---
_id: '7541'
abstract:
- lang: eng
text: Semiconductor nanowires have been playing a crucial role in the development
of nanoscale devices for the realization of spin qubits, Majorana fermions, single
photon emitters, nanoprocessors, etc. The monolithic growth of site‐controlled
nanowires is a prerequisite toward the next generation of devices that will require
addressability and scalability. Here, combining top‐down nanofabrication and bottom‐up
self‐assembly, the growth of Ge wires on prepatterned Si (001) substrates with
controllable position, distance, length, and structure is reported. This is achieved
by a novel growth process that uses a SiGe strain‐relaxation template and can
be potentially generalized to other material combinations. Transport measurements
show an electrically tunable spin–orbit coupling, with a spin–orbit length similar
to that of III–V materials. Also, charge sensing between quantum dots in closely
spaced wires is observed, which underlines their potential for the realization
of advanced quantum devices. The reported results open a path toward scalable
qubit devices using nanowires on silicon.
acknowledged_ssus:
- _id: NanoFab
- _id: M-Shop
acknowledgement: 'This work was supported by the National Key R&D Program of China
(Grant Nos. 2016YFA0301701 and 2016YFA0300600), the NSFC (Grant Nos. 11574356, 11434010,
and 11404252), the Strategic Priority Research Program of CAS (Grant No. XDB30000000),
the ERC Starting Grant No. 335497, the FWF P32235 project, and the European Union''s
Horizon 2020 research and innovation program under Grant Agreement #862046. This
research was supported by the Scientific Service Units of IST Austria through resources
provided by the MIBA Machine Shop and the nanofabrication facility. F.L. thanks
support from DOE (Grant No. DE‐FG02‐04ER46148). H.H. thanks the Startup Funding
from Xi''an Jiaotong University.'
article_number: '1906523'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Fei
full_name: Gao, Fei
last_name: Gao
- first_name: Jian-Huan
full_name: Wang, Jian-Huan
last_name: Wang
- first_name: Hannes
full_name: Watzinger, Hannes
id: 35DF8E50-F248-11E8-B48F-1D18A9856A87
last_name: Watzinger
- first_name: Hao
full_name: Hu, Hao
last_name: Hu
- first_name: Marko J.
full_name: Rančić, Marko J.
last_name: Rančić
- first_name: Jie-Yin
full_name: Zhang, Jie-Yin
last_name: Zhang
- first_name: Ting
full_name: Wang, Ting
last_name: Wang
- first_name: Yuan
full_name: Yao, Yuan
last_name: Yao
- first_name: Gui-Lei
full_name: Wang, Gui-Lei
last_name: Wang
- first_name: Josip
full_name: Kukucka, Josip
id: 3F5D8856-F248-11E8-B48F-1D18A9856A87
last_name: Kukucka
- first_name: Lada
full_name: Vukušić, Lada
id: 31E9F056-F248-11E8-B48F-1D18A9856A87
last_name: Vukušić
orcid: 0000-0003-2424-8636
- first_name: Christoph
full_name: Kloeffel, Christoph
last_name: Kloeffel
- first_name: Daniel
full_name: Loss, Daniel
last_name: Loss
- first_name: Feng
full_name: Liu, Feng
last_name: Liu
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
- first_name: Jian-Jun
full_name: Zhang, Jian-Jun
last_name: Zhang
citation:
ama: Gao F, Wang J-H, Watzinger H, et al. Site-controlled uniform Ge/Si hut wires
with electrically tunable spin-orbit coupling. Advanced Materials. 2020;32(16).
doi:10.1002/adma.201906523
apa: Gao, F., Wang, J.-H., Watzinger, H., Hu, H., Rančić, M. J., Zhang, J.-Y., …
Zhang, J.-J. (2020). Site-controlled uniform Ge/Si hut wires with electrically
tunable spin-orbit coupling. Advanced Materials. Wiley. https://doi.org/10.1002/adma.201906523
chicago: Gao, Fei, Jian-Huan Wang, Hannes Watzinger, Hao Hu, Marko J. Rančić, Jie-Yin
Zhang, Ting Wang, et al. “Site-Controlled Uniform Ge/Si Hut Wires with Electrically
Tunable Spin-Orbit Coupling.” Advanced Materials. Wiley, 2020. https://doi.org/10.1002/adma.201906523.
ieee: F. Gao et al., “Site-controlled uniform Ge/Si hut wires with electrically
tunable spin-orbit coupling,” Advanced Materials, vol. 32, no. 16. Wiley,
2020.
ista: Gao F, Wang J-H, Watzinger H, Hu H, Rančić MJ, Zhang J-Y, Wang T, Yao Y, Wang
G-L, Kukucka J, Vukušić L, Kloeffel C, Loss D, Liu F, Katsaros G, Zhang J-J. 2020.
Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling.
Advanced Materials. 32(16), 1906523.
mla: Gao, Fei, et al. “Site-Controlled Uniform Ge/Si Hut Wires with Electrically
Tunable Spin-Orbit Coupling.” Advanced Materials, vol. 32, no. 16, 1906523,
Wiley, 2020, doi:10.1002/adma.201906523.
short: F. Gao, J.-H. Wang, H. Watzinger, H. Hu, M.J. Rančić, J.-Y. Zhang, T. Wang,
Y. Yao, G.-L. Wang, J. Kukucka, L. Vukušić, C. Kloeffel, D. Loss, F. Liu, G. Katsaros,
J.-J. Zhang, Advanced Materials 32 (2020).
date_created: 2020-02-28T09:47:00Z
date_published: 2020-04-23T00:00:00Z
date_updated: 2024-02-21T12:42:12Z
day: '23'
ddc:
- '530'
department:
- _id: GeKa
doi: 10.1002/adma.201906523
ec_funded: 1
external_id:
isi:
- '000516660900001'
file:
- access_level: open_access
checksum: c622737dc295972065782558337124a2
content_type: application/pdf
creator: dernst
date_created: 2020-11-20T10:11:35Z
date_updated: 2020-11-20T10:11:35Z
file_id: '8782'
file_name: 2020_AdvancedMaterials_Gao.pdf
file_size: 5242880
relation: main_file
success: 1
file_date_updated: 2020-11-20T10:11:35Z
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
issue: '16'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 25517E86-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '335497'
name: Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires
- _id: 237B3DA4-32DE-11EA-91FC-C7463DDC885E
call_identifier: FWF
grant_number: P32235
name: Towards scalable hut wire quantum devices
- _id: 237E5020-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '862046'
name: TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS
publication: Advanced Materials
publication_identifier:
issn:
- 0935-9648
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '7996'
relation: dissertation_contains
status: public
- id: '9222'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit
coupling
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 32
year: '2020'
...
---
_id: '7545'
abstract:
- lang: eng
text: Neuronal activity often leads to alterations in gene expression and cellular
architecture. The nematode Caenorhabditis elegans, owing to its compact translucent
nervous system, is a powerful system in which to study conserved aspects of the
development and plasticity of neuronal morphology. Here we focus on one pair of
sensory neurons, termed URX, which the worm uses to sense and avoid high levels
of environmental oxygen. Previous studies have reported that the URX neuron pair
has variable branched endings at its dendritic sensory tip. By controlling oxygen
levels and analyzing mutants, we found that these microtubule-rich branched endings
grow over time as a consequence of neuronal activity in adulthood. We also find
that the growth of these branches correlates with an increase in cellular sensitivity
to particular ranges of oxygen that is observable in the behavior of older worms.
Given the strengths of C. elegans as a model organism, URX may serve as a potent
system for uncovering genes and mechanisms involved in activity-dependent morphological
changes in neurons and possible adaptive changes in the aging nervous system.
article_processing_charge: No
article_type: original
author:
- first_name: Jesse A.
full_name: Cohn, Jesse A.
last_name: Cohn
- first_name: Elizabeth R.
full_name: Cebul, Elizabeth R.
last_name: Cebul
- first_name: Giulio
full_name: Valperga, Giulio
last_name: Valperga
- first_name: Lotti
full_name: Brose, Lotti
last_name: Brose
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
- first_name: Maxwell G.
full_name: Heiman, Maxwell G.
last_name: Heiman
- first_name: Jonathan T.
full_name: Pierce, Jonathan T.
last_name: Pierce
citation:
ama: Cohn JA, Cebul ER, Valperga G, et al. Long-term activity drives dendritic branch
elaboration of a C. elegans sensory neuron. Developmental Biology. 2020;461(1):66-74.
doi:10.1016/j.ydbio.2020.01.005
apa: Cohn, J. A., Cebul, E. R., Valperga, G., Brose, L., de Bono, M., Heiman, M.
G., & Pierce, J. T. (2020). Long-term activity drives dendritic branch elaboration
of a C. elegans sensory neuron. Developmental Biology. Elsevier. https://doi.org/10.1016/j.ydbio.2020.01.005
chicago: Cohn, Jesse A., Elizabeth R. Cebul, Giulio Valperga, Lotti Brose, Mario
de Bono, Maxwell G. Heiman, and Jonathan T. Pierce. “Long-Term Activity Drives
Dendritic Branch Elaboration of a C. Elegans Sensory Neuron.” Developmental
Biology. Elsevier, 2020. https://doi.org/10.1016/j.ydbio.2020.01.005.
ieee: J. A. Cohn et al., “Long-term activity drives dendritic branch elaboration
of a C. elegans sensory neuron,” Developmental Biology, vol. 461, no. 1.
Elsevier, pp. 66–74, 2020.
ista: Cohn JA, Cebul ER, Valperga G, Brose L, de Bono M, Heiman MG, Pierce JT. 2020.
Long-term activity drives dendritic branch elaboration of a C. elegans sensory
neuron. Developmental Biology. 461(1), 66–74.
mla: Cohn, Jesse A., et al. “Long-Term Activity Drives Dendritic Branch Elaboration
of a C. Elegans Sensory Neuron.” Developmental Biology, vol. 461, no. 1,
Elsevier, 2020, pp. 66–74, doi:10.1016/j.ydbio.2020.01.005.
short: J.A. Cohn, E.R. Cebul, G. Valperga, L. Brose, M. de Bono, M.G. Heiman, J.T.
Pierce, Developmental Biology 461 (2020) 66–74.
date_created: 2020-02-28T10:38:32Z
date_published: 2020-05-01T00:00:00Z
date_updated: 2021-01-12T08:14:06Z
day: '01'
doi: 10.1016/j.ydbio.2020.01.005
extern: '1'
intvolume: ' 461'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/685339
month: '05'
oa: 1
oa_version: Preprint
page: 66-74
publication: Developmental Biology
publication_identifier:
issn:
- 0012-1606
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Long-term activity drives dendritic branch elaboration of a C. elegans sensory
neuron
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 461
year: '2020'
...
---
_id: '7546'
abstract:
- lang: eng
text: The extent to which behavior is shaped by experience varies between individuals.
Genetic differences contribute to this variation, but the neural mechanisms are
not understood. Here, we dissect natural variation in the behavioral flexibility
of two Caenorhabditis elegans wild strains. In one strain, a memory of exposure
to 21% O2 suppresses CO2-evoked locomotory arousal; in the other, CO2 evokes arousal
regardless of previous O2 experience. We map that variation to a polymorphic dendritic
scaffold protein, ARCP-1, expressed in sensory neurons. ARCP-1 binds the Ca2+-dependent
phosphodiesterase PDE-1 and co-localizes PDE-1 with molecular sensors for CO2
at dendritic ends. Reducing ARCP-1 or PDE-1 activity promotes CO2 escape by altering
neuropeptide expression in the BAG CO2 sensors. Variation in ARCP-1 alters behavioral
plasticity in multiple paradigms. Our findings are reminiscent of genetic accommodation,
an evolutionary process by which phenotypic flexibility in response to environmental
variation is reset by genetic change.
article_processing_charge: No
article_type: original
author:
- first_name: Isabel
full_name: Beets, Isabel
last_name: Beets
- first_name: Gaotian
full_name: Zhang, Gaotian
last_name: Zhang
- first_name: Lorenz A.
full_name: Fenk, Lorenz A.
last_name: Fenk
- first_name: Changchun
full_name: Chen, Changchun
last_name: Chen
- first_name: Geoffrey M.
full_name: Nelson, Geoffrey M.
last_name: Nelson
- first_name: Marie-Anne
full_name: Félix, Marie-Anne
last_name: Félix
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Beets I, Zhang G, Fenk LA, et al. Natural variation in a dendritic scaffold
protein remodels experience-dependent plasticity by altering neuropeptide expression.
Neuron. 2020;105(1):106-121.e10. doi:10.1016/j.neuron.2019.10.001
apa: Beets, I., Zhang, G., Fenk, L. A., Chen, C., Nelson, G. M., Félix, M.-A., &
de Bono, M. (2020). Natural variation in a dendritic scaffold protein remodels
experience-dependent plasticity by altering neuropeptide expression. Neuron.
Cell Press. https://doi.org/10.1016/j.neuron.2019.10.001
chicago: Beets, Isabel, Gaotian Zhang, Lorenz A. Fenk, Changchun Chen, Geoffrey
M. Nelson, Marie-Anne Félix, and Mario de Bono. “Natural Variation in a Dendritic
Scaffold Protein Remodels Experience-Dependent Plasticity by Altering Neuropeptide
Expression.” Neuron. Cell Press, 2020. https://doi.org/10.1016/j.neuron.2019.10.001.
ieee: I. Beets et al., “Natural variation in a dendritic scaffold protein
remodels experience-dependent plasticity by altering neuropeptide expression,”
Neuron, vol. 105, no. 1. Cell Press, p. 106–121.e10, 2020.
ista: Beets I, Zhang G, Fenk LA, Chen C, Nelson GM, Félix M-A, de Bono M. 2020.
Natural variation in a dendritic scaffold protein remodels experience-dependent
plasticity by altering neuropeptide expression. Neuron. 105(1), 106–121.e10.
mla: Beets, Isabel, et al. “Natural Variation in a Dendritic Scaffold Protein Remodels
Experience-Dependent Plasticity by Altering Neuropeptide Expression.” Neuron,
vol. 105, no. 1, Cell Press, 2020, p. 106–121.e10, doi:10.1016/j.neuron.2019.10.001.
short: I. Beets, G. Zhang, L.A. Fenk, C. Chen, G.M. Nelson, M.-A. Félix, M. de Bono,
Neuron 105 (2020) 106–121.e10.
date_created: 2020-02-28T10:43:39Z
date_published: 2020-01-08T00:00:00Z
date_updated: 2023-08-18T06:46:23Z
day: '08'
ddc:
- '570'
department:
- _id: MaDe
doi: 10.1016/j.neuron.2019.10.001
external_id:
isi:
- '000507341300012'
pmid:
- '31757604'
file:
- access_level: open_access
checksum: 799bfd297a008753a688b30d3958fa48
content_type: application/pdf
creator: dernst
date_created: 2020-03-02T15:43:57Z
date_updated: 2020-07-14T12:48:00Z
file_id: '7558'
file_name: 2020_Neuron_Beets.pdf
file_size: 3294066
relation: main_file
file_date_updated: 2020-07-14T12:48:00Z
has_accepted_license: '1'
intvolume: ' 105'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 106-121.e10
pmid: 1
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Cell Press
quality_controlled: '1'
status: public
title: Natural variation in a dendritic scaffold protein remodels experience-dependent
plasticity by altering neuropeptide expression
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 105
year: '2020'
...
---
_id: '7554'
abstract:
- lang: eng
text: Slicing a Voronoi tessellation in ${R}^n$ with a $k$-plane gives a $k$-dimensional
weighted Voronoi tessellation, also known as a power diagram or Laguerre tessellation.
Mapping every simplex of the dual weighted Delaunay mosaic to the radius of the
smallest empty circumscribed sphere whose center lies in the $k$-plane gives a
generalized discrete Morse function. Assuming the Voronoi tessellation is generated
by a Poisson point process in ${R}^n$, we study the expected number of simplices
in the $k$-dimensional weighted Delaunay mosaic as well as the expected number
of intervals of the Morse function, both as functions of a radius threshold. As
a by-product, we obtain a new proof for the expected number of connected components
(clumps) in a line section of a circular Boolean model in ${R}^n$.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Anton
full_name: Nikitenko, Anton
id: 3E4FF1BA-F248-11E8-B48F-1D18A9856A87
last_name: Nikitenko
orcid: 0000-0002-0659-3201
citation:
ama: Edelsbrunner H, Nikitenko A. Weighted Poisson–Delaunay mosaics. Theory of
Probability and its Applications. 2020;64(4):595-614. doi:10.1137/S0040585X97T989726
apa: Edelsbrunner, H., & Nikitenko, A. (2020). Weighted Poisson–Delaunay mosaics.
Theory of Probability and Its Applications. SIAM. https://doi.org/10.1137/S0040585X97T989726
chicago: Edelsbrunner, Herbert, and Anton Nikitenko. “Weighted Poisson–Delaunay
Mosaics.” Theory of Probability and Its Applications. SIAM, 2020. https://doi.org/10.1137/S0040585X97T989726.
ieee: H. Edelsbrunner and A. Nikitenko, “Weighted Poisson–Delaunay mosaics,” Theory
of Probability and its Applications, vol. 64, no. 4. SIAM, pp. 595–614, 2020.
ista: Edelsbrunner H, Nikitenko A. 2020. Weighted Poisson–Delaunay mosaics. Theory
of Probability and its Applications. 64(4), 595–614.
mla: Edelsbrunner, Herbert, and Anton Nikitenko. “Weighted Poisson–Delaunay Mosaics.”
Theory of Probability and Its Applications, vol. 64, no. 4, SIAM, 2020,
pp. 595–614, doi:10.1137/S0040585X97T989726.
short: H. Edelsbrunner, A. Nikitenko, Theory of Probability and Its Applications
64 (2020) 595–614.
date_created: 2020-03-01T23:00:39Z
date_published: 2020-02-13T00:00:00Z
date_updated: 2023-08-18T06:45:48Z
day: '13'
department:
- _id: HeEd
doi: 10.1137/S0040585X97T989726
ec_funded: 1
external_id:
arxiv:
- '1705.08735'
isi:
- '000551393100007'
intvolume: ' 64'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.08735
month: '02'
oa: 1
oa_version: Preprint
page: 595-614
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication: Theory of Probability and its Applications
publication_identifier:
eissn:
- '10957219'
issn:
- 0040585X
publication_status: published
publisher: SIAM
quality_controlled: '1'
scopus_import: '1'
status: public
title: Weighted Poisson–Delaunay mosaics
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 64
year: '2020'
...
---
_id: '7563'
abstract:
- lang: eng
text: "We introduce “state space persistence analysis” for deducing the symbolic
dynamics of time series data obtained from high-dimensional chaotic attractors.
To this end, we adapt a topological data analysis technique known as persistent
homology for the characterization of state space projections of chaotic trajectories
and periodic orbits. By comparing the shapes along a chaotic trajectory to those
of the periodic orbits, state space persistence analysis quantifies the shape
similarity of chaotic trajectory segments and periodic orbits. We demonstrate
the method by applying it to the three-dimensional Rössler system and a 30-dimensional
discretization of the Kuramoto–Sivashinsky partial differential equation in (1+1)
dimensions.\r\nOne way of studying chaotic attractors systematically is through
their symbolic dynamics, in which one partitions the state space into qualitatively
different regions and assigns a symbol to each such region.1–3 This yields a “coarse-grained”
state space of the system, which can then be reduced to a Markov chain encoding
all possible transitions between the states of the system. While it is possible
to obtain the symbolic dynamics of low-dimensional chaotic systems with standard
tools such as Poincaré maps, when applied to high-dimensional systems such as
turbulent flows, these tools alone are not sufficient to determine symbolic dynamics.4,5
In this paper, we develop “state space persistence analysis” and demonstrate that
it can be utilized to infer the symbolic dynamics in very high-dimensional settings."
article_number: '033109'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Gökhan
full_name: Yalniz, Gökhan
id: 66E74FA2-D8BF-11E9-8249-8DE2E5697425
last_name: Yalniz
orcid: 0000-0002-8490-9312
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
citation:
ama: Yalniz G, Budanur NB. Inferring symbolic dynamics of chaotic flows from persistence.
Chaos. 2020;30(3). doi:10.1063/1.5122969
apa: Yalniz, G., & Budanur, N. B. (2020). Inferring symbolic dynamics of chaotic
flows from persistence. Chaos. AIP Publishing. https://doi.org/10.1063/1.5122969
chicago: Yalniz, Gökhan, and Nazmi B Budanur. “Inferring Symbolic Dynamics of Chaotic
Flows from Persistence.” Chaos. AIP Publishing, 2020. https://doi.org/10.1063/1.5122969.
ieee: G. Yalniz and N. B. Budanur, “Inferring symbolic dynamics of chaotic flows
from persistence,” Chaos, vol. 30, no. 3. AIP Publishing, 2020.
ista: Yalniz G, Budanur NB. 2020. Inferring symbolic dynamics of chaotic flows from
persistence. Chaos. 30(3), 033109.
mla: Yalniz, Gökhan, and Nazmi B. Budanur. “Inferring Symbolic Dynamics of Chaotic
Flows from Persistence.” Chaos, vol. 30, no. 3, 033109, AIP Publishing,
2020, doi:10.1063/1.5122969.
short: G. Yalniz, N.B. Budanur, Chaos 30 (2020).
date_created: 2020-03-04T08:06:25Z
date_published: 2020-03-03T00:00:00Z
date_updated: 2023-08-18T06:47:16Z
day: '03'
department:
- _id: BjHo
doi: 10.1063/1.5122969
external_id:
arxiv:
- '1910.04584'
isi:
- '000519254800002'
intvolume: ' 30'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1063/1.5122969
month: '03'
oa: 1
oa_version: Published Version
publication: Chaos
publication_identifier:
eissn:
- 1089-7682
issn:
- 1054-1500
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inferring symbolic dynamics of chaotic flows from persistence
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 30
year: '2020'
...
---
_id: '7567'
abstract:
- lang: eng
text: Coxeter triangulations are triangulations of Euclidean space based on a single
simplex. By this we mean that given an individual simplex we can recover the entire
triangulation of Euclidean space by inductively reflecting in the faces of the
simplex. In this paper we establish that the quality of the simplices in all Coxeter
triangulations is O(1/d−−√) of the quality of regular simplex. We further investigate
the Delaunay property for these triangulations. Moreover, we consider an extension
of the Delaunay property, namely protection, which is a measure of non-degeneracy
of a Delaunay triangulation. In particular, one family of Coxeter triangulations
achieves the protection O(1/d2). We conjecture that both bounds are optimal for
triangulations in Euclidean space.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Aruni
full_name: Choudhary, Aruni
last_name: Choudhary
- first_name: Siargey
full_name: Kachanovich, Siargey
last_name: Kachanovich
- first_name: Mathijs
full_name: Wintraecken, Mathijs
id: 307CFBC8-F248-11E8-B48F-1D18A9856A87
last_name: Wintraecken
orcid: 0000-0002-7472-2220
citation:
ama: Choudhary A, Kachanovich S, Wintraecken M. Coxeter triangulations have good
quality. Mathematics in Computer Science. 2020;14:141-176. doi:10.1007/s11786-020-00461-5
apa: Choudhary, A., Kachanovich, S., & Wintraecken, M. (2020). Coxeter triangulations
have good quality. Mathematics in Computer Science. Springer Nature. https://doi.org/10.1007/s11786-020-00461-5
chicago: Choudhary, Aruni, Siargey Kachanovich, and Mathijs Wintraecken. “Coxeter
Triangulations Have Good Quality.” Mathematics in Computer Science. Springer
Nature, 2020. https://doi.org/10.1007/s11786-020-00461-5.
ieee: A. Choudhary, S. Kachanovich, and M. Wintraecken, “Coxeter triangulations
have good quality,” Mathematics in Computer Science, vol. 14. Springer
Nature, pp. 141–176, 2020.
ista: Choudhary A, Kachanovich S, Wintraecken M. 2020. Coxeter triangulations have
good quality. Mathematics in Computer Science. 14, 141–176.
mla: Choudhary, Aruni, et al. “Coxeter Triangulations Have Good Quality.” Mathematics
in Computer Science, vol. 14, Springer Nature, 2020, pp. 141–76, doi:10.1007/s11786-020-00461-5.
short: A. Choudhary, S. Kachanovich, M. Wintraecken, Mathematics in Computer Science
14 (2020) 141–176.
date_created: 2020-03-05T13:30:18Z
date_published: 2020-03-01T00:00:00Z
date_updated: 2021-01-12T08:14:13Z
day: '01'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.1007/s11786-020-00461-5
ec_funded: 1
file:
- access_level: open_access
checksum: 1d145f3ab50ccee735983cb89236e609
content_type: application/pdf
creator: dernst
date_created: 2020-11-20T10:18:02Z
date_updated: 2020-11-20T10:18:02Z
file_id: '8783'
file_name: 2020_MathCompScie_Choudhary.pdf
file_size: 872275
relation: main_file
success: 1
file_date_updated: 2020-11-20T10:18:02Z
has_accepted_license: '1'
intvolume: ' 14'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 141-176
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Mathematics in Computer Science
publication_identifier:
eissn:
- 1661-8289
issn:
- 1661-8270
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Coxeter triangulations have good quality
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: 14
year: '2020'
...
---
_id: '7569'
abstract:
- lang: eng
text: 'Genes differ in the frequency at which they are expressed and in the form
of regulation used to control their activity. In particular, positive or negative
regulation can lead to activation of a gene in response to an external signal.
Previous works proposed that the form of regulation of a gene correlates with
its frequency of usage: positive regulation when the gene is frequently expressed
and negative regulation when infrequently expressed. Such network design means
that, in the absence of their regulators, the genes are found in their least required
activity state, hence regulatory intervention is often necessary. Due to the multitude
of genes and regulators, spurious binding and unbinding events, called “crosstalk”,
could occur. To determine how the form of regulation affects the global crosstalk
in the network, we used a mathematical model that includes multiple regulators
and multiple target genes. We found that crosstalk depends non-monotonically on
the availability of regulators. Our analysis showed that excess use of regulation
entailed by the formerly suggested network design caused high crosstalk levels
in a large part of the parameter space. We therefore considered the opposite ‘idle’
design, where the default unregulated state of genes is their frequently required
activity state. We found, that ‘idle’ design minimized the use of regulation and
thus minimized crosstalk. In addition, we estimated global crosstalk of S. cerevisiae
using transcription factors binding data. We demonstrated that even partial network
data could suffice to estimate its global crosstalk, suggesting its applicability
to additional organisms. We found that S. cerevisiae estimated crosstalk is lower
than that of a random network, suggesting that natural selection reduces crosstalk.
In summary, our study highlights a new type of protein production cost which is
typically overlooked: that of regulatory interference caused by the presence of
excess regulators in the cell. It demonstrates the importance of whole-network
descriptions, which could show effects missed by single-gene models.'
article_number: e1007642
article_processing_charge: No
article_type: original
author:
- first_name: Rok
full_name: Grah, Rok
id: 483E70DE-F248-11E8-B48F-1D18A9856A87
last_name: Grah
orcid: 0000-0003-2539-3560
- first_name: Tamar
full_name: Friedlander, Tamar
last_name: Friedlander
citation:
ama: Grah R, Friedlander T. The relation between crosstalk and gene regulation form
revisited. PLOS Computational Biology. 2020;16(2). doi:10.1371/journal.pcbi.1007642
apa: Grah, R., & Friedlander, T. (2020). The relation between crosstalk and
gene regulation form revisited. PLOS Computational Biology. Public Library
of Science. https://doi.org/10.1371/journal.pcbi.1007642
chicago: Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene
Regulation Form Revisited.” PLOS Computational Biology. Public Library
of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.
ieee: R. Grah and T. Friedlander, “The relation between crosstalk and gene regulation
form revisited,” PLOS Computational Biology, vol. 16, no. 2. Public Library
of Science, 2020.
ista: Grah R, Friedlander T. 2020. The relation between crosstalk and gene regulation
form revisited. PLOS Computational Biology. 16(2), e1007642.
mla: Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene
Regulation Form Revisited.” PLOS Computational Biology, vol. 16, no. 2,
e1007642, Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.
short: R. Grah, T. Friedlander, PLOS Computational Biology 16 (2020).
date_created: 2020-03-06T07:39:38Z
date_published: 2020-02-25T00:00:00Z
date_updated: 2023-09-12T11:02:24Z
day: '25'
ddc:
- '000'
- '570'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1371/journal.pcbi.1007642
external_id:
isi:
- '000526725200019'
file:
- access_level: open_access
checksum: 5239dd134dc6e1c71fe7b3ce2953da37
content_type: application/pdf
creator: dernst
date_created: 2020-03-09T15:12:21Z
date_updated: 2020-07-14T12:48:00Z
file_id: '7579'
file_name: 2020_PlosCompBio_Grah.pdf
file_size: 2209325
relation: main_file
file_date_updated: 2020-07-14T12:48:00Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: PLOS Computational Biology
publication_identifier:
issn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
record:
- id: '9716'
relation: research_data
status: deleted
- id: '9776'
relation: research_data
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- id: '9779'
relation: used_in_publication
status: public
- id: '8155'
relation: dissertation_contains
status: public
- id: '9777'
relation: research_data
status: public
scopus_import: '1'
status: public
title: The relation between crosstalk and gene regulation form revisited
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 16
year: '2020'
...
---
_id: '7570'
abstract:
- lang: eng
text: The relaxation of few-body quantum systems can strongly depend on the initial
state when the system’s semiclassical phase space is mixed; i.e., regions of chaotic
motion coexist with regular islands. In recent years, there has been much effort
to understand the process of thermalization in strongly interacting quantum systems
that often lack an obvious semiclassical limit. The time-dependent variational
principle (TDVP) allows one to systematically derive an effective classical (nonlinear)
dynamical system by projecting unitary many-body dynamics onto a manifold of weakly
entangled variational states. We demonstrate that such dynamical systems generally
possess mixed phase space. When TDVP errors are small, the mixed phase space leaves
a footprint on the exact dynamics of the quantum model. For example, when the
system is initialized in a state belonging to a stable periodic orbit or the surrounding
regular region, it exhibits persistent many-body quantum revivals. As a proof
of principle, we identify new types of “quantum many-body scars,” i.e., initial
states that lead to long-time oscillations in a model of interacting Rydberg atoms
in one and two dimensions. Intriguingly, the initial states that give rise to
most robust revivals are typically entangled states. On the other hand, even when
TDVP errors are large, as in the thermalizing tilted-field Ising model, initializing
the system in a regular region of phase space leads to a surprising slowdown of
thermalization. Our work establishes TDVP as a method for identifying interacting
quantum systems with anomalous dynamics in arbitrary dimensions. Moreover, the
mixed phase space classical variational equations allow one to find slowly thermalizing
initial conditions in interacting models. Our results shed light on a link between
classical and quantum chaos, pointing toward possible extensions of the classical
Kolmogorov-Arnold-Moser theorem to quantum systems.
article_number: '011055'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Alexios
full_name: Michailidis, Alexios
id: 36EBAD38-F248-11E8-B48F-1D18A9856A87
last_name: Michailidis
orcid: 0000-0002-8443-1064
- first_name: C. J.
full_name: Turner, C. J.
last_name: Turner
- first_name: Z.
full_name: Papić, Z.
last_name: Papić
- first_name: D. A.
full_name: Abanin, D. A.
last_name: Abanin
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Michailidis A, Turner CJ, Papić Z, Abanin DA, Serbyn M. Slow quantum thermalization
and many-body revivals from mixed phase space. Physical Review X. 2020;10(1).
doi:10.1103/physrevx.10.011055
apa: Michailidis, A., Turner, C. J., Papić, Z., Abanin, D. A., & Serbyn, M.
(2020). Slow quantum thermalization and many-body revivals from mixed phase space.
Physical Review X. American Physical Society. https://doi.org/10.1103/physrevx.10.011055
chicago: Michailidis, Alexios, C. J. Turner, Z. Papić, D. A. Abanin, and Maksym
Serbyn. “Slow Quantum Thermalization and Many-Body Revivals from Mixed Phase Space.”
Physical Review X. American Physical Society, 2020. https://doi.org/10.1103/physrevx.10.011055.
ieee: A. Michailidis, C. J. Turner, Z. Papić, D. A. Abanin, and M. Serbyn, “Slow
quantum thermalization and many-body revivals from mixed phase space,” Physical
Review X, vol. 10, no. 1. American Physical Society, 2020.
ista: Michailidis A, Turner CJ, Papić Z, Abanin DA, Serbyn M. 2020. Slow quantum
thermalization and many-body revivals from mixed phase space. Physical Review
X. 10(1), 011055.
mla: Michailidis, Alexios, et al. “Slow Quantum Thermalization and Many-Body Revivals
from Mixed Phase Space.” Physical Review X, vol. 10, no. 1, 011055, American
Physical Society, 2020, doi:10.1103/physrevx.10.011055.
short: A. Michailidis, C.J. Turner, Z. Papić, D.A. Abanin, M. Serbyn, Physical Review
X 10 (2020).
date_created: 2020-03-08T18:02:01Z
date_published: 2020-03-04T00:00:00Z
date_updated: 2023-08-18T07:01:07Z
day: '04'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.1103/physrevx.10.011055
external_id:
arxiv:
- '1905.08564'
isi:
- '000517969300001'
file:
- access_level: open_access
checksum: 4b3f2c13873d35230173c73d0e11c408
content_type: application/pdf
creator: dernst
date_created: 2020-03-12T12:13:07Z
date_updated: 2020-07-14T12:48:00Z
file_id: '7581'
file_name: 2020_PhysicalReviewX_Michailidis.pdf
file_size: 17828638
relation: main_file
file_date_updated: 2020-07-14T12:48:00Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: Physical Review X
publication_identifier:
issn:
- 2160-3308
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/classical-physics-helps-predict-fate-of-interacting-quantum-systems/
scopus_import: '1'
status: public
title: Slow quantum thermalization and many-body revivals from mixed phase space
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2020'
...
---
_id: '7572'
abstract:
- lang: eng
text: The polymerization–depolymerization dynamics of cytoskeletal proteins play
essential roles in the self-organization of cytoskeletal structures, in eukaryotic
as well as prokaryotic cells. While advances in fluorescence microscopy and in
vitro reconstitution experiments have helped to study the dynamic properties of
these complex systems, methods that allow to collect and analyze large quantitative
datasets of the underlying polymer dynamics are still missing. Here, we present
a novel image analysis workflow to study polymerization dynamics of active filaments
in a nonbiased, highly automated manner. Using treadmilling filaments of the bacterial
tubulin FtsZ as an example, we demonstrate that our method is able to specifically
detect, track and analyze growth and shrinkage of polymers, even in dense networks
of filaments. We believe that this automated method can facilitate the analysis
of a large variety of dynamic cytoskeletal systems, using standard time-lapse
movies obtained from experiments in vitro as well as in the living cell. Moreover,
we provide scripts implementing this method as supplementary material.
alternative_title:
- Methods in Cell Biology
article_processing_charge: No
author:
- first_name: Paulo R
full_name: Dos Santos Caldas, Paulo R
id: 38FCDB4C-F248-11E8-B48F-1D18A9856A87
last_name: Dos Santos Caldas
orcid: 0000-0001-6730-4461
- first_name: Philipp
full_name: Radler, Philipp
id: 40136C2A-F248-11E8-B48F-1D18A9856A87
last_name: Radler
orcid: '0000-0001-9198-2182 '
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
citation:
ama: 'Dos Santos Caldas PR, Radler P, Sommer CM, Loose M. Computational analysis
of filament polymerization dynamics in cytoskeletal networks. In: Tran P, ed.
Methods in Cell Biology. Vol 158. Elsevier; 2020:145-161. doi:10.1016/bs.mcb.2020.01.006'
apa: Dos Santos Caldas, P. R., Radler, P., Sommer, C. M., & Loose, M. (2020).
Computational analysis of filament polymerization dynamics in cytoskeletal networks.
In P. Tran (Ed.), Methods in Cell Biology (Vol. 158, pp. 145–161). Elsevier.
https://doi.org/10.1016/bs.mcb.2020.01.006
chicago: Dos Santos Caldas, Paulo R, Philipp Radler, Christoph M Sommer, and Martin
Loose. “Computational Analysis of Filament Polymerization Dynamics in Cytoskeletal
Networks.” In Methods in Cell Biology, edited by Phong Tran, 158:145–61.
Elsevier, 2020. https://doi.org/10.1016/bs.mcb.2020.01.006.
ieee: P. R. Dos Santos Caldas, P. Radler, C. M. Sommer, and M. Loose, “Computational
analysis of filament polymerization dynamics in cytoskeletal networks,” in Methods
in Cell Biology, vol. 158, P. Tran, Ed. Elsevier, 2020, pp. 145–161.
ista: 'Dos Santos Caldas PR, Radler P, Sommer CM, Loose M. 2020.Computational analysis
of filament polymerization dynamics in cytoskeletal networks. In: Methods in Cell
Biology. Methods in Cell Biology, vol. 158, 145–161.'
mla: Dos Santos Caldas, Paulo R., et al. “Computational Analysis of Filament Polymerization
Dynamics in Cytoskeletal Networks.” Methods in Cell Biology, edited by
Phong Tran, vol. 158, Elsevier, 2020, pp. 145–61, doi:10.1016/bs.mcb.2020.01.006.
short: P.R. Dos Santos Caldas, P. Radler, C.M. Sommer, M. Loose, in:, P. Tran (Ed.),
Methods in Cell Biology, Elsevier, 2020, pp. 145–161.
date_created: 2020-03-08T23:00:47Z
date_published: 2020-02-27T00:00:00Z
date_updated: 2023-10-04T09:50:24Z
day: '27'
department:
- _id: MaLo
doi: 10.1016/bs.mcb.2020.01.006
ec_funded: 1
editor:
- first_name: 'Phong '
full_name: 'Tran, Phong '
last_name: Tran
external_id:
isi:
- '000611826500008'
intvolume: ' 158'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/839571
month: '02'
oa: 1
oa_version: Preprint
page: 145-161
project:
- _id: 2595697A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '679239'
name: Self-Organization of the Bacterial Cell
- _id: 260D98C8-B435-11E9-9278-68D0E5697425
name: Reconstitution of Bacterial Cell Division Using Purified Components
publication: Methods in Cell Biology
publication_identifier:
issn:
- 0091679X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '8358'
relation: part_of_dissertation
status: public
scopus_import: '1'
status: public
title: Computational analysis of filament polymerization dynamics in cytoskeletal
networks
type: book_chapter
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 158
year: '2020'
...
---
_id: '7573'
abstract:
- lang: eng
text: This paper deals with dynamical optimal transport metrics defined by spatial
discretisation of the Benamou–Benamou formula for the Kantorovich metric . Such
metrics appear naturally in discretisations of -gradient flow formulations for
dissipative PDE. However, it has recently been shown that these metrics do not
in general converge to , unless strong geometric constraints are imposed on the
discrete mesh. In this paper we prove that, in a 1-dimensional periodic setting,
discrete transport metrics converge to a limiting transport metric with a non-trivial
effective mobility. This mobility depends sensitively on the geometry of the mesh
and on the non-local mobility at the discrete level. Our result quantifies to
what extent discrete transport can make use of microstructure in the mesh to reduce
the cost of transport.
acknowledgement: J.M. gratefully acknowledges support by the European Research Council
(ERC) under the European Union's Horizon 2020 research and innovation programme
(grant agreement No 716117). J.M. and L.P. also acknowledge support from the Austrian
Science Fund (FWF), grants No F65 and W1245. E.K. gratefully acknowledges support
by the German Research Foundation through the Hausdorff Center for Mathematics and
the Collaborative Research Center 1060. P.G. is partially funded by the Deutsche
Forschungsgemeinschaft (DFG, German Research Foundation) – 350398276.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Peter
full_name: Gladbach, Peter
last_name: Gladbach
- first_name: Eva
full_name: Kopfer, Eva
last_name: Kopfer
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
- first_name: Lorenzo
full_name: Portinale, Lorenzo
id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87
last_name: Portinale
citation:
ama: Gladbach P, Kopfer E, Maas J, Portinale L. Homogenisation of one-dimensional
discrete optimal transport. Journal de Mathematiques Pures et Appliquees.
2020;139(7):204-234. doi:10.1016/j.matpur.2020.02.008
apa: Gladbach, P., Kopfer, E., Maas, J., & Portinale, L. (2020). Homogenisation
of one-dimensional discrete optimal transport. Journal de Mathematiques Pures
et Appliquees. Elsevier. https://doi.org/10.1016/j.matpur.2020.02.008
chicago: Gladbach, Peter, Eva Kopfer, Jan Maas, and Lorenzo Portinale. “Homogenisation
of One-Dimensional Discrete Optimal Transport.” Journal de Mathematiques Pures
et Appliquees. Elsevier, 2020. https://doi.org/10.1016/j.matpur.2020.02.008.
ieee: P. Gladbach, E. Kopfer, J. Maas, and L. Portinale, “Homogenisation of one-dimensional
discrete optimal transport,” Journal de Mathematiques Pures et Appliquees,
vol. 139, no. 7. Elsevier, pp. 204–234, 2020.
ista: Gladbach P, Kopfer E, Maas J, Portinale L. 2020. Homogenisation of one-dimensional
discrete optimal transport. Journal de Mathematiques Pures et Appliquees. 139(7),
204–234.
mla: Gladbach, Peter, et al. “Homogenisation of One-Dimensional Discrete Optimal
Transport.” Journal de Mathematiques Pures et Appliquees, vol. 139, no.
7, Elsevier, 2020, pp. 204–34, doi:10.1016/j.matpur.2020.02.008.
short: P. Gladbach, E. Kopfer, J. Maas, L. Portinale, Journal de Mathematiques Pures
et Appliquees 139 (2020) 204–234.
date_created: 2020-03-08T23:00:47Z
date_published: 2020-07-01T00:00:00Z
date_updated: 2023-09-07T13:31:05Z
day: '01'
department:
- _id: JaMa
doi: 10.1016/j.matpur.2020.02.008
ec_funded: 1
external_id:
arxiv:
- '1905.05757'
isi:
- '000539439400008'
intvolume: ' 139'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1905.05757
month: '07'
oa: 1
oa_version: Preprint
page: 204-234
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: 260482E2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: ' F06504'
name: Taming Complexity in Partial Di erential Systems
- _id: 260788DE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
name: Dissipation and Dispersion in Nonlinear Partial Differential Equations
publication: Journal de Mathematiques Pures et Appliquees
publication_identifier:
issn:
- '00217824'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '10030'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Homogenisation of one-dimensional discrete optimal transport
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 139
year: '2020'
...
---
_id: '7580'
abstract:
- lang: eng
text: The eukaryotic endomembrane system is controlled by small GTPases of the Rab
family, which are activated at defined times and locations in a switch-like manner.
While this switch is well understood for an individual protein, how regulatory
networks produce intracellular activity patterns is currently not known. Here,
we combine in vitro reconstitution experiments with computational modeling to
study a minimal Rab5 activation network. We find that the molecular interactions
in this system give rise to a positive feedback and bistable collective switching
of Rab5. Furthermore, we find that switching near the critical point is intrinsically
stochastic and provide evidence that controlling the inactive population of Rab5
on the membrane can shape the network response. Notably, we demonstrate that collective
switching can spread on the membrane surface as a traveling wave of Rab5 activation.
Together, our findings reveal how biochemical signaling networks control vesicle
trafficking pathways and how their nonequilibrium properties define the spatiotemporal
organization of the cell.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
article_processing_charge: No
article_type: original
author:
- first_name: Urban
full_name: Bezeljak, Urban
id: 2A58201A-F248-11E8-B48F-1D18A9856A87
last_name: Bezeljak
orcid: 0000-0003-1365-5631
- first_name: Hrushikesh
full_name: Loya, Hrushikesh
last_name: Loya
- first_name: Beata M
full_name: Kaczmarek, Beata M
id: 36FA4AFA-F248-11E8-B48F-1D18A9856A87
last_name: Kaczmarek
- first_name: Timothy E.
full_name: Saunders, Timothy E.
last_name: Saunders
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
citation:
ama: Bezeljak U, Loya H, Kaczmarek BM, Saunders TE, Loose M. Stochastic activation
and bistability in a Rab GTPase regulatory network. Proceedings of the National
Academy of Sciences. 2020;117(12):6504-6549. doi:10.1073/pnas.1921027117
apa: Bezeljak, U., Loya, H., Kaczmarek, B. M., Saunders, T. E., & Loose, M.
(2020). Stochastic activation and bistability in a Rab GTPase regulatory network.
Proceedings of the National Academy of Sciences. Proceedings of the National
Academy of Sciences. https://doi.org/10.1073/pnas.1921027117
chicago: Bezeljak, Urban, Hrushikesh Loya, Beata M Kaczmarek, Timothy E. Saunders,
and Martin Loose. “Stochastic Activation and Bistability in a Rab GTPase Regulatory
Network.” Proceedings of the National Academy of Sciences. Proceedings
of the National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1921027117.
ieee: U. Bezeljak, H. Loya, B. M. Kaczmarek, T. E. Saunders, and M. Loose, “Stochastic
activation and bistability in a Rab GTPase regulatory network,” Proceedings
of the National Academy of Sciences, vol. 117, no. 12. Proceedings of the
National Academy of Sciences, pp. 6504–6549, 2020.
ista: Bezeljak U, Loya H, Kaczmarek BM, Saunders TE, Loose M. 2020. Stochastic activation
and bistability in a Rab GTPase regulatory network. Proceedings of the National
Academy of Sciences. 117(12), 6504–6549.
mla: Bezeljak, Urban, et al. “Stochastic Activation and Bistability in a Rab GTPase
Regulatory Network.” Proceedings of the National Academy of Sciences, vol.
117, no. 12, Proceedings of the National Academy of Sciences, 2020, pp. 6504–49,
doi:10.1073/pnas.1921027117.
short: U. Bezeljak, H. Loya, B.M. Kaczmarek, T.E. Saunders, M. Loose, Proceedings
of the National Academy of Sciences 117 (2020) 6504–6549.
date_created: 2020-03-12T05:32:26Z
date_published: 2020-03-24T00:00:00Z
date_updated: 2023-09-07T13:17:06Z
day: '24'
department:
- _id: MaLo
- _id: CaBe
doi: 10.1073/pnas.1921027117
external_id:
isi:
- '000521821800040'
intvolume: ' 117'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/776567
month: '03'
oa: 1
oa_version: Preprint
page: 6504-6549
project:
- _id: 2599F062-B435-11E9-9278-68D0E5697425
grant_number: RGY0083/2016
name: Reconstitution of cell polarity and axis determination in a cell-free system
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/proteins-as-molecular-switches/
record:
- id: '8341'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Stochastic activation and bistability in a Rab GTPase regulatory network
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 117
year: '2020'
...
---
_id: '7582'
abstract:
- lang: eng
text: Small RNAs (smRNA, 19–25 nucleotides long), which are transcribed by RNA polymerase
II, regulate the expression of genes involved in a multitude of processes in eukaryotes.
miRNA biogenesis and the proteins involved in the biogenesis pathway differ across
plant and animal lineages. The major proteins constituting the biogenesis pathway,
namely, the Dicers (DCL/DCR) and Argonautes (AGOs), have been extensively studied.
However, the accessory proteins (DAWDLE (DDL), SERRATE (SE), and TOUGH (TGH))
of the pathway that differs across the two lineages remain largely uncharacterized.
We present the first detailed report on the molecular evolution and divergence
of these proteins across eukaryotes. Although DDL is present in eukaryotes and
prokaryotes, SE and TGH appear to be specific to eukaryotes. The addition/deletion
of specific domains and/or domain-specific sequence divergence in the three proteins
points to the observed functional divergence of these proteins across the two
lineages, which correlates with the differences in miRNA length across the two
lineages. Our data enhance the current understanding of the structure–function
relationship of these proteins and reveals previous unexplored crucial residues
in the three proteins that can be used as a basis for further functional characterization.
The data presented here on the number of miRNAs in crown eukaryotic lineages are
consistent with the notion of the expansion of the number of miRNA-coding genes
in animal and plant lineages correlating with organismal complexity. Whether this
difference in functionally correlates with the diversification (or presence/absence)
of the three proteins studied here or the miRNA signaling in the plant and animal
lineages is unclear. Based on our results of the three proteins studied here and
previously available data concerning the evolution of miRNA genes in the plant
and animal lineages, we believe that miRNAs probably evolved once in the ancestor
to crown eukaryotes and have diversified independently in the eukaryotes.
article_number: '299'
article_processing_charge: No
article_type: original
author:
- first_name: Taraka Ramji
full_name: Moturu, Taraka Ramji
last_name: Moturu
- first_name: Sansrity
full_name: Sinha, Sansrity
last_name: Sinha
- first_name: Hymavathi
full_name: Salava, Hymavathi
last_name: Salava
- first_name: Sravankumar
full_name: Thula, Sravankumar
last_name: Thula
- first_name: Tomasz
full_name: Nodzyński, Tomasz
last_name: Nodzyński
- first_name: Radka Svobodová
full_name: Vařeková, Radka Svobodová
last_name: Vařeková
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Sibu
full_name: Simon, Sibu
id: 4542EF9A-F248-11E8-B48F-1D18A9856A87
last_name: Simon
orcid: 0000-0002-1998-6741
citation:
ama: Moturu TR, Sinha S, Salava H, et al. Molecular evolution and diversification
of proteins involved in miRNA maturation pathway. Plants. 2020;9(3). doi:10.3390/plants9030299
apa: Moturu, T. R., Sinha, S., Salava, H., Thula, S., Nodzyński, T., Vařeková, R.
S., … Simon, S. (2020). Molecular evolution and diversification of proteins involved
in miRNA maturation pathway. Plants. MDPI. https://doi.org/10.3390/plants9030299
chicago: Moturu, Taraka Ramji, Sansrity Sinha, Hymavathi Salava, Sravankumar Thula,
Tomasz Nodzyński, Radka Svobodová Vařeková, Jiří Friml, and Sibu Simon. “Molecular
Evolution and Diversification of Proteins Involved in MiRNA Maturation Pathway.”
Plants. MDPI, 2020. https://doi.org/10.3390/plants9030299.
ieee: T. R. Moturu et al., “Molecular evolution and diversification of proteins
involved in miRNA maturation pathway,” Plants, vol. 9, no. 3. MDPI, 2020.
ista: Moturu TR, Sinha S, Salava H, Thula S, Nodzyński T, Vařeková RS, Friml J,
Simon S. 2020. Molecular evolution and diversification of proteins involved in
miRNA maturation pathway. Plants. 9(3), 299.
mla: Moturu, Taraka Ramji, et al. “Molecular Evolution and Diversification of Proteins
Involved in MiRNA Maturation Pathway.” Plants, vol. 9, no. 3, 299, MDPI,
2020, doi:10.3390/plants9030299.
short: T.R. Moturu, S. Sinha, H. Salava, S. Thula, T. Nodzyński, R.S. Vařeková,
J. Friml, S. Simon, Plants 9 (2020).
date_created: 2020-03-15T23:00:52Z
date_published: 2020-03-01T00:00:00Z
date_updated: 2025-05-07T11:12:28Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.3390/plants9030299
ec_funded: 1
external_id:
isi:
- '000525315000035'
pmid:
- '32121542'
file:
- access_level: open_access
checksum: 6d5af3e17266a48996b4af4e67e88a85
content_type: application/pdf
creator: dernst
date_created: 2020-03-23T13:37:00Z
date_updated: 2020-07-14T12:48:00Z
file_id: '7614'
file_name: 2020_Plants_Moturu.pdf
file_size: 2373484
relation: main_file
file_date_updated: 2020-07-14T12:48:00Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Plants
publication_identifier:
eissn:
- '22237747'
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Molecular evolution and diversification of proteins involved in miRNA maturation
pathway
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2020'
...
---
_id: '7586'
abstract:
- lang: eng
text: CLC chloride/proton exchangers may support acidification of endolysosomes
and raise their luminal Cl− concentration. Disruption of endosomal ClC‐3 causes
severe neurodegeneration. To assess the importance of ClC‐3 Cl−/H+ exchange, we
now generate Clcn3unc/unc mice in which ClC‐3 is converted into a Cl− channel.
Unlike Clcn3−/− mice, Clcn3unc/unc mice appear normal owing to compensation by
ClC‐4 with which ClC‐3 forms heteromers. ClC‐4 protein levels are strongly reduced
in Clcn3−/−, but not in Clcn3unc/unc mice because ClC‐3unc binds and stabilizes
ClC‐4 like wild‐type ClC‐3. Although mice lacking ClC‐4 appear healthy, its absence
in Clcn3unc/unc/Clcn4−/− mice entails even stronger neurodegeneration than observed
in Clcn3−/− mice. A fraction of ClC‐3 is found on synaptic vesicles, but miniature
postsynaptic currents and synaptic vesicle acidification are not affected in Clcn3unc/unc
or Clcn3−/− mice before neurodegeneration sets in. Both, Cl−/H+‐exchange activity
and the stabilizing effect on ClC‐4, are central to the biological function of
ClC‐3.
acknowledgement: "We thank T. Stauber and T. Breiderhoff for cloning expression constructs;
K. Räbel, S. Hohensee, and C. Backhaus for technical assistance; R. Jahn (MPIbpc,
Göttingen) for providing the equipment required for SV purification; and A\r\nWoehler
(MDC, Berlin) for assistance with SV imaging. Supported, in part, by grants from
the Deutsche Forschungsgemeinschaft (JE164/9-2, SFB740 TP C5, FOR 2625 (JE164/14-1),
NeuroCure Cluster of Excellence), the European Research Council Advanced Grant CYTOVOLION
(ERC 294435) and the Prix Louis-Jeantet de Médecine to TJJ, and Peter and Traudl
Engelhorn fellowship to ZF."
article_number: e103358
article_processing_charge: No
article_type: original
author:
- first_name: Stefanie
full_name: Weinert, Stefanie
last_name: Weinert
- first_name: Niclas
full_name: Gimber, Niclas
last_name: Gimber
- first_name: Dorothea
full_name: Deuschel, Dorothea
last_name: Deuschel
- first_name: Till
full_name: Stuhlmann, Till
last_name: Stuhlmann
- first_name: Dmytro
full_name: Puchkov, Dmytro
last_name: Puchkov
- first_name: Zohreh
full_name: Farsi, Zohreh
last_name: Farsi
- first_name: Carmen F.
full_name: Ludwig, Carmen F.
last_name: Ludwig
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Karen I.
full_name: López-Cayuqueo, Karen I.
last_name: López-Cayuqueo
- first_name: Rosa
full_name: Planells-Cases, Rosa
last_name: Planells-Cases
- first_name: Thomas J.
full_name: Jentsch, Thomas J.
last_name: Jentsch
citation:
ama: Weinert S, Gimber N, Deuschel D, et al. Uncoupling endosomal CLC chloride/proton
exchange causes severe neurodegeneration. EMBO Journal. 2020;39. doi:10.15252/embj.2019103358
apa: Weinert, S., Gimber, N., Deuschel, D., Stuhlmann, T., Puchkov, D., Farsi, Z.,
… Jentsch, T. J. (2020). Uncoupling endosomal CLC chloride/proton exchange causes
severe neurodegeneration. EMBO Journal. EMBO Press. https://doi.org/10.15252/embj.2019103358
chicago: Weinert, Stefanie, Niclas Gimber, Dorothea Deuschel, Till Stuhlmann, Dmytro
Puchkov, Zohreh Farsi, Carmen F. Ludwig, et al. “Uncoupling Endosomal CLC Chloride/Proton
Exchange Causes Severe Neurodegeneration.” EMBO Journal. EMBO Press, 2020.
https://doi.org/10.15252/embj.2019103358.
ieee: S. Weinert et al., “Uncoupling endosomal CLC chloride/proton exchange
causes severe neurodegeneration,” EMBO Journal, vol. 39. EMBO Press, 2020.
ista: Weinert S, Gimber N, Deuschel D, Stuhlmann T, Puchkov D, Farsi Z, Ludwig CF,
Novarino G, López-Cayuqueo KI, Planells-Cases R, Jentsch TJ. 2020. Uncoupling
endosomal CLC chloride/proton exchange causes severe neurodegeneration. EMBO Journal.
39, e103358.
mla: Weinert, Stefanie, et al. “Uncoupling Endosomal CLC Chloride/Proton Exchange
Causes Severe Neurodegeneration.” EMBO Journal, vol. 39, e103358, EMBO
Press, 2020, doi:10.15252/embj.2019103358.
short: S. Weinert, N. Gimber, D. Deuschel, T. Stuhlmann, D. Puchkov, Z. Farsi, C.F.
Ludwig, G. Novarino, K.I. López-Cayuqueo, R. Planells-Cases, T.J. Jentsch, EMBO
Journal 39 (2020).
date_created: 2020-03-15T23:00:55Z
date_published: 2020-03-02T00:00:00Z
date_updated: 2023-08-18T07:07:36Z
day: '02'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.15252/embj.2019103358
external_id:
isi:
- '000517335000001'
pmid:
- '32118314'
file:
- access_level: open_access
checksum: 82750a7a93e3740decbce8474004111a
content_type: application/pdf
creator: dernst
date_created: 2020-03-23T13:51:11Z
date_updated: 2020-07-14T12:48:00Z
file_id: '7615'
file_name: 2020_EMBO_Weinert.pdf
file_size: 12243278
relation: main_file
file_date_updated: 2020-07-14T12:48:00Z
has_accepted_license: '1'
intvolume: ' 39'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: EMBO Journal
publication_identifier:
eissn:
- '14602075'
issn:
- '02614189'
publication_status: published
publisher: EMBO Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Uncoupling endosomal CLC chloride/proton exchange causes severe neurodegeneration
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 39
year: '2020'
...
---
_id: '7591'
abstract:
- lang: eng
text: Rechargeable Li–O2 batteries have gathered enormous attention in the research
community for having amongst the highest theoretical energy storage. Realizing
the promise, even in part, in practice could produce a device that stores significantly
more energy than other rechargeable batteries. Fundamental understanding of the
reaction mechanisms is now realized to be key to overcome many challenges. We
give a critical overview of the current understanding of the chemistry underpinning
the Li–O2 cell with focus on the cathode and give a perspective on the most important
research needs. Since performance and reversibility are often grossly misunderstood,
we put emphasis on realistic performances to be achieved by Li–O2 cells and on
means to identify reversibility. Parasitic chemistry is the foremost barrier for
reversible cycling and now realized to be predominantly caused by singlet oxygen
rather than by the previously thought superoxide or peroxide. This finding profoundly
affects any other area of research from reaction mechanisms, to electrolytes and
catalysts and dominates future research needs.
article_processing_charge: No
author:
- first_name: Yann K.
full_name: Petit, Yann K.
last_name: Petit
- first_name: Eléonore
full_name: Mourad, Eléonore
last_name: Mourad
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
citation:
ama: 'Petit YK, Mourad E, Freunberger SA. Lithium–Oxygen batteries. In: Encyclopedia
of Electrochemistry. Wiley; 2020:1-42. doi:10.1002/9783527610426.bard110017'
apa: Petit, Y. K., Mourad, E., & Freunberger, S. A. (2020). Lithium–Oxygen batteries.
In Encyclopedia of Electrochemistry (pp. 1–42). Wiley. https://doi.org/10.1002/9783527610426.bard110017
chicago: Petit, Yann K., Eléonore Mourad, and Stefan Alexander Freunberger. “Lithium–Oxygen
Batteries.” In Encyclopedia of Electrochemistry, 1–42. Wiley, 2020. https://doi.org/10.1002/9783527610426.bard110017.
ieee: Y. K. Petit, E. Mourad, and S. A. Freunberger, “Lithium–Oxygen batteries,”
in Encyclopedia of Electrochemistry, Wiley, 2020, pp. 1–42.
ista: 'Petit YK, Mourad E, Freunberger SA. 2020.Lithium–Oxygen batteries. In: Encyclopedia
of Electrochemistry. , 1–42.'
mla: Petit, Yann K., et al. “Lithium–Oxygen Batteries.” Encyclopedia of Electrochemistry,
Wiley, 2020, pp. 1–42, doi:10.1002/9783527610426.bard110017.
short: Y.K. Petit, E. Mourad, S.A. Freunberger, in:, Encyclopedia of Electrochemistry,
Wiley, 2020, pp. 1–42.
date_created: 2020-03-19T15:54:34Z
date_published: 2020-03-18T00:00:00Z
date_updated: 2021-01-12T08:14:22Z
day: '18'
doi: 10.1002/9783527610426.bard110017
extern: '1'
language:
- iso: eng
month: '03'
oa_version: None
page: 1-42
publication: Encyclopedia of Electrochemistry
publication_identifier:
eisbn:
- '9783527610426'
isbn:
- '9783527302505'
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Lithium–Oxygen batteries
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '7593'
abstract:
- lang: eng
text: Heterozygous loss of human PAFAH1B1 (coding for LIS1) results in the disruption
of neurogenesis and neuronal migration via dysregulation of microtubule (MT) stability
and dynein motor function/localization that alters mitotic spindle orientation,
chromosomal segregation, and nuclear migration. Recently, human induced pluripotent
stem cell (iPSC) models revealed an important role for LIS1 in controlling the
length of terminal cell divisions of outer radial glial (oRG) progenitors, suggesting
cellular functions of LIS1 in regulating neural progenitor cell (NPC) daughter
cell separation. Here we examined the late mitotic stages NPCs in vivo and mouse
embryonic fibroblasts (MEFs) in vitro from Pafah1b1-deficient mutants. Pafah1b1-deficient
neocortical NPCs and MEFs similarly exhibited cleavage plane displacement with
mislocalization of furrow-associated markers, associated with actomyosin dysfunction
and cell membrane hyper-contractility. Thus, it suggests LIS1 acts as a key molecular
link connecting MTs/dynein and actomyosin, ensuring that cell membrane contractility
is tightly controlled to execute proper daughter cell separation.
article_number: '51512'
article_processing_charge: No
article_type: original
author:
- first_name: Hyang Mi
full_name: Moon, Hyang Mi
last_name: Moon
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Liqun
full_name: Luo, Liqun
last_name: Luo
- first_name: Anthony
full_name: Wynshaw-Boris, Anthony
last_name: Wynshaw-Boris
citation:
ama: Moon HM, Hippenmeyer S, Luo L, Wynshaw-Boris A. LIS1 determines cleavage plane
positioning by regulating actomyosin-mediated cell membrane contractility. eLife.
2020;9. doi:10.7554/elife.51512
apa: Moon, H. M., Hippenmeyer, S., Luo, L., & Wynshaw-Boris, A. (2020). LIS1
determines cleavage plane positioning by regulating actomyosin-mediated cell membrane
contractility. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.51512
chicago: Moon, Hyang Mi, Simon Hippenmeyer, Liqun Luo, and Anthony Wynshaw-Boris.
“LIS1 Determines Cleavage Plane Positioning by Regulating Actomyosin-Mediated
Cell Membrane Contractility.” ELife. eLife Sciences Publications, 2020.
https://doi.org/10.7554/elife.51512.
ieee: H. M. Moon, S. Hippenmeyer, L. Luo, and A. Wynshaw-Boris, “LIS1 determines
cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility,”
eLife, vol. 9. eLife Sciences Publications, 2020.
ista: Moon HM, Hippenmeyer S, Luo L, Wynshaw-Boris A. 2020. LIS1 determines cleavage
plane positioning by regulating actomyosin-mediated cell membrane contractility.
eLife. 9, 51512.
mla: Moon, Hyang Mi, et al. “LIS1 Determines Cleavage Plane Positioning by Regulating
Actomyosin-Mediated Cell Membrane Contractility.” ELife, vol. 9, 51512,
eLife Sciences Publications, 2020, doi:10.7554/elife.51512.
short: H.M. Moon, S. Hippenmeyer, L. Luo, A. Wynshaw-Boris, ELife 9 (2020).
date_created: 2020-03-20T13:16:41Z
date_published: 2020-03-11T00:00:00Z
date_updated: 2023-08-18T07:06:31Z
day: '11'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.7554/elife.51512
external_id:
isi:
- '000522835800001'
pmid:
- '32159512'
file:
- access_level: open_access
checksum: 396ceb2dd10b102ef4e699666b9342c3
content_type: application/pdf
creator: dernst
date_created: 2020-09-24T07:03:20Z
date_updated: 2020-09-24T07:03:20Z
file_id: '8567'
file_name: 2020_elife_Moon.pdf
file_size: 15089438
relation: main_file
success: 1
file_date_updated: 2020-09-24T07:03:20Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/751958
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: LIS1 determines cleavage plane positioning by regulating actomyosin-mediated
cell membrane contractility
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2020'
...
---
_id: '7594'
abstract:
- lang: eng
text: The concept of the entanglement between spin and orbital degrees of freedom
plays a crucial role in our understanding of various phases and exotic ground
states in a broad class of materials, including orbitally ordered materials and
spin liquids. We investigate how the spin-orbital entanglement in a Mott insulator
depends on the value of the spin-orbit coupling of the relativistic origin. To
this end, we numerically diagonalize a one-dimensional spin-orbital model with
Kugel-Khomskii exchange interactions between spins and orbitals on different sites
supplemented by the on-site spin-orbit coupling. In the regime of small spin-orbit
coupling with regard to the spin-orbital exchange, the ground state to a large
extent resembles the one obtained in the limit of vanishing spin-orbit coupling.
On the other hand, for large spin-orbit coupling the ground state can, depending
on the model parameters, either still show negligible spin-orbital entanglement
or evolve to a highly spin-orbitally-entangled phase with completely distinct
properties that are described by an effective XXZ model. The presented results
suggest that (i) the spin-orbital entanglement may be induced by large on-site
spin-orbit coupling, as found in the 5d transition metal oxides, such as the iridates;
(ii) for Mott insulators with weak spin-orbit coupling of Ising type, such as,
e.g., the alkali hyperoxides, the effects of the spin-orbit coupling on the ground
state can, in the first order of perturbation theory, be neglected.
article_number: '013353'
article_processing_charge: No
article_type: original
author:
- first_name: Dorota
full_name: Gotfryd, Dorota
last_name: Gotfryd
- first_name: Ekaterina
full_name: Paerschke, Ekaterina
id: 8275014E-6063-11E9-9B7F-6338E6697425
last_name: Paerschke
orcid: 0000-0003-0853-8182
- first_name: Jiri
full_name: Chaloupka, Jiri
last_name: Chaloupka
- first_name: Andrzej M.
full_name: Oles, Andrzej M.
last_name: Oles
- first_name: Krzysztof
full_name: Wohlfeld, Krzysztof
last_name: Wohlfeld
citation:
ama: Gotfryd D, Paerschke E, Chaloupka J, Oles AM, Wohlfeld K. How spin-orbital
entanglement depends on the spin-orbit coupling in a Mott insulator. Physical
Review Research. 2020;2(1). doi:10.1103/PhysRevResearch.2.013353
apa: Gotfryd, D., Paerschke, E., Chaloupka, J., Oles, A. M., & Wohlfeld, K.
(2020). How spin-orbital entanglement depends on the spin-orbit coupling in a
Mott insulator. Physical Review Research. American Physical Society. https://doi.org/10.1103/PhysRevResearch.2.013353
chicago: Gotfryd, Dorota, Ekaterina Paerschke, Jiri Chaloupka, Andrzej M. Oles,
and Krzysztof Wohlfeld. “How Spin-Orbital Entanglement Depends on the Spin-Orbit
Coupling in a Mott Insulator.” Physical Review Research. American Physical
Society, 2020. https://doi.org/10.1103/PhysRevResearch.2.013353.
ieee: D. Gotfryd, E. Paerschke, J. Chaloupka, A. M. Oles, and K. Wohlfeld, “How
spin-orbital entanglement depends on the spin-orbit coupling in a Mott insulator,”
Physical Review Research, vol. 2, no. 1. American Physical Society, 2020.
ista: Gotfryd D, Paerschke E, Chaloupka J, Oles AM, Wohlfeld K. 2020. How spin-orbital
entanglement depends on the spin-orbit coupling in a Mott insulator. Physical
Review Research. 2(1), 013353.
mla: Gotfryd, Dorota, et al. “How Spin-Orbital Entanglement Depends on the Spin-Orbit
Coupling in a Mott Insulator.” Physical Review Research, vol. 2, no. 1,
013353, American Physical Society, 2020, doi:10.1103/PhysRevResearch.2.013353.
short: D. Gotfryd, E. Paerschke, J. Chaloupka, A.M. Oles, K. Wohlfeld, Physical
Review Research 2 (2020).
date_created: 2020-03-20T15:21:10Z
date_published: 2020-03-20T00:00:00Z
date_updated: 2021-01-12T08:14:23Z
day: '20'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1103/PhysRevResearch.2.013353
ec_funded: 1
file:
- access_level: open_access
checksum: 1be551fd5f5583635076017d7391ffdc
content_type: application/pdf
creator: dernst
date_created: 2020-03-23T10:18:38Z
date_updated: 2020-07-14T12:48:00Z
file_id: '7610'
file_name: 2020_PhysRevResearch_Gotfryd.pdf
file_size: 1436735
relation: main_file
file_date_updated: 2020-07-14T12:48:00Z
has_accepted_license: '1'
intvolume: ' 2'
issue: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Physical Review Research
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: How spin-orbital entanglement depends on the spin-orbit coupling in a Mott
insulator
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: 2
year: '2020'
...
---
_id: '7600'
abstract:
- lang: eng
text: Directional intercellular transport of the phytohormone auxin mediated by
PIN FORMED (PIN) efflux carriers plays essential roles in both coordinating patterning
processes and integrating multiple external cues by rapidly redirecting auxin
fluxes. Multilevel regulations of PIN activity under internal and external cues
are complicated; however, the underlying molecular mechanism remains elusive.
Here we demonstrate that 3’-Phosphoinositide-Dependent Protein Kinase1 (PDK1),
which is conserved in plants and mammals, functions as a molecular hub integrating
the upstream lipid signalling and the downstream substrate activity through phosphorylation.
Genetic analysis uncovers that loss-of-function Arabidopsis mutant pdk1.1 pdk1.2
exhibits a plethora of abnormalities in organogenesis and growth, due to the defective
PIN-dependent auxin transport. Further cellular and biochemical analyses reveal
that PDK1 phosphorylates D6 Protein Kinase to facilitate its activity towards
PIN proteins. Our studies establish a lipid-dependent phosphorylation cascade
connecting membrane composition-based cellular signalling with plant growth and
patterning by regulating morphogenetic auxin fluxes.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
article_processing_charge: No
article_type: original
author:
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: Xixi
full_name: Zhang, Xixi
id: 61A66458-47E9-11EA-85BA-8AEAAF14E49A
last_name: Zhang
orcid: 0000-0001-7048-4627
- first_name: Wei
full_name: Kong, Wei
last_name: Kong
- first_name: Xiao-Li
full_name: Yang, Xiao-Li
last_name: Yang
- first_name: Gergely
full_name: Molnar, Gergely
id: 34F1AF46-F248-11E8-B48F-1D18A9856A87
last_name: Molnar
- first_name: Zuzana
full_name: Vondráková, Zuzana
last_name: Vondráková
- first_name: Roberta
full_name: Filepová, Roberta
last_name: Filepová
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Hong-Wei
full_name: Xue, Hong-Wei
last_name: Xue
citation:
ama: Tan S, Zhang X, Kong W, et al. The lipid code-dependent phosphoswitch PDK1–D6PK
activates PIN-mediated auxin efflux in Arabidopsis. Nature Plants. 2020;6:556-569.
doi:10.1038/s41477-020-0648-9
apa: Tan, S., Zhang, X., Kong, W., Yang, X.-L., Molnar, G., Vondráková, Z., … Xue,
H.-W. (2020). The lipid code-dependent phosphoswitch PDK1–D6PK activates PIN-mediated
auxin efflux in Arabidopsis. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-020-0648-9
chicago: Tan, Shutang, Xixi Zhang, Wei Kong, Xiao-Li Yang, Gergely Molnar, Zuzana
Vondráková, Roberta Filepová, Jan Petrášek, Jiří Friml, and Hong-Wei Xue. “The
Lipid Code-Dependent Phosphoswitch PDK1–D6PK Activates PIN-Mediated Auxin Efflux
in Arabidopsis.” Nature Plants. Springer Nature, 2020. https://doi.org/10.1038/s41477-020-0648-9.
ieee: S. Tan et al., “The lipid code-dependent phosphoswitch PDK1–D6PK activates
PIN-mediated auxin efflux in Arabidopsis,” Nature Plants, vol. 6. Springer
Nature, pp. 556–569, 2020.
ista: Tan S, Zhang X, Kong W, Yang X-L, Molnar G, Vondráková Z, Filepová R, Petrášek
J, Friml J, Xue H-W. 2020. The lipid code-dependent phosphoswitch PDK1–D6PK activates
PIN-mediated auxin efflux in Arabidopsis. Nature Plants. 6, 556–569.
mla: Tan, Shutang, et al. “The Lipid Code-Dependent Phosphoswitch PDK1–D6PK Activates
PIN-Mediated Auxin Efflux in Arabidopsis.” Nature Plants, vol. 6, Springer
Nature, 2020, pp. 556–69, doi:10.1038/s41477-020-0648-9.
short: S. Tan, X. Zhang, W. Kong, X.-L. Yang, G. Molnar, Z. Vondráková, R. Filepová,
J. Petrášek, J. Friml, H.-W. Xue, Nature Plants 6 (2020) 556–569.
date_created: 2020-03-21T16:34:16Z
date_published: 2020-05-01T00:00:00Z
date_updated: 2023-08-18T07:05:57Z
day: '01'
department:
- _id: JiFr
doi: 10.1038/s41477-020-0648-9
ec_funded: 1
external_id:
isi:
- '000531787500006'
pmid:
- '32393881'
intvolume: ' 6'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/755504
month: '05'
oa: 1
oa_version: Preprint
page: 556-569
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 256FEF10-B435-11E9-9278-68D0E5697425
grant_number: 723-2015
name: Long Term Fellowship
publication: Nature Plants
publication_identifier:
eissn:
- '20550278'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41477-020-0719-y
scopus_import: '1'
status: public
title: The lipid code-dependent phosphoswitch PDK1–D6PK activates PIN-mediated auxin
efflux in Arabidopsis
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 6
year: '2020'
...
---
_id: '7601'
abstract:
- lang: eng
text: Plasmodesmata (PD) are crucial structures for intercellular communication
in multicellular plants with remorins being their crucial plant-specific structural
and functional constituents. The PD biogenesis is an intriguing but poorly understood
process. By expressing an Arabidopsis remorin protein in mammalian cells, we have
reconstituted a PD-like filamentous structure, termed remorin filament (RF), connecting
neighboring cells physically and physiologically. Notably, RFs are capable of
transporting macromolecules intercellularly, in a way similar to plant PD. With
further super-resolution microscopic analysis and biochemical characterization,
we found that RFs are also composed of actin filaments, forming the core skeleton
structure, aligned with the remorin protein. This unique heterologous filamentous
structure might explain the molecular mechanism for remorin function as well as
PD construction. Furthermore, remorin protein exhibits a specific distribution
manner in the plasma membrane in mammalian cells, representing a lipid nanodomain,
depending on its lipid modification status. Our studies not only provide crucial
insights into the mechanism of PD biogenesis, but also uncovers unsuspected fundamental
mechanistic and evolutionary links between intercellular communication systems
of plants and animals.
article_processing_charge: No
author:
- first_name: Zhuang
full_name: Wei, Zhuang
last_name: Wei
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: Tao
full_name: Liu, Tao
last_name: Liu
- first_name: Yuan
full_name: Wu, Yuan
last_name: Wu
- first_name: Ji-Gang
full_name: Lei, Ji-Gang
last_name: Lei
- first_name: ZhengJun
full_name: Chen, ZhengJun
last_name: Chen
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Hong-Wei
full_name: Xue, Hong-Wei
last_name: Xue
- first_name: Kan
full_name: Liao, Kan
last_name: Liao
citation:
ama: Wei Z, Tan S, Liu T, et al. Plasmodesmata-like intercellular connections by
plant remorin in animal cells. bioRxiv. 2020. doi:10.1101/791137
apa: Wei, Z., Tan, S., Liu, T., Wu, Y., Lei, J.-G., Chen, Z., … Liao, K. (2020).
Plasmodesmata-like intercellular connections by plant remorin in animal cells.
bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/791137
chicago: Wei, Zhuang, Shutang Tan, Tao Liu, Yuan Wu, Ji-Gang Lei, ZhengJun Chen,
Jiří Friml, Hong-Wei Xue, and Kan Liao. “Plasmodesmata-like Intercellular Connections
by Plant Remorin in Animal Cells.” BioRxiv. Cold Spring Harbor Laboratory,
2020. https://doi.org/10.1101/791137.
ieee: Z. Wei et al., “Plasmodesmata-like intercellular connections by plant
remorin in animal cells,” bioRxiv. Cold Spring Harbor Laboratory, 2020.
ista: Wei Z, Tan S, Liu T, Wu Y, Lei J-G, Chen Z, Friml J, Xue H-W, Liao K. 2020.
Plasmodesmata-like intercellular connections by plant remorin in animal cells.
bioRxiv, 10.1101/791137.
mla: Wei, Zhuang, et al. “Plasmodesmata-like Intercellular Connections by Plant
Remorin in Animal Cells.” BioRxiv, Cold Spring Harbor Laboratory, 2020,
doi:10.1101/791137.
short: Z. Wei, S. Tan, T. Liu, Y. Wu, J.-G. Lei, Z. Chen, J. Friml, H.-W. Xue, K.
Liao, BioRxiv (2020).
date_created: 2020-03-21T16:34:42Z
date_published: 2020-02-19T00:00:00Z
date_updated: 2021-01-12T08:14:26Z
day: '19'
department:
- _id: JiFr
doi: 10.1101/791137
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/791137
month: '02'
oa: 1
oa_version: Preprint
page: '22'
publication: bioRxiv
publication_status: published
publisher: Cold Spring Harbor Laboratory
status: public
title: Plasmodesmata-like intercellular connections by plant remorin in animal cells
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '7603'
abstract:
- lang: eng
text: Plants are exposed to a variety of abiotic and biotic stresses that may result
in DNA damage. Endogenous processes - such as DNA replication, DNA recombination,
respiration, or photosynthesis - are also a threat to DNA integrity. It is therefore
essential to understand the strategies plants have developed for DNA damage detection,
signaling, and repair. Alternative splicing (AS) is a key post-transcriptional
process with a role in regulation of gene expression. Recent studies demonstrate
that the majority of intron-containing genes in plants are alternatively spliced,
highlighting the importance of AS in plant development and stress response. Not
only does AS ensure a versatile proteome and influence the abundance and availability
of proteins greatly, it has also emerged as an important player in the DNA damage
response (DDR) in animals. Despite extensive studies of DDR carried out in plants,
its regulation at the level of AS has not been comprehensively addressed. Here,
we provide some insights into the interplay between AS and DDR in plants.
article_number: '91'
article_processing_charge: No
article_type: original
author:
- first_name: Barbara Anna
full_name: Nimeth, Barbara Anna
last_name: Nimeth
- first_name: Stefan
full_name: Riegler, Stefan
id: FF6018E0-D806-11E9-8E43-0B14E6697425
last_name: Riegler
orcid: 0000-0003-3413-1343
- first_name: Maria
full_name: Kalyna, Maria
last_name: Kalyna
citation:
ama: Nimeth BA, Riegler S, Kalyna M. Alternative splicing and DNA damage response
in plants. Frontiers in Plant Science. 2020;11. doi:10.3389/fpls.2020.00091
apa: Nimeth, B. A., Riegler, S., & Kalyna, M. (2020). Alternative splicing and
DNA damage response in plants. Frontiers in Plant Science. Frontiers. https://doi.org/10.3389/fpls.2020.00091
chicago: Nimeth, Barbara Anna, Stefan Riegler, and Maria Kalyna. “Alternative Splicing
and DNA Damage Response in Plants.” Frontiers in Plant Science. Frontiers,
2020. https://doi.org/10.3389/fpls.2020.00091.
ieee: B. A. Nimeth, S. Riegler, and M. Kalyna, “Alternative splicing and DNA damage
response in plants,” Frontiers in Plant Science, vol. 11. Frontiers, 2020.
ista: Nimeth BA, Riegler S, Kalyna M. 2020. Alternative splicing and DNA damage
response in plants. Frontiers in Plant Science. 11, 91.
mla: Nimeth, Barbara Anna, et al. “Alternative Splicing and DNA Damage Response
in Plants.” Frontiers in Plant Science, vol. 11, 91, Frontiers, 2020, doi:10.3389/fpls.2020.00091.
short: B.A. Nimeth, S. Riegler, M. Kalyna, Frontiers in Plant Science 11 (2020).
date_created: 2020-03-22T23:00:46Z
date_published: 2020-02-19T00:00:00Z
date_updated: 2023-08-18T07:05:18Z
day: '19'
ddc:
- '580'
department:
- _id: FyKo
doi: 10.3389/fpls.2020.00091
external_id:
isi:
- '000518903600001'
file:
- access_level: open_access
checksum: 57c37209f7b6712ced86c0f11b2be74e
content_type: application/pdf
creator: dernst
date_created: 2020-03-23T09:03:40Z
date_updated: 2020-07-14T12:48:01Z
file_id: '7607'
file_name: 2020_FrontiersPlants_Nimeth.pdf
file_size: 507414
relation: main_file
file_date_updated: 2020-07-14T12:48:01Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: Frontiers in Plant Science
publication_identifier:
eissn:
- 1664462X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Alternative splicing and DNA damage response in plants
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2020'
...
---
_id: '7605'
abstract:
- lang: eng
text: 'Union-Find (or Disjoint-Set Union) is one of the fundamental problems in
computer science; it has been well-studied from both theoretical and practical
perspectives in the sequential case. Recently, there has been mounting interest
in analyzing this problem in the concurrent scenario, and several asymptotically-efficient
algorithms have been proposed. Yet, to date, there is very little known about
the practical performance of concurrent Union-Find. This work addresses this gap.
We evaluate and analyze the performance of several concurrent Union-Find algorithms
and optimization strategies across a wide range of platforms (Intel, AMD, and
ARM) and workloads (social, random, and road networks, as well as integrations
into more complex algorithms). We first observe that, due to the limited computational
cost, the number of induced cache misses is the critical determining factor for
the performance of existing algorithms. We introduce new techniques to reduce
this cost by storing node priorities implicitly and by using plain reads and writes
in a way that does not affect the correctness of the algorithms. Finally, we show
that Union-Find implementations are an interesting application for Transactional
Memory (TM): one of the fastest algorithm variants we discovered is a sequential
one that uses coarse-grained locking with the lock elision optimization to reduce
synchronization cost and increase scalability. '
alternative_title:
- LIPIcs
article_processing_charge: No
arxiv: 1
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Alexander
full_name: Fedorov, Alexander
last_name: Fedorov
- first_name: Nikita
full_name: Koval, Nikita
id: 2F4DB10C-F248-11E8-B48F-1D18A9856A87
last_name: Koval
citation:
ama: 'Alistarh D-A, Fedorov A, Koval N. In search of the fastest concurrent union-find
algorithm. In: 23rd International Conference on Principles of Distributed Systems.
Vol 153. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020:15:1-15:16. doi:10.4230/LIPIcs.OPODIS.2019.15'
apa: 'Alistarh, D.-A., Fedorov, A., & Koval, N. (2020). In search of the fastest
concurrent union-find algorithm. In 23rd International Conference on Principles
of Distributed Systems (Vol. 153, p. 15:1-15:16). Neuchatal, Switzerland:
Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.OPODIS.2019.15'
chicago: Alistarh, Dan-Adrian, Alexander Fedorov, and Nikita Koval. “In Search of
the Fastest Concurrent Union-Find Algorithm.” In 23rd International Conference
on Principles of Distributed Systems, 153:15:1-15:16. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2020. https://doi.org/10.4230/LIPIcs.OPODIS.2019.15.
ieee: D.-A. Alistarh, A. Fedorov, and N. Koval, “In search of the fastest concurrent
union-find algorithm,” in 23rd International Conference on Principles of Distributed
Systems, Neuchatal, Switzerland, 2020, vol. 153, p. 15:1-15:16.
ista: 'Alistarh D-A, Fedorov A, Koval N. 2020. In search of the fastest concurrent
union-find algorithm. 23rd International Conference on Principles of Distributed
Systems. OPODIS: International Conference on Principles of Distributed Systems,
LIPIcs, vol. 153, 15:1-15:16.'
mla: Alistarh, Dan-Adrian, et al. “In Search of the Fastest Concurrent Union-Find
Algorithm.” 23rd International Conference on Principles of Distributed Systems,
vol. 153, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, p. 15:1-15:16,
doi:10.4230/LIPIcs.OPODIS.2019.15.
short: D.-A. Alistarh, A. Fedorov, N. Koval, in:, 23rd International Conference
on Principles of Distributed Systems, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2020, p. 15:1-15:16.
conference:
end_date: 2019-12-19
location: Neuchatal, Switzerland
name: 'OPODIS: International Conference on Principles of Distributed Systems'
start_date: 2019-12-17
date_created: 2020-03-22T23:00:46Z
date_published: 2020-02-01T00:00:00Z
date_updated: 2023-02-23T13:12:12Z
day: '01'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.4230/LIPIcs.OPODIS.2019.15
external_id:
arxiv:
- '1911.06347'
file:
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creator: dernst
date_created: 2020-03-23T09:22:48Z
date_updated: 2020-07-14T12:48:01Z
file_id: '7609'
file_name: 2019_LIPIcs_Alistarh.pdf
file_size: 13074131
relation: main_file
file_date_updated: 2020-07-14T12:48:01Z
has_accepted_license: '1'
intvolume: ' 153'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '02'
oa: 1
oa_version: Published Version
page: 15:1-15:16
publication: 23rd International Conference on Principles of Distributed Systems
publication_identifier:
isbn:
- '9783959771337'
issn:
- '18688969'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: In search of the fastest concurrent union-find algorithm
tmp:
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legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 153
year: '2020'
...