: Bergès, Alexis
last_name: Bergès
- first_name: Mathieu
full_name: Bancelin, Mathieu
last_name: Bancelin
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
citation:
ama: Boubaker R, Platel V, Bergès A, Bancelin M, Hannezo EB. Dynamic model of heat
and mass transfer in an unsaturated porous wick of capillary pumped loop. Applied
Thermal Engineering. 2015;76:1-8. doi:10.1016/j.applthermaleng.2014.10.009
apa: Boubaker, R., Platel, V., Bergès, A., Bancelin, M., & Hannezo, E. B. (2015).
Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary
pumped loop. Applied Thermal Engineering. Elsevier. https://doi.org/10.1016/j.applthermaleng.2014.10.009
chicago: Boubaker, Riadh, Vincent Platel, Alexis Bergès, Mathieu Bancelin, and Edouard
B Hannezo. “Dynamic Model of Heat and Mass Transfer in an Unsaturated Porous Wick
of Capillary Pumped Loop.” Applied Thermal Engineering. Elsevier, 2015.
https://doi.org/10.1016/j.applthermaleng.2014.10.009.
ieee: R. Boubaker, V. Platel, A. Bergès, M. Bancelin, and E. B. Hannezo, “Dynamic
model of heat and mass transfer in an unsaturated porous wick of capillary pumped
loop,” Applied Thermal Engineering, vol. 76. Elsevier, pp. 1–8, 2015.
ista: Boubaker R, Platel V, Bergès A, Bancelin M, Hannezo EB. 2015. Dynamic model
of heat and mass transfer in an unsaturated porous wick of capillary pumped loop.
Applied Thermal Engineering. 76, 1–8.
mla: Boubaker, Riadh, et al. “Dynamic Model of Heat and Mass Transfer in an Unsaturated
Porous Wick of Capillary Pumped Loop.” Applied Thermal Engineering, vol.
76, Elsevier, 2015, pp. 1–8, doi:10.1016/j.applthermaleng.2014.10.009.
short: R. Boubaker, V. Platel, A. Bergès, M. Bancelin, E.B. Hannezo, Applied Thermal
Engineering 76 (2015) 1–8.
date_created: 2018-12-11T11:49:13Z
date_published: 2015-02-05T00:00:00Z
date_updated: 2021-01-12T08:21:56Z
day: '05'
doi: 10.1016/j.applthermaleng.2014.10.009
extern: '1'
intvolume: ' 76'
language:
- iso: eng
month: '02'
oa_version: None
page: 1 - 8
publication: Applied Thermal Engineering
publication_status: published
publisher: Elsevier
publist_id: '6514'
status: public
title: Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary
pumped loop
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 76
year: '2015'
...
---
_id: '928'
abstract:
- lang: eng
text: The actomyosin cytoskeleton is a primary force-generating mechanism in morphogenesis,
thus a robust spatial control of cytoskeletal positioning is essential. In this
report, we demonstrate that actomyosin contractility and planar cell polarity
(PCP) interact in post-mitotic Ciona notochord cells to self-assemble and reposition
actomyosin rings, which play an essential role for cell elongation. Intriguingly,
rings always form at the cells′ anterior edge before migrating towards the center
as contractility increases, reflecting a novel dynamical property of the cortex.
Our drug and genetic manipulations uncover a tug-of-war between contractility,
which localizes cortical flows toward the equator and PCP, which tries to reposition
them. We develop a simple model of the physical forces underlying this tug-of-war,
which quantitatively reproduces our results. We thus propose a quantitative framework
for dissecting the relative contribution of contractility and PCP to the self-assembly
and repositioning of cytoskeletal structures, which should be applicable to other
morphogenetic events.
article_number: e09206
author:
- first_name: Ivonne
full_name: Sehring, Ivonne
last_name: Sehring
- first_name: Pierre
full_name: Recho, Pierre
last_name: Recho
- first_name: Elsa
full_name: Denker, Elsa
last_name: Denker
- first_name: Matthew
full_name: Kourakis, Matthew
last_name: Kourakis
- first_name: Birthe
full_name: Mathiesen, Birthe
last_name: Mathiesen
- 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: Bo
full_name: Dong, Bo
last_name: Dong
- first_name: Di
full_name: Jiang, Di
last_name: Jiang
citation:
ama: Sehring I, Recho P, Denker E, et al. Assembly and positioning of actomyosin
rings by contractility and planar cell polarity. eLife. 2015;4. doi:10.7554/eLife.09206
apa: Sehring, I., Recho, P., Denker, E., Kourakis, M., Mathiesen, B., Hannezo, E.
B., … Jiang, D. (2015). Assembly and positioning of actomyosin rings by contractility
and planar cell polarity. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.09206
chicago: Sehring, Ivonne, Pierre Recho, Elsa Denker, Matthew Kourakis, Birthe Mathiesen,
Edouard B Hannezo, Bo Dong, and Di Jiang. “Assembly and Positioning of Actomyosin
Rings by Contractility and Planar Cell Polarity.” ELife. eLife Sciences
Publications, 2015. https://doi.org/10.7554/eLife.09206.
ieee: I. Sehring et al., “Assembly and positioning of actomyosin rings by
contractility and planar cell polarity,” eLife, vol. 4. eLife Sciences
Publications, 2015.
ista: Sehring I, Recho P, Denker E, Kourakis M, Mathiesen B, Hannezo EB, Dong B,
Jiang D. 2015. Assembly and positioning of actomyosin rings by contractility and
planar cell polarity. eLife. 4, e09206.
mla: Sehring, Ivonne, et al. “Assembly and Positioning of Actomyosin Rings by Contractility
and Planar Cell Polarity.” ELife, vol. 4, e09206, eLife Sciences Publications,
2015, doi:10.7554/eLife.09206.
short: I. Sehring, P. Recho, E. Denker, M. Kourakis, B. Mathiesen, E.B. Hannezo,
B. Dong, D. Jiang, ELife 4 (2015).
date_created: 2018-12-11T11:49:15Z
date_published: 2015-10-21T00:00:00Z
date_updated: 2021-01-12T08:21:58Z
day: '21'
ddc:
- '539'
- '570'
doi: 10.7554/eLife.09206
extern: '1'
file:
- access_level: open_access
checksum: 1e4024b3161adcae4a53a0b3dc8a946e
content_type: application/pdf
creator: dernst
date_created: 2018-12-20T15:50:56Z
date_updated: 2020-07-14T12:48:15Z
file_id: '5769'
file_name: 2015_eLife_Sehring.pdf
file_size: 7202224
relation: main_file
file_date_updated: 2020-07-14T12:48:15Z
has_accepted_license: '1'
intvolume: ' 4'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
publist_id: '6512'
quality_controlled: '1'
status: public
title: Assembly and positioning of actomyosin rings by contractility and planar cell
polarity
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
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2015'
...
---
_id: '929'
abstract:
- lang: eng
text: 'An essential question of morphogenesis is how patterns arise without preexisting
positional information, as inspired by Turing. In the past few years, cytoskeletal
flows in the cell cortex have been identified as a key mechanism of molecular
patterning at the subcellular level. Theoretical and in vitro studies have suggested
that biological polymers such as actomyosin gels have the property to self-organize,
but the applicability of this concept in an in vivo setting remains unclear. Here,
we report that the regular spacing pattern of supracellular actin rings in the
Drosophila tracheal tubule is governed by a self-organizing principle. We propose
a simple biophysical model where pattern formation arises from the interplay of
myosin contractility and actin turnover. We validate the hypotheses of the model
using photobleaching experiments and report that the formation of actin rings
is contractility dependent. Moreover, genetic and pharmacological perturbations
of the physical properties of the actomyosin gel modify the spacing of the pattern,
as the model predicted. In addition, our model posited a role of cortical friction
in stabilizing the spacing pattern of actin rings. Consistently, genetic depletion
of apical extracellular matrix caused strikingly dynamic movements of actin rings,
mirroring our model prediction of a transition from steady to chaotic actin patterns
at low cortical friction. Our results therefore demonstrate quantitatively that
a hydrodynamical instability of the actin cortex can trigger regular pattern formation
and drive morphogenesis in an in vivo setting. '
acknowledgement: We thank H. Oda, R. E. Ward, K. Saigo, T. Nishimura, D. Pinheiro,
Y. Bellaiche, the Bloomington Stock Center, Drosophila Genetic Resource Center (Kyoto),
and the Developmental Studies Hybridoma Bank for generously providing antibodies
and fly stocks; A. Hayashi for sharing phalloidin staining samples; Y. H. Zhang
for plasmid and protocol for CBP preparation; and T. Kondo and J. Prost for suggestions
and discussion. This work was supported by the Taishan Scholar Program of Shandong
and the Fundamental Research Funds for the Central Universities in China (3005000-841412019)
(to B.D.) and a Grant-in-Aid for Scientific Research on Innovative Areas from Ministry
of Education, Culture, Sports, Science and Technology of Japan (to S.H.). E.H. acknowledges
support from the Young Researcher Prize of the Bettencourt-Schueller Foundation.
article_processing_charge: No
author:
- 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: Bo
full_name: Dong, Bo
last_name: Dong
- first_name: Pierre
full_name: Recho, Pierre
last_name: Recho
- first_name: Jean
full_name: Joanny, Jean
last_name: Joanny
- first_name: Shigeo
full_name: Hayashi, Shigeo
last_name: Hayashi
citation:
ama: Hannezo EB, Dong B, Recho P, Joanny J, Hayashi S. Cortical instability drives
periodic supracellular actin pattern formation in epithelial tubes. PNAS.
2015;112(28):8620-8625. doi:10.1073/pnas.1504762112
apa: Hannezo, E. B., Dong, B., Recho, P., Joanny, J., & Hayashi, S. (2015).
Cortical instability drives periodic supracellular actin pattern formation in
epithelial tubes. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1504762112
chicago: Hannezo, Edouard B, Bo Dong, Pierre Recho, Jean Joanny, and Shigeo Hayashi.
“Cortical Instability Drives Periodic Supracellular Actin Pattern Formation in
Epithelial Tubes.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1504762112.
ieee: E. B. Hannezo, B. Dong, P. Recho, J. Joanny, and S. Hayashi, “Cortical instability
drives periodic supracellular actin pattern formation in epithelial tubes,” PNAS,
vol. 112, no. 28. National Academy of Sciences, pp. 8620–8625, 2015.
ista: Hannezo EB, Dong B, Recho P, Joanny J, Hayashi S. 2015. Cortical instability
drives periodic supracellular actin pattern formation in epithelial tubes. PNAS.
112(28), 8620–8625.
mla: Hannezo, Edouard B., et al. “Cortical Instability Drives Periodic Supracellular
Actin Pattern Formation in Epithelial Tubes.” PNAS, vol. 112, no. 28, National
Academy of Sciences, 2015, pp. 8620–25, doi:10.1073/pnas.1504762112.
short: E.B. Hannezo, B. Dong, P. Recho, J. Joanny, S. Hayashi, PNAS 112 (2015) 8620–8625.
date_created: 2018-12-11T11:49:15Z
date_published: 2015-07-14T00:00:00Z
date_updated: 2021-01-12T08:21:59Z
day: '14'
doi: 10.1073/pnas.1504762112
extern: '1'
intvolume: ' 112'
issue: '28'
language:
- iso: eng
month: '07'
oa_version: None
page: 8620 - 8625
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6513'
status: public
title: Cortical instability drives periodic supracellular actin pattern formation
in epithelial tubes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '933'
abstract:
- lang: eng
text: Although collective cell motion plays an important role, for example during
wound healing, embryogenesis, or cancer progression, the fundamental rules governing
this motion are still not well understood, in particular at high cell density.
We study here the motion of human bronchial epithelial cells within a monolayer,
over long times. We observe that, as the monolayer ages, the cells slow down monotonously,
while the velocity correlation length first increases as the cells slow down but
eventually decreases at the slowest motions. By comparing experiments, analytic
model, and detailed particle-based simulations, we shed light on this biological
amorphous solidification process, demonstrating that the observed dynamics can
be explained as a consequence of the combined maturation and strengthening of
cell-cell and cell-substrate adhesions. Surprisingly, the increase of cell surface
density due to proliferation is only secondary in this process. This analysis
is confirmed with two other cell types. The very general relations between the
mean cell velocity and velocity correlation lengths, which apply for aggregates
of self-propelled particles, as well as motile cells, can possibly be used to
discriminate between various parameter changes in vivo, from noninvasive microscopy
data.
author:
- first_name: Simón
full_name: García, Simón
last_name: García
- 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: Jens
full_name: Elgeti, Jens
last_name: Elgeti
- first_name: Jean
full_name: Joanny, Jean
last_name: Joanny
- first_name: Pascal
full_name: Silberzan, Pascal
last_name: Silberzan
- first_name: Nir
full_name: Gov, Nir
last_name: Gov
citation:
ama: García S, Hannezo EB, Elgeti J, Joanny J, Silberzan P, Gov N. Physics of active
jamming during collective cellular motion in a monolayer. PNAS. 2015;112(50):15314-15319.
doi:10.1073/pnas.1510973112
apa: García, S., Hannezo, E. B., Elgeti, J., Joanny, J., Silberzan, P., & Gov,
N. (2015). Physics of active jamming during collective cellular motion in a monolayer.
PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1510973112
chicago: García, Simón, Edouard B Hannezo, Jens Elgeti, Jean Joanny, Pascal Silberzan,
and Nir Gov. “Physics of Active Jamming during Collective Cellular Motion in a
Monolayer.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1510973112.
ieee: S. García, E. B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, and N. Gov,
“Physics of active jamming during collective cellular motion in a monolayer,”
PNAS, vol. 112, no. 50. National Academy of Sciences, pp. 15314–15319,
2015.
ista: García S, Hannezo EB, Elgeti J, Joanny J, Silberzan P, Gov N. 2015. Physics
of active jamming during collective cellular motion in a monolayer. PNAS. 112(50),
15314–15319.
mla: García, Simón, et al. “Physics of Active Jamming during Collective Cellular
Motion in a Monolayer.” PNAS, vol. 112, no. 50, National Academy of Sciences,
2015, pp. 15314–19, doi:10.1073/pnas.1510973112.
short: S. García, E.B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, N. Gov, PNAS
112 (2015) 15314–15319.
date_created: 2018-12-11T11:49:16Z
date_published: 2015-12-15T00:00:00Z
date_updated: 2021-01-12T08:22:01Z
day: '15'
doi: 10.1073/pnas.1510973112
extern: '1'
external_id:
pmid:
- '26627719'
intvolume: ' 112'
issue: '50'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.pnas.org/content/pnas/112/50/15314.full.pdf
month: '12'
oa: 1
oa_version: None
page: 15314 - 15319
pmid: 1
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6511'
quality_controlled: '1'
status: public
title: Physics of active jamming during collective cellular motion in a monolayer
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '9532'
abstract:
- lang: eng
text: Genomic imprinting, an inherently epigenetic phenomenon defined by parent
of origin-dependent gene expression, is observed in mammals and flowering plants.
Genome-scale surveys of imprinted expression and the underlying differential epigenetic
marks have led to the discovery of hundreds of imprinted plant genes and confirmed
DNA and histone methylation as key regulators of plant imprinting. However, the
biological roles of the vast majority of imprinted plant genes are unknown, and
the evolutionary forces shaping plant imprinting remain rather opaque. Here, we
review the mechanisms of plant genomic imprinting and discuss theories of imprinting
evolution and biological significance in light of recent findings.
article_processing_charge: No
article_type: review
author:
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Rodrigues JA, Zilberman D. Evolution and function of genomic imprinting in
plants. Genes and Development. 2015;29(24):2517–2531. doi:10.1101/gad.269902.115
apa: Rodrigues, J. A., & Zilberman, D. (2015). Evolution and function of genomic
imprinting in plants. Genes and Development. Cold Spring Harbor Laboratory
Press. https://doi.org/10.1101/gad.269902.115
chicago: Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of
Genomic Imprinting in Plants.” Genes and Development. Cold Spring Harbor
Laboratory Press, 2015. https://doi.org/10.1101/gad.269902.115.
ieee: J. A. Rodrigues and D. Zilberman, “Evolution and function of genomic imprinting
in plants,” Genes and Development, vol. 29, no. 24. Cold Spring Harbor
Laboratory Press, pp. 2517–2531, 2015.
ista: Rodrigues JA, Zilberman D. 2015. Evolution and function of genomic imprinting
in plants. Genes and Development. 29(24), 2517–2531.
mla: Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic
Imprinting in Plants.” Genes and Development, vol. 29, no. 24, Cold Spring
Harbor Laboratory Press, 2015, pp. 2517–2531, doi:10.1101/gad.269902.115.
short: J.A. Rodrigues, D. Zilberman, Genes and Development 29 (2015) 2517–2531.
date_created: 2021-06-08T09:56:24Z
date_published: 2015-12-15T00:00:00Z
date_updated: 2021-12-14T07:58:15Z
day: '15'
ddc:
- '570'
department:
- _id: DaZi
doi: 10.1101/gad.269902.115
extern: '1'
external_id:
pmid:
- '26680300'
file:
- access_level: open_access
checksum: 086a88cfca4677646da26ed960cb02e9
content_type: application/pdf
creator: asandaue
date_created: 2021-06-08T09:55:10Z
date_updated: 2021-06-08T09:55:10Z
file_id: '9533'
file_name: 2015_GenesAndDevelopment_Rodrigues.pdf
file_size: 1116846
relation: main_file
success: 1
file_date_updated: 2021-06-08T09:55:10Z
has_accepted_license: '1'
intvolume: ' 29'
issue: '24'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 2517–2531
pmid: 1
publication: Genes and Development
publication_identifier:
eissn:
- 1549-5477
issn:
- 0890-9369
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolution and function of genomic imprinting in plants
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 29
year: '2015'
...
---
_id: '9575'
abstract:
- lang: eng
text: We give several results showing that different discrete structures typically
gain certain spanning substructures (in particular, Hamilton cycles) after a modest
random perturbation. First, we prove that adding linearly many random edges to
a dense k-uniform hypergraph ensures the (asymptotically almost sure) existence
of a perfect matching or a loose Hamilton cycle. The proof involves an interesting
application of Szemerédi's Regularity Lemma, which might be independently useful.
We next prove that digraphs with certain strong expansion properties are pancyclic,
and use this to show that adding a linear number of random edges typically makes
a dense digraph pancyclic. Finally, we prove that perturbing a certain (minimum-degree-dependent)
number of random edges in a tournament typically ensures the existence of multiple
edge-disjoint Hamilton cycles. All our results are tight.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Michael
full_name: Krivelevich, Michael
last_name: Krivelevich
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Benny
full_name: Sudakov, Benny
last_name: Sudakov
citation:
ama: Krivelevich M, Kwan MA, Sudakov B. Cycles and matchings in randomly perturbed
digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. 2015;49:181-187.
doi:10.1016/j.endm.2015.06.027
apa: Krivelevich, M., Kwan, M. A., & Sudakov, B. (2015). Cycles and matchings
in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete
Mathematics. Elsevier. https://doi.org/10.1016/j.endm.2015.06.027
chicago: Krivelevich, Michael, Matthew Alan Kwan, and Benny Sudakov. “Cycles and
Matchings in Randomly Perturbed Digraphs and Hypergraphs.” Electronic Notes
in Discrete Mathematics. Elsevier, 2015. https://doi.org/10.1016/j.endm.2015.06.027.
ieee: M. Krivelevich, M. A. Kwan, and B. Sudakov, “Cycles and matchings in randomly
perturbed digraphs and hypergraphs,” Electronic Notes in Discrete Mathematics,
vol. 49. Elsevier, pp. 181–187, 2015.
ista: Krivelevich M, Kwan MA, Sudakov B. 2015. Cycles and matchings in randomly
perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics.
49, 181–187.
mla: Krivelevich, Michael, et al. “Cycles and Matchings in Randomly Perturbed Digraphs
and Hypergraphs.” Electronic Notes in Discrete Mathematics, vol. 49, Elsevier,
2015, pp. 181–87, doi:10.1016/j.endm.2015.06.027.
short: M. Krivelevich, M.A. Kwan, B. Sudakov, Electronic Notes in Discrete Mathematics
49 (2015) 181–187.
date_created: 2021-06-21T06:40:34Z
date_published: 2015-11-01T00:00:00Z
date_updated: 2023-02-23T14:01:28Z
day: '01'
doi: 10.1016/j.endm.2015.06.027
extern: '1'
external_id:
arxiv:
- '1501.04816'
intvolume: ' 49'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1501.04816
month: '11'
oa: 1
oa_version: Preprint
page: 181-187
publication: Electronic Notes in Discrete Mathematics
publication_identifier:
issn:
- 1571-0653
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cycles and matchings in randomly perturbed digraphs and hypergraphs
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 49
year: '2015'
...
---
_id: '9673'
abstract:
- lang: eng
text: Current strategies of computational crystal plasticity that focus on individual
atoms or dislocations are impractical for real-scale, large-strain problems even
with today’s computing power. Dislocation-density based approaches are a way forward
but a critical issue to address is a realistic description of the interactions
between dislocations. In this paper, a new scheme for computational dynamics of
dislocation-density functions is proposed, which takes full consideration of the
mutual elastic interactions between dislocations based on the Hirth–Lothe formulation.
Other features considered include (i) the continuity nature of the movements of
dislocation densities, (ii) forest hardening, (iii) generation according to high
spatial gradients in dislocation densities, and (iv) annihilation. Numerical implementation
by the finite-volume method, which is well suited for flow problems with high
gradients, is discussed. Numerical examples performed for a single-crystal aluminum
model show typical strength anisotropy behavior comparable to experimental observations.
Furthermore, a detailed case study on small-scale crystal plasticity successfully
captures a number of key experimental features, including power-law relation between
strength and size, low dislocation storage and jerky deformation.
article_processing_charge: No
article_type: original
author:
- first_name: H.S.
full_name: Leung, H.S.
last_name: Leung
- first_name: P.S.S.
full_name: Leung, P.S.S.
last_name: Leung
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: A.H.W.
full_name: Ngan, A.H.W.
last_name: Ngan
citation:
ama: Leung HS, Leung PSS, Cheng B, Ngan AHW. A new dislocation-density-function
dynamics scheme for computational crystal plasticity by explicit consideration
of dislocation elastic interactions. International Journal of Plasticity.
2015;67:1-25. doi:10.1016/j.ijplas.2014.09.009
apa: Leung, H. S., Leung, P. S. S., Cheng, B., & Ngan, A. H. W. (2015). A new
dislocation-density-function dynamics scheme for computational crystal plasticity
by explicit consideration of dislocation elastic interactions. International
Journal of Plasticity. Elsevier. https://doi.org/10.1016/j.ijplas.2014.09.009
chicago: Leung, H.S., P.S.S. Leung, Bingqing Cheng, and A.H.W. Ngan. “A New Dislocation-Density-Function
Dynamics Scheme for Computational Crystal Plasticity by Explicit Consideration
of Dislocation Elastic Interactions.” International Journal of Plasticity.
Elsevier, 2015. https://doi.org/10.1016/j.ijplas.2014.09.009.
ieee: H. S. Leung, P. S. S. Leung, B. Cheng, and A. H. W. Ngan, “A new dislocation-density-function
dynamics scheme for computational crystal plasticity by explicit consideration
of dislocation elastic interactions,” International Journal of Plasticity,
vol. 67. Elsevier, pp. 1–25, 2015.
ista: Leung HS, Leung PSS, Cheng B, Ngan AHW. 2015. A new dislocation-density-function
dynamics scheme for computational crystal plasticity by explicit consideration
of dislocation elastic interactions. International Journal of Plasticity. 67,
1–25.
mla: Leung, H. S., et al. “A New Dislocation-Density-Function Dynamics Scheme for
Computational Crystal Plasticity by Explicit Consideration of Dislocation Elastic
Interactions.” International Journal of Plasticity, vol. 67, Elsevier,
2015, pp. 1–25, doi:10.1016/j.ijplas.2014.09.009.
short: H.S. Leung, P.S.S. Leung, B. Cheng, A.H.W. Ngan, International Journal of
Plasticity 67 (2015) 1–25.
date_created: 2021-07-15T14:09:32Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2023-02-23T14:04:28Z
day: '01'
doi: 10.1016/j.ijplas.2014.09.009
extern: '1'
intvolume: ' 67'
language:
- iso: eng
month: '04'
oa_version: None
page: 1-25
publication: International Journal of Plasticity
publication_identifier:
issn:
- 0749-6419
publication_status: published
publisher: Elsevier
scopus_import: '1'
status: public
title: A new dislocation-density-function dynamics scheme for computational crystal
plasticity by explicit consideration of dislocation elastic interactions
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 67
year: '2015'
...