---
_id: '14530'
abstract:
- lang: eng
text: 'Most motions of many-body systems at any scale in nature with sufficient
degrees of freedom tend to be chaotic; reaching from the orbital motion of planets,
the air currents in our atmosphere, down to the water flowing through our pipelines
or the movement of a population of bacteria. To the observer it is therefore intriguing
when a moving collective exhibits order. Collective motion of flocks of birds,
schools of fish or swarms of self-propelled particles or robots have been studied
extensively over the past decades but the mechanisms involved in the transition
from chaos to order remain unclear. Here, the interactions, that in most systems
give rise to chaos, sustain order. In this thesis we investigate mechanisms that
preserve, destabilize or lead to the ordered state. We show that endothelial cells
migrating in circular confinements transition to a collective rotating state and
concomitantly synchronize the frequencies of nucleating actin waves within individual
cells. Consequently, the frequency dependent cell migration speed uniformizes
across the population. Complementary to the WAVE dependent nucleation of traveling
actin waves, we show that in leukocytes the actin polymerization depending on
WASp generates pushing forces locally at stationary patches. Next, in pipe flows,
we study methods to disrupt the self--sustaining cycle of turbulence and therefore
relaminarize the flow. While we find in pulsating flow conditions that turbulence
emerges through a helical instability during the decelerating phase. Finally,
we show quantitatively in brain slices of mice that wild-type control neurons
can compensate the migratory deficits of a genetically modified neuronal sub--population
in the developing cortex. '
acknowledged_ssus:
- _id: M-Shop
- _id: Bio
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Michael
full_name: Riedl, Michael
id: 3BE60946-F248-11E8-B48F-1D18A9856A87
last_name: Riedl
orcid: 0000-0003-4844-6311
citation:
ama: Riedl M. Synchronization in collectively moving active matter. 2023. doi:10.15479/14530
apa: Riedl, M. (2023). Synchronization in collectively moving active matter.
Institute of Science and Technology Austria. https://doi.org/10.15479/14530
chicago: Riedl, Michael. “Synchronization in Collectively Moving Active Matter.”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14530.
ieee: M. Riedl, “Synchronization in collectively moving active matter,” Institute
of Science and Technology Austria, 2023.
ista: Riedl M. 2023. Synchronization in collectively moving active matter. Institute
of Science and Technology Austria.
mla: Riedl, Michael. Synchronization in Collectively Moving Active Matter.
Institute of Science and Technology Austria, 2023, doi:10.15479/14530.
short: M. Riedl, Synchronization in Collectively Moving Active Matter, Institute
of Science and Technology Austria, 2023.
date_created: 2023-11-15T09:59:03Z
date_published: 2023-11-16T00:00:00Z
date_updated: 2023-11-30T10:55:13Z
day: '16'
ddc:
- '530'
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MiSi
doi: 10.15479/14530
file:
- access_level: open_access
checksum: 52e1d0ab6c1abe59c82dfe8c9ff5f83a
content_type: application/pdf
creator: mriedl
date_created: 2023-11-15T09:52:54Z
date_updated: 2023-11-15T09:52:54Z
file_id: '14536'
file_name: Thesis_Riedl_2023_corr.pdf
file_size: 36743942
relation: main_file
success: 1
file_date_updated: 2023-11-15T09:52:54Z
has_accepted_license: '1'
keyword:
- Synchronization
- Collective Movement
- Active Matter
- Cell Migration
- Active Colloids
language:
- iso: eng
month: '11'
oa: 1
oa_version: Updated Version
page: '260'
publication_identifier:
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10703'
relation: part_of_dissertation
status: public
- id: '10791'
relation: part_of_dissertation
status: public
- id: '7932'
relation: part_of_dissertation
status: public
- id: '461'
relation: part_of_dissertation
status: public
- id: '12726'
relation: old_edition
status: public
status: public
supervisor:
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
title: Synchronization in collectively moving active matter
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14547'
abstract:
- lang: eng
text: "Superconductor-semiconductor heterostructures currently capture a significant
amount of research interest and they serve as the physical platform in many proposals
towards topological quantum computation.\r\nDespite being under extensive investigations,
historically using transport techniques, the basic properties of the interface
between the superconductor and the semiconductor remain to be understood.\r\n\r\nIn
this thesis, two separate studies on the Al-InAs heterostructures are reported
with the first focusing on the physics of the material motivated by the emergence
of a new phase, the Bogoliubov-Fermi surface. \r\nThe second focuses on a technological
application, a gate-tunable Josephson parametric amplifier.\r\n\r\nIn the first
study, we investigate the hypothesized unconventional nature of the induced superconductivity
at the interface between the Al thin film and the InAs quantum well.\r\nWe embed
a two-dimensional Al-InAs hybrid system in a resonant microwave circuit allowing
measurements of change in inductance.\r\nThe behaviour of the resonance in a range
of temperature and in-plane magnetic field has been studied and compared with
the theory of conventional s-wave superconductor and a two-component theory that
includes both contribution of the $s$-wave pairing in Al and the intraband $p
\\pm ip$ pairing in InAs.\r\nMeasuring the temperature dependence of resonant
frequency, no discrepancy is found between data and the conventional theory.\r\nWe
observe the breakdown of superconductivity due to an applied magnetic field which
contradicts the conventional theory.\r\nIn contrast, the data can be captured
quantitatively by fitting to a two-component model.\r\nWe find the evidence of
the intraband $p \\pm ip$ pairing in the InAs and the emergence of the Bogoliubov-Fermi
surfaces due to magnetic field with the characteristic value $B^* = 0.33~\\mathrm{T}$.\r\nFrom
the fits, the sheet resistance of Al, the carrier density and mobility in InAs
are determined.\r\nBy systematically studying the anisotropy of the circuit response,
we find weak anisotropy for $B < B^*$ and increasingly strong anisotropy for $B
> B^*$ resulting in a pronounced two-lobe structure in polar plot of frequency
versus field angle.\r\nStrong resemblance between the field dependence of dissipation
and superfluid density hints at a hidden signature of the Bogoliubov-Fermi surface
that is burried in the dissipation data.\r\n\r\nIn the second study, we realize
a parametric amplifier with a Josephson field effect transistor as the active
element.\r\nThe device's modest construction consists of a gated SNS weak link
embedded at the center of a coplanar waveguide resonator.\r\nBy applying a gate
voltage, the resonant frequency is field-effect tunable over a range of 2 GHz.\r\nModelling
the JoFET minimally as a parallel RL circuit, the dissipation introduced by the
JoFET can be quantitatively related to the gate voltage.\r\nWe observed gate-tunable
Kerr nonlinearity qualitatively in line with expectation.\r\nThe JoFET amplifier
has 20 dB of gain, 4 MHz of instantaneous bandwidth, and a 1dB compression point
of -125.5 dBm when operated at a fixed resonant frequency.\r\nIn general, the
signal-to-noise ratio is improved by 5-7 dB when the JoFET amplifier is activated
compared.\r\nThe noise of the measurement chain and insertion loss of relevant
circuit elements are calibrated to determine the expected and the real noise performance
of the JoFET amplifier.\r\nAs a quantification of the noise performance, the measured
total input-referred noise of the JoFET amplifier is in good agreement with the
estimated expectation which takes device loss into account.\r\nWe found that the
noise performance of the device reported in this document approaches one photon
of total input-referred added noise which is the quantum limit imposed in nondegenerate
parametric amplifier."
acknowledged_ssus:
- _id: NanoFab
- _id: Bio
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Duc T
full_name: Phan, Duc T
id: 29C8C0B4-F248-11E8-B48F-1D18A9856A87
last_name: Phan
citation:
ama: Phan DT. Resonant microwave spectroscopy of Al-InAs. 2023. doi:10.15479/14547
apa: Phan, D. T. (2023). Resonant microwave spectroscopy of Al-InAs. Institute
of Science and Technology Austria. https://doi.org/10.15479/14547
chicago: Phan, Duc T. “Resonant Microwave Spectroscopy of Al-InAs.” Institute of
Science and Technology Austria, 2023. https://doi.org/10.15479/14547.
ieee: D. T. Phan, “Resonant microwave spectroscopy of Al-InAs,” Institute of Science
and Technology Austria, 2023.
ista: Phan DT. 2023. Resonant microwave spectroscopy of Al-InAs. Institute of Science
and Technology Austria.
mla: Phan, Duc T. Resonant Microwave Spectroscopy of Al-InAs. Institute of
Science and Technology Austria, 2023, doi:10.15479/14547.
short: D.T. Phan, Resonant Microwave Spectroscopy of Al-InAs, Institute of Science
and Technology Austria, 2023.
date_created: 2023-11-17T13:45:26Z
date_published: 2023-11-16T00:00:00Z
date_updated: 2023-11-30T10:56:04Z
day: '16'
ddc:
- '530'
degree_awarded: PhD
department:
- _id: GradSch
- _id: AnHi
doi: 10.15479/14547
file:
- access_level: open_access
checksum: db0c37d213bc002125bd59690e9db246
content_type: application/pdf
creator: pduc
date_created: 2023-11-17T13:36:44Z
date_updated: 2023-11-22T09:46:06Z
file_id: '14548'
file_name: Phan_Thesis_pdfa.pdf
file_size: 34828019
relation: main_file
- access_level: closed
checksum: 8d3bd6afa279a0078ffd13e06bb6d56d
content_type: application/zip
creator: pduc
date_created: 2023-11-17T13:44:53Z
date_updated: 2023-11-17T13:47:54Z
file_id: '14549'
file_name: dissertation_src.zip
file_size: 279319709
relation: source_file
file_date_updated: 2023-11-22T09:46:06Z
has_accepted_license: '1'
keyword:
- superconductor-semiconductor
- superconductivity
- Al
- InAs
- p-wave
- superconductivity
- JPA
- microwave
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '11'
oa: 1
oa_version: Published Version
page: '80'
publication_identifier:
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10851'
relation: part_of_dissertation
status: public
- id: '13264'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
title: Resonant microwave spectroscopy of Al-InAs
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '13264'
abstract:
- lang: eng
text: "We build a parametric amplifier with a Josephson field-effect transistor
(JoFET) as the active element. The resonant frequency of the device is field-effect
tunable over a range of 2 GHz. The JoFET amplifier has 20 dB of gain, 4 MHz of
instantaneous bandwidth, and a 1-dB compression point of -125.5 dBm when operated
at a fixed resonance frequency.\r\n\r\n"
acknowledged_ssus:
- _id: NanoFab
- _id: M-Shop
acknowledgement: We thank Shyam Shankar for helpful feedback on the manuscript. We
gratefully acknowledge the support of the ISTA nanofabrication facility, the Miba
Machine Shop, and the eMachine Shop. The NYU team acknowledges support from Army
Research Office Grant No. W911NF2110303.
article_number: '064032'
article_processing_charge: No
article_type: original
author:
- first_name: Duc T
full_name: Phan, Duc T
id: 29C8C0B4-F248-11E8-B48F-1D18A9856A87
last_name: Phan
- first_name: Paul
full_name: Falthansl-Scheinecker, Paul
id: 85b43b21-15b2-11ec-abd3-e2c252cc2285
last_name: Falthansl-Scheinecker
- first_name: Umang
full_name: Mishra, Umang
id: 4328fa4c-f128-11eb-9611-c107b0fe4d51
last_name: Mishra
- first_name: W. M.
full_name: Strickland, W. M.
last_name: Strickland
- first_name: D.
full_name: Langone, D.
last_name: Langone
- first_name: J.
full_name: Shabani, J.
last_name: Shabani
- 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: Phan DT, Falthansl-Scheinecker P, Mishra U, et al. Gate-tunable superconductor-semiconductor
parametric amplifier. Physical Review Applied. 2023;19(6). doi:10.1103/PhysRevApplied.19.064032
apa: Phan, D. T., Falthansl-Scheinecker, P., Mishra, U., Strickland, W. M., Langone,
D., Shabani, J., & Higginbotham, A. P. (2023). Gate-tunable superconductor-semiconductor
parametric amplifier. Physical Review Applied. American Physical Society.
https://doi.org/10.1103/PhysRevApplied.19.064032
chicago: Phan, Duc T, Paul Falthansl-Scheinecker, Umang Mishra, W. M. Strickland,
D. Langone, J. Shabani, and Andrew P Higginbotham. “Gate-Tunable Superconductor-Semiconductor
Parametric Amplifier.” Physical Review Applied. American Physical Society,
2023. https://doi.org/10.1103/PhysRevApplied.19.064032.
ieee: D. T. Phan et al., “Gate-tunable superconductor-semiconductor parametric
amplifier,” Physical Review Applied, vol. 19, no. 6. American Physical
Society, 2023.
ista: Phan DT, Falthansl-Scheinecker P, Mishra U, Strickland WM, Langone D, Shabani
J, Higginbotham AP. 2023. Gate-tunable superconductor-semiconductor parametric
amplifier. Physical Review Applied. 19(6), 064032.
mla: Phan, Duc T., et al. “Gate-Tunable Superconductor-Semiconductor Parametric
Amplifier.” Physical Review Applied, vol. 19, no. 6, 064032, American Physical
Society, 2023, doi:10.1103/PhysRevApplied.19.064032.
short: D.T. Phan, P. Falthansl-Scheinecker, U. Mishra, W.M. Strickland, D. Langone,
J. Shabani, A.P. Higginbotham, Physical Review Applied 19 (2023).
date_created: 2023-07-23T22:01:12Z
date_published: 2023-06-09T00:00:00Z
date_updated: 2023-11-30T10:56:03Z
day: '09'
department:
- _id: AnHi
- _id: OnHo
doi: 10.1103/PhysRevApplied.19.064032
external_id:
arxiv:
- '2206.05746'
isi:
- '001012022600004'
intvolume: ' 19'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2206.05746
month: '06'
oa: 1
oa_version: Preprint
publication: Physical Review Applied
publication_identifier:
eissn:
- 2331-7019
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '14547'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Gate-tunable superconductor-semiconductor parametric amplifier
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 19
year: '2023'
...
---
_id: '14587'
abstract:
- lang: eng
text: "This thesis concerns the application of variational methods to the study
of evolution problems arising in fluid mechanics and in material sciences. The
main focus is on weak-strong stability properties of some curvature driven interface
evolution problems, such as the two-phase Navier–Stokes flow with surface tension
and multiphase mean curvature flow, and on the phase-field approximation of the
latter. Furthermore, we discuss a variational approach to the study of a class
of doubly nonlinear wave equations.\r\nFirst, we consider the two-phase Navier–Stokes
flow with surface tension within a bounded domain. The two fluids are immiscible
and separated by a sharp interface, which intersects the boundary of the domain
at a constant contact angle of ninety degree. We devise a suitable concept of
varifolds solutions for the associated interface evolution problem and we establish
a weak-strong uniqueness principle in case of a two dimensional ambient space.
In order to focus on the boundary effects and on the singular geometry of the
evolving domains, we work for simplicity in the regime of same viscosities for
the two fluids.\r\nThe core of the thesis consists in the rigorous proof of the
convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature
flow for a suitable class of multi- well potentials and for well-prepared initial
data. We even establish a rate of convergence. Our relative energy approach relies
on the concept of gradient-flow calibration for branching singularities in multiphase
mean curvature flow and thus enables us to overcome the limitations of other approaches.
To the best of the author’s knowledge, our result is the first quantitative and
unconditional one available in the literature for the vectorial/multiphase setting.\r\nThis
thesis also contains a first study of weak-strong stability for planar multiphase
mean curvature flow beyond the singularity resulting from a topology change. Previous
weak-strong results are indeed limited to time horizons before the first topology
change of the strong solution. We consider circular topology changes and we prove
weak-strong stability for BV solutions to planar multiphase mean curvature flow
beyond the associated singular times by dynamically adapting the strong solutions
to the weak one by means of a space-time shift.\r\nIn the context of interface
evolution problems, our proofs for the main results of this thesis are based on
the relative energy technique, relying on novel suitable notions of relative energy
functionals, which in particular measure the interface error. Our statements follow
from the resulting stability estimates for the relative energy associated to the
problem.\r\nAt last, we introduce a variational approach to the study of nonlinear
evolution problems. This approach hinges on the minimization of a parameter dependent
family of convex functionals over entire trajectories, known as Weighted Inertia-Dissipation-Energy
(WIDE) functionals. We consider a class of doubly nonlinear wave equations and
establish the convergence, up to subsequences, of the associated WIDE minimizers
to a solution of the target problem as the parameter goes to zero."
acknowledgement: The research projects contained in this thesis have received funding
from the European Research Council (ERC) under the European Union’s Horizon 2020
research and innovation programme (grant agreement No 948819).
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Alice
full_name: Marveggio, Alice
id: 25647992-AA84-11E9-9D75-8427E6697425
last_name: Marveggio
citation:
ama: Marveggio A. Weak-strong stability and phase-field approximation of interface
evolution problems in fluid mechanics and in material sciences. 2023. doi:10.15479/at:ista:14587
apa: Marveggio, A. (2023). Weak-strong stability and phase-field approximation
of interface evolution problems in fluid mechanics and in material sciences.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14587
chicago: Marveggio, Alice. “Weak-Strong Stability and Phase-Field Approximation
of Interface Evolution Problems in Fluid Mechanics and in Material Sciences.”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14587.
ieee: A. Marveggio, “Weak-strong stability and phase-field approximation of interface
evolution problems in fluid mechanics and in material sciences,” Institute of
Science and Technology Austria, 2023.
ista: Marveggio A. 2023. Weak-strong stability and phase-field approximation of
interface evolution problems in fluid mechanics and in material sciences. Institute
of Science and Technology Austria.
mla: Marveggio, Alice. Weak-Strong Stability and Phase-Field Approximation of
Interface Evolution Problems in Fluid Mechanics and in Material Sciences.
Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14587.
short: A. Marveggio, Weak-Strong Stability and Phase-Field Approximation of Interface
Evolution Problems in Fluid Mechanics and in Material Sciences, Institute of Science
and Technology Austria, 2023.
date_created: 2023-11-21T11:41:05Z
date_published: 2023-11-21T00:00:00Z
date_updated: 2023-11-30T13:25:03Z
day: '21'
ddc:
- '515'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JuFi
doi: 10.15479/at:ista:14587
ec_funded: 1
file:
- access_level: open_access
checksum: 6c7db4cc86da6cdc79f7f358dc7755d4
content_type: application/pdf
creator: amarvegg
date_created: 2023-11-29T09:09:31Z
date_updated: 2023-11-29T09:09:31Z
file_id: '14626'
file_name: thesis_Marveggio.pdf
file_size: 2881100
relation: main_file
success: 1
- access_level: open_access
checksum: 52f28bdf95ec82cff39f3685f9c48e7d
content_type: application/zip
creator: amarvegg
date_created: 2023-11-29T09:10:19Z
date_updated: 2023-11-29T09:28:30Z
file_id: '14627'
file_name: Thesis_Marveggio.zip
file_size: 10189696
relation: source_file
file_date_updated: 2023-11-29T09:28:30Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '228'
project:
- _id: 0aa76401-070f-11eb-9043-b5bb049fa26d
call_identifier: H2020
grant_number: '948819'
name: Bridging Scales in Random Materials
publication_identifier:
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11842'
relation: part_of_dissertation
status: public
- id: '14597'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
title: Weak-strong stability and phase-field approximation of interface evolution
problems in fluid mechanics and in material sciences
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14591'
abstract:
- lang: eng
text: Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth
and development by controlling plasma membrane protein composition and cargo uptake.
CME relies on the precise recruitment of regulators for vesicle maturation and
release. Homologues of components of mammalian vesicle scission are strong candidates
to be part of the scissin machinery in plants, but the precise roles of these
proteins in this process is not fully understood. Here, we characterised the roles
of Plant Dynamin-Related Proteins 2 (DRP2s) and SH3-domain containing protein
2 (SH3P2), the plant homologue to Dynamins’ recruiters, like Endophilin and Amphiphysin,
in the CME by combining high-resolution imaging of endocytic events in vivo and
characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive
similarly late during CME and physically interact, genetic analysis of the Dsh3p1,2,3
triple-mutant and complementation assays with non-SH3P2-interacting DRP2 variants
suggests that SH3P2 does not directly recruit DRP2s to the site of endocytosis.
These observations imply that despite the presence of many well-conserved endocytic
components, plants have acquired a distinct mechanism for CME. One Sentence Summary
In contrast to predictions based on mammalian systems, plant Dynamin-related proteins
2 are recruited to the site of Clathrin-mediated endocytosis independently of
BAR-SH3 proteins.
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: Bio
article_processing_charge: No
author:
- first_name: Nataliia
full_name: Gnyliukh, Nataliia
id: 390C1120-F248-11E8-B48F-1D18A9856A87
last_name: Gnyliukh
orcid: 0000-0002-2198-0509
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
- first_name: Marie-Kristin
full_name: Nagel, Marie-Kristin
last_name: Nagel
- first_name: Aline
full_name: Monzer, Aline
id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425
last_name: Monzer
- first_name: Annamaria
full_name: Hlavata, Annamaria
id: 36062FEC-F248-11E8-B48F-1D18A9856A87
last_name: Hlavata
- first_name: Erika
full_name: Isono, Erika
last_name: Isono
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Gnyliukh N, Johnson AJ, Nagel M-K, et al. Role of dynamin-related proteins
2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv. doi:10.1101/2023.10.09.561523
apa: Gnyliukh, N., Johnson, A. J., Nagel, M.-K., Monzer, A., Hlavata, A., Isono,
E., … Friml, J. (n.d.). Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated
endocytosis in plants. bioRxiv. https://doi.org/10.1101/2023.10.09.561523
chicago: Gnyliukh, Nataliia, Alexander J Johnson, Marie-Kristin Nagel, Aline Monzer,
Annamaria Hlavata, Erika Isono, Martin Loose, and Jiří Friml. “Role of Dynamin-Related
Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” BioRxiv,
n.d. https://doi.org/10.1101/2023.10.09.561523.
ieee: N. Gnyliukh et al., “Role of dynamin-related proteins 2 and SH3P2 in
clathrin-mediated endocytosis in plants,” bioRxiv. .
ista: Gnyliukh N, Johnson AJ, Nagel M-K, Monzer A, Hlavata A, Isono E, Loose M,
Friml J. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis
in plants. bioRxiv, 10.1101/2023.10.09.561523.
mla: Gnyliukh, Nataliia, et al. “Role of Dynamin-Related Proteins 2 and SH3P2 in
Clathrin-Mediated Endocytosis in Plants.” BioRxiv, doi:10.1101/2023.10.09.561523.
short: N. Gnyliukh, A.J. Johnson, M.-K. Nagel, A. Monzer, A. Hlavata, E. Isono,
M. Loose, J. Friml, BioRxiv (n.d.).
date_created: 2023-11-22T10:17:49Z
date_published: 2023-10-10T00:00:00Z
date_updated: 2023-12-01T13:51:06Z
day: '10'
department:
- _id: JiFr
- _id: MaLo
- _id: CaBe
doi: 10.1101/2023.10.09.561523
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/2023.10.09.561523v2
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: bioRxiv
publication_status: submitted
related_material:
record:
- id: '14510'
relation: dissertation_contains
status: public
status: public
title: Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis
in plants
type: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14639'
abstract:
- lang: eng
text: "Background: Biallelic variants in OGDHL, encoding part of the α-ketoglutarate
dehydrogenase complex, have been associated with highly heterogeneous neurological
and neurodevelopmental disorders. However, the validity of this association remains
to be confirmed. A second OGDHL patient cohort was recruited to carefully assess
the gene-disease relationship.\r\nMethods: Using an unbiased genotype-first approach,
we screened large, multiethnic aggregated sequencing datasets worldwide for biallelic
OGDHL variants. We used CRISPR/Cas9 to generate zebrafish knockouts of ogdhl,
ogdh paralogs, and dhtkd1 to investigate functional relationships and impact during
development. Functional complementation with patient variant transcripts was conducted
to systematically assess protein functionality as a readout for pathogenicity.\r\nResults:
A cohort of 14 individuals from 12 unrelated families exhibited highly variable
clinical phenotypes, with the majority of them presenting at least one additional
variant, potentially accounting for a blended phenotype and complicating phenotypic
understanding. We also uncovered extreme clinical heterogeneity and high allele
frequencies, occasionally incompatible with a fully penetrant recessive disorder.
Human cDNA of previously described and new variants were tested in an ogdhl zebrafish
knockout model, adding functional evidence for variant reclassification. We disclosed
evidence of hypomorphic alleles as well as a loss-of-function variant without
deleterious effects in zebrafish variant testing also showing discordant familial
segregation, challenging the relationship of OGDHL as a conventional Mendelian
gene. Going further, we uncovered evidence for a complex compensatory relationship
among OGDH, OGDHL, and DHTKD1 isoenzymes that are associated with neurodevelopmental
disorders and exhibit complex transcriptional compensation patterns with partial
functional redundancy.\r\nConclusions: Based on the results of genetic, clinical,
and functional studies, we formed three hypotheses in which to frame observations:
biallelic OGDHL variants lead to a highly variable monogenic disorder, variants
in OGDHL are following a complex pattern of inheritance, or they may not be causative
at all. Our study further highlights the continuing challenges of assessing the
validity of reported disease-gene associations and effects of variants identified
in these genes. This is particularly more complicated in making genetic diagnoses
based on identification of variants in genes presenting a highly heterogenous
phenotype such as “OGDHL-related disorders”."
article_number: '102'
article_processing_charge: Yes
article_type: original
author:
- first_name: Sheng-Jia
full_name: Lin, Sheng-Jia
last_name: Lin
- first_name: Barbara
full_name: Vona, Barbara
last_name: Vona
- first_name: Tracy
full_name: Lau, Tracy
last_name: Lau
- first_name: Kevin
full_name: Huang, Kevin
id: 3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3
last_name: Huang
orcid: 0000-0002-2512-7812
- first_name: Maha S.
full_name: Zaki, Maha S.
last_name: Zaki
- first_name: Huda Shujaa
full_name: Aldeen, Huda Shujaa
last_name: Aldeen
- first_name: Ehsan Ghayoor
full_name: Karimiani, Ehsan Ghayoor
last_name: Karimiani
- first_name: Clarissa
full_name: Rocca, Clarissa
last_name: Rocca
- first_name: Mahmoud M.
full_name: Noureldeen, Mahmoud M.
last_name: Noureldeen
- first_name: Ahmed K.
full_name: Saad, Ahmed K.
last_name: Saad
- first_name: Cassidy
full_name: Petree, Cassidy
last_name: Petree
- first_name: Tobias
full_name: Bartolomaeus, Tobias
last_name: Bartolomaeus
- first_name: Rami
full_name: Abou Jamra, Rami
last_name: Abou Jamra
- first_name: Giovanni
full_name: Zifarelli, Giovanni
last_name: Zifarelli
- first_name: Aditi
full_name: Gotkhindikar, Aditi
last_name: Gotkhindikar
- first_name: Ingrid M.
full_name: Wentzensen, Ingrid M.
last_name: Wentzensen
- first_name: Mingjuan
full_name: Liao, Mingjuan
last_name: Liao
- first_name: Emalyn Elise
full_name: Cork, Emalyn Elise
last_name: Cork
- first_name: Pratishtha
full_name: Varshney, Pratishtha
last_name: Varshney
- first_name: Narges
full_name: Hashemi, Narges
last_name: Hashemi
- first_name: Mohammad Hasan
full_name: Mohammadi, Mohammad Hasan
last_name: Mohammadi
- first_name: Aboulfazl
full_name: Rad, Aboulfazl
last_name: Rad
- first_name: Juanita
full_name: Neira, Juanita
last_name: Neira
- first_name: Mehran Beiraghi
full_name: Toosi, Mehran Beiraghi
last_name: Toosi
- first_name: Cordula
full_name: Knopp, Cordula
last_name: Knopp
- first_name: Ingo
full_name: Kurth, Ingo
last_name: Kurth
- first_name: Thomas D.
full_name: Challman, Thomas D.
last_name: Challman
- first_name: Rebecca
full_name: Smith, Rebecca
last_name: Smith
- first_name: Asmahan
full_name: Abdalla, Asmahan
last_name: Abdalla
- first_name: Thomas
full_name: Haaf, Thomas
last_name: Haaf
- first_name: Mohnish
full_name: Suri, Mohnish
last_name: Suri
- first_name: Manali
full_name: Joshi, Manali
last_name: Joshi
- first_name: Wendy K.
full_name: Chung, Wendy K.
last_name: Chung
- first_name: Andres
full_name: Moreno-De-Luca, Andres
last_name: Moreno-De-Luca
- first_name: Henry
full_name: Houlden, Henry
last_name: Houlden
- first_name: Reza
full_name: Maroofian, Reza
last_name: Maroofian
- first_name: Gaurav K.
full_name: Varshney, Gaurav K.
last_name: Varshney
citation:
ama: Lin S-J, Vona B, Lau T, et al. Evaluating the association of biallelic OGDHL
variants with significant phenotypic heterogeneity. Genome Medicine. 2023;15.
doi:10.1186/s13073-023-01258-4
apa: Lin, S.-J., Vona, B., Lau, T., Huang, K., Zaki, M. S., Aldeen, H. S., … Varshney,
G. K. (2023). Evaluating the association of biallelic OGDHL variants with significant
phenotypic heterogeneity. Genome Medicine. Springer Nature. https://doi.org/10.1186/s13073-023-01258-4
chicago: Lin, Sheng-Jia, Barbara Vona, Tracy Lau, Kevin Huang, Maha S. Zaki, Huda
Shujaa Aldeen, Ehsan Ghayoor Karimiani, et al. “Evaluating the Association of
Biallelic OGDHL Variants with Significant Phenotypic Heterogeneity.” Genome
Medicine. Springer Nature, 2023. https://doi.org/10.1186/s13073-023-01258-4.
ieee: S.-J. Lin et al., “Evaluating the association of biallelic OGDHL variants
with significant phenotypic heterogeneity,” Genome Medicine, vol. 15. Springer
Nature, 2023.
ista: Lin S-J, Vona B, Lau T, Huang K, Zaki MS, Aldeen HS, Karimiani EG, Rocca C,
Noureldeen MM, Saad AK, Petree C, Bartolomaeus T, Abou Jamra R, Zifarelli G, Gotkhindikar
A, Wentzensen IM, Liao M, Cork EE, Varshney P, Hashemi N, Mohammadi MH, Rad A,
Neira J, Toosi MB, Knopp C, Kurth I, Challman TD, Smith R, Abdalla A, Haaf T,
Suri M, Joshi M, Chung WK, Moreno-De-Luca A, Houlden H, Maroofian R, Varshney
GK. 2023. Evaluating the association of biallelic OGDHL variants with significant
phenotypic heterogeneity. Genome Medicine. 15, 102.
mla: Lin, Sheng-Jia, et al. “Evaluating the Association of Biallelic OGDHL Variants
with Significant Phenotypic Heterogeneity.” Genome Medicine, vol. 15, 102,
Springer Nature, 2023, doi:10.1186/s13073-023-01258-4.
short: S.-J. Lin, B. Vona, T. Lau, K. Huang, M.S. Zaki, H.S. Aldeen, E.G. Karimiani,
C. Rocca, M.M. Noureldeen, A.K. Saad, C. Petree, T. Bartolomaeus, R. Abou Jamra,
G. Zifarelli, A. Gotkhindikar, I.M. Wentzensen, M. Liao, E.E. Cork, P. Varshney,
N. Hashemi, M.H. Mohammadi, A. Rad, J. Neira, M.B. Toosi, C. Knopp, I. Kurth,
T.D. Challman, R. Smith, A. Abdalla, T. Haaf, M. Suri, M. Joshi, W.K. Chung, A.
Moreno-De-Luca, H. Houlden, R. Maroofian, G.K. Varshney, Genome Medicine 15 (2023).
date_created: 2023-12-04T08:10:55Z
date_published: 2023-11-23T00:00:00Z
date_updated: 2023-12-04T08:17:22Z
day: '23'
ddc:
- '570'
doi: 10.1186/s13073-023-01258-4
extern: '1'
file:
- access_level: open_access
checksum: 279efd212005549aba817a487d56d363
content_type: application/pdf
creator: dernst
date_created: 2023-12-04T08:15:43Z
date_updated: 2023-12-04T08:15:43Z
file_id: '14640'
file_name: 2023_GenomeMed_Lin.pdf
file_size: 14791081
relation: main_file
success: 1
file_date_updated: 2023-12-04T08:15:43Z
has_accepted_license: '1'
intvolume: ' 15'
keyword:
- Genetics (clinical)
- Genetics
- Molecular Biology
- Molecular Medicine
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '11'
oa: 1
oa_version: Published Version
publication: Genome Medicine
publication_identifier:
issn:
- 1756-994X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Evaluating the association of biallelic OGDHL variants with significant phenotypic
heterogeneity
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: 15
year: '2023'
...
---
_id: '14628'
abstract:
- lang: eng
text: We introduce a compact, intuitive procedural graph representation for cellular
metamaterials, which are small-scale, tileable structures that can be architected
to exhibit many useful material properties. Because the structures’ “architectures”
vary widely—with elements such as beams, thin shells, and solid bulks—it is difficult
to explore them using existing representations. Generic approaches like voxel
grids are versatile, but it is cumbersome to represent and edit individual structures;
architecture-specific approaches address these issues, but are incompatible with
one another. By contrast, our procedural graph succinctly represents the construction
process for any structure using a simple skeleton annotated with spatially varying
thickness. To express the highly constrained triply periodic minimal surfaces
(TPMS) in this manner, we present the first fully automated version of the conjugate
surface construction method, which allows novices to create complex TPMS from
intuitive input. We demonstrate our representation’s expressiveness, accuracy,
and compactness by constructing a wide range of established structures and hundreds
of novel structures with diverse architectures and material properties. We also
conduct a user study to verify our representation’s ease-of-use and ability to
expand engineers’ capacity for exploration.
acknowledgement: "The authors thank Mina Konaković Luković and Michael Foshey for
their early contributions to this project, David Palmer and Paul Zhang for their
insightful discussions about minimal surfaces and the CSCM, Julian Panetta for providing
the Elastic Textures code, and Hannes Hergeth for his feedback and support. We also
thank our user study participants and anonymous reviewers.\r\nThis material is based
upon work supported by the National Science Foundation\r\n(NSF) Graduate Research
Fellowship under Grant No. 2141064; the MIT Morningside\r\nAcademy for Design Fellowship;
the Defense Advanced Research Projects Agency\r\n(DARPA) Grant No. FA8750-20-C-0075;
the ERC Consolidator Grant No. 101045083,\r\n“CoDiNA: Computational Discovery of
Numerical Algorithms for Animation and Simulation of Natural Phenomena”; and the
NewSat project, which is co-funded by the Operational Program for Competitiveness
and Internationalisation (COMPETE2020), Portugal 2020, the European Regional Development
Fund (ERDF), and the Portuguese Foundation for Science and Technology (FTC) under
the MIT Portugal program."
article_number: '168'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Liane
full_name: Makatura, Liane
last_name: Makatura
- first_name: Bohan
full_name: Wang, Bohan
last_name: Wang
- first_name: Yi-Lu
full_name: Chen, Yi-Lu
id: 0b467602-dbcd-11ea-9d1d-ed480aa46b70
last_name: Chen
- first_name: Bolei
full_name: Deng, Bolei
last_name: Deng
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Wojciech
full_name: Matusik, Wojciech
last_name: Matusik
citation:
ama: 'Makatura L, Wang B, Chen Y-L, et al. Procedural metamaterials: A unified procedural
graph for metamaterial design. ACM Transactions on Graphics. 2023;42(5).
doi:10.1145/3605389'
apa: 'Makatura, L., Wang, B., Chen, Y.-L., Deng, B., Wojtan, C., Bickel, B., &
Matusik, W. (2023). Procedural metamaterials: A unified procedural graph for metamaterial
design. ACM Transactions on Graphics. Association for Computing Machinery.
https://doi.org/10.1145/3605389'
chicago: 'Makatura, Liane, Bohan Wang, Yi-Lu Chen, Bolei Deng, Chris Wojtan, Bernd
Bickel, and Wojciech Matusik. “Procedural Metamaterials: A Unified Procedural
Graph for Metamaterial Design.” ACM Transactions on Graphics. Association
for Computing Machinery, 2023. https://doi.org/10.1145/3605389.'
ieee: 'L. Makatura et al., “Procedural metamaterials: A unified procedural
graph for metamaterial design,” ACM Transactions on Graphics, vol. 42,
no. 5. Association for Computing Machinery, 2023.'
ista: 'Makatura L, Wang B, Chen Y-L, Deng B, Wojtan C, Bickel B, Matusik W. 2023.
Procedural metamaterials: A unified procedural graph for metamaterial design.
ACM Transactions on Graphics. 42(5), 168.'
mla: 'Makatura, Liane, et al. “Procedural Metamaterials: A Unified Procedural Graph
for Metamaterial Design.” ACM Transactions on Graphics, vol. 42, no. 5,
168, Association for Computing Machinery, 2023, doi:10.1145/3605389.'
short: L. Makatura, B. Wang, Y.-L. Chen, B. Deng, C. Wojtan, B. Bickel, W. Matusik,
ACM Transactions on Graphics 42 (2023).
date_created: 2023-11-29T15:02:03Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2023-12-04T08:09:05Z
day: '01'
ddc:
- '531'
- '006'
department:
- _id: GradSch
- _id: ChWo
- _id: BeBi
doi: 10.1145/3605389
file:
- access_level: open_access
checksum: 0192f597d7a2ceaf89baddfd6190d4c8
content_type: application/zip
creator: yichen
date_created: 2023-11-29T15:16:01Z
date_updated: 2023-11-29T15:16:01Z
file_id: '14630'
file_name: tog-22-0089-File004.zip
file_size: 95467870
relation: main_file
success: 1
- access_level: open_access
checksum: 7fb024963be81933494f38de191e4710
content_type: application/zip
creator: yichen
date_created: 2023-11-29T15:16:01Z
date_updated: 2023-11-29T15:16:01Z
file_id: '14631'
file_name: tog-22-0089-File005.zip
file_size: 103731880
relation: main_file
success: 1
- access_level: open_access
checksum: b7d6829ce396e21cac9fae0ec7130a6b
content_type: application/pdf
creator: dernst
date_created: 2023-12-04T08:04:14Z
date_updated: 2023-12-04T08:04:14Z
file_id: '14638'
file_name: 2023_ACMToG_Makatura.pdf
file_size: 57067476
relation: main_file
success: 1
file_date_updated: 2023-12-04T08:04:14Z
has_accepted_license: '1'
intvolume: ' 42'
issue: '5'
keyword:
- Computer Graphics and Computer-Aided Design
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088
grant_number: '101045083'
name: Computational Discovery of Numerical Algorithms for Animation and Simulation
of Natural Phenomena
publication: ACM Transactions on Graphics
publication_identifier:
issn:
- 0730-0301
- 1557-7368
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
status: public
title: 'Procedural metamaterials: A unified procedural graph for metamaterial design'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2023'
...
---
_id: '14644'
abstract:
- lang: eng
text: Transcription by RNA polymerase II (Pol II) can be repressed by noncoding
RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs
repress transcription remains unclear. Here we present cryo-electron microscopy
structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA
and RNA bind to Pol II during transcription elongation. Further, we show how domains
of the general transcription factor TFIIF affect complex dynamics and control
repressive activity. Together, we reveal how a non-coding RNA can regulate mammalian
gene expression.
acknowledged_ssus:
- _id: LifeSc
- _id: EM-Fac
- _id: PreCl
acknowledgement: "We thank B. Kaczmarek and other members of the Bernecky lab for
helpful discussions. We thank V.-V. Hodirnau for SerialEM data collection and support
with EPU data collection. We thank D. Slade for the wild type TFIIF expression\r\nplasmid.
We thank N. Thompson and R. Burgess for the 8WG16 hybridoma cell line. We thank
C. Plaschka and M. Loose for critical reading of the manuscript. This work was supported
by Austrian Science Fund (FWF) grant P34185. This research was further supported
by the Scientific Service Units (SSU) of IST Austria through resources provided
by the Lab Support Facility (LSF), Electron Microscopy Facility (EMF), Scientific
Computing (SciComp), and the Preclinical Facility (PCF)."
article_processing_charge: No
author:
- first_name: Katarina
full_name: Tluckova, Katarina
id: 4AC7D980-F248-11E8-B48F-1D18A9856A87
last_name: Tluckova
- first_name: Anita P
full_name: Testa Salmazo, Anita P
id: 41F1F098-F248-11E8-B48F-1D18A9856A87
last_name: Testa Salmazo
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
citation:
ama: Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional
repression by noncoding RNA. doi:10.15479/AT:ISTA:14644
apa: Tluckova, K., Testa Salmazo, A. P., & Bernecky, C. (n.d.). Mechanism of
mammalian transcriptional repression by noncoding RNA. Institute of Science and
Technology Austria. https://doi.org/10.15479/AT:ISTA:14644
chicago: Tluckova, Katarina, Anita P Testa Salmazo, and Carrie Bernecky. “Mechanism
of Mammalian Transcriptional Repression by Noncoding RNA.” Institute of Science
and Technology Austria, n.d. https://doi.org/10.15479/AT:ISTA:14644.
ieee: K. Tluckova, A. P. Testa Salmazo, and C. Bernecky, “Mechanism of mammalian
transcriptional repression by noncoding RNA.” Institute of Science and Technology
Austria.
ista: Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional
repression by noncoding RNA. 10.15479/AT:ISTA:14644.
mla: Tluckova, Katarina, et al. Mechanism of Mammalian Transcriptional Repression
by Noncoding RNA. Institute of Science and Technology Austria, doi:10.15479/AT:ISTA:14644.
short: K. Tluckova, A.P. Testa Salmazo, C. Bernecky, (n.d.).
date_created: 2023-12-04T14:51:00Z
date_published: 2023-12-05T00:00:00Z
date_updated: 2023-12-05T10:37:28Z
day: '05'
ddc:
- '572'
department:
- _id: CaBe
doi: 10.15479/AT:ISTA:14644
file:
- access_level: open_access
checksum: c45608cb97ee36d7b50ba518db8e07b0
content_type: application/pdf
creator: dernst
date_created: 2023-12-05T10:37:02Z
date_updated: 2023-12-05T10:37:02Z
file_id: '14646'
file_name: 2023_Tluckova_etal_REx.pdf
file_size: 4892920
relation: main_file
success: 1
file_date_updated: 2023-12-05T10:37:02Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '12'
oa: 1
oa_version: Submitted Version
project:
- _id: c08a6700-5a5b-11eb-8a69-82a722b2bc30
grant_number: P34185
name: Regulation of mammalian transcription by noncoding RNA
publication_status: submitted
publisher: Institute of Science and Technology Austria
status: public
title: Mechanism of mammalian transcriptional repression by noncoding RNA
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: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14641'
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
- _id: CampIT
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Mike
full_name: Hennessey-Wesen, Mike
id: 3F338C72-F248-11E8-B48F-1D18A9856A87
last_name: Hennessey-Wesen
citation:
ama: Hennessey-Wesen M. Adaptive mutation in E. coli modulated by luxS. 2023. doi:10.15479/at:ista:14641
apa: Hennessey-Wesen, M. (2023). Adaptive mutation in E. coli modulated by luxS.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14641
chicago: Hennessey-Wesen, Mike. “Adaptive Mutation in E. Coli Modulated by LuxS.”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14641.
ieee: M. Hennessey-Wesen, “Adaptive mutation in E. coli modulated by luxS,” Institute
of Science and Technology Austria, 2023.
ista: Hennessey-Wesen M. 2023. Adaptive mutation in E. coli modulated by luxS. Institute
of Science and Technology Austria.
mla: Hennessey-Wesen, Mike. Adaptive Mutation in E. Coli Modulated by LuxS.
Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14641.
short: M. Hennessey-Wesen, Adaptive Mutation in E. Coli Modulated by LuxS, Institute
of Science and Technology Austria, 2023.
date_created: 2023-12-04T13:17:37Z
date_published: 2023-11-30T00:00:00Z
date_updated: 2023-12-07T14:12:25Z
day: '30'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: BjHo
doi: 10.15479/at:ista:14641
ec_funded: 1
file:
- access_level: closed
checksum: 4127c285b34f4bf7fb31ef24f9d14c25
content_type: application/vnd.oasis.opendocument.text
creator: mhenness
date_created: 2023-12-06T13:13:26Z
date_updated: 2023-12-06T13:13:26Z
file_id: '14648'
file_name: mike_thesis_v06-12-2023.odt
file_size: 46405919
relation: source_file
- access_level: closed
checksum: f5203a61eddaf35235bbc51904d73982
content_type: application/pdf
creator: mhenness
date_created: 2023-12-06T13:14:15Z
date_updated: 2023-12-06T13:14:15Z
embargo: 2024-11-30
embargo_to: open_access
file_id: '14649'
file_name: mike_thesis_v06-12-2023.pdf
file_size: 21282155
relation: main_file
file_date_updated: 2023-12-06T13:14:15Z
has_accepted_license: '1'
keyword:
- microfluidics
- miceobiology
- mutations
- quorum sensing
language:
- iso: eng
month: '11'
oa_version: Published Version
page: '104'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
title: Adaptive mutation in E. coli modulated by luxS
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14658'
abstract:
- lang: eng
text: "We investigate spin-charge separation of a spin-\r\n1\r\n2\r\n Fermi system
confined in a triple well where multiple bands are occupied. We assume that our
finite fermionic system is close to fully spin polarized while being doped by
a hole and an impurity fermion with opposite spin. Our setup involves ferromagnetic
couplings among the particles in different bands, leading to the development of
strong spin-transport correlations in an intermediate interaction regime. Interactions
are then strong enough to lift the degeneracy among singlet and triplet spin configurations
in the well of the spin impurity but not strong enough to prohibit hole-induced
magnetic excitations to the singlet state. Despite the strong spin-hole correlations,
the system exhibits spin-charge deconfinement allowing for long-range entanglement
of the spatial and spin degrees of freedom."
acknowledgement: This work has been funded by the Cluster of Excellence “Advanced
Imaging of Matter” of the Deutsche Forschungsgemeinschaft (DFG)-EXC 2056-Project
ID No. 390715994. G.M.K. gratefully acknowledges funding from the European Union’s
Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie
Grant Agreement No. 101034413.
article_number: '043039'
article_processing_charge: Yes
article_type: original
author:
- first_name: J. M.
full_name: Becker, J. M.
last_name: Becker
- first_name: Georgios
full_name: Koutentakis, Georgios
id: d7b23d3a-9e21-11ec-b482-f76739596b95
last_name: Koutentakis
- first_name: P.
full_name: Schmelcher, P.
last_name: Schmelcher
citation:
ama: Becker JM, Koutentakis G, Schmelcher P. Spin-charge correlations in finite
one-dimensional multiband Fermi systems. Physical Review Research. 2023;5(4).
doi:10.1103/PhysRevResearch.5.043039
apa: Becker, J. M., Koutentakis, G., & Schmelcher, P. (2023). Spin-charge correlations
in finite one-dimensional multiband Fermi systems. Physical Review Research.
American Physical Society. https://doi.org/10.1103/PhysRevResearch.5.043039
chicago: Becker, J. M., Georgios Koutentakis, and P. Schmelcher. “Spin-Charge Correlations
in Finite One-Dimensional Multiband Fermi Systems.” Physical Review Research.
American Physical Society, 2023. https://doi.org/10.1103/PhysRevResearch.5.043039.
ieee: J. M. Becker, G. Koutentakis, and P. Schmelcher, “Spin-charge correlations
in finite one-dimensional multiband Fermi systems,” Physical Review Research,
vol. 5, no. 4. American Physical Society, 2023.
ista: Becker JM, Koutentakis G, Schmelcher P. 2023. Spin-charge correlations in
finite one-dimensional multiband Fermi systems. Physical Review Research. 5(4),
043039.
mla: Becker, J. M., et al. “Spin-Charge Correlations in Finite One-Dimensional Multiband
Fermi Systems.” Physical Review Research, vol. 5, no. 4, 043039, American
Physical Society, 2023, doi:10.1103/PhysRevResearch.5.043039.
short: J.M. Becker, G. Koutentakis, P. Schmelcher, Physical Review Research 5 (2023).
date_created: 2023-12-10T23:00:58Z
date_published: 2023-10-12T00:00:00Z
date_updated: 2023-12-11T10:55:52Z
day: '12'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1103/PhysRevResearch.5.043039
ec_funded: 1
external_id:
arxiv:
- '2305.09529'
file:
- access_level: open_access
checksum: ee31c0d0de5d1b65591990ae6705a601
content_type: application/pdf
creator: dernst
date_created: 2023-12-11T10:49:07Z
date_updated: 2023-12-11T10:49:07Z
file_id: '14672'
file_name: 2023_PhysReviewResearch_Becker.pdf
file_size: 2362158
relation: main_file
success: 1
file_date_updated: 2023-12-11T10:49:07Z
has_accepted_license: '1'
intvolume: ' 5'
issue: '4'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Physical Review Research
publication_identifier:
issn:
- 2643-1564
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spin-charge correlations in finite one-dimensional multiband Fermi systems
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: 5
year: '2023'
...
---
_id: '14650'
abstract:
- lang: eng
text: We study the out-of-equilibrium quantum dynamics of dipolar polarons, i.e.,
impurities immersed in a dipolar Bose-Einstein condensate, after a quench of the
impurity-boson interaction. We show that the dipolar nature of the condensate
and of the impurity results in anisotropic relaxation dynamics, in particular,
anisotropic dressing of the polaron. More relevantly for cold-atom setups, quench
dynamics is strongly affected by the interplay between dipolar anisotropy and
trap geometry. Our findings pave the way for simulating impurities in anisotropic
media utilizing experiments with dipolar mixtures.
acknowledgement: "We thank Lauriane Chomaz for useful discussions and comments on
the manuscript. We also\r\nthank Ragheed Al Hyder for comments on the manuscript.\r\nG.B.
acknowledges support from the Austrian Science Fund (FWF),\r\nunder Project No.
M2641-N27. This work is supported by the Deutsche Forschungsgemeinschaft (DFG, German
Research Foundation) under Germany’s Excellence Strategy EXC2181/1-\r\n390900948
(the Heidelberg STRUCTURES Excellence Cluster). A. G. V. acknowledges support from
the European Union’s Horizon 2020 research and innovation programme under the\r\nMarie
Skłodowska-Curie Grant Agreement No. 754411. L.A.P.A acknowledges by the PNRR\r\nMUR
project PE0000023 - NQSTI and the Deutsche Forschungsgemeinschaft (DFG, German\r\nResearch
Foundation) under Germany’s Excellence Strategy - EXC - 2123 Quantum Frontiers390837967
and FOR2247."
article_number: '232'
article_processing_charge: No
article_type: original
author:
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
- first_name: Luis
full_name: Santos, Luis
last_name: Santos
- first_name: Luisllu A.
full_name: Peña Ardila, Luisllu A.
last_name: Peña Ardila
citation:
ama: Volosniev A, Bighin G, Santos L, Peña Ardila LA. Non-equilibrium dynamics of
dipolar polarons. SciPost Physics. 2023;15(6). doi:10.21468/scipostphys.15.6.232
apa: Volosniev, A., Bighin, G., Santos, L., & Peña Ardila, L. A. (2023). Non-equilibrium
dynamics of dipolar polarons. SciPost Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.15.6.232
chicago: Volosniev, Artem, Giacomo Bighin, Luis Santos, and Luisllu A. Peña Ardila.
“Non-Equilibrium Dynamics of Dipolar Polarons.” SciPost Physics. SciPost
Foundation, 2023. https://doi.org/10.21468/scipostphys.15.6.232.
ieee: A. Volosniev, G. Bighin, L. Santos, and L. A. Peña Ardila, “Non-equilibrium
dynamics of dipolar polarons,” SciPost Physics, vol. 15, no. 6. SciPost
Foundation, 2023.
ista: Volosniev A, Bighin G, Santos L, Peña Ardila LA. 2023. Non-equilibrium dynamics
of dipolar polarons. SciPost Physics. 15(6), 232.
mla: Volosniev, Artem, et al. “Non-Equilibrium Dynamics of Dipolar Polarons.” SciPost
Physics, vol. 15, no. 6, 232, SciPost Foundation, 2023, doi:10.21468/scipostphys.15.6.232.
short: A. Volosniev, G. Bighin, L. Santos, L.A. Peña Ardila, SciPost Physics 15
(2023).
date_created: 2023-12-10T13:03:07Z
date_published: 2023-12-07T00:00:00Z
date_updated: 2023-12-11T07:44:08Z
day: '07'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.21468/scipostphys.15.6.232
ec_funded: 1
external_id:
arxiv:
- '2305.17969'
file:
- access_level: open_access
checksum: e664372a1fe9d628a9bb1d135ebab7d8
content_type: application/pdf
creator: dernst
date_created: 2023-12-11T07:42:04Z
date_updated: 2023-12-11T07:42:04Z
file_id: '14669'
file_name: 2023_SciPostPhysics_Volosniev.pdf
file_size: 3543541
relation: main_file
success: 1
file_date_updated: 2023-12-11T07:42:04Z
has_accepted_license: '1'
intvolume: ' 15'
issue: '6'
keyword:
- General Physics and Astronomy
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 26986C82-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02641
name: A path-integral approach to composite impurities
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: SciPost Physics
publication_identifier:
issn:
- 2542-4653
publication_status: published
publisher: SciPost Foundation
quality_controlled: '1'
status: public
title: Non-equilibrium dynamics of dipolar polarons
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: 15
year: '2023'
...
---
_id: '14653'
abstract:
- lang: eng
text: 'Mass spectrometry imaging (MSI) is a powerful analytical technique for the
two-dimensional (2D) localization of chemicals on surfaces. Conventional MSI experiments
require to predefine the surface of interest based on photographic or microscopic
images. Typically, these boundaries can no longer be changed or adjusted once
the experiment has been started. In terms of a more interactive approach we recently
developed a pen-like ionization interface which is directly connected to the mass
spectrometer. The device allows the user to ionize chemicals by desorption electrospray
ionization (DESI) and to freely move the interface over a surface of interest.
A mini camera, which is mounted on the tip of the pen, magnifies the desorption
area and enables a simple positioning of the pen. The combination of optical data
from the camera module and chemical data obtained by mass analysis facilitates
a novel type of imaging experiment: interactive mass spectrometry imaging (IMSI).
For this application, we present a novel approach for a robust, optical flow-based
motion detection. While the live video stream from the camera is used to track
the pen''s motion across the surface a post-acquisition algorithm correlates the
coordinates of the pen trajectory with respective mass spectra obtained from a
simultaneous mass spectrometric data acquisition. This algorithm is no longer
dependent on a single, manually applied optical marker on the sample surface,
which has to be visible on all video frames throughout the analysis. The advanced
DESI-IMSI method was successfully tested on inkjet-printed letters as well as
mouse brain tissue samples. Validation of the results was done by comparing DESI-IMSI
with standard DESI-MSI data.'
acknowledgement: We would like to thank Marco Sealey Cardona, PhD for help with the
mouse brain samples and acknowledge the financial support by 1669 Förderkreis of
the University of Innsbruck, Austria Wirtschaftsservice (AWS), D. Swarovski KG and
Tyrolean Science Fund (TWF).
article_number: '117168'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Florian
full_name: Kluibenschedl, Florian
id: 7499e70e-eb2c-11ec-b98b-f925648bc9d9
last_name: Kluibenschedl
- first_name: Anna
full_name: Ploner, Anna
last_name: Ploner
- first_name: Christina
full_name: Meisenbichler, Christina
last_name: Meisenbichler
- first_name: Robert
full_name: Konrat, Robert
last_name: Konrat
- first_name: Thomas
full_name: Müller, Thomas
last_name: Müller
citation:
ama: Kluibenschedl F, Ploner A, Meisenbichler C, Konrat R, Müller T. Advanced motion
tracking for interactive mass spectrometry imaging (IMSI). International Journal
of Mass Spectrometry. 2023;495. doi:10.1016/j.ijms.2023.117168
apa: Kluibenschedl, F., Ploner, A., Meisenbichler, C., Konrat, R., & Müller,
T. (2023). Advanced motion tracking for interactive mass spectrometry imaging
(IMSI). International Journal of Mass Spectrometry. Elsevier. https://doi.org/10.1016/j.ijms.2023.117168
chicago: Kluibenschedl, Florian, Anna Ploner, Christina Meisenbichler, Robert Konrat,
and Thomas Müller. “Advanced Motion Tracking for Interactive Mass Spectrometry
Imaging (IMSI).” International Journal of Mass Spectrometry. Elsevier,
2023. https://doi.org/10.1016/j.ijms.2023.117168.
ieee: F. Kluibenschedl, A. Ploner, C. Meisenbichler, R. Konrat, and T. Müller, “Advanced
motion tracking for interactive mass spectrometry imaging (IMSI),” International
Journal of Mass Spectrometry, vol. 495. Elsevier, 2023.
ista: Kluibenschedl F, Ploner A, Meisenbichler C, Konrat R, Müller T. 2023. Advanced
motion tracking for interactive mass spectrometry imaging (IMSI). International
Journal of Mass Spectrometry. 495, 117168.
mla: Kluibenschedl, Florian, et al. “Advanced Motion Tracking for Interactive Mass
Spectrometry Imaging (IMSI).” International Journal of Mass Spectrometry,
vol. 495, 117168, Elsevier, 2023, doi:10.1016/j.ijms.2023.117168.
short: F. Kluibenschedl, A. Ploner, C. Meisenbichler, R. Konrat, T. Müller, International
Journal of Mass Spectrometry 495 (2023).
date_created: 2023-12-10T23:00:57Z
date_published: 2023-11-23T00:00:00Z
date_updated: 2023-12-11T08:16:35Z
day: '23'
department:
- _id: GradSch
doi: 10.1016/j.ijms.2023.117168
intvolume: ' 495'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.ijms.2023.117168
month: '11'
oa: 1
oa_version: Published Version
publication: International Journal of Mass Spectrometry
publication_identifier:
issn:
- 1387-3806
publication_status: epub_ahead
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Advanced motion tracking for interactive mass spectrometry imaging (IMSI)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 495
year: '2023'
...
---
_id: '14647'
abstract:
- lang: eng
text: In the developing vertebrate central nervous system, neurons and glia typically
arise sequentially from common progenitors. Here, we report that the transcription
factor Forkhead Box G1 (Foxg1) regulates gliogenesis in the mouse neocortex via
distinct cell-autonomous roles in progenitors and in postmitotic neurons that
regulate different aspects of the gliogenic FGF signalling pathway. We demonstrate
that loss of Foxg1 in cortical progenitors at neurogenic stages causes premature
astrogliogenesis. We identify a novel FOXG1 target, the pro-gliogenic FGF pathway
component Fgfr3, which is suppressed by FOXG1 cell-autonomously to maintain neurogenesis.
Furthermore, FOXG1 can also suppress premature astrogliogenesis triggered by the
augmentation of FGF signalling. We identify a second novel function of FOXG1 in
regulating the expression of gliogenic ligand FGF18 in new born neocortical upper-layer
neurons. Loss of FOXG1 in postmitotic neurons increases Fgf18 expression and enhances
gliogenesis in the progenitors. These results fit well with the model that new
born neurons secrete cues that trigger progenitors to produce the next wave of
cell types, astrocytes. If FGF signalling is attenuated in Foxg1 null progenitors,
they progress to oligodendrocyte production. Therefore, loss of FOXG1 transitions
the progenitor to a gliogenic state, producing either astrocytes or oligodendrocytes
depending on FGF signalling levels. Our results uncover how FOXG1 integrates extrinsic
signalling via the FGF pathway to regulate the sequential generation of neurons,
astrocytes, and oligodendrocytes in the cerebral cortex.
acknowledgement: "We thank Dr. Shital Suryavanshi and the animal house staff of the
Tata Institute of\r\nFundamental Research (TIFR) for their excellent support; Gord
Fishell and Goichi Miyoshi for\r\nthe Foxg1 floxed mouse line; Hiroshi Kawasaki
for the plasmids pCAG-FGF8 and pCAGsFGFR3c. We thank Prof. S.K. Lee for the Foxg1lox/lox
genotyping primers and protocol. We thank Dr. Deepak Modi and Dr. Vainav Patel for
allowing us to use the NIRRCH FACS Facility and the staff of the NIRRCH and TIFR
FACS facilities for their assistance.\r\nWe thank Denis Jabaudon for his critical
comments on the manuscript and members of the\r\nJabaudon lab for helpful discussions.
This work was funded by the Department of Atomic\r\nEnergy (DAE), Govt. of India
(Project Identification no. RTI4003, DAE OM no.\r\n1303/2/2019/R&D-II/DAE/2079)."
article_processing_charge: No
author:
- first_name: Mahima
full_name: Bose, Mahima
last_name: Bose
- first_name: Varun
full_name: Suresh, Varun
last_name: Suresh
- first_name: Urvi
full_name: Mishra, Urvi
last_name: Mishra
- first_name: Ishita
full_name: Talwar, Ishita
last_name: Talwar
- first_name: Anuradha
full_name: Yadav, Anuradha
last_name: Yadav
- first_name: Shiona
full_name: Biswas, Shiona
last_name: Biswas
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Shubha
full_name: Tole, Shubha
last_name: Tole
citation:
ama: Bose M, Suresh V, Mishra U, et al. Dual role of FOXG1 in regulating gliogenesis
in the developing neocortex via the FGF signalling pathway. bioRxiv. doi:10.1101/2023.11.30.569337
apa: Bose, M., Suresh, V., Mishra, U., Talwar, I., Yadav, A., Biswas, S., … Tole,
S. (n.d.). Dual role of FOXG1 in regulating gliogenesis in the developing neocortex
via the FGF signalling pathway. bioRxiv. Cold Spring Harbor Laboratory.
https://doi.org/10.1101/2023.11.30.569337
chicago: Bose, Mahima, Varun Suresh, Urvi Mishra, Ishita Talwar, Anuradha Yadav,
Shiona Biswas, Simon Hippenmeyer, and Shubha Tole. “Dual Role of FOXG1 in Regulating
Gliogenesis in the Developing Neocortex via the FGF Signalling Pathway.” BioRxiv.
Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2023.11.30.569337.
ieee: M. Bose et al., “Dual role of FOXG1 in regulating gliogenesis in the
developing neocortex via the FGF signalling pathway,” bioRxiv. Cold Spring
Harbor Laboratory.
ista: Bose M, Suresh V, Mishra U, Talwar I, Yadav A, Biswas S, Hippenmeyer S, Tole
S. Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via
the FGF signalling pathway. bioRxiv, 10.1101/2023.11.30.569337.
mla: Bose, Mahima, et al. “Dual Role of FOXG1 in Regulating Gliogenesis in the Developing
Neocortex via the FGF Signalling Pathway.” BioRxiv, Cold Spring Harbor
Laboratory, doi:10.1101/2023.11.30.569337.
short: M. Bose, V. Suresh, U. Mishra, I. Talwar, A. Yadav, S. Biswas, S. Hippenmeyer,
S. Tole, BioRxiv (n.d.).
date_created: 2023-12-06T13:07:01Z
date_published: 2023-12-01T00:00:00Z
date_updated: 2023-12-11T07:37:17Z
day: '01'
department:
- _id: SiHi
doi: 10.1101/2023.11.30.569337
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2023.11.30.569337
month: '12'
oa: 1
oa_version: Preprint
publication: bioRxiv
publication_status: submitted
publisher: Cold Spring Harbor Laboratory
status: public
title: Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via
the FGF signalling pathway
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14655'
abstract:
- lang: eng
text: The kinetics of the assembly of semiflexible filaments through end-to-end
annealing is key to the structure of the cytoskeleton, but is not understood.
We analyze this problem through scaling theory and simulations, and uncover a
regime where filaments’ ends find each other through bending fluctuations without
the need for the whole filament to diffuse. This results in a very substantial
speedup of assembly in physiological regimes, and could help with understanding
the dynamics of actin and intermediate filaments in biological processes such
as wound healing and cell division.
acknowledgement: The authors thank C´ecile Leduc and Duc-Quang Tran for invaluable
help with understanding the experimental behavior of intermediate filaments, and
Raphael Voituriez, Nicolas Levernier, and Alexander Grosberg for fruitful discussion
on the theoretical model. V. S. also thanks Davide Michieletto, Maria Panoukidou,
and Lorenzo Rovigatti for very helpful suggestions on the simulation model. M. L.
was supported by Marie Curie Integration Grant No. PCIG12-GA-2012-334053, “Investissements
d’Avenir” LabEx PALM (ANR-10-LABX- 0039-PALM), ANR Grants No. ANR-15-CE13-0004-03,
No. ANR-21-CE11-0004-02 and No. ANR-22-CE30-0024, as well as ERC Starting Grant
No. 677532. M.L.’s group belongs to the CNRS consortium AQV. Part of this work was
performed using HPC resources from GENCI–IDRIS (Grants No. 2020-A0090712066 and
No. 2021-A0110712066).
article_number: '228401'
article_processing_charge: No
article_type: original
author:
- first_name: Valerio
full_name: Sorichetti, Valerio
id: ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b
last_name: Sorichetti
orcid: 0000-0002-9645-6576
- first_name: Martin
full_name: Lenz, Martin
last_name: Lenz
citation:
ama: Sorichetti V, Lenz M. Transverse fluctuations control the assembly of semiflexible
filaments. Physical Review Letters. 2023;131(22). doi:10.1103/PhysRevLett.131.228401
apa: Sorichetti, V., & Lenz, M. (2023). Transverse fluctuations control the
assembly of semiflexible filaments. Physical Review Letters. American Physical
Society. https://doi.org/10.1103/PhysRevLett.131.228401
chicago: Sorichetti, Valerio, and Martin Lenz. “Transverse Fluctuations Control
the Assembly of Semiflexible Filaments.” Physical Review Letters. American
Physical Society, 2023. https://doi.org/10.1103/PhysRevLett.131.228401.
ieee: V. Sorichetti and M. Lenz, “Transverse fluctuations control the assembly of
semiflexible filaments,” Physical Review Letters, vol. 131, no. 22. American
Physical Society, 2023.
ista: Sorichetti V, Lenz M. 2023. Transverse fluctuations control the assembly of
semiflexible filaments. Physical Review Letters. 131(22), 228401.
mla: Sorichetti, Valerio, and Martin Lenz. “Transverse Fluctuations Control the
Assembly of Semiflexible Filaments.” Physical Review Letters, vol. 131,
no. 22, 228401, American Physical Society, 2023, doi:10.1103/PhysRevLett.131.228401.
short: V. Sorichetti, M. Lenz, Physical Review Letters 131 (2023).
date_created: 2023-12-10T23:00:57Z
date_published: 2023-12-01T00:00:00Z
date_updated: 2023-12-11T07:59:25Z
day: '01'
department:
- _id: AnSa
doi: 10.1103/PhysRevLett.131.228401
external_id:
arxiv:
- '2303.03088'
intvolume: ' 131'
issue: '22'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2303.03088
month: '12'
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: Transverse fluctuations control the assembly of semiflexible filaments
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 131
year: '2023'
...
---
_id: '14660'
abstract:
- lang: eng
text: "The classical Steinitz theorem states that if the origin belongs to the interior
of the convex hull of a set \U0001D446⊂ℝ\U0001D451, then there are at most 2\U0001D451
points of \U0001D446 whose convex hull contains the origin in the interior. Bárány,
Katchalski,and Pach proved the following quantitative version of Steinitz’s theorem.
Let \U0001D444 be a convex polytope in ℝ\U0001D451 containing the standard Euclidean
unit ball \U0001D401\U0001D451. Then there exist at most 2\U0001D451 vertices
of \U0001D444 whose convex hull \U0001D444′ satisfies \U0001D45F\U0001D401\U0001D451⊂\U0001D444′
with \U0001D45F⩾\U0001D451−2\U0001D451. They conjectured that \U0001D45F⩾\U0001D450\U0001D451−1∕2
holds with a universal constant \U0001D450>0. We prove \U0001D45F⩾15\U0001D4512,
the first polynomial lower bound on \U0001D45F. Furthermore, we show that \U0001D45F
is not greater than 2/√\U0001D451."
acknowledgement: M.N. was supported by the János Bolyai Scholarship of the Hungarian
Academy of Sciences aswell as the National Research, Development and Innovation
Fund (NRDI) grants K119670 andK131529, and the ÚNKP-22-5 New National Excellence
Program of the Ministry for Innovationand Technology from the source of the NRDI
as well as the ELTE TKP 2021-NKTA-62 fundingscheme
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Grigory
full_name: Ivanov, Grigory
id: 87744F66-5C6F-11EA-AFE0-D16B3DDC885E
last_name: Ivanov
- first_name: Márton
full_name: Naszódi, Márton
last_name: Naszódi
citation:
ama: 'Ivanov G, Naszódi M. Quantitative Steinitz theorem: A polynomial bound. Bulletin
of the London Mathematical Society. 2023. doi:10.1112/blms.12965'
apa: 'Ivanov, G., & Naszódi, M. (2023). Quantitative Steinitz theorem: A polynomial
bound. Bulletin of the London Mathematical Society. London Mathematical
Society. https://doi.org/10.1112/blms.12965'
chicago: 'Ivanov, Grigory, and Márton Naszódi. “Quantitative Steinitz Theorem: A
Polynomial Bound.” Bulletin of the London Mathematical Society. London
Mathematical Society, 2023. https://doi.org/10.1112/blms.12965.'
ieee: 'G. Ivanov and M. Naszódi, “Quantitative Steinitz theorem: A polynomial bound,”
Bulletin of the London Mathematical Society. London Mathematical Society,
2023.'
ista: 'Ivanov G, Naszódi M. 2023. Quantitative Steinitz theorem: A polynomial bound.
Bulletin of the London Mathematical Society.'
mla: 'Ivanov, Grigory, and Márton Naszódi. “Quantitative Steinitz Theorem: A Polynomial
Bound.” Bulletin of the London Mathematical Society, London Mathematical
Society, 2023, doi:10.1112/blms.12965.'
short: G. Ivanov, M. Naszódi, Bulletin of the London Mathematical Society (2023).
date_created: 2023-12-10T23:00:58Z
date_published: 2023-12-04T00:00:00Z
date_updated: 2023-12-11T10:03:54Z
day: '04'
department:
- _id: UlWa
doi: 10.1112/blms.12965
external_id:
arxiv:
- '2212.04308'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.1112/blms.12965'
month: '12'
oa: 1
oa_version: Published Version
publication: Bulletin of the London Mathematical Society
publication_identifier:
eissn:
- 1469-2120
issn:
- 0024-6093
publication_status: epub_ahead
publisher: London Mathematical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Quantitative Steinitz theorem: A polynomial bound'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14666'
abstract:
- lang: eng
text: So-called spontaneous activity is a central hallmark of most nervous systems.
Such non-causal firing is contrary to the tenet of spikes as a means of communication,
and its purpose remains unclear. We propose that self-initiated firing can serve
as a release valve to protect neurons from the toxic conditions arising in mitochondria
from lower-than-baseline energy consumption. To demonstrate the viability of our
hypothesis, we built a set of models that incorporate recent experimental results
indicating homeostatic control of metabolic products—Adenosine triphosphate (ATP),
adenosine diphosphate (ADP), and reactive oxygen species (ROS)—by changes in firing.
We explore the relationship of metabolic cost of spiking with its effect on the
temporal patterning of spikes and reproduce experimentally observed changes in
intrinsic firing in the fruitfly dorsal fan-shaped body neuron in a model with
ROS-modulated potassium channels. We also show that metabolic spiking homeostasis
can produce indefinitely sustained avalanche dynamics in cortical circuits. Our
theory can account for key features of neuronal activity observed in many studies
ranging from ion channel function all the way to resting state dynamics. We finish
with a set of experimental predictions that would confirm an integrated, crucial
role for metabolically regulated spiking and firmly link metabolic homeostasis
and neuronal function.
acknowledgement: We thank Prof. C. Nazaret and Prof. J.-P. Mazat for sharing the code
of their mitochondrial model. We also thank G. Miesenböck, E. Marder, L. Abbott,
A. Kempf, P. Hasenhuetl, W. Podlaski, F. Zenke, E. Agnes, P. Bozelos, J. Watson,
B. Confavreux, and G. Christodoulou, and the rest of the Vogels Lab for their feedback.
This work was funded by Wellcome Trust and Royal Society Sir Henry Dale Research
Fellowship (WT100000), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z),
and a UK Research and Innovation, Biotechnology and Biological Sciences Research
Council grant (UKRI-BBSRC BB/N019512/1).
article_number: e2306525120
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Chaitanya
full_name: Chintaluri, Chaitanya
id: E4EDB536-3485-11EA-98D2-20AF3DDC885E
last_name: Chintaluri
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: Chintaluri C, Vogels TP. Metabolically regulated spiking could serve neuronal
energy homeostasis and protect from reactive oxygen species. Proceedings of
the National Academy of Sciences of the United States of America. 2023;120(48).
doi:10.1073/pnas.2306525120
apa: Chintaluri, C., & Vogels, T. P. (2023). Metabolically regulated spiking
could serve neuronal energy homeostasis and protect from reactive oxygen species.
Proceedings of the National Academy of Sciences of the United States of America.
National Academy of Sciences. https://doi.org/10.1073/pnas.2306525120
chicago: Chintaluri, Chaitanya, and Tim P Vogels. “Metabolically Regulated Spiking
Could Serve Neuronal Energy Homeostasis and Protect from Reactive Oxygen Species.”
Proceedings of the National Academy of Sciences of the United States of America.
National Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2306525120.
ieee: C. Chintaluri and T. P. Vogels, “Metabolically regulated spiking could serve
neuronal energy homeostasis and protect from reactive oxygen species,” Proceedings
of the National Academy of Sciences of the United States of America, vol.
120, no. 48. National Academy of Sciences, 2023.
ista: Chintaluri C, Vogels TP. 2023. Metabolically regulated spiking could serve
neuronal energy homeostasis and protect from reactive oxygen species. Proceedings
of the National Academy of Sciences of the United States of America. 120(48),
e2306525120.
mla: Chintaluri, Chaitanya, and Tim P. Vogels. “Metabolically Regulated Spiking
Could Serve Neuronal Energy Homeostasis and Protect from Reactive Oxygen Species.”
Proceedings of the National Academy of Sciences of the United States of America,
vol. 120, no. 48, e2306525120, National Academy of Sciences, 2023, doi:10.1073/pnas.2306525120.
short: C. Chintaluri, T.P. Vogels, Proceedings of the National Academy of Sciences
of the United States of America 120 (2023).
date_created: 2023-12-10T23:01:00Z
date_published: 2023-11-21T00:00:00Z
date_updated: 2023-12-11T12:47:41Z
day: '21'
ddc:
- '570'
department:
- _id: TiVo
doi: 10.1073/pnas.2306525120
external_id:
pmid:
- '37988463'
file:
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checksum: bf4ec38602a70dae4338077a5a4d497f
content_type: application/pdf
creator: dernst
date_created: 2023-12-11T12:45:12Z
date_updated: 2023-12-11T12:45:12Z
file_id: '14678'
file_name: 2023_PNAS_Chintaluri.pdf
file_size: 16891602
relation: main_file
success: 1
file_date_updated: 2023-12-11T12:45:12Z
has_accepted_license: '1'
intvolume: ' 120'
issue: '48'
language:
- iso: eng
month: '11'
oa: 1
oa_version: None
pmid: 1
project:
- _id: c084a126-5a5b-11eb-8a69-d75314a70a87
grant_number: 214316/Z/18/Z
name: What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent
neuronal networks.
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/ccluri/metabolic_spiking
scopus_import: '1'
status: public
title: Metabolically regulated spiking could serve neuronal energy homeostasis and
protect from reactive oxygen species
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: 120
year: '2023'
...
---
_id: '14656'
abstract:
- lang: eng
text: Although much is known about how single neurons in the hippocampus represent
an animal's position, how circuit interactions contribute to spatial coding is
less well understood. Using a novel statistical estimator and theoretical modeling,
both developed in the framework of maximum entropy models, we reveal highly structured
CA1 cell-cell interactions in male rats during open field exploration. The statistics
of these interactions depend on whether the animal is in a familiar or novel environment.
In both conditions the circuit interactions optimize the encoding of spatial information,
but for regimes that differ in the informativeness of their spatial inputs. This
structure facilitates linear decodability, making the information easy to read
out by downstream circuits. Overall, our findings suggest that the efficient coding
hypothesis is not only applicable to individual neuron properties in the sensory
periphery, but also to neural interactions in the central brain.
acknowledgement: M.N. was supported by the European Union Horizon 2020 Grant 665385.
J.C. was supported by the European Research Council Consolidator Grant 281511. G.T.
was supported by the Austrian Science Fund (FWF) Grant P34015. C.S. was supported
by an Institute of Science and Technology fellow award and by the National Science
Foundation (NSF) Award No. 1922658. We thank Peter Baracskay, Karola Kaefer, and
Hugo Malagon-Vina for the acquisition of the data. We also thank Federico Stella,
Wiktor Młynarski, Dori Derdikman, Colin Bredenberg, Roman Huszar, Heloisa Chiossi,
Lorenzo Posani, and Mohamady El-Gaby for comments on an earlier version of the manuscript.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Michele
full_name: Nardin, Michele
id: 30BD0376-F248-11E8-B48F-1D18A9856A87
last_name: Nardin
orcid: 0000-0001-8849-6570
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Cristina
full_name: Savin, Cristina
id: 3933349E-F248-11E8-B48F-1D18A9856A87
last_name: Savin
citation:
ama: Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1
interactions optimizes spatial coding across experience. The Journal of Neuroscience.
2023;43(48):8140-8156. doi:10.1523/JNEUROSCI.0194-23.2023
apa: Nardin, M., Csicsvari, J. L., Tkačik, G., & Savin, C. (2023). The structure
of hippocampal CA1 interactions optimizes spatial coding across experience. The
Journal of Neuroscience. Society of Neuroscience. https://doi.org/10.1523/JNEUROSCI.0194-23.2023
chicago: Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin.
“The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across
Experience.” The Journal of Neuroscience. Society of Neuroscience, 2023.
https://doi.org/10.1523/JNEUROSCI.0194-23.2023.
ieee: M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal
CA1 interactions optimizes spatial coding across experience,” The Journal of
Neuroscience, vol. 43, no. 48. Society of Neuroscience, pp. 8140–8156, 2023.
ista: Nardin M, Csicsvari JL, Tkačik G, Savin C. 2023. The structure of hippocampal
CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience.
43(48), 8140–8156.
mla: Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes
Spatial Coding across Experience.” The Journal of Neuroscience, vol. 43,
no. 48, Society of Neuroscience, 2023, pp. 8140–56, doi:10.1523/JNEUROSCI.0194-23.2023.
short: M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, The Journal of Neuroscience
43 (2023) 8140–8156.
date_created: 2023-12-10T23:00:58Z
date_published: 2023-11-29T00:00:00Z
date_updated: 2023-12-11T11:37:20Z
day: '29'
ddc:
- '570'
department:
- _id: JoCs
- _id: GaTk
doi: 10.1523/JNEUROSCI.0194-23.2023
ec_funded: 1
external_id:
pmid:
- '37758476'
file:
- access_level: closed
checksum: e2503c8f84be1050e28f64320f1d5bd2
content_type: application/pdf
creator: dernst
date_created: 2023-12-11T11:30:37Z
date_updated: 2023-12-11T11:30:37Z
embargo: 2024-06-01
embargo_to: open_access
file_id: '14674'
file_name: 2023_JourNeuroscience_Nardin.pdf
file_size: 2280632
relation: main_file
file_date_updated: 2023-12-11T11:30:37Z
has_accepted_license: '1'
intvolume: ' 43'
issue: '48'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1523/JNEUROSCI.0194-23.2023
month: '11'
oa: 1
oa_version: Published Version
page: 8140-8156
pmid: 1
project:
- _id: 257A4776-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281511'
name: Memory-related information processing in neuronal circuits of the hippocampus
and entorhinal cortex
- _id: 626c45b5-2b32-11ec-9570-e509828c1ba6
grant_number: P34015
name: Efficient coding with biophysical realism
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: The Journal of Neuroscience
publication_identifier:
eissn:
- 1529-2401
publication_status: published
publisher: Society of Neuroscience
quality_controlled: '1'
scopus_import: '1'
status: public
title: The structure of hippocampal CA1 interactions optimizes spatial coding across
experience
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: 43
year: '2023'
...
---
_id: '14657'
abstract:
- lang: eng
text: 'Natural selection is usually studied between mutants that differ in reproductive
rate, but are subject to the same population structure. Here we explore how natural
selection acts on mutants that have the same reproductive rate, but different
population structures. In our framework, population structure is given by a graph
that specifies where offspring can disperse. The invading mutant disperses offspring
on a different graph than the resident wild-type. We find that more densely connected
dispersal graphs tend to increase the invader’s fixation probability, but the
exact relationship between structure and fixation probability is subtle. We present
three main results. First, we prove that if both invader and resident are on complete
dispersal graphs, then removing a single edge in the invader’s dispersal graph
reduces its fixation probability. Second, we show that for certain island models
higher invader’s connectivity increases its fixation probability, but the magnitude
of the effect depends on the exact layout of the connections. Third, we show that
for lattices the effect of different connectivity is comparable to that of different
fitness: for large population size, the invader’s fixation probability is either
constant or exponentially small, depending on whether it is more or less connected
than the resident.'
acknowledgement: K.C. acknowledges support from the ERC CoG 863818(ForM-SMArt). J.T.
is supported by Center for Foundations ofModern Computer Science (Charles Univ.
project UNCE/SCI/004).
article_number: '20230355'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Kamran
full_name: Kaveh, Kamran
last_name: Kaveh
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin A.
full_name: Nowak, Martin A.
last_name: Nowak
citation:
ama: Tkadlec J, Kaveh K, Chatterjee K, Nowak MA. Evolutionary dynamics of mutants
that modify population structure. Journal of the Royal Society, Interface.
2023;20(208). doi:10.1098/rsif.2023.0355
apa: Tkadlec, J., Kaveh, K., Chatterjee, K., & Nowak, M. A. (2023). Evolutionary
dynamics of mutants that modify population structure. Journal of the Royal
Society, Interface. The Royal Society. https://doi.org/10.1098/rsif.2023.0355
chicago: Tkadlec, Josef, Kamran Kaveh, Krishnendu Chatterjee, and Martin A. Nowak.
“Evolutionary Dynamics of Mutants That Modify Population Structure.” Journal
of the Royal Society, Interface. The Royal Society, 2023. https://doi.org/10.1098/rsif.2023.0355.
ieee: J. Tkadlec, K. Kaveh, K. Chatterjee, and M. A. Nowak, “Evolutionary dynamics
of mutants that modify population structure,” Journal of the Royal Society,
Interface, vol. 20, no. 208. The Royal Society, 2023.
ista: Tkadlec J, Kaveh K, Chatterjee K, Nowak MA. 2023. Evolutionary dynamics of
mutants that modify population structure. Journal of the Royal Society, Interface.
20(208), 20230355.
mla: Tkadlec, Josef, et al. “Evolutionary Dynamics of Mutants That Modify Population
Structure.” Journal of the Royal Society, Interface, vol. 20, no. 208,
20230355, The Royal Society, 2023, doi:10.1098/rsif.2023.0355.
short: J. Tkadlec, K. Kaveh, K. Chatterjee, M.A. Nowak, Journal of the Royal Society,
Interface 20 (2023).
date_created: 2023-12-10T23:00:58Z
date_published: 2023-11-29T00:00:00Z
date_updated: 2023-12-11T11:17:53Z
day: '29'
ddc:
- '000'
- '570'
department:
- _id: KrCh
doi: 10.1098/rsif.2023.0355
ec_funded: 1
external_id:
pmid:
- '38016637'
file:
- access_level: open_access
checksum: 2eefab13127c7786dbd33303c482a004
content_type: application/pdf
creator: dernst
date_created: 2023-12-11T11:10:32Z
date_updated: 2023-12-11T11:10:32Z
file_id: '14673'
file_name: 2023_RoyalInterface_Tkadlec.pdf
file_size: 1720243
relation: main_file
success: 1
file_date_updated: 2023-12-11T11:10:32Z
has_accepted_license: '1'
intvolume: ' 20'
issue: '208'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Journal of the Royal Society, Interface
publication_identifier:
eissn:
- 1742-5662
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolutionary dynamics of mutants that modify population structure
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: 20
year: '2023'
...
---
_id: '14664'
abstract:
- lang: eng
text: The architecture of self-assembled host molecules can profoundly affect the
properties of the encapsulated guests. For example, a rigid cage with small windows
can efficiently protect its contents from the environment; in contrast, tube-shaped,
flexible hosts with large openings and an easily accessible cavity are ideally
suited for catalysis. Here, we report a “Janus” nature of a Pd6L4 coordination
host previously reported to exist exclusively as a tube isomer (T). We show that
upon encapsulating various tetrahedrally shaped guests, T can reconfigure into
a cage-shaped host (C) in quantitative yield. Extracting the guest affords empty
C, which is metastable and spontaneously relaxes to T, and the T⇄C interconversion
can be repeated for multiple cycles. Reversible toggling between two vastly different
isomers paves the way toward controlling functional properties of coordination
hosts “on demand”.
acknowledgement: We acknowledge funding from the European Union’s Horizon 2020 Research
and Innovation Program under the European Research Council (grant agreement 820008).We
also thank the Deutsche Forschungsgemeinschaft (DFG) for support through priority
program SPP1807(CL489/3-2) and RESOLV Cluster of Excellence EXC2033 (project number
390677874). A.B.G. acknowledges funding from the Zuckerman STEM Leadership Program.
DFT calculations were carried out using resources provided by the Wrocław Center
for Networking and Supercomputing, grant 329.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Kuntrapakam
full_name: Hema, Kuntrapakam
last_name: Hema
- first_name: Angela B.
full_name: Grommet, Angela B.
last_name: Grommet
- first_name: Michał J.
full_name: Białek, Michał J.
last_name: Białek
- first_name: Jinhua
full_name: Wang, Jinhua
last_name: Wang
- first_name: Laura
full_name: Schneider, Laura
last_name: Schneider
- first_name: Christoph
full_name: Drechsler, Christoph
last_name: Drechsler
- first_name: Oksana
full_name: Yanshyna, Oksana
last_name: Yanshyna
- first_name: Yael
full_name: Diskin-Posner, Yael
last_name: Diskin-Posner
- first_name: Guido H.
full_name: Clever, Guido H.
last_name: Clever
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Hema K, Grommet AB, Białek MJ, et al. Guest encapsulation alters the thermodynamic
landscape of a coordination host. Journal of the American Chemical Society.
2023;145(45):24755-24764. doi:10.1021/jacs.3c08666
apa: Hema, K., Grommet, A. B., Białek, M. J., Wang, J., Schneider, L., Drechsler,
C., … Klajn, R. (2023). Guest encapsulation alters the thermodynamic landscape
of a coordination host. Journal of the American Chemical Society. American
Chemical Society. https://doi.org/10.1021/jacs.3c08666
chicago: Hema, Kuntrapakam, Angela B. Grommet, Michał J. Białek, Jinhua Wang, Laura
Schneider, Christoph Drechsler, Oksana Yanshyna, Yael Diskin-Posner, Guido H.
Clever, and Rafal Klajn. “Guest Encapsulation Alters the Thermodynamic Landscape
of a Coordination Host.” Journal of the American Chemical Society. American
Chemical Society, 2023. https://doi.org/10.1021/jacs.3c08666.
ieee: K. Hema et al., “Guest encapsulation alters the thermodynamic landscape
of a coordination host,” Journal of the American Chemical Society, vol.
145, no. 45. American Chemical Society, pp. 24755–24764, 2023.
ista: Hema K, Grommet AB, Białek MJ, Wang J, Schneider L, Drechsler C, Yanshyna
O, Diskin-Posner Y, Clever GH, Klajn R. 2023. Guest encapsulation alters the thermodynamic
landscape of a coordination host. Journal of the American Chemical Society. 145(45),
24755–24764.
mla: Hema, Kuntrapakam, et al. “Guest Encapsulation Alters the Thermodynamic Landscape
of a Coordination Host.” Journal of the American Chemical Society, vol.
145, no. 45, American Chemical Society, 2023, pp. 24755–64, doi:10.1021/jacs.3c08666.
short: K. Hema, A.B. Grommet, M.J. Białek, J. Wang, L. Schneider, C. Drechsler,
O. Yanshyna, Y. Diskin-Posner, G.H. Clever, R. Klajn, Journal of the American
Chemical Society 145 (2023) 24755–24764.
date_created: 2023-12-10T23:00:59Z
date_published: 2023-11-02T00:00:00Z
date_updated: 2023-12-11T11:47:07Z
day: '02'
ddc:
- '540'
department:
- _id: RaKl
doi: 10.1021/jacs.3c08666
external_id:
pmid:
- '37917939'
file:
- access_level: open_access
checksum: a1f37df6b83f88f51ba64468ce0c1589
content_type: application/pdf
creator: dernst
date_created: 2023-12-11T11:44:54Z
date_updated: 2023-12-11T11:44:54Z
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file_name: 2023_JACS_Hema.pdf
file_size: 4304472
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intvolume: ' 145'
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language:
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month: '11'
oa: 1
oa_version: Published Version
page: 24755-24764
pmid: 1
publication: Journal of the American Chemical Society
publication_identifier:
eissn:
- 1520-5126
issn:
- 0002-7863
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Guest encapsulation alters the thermodynamic landscape of a coordination host
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: 145
year: '2023'
...
---
_id: '14663'
abstract:
- lang: eng
text: As a bottleneck in the direct synthesis of hydrogen peroxide, the development
of an efficient palladium-based catalyst has garnered great attention. However,
elusive active centers and reaction mechanism issues inhibit further optimization
of its performance. In this work, advanced microkinetic modeling with the adsorbate–adsorbate
interaction and nanoparticle size effect based on first-principles calculations
is developed. A full mechanism uncovering the significance of adsorbate–adsorbate
interaction is determined on Pd nanoparticles. We demonstrate unambiguously that
Pd(100) with main coverage species of O2 and H is beneficial to H2O2 production,
being consistent with experimental operando observation, while H2O forms on Pd(111)
covered by O species and Pd(211) covered by O and OH species. Kinetic analyses
further enable quantitative estimation of the influence of temperature, pressure,
and particle size. Large-size Pd nanoparticles are found to achieve a high H2O2
reaction rate when the operating conditions are moderate temperature and higher
oxygen partial pressure. We reveal that specific facets of the Pd nanoparticles
are crucial factors for their selectivity and activity. Consistent with the experiment,
the production of H2O2 is discovered to be more favorable on Pd nanoparticles
containing Pd(100) facets. The ratio of H2/O2 induces substantial variations in
the coverage of intermediates of O2 and H on Pd(100), resulting in a change in
product selectivity.
acknowledgement: The authors acknowledge the financial support from the National Natural
Science Foundation of China (22008211, 92045303, U21A20298), the National Key Research
and Development Project of China (2021YFA1500900, 2022YFE0113800), and Zhejiang
Innovation Team (2017R5203).
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Jinyan
full_name: Zhao, Jinyan
last_name: Zhao
- first_name: Zihao
full_name: Yao, Zihao
last_name: Yao
- first_name: Rhys
full_name: Bunting, Rhys
id: 91deeae8-1207-11ec-b130-c194ad5b50c6
last_name: Bunting
orcid: 0000-0001-6928-074X
- first_name: P.
full_name: Hu, P.
last_name: Hu
- first_name: Jianguo
full_name: Wang, Jianguo
last_name: Wang
citation:
ama: Zhao J, Yao Z, Bunting R, Hu P, Wang J. Microkinetic modeling with size-dependent
and adsorbate-adsorbate interactions for the direct synthesis of H₂O₂ over Pd
nanoparticles. ACS Catalysis. 2023;13(22):15054-15073. doi:10.1021/acscatal.3c03893
apa: Zhao, J., Yao, Z., Bunting, R., Hu, P., & Wang, J. (2023). Microkinetic
modeling with size-dependent and adsorbate-adsorbate interactions for the direct
synthesis of H₂O₂ over Pd nanoparticles. ACS Catalysis. American Chemical
Society. https://doi.org/10.1021/acscatal.3c03893
chicago: Zhao, Jinyan, Zihao Yao, Rhys Bunting, P. Hu, and Jianguo Wang. “Microkinetic
Modeling with Size-Dependent and Adsorbate-Adsorbate Interactions for the Direct
Synthesis of H₂O₂ over Pd Nanoparticles.” ACS Catalysis. American Chemical
Society, 2023. https://doi.org/10.1021/acscatal.3c03893.
ieee: J. Zhao, Z. Yao, R. Bunting, P. Hu, and J. Wang, “Microkinetic modeling with
size-dependent and adsorbate-adsorbate interactions for the direct synthesis of
H₂O₂ over Pd nanoparticles,” ACS Catalysis, vol. 13, no. 22. American Chemical
Society, pp. 15054–15073, 2023.
ista: Zhao J, Yao Z, Bunting R, Hu P, Wang J. 2023. Microkinetic modeling with size-dependent
and adsorbate-adsorbate interactions for the direct synthesis of H₂O₂ over Pd
nanoparticles. ACS Catalysis. 13(22), 15054–15073.
mla: Zhao, Jinyan, et al. “Microkinetic Modeling with Size-Dependent and Adsorbate-Adsorbate
Interactions for the Direct Synthesis of H₂O₂ over Pd Nanoparticles.” ACS Catalysis,
vol. 13, no. 22, American Chemical Society, 2023, pp. 15054–73, doi:10.1021/acscatal.3c03893.
short: J. Zhao, Z. Yao, R. Bunting, P. Hu, J. Wang, ACS Catalysis 13 (2023) 15054–15073.
date_created: 2023-12-10T23:00:59Z
date_published: 2023-11-06T00:00:00Z
date_updated: 2023-12-11T11:55:35Z
day: '06'
ddc:
- '540'
department:
- _id: MaIb
doi: 10.1021/acscatal.3c03893
file:
- access_level: open_access
checksum: a97c771077af71ddfb2249e34530895c
content_type: application/pdf
creator: dernst
date_created: 2023-12-11T11:55:09Z
date_updated: 2023-12-11T11:55:09Z
file_id: '14676'
file_name: 2023_ACSCatalysis_.pdf
file_size: 14813812
relation: main_file
success: 1
file_date_updated: 2023-12-11T11:55:09Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '22'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 15054-15073
publication: ACS Catalysis
publication_identifier:
eissn:
- 2155-5435
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Microkinetic modeling with size-dependent and adsorbate-adsorbate interactions
for the direct synthesis of H₂O₂ over Pd nanoparticles
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: 13
year: '2023'
...