---
_id: '12876'
abstract:
- lang: eng
text: "Motivation: The problem of model inference is of fundamental importance to
systems biology. Logical models (e.g. Boolean networks; BNs) represent a computationally
attractive approach capable of handling large biological networks. The models
are typically inferred from experimental data. However, even with a substantial
amount of experimental data supported by some prior knowledge, existing inference
methods often focus on a small sample of admissible candidate models only.\r\n\r\nResults:
We propose Boolean network sketches as a new formal instrument for the inference
of Boolean networks. A sketch integrates (typically partial) knowledge about the
network’s topology and the update logic (obtained through, e.g. a biological knowledge
base or a literature search), as well as further assumptions about the properties
of the network’s transitions (e.g. the form of its attractor landscape), and additional
restrictions on the model dynamics given by the measured experimental data. Our
new BNs inference algorithm starts with an ‘initial’ sketch, which is extended
by adding restrictions representing experimental data to a ‘data-informed’ sketch
and subsequently computes all BNs consistent with the data-informed sketch. Our
algorithm is based on a symbolic representation and coloured model-checking. Our
approach is unique in its ability to cover a broad spectrum of knowledge and efficiently
produce a compact representation of all inferred BNs. We evaluate the method on
a non-trivial collection of real-world and simulated data."
acknowledgement: This work was partially supported by GACR [grant No. GA22-10845S];
and Grant Agency of Masaryk University [grant No. MUNI/G/1771/2020]. This work was
partially supported by European Union’s Horizon 2020 research and innovation programme
under the Marie Skłodowska-Curie [Grant Agreement No. 101034413 to S.P.].
article_number: btad158
article_processing_charge: No
article_type: original
author:
- first_name: Nikola
full_name: Beneš, Nikola
last_name: Beneš
- first_name: Luboš
full_name: Brim, Luboš
last_name: Brim
- first_name: Ondřej
full_name: Huvar, Ondřej
last_name: Huvar
- first_name: Samuel
full_name: Pastva, Samuel
id: 07c5ea74-f61c-11ec-a664-aa7c5d957b2b
last_name: Pastva
- first_name: David
full_name: Šafránek, David
last_name: Šafránek
citation:
ama: 'Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. Boolean network sketches:
A unifying framework for logical model inference. Bioinformatics. 2023;39(4).
doi:10.1093/bioinformatics/btad158'
apa: 'Beneš, N., Brim, L., Huvar, O., Pastva, S., & Šafránek, D. (2023). Boolean
network sketches: A unifying framework for logical model inference. Bioinformatics.
Oxford Academic. https://doi.org/10.1093/bioinformatics/btad158'
chicago: 'Beneš, Nikola, Luboš Brim, Ondřej Huvar, Samuel Pastva, and David Šafránek.
“Boolean Network Sketches: A Unifying Framework for Logical Model Inference.”
Bioinformatics. Oxford Academic, 2023. https://doi.org/10.1093/bioinformatics/btad158.'
ieee: 'N. Beneš, L. Brim, O. Huvar, S. Pastva, and D. Šafránek, “Boolean network
sketches: A unifying framework for logical model inference,” Bioinformatics,
vol. 39, no. 4. Oxford Academic, 2023.'
ista: 'Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. 2023. Boolean network sketches:
A unifying framework for logical model inference. Bioinformatics. 39(4), btad158.'
mla: 'Beneš, Nikola, et al. “Boolean Network Sketches: A Unifying Framework for
Logical Model Inference.” Bioinformatics, vol. 39, no. 4, btad158, Oxford
Academic, 2023, doi:10.1093/bioinformatics/btad158.'
short: N. Beneš, L. Brim, O. Huvar, S. Pastva, D. Šafránek, Bioinformatics 39 (2023).
date_created: 2023-04-30T22:01:05Z
date_published: 2023-04-03T00:00:00Z
date_updated: 2023-08-01T14:27:28Z
day: '03'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1093/bioinformatics/btad158
ec_funded: 1
external_id:
isi:
- '000976610800001'
pmid:
- '37004199'
file:
- access_level: open_access
checksum: 2cb90ddf781baefddf47eac4b54e2a03
content_type: application/pdf
creator: dernst
date_created: 2023-05-02T07:39:04Z
date_updated: 2023-05-02T07:39:04Z
file_id: '12886'
file_name: 2023_Bioinformatics_Benes.pdf
file_size: 478740
relation: main_file
success: 1
file_date_updated: 2023-05-02T07:39:04Z
has_accepted_license: '1'
intvolume: ' 39'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Bioinformatics
publication_identifier:
eissn:
- 1367-4811
publication_status: published
publisher: Oxford Academic
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://doi.org/10.5281/zenodo.7688740
scopus_import: '1'
status: public
title: 'Boolean network sketches: A unifying framework for logical model inference'
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: 39
year: '2023'
...
---
_id: '12877'
abstract:
- lang: eng
text: We consider billiards obtained by removing from the plane finitely many strictly
convex analytic obstacles satisfying the non-eclipse condition. The restriction
of the dynamics to the set of non-escaping orbits is conjugated to a subshift,
which provides a natural labeling of periodic orbits. We show that under suitable
symmetry and genericity assumptions, the Marked Length Spectrum determines the
geometry of the billiard table.
acknowledgement: 'J.D.S. and M.L. have been partially supported by the NSERC Discovery
grant, reference number 502617-2017. M.L. was also supported by the ERC project
692925 NUHGD of Sylvain Crovisier, by the ANR AAPG 2021 PRC CoSyDy: Conformally
symplectic dynamics, beyond symplectic dynamics (ANR-CE40-0014), and by the ANR
JCJC PADAWAN: Parabolic dynamics, bifurcations and wandering domains (ANR-21-CE40-0012).
V.K. acknowledges partial support of the NSF grant DMS-1402164 and ERC Grant # 885707.'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Jacopo
full_name: De Simoi, Jacopo
last_name: De Simoi
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Martin
full_name: Leguil, Martin
last_name: Leguil
citation:
ama: De Simoi J, Kaloshin V, Leguil M. Marked Length Spectral determination of analytic
chaotic billiards with axial symmetries. Inventiones Mathematicae. 2023;233:829-901.
doi:10.1007/s00222-023-01191-8
apa: De Simoi, J., Kaloshin, V., & Leguil, M. (2023). Marked Length Spectral
determination of analytic chaotic billiards with axial symmetries. Inventiones
Mathematicae. Springer Nature. https://doi.org/10.1007/s00222-023-01191-8
chicago: De Simoi, Jacopo, Vadim Kaloshin, and Martin Leguil. “Marked Length Spectral
Determination of Analytic Chaotic Billiards with Axial Symmetries.” Inventiones
Mathematicae. Springer Nature, 2023. https://doi.org/10.1007/s00222-023-01191-8.
ieee: J. De Simoi, V. Kaloshin, and M. Leguil, “Marked Length Spectral determination
of analytic chaotic billiards with axial symmetries,” Inventiones Mathematicae,
vol. 233. Springer Nature, pp. 829–901, 2023.
ista: De Simoi J, Kaloshin V, Leguil M. 2023. Marked Length Spectral determination
of analytic chaotic billiards with axial symmetries. Inventiones Mathematicae.
233, 829–901.
mla: De Simoi, Jacopo, et al. “Marked Length Spectral Determination of Analytic
Chaotic Billiards with Axial Symmetries.” Inventiones Mathematicae, vol.
233, Springer Nature, 2023, pp. 829–901, doi:10.1007/s00222-023-01191-8.
short: J. De Simoi, V. Kaloshin, M. Leguil, Inventiones Mathematicae 233 (2023)
829–901.
date_created: 2023-04-30T22:01:05Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2023-10-04T11:25:37Z
day: '01'
department:
- _id: VaKa
doi: 10.1007/s00222-023-01191-8
ec_funded: 1
external_id:
arxiv:
- '1905.00890'
isi:
- '000978887600001'
intvolume: ' 233'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1905.00890
month: '08'
oa: 1
oa_version: Preprint
page: 829-901
project:
- _id: 9B8B92DE-BA93-11EA-9121-9846C619BF3A
call_identifier: H2020
grant_number: '885707'
name: Spectral rigidity and integrability for billiards and geodesic flows
publication: Inventiones Mathematicae
publication_identifier:
eissn:
- 1432-1297
issn:
- 0020-9910
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Marked Length Spectral determination of analytic chaotic billiards with axial
symmetries
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 233
year: '2023'
...
---
_id: '12878'
abstract:
- lang: eng
text: Salicylic acid (SA) plays important roles in different aspects of plant development,
including root growth, where auxin is also a major player by means of its asymmetric
distribution. However, the mechanism underlying the effect of SA on the development
of rice roots remains poorly understood. Here, we show that SA inhibits rice root
growth by interfering with auxin transport associated with the OsPIN3t- and clathrin-mediated
gene regulatory network (GRN). SA inhibits root growth as well as Brefeldin A-sensitive
trafficking through a non-canonical SA signaling mechanism. Transcriptome analysis
of rice seedlings treated with SA revealed that the OsPIN3t auxin transporter
is at the center of a GRN involving the coat protein clathrin. The root growth
and endocytic trafficking in both the pin3t and clathrin heavy chain mutants were
SA insensitivity. SA inhibitory effect on the endocytosis of OsPIN3t was dependent
on clathrin; however, the root growth and endocytic trafficking mediated by tyrphostin
A23 (TyrA23) were independent of the pin3t mutant under SA treatment. These data
reveal that SA affects rice root growth through the convergence of transcriptional
and non-SA signaling mechanisms involving OsPIN3t-mediated auxin transport and
clathrin-mediated trafficking as key components.
acknowledgement: The authors thank Professor Jianqiang Wu (Kunming Institute of Botany,
Chinese Academy of Sciences) for support with phytohormone measurement. Thanks also
go to Professor Pieter. B. F. Ouwerkerk (Leiden University) and Professor Jean-Benoit
Morel (Plant Health Institute of Montpellier) for provision of the rice lines NB-7B-70
and NB-7B-76 and wild-type NB-61-WT, Professor Zuhua He (Chinese Academy of Sciences)
for provision of the rice OsNPR1-RNAi mutant, and Professor Yinong Yang (The Pennsylvania
State University) for provision of the rice line NahG. This work was supported by
grants from the National Natural Science Foundation of China (Grant Nos. 32260085,
31460453, 31660501, 31860064, 31970609, 31801792 and 31960554), the Key Projects
of the Applied Basic Research Plan of Yunnan Province (202301AS070082), the Major
Special Program for Scientific Research, Education Department of Yunnan Province
(Grant No. ZD2015005), the Start-up fund from Xishuangbanna Tropical Botanical Garden,
and ‘Top Talents Program in Science and Technology’ from Yunnan Province, the SRF
for ROCS, SEM (Grant No. [2013] 1792), and the Major Science and Technology Project
in Yunnan Province (202102AE090042 and 202202AE090036); and the young and middle-aged
academic and technical leaders reserve talent program in Yunnan Province (202205AC160076).
article_processing_charge: No
article_type: original
author:
- first_name: Lihui
full_name: Jiang, Lihui
last_name: Jiang
- first_name: Baolin
full_name: Yao, Baolin
last_name: Yao
- first_name: Xiaoyan
full_name: Zhang, Xiaoyan
last_name: Zhang
- first_name: Lixia
full_name: Wu, Lixia
last_name: Wu
- first_name: Qijing
full_name: Fu, Qijing
last_name: Fu
- first_name: Yiting
full_name: Zhao, Yiting
last_name: Zhao
- first_name: Yuxin
full_name: Cao, Yuxin
last_name: Cao
- first_name: Ruomeng
full_name: Zhu, Ruomeng
last_name: Zhu
- first_name: Xinqi
full_name: Lu, Xinqi
last_name: Lu
- first_name: Wuying
full_name: Huang, Wuying
last_name: Huang
- first_name: Jianping
full_name: Zhao, Jianping
last_name: Zhao
- first_name: Kuixiu
full_name: Li, Kuixiu
last_name: Li
- first_name: Shuanglu
full_name: Zhao, Shuanglu
last_name: Zhao
- first_name: Li
full_name: Han, Li
last_name: Han
- first_name: Xuan
full_name: Zhou, Xuan
last_name: Zhou
- first_name: Chongyu
full_name: Luo, Chongyu
last_name: Luo
- first_name: Haiyan
full_name: Zhu, Haiyan
last_name: Zhu
- first_name: Jing
full_name: Yang, Jing
last_name: Yang
- first_name: Huichuan
full_name: Huang, Huichuan
last_name: Huang
- first_name: Zhengge
full_name: Zhu, Zhengge
last_name: Zhu
- first_name: Xiahong
full_name: He, Xiahong
last_name: He
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Zhongkai
full_name: Zhang, Zhongkai
last_name: Zhang
- first_name: Changning
full_name: Liu, Changning
last_name: Liu
- first_name: Yunlong
full_name: Du, Yunlong
last_name: Du
citation:
ama: Jiang L, Yao B, Zhang X, et al. Salicylic acid inhibits rice endocytic protein
trafficking mediated by OsPIN3t and clathrin to affect root growth. Plant Journal.
2023;115(1):155-174. doi:10.1111/tpj.16218
apa: Jiang, L., Yao, B., Zhang, X., Wu, L., Fu, Q., Zhao, Y., … Du, Y. (2023). Salicylic
acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin
to affect root growth. Plant Journal. Wiley. https://doi.org/10.1111/tpj.16218
chicago: Jiang, Lihui, Baolin Yao, Xiaoyan Zhang, Lixia Wu, Qijing Fu, Yiting Zhao,
Yuxin Cao, et al. “Salicylic Acid Inhibits Rice Endocytic Protein Trafficking
Mediated by OsPIN3t and Clathrin to Affect Root Growth.” Plant Journal.
Wiley, 2023. https://doi.org/10.1111/tpj.16218.
ieee: L. Jiang et al., “Salicylic acid inhibits rice endocytic protein trafficking
mediated by OsPIN3t and clathrin to affect root growth,” Plant Journal,
vol. 115, no. 1. Wiley, pp. 155–174, 2023.
ista: Jiang L, Yao B, Zhang X, Wu L, Fu Q, Zhao Y, Cao Y, Zhu R, Lu X, Huang W,
Zhao J, Li K, Zhao S, Han L, Zhou X, Luo C, Zhu H, Yang J, Huang H, Zhu Z, He
X, Friml J, Zhang Z, Liu C, Du Y. 2023. Salicylic acid inhibits rice endocytic
protein trafficking mediated by OsPIN3t and clathrin to affect root growth. Plant
Journal. 115(1), 155–174.
mla: Jiang, Lihui, et al. “Salicylic Acid Inhibits Rice Endocytic Protein Trafficking
Mediated by OsPIN3t and Clathrin to Affect Root Growth.” Plant Journal,
vol. 115, no. 1, Wiley, 2023, pp. 155–74, doi:10.1111/tpj.16218.
short: L. Jiang, B. Yao, X. Zhang, L. Wu, Q. Fu, Y. Zhao, Y. Cao, R. Zhu, X. Lu,
W. Huang, J. Zhao, K. Li, S. Zhao, L. Han, X. Zhou, C. Luo, H. Zhu, J. Yang, H.
Huang, Z. Zhu, X. He, J. Friml, Z. Zhang, C. Liu, Y. Du, Plant Journal 115 (2023)
155–174.
date_created: 2023-04-30T22:01:06Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2023-08-01T14:16:33Z
day: '01'
department:
- _id: JiFr
doi: 10.1111/tpj.16218
external_id:
isi:
- '000971861400001'
pmid:
- '37025008 '
intvolume: ' 115'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa_version: None
page: 155-174
pmid: 1
publication: Plant Journal
publication_identifier:
eissn:
- 1365-313X
issn:
- 0960-7412
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t
and clathrin to affect root growth
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 115
year: '2023'
...
---
_id: '12879'
abstract:
- lang: eng
text: Machine learning (ML) has been widely applied to chemical property prediction,
most prominently for the energies and forces in molecules and materials. The strong
interest in predicting energies in particular has led to a ‘local energy’-based
paradigm for modern atomistic ML models, which ensures size-extensivity and a
linear scaling of computational cost with system size. However, many electronic
properties (such as excitation energies or ionization energies) do not necessarily
scale linearly with system size and may even be spatially localized. Using size-extensive
models in these cases can lead to large errors. In this work, we explore different
strategies for learning intensive and localized properties, using HOMO energies
in organic molecules as a representative test case. In particular, we analyze
the pooling functions that atomistic neural networks use to predict molecular
properties, and suggest an orbital weighted average (OWA) approach that enables
the accurate prediction of orbital energies and locations.
acknowledgement: KC acknowledges funding from the China Scholarship Council. KC is
grateful for the TUM graduate school finance support to visit Bingqing Cheng's group
in IST for two months. We also thankfully acknowledge computational resources provided
by the MPCDF Supercomputing Centre.
article_processing_charge: No
article_type: original
author:
- first_name: Ke
full_name: Chen, Ke
id: c636c5ca-e8b8-11ed-b2d4-cc2c37613a8d
last_name: Chen
- first_name: Christian
full_name: Kunkel, Christian
last_name: Kunkel
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Karsten
full_name: Reuter, Karsten
last_name: Reuter
- first_name: Johannes T.
full_name: Margraf, Johannes T.
last_name: Margraf
citation:
ama: Chen K, Kunkel C, Cheng B, Reuter K, Margraf JT. Physics-inspired machine learning
of localized intensive properties. Chemical Science. 2023. doi:10.1039/d3sc00841j
apa: Chen, K., Kunkel, C., Cheng, B., Reuter, K., & Margraf, J. T. (2023). Physics-inspired
machine learning of localized intensive properties. Chemical Science. Royal
Society of Chemistry. https://doi.org/10.1039/d3sc00841j
chicago: Chen, Ke, Christian Kunkel, Bingqing Cheng, Karsten Reuter, and Johannes
T. Margraf. “Physics-Inspired Machine Learning of Localized Intensive Properties.”
Chemical Science. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d3sc00841j.
ieee: K. Chen, C. Kunkel, B. Cheng, K. Reuter, and J. T. Margraf, “Physics-inspired
machine learning of localized intensive properties,” Chemical Science.
Royal Society of Chemistry, 2023.
ista: Chen K, Kunkel C, Cheng B, Reuter K, Margraf JT. 2023. Physics-inspired machine
learning of localized intensive properties. Chemical Science.
mla: Chen, Ke, et al. “Physics-Inspired Machine Learning of Localized Intensive
Properties.” Chemical Science, Royal Society of Chemistry, 2023, doi:10.1039/d3sc00841j.
short: K. Chen, C. Kunkel, B. Cheng, K. Reuter, J.T. Margraf, Chemical Science (2023).
date_created: 2023-04-30T22:01:06Z
date_published: 2023-04-10T00:00:00Z
date_updated: 2023-08-01T14:18:10Z
day: '10'
ddc:
- '000'
- '540'
department:
- _id: BiCh
doi: 10.1039/d3sc00841j
external_id:
isi:
- '000971508100001'
file:
- access_level: open_access
checksum: 5eeec69a51e192dcd94b955d84423836
content_type: application/pdf
creator: dernst
date_created: 2023-05-02T07:17:05Z
date_updated: 2023-05-02T07:17:05Z
file_id: '12883'
file_name: 2023_ChemialScience_Chen.pdf
file_size: 1515446
relation: main_file
success: 1
file_date_updated: 2023-05-02T07:17:05Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: Chemical Science
publication_identifier:
eissn:
- 2041-6539
issn:
- 2041-6520
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Physics-inspired machine learning of localized intensive properties
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2023'
...
---
_id: '12880'
abstract:
- lang: eng
text: Peripheral heterochromatin positioning depends on nuclear envelope associated
proteins and repressive histone modifications. Here we show that overexpression
(OE) of Lamin B1 (LmnB1) leads to the redistribution of peripheral heterochromatin
into heterochromatic foci within the nucleoplasm. These changes represent a perturbation
of heterochromatin binding at the nuclear periphery (NP) through a mechanism independent
from altering other heterochromatin anchors or histone post-translational modifications.
We further show that LmnB1 OE alters gene expression. These changes do not correlate
with different levels of H3K9me3, but a significant number of the misregulated
genes were likely mislocalized away from the NP upon LmnB1 OE. We also observed
an enrichment of developmental processes amongst the upregulated genes. ~74% of
these genes were normally repressed in our cell type, suggesting that LmnB1 OE
promotes gene de-repression. This demonstrates a broader consequence of LmnB1
OE on cell fate, and highlights the importance of maintaining proper levels of
LmnB1.
acknowledgement: 'We thank members of the Hetzer lab for critical review of the manuscript;
Novogene for mRNA library preparation and sequencing; the Next-Generation Sequencing
Core Facility at the Salk Institute, with funding from NIH-NCI CCSG: P30 014195,
the Chapman Foundation, and the Helmsley Charitable Trust, for sequencing Cut&Run
libraries; and the Waitt Advanced Biophotonics Core Facility at the Salk Institute,
with funding from NIH-NCI CCSG: P30 014195, the Waitt Foundation, and the Chan-Zuckerberg
Initiative Imaging Scientist Award, for electron microscopy sample preparation and
imaging.'
article_number: '2202548'
article_processing_charge: No
article_type: original
author:
- first_name: Jeanae M.
full_name: Kaneshiro, Jeanae M.
last_name: Kaneshiro
- first_name: Juliana S.
full_name: Capitanio, Juliana S.
last_name: Capitanio
- first_name: Martin W
full_name: Hetzer, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: Hetzer
orcid: 0000-0002-2111-992X
citation:
ama: Kaneshiro JM, Capitanio JS, Hetzer M. Lamin B1 overexpression alters chromatin
organization and gene expression. Nucleus. 2023;14(1). doi:10.1080/19491034.2023.2202548
apa: Kaneshiro, J. M., Capitanio, J. S., & Hetzer, M. (2023). Lamin B1 overexpression
alters chromatin organization and gene expression. Nucleus. Taylor &
Francis. https://doi.org/10.1080/19491034.2023.2202548
chicago: Kaneshiro, Jeanae M., Juliana S. Capitanio, and Martin Hetzer. “Lamin B1
Overexpression Alters Chromatin Organization and Gene Expression.” Nucleus.
Taylor & Francis, 2023. https://doi.org/10.1080/19491034.2023.2202548.
ieee: J. M. Kaneshiro, J. S. Capitanio, and M. Hetzer, “Lamin B1 overexpression
alters chromatin organization and gene expression,” Nucleus, vol. 14, no.
1. Taylor & Francis, 2023.
ista: Kaneshiro JM, Capitanio JS, Hetzer M. 2023. Lamin B1 overexpression alters
chromatin organization and gene expression. Nucleus. 14(1), 2202548.
mla: Kaneshiro, Jeanae M., et al. “Lamin B1 Overexpression Alters Chromatin Organization
and Gene Expression.” Nucleus, vol. 14, no. 1, 2202548, Taylor & Francis,
2023, doi:10.1080/19491034.2023.2202548.
short: J.M. Kaneshiro, J.S. Capitanio, M. Hetzer, Nucleus 14 (2023).
date_created: 2023-04-30T22:01:06Z
date_published: 2023-04-18T00:00:00Z
date_updated: 2023-08-01T14:18:46Z
day: '18'
ddc:
- '570'
department:
- _id: MaHe
doi: 10.1080/19491034.2023.2202548
external_id:
isi:
- '000971629400001'
pmid:
- '37071033'
file:
- access_level: open_access
checksum: 8e707eda84f64dbad7f03545ae0a83ef
content_type: application/pdf
creator: dernst
date_created: 2023-05-02T07:24:55Z
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oa: 1
oa_version: Published Version
pmid: 1
publication: Nucleus
publication_identifier:
eissn:
- 1949-1042
issn:
- 1949-1034
publication_status: published
publisher: Taylor & Francis
quality_controlled: '1'
scopus_import: '1'
status: public
title: Lamin B1 overexpression alters chromatin organization and gene expression
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 14
year: '2023'
...
---
_id: '12885'
abstract:
- lang: eng
text: 'High-performance semiconductors rely upon precise control of heat and charge
transport. This can be achieved by precisely engineering defects in polycrystalline
solids. There are multiple approaches to preparing such polycrystalline semiconductors,
and the transformation of solution-processed colloidal nanoparticles is appealing
because colloidal nanoparticles combine low cost with structural and compositional
tunability along with rich surface chemistry. However, the multiple processes
from nanoparticle synthesis to the final bulk nanocomposites are very complex.
They involve nanoparticle purification, post-synthetic modifications, and finally
consolidation (thermal treatments and densification). All these properties dictate
the final material’s composition and microstructure, ultimately affecting its
functional properties. This thesis explores the synthesis, surface chemistry and
consolidation of colloidal semiconductor nanoparticles into dense solids. In particular,
the transformations that take place during these processes, and their effect on
the material’s transport properties are evaluated. '
acknowledged_ssus:
- _id: EM-Fac
- _id: NanoFab
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Mariano
full_name: Calcabrini, Mariano
id: 45D7531A-F248-11E8-B48F-1D18A9856A87
last_name: Calcabrini
orcid: 0000-0003-4566-5877
citation:
ama: 'Calcabrini M. Nanoparticle-based semiconductor solids: From synthesis to consolidation.
2023. doi:10.15479/at:ista:12885'
apa: 'Calcabrini, M. (2023). Nanoparticle-based semiconductor solids: From synthesis
to consolidation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12885'
chicago: 'Calcabrini, Mariano. “Nanoparticle-Based Semiconductor Solids: From Synthesis
to Consolidation.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12885.'
ieee: 'M. Calcabrini, “Nanoparticle-based semiconductor solids: From synthesis to
consolidation,” Institute of Science and Technology Austria, 2023.'
ista: 'Calcabrini M. 2023. Nanoparticle-based semiconductor solids: From synthesis
to consolidation. Institute of Science and Technology Austria.'
mla: 'Calcabrini, Mariano. Nanoparticle-Based Semiconductor Solids: From Synthesis
to Consolidation. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12885.'
short: 'M. Calcabrini, Nanoparticle-Based Semiconductor Solids: From Synthesis to
Consolidation, Institute of Science and Technology Austria, 2023.'
date_created: 2023-05-02T07:58:57Z
date_published: 2023-04-28T00:00:00Z
date_updated: 2023-08-14T07:25:26Z
day: '28'
ddc:
- '546'
- '541'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MaIb
doi: 10.15479/at:ista:12885
ec_funded: 1
file:
- access_level: closed
checksum: 9347b0e09425f56fdcede5d3528404dc
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: mcalcabr
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date_updated: 2023-05-02T07:43:18Z
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file_size: 99627036
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creator: mcalcabr
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date_updated: 2023-05-02T07:42:45Z
file_id: '12888'
file_name: Thesis_Calcabrini_pdfa.pdf
file_size: 8742220
relation: main_file
success: 1
file_date_updated: 2023-05-02T07:43:18Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '82'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
isbn:
- 978-3-99078-028-2
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10806'
relation: part_of_dissertation
status: public
- id: '10042'
relation: part_of_dissertation
status: public
- id: '12237'
relation: part_of_dissertation
status: public
- id: '9118'
relation: part_of_dissertation
status: public
- id: '10123'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
title: 'Nanoparticle-based semiconductor solids: From synthesis to consolidation'
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '12890'
abstract:
- lang: eng
text: We introduce a stochastic cellular automaton as a model for culture and border
formation. The model can be conceptualized as a game where the expansion rate
of cultures is quantified in terms of their area and perimeter in such a way that
approximately geometrically round cultures get a competitive advantage. We first
analyze the model with periodic boundary conditions, where we study how the model
can end up in a fixed state, i.e., freezes. Then we implement the model on the
European geography with mountains and rivers. We see how the model reproduces
some qualitative features of European culture formation, namely, that rivers and
mountains are more frequently borders between cultures, mountainous regions tend
to have higher cultural diversity, and the central European plain has less clear
cultural borders.
acknowledgement: Thanks to Kim Sneppen, Svend Krøjer, Peter Wildemann, Peter Rasmussen
and Kent Bækgaard Lauritsen for discussions and suggestions. FRK acknowledges support
from the Villum Foundation for support through the QMATH center of Excellence (Grant
No. 10059) and the Villum Young Investigator (Grant No. 25452) programs.
article_number: '054307'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Frederik Ravn
full_name: Klausen, Frederik Ravn
last_name: Klausen
- first_name: Asbjørn Bækgaard
full_name: Lauritsen, Asbjørn Bækgaard
id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1
last_name: Lauritsen
orcid: 0000-0003-4476-2288
citation:
ama: Klausen FR, Lauritsen AB. Stochastic cellular automaton model of culture formation.
Physical Review E. 2023;108(5). doi:10.1103/PhysRevE.108.054307
apa: Klausen, F. R., & Lauritsen, A. B. (2023). Stochastic cellular automaton
model of culture formation. Physical Review E. American Physical Society.
https://doi.org/10.1103/PhysRevE.108.054307
chicago: Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular
Automaton Model of Culture Formation.” Physical Review E. American Physical
Society, 2023. https://doi.org/10.1103/PhysRevE.108.054307.
ieee: F. R. Klausen and A. B. Lauritsen, “Stochastic cellular automaton model of
culture formation,” Physical Review E, vol. 108, no. 5. American Physical
Society, 2023.
ista: Klausen FR, Lauritsen AB. 2023. Stochastic cellular automaton model of culture
formation. Physical Review E. 108(5), 054307.
mla: Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular
Automaton Model of Culture Formation.” Physical Review E, vol. 108, no.
5, 054307, American Physical Society, 2023, doi:10.1103/PhysRevE.108.054307.
short: F.R. Klausen, A.B. Lauritsen, Physical Review E 108 (2023).
date_created: 2023-05-04T08:35:01Z
date_published: 2023-11-08T00:00:00Z
date_updated: 2023-11-13T07:47:30Z
day: '08'
department:
- _id: GradSch
- _id: RoSe
doi: 10.1103/PhysRevE.108.054307
external_id:
arxiv:
- '2305.02153'
intvolume: ' 108'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2305.02153
month: '11'
oa: 1
oa_version: Preprint
publication: Physical Review E
publication_identifier:
eissn:
- 2470-0053
issn:
- 2470-0045
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/FrederikRavnKlausen/model-for-culture-formation
record:
- id: '12869'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Stochastic cellular automaton model of culture formation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2023'
...
---
_id: '12891'
abstract:
- lang: eng
text: "The tight spatiotemporal coordination of signaling activity determining embryo\r\npatterning
and the physical processes driving embryo morphogenesis renders\r\nembryonic development
robust, such that key developmental processes can unfold\r\nrelatively normally
even outside of the full embryonic context. For instance, embryonic\r\nstem cell
cultures can recapitulate the hallmarks of gastrulation, i.e. break symmetry\r\nleading
to germ layer formation and morphogenesis, in a very reduced environment.\r\nThis
leads to questions on specific contributions of embryo-specific features, such
as\r\nthe presence of extraembryonic tissues, which are inherently involved in
gastrulation\r\nin the full embryonic context. To address this, we established
zebrafish embryonic\r\nexplants without the extraembryonic yolk cell, an important
player as a signaling\r\nsource and for morphogenesis during gastrulation, as
a model of ex vivo development.\r\nWe found that dorsal-marginal determinants
are required and sufficient in these\r\nexplants to form and pattern all three
germ layers. However, formation of tissues,\r\nwhich require the highest Nodal-signaling
levels, is variable, demonstrating a\r\ncontribution of extraembryonic tissues
for reaching peak Nodal signaling levels.\r\nBlastoderm explants also undergo
gastrulation-like axis elongation. We found that this\r\nelongation movement shows
hallmarks of oriented mesendoderm cell intercalations\r\ntypically associated
with dorsal tissues in the intact embryo. These are disrupted by\r\nuniform upregulation
of BMP signaling activity and concomitant explant ventralization,\r\nsuggesting
that tight spatial control of BMP signaling is a prerequisite for explant\r\nmorphogenesis.
This control is achieved by Nodal signaling, which is critical for\r\neffectively
downregulating BMP signaling in the mesendoderm, highlighting that Nodal\r\nsignaling
is not only directly required for mesendoderm cell fate specification and\r\nmorphogenesis,
but also by maintaining low levels of BMP signaling at the dorsal side.\r\nCollectively,
we provide insights into the capacity and organization of signaling and\r\nmorphogenetic
domains to recapitulate features of zebrafish gastrulation outside of\r\nthe full
embryonic context."
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Alexandra
full_name: Schauer, Alexandra
id: 30A536BA-F248-11E8-B48F-1D18A9856A87
last_name: Schauer
orcid: 0000-0001-7659-9142
citation:
ama: 'Schauer A. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic
tissues. 2023. doi:10.15479/at:ista:12891'
apa: 'Schauer, A. (2023). Mesendoderm formation in zebrafish gastrulation: The
role of extraembryonic tissues. Institute of Science and Technology Austria.
https://doi.org/10.15479/at:ista:12891'
chicago: 'Schauer, Alexandra. “Mesendoderm Formation in Zebrafish Gastrulation:
The Role of Extraembryonic Tissues.” Institute of Science and Technology Austria,
2023. https://doi.org/10.15479/at:ista:12891.'
ieee: 'A. Schauer, “Mesendoderm formation in zebrafish gastrulation: The role of
extraembryonic tissues,” Institute of Science and Technology Austria, 2023.'
ista: 'Schauer A. 2023. Mesendoderm formation in zebrafish gastrulation: The role
of extraembryonic tissues. Institute of Science and Technology Austria.'
mla: 'Schauer, Alexandra. Mesendoderm Formation in Zebrafish Gastrulation: The
Role of Extraembryonic Tissues. Institute of Science and Technology Austria,
2023, doi:10.15479/at:ista:12891.'
short: 'A. Schauer, Mesendoderm Formation in Zebrafish Gastrulation: The Role of
Extraembryonic Tissues, Institute of Science and Technology Austria, 2023.'
date_created: 2023-05-05T08:48:20Z
date_published: 2023-05-05T00:00:00Z
date_updated: 2023-08-21T06:25:48Z
day: '05'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: CaHe
doi: 10.15479/at:ista:12891
ec_funded: 1
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checksum: 59b0303dc483f40a96a610a90aab7ee9
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creator: aschauer
date_created: 2023-05-05T13:01:14Z
date_updated: 2023-05-05T13:01:14Z
embargo: 2024-05-05
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file_name: Thesis_Schauer_final.pdf
file_size: 31434230
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content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: aschauer
date_created: 2023-05-05T13:04:15Z
date_updated: 2023-05-05T13:04:15Z
file_id: '12908'
file_name: Thesis_Schauer_final.docx
file_size: 43809109
relation: source_file
file_date_updated: 2023-05-05T13:04:15Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa_version: Published Version
page: '190'
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
- _id: 26B1E39C-B435-11E9-9278-68D0E5697425
grant_number: '25239'
name: 'Mesendoderm specification in zebrafish: The role of extraembryonic tissues'
publication_identifier:
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8966'
relation: part_of_dissertation
status: public
- id: '7888'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
title: 'Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic
tissues'
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '12897'
abstract:
- lang: eng
text: "Inverse design problems in fabrication-aware shape optimization are typically
solved on discrete representations such as polygonal meshes. This thesis argues
that there are benefits to treating these problems in the same domain as human
designers, namely, the parametric one. One reason is that discretizing a parametric
model usually removes the capability of making further manual changes to the design,
because the human intent is captured by the shape parameters. Beyond this, knowledge
about a design problem can sometimes reveal a structure that is present in a smooth
representation, but is fundamentally altered by discretizing. In this case, working
in the parametric domain may even simplify the optimization task. We present two
lines of research that explore both of these aspects of fabrication-aware shape
optimization on parametric representations.\r\n\r\nThe first project studies the
design of plane elastic curves and Kirchhoff rods, which are common mathematical
models for describing the deformation of thin elastic rods such as beams, ribbons,
cables, and hair. Our main contribution is a characterization of all curved shapes
that can be attained by bending and twisting elastic rods having a stiffness that
is allowed to vary across the length. Elements like these can be manufactured
using digital fabrication devices such as 3d printers and digital cutters, and
have applications in free-form architecture and soft robotics.\r\n\r\nWe show
that the family of curved shapes that can be produced this way admits geometric
description that is concise and computationally convenient. In the case of plane
curves, the geometric description is intuitive enough to allow a designer to determine
whether a curved shape is physically achievable by visual inspection alone. We
also present shape optimization algorithms that convert a user-defined curve in
the plane or in three dimensions into the geometry of an elastic rod that will
naturally deform to follow this curve when its endpoints are attached to a support
structure. Implemented in an interactive software design tool, the rod geometry
is generated in real time as the user edits a curve and enables fast prototyping.
\r\n\r\nThe second project tackles the problem of general-purpose shape optimization
on CAD models using a novel variant of the extended finite element method (XFEM).
Our goal is the decoupling between the simulation mesh and the CAD model, so no
geometry-dependent meshing or remeshing needs to be performed when the CAD parameters
change during optimization. This is achieved by discretizing the embedding space
of the CAD model, and using a new high-accuracy numerical integration method to
enable XFEM on free-form elements bounded by the parametric surface patches of
the model. Our simulation is differentiable from the CAD parameters to the simulation
output, which enables us to use off-the-shelf gradient-based optimization procedures.
The result is a method that fits seamlessly into the CAD workflow because it works
on the same representation as the designer, enabling the alternation of manual
editing and fabrication-aware optimization at will."
acknowledged_ssus:
- _id: M-Shop
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Christian
full_name: Hafner, Christian
id: 400429CC-F248-11E8-B48F-1D18A9856A87
last_name: Hafner
citation:
ama: 'Hafner C. Inverse shape design with parametric representations: Kirchhoff
Rods and parametric surface models. 2023. doi:10.15479/at:ista:12897'
apa: 'Hafner, C. (2023). Inverse shape design with parametric representations:
Kirchhoff Rods and parametric surface models. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:12897'
chicago: 'Hafner, Christian. “Inverse Shape Design with Parametric Representations:
Kirchhoff Rods and Parametric Surface Models.” Institute of Science and Technology
Austria, 2023. https://doi.org/10.15479/at:ista:12897.'
ieee: 'C. Hafner, “Inverse shape design with parametric representations: Kirchhoff
Rods and parametric surface models,” Institute of Science and Technology Austria,
2023.'
ista: 'Hafner C. 2023. Inverse shape design with parametric representations: Kirchhoff
Rods and parametric surface models. Institute of Science and Technology Austria.'
mla: 'Hafner, Christian. Inverse Shape Design with Parametric Representations:
Kirchhoff Rods and Parametric Surface Models. Institute of Science and Technology
Austria, 2023, doi:10.15479/at:ista:12897.'
short: 'C. Hafner, Inverse Shape Design with Parametric Representations: Kirchhoff
Rods and Parametric Surface Models, Institute of Science and Technology Austria,
2023.'
date_created: 2023-05-05T10:40:14Z
date_published: 2023-05-05T00:00:00Z
date_updated: 2024-01-29T10:47:51Z
day: '05'
ddc:
- '516'
- '004'
- '518'
- '531'
degree_awarded: PhD
department:
- _id: GradSch
- _id: BeBi
doi: 10.15479/at:ista:12897
ec_funded: 1
file:
- access_level: open_access
checksum: cc2094e92fa27000b70eb4bfb76d6b5a
content_type: application/pdf
creator: chafner
date_created: 2023-05-11T10:43:20Z
date_updated: 2023-12-08T23:30:04Z
embargo: 2023-12-07
file_id: '12942'
file_name: thesis-hafner-2023may11-a2b.pdf
file_size: 50714445
relation: main_file
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checksum: a6b51334be2b81672357b1549afab40c
content_type: application/pdf
creator: chafner
date_created: 2023-05-11T10:43:44Z
date_updated: 2023-12-08T23:30:04Z
embargo_to: open_access
file_id: '12943'
file_name: thesis-release-form.pdf
file_size: 265319
relation: source_file
file_date_updated: 2023-12-08T23:30:04Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '180'
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication_identifier:
isbn:
- 978-3-99078-031-2
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9817'
relation: part_of_dissertation
status: public
- id: '7117'
relation: part_of_dissertation
status: public
- id: '13188'
relation: dissertation_contains
status: public
status: public
supervisor:
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
title: 'Inverse shape design with parametric representations: Kirchhoff Rods and parametric
surface models'
type: dissertation
user_id: 400429CC-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12900'
abstract:
- lang: eng
text: "About a 100 years ago, we discovered that our universe is inherently noisy,
that is, measuring any physical quantity with a precision beyond a certain point
is not possible because of an omnipresent inherent noise. We call this - the quantum
noise. Certain physical processes allow this quantum noise to get correlated in
conjugate physical variables. These quantum correlations can be used to go beyond
the potential of our inherently noisy universe and obtain a quantum advantage
over the classical applications. \r\n\r\nQuantum noise being inherent also means
that, at the fundamental level, the physical quantities are not well defined and
therefore, objects can stay in multiple states at the same time. For example,
the position of a particle not being well defined means that the particle is in
multiple positions at the same time. About 4 decades ago, we started exploring
the possibility of using objects which can be in multiple states at the same time
to increase the dimensionality in computation. Thus, the field of quantum computing
was born. We discovered that using quantum entanglement, a property closely related
to quantum correlations, can be used to speed up computation of certain problems,
such as factorisation of large numbers, faster than any known classical algorithm.
Thus began the pursuit to make quantum computers a reality. \r\n\r\nTill date,
we have explored quantum control over many physical systems including photons,
spins, atoms, ions and even simple circuits made up of superconducting material.
However, there persists one ubiquitous theme. The more readily a system interacts
with an external field or matter, the more easily we can control it. But this
also means that such a system can easily interact with a noisy environment and
quickly lose its coherence. Consequently, such systems like electron spins need
to be protected from the environment to ensure the longevity of their coherence.
Other systems like nuclear spins are naturally protected as they do not interact
easily with the environment. But, due to the same reason, it is harder to interact
with such systems. \r\n\r\nAfter decades of experimentation with various systems,
we are convinced that no one type of quantum system would be the best for all
the quantum applications. We would need hybrid systems which are all interconnected
- much like the current internet where all sorts of devices can all talk to each
other - but now for quantum devices. A quantum internet. \r\n\r\nOptical photons
are the best contenders to carry information for the quantum internet. They can
carry quantum information cheaply and without much loss - the same reasons which
has made them the backbone of our current internet. Following this direction,
many systems, like trapped ions, have already demonstrated successful quantum
links over a large distances using optical photons. However, some of the most
promising contenders for quantum computing which are based on microwave frequencies
have been left behind. This is because high energy optical photons can adversely
affect fragile low-energy microwave systems. \r\n\r\nIn this thesis, we present
substantial progress on this missing quantum link between microwave and optics
using electrooptical nonlinearities in lithium niobate. The nonlinearities are
enhanced by using resonant cavities for all the involved modes leading to observation
of strong direct coupling between optical and microwave frequencies. With this
strong coupling we are not only able to achieve almost 100\\% internal conversion
efficiency with low added noise, thus presenting a quantum-enabled transducer,
but also we are able to observe novel effects such as cooling of a microwave mode
using optics. The strong coupling regime also leads to direct observation of dynamical
backaction effect between microwave and optical frequencies which are studied
in detail here. Finally, we also report first observation of microwave-optics
entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level.
\r\nWith this new bridge between microwave and optics, the microwave-based quantum
technologies can finally be a part of a quantum network which is based on optical
photons - putting us one step closer to a future with quantum internet. "
acknowledged_ssus:
- _id: M-Shop
- _id: SSU
- _id: NanoFab
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Rishabh
full_name: Sahu, Rishabh
id: 47D26E34-F248-11E8-B48F-1D18A9856A87
last_name: Sahu
orcid: 0000-0001-6264-2162
citation:
ama: Sahu R. Cavity quantum electrooptics. 2023. doi:10.15479/at:ista:12900
apa: Sahu, R. (2023). Cavity quantum electrooptics. Institute of Science
and Technology Austria. https://doi.org/10.15479/at:ista:12900
chicago: Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and
Technology Austria, 2023. https://doi.org/10.15479/at:ista:12900.
ieee: R. Sahu, “Cavity quantum electrooptics,” Institute of Science and Technology
Austria, 2023.
ista: Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology
Austria.
mla: Sahu, Rishabh. Cavity Quantum Electrooptics. Institute of Science and
Technology Austria, 2023, doi:10.15479/at:ista:12900.
short: R. Sahu, Cavity Quantum Electrooptics, Institute of Science and Technology
Austria, 2023.
date_created: 2023-05-05T11:08:50Z
date_published: 2023-05-05T00:00:00Z
date_updated: 2024-10-29T09:11:05Z
day: '05'
ddc:
- '537'
- '535'
- '539'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoFi
doi: 10.15479/at:ista:12900
ec_funded: 1
file:
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checksum: 8cbdab9c37ee55e591092a6f66b272c4
content_type: application/x-zip-compressed
creator: rsahu
date_created: 2023-05-09T08:45:14Z
date_updated: 2023-06-06T22:30:03Z
embargo_to: open_access
file_id: '12928'
file_name: thesis.zip
file_size: 36767177
relation: source_file
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checksum: 439659ead46618147309be39d9dd5a8c
content_type: application/pdf
creator: rsahu
date_created: 2023-05-09T08:51:17Z
date_updated: 2023-07-06T11:37:40Z
file_id: '12929'
file_name: thesis_pdfa_final.pdf
file_size: 17501990
relation: main_file
file_date_updated: 2023-07-06T11:37:40Z
has_accepted_license: '1'
keyword:
- quantum optics
- electrooptics
- quantum networks
- quantum communication
- transduction
language:
- iso: eng
month: '05'
oa_version: Published Version
page: '190'
project:
- _id: 26336814-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '758053'
name: A Fiber Optic Transceiver for Superconducting Qubits
- _id: 9B868D20-BA93-11EA-9121-9846C619BF3A
call_identifier: H2020
grant_number: '899354'
name: Quantum Local Area Networks with Superconducting Qubits
- _id: bdb108fd-d553-11ed-ba76-83dc74a9864f
name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration
of Superconducting Quantum Circuits
publication_identifier:
isbn:
- 978-3-99078-030-5
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9114'
relation: part_of_dissertation
status: public
- id: '10924'
relation: part_of_dissertation
status: public
- id: '13175'
relation: new_edition
status: public
status: public
supervisor:
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
title: Cavity quantum electrooptics
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '12911'
abstract:
- lang: eng
text: 'This paper establishes new connections between many-body quantum systems,
One-body Reduced Density Matrices Functional Theory (1RDMFT) and Optimal Transport
(OT), by interpreting the problem of computing the ground-state energy of a finite-dimensional
composite quantum system at positive temperature as a non-commutative entropy
regularized Optimal Transport problem. We develop a new approach to fully characterize
the dual-primal solutions in such non-commutative setting. The mathematical formalism
is particularly relevant in quantum chemistry: numerical realizations of the many-electron
ground-state energy can be computed via a non-commutative version of Sinkhorn
algorithm. Our approach allows to prove convergence and robustness of this algorithm,
which, to our best knowledge, were unknown even in the two marginal case. Our
methods are based on a priori estimates in the dual problem, which we believe
to be of independent interest. Finally, the above results are extended in 1RDMFT
setting, where bosonic or fermionic symmetry conditions are enforced on the problem.'
acknowledgement: "This work started when A.G. was visiting the Erwin Schrödinger Institute
and then continued when D.F. and L.P visited the Theoretical Chemistry Department
of the Vrije Universiteit Amsterdam. The authors thank the hospitality of both places
and, especially, P. Gori-Giorgi and K. Giesbertz for fruitful discussions and literature
suggestions in the early state of the project. The authors also thank J. Maas and
R. Seiringer for their feedback and useful comments to a first draft of the article.
Finally, we acknowledge the high quality review done by the anonymous referee of
our paper, who we would like to thank for the excellent work and constructive feedback.\r\nD.F
acknowledges support by the European Research Council (ERC) under the European Union's
Horizon 2020 research and innovation programme (grant agreements No 716117 and No
694227). A.G. acknowledges funding by the HORIZON EUROPE European Research Council
under H2020/MSCA-IF “OTmeetsDFT” [grant ID: 795942] as well as partial support of
his research by the Canada Research Chairs Program (ID 2021-00234) and Natural Sciences
and Engineering Research Council of Canada, RGPIN-2022-05207. L.P. acknowledges
support by the Austrian Science Fund (FWF), grants No W1245 and No F65, and by the
Deutsche Forschungsgemeinschaft (DFG) - Project number 390685813."
article_number: '109963'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Dario
full_name: Feliciangeli, Dario
id: 41A639AA-F248-11E8-B48F-1D18A9856A87
last_name: Feliciangeli
orcid: 0000-0003-0754-8530
- first_name: Augusto
full_name: Gerolin, Augusto
last_name: Gerolin
- first_name: Lorenzo
full_name: Portinale, Lorenzo
id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87
last_name: Portinale
citation:
ama: Feliciangeli D, Gerolin A, Portinale L. A non-commutative entropic optimal
transport approach to quantum composite systems at positive temperature. Journal
of Functional Analysis. 2023;285(4). doi:10.1016/j.jfa.2023.109963
apa: Feliciangeli, D., Gerolin, A., & Portinale, L. (2023). A non-commutative
entropic optimal transport approach to quantum composite systems at positive temperature.
Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2023.109963
chicago: Feliciangeli, Dario, Augusto Gerolin, and Lorenzo Portinale. “A Non-Commutative
Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.”
Journal of Functional Analysis. Elsevier, 2023. https://doi.org/10.1016/j.jfa.2023.109963.
ieee: D. Feliciangeli, A. Gerolin, and L. Portinale, “A non-commutative entropic
optimal transport approach to quantum composite systems at positive temperature,”
Journal of Functional Analysis, vol. 285, no. 4. Elsevier, 2023.
ista: Feliciangeli D, Gerolin A, Portinale L. 2023. A non-commutative entropic optimal
transport approach to quantum composite systems at positive temperature. Journal
of Functional Analysis. 285(4), 109963.
mla: Feliciangeli, Dario, et al. “A Non-Commutative Entropic Optimal Transport Approach
to Quantum Composite Systems at Positive Temperature.” Journal of Functional
Analysis, vol. 285, no. 4, 109963, Elsevier, 2023, doi:10.1016/j.jfa.2023.109963.
short: D. Feliciangeli, A. Gerolin, L. Portinale, Journal of Functional Analysis
285 (2023).
date_created: 2023-05-07T22:01:02Z
date_published: 2023-08-15T00:00:00Z
date_updated: 2023-11-14T13:21:01Z
day: '15'
department:
- _id: RoSe
- _id: JaMa
doi: 10.1016/j.jfa.2023.109963
ec_funded: 1
external_id:
arxiv:
- '2106.11217'
isi:
- '000990804300001'
intvolume: ' 285'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2106.11217
month: '08'
oa: 1
oa_version: Preprint
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: 260482E2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: ' F06504'
name: Taming Complexity in Partial Di erential Systems
publication: Journal of Functional Analysis
publication_identifier:
eissn:
- 1096-0783
issn:
- 0022-1236
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '9792'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: A non-commutative entropic optimal transport approach to quantum composite
systems at positive temperature
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 285
year: '2023'
...
---
_id: '12912'
abstract:
- lang: eng
text: The chemical potential of adsorbed or confined fluids provides insight into
their unique thermodynamic properties and determines adsorption isotherms. However,
it is often difficult to compute this quantity from atomistic simulations using
existing statistical mechanical methods. We introduce a computational framework
that utilizes static structure factors, thermodynamic integration, and free energy
perturbation for calculating the absolute chemical potential of fluids. For demonstration,
we apply the method to compute the adsorption isotherms of carbon dioxide in a
metal-organic framework and water in carbon nanotubes.
acknowledgement: We thank Aleks Reinhardt and Daan Frenkel for their insightful comments
and suggestions on the article. B.C. acknowledges the resources provided by the
Cambridge Tier-2 system operated by the University of Cambridge Research Computing
Service funded by EPSRC Tier-2 capital Grant No. EP/P020259/1.
article_number: '161101 '
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Rochus
full_name: Schmid, Rochus
last_name: Schmid
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: Schmid R, Cheng B. Computing chemical potentials of adsorbed or confined fluids.
The Journal of Chemical Physics. 2023;158(16). doi:10.1063/5.0146711
apa: Schmid, R., & Cheng, B. (2023). Computing chemical potentials of adsorbed
or confined fluids. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0146711
chicago: Schmid, Rochus, and Bingqing Cheng. “Computing Chemical Potentials of Adsorbed
or Confined Fluids.” The Journal of Chemical Physics. AIP Publishing, 2023.
https://doi.org/10.1063/5.0146711.
ieee: R. Schmid and B. Cheng, “Computing chemical potentials of adsorbed or confined
fluids,” The Journal of Chemical Physics, vol. 158, no. 16. AIP Publishing,
2023.
ista: Schmid R, Cheng B. 2023. Computing chemical potentials of adsorbed or confined
fluids. The Journal of Chemical Physics. 158(16), 161101.
mla: Schmid, Rochus, and Bingqing Cheng. “Computing Chemical Potentials of Adsorbed
or Confined Fluids.” The Journal of Chemical Physics, vol. 158, no. 16,
161101, AIP Publishing, 2023, doi:10.1063/5.0146711.
short: R. Schmid, B. Cheng, The Journal of Chemical Physics 158 (2023).
date_created: 2023-05-07T22:01:03Z
date_published: 2023-04-24T00:00:00Z
date_updated: 2023-08-01T14:34:49Z
day: '24'
ddc:
- '540'
department:
- _id: BiCh
doi: 10.1063/5.0146711
external_id:
arxiv:
- '2302.01297'
isi:
- '001010676000010'
pmid:
- '37093149'
file:
- access_level: open_access
checksum: 4ab8c965f2fa4e17920bfa846847f137
content_type: application/pdf
creator: dernst
date_created: 2023-05-08T07:44:49Z
date_updated: 2023-05-08T07:44:49Z
file_id: '12918'
file_name: 2023_JourChemicalPhysics_Schmid.pdf
file_size: 6499468
relation: main_file
success: 1
file_date_updated: 2023-05-08T07:44:49Z
has_accepted_license: '1'
intvolume: ' 158'
isi: 1
issue: '16'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/BingqingCheng/mu-adsorption
- relation: software
url: https://github.com/BingqingCheng/S0
scopus_import: '1'
status: public
title: Computing chemical potentials of adsorbed or confined fluids
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: 158
year: '2023'
...
---
_id: '12913'
abstract:
- lang: eng
text: The coexistence of gate-tunable superconducting, magnetic and topological
orders in magic-angle twisted bilayer graphene provides opportunities for the
creation of hybrid Josephson junctions. Here we report the fabrication of gate-defined
symmetry-broken Josephson junctions in magic-angle twisted bilayer graphene, where
the weak link is gate-tuned close to the correlated insulator state with a moiré
filling factor of υ = −2. We observe a phase-shifted and asymmetric Fraunhofer
pattern with a pronounced magnetic hysteresis. Our theoretical calculations of
the junction weak link—with valley polarization and orbital magnetization—explain
most of these unconventional features. The effects persist up to the critical
temperature of 3.5 K, with magnetic hysteresis observed below 800 mK. We show
how the combination of magnetization and its current-induced magnetization switching
allows us to realise a programmable zero-field superconducting diode. Our results
represent a major advance towards the creation of future superconducting quantum
electronic devices.
acknowledgement: We are grateful for the fruitful discussions with Allan MacDonald
and Andrei Bernevig. D.K.E. acknowledges support from the Ministry of Economy and
Competitiveness of Spain through the “Severo Ochoa” program for Centers of Excellence
in R&D (SE5-0522), Fundació Privada Cellex, Fundació Privada Mir-Puig, the Generalitat
de Catalunya through the CERCA program, funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation program (grant
agreement no. 852927)” and the La Caixa Foundation. K.T.L. acknowledges the support
of the Ministry of Science and Technology of China and the HKRGC through grants
MOST20SC04, C6025-19G, 16310219, 16309718, and 16310520. J.D.M. acknowledges support
from the INPhINIT ‘la Caixa’ Foundation (ID 100010434) fellowship program (LCF/BQ/DI19/11730021).
Y.M.X. acknowledges the support of HKRGC through Grant No. PDFS2223-6S01.
article_number: '2396'
article_processing_charge: No
article_type: original
author:
- first_name: J.
full_name: Díez-Mérida, J.
last_name: Díez-Mérida
- first_name: A.
full_name: Díez-Carlón, A.
last_name: Díez-Carlón
- first_name: S. Y.
full_name: Yang, S. Y.
last_name: Yang
- first_name: Y. M.
full_name: Xie, Y. M.
last_name: Xie
- first_name: X. J.
full_name: Gao, X. J.
last_name: Gao
- first_name: Jorden L
full_name: Senior, Jorden L
id: 5479D234-2D30-11EA-89CC-40953DDC885E
last_name: Senior
- first_name: K.
full_name: Watanabe, K.
last_name: Watanabe
- first_name: T.
full_name: Taniguchi, T.
last_name: Taniguchi
- first_name: X.
full_name: Lu, X.
last_name: Lu
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: K. T.
full_name: Law, K. T.
last_name: Law
- first_name: Dmitri K.
full_name: Efetov, Dmitri K.
last_name: Efetov
citation:
ama: Díez-Mérida J, Díez-Carlón A, Yang SY, et al. Symmetry-broken Josephson junctions
and superconducting diodes in magic-angle twisted bilayer graphene. Nature
Communications. 2023;14. doi:10.1038/s41467-023-38005-7
apa: Díez-Mérida, J., Díez-Carlón, A., Yang, S. Y., Xie, Y. M., Gao, X. J., Senior,
J. L., … Efetov, D. K. (2023). Symmetry-broken Josephson junctions and superconducting
diodes in magic-angle twisted bilayer graphene. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-023-38005-7
chicago: Díez-Mérida, J., A. Díez-Carlón, S. Y. Yang, Y. M. Xie, X. J. Gao, Jorden
L Senior, K. Watanabe, et al. “Symmetry-Broken Josephson Junctions and Superconducting
Diodes in Magic-Angle Twisted Bilayer Graphene.” Nature Communications.
Springer Nature, 2023. https://doi.org/10.1038/s41467-023-38005-7.
ieee: J. Díez-Mérida et al., “Symmetry-broken Josephson junctions and superconducting
diodes in magic-angle twisted bilayer graphene,” Nature Communications,
vol. 14. Springer Nature, 2023.
ista: Díez-Mérida J, Díez-Carlón A, Yang SY, Xie YM, Gao XJ, Senior JL, Watanabe
K, Taniguchi T, Lu X, Higginbotham AP, Law KT, Efetov DK. 2023. Symmetry-broken
Josephson junctions and superconducting diodes in magic-angle twisted bilayer
graphene. Nature Communications. 14, 2396.
mla: Díez-Mérida, J., et al. “Symmetry-Broken Josephson Junctions and Superconducting
Diodes in Magic-Angle Twisted Bilayer Graphene.” Nature Communications,
vol. 14, 2396, Springer Nature, 2023, doi:10.1038/s41467-023-38005-7.
short: J. Díez-Mérida, A. Díez-Carlón, S.Y. Yang, Y.M. Xie, X.J. Gao, J.L. Senior,
K. Watanabe, T. Taniguchi, X. Lu, A.P. Higginbotham, K.T. Law, D.K. Efetov, Nature
Communications 14 (2023).
date_created: 2023-05-07T22:01:03Z
date_published: 2023-04-26T00:00:00Z
date_updated: 2023-08-01T14:34:00Z
day: '26'
ddc:
- '530'
department:
- _id: AnHi
doi: 10.1038/s41467-023-38005-7
external_id:
isi:
- '000979744000004'
pmid:
- '37100775'
file:
- access_level: open_access
checksum: a778105665c10beb2354c92d2b295115
content_type: application/pdf
creator: dernst
date_created: 2023-05-08T07:26:40Z
date_updated: 2023-05-08T07:26:40Z
file_id: '12917'
file_name: 2023_NatureComm_DiezMerida.pdf
file_size: 1405588
relation: main_file
success: 1
file_date_updated: 2023-05-08T07:26:40Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '04'
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: Symmetry-broken Josephson junctions and superconducting diodes in magic-angle
twisted bilayer graphene
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: 14
year: '2023'
...
---
_id: '12914'
abstract:
- lang: eng
text: We numerically study two methods of measuring tunneling times using a quantum
clock. In the conventional method using the Larmor clock, we show that the Larmor
tunneling time can be shorter for higher tunneling barriers. In the second method,
we study the probability of a spin-flip of a particle when it is transmitted through
a potential barrier including a spatially rotating field interacting with its
spin. According to the adiabatic theorem, the probability depends on the velocity
of the particle inside the barrier. It is numerically observed that the probability
increases for higher barriers, which is consistent with the result obtained by
the Larmor clock. By comparing outcomes for different initial spin states, we
suggest that one of the main causes of the apparent decrease in the tunneling
time can be the filtering effect occurring at the end of the barrier.
acknowledgement: We thank W. H. Zurek, N. Sinitsyn, M. O. Scully, M. Arndt, and C.
H. Marrows for helpful discussions. F.S. acknowledges support from the Los Alamos
National Laboratory LDRD program under Project No. 20230049DR and the Center for
Nonlinear Studies. F.S. also thanks the European Union’s Horizon 2020 research and
innovation program under the Marie Skłodowska-Curie Grant No. 754411 for support.
W.G.U. thanks the Natural Science and Engineering Research Council of Canada, the
Hagler Institute of Texas A&M University, the Helmholz Inst HZDR, Germany for support
while this work was being done.
article_number: '042216'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Fumika
full_name: Suzuki, Fumika
id: 650C99FC-1079-11EA-A3C0-73AE3DDC885E
last_name: Suzuki
orcid: 0000-0003-4982-5970
- first_name: William G.
full_name: Unruh, William G.
last_name: Unruh
citation:
ama: Suzuki F, Unruh WG. Numerical quantum clock simulations for measuring tunneling
times. Physical Review A. 2023;107(4). doi:10.1103/PhysRevA.107.042216
apa: Suzuki, F., & Unruh, W. G. (2023). Numerical quantum clock simulations
for measuring tunneling times. Physical Review A. American Physical Society.
https://doi.org/10.1103/PhysRevA.107.042216
chicago: Suzuki, Fumika, and William G. Unruh. “Numerical Quantum Clock Simulations
for Measuring Tunneling Times.” Physical Review A. American Physical Society,
2023. https://doi.org/10.1103/PhysRevA.107.042216.
ieee: F. Suzuki and W. G. Unruh, “Numerical quantum clock simulations for measuring
tunneling times,” Physical Review A, vol. 107, no. 4. American Physical
Society, 2023.
ista: Suzuki F, Unruh WG. 2023. Numerical quantum clock simulations for measuring
tunneling times. Physical Review A. 107(4), 042216.
mla: Suzuki, Fumika, and William G. Unruh. “Numerical Quantum Clock Simulations
for Measuring Tunneling Times.” Physical Review A, vol. 107, no. 4, 042216,
American Physical Society, 2023, doi:10.1103/PhysRevA.107.042216.
short: F. Suzuki, W.G. Unruh, Physical Review A 107 (2023).
date_created: 2023-05-07T22:01:03Z
date_published: 2023-04-20T00:00:00Z
date_updated: 2023-08-01T14:33:21Z
day: '20'
department:
- _id: MiLe
doi: 10.1103/PhysRevA.107.042216
ec_funded: 1
external_id:
arxiv:
- '2207.13130'
isi:
- '000975799300006'
intvolume: ' 107'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2207.13130
month: '04'
oa: 1
oa_version: Preprint
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Physical Review A
publication_identifier:
eissn:
- 2469-9934
issn:
- 2469-9926
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Numerical quantum clock simulations for measuring tunneling times
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 107
year: '2023'
...
---
_id: '12915'
abstract:
- lang: eng
text: Cu2–xS and Cu2–xSe have recently been reported as promising thermoelectric
(TE) materials for medium-temperature applications. In contrast, Cu2–xTe, another
member of the copper chalcogenide family, typically exhibits low Seebeck coefficients
that limit its potential to achieve a superior thermoelectric figure of merit,
zT, particularly in the low-temperature range where this material could be effective.
To address this, we investigated the TE performance of Cu1.5–xTe–Cu2Se nanocomposites
by consolidating surface-engineered Cu1.5Te nanocrystals. This surface engineering
strategy allows for precise adjustment of Cu/Te ratios and results in a reversible
phase transition at around 600 K in Cu1.5–xTe–Cu2Se nanocomposites, as systematically
confirmed by in situ high-temperature X-ray diffraction combined with differential
scanning calorimetry analysis. The phase transition leads to a conversion from
metallic-like to semiconducting-like TE properties. Additionally, a layer of Cu2Se
generated around Cu1.5–xTe nanoparticles effectively inhibits Cu1.5–xTe grain
growth, minimizing thermal conductivity and decreasing hole concentration. These
properties indicate that copper telluride based compounds have a promising thermoelectric
potential, translated into a high dimensionless zT of 1.3 at 560 K.
acknowledgement: 'The authors acknowledge support from the projects ENE2016-77798-C4-3-R
and NANOGEN (PID2020-116093RB-C43) funded by MCIN/AEI/10.13039/501100011033/and
by “ERDF A way of making Europe”, and by the “European Union”. K.X. and B.N. thank
the China Scholarship Council (CSC) for scholarship support. The authors acknowledge
funding from Generalitat de Catalunya 2017 SGR 327 and 2017 SGR 1246. ICN2 is supported
by the Severo Ochoa program from the Spanish MCIN/AEI (Grant No.: CEX2021-001214-S).
IREC and ICN2 are funded by the CERCA Programme/Generalitat de Catalunya. J.L. acknowledges
support from the Natural Science Foundation of Sichuan province (2022NSFSC1229).
Part of the present work was performed in the frameworks of Universitat de Barcelona
Nanoscience Ph.D. program and Universitat Autònoma de Barcelona Materials Science
Ph.D. program. Y.L. acknowledges funding from the National Natural Science Foundation
of China (Grant No. 22209034) and the Innovation and Entrepreneurship Project of
Overseas Returnees in Anhui Province (Grants No. 2022LCX002). K.H.L. acknowledges
the financial support of the National Natural Science Foundation of China (Grant
No. 22208293).'
article_processing_charge: No
article_type: original
author:
- first_name: Congcong
full_name: Xing, Congcong
last_name: Xing
- first_name: Yu
full_name: Zhang, Yu
last_name: Zhang
- first_name: Ke
full_name: Xiao, Ke
last_name: Xiao
- first_name: Xu
full_name: Han, Xu
last_name: Han
- first_name: Yu
full_name: Liu, Yu
id: 2A70014E-F248-11E8-B48F-1D18A9856A87
last_name: Liu
orcid: 0000-0001-7313-6740
- first_name: Bingfei
full_name: Nan, Bingfei
last_name: 'Nan'
- first_name: Maria Garcia
full_name: Ramon, Maria Garcia
id: 1ffff7cd-ed76-11ed-8d5f-be5e7c364eb9
last_name: Ramon
- first_name: Khak Ho
full_name: Lim, Khak Ho
last_name: Lim
- first_name: Junshan
full_name: Li, Junshan
last_name: Li
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Bed
full_name: Poudel, Bed
last_name: Poudel
- first_name: Amin
full_name: Nozariasbmarz, Amin
last_name: Nozariasbmarz
- first_name: Wenjie
full_name: Li, Wenjie
last_name: Li
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: Xing C, Zhang Y, Xiao K, et al. Thermoelectric performance of surface-engineered
Cu1.5–xTe–Cu2Se nanocomposites. ACS Nano. 2023;17(9):8442-8452. doi:10.1021/acsnano.3c00495
apa: Xing, C., Zhang, Y., Xiao, K., Han, X., Liu, Y., Nan, B., … Cabot, A. (2023).
Thermoelectric performance of surface-engineered Cu1.5–xTe–Cu2Se nanocomposites.
ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.3c00495
chicago: Xing, Congcong, Yu Zhang, Ke Xiao, Xu Han, Yu Liu, Bingfei Nan, Maria Garcia
Ramon, et al. “Thermoelectric Performance of Surface-Engineered Cu1.5–XTe–Cu2Se
Nanocomposites.” ACS Nano. American Chemical Society, 2023. https://doi.org/10.1021/acsnano.3c00495.
ieee: C. Xing et al., “Thermoelectric performance of surface-engineered Cu1.5–xTe–Cu2Se
nanocomposites,” ACS Nano, vol. 17, no. 9. American Chemical Society, pp.
8442–8452, 2023.
ista: Xing C, Zhang Y, Xiao K, Han X, Liu Y, Nan B, Ramon MG, Lim KH, Li J, Arbiol
J, Poudel B, Nozariasbmarz A, Li W, Ibáñez M, Cabot A. 2023. Thermoelectric performance
of surface-engineered Cu1.5–xTe–Cu2Se nanocomposites. ACS Nano. 17(9), 8442–8452.
mla: Xing, Congcong, et al. “Thermoelectric Performance of Surface-Engineered Cu1.5–XTe–Cu2Se
Nanocomposites.” ACS Nano, vol. 17, no. 9, American Chemical Society, 2023,
pp. 8442–52, doi:10.1021/acsnano.3c00495.
short: C. Xing, Y. Zhang, K. Xiao, X. Han, Y. Liu, B. Nan, M.G. Ramon, K.H. Lim,
J. Li, J. Arbiol, B. Poudel, A. Nozariasbmarz, W. Li, M. Ibáñez, A. Cabot, ACS
Nano 17 (2023) 8442–8452.
date_created: 2023-05-07T22:01:04Z
date_published: 2023-05-09T00:00:00Z
date_updated: 2023-10-04T11:29:22Z
day: '09'
department:
- _id: MaIb
doi: 10.1021/acsnano.3c00495
external_id:
isi:
- '000976063200001'
pmid:
- '37071412'
intvolume: ' 17'
isi: 1
issue: '9'
language:
- iso: eng
month: '05'
oa_version: None
page: 8442-8452
pmid: 1
publication: ACS Nano
publication_identifier:
eissn:
- 1936-086X
issn:
- 1936-0851
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Thermoelectric performance of surface-engineered Cu1.5–xTe–Cu2Se nanocomposites
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2023'
...
---
_id: '12916'
abstract:
- lang: eng
text: "We apply a variant of the square-sieve to produce an upper bound for the
number of rational points of bounded height on a family of surfaces that admit
a fibration over P1 whose general fibre is a hyperelliptic curve. The implied
constant does not depend on the coefficients of the polynomial defining the surface.\r\n"
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Dante
full_name: Bonolis, Dante
id: 6A459894-5FDD-11E9-AF35-BB24E6697425
last_name: Bonolis
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
citation:
ama: Bonolis D, Browning TD. Uniform bounds for rational points on hyperelliptic
fibrations. Annali della Scuola Normale Superiore di Pisa - Classe di Scienze.
2023;24(1):173-204. doi:10.2422/2036-2145.202010_018
apa: Bonolis, D., & Browning, T. D. (2023). Uniform bounds for rational points
on hyperelliptic fibrations. Annali Della Scuola Normale Superiore Di Pisa
- Classe Di Scienze. Scuola Normale Superiore - Edizioni della Normale. https://doi.org/10.2422/2036-2145.202010_018
chicago: Bonolis, Dante, and Timothy D Browning. “Uniform Bounds for Rational Points
on Hyperelliptic Fibrations.” Annali Della Scuola Normale Superiore Di Pisa
- Classe Di Scienze. Scuola Normale Superiore - Edizioni della Normale, 2023.
https://doi.org/10.2422/2036-2145.202010_018.
ieee: D. Bonolis and T. D. Browning, “Uniform bounds for rational points on hyperelliptic
fibrations,” Annali della Scuola Normale Superiore di Pisa - Classe di Scienze,
vol. 24, no. 1. Scuola Normale Superiore - Edizioni della Normale, pp. 173–204,
2023.
ista: Bonolis D, Browning TD. 2023. Uniform bounds for rational points on hyperelliptic
fibrations. Annali della Scuola Normale Superiore di Pisa - Classe di Scienze.
24(1), 173–204.
mla: Bonolis, Dante, and Timothy D. Browning. “Uniform Bounds for Rational Points
on Hyperelliptic Fibrations.” Annali Della Scuola Normale Superiore Di Pisa
- Classe Di Scienze, vol. 24, no. 1, Scuola Normale Superiore - Edizioni della
Normale, 2023, pp. 173–204, doi:10.2422/2036-2145.202010_018.
short: D. Bonolis, T.D. Browning, Annali Della Scuola Normale Superiore Di Pisa
- Classe Di Scienze 24 (2023) 173–204.
date_created: 2023-05-07T22:01:04Z
date_published: 2023-02-16T00:00:00Z
date_updated: 2023-10-18T06:54:30Z
day: '16'
department:
- _id: TiBr
doi: 10.2422/2036-2145.202010_018
external_id:
arxiv:
- '2007.14182'
intvolume: ' 24'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2007.14182
month: '02'
oa: 1
oa_version: Preprint
page: 173-204
publication: Annali della Scuola Normale Superiore di Pisa - Classe di Scienze
publication_identifier:
eissn:
- 2036-2145
issn:
- 0391-173X
publication_status: published
publisher: Scuola Normale Superiore - Edizioni della Normale
quality_controlled: '1'
scopus_import: '1'
status: public
title: Uniform bounds for rational points on hyperelliptic fibrations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2023'
...
---
_id: '12933'
abstract:
- lang: eng
text: Datasets of the publication "Sex-specific estimation of cis and trans regulation
of gene expression in heads and gonads of Drosophila melanogaster".
article_processing_charge: No
author:
- first_name: Gemma
full_name: Puixeu Sala, Gemma
id: 33AB266C-F248-11E8-B48F-1D18A9856A87
last_name: Puixeu Sala
orcid: 0000-0001-8330-1754
citation:
ama: 'Puixeu Sala G. Data from: Sex-specific estimation of cis and trans regulation
of gene expression in heads and gonads of Drosophila melanogaster. 2023. doi:10.15479/AT:ISTA:12933'
apa: 'Puixeu Sala, G. (2023). Data from: Sex-specific estimation of cis and trans
regulation of gene expression in heads and gonads of Drosophila melanogaster.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12933'
chicago: 'Puixeu Sala, Gemma. “Data from: Sex-Specific Estimation of Cis and Trans
Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12933.'
ieee: 'G. Puixeu Sala, “Data from: Sex-specific estimation of cis and trans regulation
of gene expression in heads and gonads of Drosophila melanogaster.” Institute
of Science and Technology Austria, 2023.'
ista: 'Puixeu Sala G. 2023. Data from: Sex-specific estimation of cis and trans
regulation of gene expression in heads and gonads of Drosophila melanogaster,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:12933.'
mla: 'Puixeu Sala, Gemma. Data from: Sex-Specific Estimation of Cis and Trans
Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.
Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12933.'
short: G. Puixeu Sala, (2023).
contributor:
- first_name: Ariana
id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
last_name: Macon
- first_name: Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
date_created: 2023-05-10T10:00:49Z
date_published: 2023-05-15T00:00:00Z
date_updated: 2023-12-13T12:15:36Z
day: '15'
ddc:
- '570'
department:
- _id: GradSch
- _id: NiBa
- _id: BeVi
doi: 10.15479/AT:ISTA:12933
file:
- access_level: open_access
checksum: 0ba0bcd0bb8b18d84792136a4370df90
content_type: text/csv
creator: gpuixeus
date_created: 2023-05-10T09:41:43Z
date_updated: 2023-05-10T09:41:43Z
file_id: '12934'
file_name: Dataset_S1.csv
file_size: 8029982
relation: main_file
success: 1
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checksum: a62aa9a6d4904e0fdb699cf752640863
content_type: text/csv
creator: gpuixeus
date_created: 2023-05-10T09:41:43Z
date_updated: 2023-05-10T09:41:43Z
file_id: '12935'
file_name: Dataset_S2.csv
file_size: 13667640
relation: main_file
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checksum: e20ea7f4f8a9bdf1b3849a44664ae58b
content_type: text/csv
creator: gpuixeus
date_created: 2023-05-10T09:41:48Z
date_updated: 2023-05-10T09:41:48Z
file_id: '12936'
file_name: Dataset_S3.csv
file_size: 8369141
relation: main_file
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checksum: f6156e5fc44446c907ddd0d7289d4cf8
content_type: text/csv
creator: gpuixeus
date_created: 2023-05-10T09:41:50Z
date_updated: 2023-05-10T09:41:50Z
file_id: '12937'
file_name: Dataset_S4.csv
file_size: 19543247
relation: main_file
success: 1
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checksum: ae9f54c77a1c42b666ae6c1dfd33ac86
content_type: text/plain
creator: gpuixeus
date_created: 2023-05-11T12:50:18Z
date_updated: 2023-05-11T12:50:18Z
file_id: '12944'
file_name: readme.txt
file_size: 4566
relation: main_file
success: 1
file_date_updated: 2023-05-11T12:50:18Z
has_accepted_license: '1'
month: '05'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '14058'
relation: used_in_publication
status: public
- id: '14077'
relation: used_in_publication
status: public
status: public
title: 'Data from: Sex-specific estimation of cis and trans regulation of gene expression
in heads and gonads of Drosophila melanogaster'
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: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12945'
abstract:
- lang: eng
text: "basic data for use in code for experimental data analysis for manuscript
under revision: \r\nDynamic pathogen detection and social feedback shape collective
hygiene in ants\r\nCasillas-Pérez B, Boďová K, Grasse AV, Tkačik G, Cremer S"
acknowledged_ssus:
- _id: LifeSc
acknowledgement: This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(Grant No. 771402; EPIDEMICSonCHIP) to SC, from the Scientific Grant Agency of the
Slovak Republic (Grant No. 1/0521/20) to KB, and the Human Frontier Science Program
(Grant No. RGP0065/2012) to GT.
article_processing_charge: No
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: 'Cremer S. Data from: “Dynamic pathogen detection and social feedback shape
collective hygiene in ants” . 2023. doi:10.15479/AT:ISTA:12945'
apa: 'Cremer, S. (2023). Data from: “Dynamic pathogen detection and social feedback
shape collective hygiene in ants” . Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:12945'
chicago: 'Cremer, Sylvia. “Data from: ‘Dynamic Pathogen Detection and Social Feedback
Shape Collective Hygiene in Ants’ .” Institute of Science and Technology Austria,
2023. https://doi.org/10.15479/AT:ISTA:12945.'
ieee: 'S. Cremer, “Data from: ‘Dynamic pathogen detection and social feedback shape
collective hygiene in ants’ .” Institute of Science and Technology Austria, 2023.'
ista: 'Cremer S. 2023. Data from: ‘Dynamic pathogen detection and social feedback
shape collective hygiene in ants’ , Institute of Science and Technology Austria,
10.15479/AT:ISTA:12945.'
mla: 'Cremer, Sylvia. Data from: “Dynamic Pathogen Detection and Social Feedback
Shape Collective Hygiene in Ants” . Institute of Science and Technology Austria,
2023, doi:10.15479/AT:ISTA:12945.'
short: S. Cremer, (2023).
contributor:
- contributor_type: data_collector
first_name: Barbara E
id: 351ED2AA-F248-11E8-B48F-1D18A9856A87
last_name: Casillas Perez
- contributor_type: data_collector
first_name: Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- contributor_type: researcher
first_name: Katarina
last_name: Bodova
- contributor_type: supervisor
first_name: Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
date_created: 2023-05-11T21:35:17Z
date_published: 2023-05-12T00:00:00Z
date_updated: 2023-08-07T13:09:09Z
day: '12'
ddc:
- '570'
department:
- _id: SyCr
doi: 10.15479/AT:ISTA:12945
file:
- access_level: open_access
checksum: 3eadf17fd59ad8c98bf10bf63061863c
content_type: application/zip
creator: scremer
date_created: 2023-05-12T08:04:04Z
date_updated: 2023-05-12T08:04:04Z
file_id: '12947'
file_name: Experimental_data.zip
file_size: 3414674
relation: main_file
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checksum: 1b5e8e01a0989154a76b44e6d8d68f89
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creator: scremer
date_created: 2023-05-12T08:04:08Z
date_updated: 2023-05-12T08:04:08Z
file_id: '12948'
file_name: README_Experimental_Data.md
file_size: 2113
relation: main_file
success: 1
file_date_updated: 2023-05-12T08:04:08Z
has_accepted_license: '1'
keyword:
- collective behavior
- host-pathogen interactions
- social immunity
- epidemiology
- social insects
- probabilistic modeling
month: '05'
oa: 1
oa_version: None
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '13127'
relation: used_in_publication
status: public
status: public
title: 'Data from: "Dynamic pathogen detection and social feedback shape collective
hygiene in ants" '
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12949'
abstract:
- lang: eng
text: The classical infinitesimal model is a simple and robust model for the inheritance
of quantitative traits. In this model, a quantitative trait is expressed as the
sum of a genetic and a non-genetic (environmental) component and the genetic component
of offspring traits within a family follows a normal distribution around the average
of the parents’ trait values, and has a variance that is independent of the trait
values of the parents. Although the trait distribution across the whole population
can be far from normal, the trait distributions within families are normally distributed
with a variance-covariance matrix that is determined entirely by that in the
ancestral population and the probabilities of identity determined by the pedigree.
Moreover, conditioning on some of the trait values within the pedigree has predictable
effects on the mean and variance within and between families. In previous work,
Barton et al. (2017), we showed that when trait values are determined by the sum
of a large number of Mendelian factors, each of small effect, one can justify
the infinitesimal model as limit of Mendelian inheritance. It was also shown that
under some forms of epistasis, trait values within a family are still normally
distributed.
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. The infinitesimal model with dominance. 2023. doi:10.15479/AT:ISTA:12949
apa: Barton, N. H. (2023). The infinitesimal model with dominance. Institute of
Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12949
chicago: Barton, Nicholas H. “The Infinitesimal Model with Dominance.” Institute
of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12949.
ieee: N. H. Barton, “The infinitesimal model with dominance.” Institute of Science
and Technology Austria, 2023.
ista: Barton NH. 2023. The infinitesimal model with dominance, Institute of Science
and Technology Austria, 10.15479/AT:ISTA:12949.
mla: Barton, Nicholas H. The Infinitesimal Model with Dominance. Institute
of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12949.
short: N.H. Barton, (2023).
contributor:
- contributor_type: researcher
first_name: Amandine
last_name: Veber
- contributor_type: researcher
first_name: Alison
last_name: Etheridge
date_created: 2023-05-13T09:49:09Z
date_published: 2023-05-13T00:00:00Z
date_updated: 2025-05-28T11:57:00Z
day: '13'
ddc:
- '576'
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status: public
title: The infinitesimal model with dominance
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...
---
_id: '12959'
abstract:
- lang: eng
text: "This paper deals with the large-scale behaviour of dynamical optimal transport
on Zd\r\n-periodic graphs with general lower semicontinuous and convex energy
densities. Our main contribution is a homogenisation result that describes the
effective behaviour of the discrete problems in terms of a continuous optimal
transport problem. The effective energy density can be explicitly expressed in
terms of a cell formula, which is a finite-dimensional convex programming problem
that depends non-trivially on the local geometry of the discrete graph and the
discrete energy density. Our homogenisation result is derived from a Γ\r\n-convergence
result for action functionals on curves of measures, which we prove under very
mild growth conditions on the energy density. We investigate the cell formula
in several cases of interest, including finite-volume discretisations of the Wasserstein
distance, where non-trivial limiting behaviour occurs."
acknowledgement: J.M. gratefully acknowledges support by the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(Grant Agreement No. 716117). J.M and L.P. also acknowledge support from the Austrian
Science Fund (FWF), grants No F65 and W1245. E.K. gratefully acknowledges support
by the German Research Foundation through the Hausdorff Center for Mathematics and
the Collaborative Research Center 1060. P.G. is partially funded by the Deutsche
Forschungsgemeinschaft (DFG, German Research Foundation)—350398276. We thank the
anonymous reviewer for the careful reading and for useful suggestions. Open access
funding provided by Austrian Science Fund (FWF).
article_number: '143'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Peter
full_name: Gladbach, Peter
last_name: Gladbach
- first_name: Eva
full_name: Kopfer, Eva
last_name: Kopfer
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
- first_name: Lorenzo
full_name: Portinale, Lorenzo
id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87
last_name: Portinale
citation:
ama: Gladbach P, Kopfer E, Maas J, Portinale L. Homogenisation of dynamical optimal
transport on periodic graphs. Calculus of Variations and Partial Differential
Equations. 2023;62(5). doi:10.1007/s00526-023-02472-z
apa: Gladbach, P., Kopfer, E., Maas, J., & Portinale, L. (2023). Homogenisation
of dynamical optimal transport on periodic graphs. Calculus of Variations and
Partial Differential Equations. Springer Nature. https://doi.org/10.1007/s00526-023-02472-z
chicago: Gladbach, Peter, Eva Kopfer, Jan Maas, and Lorenzo Portinale. “Homogenisation
of Dynamical Optimal Transport on Periodic Graphs.” Calculus of Variations
and Partial Differential Equations. Springer Nature, 2023. https://doi.org/10.1007/s00526-023-02472-z.
ieee: P. Gladbach, E. Kopfer, J. Maas, and L. Portinale, “Homogenisation of dynamical
optimal transport on periodic graphs,” Calculus of Variations and Partial Differential
Equations, vol. 62, no. 5. Springer Nature, 2023.
ista: Gladbach P, Kopfer E, Maas J, Portinale L. 2023. Homogenisation of dynamical
optimal transport on periodic graphs. Calculus of Variations and Partial Differential
Equations. 62(5), 143.
mla: Gladbach, Peter, et al. “Homogenisation of Dynamical Optimal Transport on Periodic
Graphs.” Calculus of Variations and Partial Differential Equations, vol.
62, no. 5, 143, Springer Nature, 2023, doi:10.1007/s00526-023-02472-z.
short: P. Gladbach, E. Kopfer, J. Maas, L. Portinale, Calculus of Variations and
Partial Differential Equations 62 (2023).
date_created: 2023-05-14T22:01:00Z
date_published: 2023-04-28T00:00:00Z
date_updated: 2023-10-04T11:34:49Z
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month: '04'
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oa_version: Published Version
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call_identifier: H2020
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name: Optimal Transport and Stochastic Dynamics
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publication: Calculus of Variations and Partial Differential Equations
publication_identifier:
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publisher: Springer Nature
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status: public
title: Homogenisation of dynamical optimal transport on periodic graphs
tmp:
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legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
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type: journal_article
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...