---
_id: '9645'
abstract:
- lang: eng
text: "We consider the fundamental problem of reachability analysis over imperative
programs with real variables. Previous works that tackle reachability are either
unable to handle programs consisting of general loops (e.g. symbolic execution),
or lack completeness guarantees (e.g. abstract interpretation), or are not automated
(e.g. incorrectness logic). In contrast, we propose a novel approach for reachability
analysis that can handle general and complex loops, is complete, and can be entirely
automated for a wide family of programs. Through the notion of Inductive Reachability
Witnesses (IRWs), our approach extends ideas from both invariant generation and
termination to reachability analysis.\r\n\r\nWe first show that our IRW-based
approach is sound and complete for reachability analysis of imperative programs.
Then, we focus on linear and polynomial programs and develop automated methods
for synthesizing linear and polynomial IRWs. In the linear case, we follow the
well-known approaches using Farkas' Lemma. Our main contribution is in the polynomial
case, where we present a push-button semi-complete algorithm. We achieve this
using a novel combination of classical theorems in real algebraic geometry, such
as Putinar's Positivstellensatz and Hilbert's Strong Nullstellensatz. Finally,
our experimental results show we can prove complex reachability objectives over
various benchmarks that were beyond the reach of previous methods."
acknowledgement: This research was partially supported by the ERC CoG 863818 (ForM-SMArt),
the National Natural Science Foundation of China (NSFC) Grant No. 61802254, the
Huawei Innovation Research Program, the Facebook PhD Fellowship Program, and DOC
Fellowship No. 24956 of the Austrian Academy of Sciences (ÖAW).
article_processing_charge: No
author:
- first_name: Ali
full_name: Asadi, Ali
last_name: Asadi
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Hongfei
full_name: Fu, Hongfei
id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87
last_name: Fu
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Mohammad
full_name: Mahdavi, Mohammad
last_name: Mahdavi
citation:
ama: 'Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. Polynomial reachability
witnesses via Stellensätze. In: Proceedings of the 42nd ACM SIGPLAN International
Conference on Programming Language Design and Implementation. Association
for Computing Machinery; 2021:772-787. doi:10.1145/3453483.3454076'
apa: 'Asadi, A., Chatterjee, K., Fu, H., Goharshady, A. K., & Mahdavi, M. (2021).
Polynomial reachability witnesses via Stellensätze. In Proceedings of the 42nd
ACM SIGPLAN International Conference on Programming Language Design and Implementation
(pp. 772–787). Online: Association for Computing Machinery. https://doi.org/10.1145/3453483.3454076'
chicago: Asadi, Ali, Krishnendu Chatterjee, Hongfei Fu, Amir Kafshdar Goharshady,
and Mohammad Mahdavi. “Polynomial Reachability Witnesses via Stellensätze.” In
Proceedings of the 42nd ACM SIGPLAN International Conference on Programming
Language Design and Implementation, 772–87. Association for Computing Machinery,
2021. https://doi.org/10.1145/3453483.3454076.
ieee: A. Asadi, K. Chatterjee, H. Fu, A. K. Goharshady, and M. Mahdavi, “Polynomial
reachability witnesses via Stellensätze,” in Proceedings of the 42nd ACM SIGPLAN
International Conference on Programming Language Design and Implementation,
Online, 2021, pp. 772–787.
ista: 'Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. 2021. Polynomial reachability
witnesses via Stellensätze. Proceedings of the 42nd ACM SIGPLAN International
Conference on Programming Language Design and Implementation. PLDI: Programming
Language Design and Implementation, 772–787.'
mla: Asadi, Ali, et al. “Polynomial Reachability Witnesses via Stellensätze.” Proceedings
of the 42nd ACM SIGPLAN International Conference on Programming Language Design
and Implementation, Association for Computing Machinery, 2021, pp. 772–87,
doi:10.1145/3453483.3454076.
short: A. Asadi, K. Chatterjee, H. Fu, A.K. Goharshady, M. Mahdavi, in:, Proceedings
of the 42nd ACM SIGPLAN International Conference on Programming Language Design
and Implementation, Association for Computing Machinery, 2021, pp. 772–787.
conference:
end_date: 2021-06-26
location: Online
name: ' PLDI: Programming Language Design and Implementation'
start_date: 2021-06-20
date_created: 2021-07-11T22:01:17Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2025-07-14T09:10:06Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/3453483.3454076
ec_funded: 1
external_id:
isi:
- '000723661700050'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.archives-ouvertes.fr/hal-03183862/
month: '06'
oa: 1
oa_version: Submitted Version
page: 772-787
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 267066CE-B435-11E9-9278-68D0E5697425
name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies
publication: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming
Language Design and Implementation
publication_identifier:
isbn:
- '9781450383912'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Polynomial reachability witnesses via Stellensätze
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '9646'
abstract:
- lang: eng
text: We consider the fundamental problem of deriving quantitative bounds on the
probability that a given assertion is violated in a probabilistic program. We
provide automated algorithms that obtain both lower and upper bounds on the assertion
violation probability. The main novelty of our approach is that we prove new and
dedicated fixed-point theorems which serve as the theoretical basis of our algorithms
and enable us to reason about assertion violation bounds in terms of pre and post
fixed-point functions. To synthesize such fixed-points, we devise algorithms that
utilize a wide range of mathematical tools, including repulsing ranking supermartingales,
Hoeffding's lemma, Minkowski decompositions, Jensen's inequality, and convex optimization.
On the theoretical side, we provide (i) the first automated algorithm for lower-bounds
on assertion violation probabilities, (ii) the first complete algorithm for upper-bounds
of exponential form in affine programs, and (iii) provably and significantly tighter
upper-bounds than the previous approaches. On the practical side, we show our
algorithms can handle a wide variety of programs from the literature and synthesize
bounds that are remarkably tighter than previous results, in some cases by thousands
of orders of magnitude.
acknowledgement: 'We are very thankful to the anonymous reviewers for the helpful
and valuable comments. The work was partially supported by the National Natural
Science Foundation of China (NSFC) Grant No. 61802254, the Huawei Innovation Research
Program, the ERC CoG 863818 (ForM-SMArt), the Facebook PhD Fellowship Program and
DOC Fellowship #24956 of the Austrian Academy of Sciences (ÖAW).'
article_processing_charge: No
arxiv: 1
author:
- first_name: Jinyi
full_name: Wang, Jinyi
last_name: Wang
- first_name: Yican
full_name: Sun, Yican
last_name: Sun
- first_name: Hongfei
full_name: Fu, Hongfei
id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87
last_name: Fu
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
citation:
ama: 'Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. Quantitative analysis of
assertion violations in probabilistic programs. In: Proceedings of the 42nd
ACM SIGPLAN International Conference on Programming Language Design and Implementation.
Association for Computing Machinery; 2021:1171-1186. doi:10.1145/3453483.3454102'
apa: 'Wang, J., Sun, Y., Fu, H., Chatterjee, K., & Goharshady, A. K. (2021).
Quantitative analysis of assertion violations in probabilistic programs. In Proceedings
of the 42nd ACM SIGPLAN International Conference on Programming Language Design
and Implementation (pp. 1171–1186). Online: Association for Computing Machinery.
https://doi.org/10.1145/3453483.3454102'
chicago: Wang, Jinyi, Yican Sun, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar
Goharshady. “Quantitative Analysis of Assertion Violations in Probabilistic Programs.”
In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming
Language Design and Implementation, 1171–86. Association for Computing Machinery,
2021. https://doi.org/10.1145/3453483.3454102.
ieee: J. Wang, Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Quantitative
analysis of assertion violations in probabilistic programs,” in Proceedings
of the 42nd ACM SIGPLAN International Conference on Programming Language Design
and Implementation, Online, 2021, pp. 1171–1186.
ista: 'Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. 2021. Quantitative analysis
of assertion violations in probabilistic programs. Proceedings of the 42nd ACM
SIGPLAN International Conference on Programming Language Design and Implementation.
PLDI: Programming Language Design and Implementation, 1171–1186.'
mla: Wang, Jinyi, et al. “Quantitative Analysis of Assertion Violations in Probabilistic
Programs.” Proceedings of the 42nd ACM SIGPLAN International Conference on
Programming Language Design and Implementation, Association for Computing
Machinery, 2021, pp. 1171–86, doi:10.1145/3453483.3454102.
short: J. Wang, Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Proceedings
of the 42nd ACM SIGPLAN International Conference on Programming Language Design
and Implementation, Association for Computing Machinery, 2021, pp. 1171–1186.
conference:
end_date: 2021-06-26
location: Online
name: 'PLDI: Programming Language Design and Implementation'
start_date: 2021-06-20
date_created: 2021-07-11T22:01:18Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2025-07-14T09:10:06Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/3453483.3454102
ec_funded: 1
external_id:
arxiv:
- '2011.14617'
isi:
- '000723661700076'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2011.14617
month: '06'
oa: 1
oa_version: Preprint
page: 1171-1186
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 267066CE-B435-11E9-9278-68D0E5697425
name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies
publication: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming
Language Design and Implementation
publication_identifier:
isbn:
- '9781450383912'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantitative analysis of assertion violations in probabilistic programs
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '9647'
abstract:
- lang: eng
text: 'Gene expression is regulated by the set of transcription factors (TFs) that
bind to the promoter. The ensuing regulating function is often represented as
a combinational logic circuit, where output (gene expression) is determined by
current input values (promoter bound TFs) only. However, the simultaneous arrival
of TFs is a strong assumption, since transcription and translation of genes introduce
intrinsic time delays and there is no global synchronisation among the arrival
times of different molecular species at their targets. We present an experimentally
implementable genetic circuit with two inputs and one output, which in the presence
of small delays in input arrival, exhibits qualitatively distinct population-level
phenotypes, over timescales that are longer than typical cell doubling times.
From a dynamical systems point of view, these phenotypes represent long-lived
transients: although they converge to the same value eventually, they do so after
a very long time span. The key feature of this toy model genetic circuit is that,
despite having only two inputs and one output, it is regulated by twenty-three
distinct DNA-TF configurations, two of which are more stable than others (DNA
looped states), one promoting and another blocking the expression of the output
gene. Small delays in input arrival time result in a majority of cells in the
population quickly reaching the stable state associated with the first input,
while exiting of this stable state occurs at a slow timescale. In order to mechanistically
model the behaviour of this genetic circuit, we used a rule-based modelling language,
and implemented a grid-search to find parameter combinations giving rise to long-lived
transients. Our analysis shows that in the absence of feedback, there exist path-dependent
gene regulatory mechanisms based on the long timescale of transients. The behaviour
of this toy model circuit suggests that gene regulatory networks can exploit event
timing to create phenotypes, and it opens the possibility that they could use
event timing to memorise events, without regulatory feedback. The model reveals
the importance of (i) mechanistically modelling the transitions between the different
DNA-TF states, and (ii) employing transient analysis thereof.'
acknowledgement: 'Tatjana Petrov’s research was supported in part by SNSF Advanced
Postdoctoral Mobility Fellowship grant number P300P2 161067, the Ministry of Science,
Research and the Arts of the state of Baden-Wurttemberg, and the DFG Centre of Excellence
2117 ‘Centre for the Advanced Study of Collective Behaviour’ (ID: 422037984). Claudia
Igler is the recipient of a DOC Fellowship of the Austrian Academy of Sciences.
Thomas A. Henzinger’s research was supported in part by the Austrian Science Fund
(FWF) under grant Z211-N23 (Wittgenstein Award).'
article_processing_charge: No
article_type: original
author:
- first_name: Tatjana
full_name: Petrov, Tatjana
last_name: Petrov
- first_name: Claudia
full_name: Igler, Claudia
id: 46613666-F248-11E8-B48F-1D18A9856A87
last_name: Igler
- first_name: Ali
full_name: Sezgin, Ali
id: 4C7638DA-F248-11E8-B48F-1D18A9856A87
last_name: Sezgin
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. Long lived transients in
gene regulation. Theoretical Computer Science. 2021;893:1-16. doi:10.1016/j.tcs.2021.05.023
apa: Petrov, T., Igler, C., Sezgin, A., Henzinger, T. A., & Guet, C. C. (2021).
Long lived transients in gene regulation. Theoretical Computer Science.
Elsevier. https://doi.org/10.1016/j.tcs.2021.05.023
chicago: Petrov, Tatjana, Claudia Igler, Ali Sezgin, Thomas A Henzinger, and Calin
C Guet. “Long Lived Transients in Gene Regulation.” Theoretical Computer Science.
Elsevier, 2021. https://doi.org/10.1016/j.tcs.2021.05.023.
ieee: T. Petrov, C. Igler, A. Sezgin, T. A. Henzinger, and C. C. Guet, “Long lived
transients in gene regulation,” Theoretical Computer Science, vol. 893.
Elsevier, pp. 1–16, 2021.
ista: Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. 2021. Long lived transients
in gene regulation. Theoretical Computer Science. 893, 1–16.
mla: Petrov, Tatjana, et al. “Long Lived Transients in Gene Regulation.” Theoretical
Computer Science, vol. 893, Elsevier, 2021, pp. 1–16, doi:10.1016/j.tcs.2021.05.023.
short: T. Petrov, C. Igler, A. Sezgin, T.A. Henzinger, C.C. Guet, Theoretical Computer
Science 893 (2021) 1–16.
date_created: 2021-07-11T22:01:18Z
date_published: 2021-06-04T00:00:00Z
date_updated: 2023-08-10T14:11:19Z
day: '04'
ddc:
- '004'
department:
- _id: ToHe
- _id: CaGu
doi: 10.1016/j.tcs.2021.05.023
external_id:
isi:
- '000710180500002'
file:
- access_level: open_access
checksum: d3aef34cfb13e53bba4cf44d01680793
content_type: application/pdf
creator: dernst
date_created: 2022-05-12T12:13:27Z
date_updated: 2022-05-12T12:13:27Z
file_id: '11364'
file_name: 2021_TheoreticalComputerScience_Petrov.pdf
file_size: 2566504
relation: main_file
success: 1
file_date_updated: 2022-05-12T12:13:27Z
has_accepted_license: '1'
intvolume: ' 893'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 1-16
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Theoretical Computer Science
publication_identifier:
issn:
- 0304-3975
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Long lived transients in gene regulation
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: 893
year: '2021'
...
---
_id: '9656'
abstract:
- lang: eng
text: Tropisms, growth responses to environmental stimuli such as light or gravity,
are spectacular examples of adaptive plant development. The plant hormone auxin
serves as a major coordinative signal. The PIN auxin exporters, through their
dynamic polar subcellular localizations, redirect auxin fluxes in response to
environmental stimuli and the resulting auxin gradients across organs underly
differential cell elongation and bending. In this review, we discuss recent advances
concerning regulations of PIN polarity during tropisms, focusing on PIN phosphorylation
and trafficking. We also cover how environmental cues regulate PIN actions during
tropisms, and a crucial role of auxin feedback on PIN polarity during bending
termination. Finally, the interactions between different tropisms are reviewed
to understand plant adaptive growth in the natural environment.
acknowledgement: We are grateful to Lukas Fiedler, Alexandra Mally (IST Austria) and
Dr. Bartel Vanholme (VIB, Ghent) for their critical comments on the manuscript.
We apologize to those researchers whose great work was not cited. This work is supported
by the European Research Council under the European Union’s Horizon 2020 research
and innovation Programme (ERC grant agreement number 742985), and the Austrian Science
Fund (FWF, grant number I 3630-B25) to JF. HH is supported by the China Scholarship
Council (CSC scholarship, 201506870018) and a starting grant from Jiangxi Agriculture
University (9232308314).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Huibin
full_name: Han, Huibin
id: 31435098-F248-11E8-B48F-1D18A9856A87
last_name: Han
- first_name: Maciek
full_name: Adamowski, Maciek
id: 45F536D2-F248-11E8-B48F-1D18A9856A87
last_name: Adamowski
orcid: 0000-0001-6463-5257
- first_name: Linlin
full_name: Qi, Linlin
id: 44B04502-A9ED-11E9-B6FC-583AE6697425
last_name: Qi
orcid: 0000-0001-5187-8401
- first_name: SS
full_name: Alotaibi, SS
last_name: Alotaibi
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Han H, Adamowski M, Qi L, Alotaibi S, Friml J. PIN-mediated polar auxin transport
regulations in plant tropic responses. New Phytologist. 2021;232(2):510-522.
doi:10.1111/nph.17617
apa: Han, H., Adamowski, M., Qi, L., Alotaibi, S., & Friml, J. (2021). PIN-mediated
polar auxin transport regulations in plant tropic responses. New Phytologist.
Wiley. https://doi.org/10.1111/nph.17617
chicago: Han, Huibin, Maciek Adamowski, Linlin Qi, SS Alotaibi, and Jiří Friml.
“PIN-Mediated Polar Auxin Transport Regulations in Plant Tropic Responses.” New
Phytologist. Wiley, 2021. https://doi.org/10.1111/nph.17617.
ieee: H. Han, M. Adamowski, L. Qi, S. Alotaibi, and J. Friml, “PIN-mediated polar
auxin transport regulations in plant tropic responses,” New Phytologist,
vol. 232, no. 2. Wiley, pp. 510–522, 2021.
ista: Han H, Adamowski M, Qi L, Alotaibi S, Friml J. 2021. PIN-mediated polar auxin
transport regulations in plant tropic responses. New Phytologist. 232(2), 510–522.
mla: Han, Huibin, et al. “PIN-Mediated Polar Auxin Transport Regulations in Plant
Tropic Responses.” New Phytologist, vol. 232, no. 2, Wiley, 2021, pp. 510–22,
doi:10.1111/nph.17617.
short: H. Han, M. Adamowski, L. Qi, S. Alotaibi, J. Friml, New Phytologist 232 (2021)
510–522.
date_created: 2021-07-14T15:29:14Z
date_published: 2021-10-01T00:00:00Z
date_updated: 2023-08-10T14:02:41Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1111/nph.17617
ec_funded: 1
external_id:
isi:
- '000680587100001'
pmid:
- '34254313'
file:
- access_level: open_access
checksum: 6422a6eb329b52d96279daaee0fcf189
content_type: application/pdf
creator: kschuh
date_created: 2021-10-07T13:42:47Z
date_updated: 2021-10-07T13:42:47Z
file_id: '10105'
file_name: 2021_NewPhytologist_Han.pdf
file_size: 1939800
relation: main_file
success: 1
file_date_updated: 2021-10-07T13:42:47Z
has_accepted_license: '1'
intvolume: ' 232'
isi: 1
issue: '2'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 510-522
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: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
publication: New Phytologist
publication_identifier:
eissn:
- 1469-8137
issn:
- 0028-646x
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: PIN-mediated polar auxin transport regulations in plant tropic responses
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: 232
year: '2021'
...
---
_id: '9657'
abstract:
- lang: eng
text: To overcome nitrogen deficiency, legume roots establish symbiotic interactions
with nitrogen-fixing rhizobia that is fostered in specialized organs (nodules).
Similar to other organs, nodule formation is determined by a local maximum of
the phytohormone auxin at the primordium site. However, how auxin regulates nodule
development remains poorly understood. Here, we found that in soybean, (Glycine
max), dynamic auxin transport driven by PIN-FORMED (PIN) transporter GmPIN1 is
involved in nodule primordium formation. GmPIN1 was specifically expressed in
nodule primordium cells and GmPIN1 was polarly localized in these cells. Two nodulation
regulators, (iso)flavonoids trigger expanded distribution of GmPIN1b to root cortical
cells, and cytokinin rearranges GmPIN1b polarity. Gmpin1abc triple mutants generated
with CRISPR-Cas9 showed impaired establishment of auxin maxima in nodule meristems
and aberrant divisions in the nodule primordium cells. Moreover, overexpression
of GmPIN1 suppressed nodule primordium initiation. GmPIN9d, an ortholog of Arabidopsis
thaliana PIN2, acts together with GmPIN1 later in nodule development to acropetally
transport auxin in vascular bundles, fine-tuning the auxin supply for nodule enlargement.
Our findings reveal how PIN-dependent auxin transport modulates different aspects
of soybean nodule development and suggest that establishment of auxin gradient
is a prerequisite for the proper interaction between legumes and rhizobia.
article_processing_charge: No
article_type: original
author:
- first_name: Z
full_name: Gao, Z
last_name: Gao
- first_name: Z
full_name: Chen, Z
last_name: Chen
- first_name: Y
full_name: Cui, Y
last_name: Cui
- first_name: M
full_name: Ke, M
last_name: Ke
- first_name: H
full_name: Xu, H
last_name: Xu
- first_name: Q
full_name: Xu, Q
last_name: Xu
- first_name: J
full_name: Chen, J
last_name: Chen
- first_name: Y
full_name: Li, Y
last_name: Li
- first_name: L
full_name: Huang, L
last_name: Huang
- first_name: H
full_name: Zhao, H
last_name: Zhao
- first_name: D
full_name: Huang, D
last_name: Huang
- first_name: S
full_name: Mai, S
last_name: Mai
- first_name: T
full_name: Xu, T
last_name: Xu
- first_name: X
full_name: Liu, X
last_name: Liu
- first_name: S
full_name: Li, S
last_name: Li
- first_name: Y
full_name: Guan, Y
last_name: Guan
- first_name: W
full_name: Yang, W
last_name: Yang
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: J
full_name: Petrášek, J
last_name: Petrášek
- first_name: J
full_name: Zhang, J
last_name: Zhang
- first_name: X
full_name: Chen, X
last_name: Chen
citation:
ama: Gao Z, Chen Z, Cui Y, et al. GmPIN-dependent polar auxin transport is involved
in soybean nodule development. Plant Cell. 2021;33(9):2981–3003. doi:10.1093/plcell/koab183
apa: Gao, Z., Chen, Z., Cui, Y., Ke, M., Xu, H., Xu, Q., … Chen, X. (2021). GmPIN-dependent
polar auxin transport is involved in soybean nodule development. Plant Cell.
American Society of Plant Biologists. https://doi.org/10.1093/plcell/koab183
chicago: Gao, Z, Z Chen, Y Cui, M Ke, H Xu, Q Xu, J Chen, et al. “GmPIN-Dependent
Polar Auxin Transport Is Involved in Soybean Nodule Development.” Plant Cell.
American Society of Plant Biologists, 2021. https://doi.org/10.1093/plcell/koab183.
ieee: Z. Gao et al., “GmPIN-dependent polar auxin transport is involved in
soybean nodule development,” Plant Cell, vol. 33, no. 9. American Society
of Plant Biologists, pp. 2981–3003, 2021.
ista: Gao Z, Chen Z, Cui Y, Ke M, Xu H, Xu Q, Chen J, Li Y, Huang L, Zhao H, Huang
D, Mai S, Xu T, Liu X, Li S, Guan Y, Yang W, Friml J, Petrášek J, Zhang J, Chen
X. 2021. GmPIN-dependent polar auxin transport is involved in soybean nodule development.
Plant Cell. 33(9), 2981–3003.
mla: Gao, Z., et al. “GmPIN-Dependent Polar Auxin Transport Is Involved in Soybean
Nodule Development.” Plant Cell, vol. 33, no. 9, American Society of Plant
Biologists, 2021, pp. 2981–3003, doi:10.1093/plcell/koab183.
short: Z. Gao, Z. Chen, Y. Cui, M. Ke, H. Xu, Q. Xu, J. Chen, Y. Li, L. Huang, H.
Zhao, D. Huang, S. Mai, T. Xu, X. Liu, S. Li, Y. Guan, W. Yang, J. Friml, J. Petrášek,
J. Zhang, X. Chen, Plant Cell 33 (2021) 2981–3003.
date_created: 2021-07-14T15:32:43Z
date_published: 2021-07-07T00:00:00Z
date_updated: 2023-08-10T14:01:41Z
day: '07'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1093/plcell/koab183
external_id:
isi:
- '000702165300012'
pmid:
- '34240197'
file:
- access_level: open_access
checksum: 6715712ec306c321f0204c817b7f8ae7
content_type: application/pdf
creator: cziletti
date_created: 2021-07-19T12:13:34Z
date_updated: 2021-07-19T12:13:34Z
file_id: '9691'
file_name: 2021_PlantCell_Gao.pdf
file_size: 10566921
relation: main_file
success: 1
file_date_updated: 2021-07-19T12:13:34Z
has_accepted_license: '1'
intvolume: ' 33'
isi: 1
issue: '9'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 2981–3003
pmid: 1
publication: Plant Cell
publication_identifier:
eissn:
- 1532-298x
issn:
- 1040-4651
publication_status: published
publisher: American Society of Plant Biologists
quality_controlled: '1'
status: public
title: GmPIN-dependent polar auxin transport is involved in soybean nodule development
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: 33
year: '2021'
...
---
_id: '9669'
abstract:
- lang: eng
text: The set of known stable phases of water may not be complete, and some of the
phase boundaries between them are fuzzy. Starting from liquid water and a comprehensive
set of 50 ice structures, we compute the phase diagram at three hybrid density-functional-theory
levels of approximation, accounting for thermal and nuclear fluctuations as well
as proton disorder. Such calculations are only made tractable because we combine
machine-learning methods and advanced free-energy techniques. The computed phase
diagram is in qualitative agreement with experiment, particularly at pressures ≲ 8000
bar, and the discrepancy in chemical potential is comparable with the subtle uncertainties
introduced by proton disorder and the spread between the three hybrid functionals.
None of the hypothetical ice phases considered is thermodynamically stable in
our calculations, suggesting the completeness of the experimental water phase
diagram in the region considered. Our work demonstrates the feasibility of predicting
the phase diagram of a polymorphic system from first principles and provides a
thermodynamic way of testing the limits of quantum-mechanical calculations.
article_number: '588'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Aleks
full_name: Reinhardt, Aleks
last_name: Reinhardt
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: Reinhardt A, Cheng B. Quantum-mechanical exploration of the phase diagram of
water. Nature Communications. 2021;12(1). doi:10.1038/s41467-020-20821-w
apa: Reinhardt, A., & Cheng, B. (2021). Quantum-mechanical exploration of the
phase diagram of water. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-20821-w
chicago: Reinhardt, Aleks, and Bingqing Cheng. “Quantum-Mechanical Exploration of
the Phase Diagram of Water.” Nature Communications. Springer Nature, 2021.
https://doi.org/10.1038/s41467-020-20821-w.
ieee: A. Reinhardt and B. Cheng, “Quantum-mechanical exploration of the phase diagram
of water,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.
ista: Reinhardt A, Cheng B. 2021. Quantum-mechanical exploration of the phase diagram
of water. Nature Communications. 12(1), 588.
mla: Reinhardt, Aleks, and Bingqing Cheng. “Quantum-Mechanical Exploration of the
Phase Diagram of Water.” Nature Communications, vol. 12, no. 1, 588, Springer
Nature, 2021, doi:10.1038/s41467-020-20821-w.
short: A. Reinhardt, B. Cheng, Nature Communications 12 (2021).
date_created: 2021-07-15T13:48:13Z
date_published: 2021-01-26T00:00:00Z
date_updated: 2023-02-23T14:04:20Z
day: '26'
ddc:
- '530'
- '540'
doi: 10.1038/s41467-020-20821-w
extern: '1'
external_id:
arxiv:
- '2010.13729'
pmid:
- '33500405'
file:
- access_level: open_access
checksum: 8b5e1fbe2f1ab936047008043150e894
content_type: application/pdf
creator: asandaue
date_created: 2021-07-15T13:55:46Z
date_updated: 2021-07-15T13:55:46Z
file_id: '9670'
file_name: 2021_NatureCommunications_Reinhardt.pdf
file_size: 1180227
relation: main_file
success: 1
file_date_updated: 2021-07-15T13:55:46Z
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issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantum-mechanical exploration of the phase diagram of water
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: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 12
year: '2021'
...
---
_id: '9678'
abstract:
- lang: eng
text: We introduce a new graph problem, the token dropping game, and we show how
to solve it efficiently in a distributed setting. We use the token dropping game
as a tool to design an efficient distributed algorithm for stable orientations
and more generally for locally optimal semi-matchings. The prior work by Czygrinow
et al. (DISC 2012) finds a stable orientation in O(Δ^5) rounds in graphs of maximum
degree Δ, while we improve it to O(Δ^4) and also prove a lower bound of Ω(Δ).
For the more general problem of locally optimal semi-matchings, the prior upper
bound is O(S^5) and our new algorithm runs in O(C · S^4) rounds, which is an improvement
for C = o(S); here C and S are the maximum degrees of customers and servers, respectively.
acknowledgement: We thank Orr Fischer, Juho Hirvonen, and Tuomo Lempiäinen for valuable
discussions. This project has received funding from the European Union’s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement
No. 840605.
article_processing_charge: No
arxiv: 1
author:
- first_name: Sebastian
full_name: Brandt, Sebastian
last_name: Brandt
- first_name: Barbara
full_name: Keller, Barbara
last_name: Keller
- first_name: Joel
full_name: Rybicki, Joel
id: 334EFD2E-F248-11E8-B48F-1D18A9856A87
last_name: Rybicki
orcid: 0000-0002-6432-6646
- first_name: Jukka
full_name: Suomela, Jukka
last_name: Suomela
- first_name: Jara
full_name: Uitto, Jara
last_name: Uitto
citation:
ama: 'Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. Efficient load-balancing
through distributed token dropping. In: Annual ACM Symposium on Parallelism
in Algorithms and Architectures. ; 2021:129-139. doi:10.1145/3409964.3461785'
apa: Brandt, S., Keller, B., Rybicki, J., Suomela, J., & Uitto, J. (2021). Efficient
load-balancing through distributed token dropping. In Annual ACM Symposium
on Parallelism in Algorithms and Architectures (pp. 129–139). Virtual Event,
United States. https://doi.org/10.1145/3409964.3461785
chicago: Brandt, Sebastian, Barbara Keller, Joel Rybicki, Jukka Suomela, and Jara
Uitto. “Efficient Load-Balancing through Distributed Token Dropping.” In Annual
ACM Symposium on Parallelism in Algorithms and Architectures, 129–39, 2021.
https://doi.org/10.1145/3409964.3461785.
ieee: S. Brandt, B. Keller, J. Rybicki, J. Suomela, and J. Uitto, “Efficient load-balancing
through distributed token dropping,” in Annual ACM Symposium on Parallelism
in Algorithms and Architectures, Virtual Event, United States, 2021, pp.
129–139.
ista: 'Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. 2021. Efficient load-balancing
through distributed token dropping. Annual ACM Symposium on Parallelism in Algorithms
and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures
, 129–139.'
mla: Brandt, Sebastian, et al. “Efficient Load-Balancing through Distributed Token
Dropping.” Annual ACM Symposium on Parallelism in Algorithms and Architectures,
2021, pp. 129–39, doi:10.1145/3409964.3461785.
short: S. Brandt, B. Keller, J. Rybicki, J. Suomela, J. Uitto, in:, Annual ACM Symposium
on Parallelism in Algorithms and Architectures, 2021, pp. 129–139.
conference:
end_date: 2021-07-08
location: ' Virtual Event, United States'
name: 'SPAA: Symposium on Parallelism in Algorithms and Architectures '
start_date: 2021-07-06
date_created: 2021-07-18T22:01:22Z
date_published: 2021-07-06T00:00:00Z
date_updated: 2024-03-05T07:13:12Z
day: '06'
department:
- _id: DaAl
doi: 10.1145/3409964.3461785
ec_funded: 1
external_id:
arxiv:
- '2005.07761'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2005.07761
month: '07'
oa: 1
oa_version: Preprint
page: 129-139
project:
- _id: 26A5D39A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '840605'
name: Coordination in constrained and natural distributed systems
publication: Annual ACM Symposium on Parallelism in Algorithms and Architectures
publication_identifier:
isbn:
- '9781450380706'
publication_status: published
quality_controlled: '1'
related_material:
record:
- id: '15074'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Efficient load-balancing through distributed token dropping
type: conference
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
year: '2021'
...
---
_id: '9679'
abstract:
- lang: eng
text: The relative motion of three impenetrable particles on a ring, in our case
two identical fermions and one impurity, is isomorphic to a triangular quantum
billiard. Depending on the ratio κ of the impurity and fermion masses, the billiards
can be integrable or non-integrable (also referred to in the main text as chaotic).
To set the stage, we first investigate the energy level distributions of the billiards
as a function of 1/κ ∈ [0, 1] and find no evidence of integrable cases beyond
the limiting values 1/κ = 1 and 1/κ = 0. Then, we use machine learning tools to
analyze properties of probability distributions of individual quantum states.
We find that convolutional neural networks can correctly classify integrable and
non-integrable states. The decisive features of the wave functions are the normalization
and a large number of zero elements, corresponding to the existence of a nodal
line. The network achieves typical accuracies of 97%, suggesting that machine
learning tools can be used to analyze and classify the morphology of probability
densities obtained in theory or experiment.
acknowledgement: We thank Aidan Tracy for his input during the initial stages of this
project. We thank Nathan Harshman, Achim Richter, Wojciech Rzadkowski, and Dane
Hudson Smith for helpful discussions and comments on the manuscript. This work has
been supported by European Union's Horizon 2020 research and innovation program
under the Marie Skłodowska-Curie Grant Agreement No. 754411 (AGV); by the German
Aeronautics and Space Administration (DLR) through Grant No. 50 WM 1957 (OVM); by
the Deutsche Forschungsgemeinschaft through Project VO 2437/1-1 (Project No. 413495248)
(AGV and HWH); by the Deutsche Forschungsgemeinschaft through Collaborative Research
Center SFB 1245 (Project No. 279384907) and by the Bundesministerium für Bildung
und Forschung under Contract 05P18RDFN1 (HWH). HWH also thanks the ECT* for hospitality
during the workshop 'Universal physics in Many-Body Quantum Systems—From Atoms to
Quarks'. This infrastructure is part of a project that has received funding from
the European Union's Horizon 2020 research and innovation program under Grant Agreement
No. 824093. We acknowledge support by the Deutsche Forschungsgemeinschaft and the
Open Access Publishing Fund of Technische Universität Darmstadt.
article_number: '065009'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: David
full_name: Huber, David
last_name: Huber
- first_name: Oleksandr V.
full_name: Marchukov, Oleksandr V.
last_name: Marchukov
- first_name: Hans Werner
full_name: Hammer, Hans Werner
last_name: Hammer
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Huber D, Marchukov OV, Hammer HW, Volosniev A. Morphology of three-body quantum
states from machine learning. New Journal of Physics. 2021;23(6). doi:10.1088/1367-2630/ac0576
apa: Huber, D., Marchukov, O. V., Hammer, H. W., & Volosniev, A. (2021). Morphology
of three-body quantum states from machine learning. New Journal of Physics.
IOP Publishing. https://doi.org/10.1088/1367-2630/ac0576
chicago: Huber, David, Oleksandr V. Marchukov, Hans Werner Hammer, and Artem Volosniev.
“Morphology of Three-Body Quantum States from Machine Learning.” New Journal
of Physics. IOP Publishing, 2021. https://doi.org/10.1088/1367-2630/ac0576.
ieee: D. Huber, O. V. Marchukov, H. W. Hammer, and A. Volosniev, “Morphology of
three-body quantum states from machine learning,” New Journal of Physics,
vol. 23, no. 6. IOP Publishing, 2021.
ista: Huber D, Marchukov OV, Hammer HW, Volosniev A. 2021. Morphology of three-body
quantum states from machine learning. New Journal of Physics. 23(6), 065009.
mla: Huber, David, et al. “Morphology of Three-Body Quantum States from Machine
Learning.” New Journal of Physics, vol. 23, no. 6, 065009, IOP Publishing,
2021, doi:10.1088/1367-2630/ac0576.
short: D. Huber, O.V. Marchukov, H.W. Hammer, A. Volosniev, New Journal of Physics
23 (2021).
date_created: 2021-07-18T22:01:22Z
date_published: 2021-06-23T00:00:00Z
date_updated: 2023-08-10T13:58:09Z
day: '23'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1088/1367-2630/ac0576
ec_funded: 1
external_id:
arxiv:
- '2102.04961'
isi:
- '000664736300001'
file:
- access_level: open_access
checksum: e39164ce7ea228d287cf8924e1a0f9fe
content_type: application/pdf
creator: cziletti
date_created: 2021-07-19T11:47:16Z
date_updated: 2021-07-19T11:47:16Z
file_id: '9690'
file_name: 2021_NewJPhys_Huber.pdf
file_size: 3868445
relation: main_file
success: 1
file_date_updated: 2021-07-19T11:47:16Z
has_accepted_license: '1'
intvolume: ' 23'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: New Journal of Physics
publication_identifier:
eissn:
- '13672630'
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Morphology of three-body quantum states from machine learning
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: 23
year: '2021'
...
---
_id: '9695'
abstract:
- lang: eng
text: Real-world data typically contain a large number of features that are often
heterogeneous in nature, relevance, and also units of measure. When assessing
the similarity between data points, one can build various distance measures using
subsets of these features. Using the fewest features but still retaining sufficient
information about the system is crucial in many statistical learning approaches,
particularly when data are sparse. We introduce a statistical test that can assess
the relative information retained when using two different distance measures,
and determine if they are equivalent, independent, or if one is more informative
than the other. This in turn allows finding the most informative distance measure
out of a pool of candidates. The approach is applied to find the most relevant
policy variables for controlling the Covid-19 epidemic and to find compact yet
informative representations of atomic structures, but its potential applications
are wide ranging in many branches of science.
article_number: '2104.15079'
article_processing_charge: No
arxiv: 1
author:
- first_name: Aldo
full_name: Glielmo, Aldo
last_name: Glielmo
- first_name: Claudio
full_name: Zeni, Claudio
last_name: Zeni
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Gabor
full_name: Csanyi, Gabor
last_name: Csanyi
- first_name: Alessandro
full_name: Laio, Alessandro
last_name: Laio
citation:
ama: Glielmo A, Zeni C, Cheng B, Csanyi G, Laio A. Ranking the information content
of distance measures. arXiv.
apa: Glielmo, A., Zeni, C., Cheng, B., Csanyi, G., & Laio, A. (n.d.). Ranking
the information content of distance measures. arXiv.
chicago: Glielmo, Aldo, Claudio Zeni, Bingqing Cheng, Gabor Csanyi, and Alessandro
Laio. “Ranking the Information Content of Distance Measures.” ArXiv, n.d.
ieee: A. Glielmo, C. Zeni, B. Cheng, G. Csanyi, and A. Laio, “Ranking the information
content of distance measures,” arXiv. .
ista: Glielmo A, Zeni C, Cheng B, Csanyi G, Laio A. Ranking the information content
of distance measures. arXiv, 2104.15079.
mla: Glielmo, Aldo, et al. “Ranking the Information Content of Distance Measures.”
ArXiv, 2104.15079.
short: A. Glielmo, C. Zeni, B. Cheng, G. Csanyi, A. Laio, ArXiv (n.d.).
date_created: 2021-07-20T06:31:53Z
date_published: 2021-04-30T00:00:00Z
date_updated: 2023-02-23T14:05:13Z
day: '30'
extern: '1'
external_id:
arxiv:
- '2104.15079'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2104.15079
month: '04'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: Ranking the information content of distance measures
type: preprint
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2021'
...
---
_id: '9696'
abstract:
- lang: eng
text: Most water in the universe may be superionic, and its thermodynamic and transport
properties are crucial for planetary science but difficult to probe experimentally
or theoretically. We use machine learning and free energy methods to overcome
the limitations of quantum mechanical simulations, and characterize hydrogen diffusion,
superionic transitions, and phase behaviors of water at extreme conditions. We
predict that a close-packed superionic phase with mixed stacking is stable over
a wide temperature and pressure range, while a body-centered cubic phase is only
thermodynamically stable in a small window but is kinetically favored. Our phase
boundaries, which are consistent with the existing-albeit scarce-experimental
observations, help resolve the fractions of insulating ice, different superionic
phases, and liquid water inside of ice giants.
article_number: '2103.09035'
article_processing_charge: No
arxiv: 1
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Mandy
full_name: Bethkenhagen, Mandy
last_name: Bethkenhagen
- first_name: Chris J.
full_name: Pickard, Chris J.
last_name: Pickard
- first_name: Sebastien
full_name: Hamel, Sebastien
last_name: Hamel
citation:
ama: Cheng B, Bethkenhagen M, Pickard CJ, Hamel S. Predicting the phase behaviors
of superionic water at planetary conditions. arXiv.
apa: Cheng, B., Bethkenhagen, M., Pickard, C. J., & Hamel, S. (n.d.). Predicting
the phase behaviors of superionic water at planetary conditions. arXiv.
chicago: Cheng, Bingqing, Mandy Bethkenhagen, Chris J. Pickard, and Sebastien Hamel.
“Predicting the Phase Behaviors of Superionic Water at Planetary Conditions.”
ArXiv, n.d.
ieee: B. Cheng, M. Bethkenhagen, C. J. Pickard, and S. Hamel, “Predicting the phase
behaviors of superionic water at planetary conditions,” arXiv. .
ista: Cheng B, Bethkenhagen M, Pickard CJ, Hamel S. Predicting the phase behaviors
of superionic water at planetary conditions. arXiv, 2103.09035.
mla: Cheng, Bingqing, et al. “Predicting the Phase Behaviors of Superionic Water
at Planetary Conditions.” ArXiv, 2103.09035.
short: B. Cheng, M. Bethkenhagen, C.J. Pickard, S. Hamel, ArXiv (n.d.).
date_created: 2021-07-20T06:42:29Z
date_published: 2021-03-16T00:00:00Z
date_updated: 2023-02-23T14:05:16Z
day: '16'
extern: '1'
external_id:
arxiv:
- '2103.09035'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2103.09035
month: '03'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: Predicting the phase behaviors of superionic water at planetary conditions
type: preprint
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2021'
...
---
_id: '9698'
abstract:
- lang: eng
text: Machine learning models are poised to make a transformative impact on chemical
sciences by dramatically accelerating computational algorithms and amplifying
insights available from computational chemistry methods. However, achieving this
requires a confluence and coaction of expertise in computer science and physical
sciences. This review is written for new and experienced researchers working at
the intersection of both fields. We first provide concise tutorials of computational
chemistry and machine learning methods, showing how insights involving both can
be achieved. We then follow with a critical review of noteworthy applications
that demonstrate how computational chemistry and machine learning can be used
together to provide insightful (and useful) predictions in molecular and materials
modeling, retrosyntheses, catalysis, and drug design.
article_processing_charge: No
article_type: review
arxiv: 1
author:
- first_name: John A.
full_name: Keith, John A.
last_name: Keith
- first_name: Valentin
full_name: Valentin Vassilev-Galindo, Valentin
last_name: Valentin Vassilev-Galindo
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Stefan
full_name: Chmiela, Stefan
last_name: Chmiela
- first_name: Michael
full_name: Gastegger, Michael
last_name: Gastegger
- first_name: Klaus-Robert
full_name: Müller, Klaus-Robert
last_name: Müller
- first_name: Alexandre
full_name: Tkatchenko, Alexandre
last_name: Tkatchenko
citation:
ama: Keith JA, Valentin Vassilev-Galindo V, Cheng B, et al. Combining machine learning
and computational chemistry for predictive insights into chemical systems. Chemical
Reviews. 2021;121(16):9816-9872. doi:10.1021/acs.chemrev.1c00107
apa: Keith, J. A., Valentin Vassilev-Galindo, V., Cheng, B., Chmiela, S., Gastegger,
M., Müller, K.-R., & Tkatchenko, A. (2021). Combining machine learning and
computational chemistry for predictive insights into chemical systems. Chemical
Reviews. American Chemical Society. https://doi.org/10.1021/acs.chemrev.1c00107
chicago: Keith, John A., Valentin Valentin Vassilev-Galindo, Bingqing Cheng, Stefan
Chmiela, Michael Gastegger, Klaus-Robert Müller, and Alexandre Tkatchenko. “Combining
Machine Learning and Computational Chemistry for Predictive Insights into Chemical
Systems.” Chemical Reviews. American Chemical Society, 2021. https://doi.org/10.1021/acs.chemrev.1c00107.
ieee: J. A. Keith et al., “Combining machine learning and computational chemistry
for predictive insights into chemical systems,” Chemical Reviews, vol.
121, no. 16. American Chemical Society, pp. 9816–9872, 2021.
ista: Keith JA, Valentin Vassilev-Galindo V, Cheng B, Chmiela S, Gastegger M, Müller
K-R, Tkatchenko A. 2021. Combining machine learning and computational chemistry
for predictive insights into chemical systems. Chemical Reviews. 121(16), 9816–9872.
mla: Keith, John A., et al. “Combining Machine Learning and Computational Chemistry
for Predictive Insights into Chemical Systems.” Chemical Reviews, vol.
121, no. 16, American Chemical Society, 2021, pp. 9816–72, doi:10.1021/acs.chemrev.1c00107.
short: J.A. Keith, V. Valentin Vassilev-Galindo, B. Cheng, S. Chmiela, M. Gastegger,
K.-R. Müller, A. Tkatchenko, Chemical Reviews 121 (2021) 9816–9872.
date_created: 2021-07-20T11:18:37Z
date_published: 2021-07-07T00:00:00Z
date_updated: 2023-05-08T11:31:03Z
day: '07'
doi: 10.1021/acs.chemrev.1c00107
extern: '1'
external_id:
arxiv:
- '2102.06321'
intvolume: ' 121'
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1021/acs.chemrev.1c00107
month: '07'
oa: 1
oa_version: Published Version
page: 9816-9872
publication: Chemical Reviews
publication_identifier:
eissn:
- 1520-6890
issn:
- 0009-2665
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Combining machine learning and computational chemistry for predictive insights
into chemical systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 121
year: '2021'
...
---
_id: '9728'
abstract:
- lang: eng
text: "Most real-world flows are multiphase, yet we know little about them compared
to their single-phase counterparts. Multiphase flows are more difficult to investigate
as their dynamics occur in large parameter space and involve complex phenomena
such as preferential concentration, turbulence modulation, non-Newtonian rheology,
etc. Over the last few decades, experiments in particle-laden flows have taken
a back seat in favour of ever-improving computational resources. However, computers
are still not powerful enough to simulate a real-world fluid with millions of
finite-size particles. Experiments are essential not only because they offer a
reliable way to investigate real-world multiphase flows but also because they
serve to validate numerical studies and steer the research in a relevant direction.
In this work, we have experimentally investigated particle-laden flows in pipes,
and in particular, examined the effect of particles on the laminar-turbulent transition
and the drag scaling in turbulent flows.\r\n\r\nFor particle-laden pipe flows,
an earlier study [Matas et al., 2003] reported how the sub-critical (i.e., hysteretic)
transition that occurs via localised turbulent structures called puffs is affected
by the addition of particles. In this study, in addition to this known transition,
we found a super-critical transition to a globally fluctuating state with increasing
particle concentration. At the same time, the Newtonian-type transition via puffs
is delayed to larger Reynolds numbers. At an even higher concentration, only the
globally fluctuating state is found. The dynamics of particle-laden flows are
hence determined by two competing instabilities that give rise to three flow regimes:
Newtonian-type turbulence at low, a particle-induced globally fluctuating state
at high, and a coexistence state at intermediate concentrations.\r\n\r\nThe effect
of particles on turbulent drag is ambiguous, with studies reporting drag reduction,
no net change, and even drag increase. The ambiguity arises because, in addition
to particle concentration, particle shape, size, and density also affect the net
drag. Even similar particles might affect the flow dissimilarly in different Reynolds
number and concentration ranges. In the present study, we explored a wide range
of both Reynolds number and concentration, using spherical as well as cylindrical
particles. We found that the spherical particles do not reduce drag while the
cylindrical particles are drag-reducing within a specific Reynolds number interval.
The interval strongly depends on the particle concentration and the relative size
of the pipe and particles. Within this interval, the magnitude of drag reduction
reaches a maximum. These drag reduction maxima appear to fall onto a distinct
power-law curve irrespective of the pipe diameter and particle concentration,
and this curve can be considered as the maximum drag reduction asymptote for a
given fibre shape. Such an asymptote is well known for polymeric flows but had
not been identified for particle-laden flows prior to this work."
acknowledged_ssus:
- _id: M-Shop
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Nishchal
full_name: Agrawal, Nishchal
id: 469E6004-F248-11E8-B48F-1D18A9856A87
last_name: Agrawal
citation:
ama: Agrawal N. Transition to turbulence and drag reduction in particle-laden pipe
flows. 2021. doi:10.15479/at:ista:9728
apa: Agrawal, N. (2021). Transition to turbulence and drag reduction in particle-laden
pipe flows. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9728
chicago: Agrawal, Nishchal. “Transition to Turbulence and Drag Reduction in Particle-Laden
Pipe Flows.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9728.
ieee: N. Agrawal, “Transition to turbulence and drag reduction in particle-laden
pipe flows,” Institute of Science and Technology Austria, 2021.
ista: Agrawal N. 2021. Transition to turbulence and drag reduction in particle-laden
pipe flows. Institute of Science and Technology Austria.
mla: Agrawal, Nishchal. Transition to Turbulence and Drag Reduction in Particle-Laden
Pipe Flows. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9728.
short: N. Agrawal, Transition to Turbulence and Drag Reduction in Particle-Laden
Pipe Flows, Institute of Science and Technology Austria, 2021.
date_created: 2021-07-27T13:40:30Z
date_published: 2021-07-29T00:00:00Z
date_updated: 2024-02-28T13:14:39Z
day: '29'
ddc:
- '532'
degree_awarded: PhD
department:
- _id: GradSch
- _id: BjHo
doi: 10.15479/at:ista:9728
file:
- access_level: closed
checksum: 77436be3563a90435024307b1b5ee7e8
content_type: application/x-zip-compressed
creator: nagrawal
date_created: 2021-07-28T13:32:02Z
date_updated: 2022-07-29T22:30:05Z
embargo_to: open_access
file_id: '9744'
file_name: Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.zip
file_size: 22859658
relation: source_file
- access_level: open_access
checksum: 72a891d7daba85445c29b868c22575ed
content_type: application/pdf
creator: nagrawal
date_created: 2021-07-28T13:32:05Z
date_updated: 2022-07-29T22:30:05Z
embargo: 2022-07-28
file_id: '9745'
file_name: Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.pdf
file_size: 18658048
relation: main_file
file_date_updated: 2022-07-29T22:30:05Z
has_accepted_license: '1'
keyword:
- Drag Reduction
- Transition to Turbulence
- Multiphase Flows
- particle Laden Flows
- Complex Flows
- Experiments
- Fluid Dynamics
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '118'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6189'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
title: Transition to turbulence and drag reduction in particle-laden pipe flows
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '9733'
abstract:
- lang: eng
text: This thesis is the result of the research carried out by the author during
his PhD at IST Austria between 2017 and 2021. It mainly focuses on the Fröhlich
polaron model, specifically to its regime of strong coupling. This model, which
is rigorously introduced and discussed in the introduction, has been of great
interest in condensed matter physics and field theory for more than eighty years.
It is used to describe an electron interacting with the atoms of a solid material
(the strength of this interaction is modeled by the presence of a coupling constant
α in the Hamiltonian of the system). The particular regime examined here, which
is mathematically described by considering the limit α →∞, displays many interesting
features related to the emergence of classical behavior, which allows for a simplified
effective description of the system under analysis. The properties, the range
of validity and a quantitative analysis of the precision of such classical approximations
are the main object of the present work. We specify our investigation to the study
of the ground state energy of the system, its dynamics and its effective mass.
For each of these problems, we provide in the introduction an overview of the
previously known results and a detailed account of the original contributions
by the author.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Dario
full_name: Feliciangeli, Dario
id: 41A639AA-F248-11E8-B48F-1D18A9856A87
last_name: Feliciangeli
orcid: 0000-0003-0754-8530
citation:
ama: Feliciangeli D. The polaron at strong coupling. 2021. doi:10.15479/at:ista:9733
apa: Feliciangeli, D. (2021). The polaron at strong coupling. Institute of
Science and Technology Austria. https://doi.org/10.15479/at:ista:9733
chicago: Feliciangeli, Dario. “The Polaron at Strong Coupling.” Institute of Science
and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9733.
ieee: D. Feliciangeli, “The polaron at strong coupling,” Institute of Science and
Technology Austria, 2021.
ista: Feliciangeli D. 2021. The polaron at strong coupling. Institute of Science
and Technology Austria.
mla: Feliciangeli, Dario. The Polaron at Strong Coupling. Institute of Science
and Technology Austria, 2021, doi:10.15479/at:ista:9733.
short: D. Feliciangeli, The Polaron at Strong Coupling, Institute of Science and
Technology Austria, 2021.
date_created: 2021-07-27T15:48:30Z
date_published: 2021-08-20T00:00:00Z
date_updated: 2024-03-06T12:30:44Z
day: '20'
ddc:
- '515'
- '519'
- '539'
degree_awarded: PhD
department:
- _id: GradSch
- _id: RoSe
- _id: JaMa
doi: 10.15479/at:ista:9733
ec_funded: 1
file:
- access_level: open_access
checksum: e88bb8ca43948abe060eb2d2fa719881
content_type: application/pdf
creator: dfelicia
date_created: 2021-08-19T14:03:48Z
date_updated: 2021-09-06T09:28:56Z
file_id: '9944'
file_name: Thesis_FeliciangeliA.pdf
file_size: 1958710
relation: main_file
- access_level: closed
checksum: 72810843abee83705853505b3f8348aa
content_type: application/octet-stream
creator: dfelicia
date_created: 2021-08-19T14:06:35Z
date_updated: 2022-03-10T12:13:57Z
file_id: '9945'
file_name: thesis.7z
file_size: 3771669
relation: source_file
file_date_updated: 2022-03-10T12:13:57Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '180'
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9787'
relation: part_of_dissertation
status: public
- id: '9792'
relation: part_of_dissertation
status: public
- id: '9225'
relation: part_of_dissertation
status: public
- id: '9781'
relation: part_of_dissertation
status: public
- id: '9791'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
title: The polaron at strong coupling
tmp:
image: /image/cc_by_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
short: CC BY-ND (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '9746'
abstract:
- lang: eng
text: Evolutionary adaptation is a major source of antibiotic resistance in bacterial
pathogens. Evolution-informed therapy aims to constrain resistance by accounting
for bacterial evolvability. Sequential treatments with antibiotics that target
different bacterial processes were previously shown to limit adaptation through
genetic resistance trade-offs and negative hysteresis. Treatment with homogeneous
sets of antibiotics is generally viewed to be disadvantageous, as it should rapidly
lead to cross-resistance. We here challenged this assumption by determining the
evolutionary response of Pseudomonas aeruginosa to experimental sequential treatments
involving both heterogenous and homogeneous antibiotic sets. To our surprise,
we found that fast switching between only β-lactam antibiotics resulted in increased
extinction of bacterial populations. We demonstrate that extinction is favored
by low rates of spontaneous resistance emergence and low levels of spontaneous
cross-resistance among the antibiotics in sequence. The uncovered principles may
help to guide the optimized use of available antibiotics in highly potent, evolution-informed
treatment designs.
acknowledgement: We would like to thank Leif Tueffers and João Botelho for discussions
and suggestions as well as Kira Haas and Julia Bunk for technical support. We acknowledge
financial support from the German Science Foundation (grant SCHU 1415/12-2 to HS,
and funding under Germany’s Excellence Strategy EXC 2167–390884018 as well as the
Research Training Group 2501 TransEvo to HS and SN), the Max Planck Society (IMPRS
scholarship to AB; Max-Planck fellowship to HS), and the Leibniz Science Campus
Evolutionary Medicine of the Lung (EvoLUNG, to HS and SN). This work was further
supported by the German Science Foundation Research Infrastructure NGS_CC (project
407495230) as part of the Next Generation Sequencing Competence Network (project
423957469). NGS analyses were carried out at the Competence Centre for Genomic Analysis
Kiel (CCGA Kiel).
article_number: e68876
article_processing_charge: No
article_type: original
author:
- first_name: Aditi
full_name: Batra, Aditi
last_name: Batra
- first_name: Roderich
full_name: Römhild, Roderich
id: 68E56E44-62B0-11EA-B963-444F3DDC885E
last_name: Römhild
orcid: 0000-0001-9480-5261
- first_name: Emilie
full_name: Rousseau, Emilie
last_name: Rousseau
- first_name: Sören
full_name: Franzenburg, Sören
last_name: Franzenburg
- first_name: Stefan
full_name: Niemann, Stefan
last_name: Niemann
- first_name: Hinrich
full_name: Schulenburg, Hinrich
last_name: Schulenburg
citation:
ama: Batra A, Römhild R, Rousseau E, Franzenburg S, Niemann S, Schulenburg H. High
potency of sequential therapy with only beta-lactam antibiotics. eLife.
2021;10. doi:10.7554/elife.68876
apa: Batra, A., Römhild, R., Rousseau, E., Franzenburg, S., Niemann, S., & Schulenburg,
H. (2021). High potency of sequential therapy with only beta-lactam antibiotics.
ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.68876
chicago: Batra, Aditi, Roderich Römhild, Emilie Rousseau, Sören Franzenburg, Stefan
Niemann, and Hinrich Schulenburg. “High Potency of Sequential Therapy with Only
Beta-Lactam Antibiotics.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.68876.
ieee: A. Batra, R. Römhild, E. Rousseau, S. Franzenburg, S. Niemann, and H. Schulenburg,
“High potency of sequential therapy with only beta-lactam antibiotics,” eLife,
vol. 10. eLife Sciences Publications, 2021.
ista: Batra A, Römhild R, Rousseau E, Franzenburg S, Niemann S, Schulenburg H. 2021.
High potency of sequential therapy with only beta-lactam antibiotics. eLife. 10,
e68876.
mla: Batra, Aditi, et al. “High Potency of Sequential Therapy with Only Beta-Lactam
Antibiotics.” ELife, vol. 10, e68876, eLife Sciences Publications, 2021,
doi:10.7554/elife.68876.
short: A. Batra, R. Römhild, E. Rousseau, S. Franzenburg, S. Niemann, H. Schulenburg,
ELife 10 (2021).
date_created: 2021-07-28T13:36:57Z
date_published: 2021-07-28T00:00:00Z
date_updated: 2023-08-11T10:26:29Z
day: '28'
department:
- _id: CaGu
doi: 10.7554/elife.68876
external_id:
isi:
- '000692027800001'
pmid:
- '34318749'
intvolume: ' 10'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.7554/eLife.68876
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: High potency of sequential therapy with only beta-lactam antibiotics
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2021'
...
---
_id: '9756'
abstract:
- lang: eng
text: High-resolution visualization and quantification of membrane proteins contribute
to the understanding of their functions and the roles they play in physiological
and pathological conditions. Sodium dodecyl sulfate-digested freeze-fracture replica
labeling (SDS-FRL) is a powerful electron microscopy method to study quantitatively
the two-dimensional distribution of transmembrane proteins and their tightly associated
proteins. During treatment with SDS, intracellular organelles and proteins not
anchored to the replica are dissolved, whereas integral membrane proteins captured
and stabilized by carbon/platinum deposition remain on the replica. Their intra-
and extracellular domains become exposed on the surface of the replica, facilitating
the accessibility of antibodies and, therefore, providing higher labeling efficiency
than those obtained with other immunoelectron microscopy techniques. In this chapter,
we describe the protocols of SDS-FRL adapted for mammalian brain samples, and
optimization of the SDS treatment to increase the labeling efficiency for quantification
of Cav2.1, the alpha subunit of P/Q-type voltage-dependent calcium channels utilizing
deep learning algorithms.
acknowledgement: This work was supported by the European Union (European Research
Council Advanced grant no. 694539 and Human Brain Project Ref. 720270 to R. S.)
and the Austrian Academy of Sciences (DOC fellowship to D.K.).
alternative_title:
- Neuromethods
article_processing_charge: No
author:
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: David
full_name: Kleindienst, David
id: 42E121A4-F248-11E8-B48F-1D18A9856A87
last_name: Kleindienst
- first_name: Harumi
full_name: Harada, Harumi
id: 2E55CDF2-F248-11E8-B48F-1D18A9856A87
last_name: Harada
orcid: 0000-0001-7429-7896
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: 'Kaufmann W, Kleindienst D, Harada H, Shigemoto R. High-Resolution localization
and quantitation of membrane proteins by SDS-digested freeze-fracture replica
labeling (SDS-FRL). In: Receptor and Ion Channel Detection in the Brain.
Vol 169. Neuromethods. New York: Humana; 2021:267-283. doi:10.1007/978-1-0716-1522-5_19'
apa: 'Kaufmann, W., Kleindienst, D., Harada, H., & Shigemoto, R. (2021). High-Resolution
localization and quantitation of membrane proteins by SDS-digested freeze-fracture
replica labeling (SDS-FRL). In Receptor and Ion Channel Detection in the Brain
(Vol. 169, pp. 267–283). New York: Humana. https://doi.org/10.1007/978-1-0716-1522-5_19'
chicago: 'Kaufmann, Walter, David Kleindienst, Harumi Harada, and Ryuichi Shigemoto.
“High-Resolution Localization and Quantitation of Membrane Proteins by SDS-Digested
Freeze-Fracture Replica Labeling (SDS-FRL).” In Receptor and Ion Channel Detection
in the Brain, 169:267–83. Neuromethods. New York: Humana, 2021. https://doi.org/10.1007/978-1-0716-1522-5_19.'
ieee: 'W. Kaufmann, D. Kleindienst, H. Harada, and R. Shigemoto, “High-Resolution
localization and quantitation of membrane proteins by SDS-digested freeze-fracture
replica labeling (SDS-FRL),” in Receptor and Ion Channel Detection in the
Brain, vol. 169, New York: Humana, 2021, pp. 267–283.'
ista: 'Kaufmann W, Kleindienst D, Harada H, Shigemoto R. 2021.High-Resolution localization
and quantitation of membrane proteins by SDS-digested freeze-fracture replica
labeling (SDS-FRL). In: Receptor and Ion Channel Detection in the Brain. Neuromethods,
vol. 169, 267–283.'
mla: Kaufmann, Walter, et al. “High-Resolution Localization and Quantitation of
Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).”
Receptor and Ion Channel Detection in the Brain, vol. 169, Humana, 2021,
pp. 267–83, doi:10.1007/978-1-0716-1522-5_19.
short: W. Kaufmann, D. Kleindienst, H. Harada, R. Shigemoto, in:, Receptor and
Ion Channel Detection in the Brain, Humana, New York, 2021, pp. 267–283.
date_created: 2021-07-30T09:34:56Z
date_published: 2021-07-27T00:00:00Z
date_updated: 2024-03-25T23:30:16Z
day: '27'
ddc:
- '573'
department:
- _id: RySh
- _id: EM-Fac
doi: 10.1007/978-1-0716-1522-5_19
ec_funded: 1
has_accepted_license: '1'
intvolume: ' 169'
keyword:
- 'Freeze-fracture replica: Deep learning'
- Immunogold labeling
- Integral membrane protein
- Electron microscopy
language:
- iso: eng
month: '07'
oa_version: None
page: 267-283
place: New York
project:
- _id: 25CA28EA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694539'
name: 'In situ analysis of single channel subunit composition in neurons: physiological
implication in synaptic plasticity and behaviour'
- _id: 25CBA828-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '720270'
name: Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)
publication: ' Receptor and Ion Channel Detection in the Brain'
publication_identifier:
eisbn:
- '9781071615225'
isbn:
- '9781071615218'
publication_status: published
publisher: Humana
quality_controlled: '1'
related_material:
record:
- id: '9562'
relation: dissertation_contains
status: public
series_title: Neuromethods
status: public
title: High-Resolution localization and quantitation of membrane proteins by SDS-digested
freeze-fracture replica labeling (SDS-FRL)
type: book_chapter
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 169
year: '2021'
...
---
_id: '9759'
acknowledgement: The authors thank Inez Lam of Johns Hopkins University for valuable
comments on an earlier version of the manuscript. We also thank the facilitators
of the 2019–2020 eLife Community Ambassador program.
article_number: e1009124
article_processing_charge: Yes
article_type: letter_note
author:
- first_name: Michael John
full_name: Bartlett, Michael John
last_name: Bartlett
- first_name: Feyza N
full_name: Arslan, Feyza N
id: 49DA7910-F248-11E8-B48F-1D18A9856A87
last_name: Arslan
orcid: 0000-0001-5809-9566
- first_name: Adriana
full_name: Bankston, Adriana
last_name: Bankston
- first_name: Sarvenaz
full_name: Sarabipour, Sarvenaz
last_name: Sarabipour
citation:
ama: Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. Ten simple rules to improve
academic work- life balance. PLoS Computational Biology. 2021;17(7). doi:10.1371/journal.pcbi.1009124
apa: Bartlett, M. J., Arslan, F. N., Bankston, A., & Sarabipour, S. (2021).
Ten simple rules to improve academic work- life balance. PLoS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1009124
chicago: Bartlett, Michael John, Feyza N Arslan, Adriana Bankston, and Sarvenaz
Sarabipour. “Ten Simple Rules to Improve Academic Work- Life Balance.” PLoS
Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1009124.
ieee: M. J. Bartlett, F. N. Arslan, A. Bankston, and S. Sarabipour, “Ten simple
rules to improve academic work- life balance,” PLoS Computational Biology,
vol. 17, no. 7. Public Library of Science, 2021.
ista: Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. 2021. Ten simple rules to
improve academic work- life balance. PLoS Computational Biology. 17(7), e1009124.
mla: Bartlett, Michael John, et al. “Ten Simple Rules to Improve Academic Work-
Life Balance.” PLoS Computational Biology, vol. 17, no. 7, e1009124, Public
Library of Science, 2021, doi:10.1371/journal.pcbi.1009124.
short: M.J. Bartlett, F.N. Arslan, A. Bankston, S. Sarabipour, PLoS Computational
Biology 17 (2021).
date_created: 2021-08-01T22:01:21Z
date_published: 2021-07-15T00:00:00Z
date_updated: 2023-08-10T14:16:46Z
day: '15'
ddc:
- '613'
department:
- _id: CaHe
doi: 10.1371/journal.pcbi.1009124
external_id:
isi:
- '000677713500008'
pmid:
- '34264932'
file:
- access_level: open_access
checksum: e56d91f0eeadb36f143a90e2c1b3ab63
content_type: application/pdf
creator: cchlebak
date_created: 2021-08-05T12:06:49Z
date_updated: 2021-08-05T12:06:49Z
file_id: '9771'
file_name: 2021_PlosCompBio_Bartlett.pdf
file_size: 693633
relation: main_file
file_date_updated: 2021-08-05T12:06:49Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Computational Biology
publication_identifier:
eissn:
- '15537358'
issn:
- 1553734X
publication_status: published
publisher: Public Library of Science
scopus_import: '1'
status: public
title: Ten simple rules to improve academic work- life balance
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: 17
year: '2021'
...
---
_id: '9760'
abstract:
- lang: eng
text: "The quantum approximate optimization algorithm (QAOA) is a prospective near-term
quantum algorithm due to its modest circuit depth and promising benchmarks. However,
an external parameter optimization required in the QAOA could become a performance
bottleneck. This motivates studies of the optimization landscape and search for
heuristic ways of parameter initialization. In this work we visualize the optimization
landscape of the QAOA applied to the MaxCut problem on random graphs, demonstrating
that random initialization of the QAOA is prone to converging to local minima
with suboptimal performance. We introduce the initialization of QAOA parameters
based on the Trotterized quantum annealing (TQA) protocol, parameterized by the
Trotter time step. We find that the TQA initialization allows to circumvent\r\nthe
issue of false minima for a broad range of time steps, yielding the same performance
as the best result out of an exponentially scaling number of random initializations.
Moreover, we demonstrate that the optimal value of the time step coincides with
the point of proliferation of Trotter errors in quantum annealing. Our results
suggest practical ways of initializing QAOA protocols on near-term quantum devices
and reveal new connections between QAOA and quantum annealing."
acknowledgement: We would like to thank D. Abanin and R. Medina for fruitful discussions
and A. Smith and I. Kim for valuable feedback on the manuscript. We acknowledge
support by the European Research Council (ERC) under the European Union’s Horizon
2020 research and innovation program (Grant Agreement No. 850899).
article_number: '491'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Stefan
full_name: Sack, Stefan
id: dd622248-f6e0-11ea-865d-ce382a1c81a5
last_name: Sack
orcid: 0000-0001-5400-8508
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Sack S, Serbyn M. Quantum annealing initialization of the quantum approximate
optimization algorithm. Quantum. 2021;5. doi:10.22331/Q-2021-07-01-491
apa: Sack, S., & Serbyn, M. (2021). Quantum annealing initialization of the
quantum approximate optimization algorithm. Quantum. Verein zur Förderung
des Open Access Publizierens in den Quantenwissenschaften. https://doi.org/10.22331/Q-2021-07-01-491
chicago: Sack, Stefan, and Maksym Serbyn. “Quantum Annealing Initialization of the
Quantum Approximate Optimization Algorithm.” Quantum. Verein zur Förderung
des Open Access Publizierens in den Quantenwissenschaften, 2021. https://doi.org/10.22331/Q-2021-07-01-491.
ieee: S. Sack and M. Serbyn, “Quantum annealing initialization of the quantum approximate
optimization algorithm,” Quantum, vol. 5. Verein zur Förderung des Open
Access Publizierens in den Quantenwissenschaften, 2021.
ista: Sack S, Serbyn M. 2021. Quantum annealing initialization of the quantum approximate
optimization algorithm. Quantum. 5, 491.
mla: Sack, Stefan, and Maksym Serbyn. “Quantum Annealing Initialization of the Quantum
Approximate Optimization Algorithm.” Quantum, vol. 5, 491, Verein zur Förderung
des Open Access Publizierens in den Quantenwissenschaften, 2021, doi:10.22331/Q-2021-07-01-491.
short: S. Sack, M. Serbyn, Quantum 5 (2021).
date_created: 2021-08-01T22:01:21Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2023-12-13T14:47:25Z
day: '01'
ddc:
- '530'
department:
- _id: GradSch
- _id: MaSe
doi: 10.22331/Q-2021-07-01-491
ec_funded: 1
external_id:
arxiv:
- '2101.05742'
isi:
- '000669830600001'
file:
- access_level: open_access
checksum: 9706c2bb8e748e9b5b138381995a7f6f
content_type: application/pdf
creator: cchlebak
date_created: 2021-08-06T06:44:31Z
date_updated: 2021-08-06T06:44:31Z
file_id: '9774'
file_name: 2021_Quantum_Sack.pdf
file_size: 2312482
relation: main_file
file_date_updated: 2021-08-06T06:44:31Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Quantum
publication_identifier:
eissn:
- 2521-327X
publication_status: published
publisher: Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften
quality_controlled: '1'
related_material:
record:
- id: '14622'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Quantum annealing initialization of the quantum approximate optimization algorithm
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2021'
...
---
_id: '9761'
abstract:
- lang: eng
text: 'The important roles of mitochondrial function and dysfunction in the process
of neurodegeneration are widely acknowledged. Retinal ganglion cells (RGCs) appear
to be a highly vulnerable neuronal cell type in the central nervous system with
respect to mitochondrial dysfunction but the actual reasons for this are still
incompletely understood. These cells have a unique circumstance where unmyelinated
axons must bend nearly 90° to exit the eye and then cross a translaminar pressure
gradient before becoming myelinated in the optic nerve. This region, the optic
nerve head, contains some of the highest density of mitochondria present in these
cells. Glaucoma represents a perfect storm of events occurring at this location,
with a combination of changes in the translaminar pressure gradient and reassignment
of the metabolic support functions of supporting glia, which appears to apply
increased metabolic stress to the RGC axons leading to a failure of axonal transport
mechanisms. However, RGCs themselves are also extremely sensitive to genetic mutations,
particularly in genes affecting mitochondrial dynamics and mitochondrial clearance.
These mutations, which systemically affect the mitochondria in every cell, often
lead to an optic neuropathy as the sole pathologic defect in affected patients.
This review summarizes knowledge of mitochondrial structure and function, the
known energy demands of neurons in general, and places these in the context of
normal and pathological characteristics of mitochondria attributed to RGCs. '
acknowledgement: The authors are grateful to Kazuya Oikawa and Gillian McLellan for
generously sharing some of their data for this review, and to Janis Eells for helpful
comments on the manuscript.
article_number: '1593'
article_processing_charge: Yes
article_type: original
author:
- first_name: Nicole A.
full_name: Muench, Nicole A.
last_name: Muench
- first_name: Sonia
full_name: Patel, Sonia
last_name: Patel
- first_name: Margaret E
full_name: Maes, Margaret E
id: 3838F452-F248-11E8-B48F-1D18A9856A87
last_name: Maes
orcid: 0000-0001-9642-1085
- first_name: Ryan J.
full_name: Donahue, Ryan J.
last_name: Donahue
- first_name: Akihiro
full_name: Ikeda, Akihiro
last_name: Ikeda
- first_name: Robert W.
full_name: Nickells, Robert W.
last_name: Nickells
citation:
ama: Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. The influence
of mitochondrial dynamics and function on retinal ganglion cell susceptibility
in optic nerve disease. Cells. 2021;10(7). doi:10.3390/cells10071593
apa: Muench, N. A., Patel, S., Maes, M. E., Donahue, R. J., Ikeda, A., & Nickells,
R. W. (2021). The influence of mitochondrial dynamics and function on retinal
ganglion cell susceptibility in optic nerve disease. Cells. MDPI. https://doi.org/10.3390/cells10071593
chicago: Muench, Nicole A., Sonia Patel, Margaret E Maes, Ryan J. Donahue, Akihiro
Ikeda, and Robert W. Nickells. “The Influence of Mitochondrial Dynamics and Function
on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” Cells.
MDPI, 2021. https://doi.org/10.3390/cells10071593.
ieee: N. A. Muench, S. Patel, M. E. Maes, R. J. Donahue, A. Ikeda, and R. W. Nickells,
“The influence of mitochondrial dynamics and function on retinal ganglion cell
susceptibility in optic nerve disease,” Cells, vol. 10, no. 7. MDPI, 2021.
ista: Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. 2021. The influence
of mitochondrial dynamics and function on retinal ganglion cell susceptibility
in optic nerve disease. Cells. 10(7), 1593.
mla: Muench, Nicole A., et al. “The Influence of Mitochondrial Dynamics and Function
on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” Cells,
vol. 10, no. 7, 1593, MDPI, 2021, doi:10.3390/cells10071593.
short: N.A. Muench, S. Patel, M.E. Maes, R.J. Donahue, A. Ikeda, R.W. Nickells,
Cells 10 (2021).
date_created: 2021-08-01T22:01:22Z
date_published: 2021-06-25T00:00:00Z
date_updated: 2023-08-10T14:14:53Z
day: '25'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.3390/cells10071593
external_id:
isi:
- '000678193300001'
pmid:
- '34201955'
file:
- access_level: open_access
checksum: e0497ce5c77fa3b65a538c7d6e0f6c66
content_type: application/pdf
creator: cziletti
date_created: 2021-08-04T14:01:30Z
date_updated: 2021-08-04T14:01:30Z
file_id: '9768'
file_name: 2021_Cells_Muench.pdf
file_size: 4555611
relation: main_file
success: 1
file_date_updated: 2021-08-04T14:01:30Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '7'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Cells
publication_identifier:
eissn:
- '20734409'
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: The influence of mitochondrial dynamics and function on retinal ganglion cell
susceptibility in optic nerve disease
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: '2021'
...
---
_id: '9769'
abstract:
- lang: eng
text: A few years ago, flow equations were introduced as a technique for calculating
the ground-state energies of cold Bose gases with and without impurities. In this
paper, we extend this approach to compute observables other than the energy. As
an example, we calculate the densities, and phase fluctuations of one-dimensional
Bose gases with one and two impurities. For a single mobile impurity, we use flow
equations to validate the mean-field results obtained upon the Lee-Low-Pines transformation.
We show that the mean-field approximation is accurate for all values of the boson-impurity
interaction strength as long as the phase coherence length is much larger than
the healing length of the condensate. For two static impurities, we calculate
impurity-impurity interactions induced by the Bose gas. We find that leading order
perturbation theory fails when boson-impurity interactions are stronger than boson-boson
interactions. The mean-field approximation reproduces the flow equation results
for all values of the boson-impurity interaction strength as long as boson-boson
interactions are weak.
acknowledgement: We thank Matthias Heinz and Volker Karle for helpful comments on
the manuscript; Zoran Ristivojevic for useful correspondence regarding mean-field
calculations of induced impurity-impurity interactions; Fabian Grusdt for sharing
with us the data for the densities presented in Ref. [14]. This work has received
funding from the DFG Project No. 413495248 [VO 2437/1-1] (F. B., H.-W. H., A. G.
V.) and European Union’s Horizon 2020 research and innovation programme under the
Marie Skłodowska-Curie Grant Agreement No. 754411 (A. G. V.). M. L. acknowledges
support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).
H.-W.H. thanks the ECT* for hospitality during the workshop “Universal physics in
Many-Body Quantum Systems – From Atoms to Quarks". This infrastructure is part of
a project that has received funding from the European Union’s Horizon 2020 research
and innovation programme under grant agreement No 824093. H.-W.H. was supported
by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Project-ID
279384907 - SFB 1245.
article_number: '008'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Fabian
full_name: Brauneis, Fabian
last_name: Brauneis
- first_name: Hans-Werner
full_name: Hammer, Hans-Werner
last_name: Hammer
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: 'Brauneis F, Hammer H-W, Lemeshko M, Volosniev A. Impurities in a one-dimensional
Bose gas: The flow equation approach. SciPost Physics. 2021;11(1). doi:10.21468/scipostphys.11.1.008'
apa: 'Brauneis, F., Hammer, H.-W., Lemeshko, M., & Volosniev, A. (2021). Impurities
in a one-dimensional Bose gas: The flow equation approach. SciPost Physics.
SciPost. https://doi.org/10.21468/scipostphys.11.1.008'
chicago: 'Brauneis, Fabian, Hans-Werner Hammer, Mikhail Lemeshko, and Artem Volosniev.
“Impurities in a One-Dimensional Bose Gas: The Flow Equation Approach.” SciPost
Physics. SciPost, 2021. https://doi.org/10.21468/scipostphys.11.1.008.'
ieee: 'F. Brauneis, H.-W. Hammer, M. Lemeshko, and A. Volosniev, “Impurities in
a one-dimensional Bose gas: The flow equation approach,” SciPost Physics,
vol. 11, no. 1. SciPost, 2021.'
ista: 'Brauneis F, Hammer H-W, Lemeshko M, Volosniev A. 2021. Impurities in a one-dimensional
Bose gas: The flow equation approach. SciPost Physics. 11(1), 008.'
mla: 'Brauneis, Fabian, et al. “Impurities in a One-Dimensional Bose Gas: The Flow
Equation Approach.” SciPost Physics, vol. 11, no. 1, 008, SciPost, 2021,
doi:10.21468/scipostphys.11.1.008.'
short: F. Brauneis, H.-W. Hammer, M. Lemeshko, A. Volosniev, SciPost Physics 11
(2021).
date_created: 2021-08-04T15:00:55Z
date_published: 2021-07-13T00:00:00Z
date_updated: 2023-08-11T10:25:44Z
day: '13'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.21468/scipostphys.11.1.008
ec_funded: 1
external_id:
arxiv:
- '2101.10958'
isi:
- '000680039500013'
file:
- access_level: open_access
checksum: eaa847346b1a023d97bbb291779610ed
content_type: application/pdf
creator: asandaue
date_created: 2021-08-10T11:44:59Z
date_updated: 2021-08-10T11:44:59Z
file_id: '9875'
file_name: 2021_SciPostPhysics_Brauneis.pdf
file_size: 1085300
relation: main_file
success: 1
file_date_updated: 2021-08-10T11:44:59Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: SciPost Physics
publication_identifier:
eissn:
- 2542-4653
publication_status: published
publisher: SciPost
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Impurities in a one-dimensional Bose gas: The flow equation approach'
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: '2021'
...
---
_id: '9770'
abstract:
- lang: eng
text: We study an effective one-dimensional quantum model that includes friction
and spin-orbit coupling (SOC), and show that the model exhibits spin polarization
when both terms are finite. Most important, strong spin polarization can be observed
even for moderate SOC, provided that the friction is strong. Our findings might
help to explain the pronounced effect of chirality on spin distribution and transport
in chiral molecules. In particular, our model implies static magnetic properties
of a chiral molecule, which lead to Shiba-like states when a molecule is placed
on a superconductor, in accordance with recent experimental data.
acknowledgement: "We thank Rafael Barfknecht for useful discussions. This work has
received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A.G.\r\nand
A.G.V.). M.L. acknowledges support by the European Research Council (ERC) Starting
Grant No. 801770 (ANGULON). Y.P. and O.M. acknowledge funding from the Nidersachsen
Ministry of Science and Culture, and from the\r\nAcademia Sinica Research Program.
O.M. is thankful for support through the Harry de Jur Chair in Applied Science."
article_number: '024430'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
- first_name: Hen
full_name: Alpern, Hen
last_name: Alpern
- first_name: Yossi
full_name: Paltiel, Yossi
last_name: Paltiel
- first_name: Oded
full_name: Millo, Oded
last_name: Millo
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
citation:
ama: Volosniev A, Alpern H, Paltiel Y, Millo O, Lemeshko M, Ghazaryan A. Interplay
between friction and spin-orbit coupling as a source of spin polarization. Physical
Review B. 2021;104(2). doi:10.1103/physrevb.104.024430
apa: Volosniev, A., Alpern, H., Paltiel, Y., Millo, O., Lemeshko, M., & Ghazaryan,
A. (2021). Interplay between friction and spin-orbit coupling as a source of spin
polarization. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.104.024430
chicago: Volosniev, Artem, Hen Alpern, Yossi Paltiel, Oded Millo, Mikhail Lemeshko,
and Areg Ghazaryan. “Interplay between Friction and Spin-Orbit Coupling as a Source
of Spin Polarization.” Physical Review B. American Physical Society, 2021.
https://doi.org/10.1103/physrevb.104.024430.
ieee: A. Volosniev, H. Alpern, Y. Paltiel, O. Millo, M. Lemeshko, and A. Ghazaryan,
“Interplay between friction and spin-orbit coupling as a source of spin polarization,”
Physical Review B, vol. 104, no. 2. American Physical Society, 2021.
ista: Volosniev A, Alpern H, Paltiel Y, Millo O, Lemeshko M, Ghazaryan A. 2021.
Interplay between friction and spin-orbit coupling as a source of spin polarization.
Physical Review B. 104(2), 024430.
mla: Volosniev, Artem, et al. “Interplay between Friction and Spin-Orbit Coupling
as a Source of Spin Polarization.” Physical Review B, vol. 104, no. 2,
024430, American Physical Society, 2021, doi:10.1103/physrevb.104.024430.
short: A. Volosniev, H. Alpern, Y. Paltiel, O. Millo, M. Lemeshko, A. Ghazaryan,
Physical Review B 104 (2021).
date_created: 2021-08-04T15:05:32Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2023-08-10T14:27:07Z
day: '01'
department:
- _id: MiLe
doi: 10.1103/physrevb.104.024430
ec_funded: 1
external_id:
arxiv:
- '2101.05173'
isi:
- '000678780800003'
intvolume: ' 104'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2101.05173
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Interplay between friction and spin-orbit coupling as a source of spin polarization
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 104
year: '2021'
...