---
_id: '6779'
abstract:
- lang: eng
text: "Recent studies suggest that unstable recurrent solutions of the Navier-Stokes
equation provide new insights\r\ninto dynamics of turbulent flows. In this study,
we compute an extensive network of dynamical connections\r\nbetween such solutions
in a weakly turbulent quasi-two-dimensional Kolmogorov flow that lies in the inversion
symmetric subspace. In particular, we find numerous isolated heteroclinic connections
between different\r\ntypes of solutions—equilibria, periodic, and quasiperiodic
orbits—as well as continua of connections forming\r\nhigher-dimensional connecting
manifolds. We also compute a homoclinic connection of a periodic orbit and\r\nprovide
strong evidence that the associated homoclinic tangle forms the chaotic repeller
that underpins transient\r\nturbulence in the symmetric subspace."
article_number: '013112'
article_processing_charge: No
article_type: original
author:
- first_name: Balachandra
full_name: Suri, Balachandra
id: 47A5E706-F248-11E8-B48F-1D18A9856A87
last_name: Suri
- first_name: Ravi Kumar
full_name: Pallantla, Ravi Kumar
last_name: Pallantla
- first_name: Michael F.
full_name: Schatz, Michael F.
last_name: Schatz
- first_name: Roman O.
full_name: Grigoriev, Roman O.
last_name: Grigoriev
citation:
ama: Suri B, Pallantla RK, Schatz MF, Grigoriev RO. Heteroclinic and homoclinic
connections in a Kolmogorov-like flow. Physical Review E. 2019;100(1).
doi:10.1103/physreve.100.013112
apa: Suri, B., Pallantla, R. K., Schatz, M. F., & Grigoriev, R. O. (2019). Heteroclinic
and homoclinic connections in a Kolmogorov-like flow. Physical Review E.
American Physical Society. https://doi.org/10.1103/physreve.100.013112
chicago: Suri, Balachandra, Ravi Kumar Pallantla, Michael F. Schatz, and Roman O.
Grigoriev. “Heteroclinic and Homoclinic Connections in a Kolmogorov-like Flow.”
Physical Review E. American Physical Society, 2019. https://doi.org/10.1103/physreve.100.013112.
ieee: B. Suri, R. K. Pallantla, M. F. Schatz, and R. O. Grigoriev, “Heteroclinic
and homoclinic connections in a Kolmogorov-like flow,” Physical Review E,
vol. 100, no. 1. American Physical Society, 2019.
ista: Suri B, Pallantla RK, Schatz MF, Grigoriev RO. 2019. Heteroclinic and homoclinic
connections in a Kolmogorov-like flow. Physical Review E. 100(1), 013112.
mla: Suri, Balachandra, et al. “Heteroclinic and Homoclinic Connections in a Kolmogorov-like
Flow.” Physical Review E, vol. 100, no. 1, 013112, American Physical Society,
2019, doi:10.1103/physreve.100.013112.
short: B. Suri, R.K. Pallantla, M.F. Schatz, R.O. Grigoriev, Physical Review E 100
(2019).
date_created: 2019-08-09T09:40:41Z
date_published: 2019-07-25T00:00:00Z
date_updated: 2024-02-28T13:13:00Z
day: '25'
ddc:
- '532'
department:
- _id: BjHo
doi: 10.1103/physreve.100.013112
ec_funded: 1
external_id:
arxiv:
- '1907.05860'
isi:
- '000477911800012'
intvolume: ' 100'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1907.05860
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Physical Review E
publication_identifier:
eissn:
- 2470-0053
issn:
- 2470-0045
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Heteroclinic and homoclinic connections in a Kolmogorov-like flow
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 100
year: '2019'
...
---
_id: '7015'
abstract:
- lang: eng
text: We modify the "floating crystal" trial state for the classical homogeneous
electron gas (also known as jellium), in order to suppress the boundary charge
fluctuations that are known to lead to a macroscopic increase of the energy. The
argument is to melt a thin layer of the crystal close to the boundary and consequently
replace it by an incompressible fluid. With the aid of this trial state we show
that three different definitions of the ground-state energy of jellium coincide.
In the first point of view the electrons are placed in a neutralizing uniform
background. In the second definition there is no background but the electrons
are submitted to the constraint that their density is constant, as is appropriate
in density functional theory. Finally, in the third system each electron interacts
with a periodic image of itself; that is, periodic boundary conditions are imposed
on the interaction potential.
article_number: '035127'
article_processing_charge: No
article_type: original
author:
- first_name: Mathieu
full_name: Lewin, Mathieu
last_name: Lewin
- first_name: Elliott H.
full_name: Lieb, Elliott H.
last_name: Lieb
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Lewin M, Lieb EH, Seiringer R. Floating Wigner crystal with no boundary charge
fluctuations. Physical Review B. 2019;100(3). doi:10.1103/physrevb.100.035127
apa: Lewin, M., Lieb, E. H., & Seiringer, R. (2019). Floating Wigner crystal
with no boundary charge fluctuations. Physical Review B. American Physical
Society. https://doi.org/10.1103/physrevb.100.035127
chicago: Lewin, Mathieu, Elliott H. Lieb, and Robert Seiringer. “Floating Wigner
Crystal with No Boundary Charge Fluctuations.” Physical Review B. American
Physical Society, 2019. https://doi.org/10.1103/physrevb.100.035127.
ieee: M. Lewin, E. H. Lieb, and R. Seiringer, “Floating Wigner crystal with no boundary
charge fluctuations,” Physical Review B, vol. 100, no. 3. American Physical
Society, 2019.
ista: Lewin M, Lieb EH, Seiringer R. 2019. Floating Wigner crystal with no boundary
charge fluctuations. Physical Review B. 100(3), 035127.
mla: Lewin, Mathieu, et al. “Floating Wigner Crystal with No Boundary Charge Fluctuations.”
Physical Review B, vol. 100, no. 3, 035127, American Physical Society,
2019, doi:10.1103/physrevb.100.035127.
short: M. Lewin, E.H. Lieb, R. Seiringer, Physical Review B 100 (2019).
date_created: 2019-11-13T08:41:48Z
date_published: 2019-07-25T00:00:00Z
date_updated: 2024-02-28T13:13:23Z
day: '25'
department:
- _id: RoSe
doi: 10.1103/physrevb.100.035127
ec_funded: 1
external_id:
arxiv:
- '1905.09138'
isi:
- '000477888200001'
intvolume: ' 100'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1905.09138
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Floating Wigner crystal with no boundary charge fluctuations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 100
year: '2019'
...
---
_id: '7145'
abstract:
- lang: eng
text: End-to-end correlated bound states are investigated in superconductor-semiconductor
hybrid nanowires at zero magnetic field. Peaks in subgap conductance are independently
identified from each wire end, and a cross-correlation function is computed that
counts end-to-end coincidences, averaging over thousands of subgap features. Strong
correlations in a short, 300-nm device are reduced by a factor of 4 in a long,
900-nm device. In addition, subgap conductance distributions are investigated,
and correlations between the left and right distributions are identified based
on their mutual information.
article_number: '205412'
article_processing_charge: No
article_type: original
author:
- first_name: G. L. R.
full_name: Anselmetti, G. L. R.
last_name: Anselmetti
- first_name: E. A.
full_name: Martinez, E. A.
last_name: Martinez
- first_name: G. C.
full_name: Ménard, G. C.
last_name: Ménard
- first_name: D.
full_name: Puglia, D.
last_name: Puglia
- first_name: F. K.
full_name: Malinowski, F. K.
last_name: Malinowski
- first_name: J. S.
full_name: Lee, J. S.
last_name: Lee
- first_name: S.
full_name: Choi, S.
last_name: Choi
- first_name: M.
full_name: Pendharkar, M.
last_name: Pendharkar
- first_name: C. J.
full_name: Palmstrøm, C. J.
last_name: Palmstrøm
- first_name: C. M.
full_name: Marcus, C. M.
last_name: Marcus
- first_name: L.
full_name: Casparis, L.
last_name: Casparis
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
citation:
ama: Anselmetti GLR, Martinez EA, Ménard GC, et al. End-to-end correlated subgap
states in hybrid nanowires. Physical Review B. 2019;100(20). doi:10.1103/physrevb.100.205412
apa: Anselmetti, G. L. R., Martinez, E. A., Ménard, G. C., Puglia, D., Malinowski,
F. K., Lee, J. S., … Higginbotham, A. P. (2019). End-to-end correlated subgap
states in hybrid nanowires. Physical Review B. American Physical Society.
https://doi.org/10.1103/physrevb.100.205412
chicago: Anselmetti, G. L. R., E. A. Martinez, G. C. Ménard, D. Puglia, F. K. Malinowski,
J. S. Lee, S. Choi, et al. “End-to-End Correlated Subgap States in Hybrid Nanowires.”
Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/physrevb.100.205412.
ieee: G. L. R. Anselmetti et al., “End-to-end correlated subgap states in
hybrid nanowires,” Physical Review B, vol. 100, no. 20. American Physical
Society, 2019.
ista: Anselmetti GLR, Martinez EA, Ménard GC, Puglia D, Malinowski FK, Lee JS, Choi
S, Pendharkar M, Palmstrøm CJ, Marcus CM, Casparis L, Higginbotham AP. 2019. End-to-end
correlated subgap states in hybrid nanowires. Physical Review B. 100(20), 205412.
mla: Anselmetti, G. L. R., et al. “End-to-End Correlated Subgap States in Hybrid
Nanowires.” Physical Review B, vol. 100, no. 20, 205412, American Physical
Society, 2019, doi:10.1103/physrevb.100.205412.
short: G.L.R. Anselmetti, E.A. Martinez, G.C. Ménard, D. Puglia, F.K. Malinowski,
J.S. Lee, S. Choi, M. Pendharkar, C.J. Palmstrøm, C.M. Marcus, L. Casparis, A.P.
Higginbotham, Physical Review B 100 (2019).
date_created: 2019-12-04T16:02:25Z
date_published: 2019-11-15T00:00:00Z
date_updated: 2024-02-28T13:13:51Z
day: '15'
department:
- _id: AnHi
doi: 10.1103/physrevb.100.205412
external_id:
arxiv:
- '1908.05549'
isi:
- '000495967500006'
intvolume: ' 100'
isi: 1
issue: '20'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1908.05549
month: '11'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: End-to-end correlated subgap states in hybrid nanowires
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 100
year: '2019'
...
---
_id: '5906'
abstract:
- lang: eng
text: We introduce a simple, exactly solvable strong-randomness renormalization
group (RG) model for the many-body localization (MBL) transition in one dimension.
Our approach relies on a family of RG flows parametrized by the asymmetry between
thermal and localized phases. We identify the physical MBL transition in the limit
of maximal asymmetry, reflecting the instability of MBL against rare thermal inclusions.
We find a critical point that is localized with power-law distributed thermal
inclusions. The typical size of critical inclusions remains finite at the transition,
while the average size is logarithmically diverging. We propose a two-parameter
scaling theory for the many-body localization transition that falls into the Kosterlitz-Thouless
universality class, with the MBL phase corresponding to a stable line of fixed
points with multifractal behavior.
article_number: '040601'
article_processing_charge: No
article_type: original
author:
- first_name: Anna
full_name: Goremykina, Anna
last_name: Goremykina
- first_name: Romain
full_name: Vasseur, Romain
last_name: Vasseur
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Goremykina A, Vasseur R, Serbyn M. Analytically solvable renormalization group
for the many-body localization transition. Physical Review Letters. 2019;122(4).
doi:10.1103/physrevlett.122.040601
apa: Goremykina, A., Vasseur, R., & Serbyn, M. (2019). Analytically solvable
renormalization group for the many-body localization transition. Physical Review
Letters. American Physical Society. https://doi.org/10.1103/physrevlett.122.040601
chicago: Goremykina, Anna, Romain Vasseur, and Maksym Serbyn. “Analytically Solvable
Renormalization Group for the Many-Body Localization Transition.” Physical
Review Letters. American Physical Society, 2019. https://doi.org/10.1103/physrevlett.122.040601.
ieee: A. Goremykina, R. Vasseur, and M. Serbyn, “Analytically solvable renormalization
group for the many-body localization transition,” Physical Review Letters,
vol. 122, no. 4. American Physical Society, 2019.
ista: Goremykina A, Vasseur R, Serbyn M. 2019. Analytically solvable renormalization
group for the many-body localization transition. Physical Review Letters. 122(4),
040601.
mla: Goremykina, Anna, et al. “Analytically Solvable Renormalization Group for the
Many-Body Localization Transition.” Physical Review Letters, vol. 122,
no. 4, 040601, American Physical Society, 2019, doi:10.1103/physrevlett.122.040601.
short: A. Goremykina, R. Vasseur, M. Serbyn, Physical Review Letters 122 (2019).
date_created: 2019-02-01T08:22:28Z
date_published: 2019-02-01T00:00:00Z
date_updated: 2024-02-28T13:13:38Z
day: '01'
department:
- _id: MaSe
doi: 10.1103/physrevlett.122.040601
external_id:
arxiv:
- '1807.04285'
isi:
- '000456783700001'
intvolume: ' 122'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1807.04285
month: '02'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Analytically solvable renormalization group for the many-body localization
transition
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 122
year: '2019'
...
---
_id: '6632'
abstract:
- lang: eng
text: We consider a two-component Bose gas in two dimensions at a low temperature
with short-range repulsive interaction. In the coexistence phase where both components
are superfluid, interspecies interactions induce a nondissipative drag between
the two superfluid flows (Andreev-Bashkin effect). We show that this behavior
leads to a modification of the usual Berezinskii-Kosterlitz-Thouless (BKT) transition
in two dimensions. We extend the renormalization of the superfluid densities at
finite temperature using the renormalization-group approach and find that the
vortices of one component have a large influence on the superfluid properties
of the other, mediated by the nondissipative drag. The extended BKT flow equations indicate that the occurrence of the
vortex unbinding transition in one of the components can induce the breakdown
of superfluidity also in the other, leading to a locking phenomenon for the critical
temperatures of the two gases.
article_number: '063627'
article_processing_charge: No
author:
- first_name: Volker
full_name: Karle, Volker
last_name: Karle
- first_name: Nicolò
full_name: Defenu, Nicolò
last_name: Defenu
- first_name: Tilman
full_name: Enss, Tilman
last_name: Enss
citation:
ama: Karle V, Defenu N, Enss T. Coupled superfluidity of binary Bose mixtures in
two dimensions. Physical Review A. 2019;99(6). doi:10.1103/PhysRevA.99.063627
apa: Karle, V., Defenu, N., & Enss, T. (2019). Coupled superfluidity of binary
Bose mixtures in two dimensions. Physical Review A. American Physical Society.
https://doi.org/10.1103/PhysRevA.99.063627
chicago: Karle, Volker, Nicolò Defenu, and Tilman Enss. “Coupled Superfluidity of
Binary Bose Mixtures in Two Dimensions.” Physical Review A. American Physical
Society, 2019. https://doi.org/10.1103/PhysRevA.99.063627.
ieee: V. Karle, N. Defenu, and T. Enss, “Coupled superfluidity of binary Bose mixtures
in two dimensions,” Physical Review A, vol. 99, no. 6. American Physical
Society, 2019.
ista: Karle V, Defenu N, Enss T. 2019. Coupled superfluidity of binary Bose mixtures
in two dimensions. Physical Review A. 99(6), 063627.
mla: Karle, Volker, et al. “Coupled Superfluidity of Binary Bose Mixtures in Two
Dimensions.” Physical Review A, vol. 99, no. 6, 063627, American Physical
Society, 2019, doi:10.1103/PhysRevA.99.063627.
short: V. Karle, N. Defenu, T. Enss, Physical Review A 99 (2019).
date_created: 2019-07-14T21:59:17Z
date_published: 2019-06-28T00:00:00Z
date_updated: 2024-02-28T13:12:34Z
day: '28'
department:
- _id: MiLe
doi: 10.1103/PhysRevA.99.063627
external_id:
arxiv:
- '1903.06759'
isi:
- '000473133600007'
intvolume: ' 99'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1903.06759
month: '06'
oa: 1
oa_version: Preprint
publication: Physical Review A
publication_identifier:
eissn:
- '24699934'
issn:
- '24699926'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Coupled superfluidity of binary Bose mixtures in two dimensions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 99
year: '2019'
...
---
_id: '7396'
abstract:
- lang: eng
text: The angular momentum of molecules, or, equivalently, their rotation in three-dimensional
space, is ideally suited for quantum control. Molecular angular momentum is naturally
quantized, time evolution is governed by a well-known Hamiltonian with only a
few accurately known parameters, and transitions between rotational levels can
be driven by external fields from various parts of the electromagnetic spectrum.
Control over the rotational motion can be exerted in one-, two-, and many-body
scenarios, thereby allowing one to probe Anderson localization, target stereoselectivity
of bimolecular reactions, or encode quantum information to name just a few examples.
The corresponding approaches to quantum control are pursued within separate, and
typically disjoint, subfields of physics, including ultrafast science, cold collisions,
ultracold gases, quantum information science, and condensed-matter physics. It
is the purpose of this review to present the various control phenomena, which
all rely on the same underlying physics, within a unified framework. To this end,
recall the Hamiltonian for free rotations, assuming the rigid rotor approximation
to be valid, and summarize the different ways for a rotor to interact with external
electromagnetic fields. These interactions can be exploited for control—from achieving
alignment, orientation, or laser cooling in a one-body framework, steering bimolecular
collisions, or realizing a quantum computer or quantum simulator in the many-body
setting.
article_number: '035005 '
article_processing_charge: No
article_type: original
author:
- first_name: Christiane P.
full_name: Koch, Christiane P.
last_name: Koch
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Dominique
full_name: Sugny, Dominique
last_name: Sugny
citation:
ama: Koch CP, Lemeshko M, Sugny D. Quantum control of molecular rotation. Reviews
of Modern Physics. 2019;91(3). doi:10.1103/revmodphys.91.035005
apa: Koch, C. P., Lemeshko, M., & Sugny, D. (2019). Quantum control of molecular
rotation. Reviews of Modern Physics. American Physical Society. https://doi.org/10.1103/revmodphys.91.035005
chicago: Koch, Christiane P., Mikhail Lemeshko, and Dominique Sugny. “Quantum Control
of Molecular Rotation.” Reviews of Modern Physics. American Physical Society,
2019. https://doi.org/10.1103/revmodphys.91.035005.
ieee: C. P. Koch, M. Lemeshko, and D. Sugny, “Quantum control of molecular rotation,”
Reviews of Modern Physics, vol. 91, no. 3. American Physical Society, 2019.
ista: Koch CP, Lemeshko M, Sugny D. 2019. Quantum control of molecular rotation.
Reviews of Modern Physics. 91(3), 035005.
mla: Koch, Christiane P., et al. “Quantum Control of Molecular Rotation.” Reviews
of Modern Physics, vol. 91, no. 3, 035005, American Physical Society, 2019,
doi:10.1103/revmodphys.91.035005.
short: C.P. Koch, M. Lemeshko, D. Sugny, Reviews of Modern Physics 91 (2019).
date_created: 2020-01-29T16:04:19Z
date_published: 2019-09-18T00:00:00Z
date_updated: 2024-02-28T13:15:33Z
day: '18'
department:
- _id: MiLe
doi: 10.1103/revmodphys.91.035005
external_id:
arxiv:
- '1810.11338'
isi:
- '000486661700001'
intvolume: ' 91'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1810.11338
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
publication: Reviews of Modern Physics
publication_identifier:
eissn:
- 1539-0756
issn:
- 0034-6861
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantum control of molecular rotation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 91
year: '2019'
...
---
_id: '7606'
abstract:
- lang: eng
text: We derive a tight lower bound on equivocation (conditional entropy), or equivalently
a tight upper bound on mutual information between a signal variable and channel
outputs. The bound is in terms of the joint distribution of the signals and maximum
a posteriori decodes (most probable signals given channel output). As part of
our derivation, we describe the key properties of the distribution of signals,
channel outputs and decodes, that minimizes equivocation and maximizes mutual
information. This work addresses a problem in data analysis, where mutual information
between signals and decodes is sometimes used to lower bound the mutual information
between signals and channel outputs. Our result provides a corresponding upper
bound.
article_number: '8989292'
article_processing_charge: No
author:
- first_name: Michal
full_name: Hledik, Michal
id: 4171253A-F248-11E8-B48F-1D18A9856A87
last_name: Hledik
- first_name: Thomas R
full_name: Sokolowski, Thomas R
id: 3E999752-F248-11E8-B48F-1D18A9856A87
last_name: Sokolowski
orcid: 0000-0002-1287-3779
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: 'Hledik M, Sokolowski TR, Tkačik G. A tight upper bound on mutual information.
In: IEEE Information Theory Workshop, ITW 2019. IEEE; 2019. doi:10.1109/ITW44776.2019.8989292'
apa: 'Hledik, M., Sokolowski, T. R., & Tkačik, G. (2019). A tight upper bound
on mutual information. In IEEE Information Theory Workshop, ITW 2019. Visby,
Sweden: IEEE. https://doi.org/10.1109/ITW44776.2019.8989292'
chicago: Hledik, Michal, Thomas R Sokolowski, and Gašper Tkačik. “A Tight Upper
Bound on Mutual Information.” In IEEE Information Theory Workshop, ITW 2019.
IEEE, 2019. https://doi.org/10.1109/ITW44776.2019.8989292.
ieee: M. Hledik, T. R. Sokolowski, and G. Tkačik, “A tight upper bound on mutual
information,” in IEEE Information Theory Workshop, ITW 2019, Visby, Sweden,
2019.
ista: Hledik M, Sokolowski TR, Tkačik G. 2019. A tight upper bound on mutual information.
IEEE Information Theory Workshop, ITW 2019. Information Theory Workshop, 8989292.
mla: Hledik, Michal, et al. “A Tight Upper Bound on Mutual Information.” IEEE
Information Theory Workshop, ITW 2019, 8989292, IEEE, 2019, doi:10.1109/ITW44776.2019.8989292.
short: M. Hledik, T.R. Sokolowski, G. Tkačik, in:, IEEE Information Theory Workshop,
ITW 2019, IEEE, 2019.
conference:
end_date: 2019-08-28
location: Visby, Sweden
name: Information Theory Workshop
start_date: 2019-08-25
date_created: 2020-03-22T23:00:47Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2024-03-06T14:22:51Z
day: '01'
department:
- _id: GaTk
doi: 10.1109/ITW44776.2019.8989292
ec_funded: 1
external_id:
arxiv:
- '1812.01475'
isi:
- '000540384500015'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1812.01475
month: '08'
oa: 1
oa_version: Preprint
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: IEEE Information Theory Workshop, ITW 2019
publication_identifier:
isbn:
- '9781538669006'
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '15020'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: A tight upper bound on mutual information
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6933'
abstract:
- lang: eng
text: "We design fast deterministic algorithms for distance computation in the CONGESTED
CLIQUE model. Our key contributions include:\r\n\r\n - A (2+ε)-approximation for
all-pairs shortest paths problem in O(log²n / ε) rounds on unweighted undirected
graphs. With a small additional additive factor, this also applies for weighted
graphs. This is the first sub-polynomial constant-factor approximation for APSP
in this model.\r\n - A (1+ε)-approximation for multi-source shortest paths problem
from O(√n) sources in O(log² n / ε) rounds on weighted undirected graphs. This
is the first sub-polynomial algorithm obtaining this approximation for a set of
sources of polynomial size.\r\n\r\nOur main techniques are new distance tools
that are obtained via improved algorithms for sparse matrix multiplication, which
we leverage to construct efficient hopsets and shortest paths. Furthermore, our
techniques extend to additional distance problems for which we improve upon the
state-of-the-art, including diameter approximation, and an exact single-source
shortest paths algorithm for weighted undirected graphs in Õ(n^{1/6}) rounds."
article_processing_charge: No
author:
- first_name: Keren
full_name: Censor-Hillel, Keren
last_name: Censor-Hillel
- first_name: Michal
full_name: Dory, Michal
last_name: Dory
- first_name: Janne
full_name: Korhonen, Janne
id: C5402D42-15BC-11E9-A202-CA2BE6697425
last_name: Korhonen
- first_name: Dean
full_name: Leitersdorf, Dean
last_name: Leitersdorf
citation:
ama: 'Censor-Hillel K, Dory M, Korhonen J, Leitersdorf D. Fast approximate shortest
paths in the congested clique. In: Proceedings of the 2019 ACM Symposium on
Principles of Distributed Computin. ACM; 2019:74-83. doi:10.1145/3293611.3331633'
apa: 'Censor-Hillel, K., Dory, M., Korhonen, J., & Leitersdorf, D. (2019). Fast
approximate shortest paths in the congested clique. In Proceedings of the 2019
ACM Symposium on Principles of Distributed Computin (pp. 74–83). Toronto,
ON, Canada: ACM. https://doi.org/10.1145/3293611.3331633'
chicago: Censor-Hillel, Keren, Michal Dory, Janne Korhonen, and Dean Leitersdorf.
“Fast Approximate Shortest Paths in the Congested Clique.” In Proceedings of
the 2019 ACM Symposium on Principles of Distributed Computin, 74–83. ACM,
2019. https://doi.org/10.1145/3293611.3331633.
ieee: K. Censor-Hillel, M. Dory, J. Korhonen, and D. Leitersdorf, “Fast approximate
shortest paths in the congested clique,” in Proceedings of the 2019 ACM Symposium
on Principles of Distributed Computin, Toronto, ON, Canada, 2019, pp. 74–83.
ista: 'Censor-Hillel K, Dory M, Korhonen J, Leitersdorf D. 2019. Fast approximate
shortest paths in the congested clique. Proceedings of the 2019 ACM Symposium
on Principles of Distributed Computin. PODC: Symposium on Principles of Distributed
Computing, 74–83.'
mla: Censor-Hillel, Keren, et al. “Fast Approximate Shortest Paths in the Congested
Clique.” Proceedings of the 2019 ACM Symposium on Principles of Distributed
Computin, ACM, 2019, pp. 74–83, doi:10.1145/3293611.3331633.
short: K. Censor-Hillel, M. Dory, J. Korhonen, D. Leitersdorf, in:, Proceedings
of the 2019 ACM Symposium on Principles of Distributed Computin, ACM, 2019, pp.
74–83.
conference:
end_date: 2019-08-02
location: Toronto, ON, Canada
name: 'PODC: Symposium on Principles of Distributed Computing'
start_date: 2019-07-29
date_created: 2019-10-08T12:48:42Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2024-03-07T14:43:38Z
day: '01'
department:
- _id: DaAl
doi: 10.1145/3293611.3331633
external_id:
arxiv:
- '1903.05956'
isi:
- '000570442000011'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1903.05956
month: '08'
oa: 1
oa_version: Preprint
page: 74-83
publication: Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin
publication_identifier:
isbn:
- '9781450362177'
publication_status: published
publisher: ACM
quality_controlled: '1'
related_material:
record:
- id: '7939'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Fast approximate shortest paths in the congested clique
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2019'
...
---
_id: '15147'
abstract:
- lang: eng
text: Circadian rhythms are generated by a transcription-based feedback loop where
CLOCK:BMAL1 drive transcription of their repressors (PER1/2, CRY1/2), which bind
to CLOCK:BMAL1 to close the feedback loop with ~24-hour periodicity. Here we identify
a key biochemical and structural difference between CRY1 and CRY2 that underlies
their differential strengths as transcriptional repressors. While both cryptochromes
bind the BMAL1 transactivation domain with similar affinity to sequester it from
coactivators, CRY1 is recruited with much higher affinity to the PAS domain core
of CLOCK:BMAL1, allowing it to serve as a stronger repressor that lengthens circadian
period. We identify a dynamic loop in the secondary pocket that regulates differential
binding of cryptochromes to the PAS domain core. Notably, PER2 binding remodels
this loop in CRY2 to enhance its affinity for CLOCK:BMAL1, explaining why CRY2
forms an obligate heterodimer with PER2, while CRY1 is capable of repressing CLOCK:BMAL1
both with and without PER2.
article_processing_charge: No
author:
- first_name: Jennifer L.
full_name: Fribourgh, Jennifer L.
last_name: Fribourgh
- first_name: Ashutosh
full_name: Srivastava, Ashutosh
last_name: Srivastava
- first_name: Colby R.
full_name: Sandate, Colby R.
last_name: Sandate
- first_name: Alicia
full_name: Michael, Alicia
id: 6437c950-2a03-11ee-914d-d6476dd7b75c
last_name: Michael
orcid: 0000-0002-6080-839X
- first_name: Peter L.
full_name: Hsu, Peter L.
last_name: Hsu
- first_name: Christin
full_name: Rakers, Christin
last_name: Rakers
- first_name: Leslee T.
full_name: Nguyen, Leslee T.
last_name: Nguyen
- first_name: Megan R.
full_name: Torgrimson, Megan R.
last_name: Torgrimson
- first_name: Gian Carlo G.
full_name: Parico, Gian Carlo G.
last_name: Parico
- first_name: Sarvind
full_name: Tripathi, Sarvind
last_name: Tripathi
- first_name: Ning
full_name: Zheng, Ning
last_name: Zheng
- first_name: Gabriel C.
full_name: Lander, Gabriel C.
last_name: Lander
- first_name: Tsuyoshi
full_name: Hirota, Tsuyoshi
last_name: Hirota
- first_name: Florence
full_name: Tama, Florence
last_name: Tama
- first_name: Carrie L.
full_name: Partch, Carrie L.
last_name: Partch
citation:
ama: Fribourgh JL, Srivastava A, Sandate CR, et al. Protein dynamics regulate distinct
biochemical properties of cryptochromes in mammalian circadian rhythms. bioRxiv.
2019. doi:10.1101/740464
apa: Fribourgh, J. L., Srivastava, A., Sandate, C. R., Michael, A. K., Hsu, P. L.,
Rakers, C., … Partch, C. L. (2019). Protein dynamics regulate distinct biochemical
properties of cryptochromes in mammalian circadian rhythms. bioRxiv. https://doi.org/10.1101/740464
chicago: Fribourgh, Jennifer L., Ashutosh Srivastava, Colby R. Sandate, Alicia K.
Michael, Peter L. Hsu, Christin Rakers, Leslee T. Nguyen, et al. “Protein Dynamics
Regulate Distinct Biochemical Properties of Cryptochromes in Mammalian Circadian
Rhythms.” BioRxiv, 2019. https://doi.org/10.1101/740464.
ieee: J. L. Fribourgh et al., “Protein dynamics regulate distinct biochemical
properties of cryptochromes in mammalian circadian rhythms,” bioRxiv. 2019.
ista: Fribourgh JL, Srivastava A, Sandate CR, Michael AK, Hsu PL, Rakers C, Nguyen
LT, Torgrimson MR, Parico GCG, Tripathi S, Zheng N, Lander GC, Hirota T, Tama
F, Partch CL. 2019. Protein dynamics regulate distinct biochemical properties
of cryptochromes in mammalian circadian rhythms. bioRxiv, 10.1101/740464.
mla: Fribourgh, Jennifer L., et al. “Protein Dynamics Regulate Distinct Biochemical
Properties of Cryptochromes in Mammalian Circadian Rhythms.” BioRxiv, 2019,
doi:10.1101/740464.
short: J.L. Fribourgh, A. Srivastava, C.R. Sandate, A.K. Michael, P.L. Hsu, C. Rakers,
L.T. Nguyen, M.R. Torgrimson, G.C.G. Parico, S. Tripathi, N. Zheng, G.C. Lander,
T. Hirota, F. Tama, C.L. Partch, BioRxiv (2019).
date_created: 2024-03-21T07:51:10Z
date_published: 2019-08-20T00:00:00Z
date_updated: 2024-03-25T12:44:44Z
day: '20'
doi: 10.1101/740464
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/740464
month: '08'
oa: 1
oa_version: None
publication: bioRxiv
publication_status: published
status: public
title: Protein dynamics regulate distinct biochemical properties of cryptochromes
in mammalian circadian rhythms
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '6392'
abstract:
- lang: eng
text: "The regulation of gene expression is one of the most fundamental processes
in living systems. In recent years, thanks to advances in sequencing technology
and automation, it has become possible to study gene expression quantitatively,
genome-wide and in high-throughput. This leads to the possibility of exploring
changes in gene expression in the context of many external perturbations and their
combinations, and thus of characterising the basic principles governing gene regulation.
In this thesis, I present quantitative experimental approaches to studying transcriptional
and protein level changes in response to combinatorial drug treatment, as well
as a theoretical data-driven approach to analysing thermodynamic principles guiding
transcription of protein coding genes. \r\nIn the first part of this work, I
present a novel methodological framework for quantifying gene expression changes
in drug combinations, termed isogrowth profiling. External perturbations through
small molecule drugs influence the growth rate of the cell, leading to wide-ranging
changes in cellular physiology and gene expression. This confounds the gene expression
changes specifically elicited by the particular drug. Combinatorial perturbations,
owing to the increased stress they exert, influence the growth rate even more
strongly and hence suffer the convolution problem to a greater extent when measuring
gene expression changes. Isogrowth profiling is a way to experimentally abstract
non-specific, growth rate related changes, by performing the measurement using
varying ratios of two drugs at such concentrations that the overall inhibition
rate is constant. Using a robotic setup for automated high-throughput re-dilution
culture of Saccharomyces cerevisiae, the budding yeast, I investigate all pairwise
interactions of four small molecule drugs through sequencing RNA along a growth
isobole. Through principal component analysis, I demonstrate here that isogrowth
profiling can uncover drug-specific as well as drug-interaction-specific gene
expression changes. I show that drug-interaction-specific gene expression changes
can be used for prediction of higher-order drug interactions. I propose a simplified
generalised framework of isogrowth profiling, with few measurements needed for
each drug pair, enabling the broad application of isogrowth profiling to high-throughput
screening of inhibitors of cellular growth and beyond. Such high-throughput screenings
of gene expression changes specific to pairwise drug interactions will be instrumental
for predicting the higher-order interactions of the drugs.\r\n\r\nIn the second
part of this work, I extend isogrowth profiling to single-cell measurements of
gene expression, characterising population heterogeneity in the budding yeast
in response to combinatorial drug perturbation while controlling for non-specific
growth rate effects. Through flow cytometry of strains with protein products fused
to green fluorescent protein, I discover multiple proteins with bi-modally distributed
expression levels in the population in response to drug treatment. I characterize
more closely the effect of an ionic stressor, lithium chloride, and find that
it inhibits the splicing of mRNA, most strongly affecting ribosomal protein transcripts
and leading to a bi-stable behaviour of a small ribosomal subunit protein Rps22B.
Time-lapse microscopy of a microfluidic culture system revealed that the induced
Rps22B heterogeneity leads to preferential survival of Rps22B-low cells after
long starvation, but to preferential proliferation of Rps22B-high cells after
short starvation. Overall, this suggests that yeast cells might use splicing of
ribosomal genes for bet-hedging in fluctuating environments. I give specific examples
of how further exploration of cellular heterogeneity in yeast in response to external
perturbation has the potential to reveal yet-undiscovered gene regulation circuitry.\r\n\r\nIn
the last part of this thesis, a re-analysis of a published sequencing dataset
of nascent elongating transcripts is used to characterise the thermodynamic constraints
for RNA polymerase II (RNAP) elongation. Population-level data on RNAP position
throughout the transcribed genome with single nucleotide resolution are used to
infer the sequence specific thermodynamic determinants of RNAP pausing and backtracking.
This analysis reveals that the basepairing strength of the eight nucleotide-long
RNA:DNA duplex relative to the basepairing strength of the same sequence when
in DNA:DNA duplex, and the change in this quantity during RNA polymerase movement,
is the key determinant of RNAP pausing. This is true for RNAP pausing while elongating,
but also of RNAP pausing while backtracking and of the backtracking length. The
quantitative dependence of RNAP pausing on basepairing energetics is used to infer
the increase in pausing due to transcriptional mismatches, leading to a hypothesis
that pervasive RNA polymerase II pausing is due to basepairing energetics, as
an evolutionary cost for increased RNA polymerase II fidelity.\r\n\r\nThis work
advances our understanding of the general principles governing gene expression,
with the goal of making computational predictions of single-cell gene expression
responses to combinatorial perturbations based on the individual perturbations
possible. This ability would substantially facilitate the design of drug combination
treatments and, in the long term, lead to our increased ability to more generally
design targeted manipulations to any biological system. "
acknowledged_ssus:
- _id: LifeSc
- _id: M-Shop
- _id: Bio
alternative_title:
- IST Austria Thesis
author:
- first_name: Martin
full_name: Lukacisin, Martin
id: 298FFE8C-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisin
orcid: 0000-0001-6549-4177
citation:
ama: Lukacisin M. Quantitative investigation of gene expression principles through
combinatorial drug perturbation and theory. 2019. doi:10.15479/AT:ISTA:6392
apa: Lukacisin, M. (2019). Quantitative investigation of gene expression principles
through combinatorial drug perturbation and theory. IST Austria. https://doi.org/10.15479/AT:ISTA:6392
chicago: Lukacisin, Martin. “Quantitative Investigation of Gene Expression Principles
through Combinatorial Drug Perturbation and Theory.” IST Austria, 2019. https://doi.org/10.15479/AT:ISTA:6392.
ieee: M. Lukacisin, “Quantitative investigation of gene expression principles through
combinatorial drug perturbation and theory,” IST Austria, 2019.
ista: Lukacisin M. 2019. Quantitative investigation of gene expression principles
through combinatorial drug perturbation and theory. IST Austria.
mla: Lukacisin, Martin. Quantitative Investigation of Gene Expression Principles
through Combinatorial Drug Perturbation and Theory. IST Austria, 2019, doi:10.15479/AT:ISTA:6392.
short: M. Lukacisin, Quantitative Investigation of Gene Expression Principles through
Combinatorial Drug Perturbation and Theory, IST Austria, 2019.
date_created: 2019-05-09T19:53:00Z
date_published: 2019-05-09T00:00:00Z
date_updated: 2023-09-22T09:19:41Z
day: '09'
ddc:
- '570'
department:
- _id: ToBo
doi: 10.15479/AT:ISTA:6392
extern: '1'
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date_created: 2019-05-10T13:51:49Z
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date_created: 2019-05-10T14:13:42Z
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embargo: 2020-04-17
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file_date_updated: 2021-02-11T11:17:16Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '103'
publication_identifier:
isbn:
- 978-3-99078-001-5
issn:
- 2663-337X
publication_status: published
publisher: IST Austria
related_material:
record:
- id: '1029'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
title: Quantitative investigation of gene expression principles through combinatorial
drug perturbation and theory
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...