---
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '22247'
abstract:
- lang: eng
  text: "A linearly ordered (LO) k-colouring of a hypergraph is a colouring of its
    vertices with colours 1, …, k such that each edge contains a unique maximal colour.
    Deciding whether an input hypergraph admits LO k-colouring with a fixed number
    of colours is NP-complete (and in the special case of graphs, LO colouring coincides
    with the usual graph colouring).\r\nHere, we investigate the complexity of approximating
    the “linearly ordered chromatic number” of a hypergraph. We prove that the following
    promise problem is NP-complete: Given a 3-uniform hypergraph, distinguish between
    the case that it is LO 3-colourable, and the case that it is not even LO 4-colourable.
    We prove this result by a combination of algebraic, topological, and combinatorial
    methods, building on and extending a topological approach for studying approximate
    graph colouring introduced by Krokhin, Opršal, Wrochna, and Živný (2023)."
acknowledgement: "This research was supported by the Charles University project PRIMUS/21/SCI/014,
  by the Ministry of Education, Youth\r\nand Sports of the Czech Republic under the
  project MSCAfellow5_MUNI (CZ.02.01.01/00/22_010/0003229), and by the\r\nAustrian
  Science Fund (FWF project P31312-N35). This research was funded by UKRI EP/X024431/1
  and by a Clarendon\r\nFund Scholarship. This project has received funding from the
  European Union’s Horizon 2020 research and innovation\r\nprogramme under the Marie
  Skłodowska-Curie Grant Agreement No 101034413.\r\n"
article_number: '10'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Marek
  full_name: Filakovský, Marek
  id: 3E8AF77E-F248-11E8-B48F-1D18A9856A87
  last_name: Filakovský
- first_name: Tamio Vesa
  full_name: Nakajima, Tamio Vesa
  last_name: Nakajima
- first_name: Jakub
  full_name: Opršal, Jakub
  id: ec596741-c539-11ec-b829-c79322a91242
  last_name: Opršal
  orcid: 0000-0003-1245-3456
- first_name: Gianluca
  full_name: Tasinato, Gianluca
  id: 0433290C-AF8F-11E9-A4C7-F729E6697425
  last_name: Tasinato
- first_name: Uli
  full_name: Wagner, Uli
  id: 36690CA2-F248-11E8-B48F-1D18A9856A87
  last_name: Wagner
  orcid: 0000-0002-1494-0568
citation:
  ama: Filakovský M, Nakajima TV, Opršal J, Tasinato G, Wagner U. Hardness of linearly
    ordered 4-colouring of 3-colourable 3-uniform hypergraphs. <i>ACM Transactions
    on Computation Theory</i>. 2026;18(2). doi:<a href="https://doi.org/10.1145/3779121">10.1145/3779121</a>
  apa: Filakovský, M., Nakajima, T. V., Opršal, J., Tasinato, G., &#38; Wagner, U.
    (2026). Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs.
    <i>ACM Transactions on Computation Theory</i>. Association for Computing Machinery.
    <a href="https://doi.org/10.1145/3779121">https://doi.org/10.1145/3779121</a>
  chicago: Filakovský, Marek, Tamio Vesa Nakajima, Jakub Opršal, Gianluca Tasinato,
    and Uli Wagner. “Hardness of Linearly Ordered 4-Colouring of 3-Colourable 3-Uniform
    Hypergraphs.” <i>ACM Transactions on Computation Theory</i>. Association for Computing
    Machinery, 2026. <a href="https://doi.org/10.1145/3779121">https://doi.org/10.1145/3779121</a>.
  ieee: M. Filakovský, T. V. Nakajima, J. Opršal, G. Tasinato, and U. Wagner, “Hardness
    of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs,” <i>ACM
    Transactions on Computation Theory</i>, vol. 18, no. 2. Association for Computing
    Machinery, 2026.
  ista: Filakovský M, Nakajima TV, Opršal J, Tasinato G, Wagner U. 2026. Hardness
    of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs. ACM Transactions
    on Computation Theory. 18(2), 10.
  mla: Filakovský, Marek, et al. “Hardness of Linearly Ordered 4-Colouring of 3-Colourable
    3-Uniform Hypergraphs.” <i>ACM Transactions on Computation Theory</i>, vol. 18,
    no. 2, 10, Association for Computing Machinery, 2026, doi:<a href="https://doi.org/10.1145/3779121">10.1145/3779121</a>.
  short: M. Filakovský, T.V. Nakajima, J. Opršal, G. Tasinato, U. Wagner, ACM Transactions
    on Computation Theory 18 (2026).
corr_author: '1'
das_tickbox: '0'
date_created: 2026-07-05T22:01:37Z
date_published: 2026-05-04T00:00:00Z
date_updated: 2026-10-21T13:23:55Z
day: '04'
ddc:
- '500'
department:
- _id: UlWa
doi: 10.1145/3779121
ec_funded: 1
external_id:
  arxiv:
  - '2312.12981'
file:
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fulldoi: https://doi.org/10.1145/3779121
has_accepted_license: '1'
intvolume: '        18'
issue: '2'
keyword:
- Constraint satisfaction problem
- hypergraph colouring
- promise problem
- topological methods
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 26611F5C-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: P31312
  name: Algorithms for Embeddings and Homotopy Theory
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
  call_identifier: H2020
  grant_number: '101034413'
  name: 'IST-BRIDGE: International postdoctoral program'
publication: ACM Transactions on Computation Theory
publication_identifier:
  eissn:
  - 1942-3462
  issn:
  - 1942-3454
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
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supplementarymaterial: no
title: Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs
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type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
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_id: '19860'
abstract:
- lang: eng
  text: "An eight-partition of a finite set of points (respectively, of a continuous
    mass distribution) in R^3\r\n consists of three planes that divide the space into
    8 octants, such that each open octant contains at most 1/8 of the points (respectively,
    of the mass). In 1966, Hadwiger showed that any mass distribution in R^3 admits
    an eight-partition; moreover, one can prescribe the normal direction of one of
    the three planes. The analogous result for finite point sets follows by a standard
    limit argument. We prove the following variant of this result: any mass distribution
    (or point set) in R^3 admits an eight-partition for which the intersection of
    two of the planes is a line with a prescribed direction. Moreover, we present
    an efficient algorithm for calculating an eight-partition of a set of n points
    in R^3 (with prescribed normal direction of one of the planes) in time O(n^7/3).
    A preliminary version of this work appeared in SoCG’24 (Aronov et al., 40th International
    Symposium on Computational Geometry, 2024)."
acknowledgement: Work by BA was supported by NSF grants CCF 15-40656 and CCF 20-08551,
  and by grant 2014/170 from the US-Israel Binational Science Foundation. Part of
  this research was conducted while BA was visiting ISTA in the summers of 2022 and
  2023. The visit of BA to ISTA in the summer of 2022 was supported by an ISTA Visiting
  Professorship. Research of BA also partially supported by ERC grant no. 882971,
  “GeoScape,” and by the Erdős Center. Work by AB was supported by Australian Research
  Council grant DP220102212. Work by IR was supported by a Tandon School of Engineering
  Fellowship and by NSF Grant CCF-20-08551. BA and AB would like to thank William
  Steiger for insightful initial discussions of the problems addressed in this work.
  Open Access funding enabled and organized by CAUL and its Member Institutions.
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Boris
  full_name: Aronov, Boris
  last_name: Aronov
- first_name: Abdul
  full_name: Basit, Abdul
  last_name: Basit
- first_name: Indu
  full_name: Ramesh, Indu
  last_name: Ramesh
- first_name: Gianluca
  full_name: Tasinato, Gianluca
  id: 0433290C-AF8F-11E9-A4C7-F729E6697425
  last_name: Tasinato
- first_name: Uli
  full_name: Wagner, Uli
  id: 36690CA2-F248-11E8-B48F-1D18A9856A87
  last_name: Wagner
  orcid: 0000-0002-1494-0568
citation:
  ama: Aronov B, Basit A, Ramesh I, Tasinato G, Wagner U. Eight-partitioning points
    in 3D, and efficiently too. <i>Discrete &#38; Computational Geometry</i>. 2026;75:1331-1355.
    doi:<a href="https://doi.org/10.1007/s00454-025-00739-0">10.1007/s00454-025-00739-0</a>
  apa: Aronov, B., Basit, A., Ramesh, I., Tasinato, G., &#38; Wagner, U. (2026). Eight-partitioning
    points in 3D, and efficiently too. <i>Discrete &#38; Computational Geometry</i>.
    Springer Nature. <a href="https://doi.org/10.1007/s00454-025-00739-0">https://doi.org/10.1007/s00454-025-00739-0</a>
  chicago: Aronov, Boris, Abdul Basit, Indu Ramesh, Gianluca Tasinato, and Uli Wagner.
    “Eight-Partitioning Points in 3D, and Efficiently Too.” <i>Discrete &#38; Computational
    Geometry</i>. Springer Nature, 2026. <a href="https://doi.org/10.1007/s00454-025-00739-0">https://doi.org/10.1007/s00454-025-00739-0</a>.
  ieee: B. Aronov, A. Basit, I. Ramesh, G. Tasinato, and U. Wagner, “Eight-partitioning
    points in 3D, and efficiently too,” <i>Discrete &#38; Computational Geometry</i>,
    vol. 75. Springer Nature, pp. 1331–1355, 2026.
  ista: Aronov B, Basit A, Ramesh I, Tasinato G, Wagner U. 2026. Eight-partitioning
    points in 3D, and efficiently too. Discrete &#38; Computational Geometry. 75,
    1331–1355.
  mla: Aronov, Boris, et al. “Eight-Partitioning Points in 3D, and Efficiently Too.”
    <i>Discrete &#38; Computational Geometry</i>, vol. 75, Springer Nature, 2026,
    pp. 1331–55, doi:<a href="https://doi.org/10.1007/s00454-025-00739-0">10.1007/s00454-025-00739-0</a>.
  short: B. Aronov, A. Basit, I. Ramesh, G. Tasinato, U. Wagner, Discrete &#38; Computational
    Geometry 75 (2026) 1331–1355.
das_tickbox: '0'
date_created: 2025-06-22T22:02:07Z
date_published: 2026-06-01T00:00:00Z
date_updated: 2026-10-21T13:38:17Z
day: '01'
ddc:
- '500'
department:
- _id: UlWa
doi: 10.1007/s00454-025-00739-0
external_id:
  arxiv:
  - '2403.02627'
  isi:
  - '001506904300001'
file:
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  date_updated: 2026-07-23T11:14:05Z
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language:
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month: '06'
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page: 1331-1355
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publication_status: published
publisher: Springer Nature
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status: public
supplementarymaterial: yes
title: Eight-partitioning points in 3D, and efficiently too
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 75
year: '2026'
...
---
OA_place: repository
OA_type: green
_id: '21763'
abstract:
- lang: eng
  text: Reactive oxygen species (ROS) have been implicated in multiple signaling processes
    in plants, but the underlying mechanisms and roles remain enigmatic. In this study,
    we developed a method of live imaging of apoplastic ROS at the root surface. Distinct
    signals, including auxin, extracellular adenosine triphosphate, and rapid alkalinization
    factor 1 peptide, induce cytosolic calcium transients and apoplastic ROS bursts.
    Genetic and optogenetic manipulations of Arabidopsis identified calcium transients
    as necessary and sufficient for ROS bursts through activation of reduced nicotinamide
    adenine dinucleotide phosphate (NADPH) oxidases RBOHC and RBOHF. Apoplastic ROS
    bursts are not required, but they do limit gravity-induced root bending. Root
    bending is sensed by the stretch-activated calcium channel MCA1, leading to NADPH
    oxidase activation. The resulting ROS production stiffens cell walls to facilitate
    soil penetration. Apoplastic ROS thus provides a means to balance tissue flexibility
    and stiffness to navigate soil.
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
acknowledgement: "We gratefully acknowledge the Lab Support Facility (LSF) and the
  Imaging and Optics Facility (IOF) (both of ISTA) and the Hounsfield CT Facility
  (University of Nottingham) for support with imaging and the Growth Facility (IPMB)
  for plant cultivation. We thank M. Fendrych and his team for help with the microfluidics
  upgrades and J. Atkinson at the University of Nottingham MakerSpace for 3D printing
  of Arabidopsis mini-soil columns.\r\nThis project received funding from the European
  Research Council (ERC; 101142681 CYNIPS) and the Austrian Science Fund (FWF; P 37051-B).
  I.K. was cofunded by the European Union, Horizon Europe, project MOLIPEC, ID 101087030
  and CSF project 25-16449S. L.V. and B.K.P. acknowledge funding from UK Research
  and Innovation (UKRI) Frontiers Research (EP/Y036697/1). M.J.B. acknowledges funding
  from ERC SYNERGY (grant 101118769 HYDROSENSING). The study was partially supported
  by the Université Paris Cité, Idex ANR-18-IDEX-0001, funded by the French Government
  through its “Investments for the Future” program and also by the projects “Mecha-Nuc”
  ANR-20-CE13-0025-03 and “scEm-bryoMech” ANR-21-CE13-0046. P.D. acknowledges support
  by Human Frontier Science Program Organization grant 2022-RG107. P.V. acknowledges
  support provided by “Programme blanc” of the Graduate School BIOSPHERA, Université
  Paris-Saclay. Phytohormonal analysis was performed using the service laboratory
  funded by Toward Next GENeration Crops, reg. no. CZ.02.01.01/00/22_008/0004581 of
  the European Regional Development Fund (ERDF) program Johannes Amos Comenius. This
  research was funded in whole or in part by the Austrian Science Fund (P 37051-B)
  and UK Research and Innovation (EP/Y036697/1), cOAlition S organizations, and by
  the European Research Council (101142681 CYNIPS, 101118769 HYDROSENSING); as required,
  the author will make the Author Accepted Manuscript (AAM) version available under
  a CC BY public copyright license."
article_processing_charge: No
article_type: original
author:
- first_name: Ivan
  full_name: Kulich, Ivan
  id: 57a1567c-8314-11eb-9063-c9ddc3451a54
  last_name: Kulich
- first_name: Dmitrii
  full_name: Vladimirtsev, Dmitrii
  id: 60466724-5355-11ee-ae5a-fa55e8f99c3d
  last_name: Vladimirtsev
- first_name: Marek
  full_name: Randuch, Marek
  id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae
  last_name: Randuch
- first_name: Shiqiang
  full_name: Gao, Shiqiang
  last_name: Gao
- first_name: Matteo
  full_name: Citterico, Matteo
  last_name: Citterico
- first_name: Kai R.
  full_name: Konrad, Kai R.
  last_name: Konrad
- first_name: Georg
  full_name: Nagel, Georg
  last_name: Nagel
- first_name: Michael
  full_name: Wrzaczek, Michael
  last_name: Wrzaczek
- first_name: Léa
  full_name: Cascaro, Léa
  last_name: Cascaro
- first_name: Pauline
  full_name: Vinet, Pauline
  last_name: Vinet
- first_name: Pauline
  full_name: Durand, Pauline
  last_name: Durand
- first_name: Atef
  full_name: Asnacios, Atef
  last_name: Asnacios
- first_name: Lokesh
  full_name: Verma, Lokesh
  last_name: Verma
- first_name: Malcolm J.
  full_name: Bennett, Malcolm J.
  last_name: Bennett
- first_name: Bipin K.
  full_name: Pandey, Bipin K.
  last_name: Pandey
- first_name: Jiří
  full_name: Friml, Jiří
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
citation:
  ama: Kulich I, Vladimirtsev D, Randuch M, et al. Calcium-triggered apoplastic ROS
    bursts balance gravity and mechanical signals for soil navigation. <i>Science</i>.
    2026;392(6795):296-300. doi:<a href="https://doi.org/10.1126/science.adu8197">10.1126/science.adu8197</a>
  apa: Kulich, I., Vladimirtsev, D., Randuch, M., Gao, S., Citterico, M., Konrad,
    K. R., … Friml, J. (2026). Calcium-triggered apoplastic ROS bursts balance gravity
    and mechanical signals for soil navigation. <i>Science</i>. AAAS. <a href="https://doi.org/10.1126/science.adu8197">https://doi.org/10.1126/science.adu8197</a>
  chicago: Kulich, Ivan, Dmitrii Vladimirtsev, Marek Randuch, Shiqiang Gao, Matteo
    Citterico, Kai R. Konrad, Georg Nagel, et al. “Calcium-Triggered Apoplastic ROS
    Bursts Balance Gravity and Mechanical Signals for Soil Navigation.” <i>Science</i>.
    AAAS, 2026. <a href="https://doi.org/10.1126/science.adu8197">https://doi.org/10.1126/science.adu8197</a>.
  ieee: I. Kulich <i>et al.</i>, “Calcium-triggered apoplastic ROS bursts balance
    gravity and mechanical signals for soil navigation,” <i>Science</i>, vol. 392,
    no. 6795. AAAS, pp. 296–300, 2026.
  ista: Kulich I, Vladimirtsev D, Randuch M, Gao S, Citterico M, Konrad KR, Nagel
    G, Wrzaczek M, Cascaro L, Vinet P, Durand P, Asnacios A, Verma L, Bennett MJ,
    Pandey BK, Friml J. 2026. Calcium-triggered apoplastic ROS bursts balance gravity
    and mechanical signals for soil navigation. Science. 392(6795), 296–300.
  mla: Kulich, Ivan, et al. “Calcium-Triggered Apoplastic ROS Bursts Balance Gravity
    and Mechanical Signals for Soil Navigation.” <i>Science</i>, vol. 392, no. 6795,
    AAAS, 2026, pp. 296–300, doi:<a href="https://doi.org/10.1126/science.adu8197">10.1126/science.adu8197</a>.
  short: I. Kulich, D. Vladimirtsev, M. Randuch, S. Gao, M. Citterico, K.R. Konrad,
    G. Nagel, M. Wrzaczek, L. Cascaro, P. Vinet, P. Durand, A. Asnacios, L. Verma,
    M.J. Bennett, B.K. Pandey, J. Friml, Science 392 (2026) 296–300.
corr_author: '1'
date_created: 2026-04-26T22:01:47Z
date_published: 2026-04-16T00:00:00Z
date_updated: 2026-10-22T09:15:44Z
day: '16'
ddc:
- '580'
department:
- _id: JiFr
- _id: GradSch
doi: 10.1126/science.adu8197
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month: '04'
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oa_version: Accepted Version
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project:
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  grant_number: '101142681'
  name: Cyclic nucleotides as second messengers in plants
- _id: 7bcece63-9f16-11ee-852c-ae94e099eeb6
  grant_number: P37051
  name: Guanylate cyclase activity of TIR1/AFBs auxin receptors
publication: Science
publication_identifier:
  eissn:
  - 1095-9203
  issn:
  - 0036-8075
publication_status: published
publisher: AAAS
quality_controlled: '1'
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    status: public
scopus_import: '1'
status: public
title: Calcium-triggered apoplastic ROS bursts balance gravity and mechanical signals
  for soil navigation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 392
year: '2026'
...
---
OA_place: publisher
_id: '23145'
acknowledged_ssus:
- _id: LifeSc
- _id: M-Shop
- _id: CampIT
- _id: Bio
acknowledgement: "European Research Council (101142681 CYNIPS), Cyclic nucleotides
  as second messengers \r\nin plants, DOI: https://doi.org/10.3030/101142681 \r\nAustrian
  Science Fund (P 37051-B), Guanylate cyclase activity of TIR1/AFBs auxin receptors,
  \r\nDOI: https://doi.org/10.55776/P37051 "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Marek
  full_name: Randuch, Marek
  id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae
  last_name: Randuch
citation:
  ama: 'Randuch M. Fast growth responses in plants: Growth regulation and phospho-proteomic
    . 2026. doi:<a href="https://doi.org/10.15479/AT-ISTA-23145">10.15479/AT-ISTA-23145</a>'
  apa: 'Randuch, M. (2026). <i>Fast growth responses in plants: Growth regulation
    and phospho-proteomic </i>. Institute of Science and Technology Austria. <a href="https://doi.org/10.15479/AT-ISTA-23145">https://doi.org/10.15479/AT-ISTA-23145</a>'
  chicago: 'Randuch, Marek. “Fast Growth Responses in Plants: Growth Regulation and
    Phospho-Proteomic .” Institute of Science and Technology Austria, 2026. <a href="https://doi.org/10.15479/AT-ISTA-23145">https://doi.org/10.15479/AT-ISTA-23145</a>.'
  ieee: 'M. Randuch, “Fast growth responses in plants: Growth regulation and phospho-proteomic
    ,” Institute of Science and Technology Austria, 2026.'
  ista: 'Randuch M. 2026. Fast growth responses in plants: Growth regulation and phospho-proteomic
    . Institute of Science and Technology Austria.'
  mla: 'Randuch, Marek. <i>Fast Growth Responses in Plants: Growth Regulation and
    Phospho-Proteomic </i>. Institute of Science and Technology Austria, 2026, doi:<a
    href="https://doi.org/10.15479/AT-ISTA-23145">10.15479/AT-ISTA-23145</a>.'
  short: 'M. Randuch, Fast Growth Responses in Plants: Growth Regulation and Phospho-Proteomic
    , Institute of Science and Technology Austria, 2026.'
corr_author: '1'
date_created: 2026-10-16T17:14:40Z
date_published: 2026-10-18T00:00:00Z
date_updated: 2026-10-22T09:15:44Z
day: '18'
ddc:
- '580'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JiFr
doi: 10.15479/AT-ISTA-23145
doi_confirm: '1'
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language:
- iso: eng
license: https://creativecommons.org/licenses/by-sa/4.0/
month: '10'
oa_version: Published Version
page: '289'
project:
- _id: 7bcece63-9f16-11ee-852c-ae94e099eeb6
  grant_number: P37051
  name: Guanylate cyclase activity of TIR1/AFBs auxin receptors
- _id: 8f347782-16d5-11f0-9cad-8c19706ee739
  grant_number: '101142681'
  name: Cyclic nucleotides as second messengers in plants
publication_identifier:
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
  record:
  - id: '12291'
    relation: part_of_dissertation
    status: public
  - id: '21763'
    relation: part_of_dissertation
    status: public
  - id: '23175'
    relation: part_of_dissertation
    status: public
  - id: '23174'
    relation: part_of_dissertation
    status: public
  - id: '20656'
    relation: part_of_dissertation
    status: public
status: public
supervisor:
- first_name: Jiří
  full_name: Friml, Jiří
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
title: 'Fast growth responses in plants: Growth regulation and phospho-proteomic '
tmp:
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    BY-SA 4.0)
  short: CC BY-SA (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2026'
...
---
OA_place: repository
OA_type: green
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abstract:
- lang: eng
  text: Plants must continually balance growth with arrest, especially under stress.
    Auxin signaling acts as a central regulatory hub in this process, yet the mechanisms
    that dynamically tune early auxin signalling in real time remain unknown. Here,
    we used the light-gated, Ca2+-permeable Channelrhodopsin 2 variant XXM2.0 to optogenetically
    impose defined Ca2+ signatures on Arabidopsis root cells. Repetitive light activation
    triggered cytosolic Ca2+ signals that in turn suppressed auxin-induced membrane
    depolarization and Ca2+ transients. Moreover, prolonged optogenetic Ca2+ stimulation
    affects auxin-responsive transcriptional reprogramming. As phenotypic output,
    reversible inhibition of root growth by suppressing cell division and elongation
    was observed. We further identify a candidate CaM7–CNGC14 module that likely mediates
    Ca2+-dependent gating of early auxin signalling. Our study thus introduces a synthetic
    biology approach to decompose calcium–auxin crosstalk in plant cells, and demonstrates
    that optogenetically imposed cytosolic Ca2+ signals act as dynamic regulators
    of auxin susceptibility in roots.
acknowledgement: "We would like to thank Dirk Becker (University of Wuerzburg) for
  his help in making the optogenetic constructs and for his comments on the manuscript.
  We also appreciate Rob Roelfsema (University of Wuerzburg) for his feedback on the
  manuscript. We sincerely thank the anonymous reviewers for the thoughtful and inspiring
  suggestions that helped broaden the discussion and identify important future research
  directions. Funding\r\nNational Key R&D Program of China, 2025YFA0923400 (RH)\r\n\r\nNational
  Natural Science Foundation of China (NSFC), W2531024 (RH); 32271501(NL)\r\n\r\nNSFC-Excellent
  Young Scientists Fund Program (overseas) (SH)\r\n\r\nNSFC-RFIS, ZB2025101410702
  (RH)\r\n\r\nGuangdong Pearl River Talents Program, 2023ZT10N033\r\n\r\nChina Scholarship
  Council no. 202306510063 (HS)\r\n\r\nThe European Research Council grant 101142681
  CYNIPS (JF)\r\n\r\nAustrian Science Fund grant FWF; P 37051-B (JF)\r\n\r\nGerman
  Research Foundation grant CRC 1644 (512328399; 512328399) (KK, ZH)\r\n\r\nERC Synergy
  project STARMORPH, reg. no. 101166880 (AP, ON)"
article_processing_charge: No
author:
- first_name: Huifang
  full_name: Song, Huifang
  last_name: Song
- first_name: Angel
  full_name: Baudon, Angel
  last_name: Baudon
- first_name: Matthias
  full_name: Freund, Matthias
  last_name: Freund
- first_name: Marek
  full_name: Randuch, Marek
  id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae
  last_name: Randuch
- first_name: Aleš
  full_name: Pěnčík, Aleš
  last_name: Pěnčík
- first_name: Novák
  full_name: Ondřej, Novák
  last_name: Ondřej
- first_name: Zhaohui
  full_name: He, Zhaohui
  last_name: He
- first_name: Kerstin
  full_name: Kaufmann, Kerstin
  last_name: Kaufmann
- first_name: 'Nan'
  full_name: Li, Nan
  last_name: Li
- first_name: Matthew
  full_name: Gilliham, Matthew
  last_name: Gilliham
- first_name: Jiří
  full_name: Friml, Jiří
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
- first_name: Rainer
  full_name: Hedrich, Rainer
  last_name: Hedrich
- first_name: Shouguang
  full_name: Huang, Shouguang
  last_name: Huang
biorxivid: 1
citation:
  ama: Song H, Baudon A, Freund M, et al. Ca2+ signature gates early auxin signaling
    in Arabidopsis roots. <i>bioRxiv</i>. doi:<a href="https://doi.org/10.1101/2025.10.04.680446">10.1101/2025.10.04.680446</a>
  apa: Song, H., Baudon, A., Freund, M., Randuch, M., Pěnčík, A., Ondřej, N., … Huang,
    S. (n.d.). Ca2+ signature gates early auxin signaling in Arabidopsis roots. <i>bioRxiv</i>.
    <a href="https://doi.org/10.1101/2025.10.04.680446">https://doi.org/10.1101/2025.10.04.680446</a>
  chicago: Song, Huifang, Angel Baudon, Matthias Freund, Marek Randuch, Aleš Pěnčík,
    Novák Ondřej, Zhaohui He, et al. “Ca2+ Signature Gates Early Auxin Signaling in
    Arabidopsis Roots.” <i>BioRxiv</i>, n.d. <a href="https://doi.org/10.1101/2025.10.04.680446">https://doi.org/10.1101/2025.10.04.680446</a>.
  ieee: H. Song <i>et al.</i>, “Ca2+ signature gates early auxin signaling in Arabidopsis
    roots,” <i>bioRxiv</i>. .
  ista: Song H, Baudon A, Freund M, Randuch M, Pěnčík A, Ondřej N, He Z, Kaufmann
    K, Li N, Gilliham M, Friml J, Hedrich R, Huang S. Ca2+ signature gates early auxin
    signaling in Arabidopsis roots. bioRxiv, <a href="https://doi.org/10.1101/2025.10.04.680446">10.1101/2025.10.04.680446</a>.
  mla: Song, Huifang, et al. “Ca2+ Signature Gates Early Auxin Signaling in Arabidopsis
    Roots.” <i>BioRxiv</i>, doi:<a href="https://doi.org/10.1101/2025.10.04.680446">10.1101/2025.10.04.680446</a>.
  short: H. Song, A. Baudon, M. Freund, M. Randuch, A. Pěnčík, N. Ondřej, Z. He, K.
    Kaufmann, N. Li, M. Gilliham, J. Friml, R. Hedrich, S. Huang, BioRxiv (n.d.).
corr_author: '1'
date_created: 2026-10-19T11:51:47Z
date_published: 2026-08-26T00:00:00Z
date_updated: 2026-10-22T09:15:44Z
day: '26'
department:
- _id: JiFr
doi: 10.1101/2025.10.04.680446
external_id:
  biorxivid:
  - 10.1101/2025.10.04.680446
fulldoi: https://doi.org/10.1101/2025.10.04.680446
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1101/2025.10.04.680446
month: '08'
oa: 1
oa_version: Preprint
project:
- _id: 8f347782-16d5-11f0-9cad-8c19706ee739
  grant_number: '101142681'
  name: Cyclic nucleotides as second messengers in plants
- _id: 7bcece63-9f16-11ee-852c-ae94e099eeb6
  grant_number: P37051
  name: Guanylate cyclase activity of TIR1/AFBs auxin receptors
publication: bioRxiv
publication_status: draft
related_material:
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  - id: '23145'
    relation: dissertation_contains
    status: public
status: public
title: Ca2+ signature gates early auxin signaling in Arabidopsis roots
tmp:
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  short: CC BY-NC-ND (4.0)
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '18706'
abstract:
- lang: eng
  text: "We prove discrete-to-continuum convergence for dynamical optimal transport
    on  Zd\r\n -periodic graphs with cost functional having linear growth at infinity.
    This result provides an answer to a problem left open by Gladbach, Kopfer, Maas,
    and Portinale (Calc Var Partial Differential Equations 62(5), 2023), where the
    convergence behaviour of discrete boundary-value dynamical transport problems
    is proved under the stronger assumption of superlinear growth. Our result extends
    the known literature to some important classes of examples, such as scaling limits
    of  1 -Wasserstein transport problems. Similarly to what happens in the quadratic
    case, the geometry of the graph plays a crucial role in the structure of the limit
    cost function, as we discuss in the final part of this work, which includes some
    visual representations."
acknowledgement: L.P. gratefully acknowledges fundings from the Deutsche Forschungsgemeinschaft
  (DFG, German Research Foundation) under Germany’s Excellence Strategy – GZ 2047/1,
  Projekt-ID 390685813. F.Q. gratefully acknowledges support from the Austrian Science
  Fund (FWF) project 10.55776/F65.
article_processing_charge: Yes
article_type: original
author:
- first_name: Lorenzo
  full_name: Portinale, Lorenzo
  id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87
  last_name: Portinale
- first_name: Filippo
  full_name: Quattrocchi, Filippo
  id: 3ebd6ba8-edfb-11eb-afb5-91a9745ba308
  last_name: Quattrocchi
  orcid: 0009-0000-9773-1931
citation:
  ama: Portinale L, Quattrocchi F. Discrete-to-continuum limits of optimal transport
    with linear growth on periodic graphs. <i>European Journal of Applied Mathematics</i>.
    2026;37(3):614-642. doi:<a href="https://doi.org/10.1017/s0956792524000810">10.1017/s0956792524000810</a>
  apa: Portinale, L., &#38; Quattrocchi, F. (2026). Discrete-to-continuum limits of
    optimal transport with linear growth on periodic graphs. <i>European Journal of
    Applied Mathematics</i>. Cambridge University Press. <a href="https://doi.org/10.1017/s0956792524000810">https://doi.org/10.1017/s0956792524000810</a>
  chicago: Portinale, Lorenzo, and Filippo Quattrocchi. “Discrete-to-Continuum Limits
    of Optimal Transport with Linear Growth on Periodic Graphs.” <i>European Journal
    of Applied Mathematics</i>. Cambridge University Press, 2026. <a href="https://doi.org/10.1017/s0956792524000810">https://doi.org/10.1017/s0956792524000810</a>.
  ieee: L. Portinale and F. Quattrocchi, “Discrete-to-continuum limits of optimal
    transport with linear growth on periodic graphs,” <i>European Journal of Applied
    Mathematics</i>, vol. 37, no. 3. Cambridge University Press, pp. 614–642, 2026.
  ista: Portinale L, Quattrocchi F. 2026. Discrete-to-continuum limits of optimal
    transport with linear growth on periodic graphs. European Journal of Applied Mathematics.
    37(3), 614–642.
  mla: Portinale, Lorenzo, and Filippo Quattrocchi. “Discrete-to-Continuum Limits
    of Optimal Transport with Linear Growth on Periodic Graphs.” <i>European Journal
    of Applied Mathematics</i>, vol. 37, no. 3, Cambridge University Press, 2026,
    pp. 614–42, doi:<a href="https://doi.org/10.1017/s0956792524000810">10.1017/s0956792524000810</a>.
  short: L. Portinale, F. Quattrocchi, European Journal of Applied Mathematics 37
    (2026) 614–642.
das_tickbox: '0'
date_created: 2024-12-23T11:03:59Z
date_published: 2026-06-01T00:00:00Z
date_updated: 2026-10-22T22:31:21Z
day: '01'
ddc:
- '500'
department:
- _id: GradSch
- _id: JaMa
doi: 10.1017/s0956792524000810
external_id:
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  - '001381435800001'
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  date_created: 2026-07-23T05:55:03Z
  date_updated: 2026-07-23T05:55:03Z
  file_id: '22386'
  file_name: 2026_EuropJourAppliedMath_Portinale.pdf
  file_size: 612317
  relation: main_file
  success: 1
file_date_updated: 2026-07-23T05:55:03Z
fulldoi: https://doi.org/10.1017/s0956792524000810
has_accepted_license: '1'
intvolume: '        37'
isi: 1
issue: '3'
keyword:
- optimal transport
- discrete-to-continuum
- homogenisation
- linear growth
- gamma-convergence
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 614-642
project:
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
  grant_number: F6504
  name: Taming Complexity in Partial Differential Systems
publication: European Journal of Applied Mathematics
publication_identifier:
  eissn:
  - 1469-4425
  issn:
  - 0956-7925
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
related_material:
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  - id: '20563'
    relation: dissertation_contains
    status: public
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Discrete-to-continuum limits of optimal transport with linear growth on periodic
  graphs
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 37
year: '2026'
...
---
OA_place: repository
_id: '21423'
abstract:
- lang: eng
  text: "Biological systems, such as cytoskeletal filaments and multicellular collectives,
    exhibit rich \r\nself-organization driven by their intrinsic activity and physical
    constraints. Across scales, \r\ngeometry plays a central role: the shape of active
    units and the structure of their environment \r\nstrongly influence how order
    emerges in these far-from-equilibrium systems. In this thesis, \r\nwe combine
    minimal active-matter models with bottom-up in vitro experiments to identify \r\nthe
    principles by which geometry and activity shape collective behavior in biological
    matter. \r\nAt the subcellular scale, we investigate how the physical properties
    of chiral FtsZ filaments \r\ngovern their large-scale organization. Using a mesoscopic
    model validated by reconstituted \r\nfilament assays, we show that filament shape,
    intrinsic curvature, and flexibility, together with \r\nactivity-driven straightening,
    determine whether filaments form chiral rings, polar bands, or \r\nnematic-like
    states. Our model shows that small changes in filament mechanics produce large
    \r\nshifts in collective structures, revealing how the geometry of individual
    filaments amplifies \r\nthrough activity to control patterns relevant for bacterial
    cytokinesis. \r\nAt the cellular scale, we examine how geometry of the external
    environment influences \r\ncollective cancer cell migration. Experiments in controlled
    microfabricated obstacle \r\nenvironments demonstrate that geometric disorder
    alone can induce a transition from \r\ncollective to single-cell invasion. A minimal
    model of active particles in disordered geometries \r\nreproduces these effects,
    demonstrating that cell dissemination results both from local \r\ngeometrical
    constraints and a global integration of spatial disorder over time. Surprisingly,
    \r\nthis transition is accompanied by a change in the universality class of interface
    dynamics, \r\nrevealing that cell-environment interactions can shift the collective
    behavior of an invasive \r\nfront purely through mechanics.  \r\nIn the last system,
    we study how cell-intrinsic geometry and chirality affect collective motion \r\nin
    confined and unconfined settings. Using a minimal model inspired by in vitro experiments,
    \r\nwe analyze motile cells that exhibit persistent rotation due to intrinsic
    left-right asymmetry. \r\nIn circular confinement, this simplified chiral model
    reproduces several experimentally \r\nobserved features within specific parameter
    regimes. At high densities in unconfined \r\nenvironments, however, intrinsic
    chirality becomes masked even before the onset of the \r\njamming transition.
    These results show that single-cell geometric asymmetry does not \r\nnecessarily
    translate into large-scale chiral flows, offering new insight into how forces
    and \r\nsymmetries shape collective motion in dense cellular systems. \r\nOverall,
    this work uncovers how geometric constraints – embedded in the intrinsic \r\narchitecture
    of an active filament or encoded in the complexity of a microenvironment \r\ncouple
    to active forces to generate different classes of complex behaviors. "
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "Finally, I gratefully acknowledge funding from the DOC Fellowship
  of the Austrian Academy\r\nof Sciences (OeAW): grant agreement 26360."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Zuzana
  full_name: Dunajova, Zuzana
  id: 4B39F286-F248-11E8-B48F-1D18A9856A87
  last_name: Dunajova
citation:
  ama: Dunajova Z. Geometry-driven self-organization of migrating cells and chiral
    filaments. 2026. doi:<a href="https://doi.org/10.15479/AT-ISTA-21423">10.15479/AT-ISTA-21423</a>
  apa: Dunajova, Z. (2026). <i>Geometry-driven self-organization of migrating cells
    and chiral filaments</i>. Institute of Science and Technology Austria. <a href="https://doi.org/10.15479/AT-ISTA-21423">https://doi.org/10.15479/AT-ISTA-21423</a>
  chicago: Dunajova, Zuzana. “Geometry-Driven Self-Organization of Migrating Cells
    and Chiral Filaments.” Institute of Science and Technology Austria, 2026. <a href="https://doi.org/10.15479/AT-ISTA-21423">https://doi.org/10.15479/AT-ISTA-21423</a>.
  ieee: Z. Dunajova, “Geometry-driven self-organization of migrating cells and chiral
    filaments,” Institute of Science and Technology Austria, 2026.
  ista: Dunajova Z. 2026. Geometry-driven self-organization of migrating cells and
    chiral filaments. Institute of Science and Technology Austria.
  mla: Dunajova, Zuzana. <i>Geometry-Driven Self-Organization of Migrating Cells and
    Chiral Filaments</i>. Institute of Science and Technology Austria, 2026, doi:<a
    href="https://doi.org/10.15479/AT-ISTA-21423">10.15479/AT-ISTA-21423</a>.
  short: Z. Dunajova, Geometry-Driven Self-Organization of Migrating Cells and Chiral
    Filaments, Institute of Science and Technology Austria, 2026.
corr_author: '1'
date_created: 2026-03-11T08:30:49Z
date_published: 2026-03-11T00:00:00Z
date_updated: 2026-10-16T08:12:11Z
day: '11'
ddc:
- '539'
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: EdHa
doi: 10.15479/AT-ISTA-21423
doi_confirm: '1'
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  date_updated: 2026-09-11T22:30:02Z
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fulldoi: https://doi.org/10.15479/AT-ISTA-21423
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '110'
project:
- _id: 34d75525-11ca-11ed-8bc3-89b6307fee9d
  grant_number: '26360'
  name: Motile active matter models of migrating cells and chiral filaments
publication_identifier:
  isbn:
  - 978-3-99078-076-3
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
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    relation: part_of_dissertation
    status: public
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    relation: research_data
    status: public
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    status: public
status: public
supervisor:
- first_name: Edouard B
  full_name: Hannezo, Edouard B
  id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
  last_name: Hannezo
  orcid: 0000-0001-6005-1561
title: Geometry-driven self-organization of migrating cells and chiral filaments
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  short: CC BY-NC-SA (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2026'
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---
OA_place: repository
OA_type: free access
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abstract:
- lang: eng
  text: These files contain supplementary movies accompanying the PhD thesis “Geometry-driven
    self-organization of migrating cells and chiral filaments” by Zuzana Dunajova
    (2026). The videos provide additional visual material supporting the experiments
    and results described in the thesis.
acknowledged_ssus:
- _id: Bio
- _id: ScienComp
article_processing_charge: No
author:
- first_name: Zuzana
  full_name: Dunajova, Zuzana
  id: 4B39F286-F248-11E8-B48F-1D18A9856A87
  last_name: Dunajova
citation:
  ama: Dunajova Z. Supplementary movies to PhD thesis “Geometry-driven self-organization
    of migrating cells and chiral filaments.” 2026. doi:<a href="https://doi.org/10.15479/AT-ISTA-21439">10.15479/AT-ISTA-21439</a>
  apa: Dunajova, Z. (2026). Supplementary movies to PhD thesis “Geometry-driven self-organization
    of migrating cells and chiral filaments.” Institute of Science and Technology
    Austria. <a href="https://doi.org/10.15479/AT-ISTA-21439">https://doi.org/10.15479/AT-ISTA-21439</a>
  chicago: Dunajova, Zuzana. “Supplementary Movies to PhD Thesis ‘Geometry-Driven
    Self-Organization of Migrating Cells and Chiral Filaments.’” Institute of Science
    and Technology Austria, 2026. <a href="https://doi.org/10.15479/AT-ISTA-21439">https://doi.org/10.15479/AT-ISTA-21439</a>.
  ieee: Z. Dunajova, “Supplementary movies to PhD thesis ‘Geometry-driven self-organization
    of migrating cells and chiral filaments.’” Institute of Science and Technology
    Austria, 2026.
  ista: Dunajova Z. 2026. Supplementary movies to PhD thesis “Geometry-driven self-organization
    of migrating cells and chiral filaments”, Institute of Science and Technology
    Austria, <a href="https://doi.org/10.15479/AT-ISTA-21439">10.15479/AT-ISTA-21439</a>.
  mla: Dunajova, Zuzana. <i>Supplementary Movies to PhD Thesis “Geometry-Driven Self-Organization
    of Migrating Cells and Chiral Filaments.”</i> Institute of Science and Technology
    Austria, 2026, doi:<a href="https://doi.org/10.15479/AT-ISTA-21439">10.15479/AT-ISTA-21439</a>.
  short: Z. Dunajova, (2026).
contributor:
- contributor_type: researcher
  first_name: Saren
  id: 4323B49C-F248-11E8-B48F-1D18A9856A87
  last_name: Tasciyan
  orcid: 0000-0003-1671-393X
- contributor_type: researcher
  first_name: Philipp
  id: 40136C2A-F248-11E8-B48F-1D18A9856A87
  last_name: Radler
  orcid: '0000-0001-9198-2182 '
corr_author: '1'
date_created: 2026-03-11T21:05:20Z
date_published: 2026-03-12T00:00:00Z
date_updated: 2026-10-22T22:31:26Z
day: '12'
ddc:
- '570'
department:
- _id: GradSch
- _id: EdHa
doi: 10.15479/AT-ISTA-21439
file:
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  checksum: 47809a9a31b748b16e21e92d11ddc87f
  content_type: application/zip
  creator: zdunajov
  date_created: 2026-03-11T20:41:28Z
  date_updated: 2026-03-11T20:41:28Z
  file_id: '21440'
  file_name: Supplementary_movies_Thesis_Dunajova.zip
  file_size: 154465214
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  creator: zdunajov
  date_created: 2026-03-11T20:52:39Z
  date_updated: 2026-03-11T20:52:39Z
  file_id: '21441'
  file_name: readme.txt
  file_size: 2289
  relation: main_file
  success: 1
file_date_updated: 2026-03-11T20:52:39Z
fulldoi: https://doi.org/10.15479/AT-ISTA-21439
has_accepted_license: '1'
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 34d75525-11ca-11ed-8bc3-89b6307fee9d
  grant_number: '26360'
  name: Motile active matter models of migrating cells and chiral filaments
publisher: Institute of Science and Technology Austria
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status: public
title: Supplementary movies to PhD thesis “Geometry-driven self-organization of migrating
  cells and chiral filaments”
tmp:
  image: /images/cc_by_nc_sa.png
  legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
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