---
OA_place: repository
OA_type: green
_id: '19399'
abstract:
- lang: eng
text: Phytohormone auxin and its directional transport mediate much of the remarkably
plastic development of higher plants. Positive feedback between auxin signaling
and transport is a key prerequisite for (i) self-organizing processes including
vascular tissue formation and (ii) directional growth responses such as gravitropism.
Here we identify a mechanism, by which auxin signaling directly targets PIN auxin
transporters. Via the cell-surface ABP1-TMK1 receptor module, auxin rapidly induces
phosphorylation and thus stabilization of PIN2. Following gravistimulation, initial
auxin asymmetry activates autophosphorylation of the TMK1 kinase. This induces
TMK1 interaction with and phosphorylation of PIN2, stabilizing PIN2 at the lower
root side, thus reinforcing asymmetric auxin flow for root bending. Upstream of
TMK1 in this regulation, ABP1 acts redundantly with the root-expressed ABP1-LIKE
auxin receptor ABL3. Such positive feedback between cell-surface auxin signaling
and PIN-mediated polar auxin transport is fundamental for robust root gravitropism
and presumably also for other self-organizing developmental phenomena.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: 'We thank W. Gray for providing material; N. Gnyliukh and E. Cervenova
for help with manuscript preparation; J. Schmid for help with cloning. We thank
Dolf Weijers, Mark Roosjen, and Andre Kuhn for discussions and support with phospho-proteomic
analyses. We thank the Bioimaging and Life Science facilities at ISTA for their
excellent service and assistance. The research leading to these results has received
funding from the European Research Council (ERC) under the European Union’s Horizon
2020 research and innovation program grant agreement No 742985 and Austrian Science
Fund (FWF): I3630-775 B25 to J.F; National Natural Science Foundation of China (Grant
32130010, 31422008), start-up funds from FAFU to T.X., Y.J. was funded by ERC no.
3363360-APPL under FP/2007-2013. L.R. was supported by FP7-PEOPLE-2011-COFUND ISTFELLOW
program (IC1023FELL01) and the European Molecular Biology Organization (EMBO) long-term
postdoctoral fellowship (ALTF 985- 2016). S.T. was supported by the National Natural
Science Foundation of China (32321001).'
article_processing_charge: No
author:
- first_name: Lesia
full_name: Rodriguez Solovey, Lesia
id: 3922B506-F248-11E8-B48F-1D18A9856A87
last_name: Rodriguez Solovey
orcid: 0000-0002-7244-7237
- first_name: Lukas
full_name: Fiedler, Lukas
id: 7c417475-8972-11ed-ae7b-8b674ca26986
last_name: Fiedler
- first_name: Minxia
full_name: Zou, Minxia
id: 5c243f41-03f3-11ec-841c-96faf48a7ef9
last_name: Zou
- first_name: Caterina
full_name: Giannini, Caterina
id: e3fdddd5-f6e0-11ea-865d-ca99ee6367f4
last_name: Giannini
- first_name: Aline
full_name: Monzer, Aline
id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425
last_name: Monzer
- 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: Yongfan
full_name: Yu, Yongfan
last_name: Yu
- first_name: Zuzana
full_name: Gelová, Zuzana
id: 0AE74790-0E0B-11E9-ABC7-1ACFE5697425
last_name: Gelová
orcid: 0000-0003-4783-1752
- first_name: Inge
full_name: Verstraeten, Inge
id: 362BF7FE-F248-11E8-B48F-1D18A9856A87
last_name: Verstraeten
orcid: 0000-0001-7241-2328
- first_name: Jakub
full_name: Hajny, Jakub
id: 4800CC20-F248-11E8-B48F-1D18A9856A87
last_name: Hajny
orcid: 0000-0003-2140-7195
- first_name: Meng
full_name: Chen, Meng
last_name: Chen
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: Lukas
full_name: Hörmayer, Lukas
id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87
last_name: Hörmayer
orcid: 0000-0001-8295-2926
- first_name: Lanxin
full_name: Li, Lanxin
id: 367EF8FA-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0002-5607-272X
- first_name: Maria Mar
full_name: Marques-Bueno, Maria Mar
last_name: Marques-Bueno
- first_name: Zainab
full_name: Quddoos, Zainab
id: 32ff3c64-04a0-11f0-a50f-d0c45bfac466
last_name: Quddoos
- first_name: Gergely
full_name: Molnar, Gergely
id: 34F1AF46-F248-11E8-B48F-1D18A9856A87
last_name: Molnar
- first_name: Tongda
full_name: Xu, Tongda
last_name: Xu
- first_name: Ivan
full_name: Kulich, Ivan
id: 57a1567c-8314-11eb-9063-c9ddc3451a54
last_name: Kulich
- first_name: Yvon
full_name: Jaillais, Yvon
last_name: Jaillais
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Rodriguez Solovey L, Fiedler L, Zou M, et al. ABP1/ABL3-TMK1 cell-surface auxin
signaling directly targets PIN2-mediated auxin fluxes for root gravitropism. bioRxiv.
doi:10.1101/2022.11.30.518503
apa: Rodriguez Solovey, L., Fiedler, L., Zou, M., Giannini, C., Monzer, A., Vladimirtsev,
D., … Friml, J. (n.d.). ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets
PIN2-mediated auxin fluxes for root gravitropism. bioRxiv. https://doi.org/10.1101/2022.11.30.518503
chicago: Rodriguez Solovey, Lesia, Lukas Fiedler, Minxia Zou, Caterina Giannini,
Aline Monzer, Dmitrii Vladimirtsev, Marek Randuch, et al. “ABP1/ABL3-TMK1 Cell-Surface
Auxin Signaling Directly Targets PIN2-Mediated Auxin Fluxes for Root Gravitropism.”
BioRxiv, n.d. https://doi.org/10.1101/2022.11.30.518503.
ieee: L. Rodriguez Solovey et al., “ABP1/ABL3-TMK1 cell-surface auxin signaling
directly targets PIN2-mediated auxin fluxes for root gravitropism,” bioRxiv.
.
ista: Rodriguez Solovey L, Fiedler L, Zou M, Giannini C, Monzer A, Vladimirtsev
D, Randuch M, Yu Y, Gelová Z, Verstraeten I, Hajny J, Chen M, Tan S, Hörmayer
L, Li L, Marques-Bueno MM, Quddoos Z, Molnar G, Xu T, Kulich I, Jaillais Y, Friml
J. ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated
auxin fluxes for root gravitropism. bioRxiv, 10.1101/2022.11.30.518503.
mla: Rodriguez Solovey, Lesia, et al. “ABP1/ABL3-TMK1 Cell-Surface Auxin Signaling
Directly Targets PIN2-Mediated Auxin Fluxes for Root Gravitropism.” BioRxiv,
doi:10.1101/2022.11.30.518503.
short: L. Rodriguez Solovey, L. Fiedler, M. Zou, C. Giannini, A. Monzer, D. Vladimirtsev,
M. Randuch, Y. Yu, Z. Gelová, I. Verstraeten, J. Hajny, M. Chen, S. Tan, L. Hörmayer,
L. Li, M.M. Marques-Bueno, Z. Quddoos, G. Molnar, T. Xu, I. Kulich, Y. Jaillais,
J. Friml, BioRxiv (n.d.).
corr_author: '1'
das_tickbox: '1'
date_created: 2025-03-13T08:36:48Z
date_published: 2025-02-20T00:00:00Z
date_updated: 2026-08-14T09:33:45Z
day: '20'
ddc:
- '580'
department:
- _id: JiFr
- _id: XiFe
doi: 10.1101/2022.11.30.518503
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2022.11.30.518503
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 26060676-B435-11E9-9278-68D0E5697425
grant_number: ALTF 985-2016
name: Cell surface receptor complexes for auxin signaling in plants
publication: bioRxiv
publication_status: draft
related_material:
record:
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relation: later_version
status: public
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relation: dissertation_contains
status: public
- id: '19395'
relation: dissertation_contains
status: public
status: public
title: ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated
auxin fluxes for root gravitropism
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '19398'
abstract:
- lang: eng
text: Receptor-like kinases (RLKs), particularly the Transmembrane Kinase (TMK)
family, play essential roles in signaling and development, with TMKs being key
components of auxin perception and downstream phosphorylation events. While TMKs’
involvement in auxin canalization, a process essential for vasculature formation
and regeneration, has been established, nonetheless, the additional signaling
and regulatory partners remain poorly understood. In this study, we identify and
characterize seven leucine-rich repeat RLKs (TINT1–TINT7) as novel interactors
of TMK1, revealing their diverse evolutionary, structural, and functional characteristics.
Our results show that TINTs interact with TMK1 and highlight their roles in regulating
various developmental processes. Majority of TINTs contributes, together with
TMK1, to auxin canalization, with TINT5 linking TMK1 to other canalization component
CAMEL. Beyond canalization, we also establish the role of TINT-TMK1 interactions
in processes such as stomatal movement and the hypocotyl’s gravitropic response.
These findings suggest that TINTs, through their interaction with TMK1, are integral
components of various signaling networks, contributing to both auxin canalization
and broader plant development.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: We deeply appreciate M. Wrzaczek’s constructive input and insightful
discussions, which significantly enriched this work. We thank L. Fiedler for helping
with the heat map and for the discussions. We also thank the facilities at ISTA,
the imaging and optics (IOF) and Lab Support (LSF) facilities for their service
and assistance.
article_processing_charge: No
author:
- first_name: Aline
full_name: Monzer, Aline
id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425
last_name: Monzer
- first_name: Ewa
full_name: Mazur, Ewa
last_name: Mazur
- first_name: Lesia
full_name: Rodriguez Solovey, Lesia
id: 3922B506-F248-11E8-B48F-1D18A9856A87
last_name: Rodriguez Solovey
orcid: 0000-0002-7244-7237
- first_name: Michelle C
full_name: Gallei, Michelle C
id: 35A03822-F248-11E8-B48F-1D18A9856A87
last_name: Gallei
orcid: 0000-0003-1286-7368
- first_name: Minxia
full_name: Zou, Minxia
id: 5c243f41-03f3-11ec-841c-96faf48a7ef9
last_name: Zou
- first_name: Michael
full_name: Smejkal, Michael
id: 79a5a1be-04a3-11f0-ba18-a1730e0b58e9
last_name: Smejkal
- first_name: Ema
full_name: Cervenova, Ema
id: 9f185b95-04a3-11f0-8245-f5e32eeb470f
last_name: Cervenova
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Monzer A, Mazur E, Rodriguez Solovey L, et al. TMK interacting network of receptor
like kinases for auxin canalization and beyond. bioRxiv. doi:10.1101/2025.02.28.640727
apa: Monzer, A., Mazur, E., Rodriguez Solovey, L., Gallei, M. C., Zou, M., Smejkal,
M., … Friml, J. (n.d.). TMK interacting network of receptor like kinases for auxin
canalization and beyond. bioRxiv. https://doi.org/10.1101/2025.02.28.640727
chicago: Monzer, Aline, Ewa Mazur, Lesia Rodriguez Solovey, Michelle C Gallei, Minxia
Zou, Michael Smejkal, Ema Cervenova, and Jiří Friml. “TMK Interacting Network
of Receptor like Kinases for Auxin Canalization and Beyond.” BioRxiv, n.d.
https://doi.org/10.1101/2025.02.28.640727.
ieee: A. Monzer et al., “TMK interacting network of receptor like kinases
for auxin canalization and beyond,” bioRxiv. .
ista: Monzer A, Mazur E, Rodriguez Solovey L, Gallei MC, Zou M, Smejkal M, Cervenova
E, Friml J. TMK interacting network of receptor like kinases for auxin canalization
and beyond. bioRxiv, 10.1101/2025.02.28.640727.
mla: Monzer, Aline, et al. “TMK Interacting Network of Receptor like Kinases for
Auxin Canalization and Beyond.” BioRxiv, doi:10.1101/2025.02.28.640727.
short: A. Monzer, E. Mazur, L. Rodriguez Solovey, M.C. Gallei, M. Zou, M. Smejkal,
E. Cervenova, J. Friml, BioRxiv (n.d.).
corr_author: '1'
das_tickbox: '1'
date_created: 2025-03-12T14:28:53Z
date_published: 2025-03-02T00:00:00Z
date_updated: 2026-08-14T09:33:45Z
day: '02'
ddc:
- '580'
department:
- _id: GradSch
- _id: JiFr
- _id: EvBe
doi: 10.1101/2025.02.28.640727
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2025.02.28.640727
month: '03'
oa: 1
oa_version: Published Version
publication: bioRxiv
publication_status: draft
related_material:
record:
- id: '19395'
relation: dissertation_contains
status: public
status: public
title: TMK interacting network of receptor like kinases for auxin canalization and
beyond
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_place: publisher
OA_type: gold
_id: '21280'
abstract:
- lang: eng
text: We give an algorithm that, with high probability, maintains a (1-ε)-approximate
s-t maximum flow in undirected, uncapacitated n-vertex graphs undergoing m edge
insertions in Õ(m+ n F^*/ε) total update time, where F^{*} is the maximum flow
on the final graph. This is the first algorithm to achieve polylogarithmic amortized
update time for dense graphs (m = Ω(n²)), and more generally, for graphs where
F^* = Õ(m/n). At the heart of our incremental algorithm is the residual graph
sparsification technique of Karger and Levine [SICOMP '15], originally designed
for computing exact maximum flows in the static setting. Our main contributions
are (i) showing how to maintain such sparsifiers for approximate maximum flows
in the incremental setting and (ii) generalizing the cut sparsification framework
of Fung et al. [SICOMP '19] from undirected graphs to balanced directed graphs.
acknowledgement: "Monika Henzinger and A. R. Sricharan: This project has received
funding from the European Research Council (ERC) under the European Union’s Horizon
2020 research and innovation\r\nprogramme (MoDynStruct, No. 101019564) and the Austrian
Science Fund (FWF) grant DOI\r\n10.55776/Z422, grant DOI 10.55776/I5982, and grant
DOI 10.55776/P33775 with additional funding from the netidee SCIENCE Stiftung, 2020–2024.
Harald Räcke: This project has received funding from the Deutsche Forschungsgemeinschaft
(DFG, German Research Foundation) – 498605858 and 470029389."
alternative_title:
- LIPIcs
article_processing_charge: No
arxiv: 1
author:
- first_name: Gramoz
full_name: Goranci, Gramoz
last_name: Goranci
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Harald
full_name: Räcke, Harald
last_name: Räcke
- first_name: A.
full_name: Sricharan, A.
last_name: Sricharan
citation:
ama: 'Goranci G, Henzinger M, Räcke H, Sricharan A. Incremental approximate maximum
flow via residual graph sparsification. In: 52nd International Colloquium on
Automata, Languages, and Programming. Vol 334. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik; 2025:91:1-91:20. doi:10.4230/lipics.icalp.2025.91'
apa: 'Goranci, G., Henzinger, M., Räcke, H., & Sricharan, A. (2025). Incremental
approximate maximum flow via residual graph sparsification. In 52nd International
Colloquium on Automata, Languages, and Programming (Vol. 334, p. 91:1-91:20).
Aarhus, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/lipics.icalp.2025.91'
chicago: Goranci, Gramoz, Monika Henzinger, Harald Räcke, and A. Sricharan. “Incremental
Approximate Maximum Flow via Residual Graph Sparsification.” In 52nd International
Colloquium on Automata, Languages, and Programming, 334:91:1-91:20. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2025. https://doi.org/10.4230/lipics.icalp.2025.91.
ieee: G. Goranci, M. Henzinger, H. Räcke, and A. Sricharan, “Incremental approximate
maximum flow via residual graph sparsification,” in 52nd International Colloquium
on Automata, Languages, and Programming, Aarhus, Denmark, 2025, vol. 334,
p. 91:1-91:20.
ista: 'Goranci G, Henzinger M, Räcke H, Sricharan A. 2025. Incremental approximate
maximum flow via residual graph sparsification. 52nd International Colloquium
on Automata, Languages, and Programming. ICALP: Automata, Languages and Programming,
LIPIcs, vol. 334, 91:1-91:20.'
mla: Goranci, Gramoz, et al. “Incremental Approximate Maximum Flow via Residual
Graph Sparsification.” 52nd International Colloquium on Automata, Languages,
and Programming, vol. 334, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2025, p. 91:1-91:20, doi:10.4230/lipics.icalp.2025.91.
short: G. Goranci, M. Henzinger, H. Räcke, A. Sricharan, in:, 52nd International
Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2025, p. 91:1-91:20.
conference:
end_date: 2025-07-11
location: Aarhus, Denmark
name: 'ICALP: Automata, Languages and Programming'
start_date: 2025-07-08
corr_author: '1'
date_created: 2026-02-17T08:26:06Z
date_published: 2025-06-30T00:00:00Z
date_updated: 2026-08-20T06:28:00Z
day: '30'
ddc:
- '000'
department:
- _id: MoHe
doi: 10.4230/lipics.icalp.2025.91
ec_funded: 1
external_id:
arxiv:
- '2502.09105'
file:
- access_level: open_access
checksum: c178cf554e44204b9f64ebd9b54cf7ba
content_type: application/pdf
creator: dernst
date_created: 2026-02-18T09:02:33Z
date_updated: 2026-02-18T09:02:33Z
file_id: '21315'
file_name: 2025_ICALP_Goranci.pdf
file_size: 944824
relation: main_file
success: 1
file_date_updated: 2026-02-18T09:02:33Z
has_accepted_license: '1'
intvolume: ' 334'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 91:1-91:20
project:
- _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62
call_identifier: H2020
grant_number: '101019564'
name: The design and evaluation of modern fully dynamic data structures
- _id: 34def286-11ca-11ed-8bc3-da5948e1613c
grant_number: Z00422
name: Efficient algorithms
- _id: bda196b2-d553-11ed-ba76-8e8ee6c21103
grant_number: I05982
name: Static and Dynamic Hierarchical Graph Decompositions
- _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe
grant_number: P33775
name: Fast Algorithms for a Reactive Network Layer
publication: 52nd International Colloquium on Automata, Languages, and Programming
publication_identifier:
isbn:
- '9783959773720'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
related_material:
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scopus_import: '1'
status: public
title: Incremental approximate maximum flow via residual graph sparsification
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: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 334
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '21262'
abstract:
- lang: eng
text: "Continuous Group Key Agreement (CGKA) is the primitive underlying secure
group messaging. It allows a large group of N users to maintain a shared secret
key that is frequently rotated by the\r\ngroup members in order to achieve forward
secrecy and post compromise security. The group messaging scheme Messaging Layer
Security (MLS) standardized by the IETF makes use of a CGKA called TreeKEM which
arranges the N group members in a binary tree. Here, each node is associated with
a public-key, each user is assigned one of the leaves, and a user knows the corresponding
secret keys from their leaf to the root. To update the key material known to them,
a user must just replace keys at log(N) nodes, which requires them to create and
upload log(N) ciphertexts. Such updates must be processed sequentially by all
users, which for large groups is impractical. To allow for concurrent updates,
TreeKEM uses the “propose and commit” paradigm, where multiple users can concurrently
propose to update (by just sampling a fresh leaf key), and a single user can then
commit to all proposals at once. Unfortunately, this process destroys the binary
tree structure as the tree gets pruned and some nodes must be “blanked” at the
cost of increasing the in-degree of others, which makes the commit operation,
as well as, future commits more costly. In the worst case, the update cost (in
terms of uploaded ciphertexts) per user can grow from log(N) to Ω(N). In this
work we provide two main contributions. First, we show that MLS’ communication
complexity is bad not only in the worst case but also if the proposers and committers
are chosen at random: even if there’s just one update proposal for every commit
the expected cost is already over √N, and it approaches N as this ratio changes
towards more proposals. Our second contribution is a new variant of propose and
commit for\r\nTreeKEM which for moderate amounts of update proposals per commit
provably achieves an update cost of Θ(log(N)) assuming the proposers and committers
are chosen at random."
acknowledgement: B. Auerbach and B. Erol—Conducted part of this work at ISTA.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Benedikt
full_name: Auerbach, Benedikt
id: D33D2B18-E445-11E9-ABB7-15F4E5697425
last_name: Auerbach
orcid: 0000-0002-7553-6606
- first_name: Miguel
full_name: Cueto Noval, Miguel
id: ffc563a3-f6e0-11ea-865d-e3cce03d17cc
last_name: Cueto Noval
orcid: 0000-0002-2505-4246
- first_name: Boran
full_name: Erol, Boran
last_name: Erol
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Auerbach B, Cueto Noval M, Erol B, Pietrzak KZ. Continuous group-key agreement:
Concurrent updates without pruning. In: 45th Annual International Cryptology
Conference. Vol 16007. Springer Nature; 2025:141-172. doi:10.1007/978-3-032-01913-4_5'
apa: 'Auerbach, B., Cueto Noval, M., Erol, B., & Pietrzak, K. Z. (2025). Continuous
group-key agreement: Concurrent updates without pruning. In 45th Annual International
Cryptology Conference (Vol. 16007, pp. 141–172). Santa Barbara, CA, United
States: Springer Nature. https://doi.org/10.1007/978-3-032-01913-4_5'
chicago: 'Auerbach, Benedikt, Miguel Cueto Noval, Boran Erol, and Krzysztof Z Pietrzak.
“Continuous Group-Key Agreement: Concurrent Updates without Pruning.” In 45th
Annual International Cryptology Conference, 16007:141–72. Springer Nature,
2025. https://doi.org/10.1007/978-3-032-01913-4_5.'
ieee: 'B. Auerbach, M. Cueto Noval, B. Erol, and K. Z. Pietrzak, “Continuous group-key
agreement: Concurrent updates without pruning,” in 45th Annual International
Cryptology Conference, Santa Barbara, CA, United States, 2025, vol. 16007,
pp. 141–172.'
ista: 'Auerbach B, Cueto Noval M, Erol B, Pietrzak KZ. 2025. Continuous group-key
agreement: Concurrent updates without pruning. 45th Annual International Cryptology
Conference. CRYPTO: International Cryptology Conference, LNCS, vol. 16007, 141–172.'
mla: 'Auerbach, Benedikt, et al. “Continuous Group-Key Agreement: Concurrent Updates
without Pruning.” 45th Annual International Cryptology Conference, vol.
16007, Springer Nature, 2025, pp. 141–72, doi:10.1007/978-3-032-01913-4_5.'
short: B. Auerbach, M. Cueto Noval, B. Erol, K.Z. Pietrzak, in:, 45th Annual International
Cryptology Conference, Springer Nature, 2025, pp. 141–172.
conference:
end_date: 2025-08-21
location: Santa Barbara, CA, United States
name: 'CRYPTO: International Cryptology Conference'
start_date: 2025-08-17
date_created: 2026-02-17T07:41:04Z
date_published: 2025-08-17T00:00:00Z
date_updated: 2026-08-21T10:53:16Z
day: '17'
department:
- _id: KrPi
doi: 10.1007/978-3-032-01913-4_5
intvolume: ' 16007'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2025/1035
month: '08'
oa: 1
oa_version: Preprint
page: 141-172
publication: 45th Annual International Cryptology Conference
publication_identifier:
eisbn:
- '9783032019134'
eissn:
- 1611-3349
isbn:
- '9783032019127'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '22664'
relation: dissertation_contains
status: public
status: public
title: 'Continuous group-key agreement: Concurrent updates without pruning'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16007
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '19278'
abstract:
- lang: eng
text: 'When two insulating, neutral materials are contacted and separated, they
exchange electrical charge1. Experiments have long suggested that this ‘contact
electrification’ is transitive, with different materials ordering into ‘triboelectric
series’ based on the sign of charge acquired2. At the same time, the effect is
plagued by unpredictability, preventing consensus on the mechanism and casting
doubt on the rhyme and reason that series imply3. Here we expose an unanticipated
connection between the unpredictability and order in contact electrification:
nominally identical materials initially exchange charge randomly and intransitively,
but—over repeated experiments—order into triboelectric series. We find that this
evolution is driven by the act of contact itself—samples with more contacts in
their history charge negatively to ones with fewer contacts. Capturing this ‘contact
bias’ in a minimal model, we recreate both the initial randomness and ultimate
order in numerical simulations and use it experimentally to force the appearance
of a triboelectric series of our choosing. With a set of surface-sensitive techniques
to search for the underlying alterations contact creates, we only find evidence
of nanoscale morphological changes, pointing to a mechanism strongly coupled with
mechanics. Our results highlight the centrality of contact history in contact
electrification and suggest that focusing on the unpredictability that has long
plagued the effect may hold the key to understanding it.'
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
- _id: ScienComp
- _id: EM-Fac
- _id: LifeSc
acknowledgement: This project has received financing from the European Research Council
grant agreement no. 949120 under the European Union’s Horizon 2020 research and
innovation programme. The Analytical Instrumentation Center of the TU Wien acknowledges
support by the FFG project ‘ELSA’ under grant no. 884672. C.M.P. and M.O. acknowledge
the state of Lower Austria and the European Regional Development Fund under grant
no. WST3-F-542638/004-2021. This research was supported by the Scientific Service
Units of the Institute of Science and Technology Austria through resources provided
by the Miba Machine Shop, Nanofabrication Facility, Scientific Computing facility,
Electron Microscopy Facility and Lab Support Facility. We thank J. Garcia-Suarez
and G. Anciaux for the suggestion to look into the roughness power spectral density.
We thank I.-M. Strugaru for help with testing the device for Young’s modulus measurements.
Open access funding provided by Institute of Science and Technology (IST Austria).
article_number: 664-669
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Juan Carlos A
full_name: Sobarzo Ponce, Juan Carlos A
id: 4B807D68-AE37-11E9-AC72-31CAE5697425
last_name: Sobarzo Ponce
- first_name: Felix
full_name: Pertl, Felix
id: 6313aec0-15b2-11ec-abd3-ed67d16139af
last_name: Pertl
orcid: 0000-0003-0463-5794
- first_name: Daniel
full_name: Balazs, Daniel
id: 302BADF6-85FC-11EA-9E3B-B9493DDC885E
last_name: Balazs
orcid: 0000-0001-7597-043X
- first_name: Tommaso
full_name: Costanzo, Tommaso
id: D93824F4-D9BA-11E9-BB12-F207E6697425
last_name: Costanzo
orcid: 0000-0001-9732-3815
- first_name: Markus
full_name: Sauer, Markus
last_name: Sauer
- first_name: Annette
full_name: Foelske, Annette
last_name: Foelske
- first_name: Markus
full_name: Ostermann, Markus
last_name: Ostermann
- first_name: Christian M.
full_name: Pichler, Christian M.
last_name: Pichler
- first_name: Yongkang
full_name: Wang, Yongkang
last_name: Wang
- first_name: Yuki
full_name: Nagata, Yuki
last_name: Nagata
- first_name: Mischa
full_name: Bonn, Mischa
last_name: Bonn
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
citation:
ama: Sobarzo Ponce JCA, Pertl F, Balazs D, et al. Spontaneous ordering of identical
materials into a triboelectric series. Nature. 2025;638(8051). doi:10.1038/s41586-024-08530-6
apa: Sobarzo Ponce, J. C. A., Pertl, F., Balazs, D., Costanzo, T., Sauer, M., Foelske,
A., … Waitukaitis, S. R. (2025). Spontaneous ordering of identical materials into
a triboelectric series. Nature. Springer Nature. https://doi.org/10.1038/s41586-024-08530-6
chicago: Sobarzo Ponce, Juan Carlos A, Felix Pertl, Daniel Balazs, Tommaso Costanzo,
Markus Sauer, Annette Foelske, Markus Ostermann, et al. “Spontaneous Ordering
of Identical Materials into a Triboelectric Series.” Nature. Springer Nature,
2025. https://doi.org/10.1038/s41586-024-08530-6.
ieee: J. C. A. Sobarzo Ponce et al., “Spontaneous ordering of identical materials
into a triboelectric series,” Nature, vol. 638, no. 8051. Springer Nature,
2025.
ista: Sobarzo Ponce JCA, Pertl F, Balazs D, Costanzo T, Sauer M, Foelske A, Ostermann
M, Pichler CM, Wang Y, Nagata Y, Bonn M, Waitukaitis SR. 2025. Spontaneous ordering
of identical materials into a triboelectric series. Nature. 638(8051), 664–669.
mla: Sobarzo Ponce, Juan Carlos A., et al. “Spontaneous Ordering of Identical Materials
into a Triboelectric Series.” Nature, vol. 638, no. 8051, 664–669, Springer
Nature, 2025, doi:10.1038/s41586-024-08530-6.
short: J.C.A. Sobarzo Ponce, F. Pertl, D. Balazs, T. Costanzo, M. Sauer, A. Foelske,
M. Ostermann, C.M. Pichler, Y. Wang, Y. Nagata, M. Bonn, S.R. Waitukaitis, Nature
638 (2025).
corr_author: '1'
date_created: 2025-03-02T23:01:52Z
date_published: 2025-02-20T00:00:00Z
date_updated: 2026-08-27T11:42:43Z
day: '20'
ddc:
- '530'
department:
- _id: ScWa
- _id: LifeSc
- _id: EM-Fac
doi: 10.1038/s41586-024-08530-6
ec_funded: 1
external_id:
isi:
- '001428076100015'
pmid:
- '39972227'
file:
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checksum: fecf302274dd3218d3e7dd22f39a6c0c
content_type: application/pdf
creator: dernst
date_created: 2025-03-04T10:05:18Z
date_updated: 2025-03-04T10:05:18Z
file_id: '19289'
file_name: 2025_Nature_Sobarzo.pdf
file_size: 3807415
relation: main_file
success: 1
file_date_updated: 2025-03-04T10:05:18Z
has_accepted_license: '1'
intvolume: ' 638'
isi: 1
issue: '8051'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 0aa60e99-070f-11eb-9043-a6de6bdc3afa
call_identifier: H2020
grant_number: '949120'
name: 'Tribocharge: a multi-scale approach to an enduring problem in physics'
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/an-electrifying-turn-in-an-age-old-quest/
record:
- id: '20203'
relation: dissertation_contains
status: public
- id: '22684'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Spontaneous ordering of identical materials into a triboelectric series
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 638
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20481'
abstract:
- lang: eng
text: 'Kelvin probe force microscopy (KPFM) is widely used in stationary and dynamic
studies of contact electrification. An obvious question that connects these two
has been overlooked: when are charge dynamics too fast for stationary studies
to be meaningful? Using a rapid transfer system to quickly perform KPFM after
contact, we find the dynamics are too fast in all but the best insulators. Our
data further suggest that dynamics are caused by bulk as opposed to surface conductivity,
and that charge-transfer heterogeneity is less prevalent than previously suggested.'
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
- _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 agreement No. 949120). This research was supported by the Scientific Service
Units of The Institute of Science and Technology Austria (ISTA) through resources
provided by the Miba Machine Shop, the Nanofabrication Facility and Lab Support
Facility.
article_number: '146202'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Felix
full_name: Pertl, Felix
id: 6313aec0-15b2-11ec-abd3-ed67d16139af
last_name: Pertl
orcid: 0000-0003-0463-5794
- first_name: Isaac C
full_name: Lenton, Isaac C
id: a550210f-223c-11ec-8182-e2d45e817efb
last_name: Lenton
orcid: 0000-0002-5010-6984
- first_name: Tobias
full_name: Cramer, Tobias
last_name: Cramer
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
citation:
ama: 'Pertl F, Lenton IC, Cramer T, Waitukaitis SR. No time for surface charge:
How bulk conductivity hides charge patterns from Kelvin probe force microscopy
in contact-electrified surfaces. Physical Review Letters. 2025;135(14).
doi:10.1103/lcsm-xxty'
apa: 'Pertl, F., Lenton, I. C., Cramer, T., & Waitukaitis, S. R. (2025). No
time for surface charge: How bulk conductivity hides charge patterns from Kelvin
probe force microscopy in contact-electrified surfaces. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/lcsm-xxty'
chicago: 'Pertl, Felix, Isaac C Lenton, Tobias Cramer, and Scott R Waitukaitis.
“No Time for Surface Charge: How Bulk Conductivity Hides Charge Patterns from
Kelvin Probe Force Microscopy in Contact-Electrified Surfaces.” Physical Review
Letters. American Physical Society, 2025. https://doi.org/10.1103/lcsm-xxty.'
ieee: 'F. Pertl, I. C. Lenton, T. Cramer, and S. R. Waitukaitis, “No time for surface
charge: How bulk conductivity hides charge patterns from Kelvin probe force microscopy
in contact-electrified surfaces,” Physical Review Letters, vol. 135, no.
14. American Physical Society, 2025.'
ista: 'Pertl F, Lenton IC, Cramer T, Waitukaitis SR. 2025. No time for surface charge:
How bulk conductivity hides charge patterns from Kelvin probe force microscopy
in contact-electrified surfaces. Physical Review Letters. 135(14), 146202.'
mla: 'Pertl, Felix, et al. “No Time for Surface Charge: How Bulk Conductivity Hides
Charge Patterns from Kelvin Probe Force Microscopy in Contact-Electrified Surfaces.”
Physical Review Letters, vol. 135, no. 14, 146202, American Physical Society,
2025, doi:10.1103/lcsm-xxty.'
short: F. Pertl, I.C. Lenton, T. Cramer, S.R. Waitukaitis, Physical Review Letters
135 (2025).
corr_author: '1'
date_created: 2025-10-16T13:13:29Z
date_published: 2025-09-30T00:00:00Z
date_updated: 2026-08-27T11:42:43Z
day: '30'
ddc:
- '530'
department:
- _id: ScWa
doi: 10.1103/lcsm-xxty
ec_funded: 1
external_id:
arxiv:
- '2502.12718'
isi:
- '001587263900003'
file:
- access_level: open_access
checksum: 7e45e89b8db0b7f01e63185c68e4b0f9
content_type: application/pdf
creator: dernst
date_created: 2025-10-23T09:32:31Z
date_updated: 2025-10-23T09:32:31Z
file_id: '20522'
file_name: 2025_PhysReviewLetters_Pertl.pdf
file_size: 1692251
relation: main_file
success: 1
file_date_updated: 2025-10-23T09:32:31Z
has_accepted_license: '1'
intvolume: ' 135'
isi: 1
issue: '14'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 0aa60e99-070f-11eb-9043-a6de6bdc3afa
call_identifier: H2020
grant_number: '949120'
name: 'Tribocharge: a multi-scale approach to an enduring problem in physics'
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '20523'
relation: research_data
status: public
- id: '22684'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'No time for surface charge: How bulk conductivity hides charge patterns from
Kelvin probe force microscopy in contact-electrified surfaces'
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: 135
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20452'
abstract:
- lang: eng
text: Accurate modeling of long-range forces is critical in atomistic simulations,
as they play a central role in determining the properties of material and chemical
systems. However, standard machine learning interatomic potentials (MLIPs) often
rely on short-range approximations, limiting their applicability to systems with
significant electrostatics and dispersion forces. We recently introduced the Latent
Ewald Summation (LES) method, which captures long-range electrostatics without
explicitly learning atomic charges or charge equilibration. We benchmark LES on
diverse and challenging systems, including charged molecules, ionic liquids, electrolyte
solutions, polar dipeptides, surface adsorption, electrolyte/solid interfaces,
and solid-solid interfaces. Here we show that LES can reproduce the exact atomic
charges for classical systems with fixed charges and can infer dipole and quadrupole
moments, as well as the dipole derivative with respect to atomic positions, for
quantum mechanical systems. Moreover, LES can achieve better accuracy in energy
and force predictions compared to methods that explicitly learn from charges.
acknowledgement: We thank Chunyi Zhang for providing the TiO2(101)/NaCl+NaOH+HCl(aq)
dataset and for useful discussions. We thank Jia-Xin Zhu for providing the Pt(111)/KF(aq)
dataset. We thank Tsz Wai Ko and Jonas Finkler for useful discussions and for the
DFT-optimized Au2-MgO(001) structures. We thank Junmin Chen for discussions. D.K
and B.C. acknowledge funding from Toyota Research Institute Synthesis Advanced Research
Challenge. D.S.K. and P.Z. acknowledge funding from BIDMaP Postdoctoral Fellowship.
article_number: '8763'
article_processing_charge: Yes
article_type: original
author:
- first_name: Daniel S.
full_name: King, Daniel S.
last_name: King
- first_name: Dongjin
full_name: Kim, Dongjin
last_name: Kim
- first_name: Peichen
full_name: Zhong, Peichen
last_name: Zhong
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: King DS, Kim D, Zhong P, Cheng B. Machine learning of charges and long-range
interactions from energies and forces. Nature Communications. 2025;16.
doi:10.1038/s41467-025-63852-x
apa: King, D. S., Kim, D., Zhong, P., & Cheng, B. (2025). Machine learning of
charges and long-range interactions from energies and forces. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-025-63852-x
chicago: King, Daniel S., Dongjin Kim, Peichen Zhong, and Bingqing Cheng. “Machine
Learning of Charges and Long-Range Interactions from Energies and Forces.” Nature
Communications. Springer Nature, 2025. https://doi.org/10.1038/s41467-025-63852-x.
ieee: D. S. King, D. Kim, P. Zhong, and B. Cheng, “Machine learning of charges and
long-range interactions from energies and forces,” Nature Communications,
vol. 16. Springer Nature, 2025.
ista: King DS, Kim D, Zhong P, Cheng B. 2025. Machine learning of charges and long-range
interactions from energies and forces. Nature Communications. 16, 8763.
mla: King, Daniel S., et al. “Machine Learning of Charges and Long-Range Interactions
from Energies and Forces.” Nature Communications, vol. 16, 8763, Springer
Nature, 2025, doi:10.1038/s41467-025-63852-x.
short: D.S. King, D. Kim, P. Zhong, B. Cheng, Nature Communications 16 (2025).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: The training sets, training scripts, MD input files, and
trained CACE potentials are available at https://github.com/BingqingCheng/cace-lr-fit;
see https://doi.org/10.5281/zenodo.16415061. Source data for all figures are provided
with this paper. Source data are provided with this paper.
date_created: 2025-10-12T22:01:25Z
date_published: 2025-10-01T00:00:00Z
date_updated: 2026-08-27T12:16:47Z
day: '01'
ddc:
- '000'
department:
- _id: BiCh
doi: 10.1038/s41467-025-63852-x
external_id:
isi:
- '001586620700015'
pmid:
- '41034200'
file:
- access_level: open_access
checksum: 34b6005d349bbff85839c4e51d6c8725
content_type: application/pdf
creator: dernst
date_created: 2025-10-13T07:54:51Z
date_updated: 2025-10-13T07:54:51Z
file_id: '20460'
file_name: 2025_NatureComm_King.pdf
file_size: 4907055
relation: main_file
success: 1
file_date_updated: 2025-10-13T07:54:51Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
language:
- iso: eng
month: '10'
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'
related_material:
record:
- id: '22770'
relation: research_data
status: public
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Machine learning of charges and long-range interactions from energies and forces
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: 16
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '22770'
article_processing_charge: No
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
last_name: Cheng
- first_name: Daniel
full_name: King, Daniel
last_name: King
- first_name: Dongjin
full_name: Kim, Dongjin
last_name: Kim
- first_name: Peichen
full_name: Zhong, Peichen
last_name: Zhong
citation:
ama: 'Cheng B, King D, Kim D, Zhong P. BingqingCheng/cace-lr-fit: V0. 2025. doi:10.5281/zenodo.16415060'
apa: 'Cheng, B., King, D., Kim, D., & Zhong, P. (2025). BingqingCheng/cace-lr-fit:
V0. Repository. https://doi.org/10.5281/zenodo.16415060'
chicago: 'Cheng, Bingqing, Daniel King, Dongjin Kim, and Peichen Zhong. “BingqingCheng/Cace-Lr-Fit:
V0.” Repository, 2025. https://doi.org/10.5281/zenodo.16415060.'
ieee: 'B. Cheng, D. King, D. Kim, and P. Zhong, “BingqingCheng/cace-lr-fit: V0.”
Repository, 2025.'
ista: 'Cheng B, King D, Kim D, Zhong P. 2025. BingqingCheng/cace-lr-fit: V0, Repository,
10.5281/zenodo.16415060.'
mla: 'Cheng, Bingqing, et al. BingqingCheng/Cace-Lr-Fit: V0. Repository,
2025, doi:10.5281/zenodo.16415060.'
short: B. Cheng, D. King, D. Kim, P. Zhong, (2025).
date_created: 2026-08-27T12:13:55Z
date_published: 2025-07-24T00:00:00Z
date_updated: 2026-08-27T12:16:48Z
day: '24'
ddc:
- '000'
department:
- _id: BiCh
doi: 10.5281/zenodo.16415060
main_file_link:
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url: https://doi.org/10.5281/zenodo.16415061
month: '07'
oa: 1
oa_version: None
publisher: Repository
related_material:
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status: public
title: 'BingqingCheng/cace-lr-fit: V0'
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year: '2025'
...
---
OA_place: publisher
_id: '19684'
abstract:
- lang: eng
text: "The overarching goal of this thesis is to break down the complexity of turbulent
flows in terms of enumerable, coherent structures and patterns. In a five-paper
series, we adopt a variety of perspectives and techniques to relate the properties
of systems of increasing complexity to their underlying coherent structures. \r\n\r\nInitially,
we take a dynamical systems point of view, seeing turbulent flow as a chaotic
trajectory bouncing between exact unstable solutions of the underlying equations
of motion. Using persistent homology, the main tool of topological data analysis
capturing the persistence across scales of topological features in a point cloud,
we introduce a method that quantifies visits of turbulent trajectories to unstable
time-periodic solutions, also called periodic orbits. We demonstrate this method
first in the Rössler and Kuramoto–Sivashinsky systems. Using this method in 3D
Kolmogorov flow, we extract a Markov chain from turbulent data, where each node
corresponds to the neighbourhood of a periodic orbit. The invariant distribution
of this Markov chain reproduces expectation values on turbulent data when it is
used to weight averages on the respective periodic orbits.\r\n\r\nIn more realistic,
wall-bounded settings, such as plane-Couette flow (pcf) driven by the relative
motion of the walls, or plane-Poiseuille flow (ppf) driven by a pressure gradient,
finding exact solutions is difficult. We use dynamic mode decomposition (DMD),
a dimensionality reduction method for sequential data, to identify and approximate
low-dimensional dynamics without knowing any exact solutions. Most spatially-extended
systems are equivariant under translations, and in such cases spatial drifts dominate
DMD, hindering its use in the search for and modelling of low-dimensional dynamics.
We augment DMD with a symmetry reduction method trained on turbulent data to stop
it from seeing translations as a feature, improving its ability to extract dynamical
information in translation-equivariant systems. We find segments of turbulent
trajectories that linearize well with their symmetry-reduced DMD spectra, akin
to dynamics near exact solutions. Searching for harmonics in the spectra gives
leads for periodic orbits with spatial drifts, one of which converges to a new
solution.\r\n\r\nIn larger domains, turbulence can localize and coexist with surrounding
laminar flow. Our preceding approaches are global, taking all of a domain into
account at once, and cannot readily treat each localized patch individually. Working
first in a minimal oblique domain that can host a single 1D-localized turbulent
patch, we find that turbulence in ppf is connected to a stable periodic orbit
at a flow velocity much lower than when turbulence is first onset. We show that,
well in advance of sustained turbulence, chaos sets in explosively, and for long
time horizons, time series are consistent with that of a random process.\r\n\r\nFinally,
in much larger domains, we study and compare 2D-localized turbulence that appears
as large-scale inclined structures, called stripes, in ppf and pcf. While appearing
similar, we find that stripes in these two settings differ significantly in terms
of how they sustain themselves, and in higher velocities, how they proliferate."
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "The work in this thesis was supported by a grant from the Simons
Foundation (662960, BH).\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Gökhan
full_name: Yalniz, Gökhan
id: 66E74FA2-D8BF-11E9-8249-8DE2E5697425
last_name: Yalniz
orcid: 0000-0002-8490-9312
citation:
ama: 'Yalniz G. Transition to turbulence: Data-, solution-, and pattern-driven approaches.
2025. doi:10.15479/AT-ISTA-19684'
apa: 'Yalniz, G. (2025). Transition to turbulence: Data-, solution-, and pattern-driven
approaches. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19684'
chicago: 'Yalniz, Gökhan. “Transition to Turbulence: Data-, Solution-, and Pattern-Driven
Approaches.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19684.'
ieee: 'G. Yalniz, “Transition to turbulence: Data-, solution-, and pattern-driven
approaches,” Institute of Science and Technology Austria, 2025.'
ista: 'Yalniz G. 2025. Transition to turbulence: Data-, solution-, and pattern-driven
approaches. Institute of Science and Technology Austria.'
mla: 'Yalniz, Gökhan. Transition to Turbulence: Data-, Solution-, and Pattern-Driven
Approaches. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19684.'
short: 'G. Yalniz, Transition to Turbulence: Data-, Solution-, and Pattern-Driven
Approaches, Institute of Science and Technology Austria, 2025.'
corr_author: '1'
date_created: 2025-05-12T15:12:28Z
date_published: 2025-05-13T00:00:00Z
date_updated: 2026-09-02T08:16:32Z
day: '13'
ddc:
- '514'
- '519'
- '532'
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degree_awarded: PhD
department:
- _id: GradSch
- _id: BjHo
doi: 10.15479/AT-ISTA-19684
doi_confirm: '1'
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content_type: video/mp4
creator: gyalniz
date_created: 2025-05-12T15:15:59Z
date_updated: 2025-05-12T15:43:28Z
description: '3D visualizations of the turbulent flow (left) and the periodic orbits
(middle) that are being shadowed along with the local state space projections
(right) onto the principal components of the respective periodic orbit. Shown
here are the isosurfaces of velocity (red/blue: ±95% of the instantaneous maximum)
and vorticity (purple/green: ±65% of the instantaneous maximum) in the x-direction.
Markers along the projections are in sync with the 3D visualizations. The movie
corresponds to the initial time interval (up to t = 100) of figure 2.2 (a,b);
periodic orbits and the state space projections are shown only through the shadowing
events indicated in figure 2.2 (b).'
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file_name: Movie 2A.1.mp4
file_size: 37763743
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title: Chapter 2 - Movie 2A.1
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content_type: video/mp4
creator: gyalniz
date_created: 2025-05-12T15:16:09Z
date_updated: 2025-05-12T15:43:28Z
description: 'Turbulent flow (left) in HKW domain and its symmetry reduction (right).
Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min
u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).'
file_id: '19687'
file_name: Movie 3A.1.mp4
file_size: 3902655
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title: Chapter 3 - Movie 3A.1
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content_type: video/mp4
creator: gyalniz
date_created: 2025-05-12T15:16:21Z
date_updated: 2025-05-12T15:43:28Z
description: 'Turbulent flow (left) in P2K domain and its symmetry reduction (right).
Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min
u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).'
file_id: '19688'
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content_type: video/mp4
creator: gyalniz
date_created: 2025-05-12T15:16:36Z
date_updated: 2025-05-12T15:43:28Z
description: 'Relative periodic orbit RPO_79.4 (left) of the plane-Couette flow
(HKW domain) and its symmetry reduction (right). Shown here are the isosurfaces
of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity
(green/purple: ω_x = 0.5 max/min ω_x).'
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content_type: video/mp4
creator: gyalniz
date_created: 2025-05-12T15:16:50Z
date_updated: 2025-05-12T15:43:28Z
description: 'Symmetry-reduced flow (left), its SRDMD approximation (middle), and
state space projection (right) showing the spiral-out episode in P2K domain (figure
3.6 (b) and figure 3.8 (b)). Shown here are the isosurfaces of streamwise velocity
(red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5
max/min ω_x).'
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creator: gyalniz
date_created: 2025-05-12T15:17:11Z
date_updated: 2025-05-12T15:43:28Z
description: Movie demonstrating the quasi-steady Reynolds number descent from turbulence
to a periodic orbit.
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file_size: 9209327
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title: Chapter 4 - Movie 4A.1
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content_type: video/mp4
creator: gyalniz
date_created: 2025-05-12T15:17:43Z
date_updated: 2025-05-12T15:43:28Z
description: Streamwise velocity fluctuations (from laminar) of plane-Couette flow
(Re^C =335) at the y = 0 wall-normal plane in coordinates stationary with respect
to the bulk velocity. Here, x is the streamwise direction (the wall at y = 1 moves
to the right) and z is the spanwise direction. Time is in advectime time units.
Shown is the full (L_x = L_z = 400) domain.
file_id: '19692'
file_name: Movie 5A.1.mp4
file_size: 5893993
relation: supplementary_material
title: Chapter 5 - Movie 5A.1
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content_type: video/mp4
creator: gyalniz
date_created: 2025-05-12T15:17:49Z
date_updated: 2025-05-12T15:43:28Z
description: Streamwise velocity fluctuations (from laminar) of plane-Poiseuille
flow (Re^P =660) at the y = 0.5 wall-normal plane in coordinates stationary with
respect to the bulk velocity. Here, x is the streamwise direction (the mean negative
pressure gradient is to the right) and z is the spanwise direction. Time is in
advectime time units. Shown is the full (L_x = L_z = 400) domain.
file_id: '19693'
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file_size: 3990352
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title: Chapter 5 - Movie 5A.2
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content_type: video/mp4
creator: gyalniz
date_created: 2025-05-12T15:17:58Z
date_updated: 2025-05-12T15:43:28Z
description: Streamwise velocity fluctuations (from laminar) of plane-Poiseuille
flow (Re^P=660) at the y = 0.5 wall-normal plane in coordinates stationary with
respect to the average velocity of the downstream tip of the stripe. Here, x is
the streamwise direction (the mean negative pressure gradient is to the right)
and z is the spanwise direction. Time is in advectime time units. Shown is a zoom-in
of the full (L_x = L_z) domain.
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creator: gyalniz
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has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '155'
project:
- _id: 238598C6-32DE-11EA-91FC-C7463DDC885E
grant_number: '662960'
name: Revisiting the Turbulence Problem Using Statistical Mechanics
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9558'
relation: part_of_dissertation
status: public
- id: '12105'
relation: part_of_dissertation
status: public
- id: '13274'
relation: part_of_dissertation
status: public
- id: '14466'
relation: part_of_dissertation
status: public
- id: '7563'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
title: 'Transition to turbulence: Data-, solution-, and pattern-driven approaches'
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '19795'
abstract:
- lang: eng
text: Super-resolution microscopy often entails long acquisition times of minutes
to hours. Since drifts during the acquisition adversely affect data quality, active
sample stabilization is commonly used for some of these techniques to reach their
full potential. Although drifts in the lateral plane can often be corrected after
acquisition, this is not always possible or may come with drawbacks. Therefore,
it is appealing to stabilize sample position in three dimensions (3D) during acquisition.
Various schemes for active sample stabilization have been demonstrated previously,
with some reaching sub-nanometer stability in 3D. Here, we present a scheme for
active drift correction that delivers the nanometer-scale 3D stability demanded
by state-of-the-art super-resolution techniques and is straightforward to implement
compared to previous schemes capable of reaching this level of stabilization precision.
Using a refined algorithm that can handle various types of reference structure,
without sparse signal peaks being mandatory, we stabilized sample position to
∼1 nm in 3D using objective lenses both with high and low numerical aperture.
Our implementation requires only the addition of a simple widefield imaging path
and we provide an open-source control software with graphical user interface to
facilitate easy adoption of the module. Finally, we demonstrate how this has the
potential to enhance data collection for diffraction-limited and super-resolution
imaging techniques using single-molecule localization microscopy and cryo-confocal
imaging as showcases.
acknowledged_ssus:
- _id: M-Shop
- _id: EM-Fac
- _id: LifeSc
acknowledgement: 'We acknowledge expert support by ISTA’s scientific service units,
including the Miba Machine Shop, the Electron Microscopy Facility, and the Lab Support
Facility. This work has been made possible in part by CZI grant DAF2021-234754 and
grant DOI: https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative
DAF, an advised fund of Silicon Valley Community Foundation (funder DOI: https://doi.org/10.13039/100014989)
(F.K.M.S. and J.G.D.). We further gratefully acknowledge funding by the following
sources: Austrian Science Fund (FWF) grant DK W1232 (M.R.T. and J.G.D.); Austrian
Academy of Sciences DOC fellowship 26137 (M.R.T.); Marie Skłodowska-Curie Actions
Fellowship GA no. 665385 under the EU Horizon 2020 program (J.L.); ISTA postdoctoral
fellowship IST fellow (A.W.); and Human Frontier Science Program postdoctoral fellowship
LT000557/2018 (W.J.).'
article_number: '100211'
article_processing_charge: Yes
article_type: original
author:
- first_name: Jakob
full_name: Vorlaufer, Jakob
id: 937696FA-C996-11E9-8C7C-CF13E6697425
last_name: Vorlaufer
orcid: 0009-0000-7590-3501
- first_name: Nikolai
full_name: Semenov, Nikolai
id: e64d39c7-72ef-11ef-b75a-ee3046860d1b
last_name: Semenov
- first_name: Caroline
full_name: Kreuzinger, Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
- first_name: Manjunath
full_name: Javoor, Manjunath
id: 305ab18b-dc7d-11ea-9b2f-b58195228ea2
last_name: Javoor
orcid: 0000-0003-2311-2112
- first_name: Bettina
full_name: Zens, Bettina
id: 45FD126C-F248-11E8-B48F-1D18A9856A87
last_name: Zens
orcid: 0000-0002-9561-1239
- first_name: Nathalie
full_name: Agudelo Duenas, Nathalie
id: 40E7F008-F248-11E8-B48F-1D18A9856A87
last_name: Agudelo Duenas
- first_name: Mojtaba
full_name: Tavakoli, Mojtaba
id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
last_name: Tavakoli
orcid: 0000-0002-7667-6854
- first_name: Marek
full_name: Suplata, Marek
id: EE8452B8-C26A-11E9-B157-E80CE6697425
last_name: Suplata
- first_name: Wiebke
full_name: Jahr, Wiebke
id: 425C1CE8-F248-11E8-B48F-1D18A9856A87
last_name: Jahr
orcid: 0000-0003-0201-2315
- first_name: Julia
full_name: Lyudchik, Julia
id: 46E28B80-F248-11E8-B48F-1D18A9856A87
last_name: Lyudchik
- first_name: Andreas
full_name: Wartak, Andreas
id: 60aaa06c-3de5-11eb-9e53-baa88e955dcb
last_name: Wartak
- first_name: Florian Km
full_name: Schur, Florian Km
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
citation:
ama: Vorlaufer J, Semenov N, Kreuzinger C, et al. Image-based 3D active sample stabilization
on the nanometer scale for optical microscopy. Biophysical Reports. 2025;5(2).
doi:10.1016/j.bpr.2025.100211
apa: Vorlaufer, J., Semenov, N., Kreuzinger, C., Javoor, M., Zens, B., Agudelo Duenas,
N., … Danzl, J. G. (2025). Image-based 3D active sample stabilization on the nanometer
scale for optical microscopy. Biophysical Reports. Elsevier. https://doi.org/10.1016/j.bpr.2025.100211
chicago: Vorlaufer, Jakob, Nikolai Semenov, Caroline Kreuzinger, Manjunath Javoor,
Bettina Zens, Nathalie Agudelo Duenas, Mojtaba Tavakoli, et al. “Image-Based 3D
Active Sample Stabilization on the Nanometer Scale for Optical Microscopy.” Biophysical
Reports. Elsevier, 2025. https://doi.org/10.1016/j.bpr.2025.100211.
ieee: J. Vorlaufer et al., “Image-based 3D active sample stabilization on
the nanometer scale for optical microscopy,” Biophysical Reports, vol.
5, no. 2. Elsevier, 2025.
ista: Vorlaufer J, Semenov N, Kreuzinger C, Javoor M, Zens B, Agudelo Duenas N,
Tavakoli M, Suplata M, Jahr W, Lyudchik J, Wartak A, Schur FK, Danzl JG. 2025.
Image-based 3D active sample stabilization on the nanometer scale for optical
microscopy. Biophysical Reports. 5(2), 100211.
mla: Vorlaufer, Jakob, et al. “Image-Based 3D Active Sample Stabilization on the
Nanometer Scale for Optical Microscopy.” Biophysical Reports, vol. 5, no.
2, 100211, Elsevier, 2025, doi:10.1016/j.bpr.2025.100211.
short: J. Vorlaufer, N. Semenov, C. Kreuzinger, M. Javoor, B. Zens, N. Agudelo Duenas,
M. Tavakoli, M. Suplata, W. Jahr, J. Lyudchik, A. Wartak, F.K. Schur, J.G. Danzl,
Biophysical Reports 5 (2025).
corr_author: '1'
date_created: 2025-06-08T22:01:22Z
date_published: 2025-06-11T00:00:00Z
date_updated: 2026-09-03T09:36:24Z
day: '11'
ddc:
- '570'
department:
- _id: JoDa
- _id: GradSch
- _id: FlSc
- _id: EM-Fac
doi: 10.1016/j.bpr.2025.100211
ec_funded: 1
file:
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checksum: 4018c833f25a3ad3b57e3577fed70334
content_type: application/pdf
creator: dernst
date_created: 2025-06-10T07:24:46Z
date_updated: 2025-06-10T07:24:46Z
file_id: '19802'
file_name: 2025_BiophysicalReports_Vorlaufer.pdf
file_size: 7238179
relation: main_file
success: 1
file_date_updated: 2025-06-10T07:24:46Z
has_accepted_license: '1'
intvolume: ' 5'
issue: '2'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 62909c6f-2b32-11ec-9570-e1476aab5308
grant_number: CZI01
name: CryoMinflux-guided in-situ molecular census and structure determination
- _id: 6285a163-2b32-11ec-9570-8e204ca2dba5
grant_number: '26137'
name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion
Microscopy
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
- _id: 2668BFA0-B435-11E9-9278-68D0E5697425
grant_number: LT00057
name: High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration
publication: Biophysical Reports
publication_identifier:
eissn:
- 2667-0747
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '20206'
relation: dissertation_contains
status: public
- id: '22744'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Image-based 3D active sample stabilization on the nanometer scale for optical
microscopy
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '15016'
abstract:
- lang: eng
text: Amphibians, by virtue of their phylogenetic position, provide invaluable insights
on nervous system evolution, development, and remodeling. The genetic toolkit
for amphibians, however, remains limited. Recombinant adeno-associated viral vectors
(AAVs) are a powerful alternative to transgenesis for labeling and manipulating
neurons. Although successful in mammals, AAVs have never been shown to transduce
amphibian cells efficiently. We screened AAVs in three amphibian species—the frogs
Xenopus laevis and Pelophylax bedriagae and the salamander Pleurodeles waltl—and
identified at least two AAV serotypes per species that transduce neurons. In developing
amphibians, AAVs labeled groups of neurons generated at the same time during development.
In the mature brain, AAVrg retrogradely traced long-range projections. Our study
introduces AAVs as a tool for amphibian research, establishes a generalizable
workflow for AAV screening in new species, and expands opportunities for cross-species
comparisons of nervous system development, function, and evolution.
acknowledged_ssus:
- _id: PreCl
- _id: Bio
acknowledgement: 'We thank members of the Sweeney, Tosches, Shein-Idelson, Yamaguchi,
Kelley, and Cline Labs for their contributions to this project, discussion, and
support. We additionally thank the Beckman Institute CLOVER Center and Viviana Gradinaru
(Caltech), Kimberly Ritola (UNC NeuroTools), and Flavia Gomez-Leite (ISTA Viral
Core) for AAV production and consultation; Andras Simon and Alberto Joven (Karolinska
Institute) for feedback; Elizabeth Bagnato-Cohen (Columbia) for project coordination;
our animal care and imaging facilities; the amphibian stock centers (NXR, EXRC,
and XenopusExpress); and our funding sources: NSF IOS 2110086 (D.B.K., L.B.S., M.A.T.,
A.Y., and H.T.C.); US-Israel Binational Science Foundation (BSF) 2020702 (M.S.-I.);
FTI Strategy Lower Austria Dissertation FT121-D-046 (D.V.); Horizon Europe ERC Starting
Grant 101041551 and Special Research Programme (SFB) of the Austrian Science Fund
(FWF) project F7814-B (L.B.S.); NIH grant R35GM146973, Rita Allen Foundation Award
GA_032522_FE, and CZI Ben Barres Early Career Acceleration Award 2023-331758 (M.A.T.);
EMBO Long-Term Fellowship ALTF 874-2021 (A.D.); and NSF GRFP DGE 2036197 (E.C.B.J.).'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Eliza C.B.
full_name: Jaeger, Eliza C.B.
last_name: Jaeger
- first_name: David
full_name: Vijatovic, David
id: cf391e77-ec3c-11ea-a124-d69323410b58
last_name: Vijatovic
orcid: 0000-0002-5494-0941
- first_name: Astrid
full_name: Deryckere, Astrid
last_name: Deryckere
- first_name: Nikol
full_name: Zorin, Nikol
last_name: Zorin
- first_name: Akemi L.
full_name: Nguyen, Akemi L.
last_name: Nguyen
- first_name: Georgiy
full_name: Ivanian, Georgiy
id: eaf2b366-cfd1-11ee-bbdf-c8790f800a05
last_name: Ivanian
orcid: 0009-0002-3999-3735
- first_name: Jamie
full_name: Woych, Jamie
last_name: Woych
- first_name: Rebecca C
full_name: Arnold, Rebecca C
id: d6cce458-14c9-11ed-a755-c1c8fc6fde6f
last_name: Arnold
- first_name: Alonso
full_name: Ortega Gurrola, Alonso
last_name: Ortega Gurrola
- first_name: Arik
full_name: Shvartsman, Arik
last_name: Shvartsman
- first_name: Francesca
full_name: Barbieri, Francesca
id: a9492887-8972-11ed-ae7b-bfae10998254
last_name: Barbieri
- first_name: Florina-Alexandra
full_name: Toma, Florina-Alexandra
id: 85dd99f2-15b2-11ec-abd3-d1ae4d57f3b5
last_name: Toma
- first_name: Gary J.
full_name: Gorbsky, Gary J.
last_name: Gorbsky
- first_name: Marko E.
full_name: Horb, Marko E.
last_name: Horb
- first_name: Hollis T.
full_name: Cline, Hollis T.
last_name: Cline
- first_name: Timothy F.
full_name: Shay, Timothy F.
last_name: Shay
- first_name: Darcy B.
full_name: Kelley, Darcy B.
last_name: Kelley
- first_name: Ayako
full_name: Yamaguchi, Ayako
last_name: Yamaguchi
- first_name: Mark
full_name: Shein-Idelson, Mark
last_name: Shein-Idelson
- first_name: Maria Antonietta
full_name: Tosches, Maria Antonietta
last_name: Tosches
- first_name: Lora Beatrice Jaeger
full_name: Sweeney, Lora Beatrice Jaeger
id: 56BE8254-C4F0-11E9-8E45-0B23E6697425
last_name: Sweeney
orcid: 0000-0001-9242-5601
citation:
ama: Jaeger ECB, Vijatovic D, Deryckere A, et al. Adeno-associated viral tools to
trace neural development and connectivity across amphibians. Developmental
Cell. 2025;60(5):794-812.e6. doi:10.1016/j.devcel.2024.10.025
apa: Jaeger, E. C. B., Vijatovic, D., Deryckere, A., Zorin, N., Nguyen, A. L., Ivanian,
G., … Sweeney, L. B. (2025). Adeno-associated viral tools to trace neural development
and connectivity across amphibians. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2024.10.025
chicago: Jaeger, Eliza C.B., David Vijatovic, Astrid Deryckere, Nikol Zorin, Akemi
L. Nguyen, Georgiy Ivanian, Jamie Woych, et al. “Adeno-Associated Viral Tools
to Trace Neural Development and Connectivity across Amphibians.” Developmental
Cell. Elsevier, 2025. https://doi.org/10.1016/j.devcel.2024.10.025.
ieee: E. C. B. Jaeger et al., “Adeno-associated viral tools to trace neural
development and connectivity across amphibians,” Developmental Cell, vol.
60, no. 5. Elsevier, p. 794–812.e6, 2025.
ista: Jaeger ECB, Vijatovic D, Deryckere A, Zorin N, Nguyen AL, Ivanian G, Woych
J, Arnold RC, Ortega Gurrola A, Shvartsman A, Barbieri F, Toma F-A, Gorbsky GJ,
Horb ME, Cline HT, Shay TF, Kelley DB, Yamaguchi A, Shein-Idelson M, Tosches MA,
Sweeney LB. 2025. Adeno-associated viral tools to trace neural development and
connectivity across amphibians. Developmental Cell. 60(5), 794–812.e6.
mla: Jaeger, Eliza C. B., et al. “Adeno-Associated Viral Tools to Trace Neural Development
and Connectivity across Amphibians.” Developmental Cell, vol. 60, no. 5,
Elsevier, 2025, p. 794–812.e6, doi:10.1016/j.devcel.2024.10.025.
short: E.C.B. Jaeger, D. Vijatovic, A. Deryckere, N. Zorin, A.L. Nguyen, G. Ivanian,
J. Woych, R.C. Arnold, A. Ortega Gurrola, A. Shvartsman, F. Barbieri, F.-A. Toma,
G.J. Gorbsky, M.E. Horb, H.T. Cline, T.F. Shay, D.B. Kelley, A. Yamaguchi, M.
Shein-Idelson, M.A. Tosches, L.B. Sweeney, Developmental Cell 60 (2025) 794–812.e6.
corr_author: '1'
date_created: 2024-02-20T09:20:32Z
date_published: 2025-03-10T00:00:00Z
date_updated: 2026-09-04T10:11:04Z
day: '10'
ddc:
- '570'
department:
- _id: LoSw
- _id: MaDe
- _id: GaNo
doi: 10.1016/j.devcel.2024.10.025
external_id:
isi:
- '001444798600001'
pmid:
- '39603234'
file:
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content_type: application/pdf
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file_size: 11936258
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isi: 1
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month: '03'
oa: 1
oa_version: Published Version
page: 794-812.e6
pmid: 1
project:
- _id: bd73af52-d553-11ed-ba76-912049f0ac7a
grant_number: FTI21-D-046
name: Development of V1 interneuron diversity during swim-to-walk transition of
Xenopus metamorphosis
- _id: ebb66355-77a9-11ec-83b8-b8ac210a4dae
grant_number: '101041551'
name: Development and Evolution of Tetrapod Motor Circuits
- _id: 8da85f50-16d5-11f0-9cad-eab8b0ff6c9e
grant_number: F7814
name: 'Stem Cell Modulation in Neural Development and Regeneration/ P14-Swim-to-limb
transition: cell type to connection diversity'
publication: Developmental Cell
publication_identifier:
eissn:
- 1878-1551
issn:
- 1534-5807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '22667'
relation: dissertation_contains
status: public
- id: '22803'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Adeno-associated viral tools to trace neural development and connectivity across
amphibians
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: 60
year: '2025'
...
---
OA_place: publisher
_id: '20292'
abstract:
- lang: eng
text: In automated decision-making, it is desirable that outputs of decision-makers
be robust to slight perturbations in their inputs, a property that may be called
input-output robustness. Input-output robustness appears in various different
forms in the literature, such as robustness of AI models to adversarial or semantic
perturbations and individual fairness of AI models that make decisions about humans.
We propose runtime monitoring of input-output robustness of deployed, black-box
AI models, where the goal is to design monitors that would observe one long execution
sequence of the model, and would raise an alarm whenever it is detected that two
similar inputs from the past led to dissimilar outputs. This way, monitoring will
complement existing offline ''robustification'' approaches to increase the trustworthiness
of AI decision-makers. We show that the monitoring problem can be cast as the
fixed-radius nearest neighbor (FRNN) search problem, which, despite being well-studied,
lacks suitable online solutions. We present our tool Clemont, which offers a number
of lightweight monitors, some of which use upgraded online variants of existing
FRNN algorithms, and one uses a novel algorithm based on binary decision diagrams--a
data-structure commonly used in software and hardware verification. We have also
developed an efficient parallelization technique that can substantially cut down
the computation time of monitors for which the distance between input-output pairs
is measured using the L∞norm. Using standard benchmarks from the literature of
adversarial and semantic robustness and individual fairness, we perform a comparative
study of different monitors in Clemont, and demonstrate their effectiveness in
correctly detecting robustness violations at runtime.
acknowledgement: This work was supported in part by the ERC project ERC-2020-AdG 101020093
and the SBI Foundation Hub for Data Science &Analytics, IIT Bombay.
article_processing_charge: No
arxiv: 1
author:
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Konstantin
full_name: Kueffner, Konstantin
id: 8121a2d0-dc85-11ea-9058-af578f3b4515
last_name: Kueffner
orcid: 0000-0001-8974-2542
- first_name: Kaushik
full_name: Mallik, Kaushik
id: 0834ff3c-6d72-11ec-94e0-b5b0a4fb8598
last_name: Mallik
orcid: 0000-0001-9864-7475
- first_name: David
full_name: Pape, David
last_name: Pape
citation:
ama: 'Gupta A, Henzinger TA, Kueffner K, Mallik K, Pape D. Monitoring robustness
and individual fairness. In: Proceedings of the 31st ACM SIGKDD Conference
on Knowledge Discovery and Data Mining. Vol 2. Association for Computing Machinery;
2025:790-801. doi:10.1145/3711896.3737054'
apa: 'Gupta, A., Henzinger, T. A., Kueffner, K., Mallik, K., & Pape, D. (2025).
Monitoring robustness and individual fairness. In Proceedings of the 31st ACM
SIGKDD Conference on Knowledge Discovery and Data Mining (Vol. 2, pp. 790–801).
Toronto, Canada: Association for Computing Machinery. https://doi.org/10.1145/3711896.3737054'
chicago: Gupta, Ashutosh, Thomas A Henzinger, Konstantin Kueffner, Kaushik Mallik,
and David Pape. “Monitoring Robustness and Individual Fairness.” In Proceedings
of the 31st ACM SIGKDD Conference on Knowledge Discovery and Data Mining,
2:790–801. Association for Computing Machinery, 2025. https://doi.org/10.1145/3711896.3737054.
ieee: A. Gupta, T. A. Henzinger, K. Kueffner, K. Mallik, and D. Pape, “Monitoring
robustness and individual fairness,” in Proceedings of the 31st ACM SIGKDD
Conference on Knowledge Discovery and Data Mining, Toronto, Canada, 2025,
vol. 2, pp. 790–801.
ista: 'Gupta A, Henzinger TA, Kueffner K, Mallik K, Pape D. 2025. Monitoring robustness
and individual fairness. Proceedings of the 31st ACM SIGKDD Conference on Knowledge
Discovery and Data Mining. KDD: Conference on Knowledge Discovery and Data Mining
vol. 2, 790–801.'
mla: Gupta, Ashutosh, et al. “Monitoring Robustness and Individual Fairness.” Proceedings
of the 31st ACM SIGKDD Conference on Knowledge Discovery and Data Mining,
vol. 2, Association for Computing Machinery, 2025, pp. 790–801, doi:10.1145/3711896.3737054.
short: A. Gupta, T.A. Henzinger, K. Kueffner, K. Mallik, D. Pape, in:, Proceedings
of the 31st ACM SIGKDD Conference on Knowledge Discovery and Data Mining, Association
for Computing Machinery, 2025, pp. 790–801.
conference:
end_date: 2025-08-07
location: Toronto, Canada
name: 'KDD: Conference on Knowledge Discovery and Data Mining'
start_date: 2025-08-03
corr_author: '1'
date_created: 2025-09-07T22:01:33Z
date_published: 2025-08-03T00:00:00Z
date_updated: 2026-09-05T15:59:18Z
day: '03'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1145/3711896.3737054
ec_funded: 1
external_id:
arxiv:
- '2506.00496'
file:
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creator: dernst
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has_accepted_license: '1'
intvolume: ' 2'
language:
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month: '08'
oa: 1
oa_version: Published Version
page: 790-801
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: Proceedings of the 31st ACM SIGKDD Conference on Knowledge Discovery
and Data Mining
publication_identifier:
isbn:
- '9798400714542'
issn:
- 2154-817X
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/ariez-xyz/clemont
record:
- id: '22808'
relation: dissertation_contains
status: for_moderation
scopus_import: '1'
status: public
title: Monitoring robustness and individual fairness
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: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '21090'
abstract:
- lang: eng
text: Fairness in AI is traditionally studied as a static property evaluated once,
over a fixed dataset. However, real-world AI systems operate sequentially, with
outcomes and environments evolving over time. This paper proposes a framework
for analysing fairness as a runtime property. Using a minimal yet expressive model
based on sequences of coin tosses with possibly evolving biases, we study the
problems of monitoring and enforcing fairness expressed in either toss outcomes
or coin biases. Since there is no one-size-fits-all solution for either problem,
we provide a summary of monitoring and enforcement strategies, parametrised by
environment dynamics, prediction horizon, and confidence thresholds. For both
problems, we present general results under simple or minimal assumptions. We survey
existing solutions for the monitoring problem for Markovian and additive dynamics,
and existing solutions for the enforcement problem in static settings with known
dynamics.
acknowledgement: 'This work is supported by the European Research Council under Grant
No.: ERC-2020-AdG 101020093.'
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Filip
full_name: Cano Cordoba, Filip
id: 708cad98-e86a-11ef-8098-bdae2d7c6af1
last_name: Cano Cordoba
orcid: 0000-0002-0783-904X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Konstantin
full_name: Kueffner, Konstantin
id: 8121a2d0-dc85-11ea-9058-af578f3b4515
last_name: Kueffner
orcid: 0000-0001-8974-2542
citation:
ama: 'Cano Cordoba F, Henzinger TA, Kueffner K. Algorithmic fairness: A runtime
perspective. In: 25th International Conference on Runtime Verification.
Vol 16087. Springer Nature; 2025:1-21. doi:10.1007/978-3-032-05435-7_1'
apa: 'Cano Cordoba, F., Henzinger, T. A., & Kueffner, K. (2025). Algorithmic
fairness: A runtime perspective. In 25th International Conference on Runtime
Verification (Vol. 16087, pp. 1–21). Graz, Austria: Springer Nature. https://doi.org/10.1007/978-3-032-05435-7_1'
chicago: 'Cano Cordoba, Filip, Thomas A Henzinger, and Konstantin Kueffner. “Algorithmic
Fairness: A Runtime Perspective.” In 25th International Conference on Runtime
Verification, 16087:1–21. Springer Nature, 2025. https://doi.org/10.1007/978-3-032-05435-7_1.'
ieee: 'F. Cano Cordoba, T. A. Henzinger, and K. Kueffner, “Algorithmic fairness:
A runtime perspective,” in 25th International Conference on Runtime Verification,
Graz, Austria, 2025, vol. 16087, pp. 1–21.'
ista: 'Cano Cordoba F, Henzinger TA, Kueffner K. 2025. Algorithmic fairness: A runtime
perspective. 25th International Conference on Runtime Verification. RV: Runtime
Verification, LNCS, vol. 16087, 1–21.'
mla: 'Cano Cordoba, Filip, et al. “Algorithmic Fairness: A Runtime Perspective.”
25th International Conference on Runtime Verification, vol. 16087, Springer
Nature, 2025, pp. 1–21, doi:10.1007/978-3-032-05435-7_1.'
short: F. Cano Cordoba, T.A. Henzinger, K. Kueffner, in:, 25th International Conference
on Runtime Verification, Springer Nature, 2025, pp. 1–21.
conference:
end_date: 2025-09-19
location: Graz, Austria
name: 'RV: Runtime Verification'
start_date: 2025-09-15
corr_author: '1'
date_created: 2026-01-29T16:01:41Z
date_published: 2025-09-13T00:00:00Z
date_updated: 2026-09-05T15:59:18Z
day: '13'
department:
- _id: ToHe
doi: 10.1007/978-3-032-05435-7_1
ec_funded: 1
external_id:
arxiv:
- '2507.20711'
intvolume: ' 16087'
language:
- iso: eng
main_file_link:
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url: https://doi.org/10.48550/arXiv.2507.20711
month: '09'
oa: 1
oa_version: Preprint
page: 1-21
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 25th International Conference on Runtime Verification
publication_identifier:
eisbn:
- '9783032054357'
eissn:
- 1611-3349
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
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relation: dissertation_contains
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status: public
title: 'Algorithmic fairness: A runtime perspective'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16087
year: '2025'
...
---
OA_place: publisher
_id: '20117'
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: PreCl
acknowledgement: "I would also like to acknowledge the invaluable assistance provided
by the Plant\r\nFacility, Imaging & Optics Facility, and the Lab Support Facility.
The technical support and\r\nresources offered by these facilities were indispensable
to the successful completion of my\r\nexperiments."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Yiqun
full_name: Wang, Yiqun
id: 82F537F2-B517-11E9-84D7-6433E6697425
last_name: Wang
citation:
ama: Wang Y. The role of dynamin related protein 2A in cytokinin regulated plant
growth and development. 2025. doi:10.15479/AT-ISTA-20117
apa: Wang, Y. (2025). The role of dynamin related protein 2A in cytokinin regulated
plant growth and development. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT-ISTA-20117
chicago: Wang, Yiqun. “The Role of Dynamin Related Protein 2A in Cytokinin Regulated
Plant Growth and Development.” Institute of Science and Technology Austria, 2025.
https://doi.org/10.15479/AT-ISTA-20117.
ieee: Y. Wang, “The role of dynamin related protein 2A in cytokinin regulated plant
growth and development,” Institute of Science and Technology Austria, 2025.
ista: Wang Y. 2025. The role of dynamin related protein 2A in cytokinin regulated
plant growth and development. Institute of Science and Technology Austria.
mla: Wang, Yiqun. The Role of Dynamin Related Protein 2A in Cytokinin Regulated
Plant Growth and Development. Institute of Science and Technology Austria,
2025, doi:10.15479/AT-ISTA-20117.
short: Y. Wang, The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant
Growth and Development, Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-08-04T15:24:21Z
date_published: 2025-08-04T00:00:00Z
date_updated: 2026-09-03T22:30:04Z
day: '04'
ddc:
- '580'
degree_awarded: PhD
department:
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- _id: EvBe
doi: 10.15479/AT-ISTA-20117
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oa: 1
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publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '18063'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
title: The role of dynamin related protein 2A in cytokinin regulated plant growth
and development
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
OA_place: publisher
_id: '20212'
acknowledged_ssus:
- _id: Bio
- _id: PreCl
acknowledgement: "I would also like to\r\nthank the Austrian Academy of Sciences for
awarding me a 2-year DOC fellowship\r\n(DOC26253)."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Osvaldo
full_name: Miranda, Osvaldo
id: 862A3C56-A8BF-11E9-B4FA-D9E3E5697425
last_name: Miranda
orcid: 0000-0001-6618-6889
citation:
ama: Miranda O. Unraveling the role of Pten in cortical stem cell lineage progression
using MADM. 2025. doi:10.15479/AT-ISTA-20212
apa: Miranda, O. (2025). Unraveling the role of Pten in cortical stem cell lineage
progression using MADM. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20212
chicago: Miranda, Osvaldo. “Unraveling the Role of Pten in Cortical Stem Cell Lineage
Progression Using MADM.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20212.
ieee: O. Miranda, “Unraveling the role of Pten in cortical stem cell lineage progression
using MADM,” Institute of Science and Technology Austria, 2025.
ista: Miranda O. 2025. Unraveling the role of Pten in cortical stem cell lineage
progression using MADM. Institute of Science and Technology Austria.
mla: Miranda, Osvaldo. Unraveling the Role of Pten in Cortical Stem Cell Lineage
Progression Using MADM. Institute of Science and Technology Austria, 2025,
doi:10.15479/AT-ISTA-20212.
short: O. Miranda, Unraveling the Role of Pten in Cortical Stem Cell Lineage Progression
Using MADM, Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-08-22T14:07:00Z
date_published: 2025-08-22T00:00:00Z
date_updated: 2026-08-26T22:30:03Z
day: '22'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: SiHi
doi: 10.15479/AT-ISTA-20212
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file_size: 28636240
relation: main_file
file_date_updated: 2026-08-26T22:30:02Z
has_accepted_license: '1'
keyword:
- Pten
- mtor
- cortical development
- MADM
- Mapk
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '119'
project:
- _id: 34c9fbcb-11ca-11ed-8bc3-98fa5658610d
grant_number: '26253'
name: Molecular Mechanisms Regulating Cortical Neural Stem Cell Lineage Progression
and Astrocyte Development
publication_identifier:
isbn:
- 978-3-99078-063-3
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '17425'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
title: Unraveling the role of Pten in cortical stem cell lineage progression using
MADM
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
OA_embargo: '12'
OA_place: publisher
_id: '19386'
abstract:
- lang: eng
text: "Crustaceans are a large group of arthropods with a great diversity of species
and\r\ndifferent types of sex determination systems and reproductive modes (Subramoniam,
2017).\r\nThis makes them a great model for exploring the evolution of sex chromosomes
and sexual\r\ndimorphism and investigating the evolutionary mechanisms driving
and maintaining the\r\ndiversity of reproductive systems. Within this taxon, Brine
shrimp of the genus Artemia, a\r\nbranchiopod crustacean, are well suited for
such explorations, as they have both highly\r\ndimorphic traits and closely related
sexual and asexual species. Although brine shrimp are\r\nknown to have ZW sex
chromosomes (Bowen, 1963; Parraguez et al., 2009), the sex\r\nchromosomes are
still not well characterized at the genomic level, the sex-determination gene\r\nis
unknown, and it is still unclear whether the same sex chromosomes as shared by
the\r\ndifferent species.\r\nThe first part of this thesis was to characterize
the Z and W chromosomes in Artemia\r\nusing an array of methods, from generating
multiple chromosome and contig level genome\r\nassemblies to identifying W-linked
scaffolds and transcripts in multiple species using k-mer\r\nbased approaches.\r\nThe
second part tackles the conservation of the cell type specific regulatory pathways\r\nin
the female reproductive system between Artemia and Drosophila, and the expression
of the\r\nZ-specific region throughout meiosis using single-nucleus RNA-seq data.
Our results show\r\nthat germline cells lack dosage compensation, with a subset
of cells showing evidence of\r\nextreme repression of the Z chromosome.\r\nWith
multiple sexual species and several asexual lineages of parthenogenetic females\r\nthat
produce rare males at low frequencies, Brine shrimp present the perfect opportunity
to\r\nexplore the transition to asexuality and shed light on the prerequisites
and repercussions of\r\nthe form of modified meiosis maintaining the asexual lineages.
The last chapter is an\r\ninvestigation of the molecular pathways involved in
asexual reproduction in Artemia using\r\nnewly generated single nucleus RNAseq
and WGS data and previously published data. "
acknowledged_ssus:
- _id: ScienComp
acknowledgement: My PhD work was funded by the Austrian science fund (FWF), as part
of the SFB Meiosis consortium (https://sfbmeiosis.org/, grant ID FWF SFB F88-10).
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Marwan N
full_name: Elkrewi, Marwan N
id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
last_name: Elkrewi
orcid: 0000-0002-5328-7231
citation:
ama: Elkrewi MN. Evolution of sex chromosomes, sex determination and asexuality
in Artemia brine shrimp. 2025. doi:10.15479/AT-ISTA-19386
apa: Elkrewi, M. N. (2025). Evolution of sex chromosomes, sex determination and
asexuality in Artemia brine shrimp. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT-ISTA-19386
chicago: Elkrewi, Marwan N. “Evolution of Sex Chromosomes, Sex Determination and
Asexuality in Artemia Brine Shrimp.” Institute of Science and Technology Austria,
2025. https://doi.org/10.15479/AT-ISTA-19386.
ieee: M. N. Elkrewi, “Evolution of sex chromosomes, sex determination and asexuality
in Artemia brine shrimp,” Institute of Science and Technology Austria, 2025.
ista: Elkrewi MN. 2025. Evolution of sex chromosomes, sex determination and asexuality
in Artemia brine shrimp. Institute of Science and Technology Austria.
mla: Elkrewi, Marwan N. Evolution of Sex Chromosomes, Sex Determination and Asexuality
in Artemia Brine Shrimp. Institute of Science and Technology Austria, 2025,
doi:10.15479/AT-ISTA-19386.
short: M.N. Elkrewi, Evolution of Sex Chromosomes, Sex Determination and Asexuality
in Artemia Brine Shrimp, Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-03-11T12:54:31Z
date_published: 2025-03-14T00:00:00Z
date_updated: 2026-07-06T13:48:33Z
day: '14'
ddc:
- '570'
- '576'
degree_awarded: PhD
department:
- _id: GradSch
- _id: BeVi
doi: 10.15479/AT-ISTA-19386
file:
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date_created: 2025-03-26T07:06:22Z
date_updated: 2026-03-26T23:30:03Z
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file_date_updated: 2026-03-26T23:30:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '170'
project:
- _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396
grant_number: F8810
name: The highjacking of meiosis for asexual reproduction
publication_identifier:
eissn:
- 2663-337X
isbn:
- '9783990780534'
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '12248'
relation: part_of_dissertation
status: public
- id: '10767'
relation: part_of_dissertation
status: public
- id: '15009'
relation: part_of_dissertation
status: public
- id: '14613'
relation: part_of_dissertation
status: public
- id: '17890'
relation: part_of_dissertation
status: public
- id: '10167'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
title: Evolution of sex chromosomes, sex determination and asexuality in Artemia brine
shrimp
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2025'
...
---
OA_embargo: '6'
OA_place: publisher
_id: '20798'
abstract:
- lang: eng
text: "Atom interferometers measure the relative phase shifts between coherent matter-wave
paths\r\nthat arise from interactions with external fields or inertial forces.
Due to their exceptional\r\nphase sensitivity, atom interferometers became an
essential tool for precision measurements\r\nand fundamental physics experiments,
finding applications in geodesy, gravimetry, and inertial\r\nnavigation. However,
their measurement precision is limited by quantum projection noise,\r\nwhich arises
from the Heisenberg uncertainty principle, preventing the measurement of atomic\r\nstates
with absolute precision. The generation of entanglement between the atoms offers
a\r\npath to surpass this so-called standard quantum limit, thereby enhancing
the interferometer’s\r\nphase sensitivity beyond classical measurement bounds.\r\nThis
thesis reports on the development of an atom interferometer experiment designed
to\r\nrealize cavity-mediated, squeezed Mach-Zehnder-type interferometry with
ultra-cold 87Rb atoms.\r\nThe experiment combines cavity-aided spin-squeezing
with cavity-mediated Mach-Zehnder\r\ninterferometry to demonstrate entanglement-enhanced
phase sensitivity. The experiment is\r\ncentered on a triangular optical cavity
that mediates all relevant atom-light interactions. The\r\ncavity provides optical
trapping, spin-squeezing, and Raman beam-splitter operations, enabling\r\nto perform
interferometry on a continuously trapped atomic ensemble.\r\nThe thesis elaborates
on the fundamental theoretical framework, the cavity design, and the full\r\noptical
setup, including the detailed configuration of the developed laser stabilization
methods.\r\nExperimentally, continuous loading methods were explored, resulting
in an accumulation of\r\nup to 4 × 106\r\natoms in the dipole trap within a cycle
time of 500 ms. The AC Stark shift\r\ncompensation method developed for continuous
loading was further applied for in-trap cooling\r\nto 10 µK, and optical pumping
for efficient atomic state preparation. Coherent state control\r\nwas verified
via observation of microwave-driven Rabi oscillations, and used to characterize\r\natom-cavity
coupling.\r\nThese presented results establish the experimental groundwork for
the future development of\r\ncavity-mediated, entanglement-enhanced Mach-Zehnder-type
atom interferometry."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Sebastian
full_name: Wald, Sebastian
id: 133F200A-B015-11E9-AD41-0EDAE5697425
last_name: Wald
orcid: 0000-0002-5869-1604
citation:
ama: Wald S. Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry.
2025. doi:10.15479/AT-ISTA-20798
apa: Wald, S. (2025). Atoms in a propagating-wave cavity for squeezed Mach-Zehnder
atom interferometry. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20798
chicago: Wald, Sebastian. “Atoms in a Propagating-Wave Cavity for Squeezed Mach-Zehnder
Atom Interferometry.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20798.
ieee: S. Wald, “Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom
interferometry,” Institute of Science and Technology Austria, 2025.
ista: Wald S. 2025. Atoms in a propagating-wave cavity for squeezed Mach-Zehnder
atom interferometry. Institute of Science and Technology Austria.
mla: Wald, Sebastian. Atoms in a Propagating-Wave Cavity for Squeezed Mach-Zehnder
Atom Interferometry. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20798.
short: S. Wald, Atoms in a Propagating-Wave Cavity for Squeezed Mach-Zehnder Atom
Interferometry, Institute of Science and Technology Austria, 2025.
corr_author: '1'
das_tickbox: '1'
date_created: 2025-12-11T11:48:11Z
date_published: 2025-12-11T00:00:00Z
date_updated: 2026-07-24T08:07:28Z
day: '11'
ddc:
- '530'
degree_awarded: PhD
department:
- _id: GradSch
- _id: OnHo
doi: 10.15479/AT-ISTA-20798
doi_confirm: '1'
file:
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checksum: 1be72faf529a5e8a2d03cb3d5f808b77
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creator: swald
date_created: 2025-12-12T11:53:42Z
date_updated: 2026-06-15T22:30:03Z
embargo: 2026-06-15
file_id: '20809'
file_name: 2025_Wald_Sebastian_Thesis.pdf
file_size: 47536855
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creator: swald
date_created: 2025-12-12T11:54:55Z
date_updated: 2026-06-15T22:30:03Z
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file_name: 2025_Wald_Sebastian_Thesis.zip
file_size: 40127601
relation: source_file
file_date_updated: 2026-06-15T22:30:03Z
has_accepted_license: '1'
keyword:
- entanglement-enhanced atom interferometry
- cavity QED
- spin-squeezing
- dipole trap
- quantum optics
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '12'
oa: 1
oa_version: Published Version
page: '152'
publication_identifier:
isbn:
- 978-3-99078-075-6
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '14759'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Onur
full_name: Hosten, Onur
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
title: Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry
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: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2025'
...
---
OA_embargo: 6 months
OA_place: publisher
OA_type: hybrid
_id: '19498'
abstract:
- lang: eng
text: A dynamic interplay between fast synaptic signals and slower neuromodulatory
signals controls the excitatory/inhibitory (E/I) balance within neuronal circuits.
The mechanisms by which neuropeptide signaling is regulated to maintain E/I balance
remain uncertain. We designed a genetic screen to isolate genes involved in the
peptidergic maintenance of the E/I balance in the C. elegans motor circuit. This
screen identified the C. elegans orthologs of the presynaptic phosphoprotein synapsin
(snn-1) and the protein phosphatase 1 (PP1) regulatory subunit PHACTR1 (phac-1).
We demonstrate that both phac-1 and snn-1 alter the motor behavior of C. elegans,
and genetic interactions suggest that SNN-1 contributes to PP1-PHAC-1 holoenzyme
signaling. De novo variants of human PHACTR1, associated with early-onset epilepsies
[developmental and epileptic encephalopathy 70 (DEE70)], when expressed in C.
elegans resulted in constitutive PP1-PHAC-1 holoenzyme activity. Unregulated PP1-PHAC-1
signaling alters the synapsin and actin cytoskeleton and increases neuropeptide
release by cholinergic motor neurons, which secondarily affects the presynaptic
vesicle cycle. Together, these results clarify the dominant mechanisms of action
of the DEE70 alleles and suggest that altered neuropeptide release may alter E/I
balance in DEE70.
acknowledgement: P.L. is a research associate of the Belgian National Fund for Scientific
Research (FRS-FNRS). K.S., M.S.-G., S.S., and P.L. are supported by grants from
the FRS-FNRS. This work was supported by an Advanced ERC Grant (269058 ACMO) to
M.D.B. We thank the team of Alexander Gottschalk for the snn-1(S9A) strain. We thank
the Imaging Facility of the Faculty of Medicine (LiMiF) of the Universite Libre
de Bruxelles, supported by FRS-FNRS. This work made use of instruments in the Electron
Microscopy Core of the University of Illinois Chicago Research Resources Center
as well as the BioCryo facility of Northwestern University's NUANCE Center, which
has received support from the SHyNE Resource (NSF ECCS-2025633), the IIN, and Northwestern's
MRSEC program (NSF DMR-2308691). Some strains were provided by the CGC, which is
funded by NIH Office of Research Infrastructure Programs (P40 OD010440).
article_number: e1767232024
article_processing_charge: No
article_type: original
author:
- first_name: Aikaterini
full_name: Stratigi, Aikaterini
last_name: Stratigi
- first_name: Miguel
full_name: Soler-García, Miguel
last_name: Soler-García
- first_name: Mia
full_name: Krout, Mia
last_name: Krout
- first_name: Shikha
full_name: Shukla, Shikha
last_name: Shukla
- first_name: Mario
full_name: De Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: De Bono
orcid: 0000-0001-8347-0443
- first_name: Janet E.
full_name: Richmond, Janet E.
last_name: Richmond
- first_name: Patrick
full_name: Laurent, Patrick
last_name: Laurent
citation:
ama: Stratigi A, Soler-García M, Krout M, et al. Neuroendocrine control of synaptic
transmission by PHAC-1 in C. elegans. Journal of Neuroscience. 2025;45(13).
doi:10.1523/JNEUROSCI.1767-23.2024
apa: Stratigi, A., Soler-García, M., Krout, M., Shukla, S., de Bono, M., Richmond,
J. E., & Laurent, P. (2025). Neuroendocrine control of synaptic transmission
by PHAC-1 in C. elegans. Journal of Neuroscience. Society for Neuroscience.
https://doi.org/10.1523/JNEUROSCI.1767-23.2024
chicago: Stratigi, Aikaterini, Miguel Soler-García, Mia Krout, Shikha Shukla, Mario
de Bono, Janet E. Richmond, and Patrick Laurent. “Neuroendocrine Control of Synaptic
Transmission by PHAC-1 in C. Elegans.” Journal of Neuroscience. Society
for Neuroscience, 2025. https://doi.org/10.1523/JNEUROSCI.1767-23.2024.
ieee: A. Stratigi et al., “Neuroendocrine control of synaptic transmission
by PHAC-1 in C. elegans,” Journal of Neuroscience, vol. 45, no. 13. Society
for Neuroscience, 2025.
ista: Stratigi A, Soler-García M, Krout M, Shukla S, de Bono M, Richmond JE, Laurent
P. 2025. Neuroendocrine control of synaptic transmission by PHAC-1 in C. elegans.
Journal of Neuroscience. 45(13), e1767232024.
mla: Stratigi, Aikaterini, et al. “Neuroendocrine Control of Synaptic Transmission
by PHAC-1 in C. Elegans.” Journal of Neuroscience, vol. 45, no. 13, e1767232024,
Society for Neuroscience, 2025, doi:10.1523/JNEUROSCI.1767-23.2024.
short: A. Stratigi, M. Soler-García, M. Krout, S. Shukla, M. de Bono, J.E. Richmond,
P. Laurent, Journal of Neuroscience 45 (2025).
date_created: 2025-04-06T22:01:32Z
date_published: 2025-03-26T00:00:00Z
date_updated: 2026-07-28T11:30:41Z
day: '26'
ddc:
- '570'
department:
- _id: MaDe
doi: 10.1523/JNEUROSCI.1767-23.2024
external_id:
isi:
- '001460952700001'
pmid:
- '39919830'
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content_type: application/pdf
creator: dernst
date_created: 2025-04-07T11:57:19Z
date_updated: 2025-09-27T22:30:02Z
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has_accepted_license: '1'
intvolume: ' 45'
isi: 1
issue: '13'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Journal of Neuroscience
publication_identifier:
eissn:
- 1529-2401
issn:
- 0270-6474
publication_status: published
publisher: Society for Neuroscience
quality_controlled: '1'
scopus_import: '1'
status: public
title: Neuroendocrine control of synaptic transmission by PHAC-1 in C. elegans
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: 45
year: '2025'
...
---
OA_place: publisher
_id: '18871'
abstract:
- lang: eng
text: "\"Can we do this with a new type of computer - a quantum computer?\". This
famous\r\nquotation of the brilliant Richard Feynman within a conference talk
on \"Simulating physics\r\nwith computers.” is often reverently praised as the
origin of the field of quantum computing.\r\nThe idea was to use quantum mechanical
systems itself to simulate \"Nature\", which is\r\ninherently quantum mechanical.
Now, 43 years later, the theoretical framework of how such\r\na computer can operate
has been developed. Two main important concepts for a potential\r\nquantum supremacy,
superposition and entanglement, have been exploited to design quantum\r\nalgorithms
to significantly speed up certain tasks. Yet, the specific hardware implementation\r\nis
still far from being certain, in fact the race between the most promising platforms
such as\r\nsuperconducting qubits, bosonic codes, cold atoms, trapped ions, optical
computing as well\r\nas spin qubits has recently intensified. If one also includes
the most mature applications of\r\nquantum communication technologies, secure
quantum key distribution and quantum random\r\nnumber generators, as part of a
quantum information technology ecosystem, we are confronted\r\nwith a plethora
of different materials, concepts, and also operation frequencies. While\r\nsuperconducting
qubits, bosonic codes and spin qubits work in the regime of approximately 5\r\nGHz
and are controlled by electrical fields, trapped ions, cold atoms, and optical
quantum\r\ncomputing operate with light in the infrared or visible range.\r\nConsequently,
a quantum frequency converter or microwave-optic transducer is required\r\nto
interface the different frequency domains or establish a long-range network connection\r\nwith
suitable telecom fibers. In fact, the combination of different frequency regimes
is also\r\nan essential part in our classical modern communication network, where
computations are\r\nperformed in electrical circuits and the information exchange
over longer distances happens\r\nvia optical fibers. However, the specific challenges
specific to building a quantum computer,\r\nalso apply to the development of such
a quantum frequency transducer: 1) As we deal with\r\nsingle excitations as the
carrier of information, i.e. the smallest possible quantity, the signal\r\ncan
easily be corrupted by other noise sources which needs to be avoided by all means.
This\r\nis also the reason why microwave quantum computers operate at temperature
environments\r\nclose to zero temperature (< 0.1 Kelvin) to avoid corruption by
thermal noise. 2) The\r\nfrequency interface generally needs to preserve the phase
of the signal as an essential part\r\nof the quantum state. And 3) Quantum signals
cannot be copied which would be a typical\r\nstrategy to account for errors in
classical computers. And finally, there is a challenge specific to\r\nmicrowave-optic
transducers: While quantum computers are operating in one specific frequency\r\ndomain,
microwave-optic transducers combine microwave and optical fields in one device.\r\nThis
results in the particular challenge that high-energy optical radiation, which
is usually\r\nwell-shielded from superconducting microwave quantum processors,
are now an essential part\r\nof the device. The concomitant optical radiation
in the operating transducer will inevitably\r\nhave a detrimental effect on the
superconducting microwave components. Together with the\r\nrequirement of minimal
background noise for quantum-limited operation as described above,\r\nv\r\nheating
from the absorption of optical photons within the same device where single microwave\r\nexcitations
are processed forms a formidable challenge.\r\nThis thesis aims to address this
challenge by developing microwave-optic transducers where\r\nthe impact of optical
absorption on superconducting circuits in general and superconducting\r\nqubits
specifically can be mitigated. In our first approach, we developed a compact device\r\nwith
optimized interaction strengths between the different frequency domains. This
minimizes\r\nthe optical powers used for transducer operation and thus the optical
absorption heating. This\r\nwork was - to the best of our knowledge - the first
comprehensive noise study, in an integrated\r\nmicrowave-optic transducer. Unfortunately,
we saw that the optical absorption heating added\r\nnoise way above a single excitation.
Consequently, a potential quantum signal would have\r\nbeen buried in the noise,
added by the transduction.\r\nBuilding on this insight, we utilized a three-dimensional
microwave-optic transducer instead\r\nof an integrated device. The larger heat
capacity of the macroscopic device with a size\r\nof a few millimeters can absorb
a larger fraction of the optical heating before it increases\r\nthe temperature
of the device. This allowed us to interface the transducer directly with a\r\nsuperconducting
qubit to readout the qubit state in a novel all-optical manner. We showed\r\nthat
the microwave-optic transducer can be operated in a regime in which optical fields
don’t\r\nharm the sensitive qubit. This is an important prerequisite for the operation
of microwave-optic\r\ntransducers in conjunction with microwave quantum processors
and brings the integration and\r\nseamless orchestration of different frequency
components in a quantum network a step closer.\r\n"
acknowledged_ssus:
- _id: SSU
- _id: M-Shop
- _id: NanoFab
acknowledgement: "This work was supported by the European Research Council under grant
agreement no. 758053\r\n(ERC StG QUNNECT) and the European Union’s Horizon 2020
research, innovation program\r\nunder grant agreement no. 899354 (FETopen SuperQuLAN)
and the Austrian Science Fund\r\n(FWF) through BeyondC (F7105). I want to acknowledge
generous support from the Austrian\r\nAcademy of Sciences from a DOC [Doctoral program
of the Austrian Academy of Sciences]\r\nfellowship (no. 25129).\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Georg M
full_name: Arnold, Georg M
id: 3770C838-F248-11E8-B48F-1D18A9856A87
last_name: Arnold
orcid: 0000-0003-1397-7876
citation:
ama: Arnold GM. Microwave-optic interconnects for superconducting circuits. 2025.
doi:10.15479/at:ista:18871
apa: Arnold, G. M. (2025). Microwave-optic interconnects for superconducting
circuits. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18871
chicago: Arnold, Georg M. “Microwave-Optic Interconnects for Superconducting Circuits.”
Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/at:ista:18871.
ieee: G. M. Arnold, “Microwave-optic interconnects for superconducting circuits,”
Institute of Science and Technology Austria, 2025.
ista: Arnold GM. 2025. Microwave-optic interconnects for superconducting circuits.
Institute of Science and Technology Austria.
mla: Arnold, Georg M. Microwave-Optic Interconnects for Superconducting Circuits.
Institute of Science and Technology Austria, 2025, doi:10.15479/at:ista:18871.
short: G.M. Arnold, Microwave-Optic Interconnects for Superconducting Circuits,
Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-01-24T10:28:39Z
date_published: 2025-01-24T00:00:00Z
date_updated: 2026-04-16T12:20:43Z
day: '24'
ddc:
- '530'
degree_awarded: PhD
department:
- _id: JoFi
- _id: GradSch
doi: 10.15479/at:ista:18871
ec_funded: 1
file:
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date_created: 2025-01-29T08:38:34Z
date_updated: 2026-01-29T23:30:03Z
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file_date_updated: 2026-01-29T23:30:03Z
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language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '01'
oa: 1
oa_version: Published Version
page: '135'
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: 2671EB66-B435-11E9-9278-68D0E5697425
name: Coherent on-chip conversion of superconducting qubit signals from microwaves
to optical frequencies
- _id: bdb108fd-d553-11ed-ba76-83dc74a9864f
grant_number: F07105
name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration
of Superconducting Quantum Circuits
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6609'
relation: part_of_dissertation
status: public
- id: '8529'
relation: part_of_dissertation
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- id: '18953'
relation: part_of_dissertation
status: public
- id: '10924'
relation: part_of_dissertation
status: public
- id: '9114'
relation: part_of_dissertation
status: public
- id: '13200'
relation: part_of_dissertation
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: Microwave-optic interconnects for superconducting circuits
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
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abstract:
- lang: eng
text: "Cell migration is a crucial process in animal development and maintenance.
It is incredibly\r\nheterogeneous, with different cell types utilizing fundamentally
distinct migration strategies.\r\nThe strategies also depend on the cellular microenvironment,
where cells can switch between\r\nmigration modes as they encounter new environmental
cues. In this thesis, we investigated\r\nhow dendritic cells adapt their migration
strategy when encountering geometrically,\r\nmechanically and chemically distinct
environments.\r\nWhen dendritic cells are embedded in a homogeneous fibrous network,
they migrate in a fast\r\nand directional amoeboid manner. In this migration strategy,
extracellular proteolysis and\r\nintegrin-mediated adhesions are dispensable.
Instead, the cells use topography of the\r\nenvironment to propel their cell body
forward. To migrate efficiently in the maze of different\r\npore sizes, they position
the nucleus ahead of the microtubule organizing center (MTOC) and\r\nuse it to
gauge the pores to identify the path of least resistance. Our aim was to identify\r\nwhether
dendritic cells adapt their migration strategy when encountering asymmetrical\r\ntransitions
into much denser environments with limited choice of large pores. In such invasive\r\ntransitions
it is unclear if the cells can cross tight pores without the use of adhesions
and\r\nextracellular proteolysis and whether they maintain the nucleus in the
cell front.\r\nUsing various cell migration assays such as fibrous 3D collagen
gels, geometrically defined\r\nmicrochannels with constrictions and simplistic
under agarose migration assay, we provide\r\na comprehensive characterization
of invasive migration of dendritic cells. We show that\r\nduring invasion the
cells stall and stretch, reflecting the difficulty to translocate the bulky cell\r\nbody
into the dense environment. In collagen gels, we show that dendritic cells can
invade\r\nwithout proteolysis and adhesions. Instead, they utilize contractility,
which can lead to largescale collagen compressions. During invasion, the nucleus
stalls at tight constrictions, leading\r\nto a transient organelle reorientation.
To resolve the stalling, upregulated rear contractility is\r\nrequired. This contractile
force is simultaneously necessary for reverting the nucleus back to\r\nthe cell
front after invasion and maintaining this positioning during permissive migration.\r\nA
functional role of the reorientation was uncovered in the first collaboration
project.\r\nA prominent central actin pool was identified around the MTOC, especially
pronounced in\r\ndense and compressive environments. The actin pool was shown
to generate pushing forces\r\nto dilate the space for cell translocation. These
forces are only necessary in non-permissive\r\nenvironments, where the nucleus
reorients to the cell rear, allowing the actin pool to\r\ngenerate space. In permissive
environments where space generation is dispensable, the\r\nMTOC is located behind
the nucleus and the actin cloud has reduced intensity, allowing more\r\nactin
to be incorporated into the lamellipodium, speeding up migration.\r\nIn the second
collaboration project, we investigated the effects of distinct chemical\r\nenvironments
on dendritic cell migration. The strikingly persistent migration of these cells\r\nwas
explained by their ability to modulate and even self-generate chemokine gradients.
This\r\nallows the cells to migrate faster and more persistent in uniform chemokine
fields compared\r\nto imposed chemokine gradients. The chemokine receptor CCR7
was identified as a crucial\r\nplayer in this process, both sensing the signal
and internalizing the chemokine to create a sink."
acknowledgement: "This project has received funding from the Austrian Science Fund
(FWF) via the doctorate\r\ncollege DK NanoCell and from the European Union’s Horizon
2020 research and innovation\r\nprogramme under the Marie Skłodowska-Curie Grant
Agreement No. 665385.\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Nikola
full_name: Canigova, Nikola
id: 3795523E-F248-11E8-B48F-1D18A9856A87
last_name: Canigova
orcid: 0000-0002-8518-5926
citation:
ama: Canigova N. Adaptive strategies of dendritic cell migration in response to
environmental cues. 2025. doi:10.15479/AT-ISTA-19745
apa: Canigova, N. (2025). Adaptive strategies of dendritic cell migration in
response to environmental cues. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT-ISTA-19745
chicago: Canigova, Nikola. “Adaptive Strategies of Dendritic Cell Migration in Response
to Environmental Cues.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19745.
ieee: N. Canigova, “Adaptive strategies of dendritic cell migration in response
to environmental cues,” Institute of Science and Technology Austria, 2025.
ista: Canigova N. 2025. Adaptive strategies of dendritic cell migration in response
to environmental cues. Institute of Science and Technology Austria.
mla: Canigova, Nikola. Adaptive Strategies of Dendritic Cell Migration in Response
to Environmental Cues. Institute of Science and Technology Austria, 2025,
doi:10.15479/AT-ISTA-19745.
short: N. Canigova, Adaptive Strategies of Dendritic Cell Migration in Response
to Environmental Cues, Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-05-26T08:49:00Z
date_published: 2025-05-27T00:00:00Z
date_updated: 2026-06-18T17:34:48Z
day: '27'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: MiSi
- _id: GradSch
doi: 10.15479/AT-ISTA-19745
ec_funded: 1
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date_created: 2025-05-28T07:38:17Z
date_updated: 2025-11-27T23:30:02Z
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file_date_updated: 2025-11-27T23:30:02Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '133'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 265E2996-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W01250-B20
name: Nano-Analytics of Cellular Systems
publication_identifier:
isbn:
- 978-3-99078-058-9
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '14274'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
title: Adaptive strategies of dendritic cell migration in response to environmental
cues
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...