---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20218'
abstract:
- lang: eng
text: Humanity has long sought inspiration from nature to innovate materials and
devices. As science advances, nature-inspired materials are becoming part of our
lives. Animate materials, characterized by their activity, adaptability, and autonomy,
emulate properties of living systems. While only biological materials fully embody
these principles, artificial versions are advancing rapidly, promising transformative
impacts in the circular economy, health and climate resilience within a generation.
This roadmap presents authoritative perspectives on animate materials across different
disciplines and scales, highlighting their interdisciplinary nature and potential
applications in diverse fields including nanotechnology, robotics and the built
environment. It underscores the need for concerted efforts to address shared challenges
such as complexity management, scalability, evolvability, interdisciplinary collaboration,
and ethical and environmental considerations. The framework defined by classifying
materials based on their level of animacy can guide this emerging field to encourage
cooperation and responsible development. By unravelling the mysteries of living
matter and leveraging its principles, we can design materials and systems that
will transform our world in a more sustainable manner.
acknowledgement: "Living Architecture is Funded by the EU Horizon 2020 Future Emerging
Technologies Open programme (2016–2019) Grant Agreement 686585 a consortium of 6
collaborating institutions—Newcastle University, University of Trento, University
of the West of England, Spanish National Research Council, Explora Biotech and Liquifer
Systems Group.\r\n\r\nThe Active Living Infrastructure: Controlled Environment (ALICE)
project is funded by an EU Innovation Award for the development of a bio-digital
‘brick’ prototype, a collaboration between Newcastle University, Translating Nature,
and the University of the West of England (2019–2021) under EU Grant Agreement No.
851246.\r\n\r\nMicrobial Hydroponics: Circular Sustainable Electrobiosynthesis (Mi-Hy)
is Funded by the European Union under Grant Agreement Number 101114746, which is
a collaboration between Beneficiaries, KU Leuven (Belgium), the University of Southampton
(UK), SONY Computer Science Laboratory (France), BioFaction KG (Austria), Spanish
National Research Council (Spain), and Associated Partners, the University of the
West of England (UK) and University of Southampton (UK). Mi-Hy is also supported
through the interdisciplinary KU Leuven Institute for Cultural Heritage (HERKUL)."
article_number: '333501'
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Giorgio
full_name: Volpe, Giorgio
last_name: Volpe
- first_name: Nuno A.M.
full_name: Araújo, Nuno A.M.
last_name: Araújo
- first_name: Maria
full_name: Guix, Maria
last_name: Guix
- first_name: Mark
full_name: Miodownik, Mark
last_name: Miodownik
- first_name: Nicolas
full_name: Martin, Nicolas
last_name: Martin
- first_name: Laura
full_name: Alvarez, Laura
last_name: Alvarez
- first_name: Juliane
full_name: Simmchen, Juliane
last_name: Simmchen
- first_name: Roberto Di
full_name: Leonardo, Roberto Di
last_name: Leonardo
- first_name: Nicola
full_name: Pellicciotta, Nicola
last_name: Pellicciotta
- first_name: Quentin
full_name: Martinet, Quentin
id: b37485a8-d343-11eb-a0e9-df8c484ef8ab
last_name: Martinet
orcid: 0000-0002-2916-6632
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
- first_name: Wai Kit
full_name: Ng, Wai Kit
last_name: Ng
- first_name: Dhruv
full_name: Saxena, Dhruv
last_name: Saxena
- first_name: Riccardo
full_name: Sapienza, Riccardo
last_name: Sapienza
- first_name: Sara
full_name: Nadine, Sara
last_name: Nadine
- first_name: João F.
full_name: Mano, João F.
last_name: Mano
- first_name: Reza
full_name: Mahdavi, Reza
last_name: Mahdavi
- first_name: Caroline
full_name: Beck Adiels, Caroline
last_name: Beck Adiels
- first_name: Joe
full_name: Forth, Joe
last_name: Forth
- first_name: Christian
full_name: Santangelo, Christian
last_name: Santangelo
- first_name: Stefano
full_name: Palagi, Stefano
last_name: Palagi
- first_name: Ji Min
full_name: Seok, Ji Min
last_name: Seok
- first_name: Victoria A.
full_name: Webster-Wood, Victoria A.
last_name: Webster-Wood
- first_name: Shuhong
full_name: Wang, Shuhong
last_name: Wang
- first_name: Lining
full_name: Yao, Lining
last_name: Yao
- first_name: Amirreza
full_name: Aghakhani, Amirreza
last_name: Aghakhani
- first_name: Thomas
full_name: Barois, Thomas
last_name: Barois
- first_name: Hamid
full_name: Kellay, Hamid
last_name: Kellay
- first_name: Corentin
full_name: Coulais, Corentin
last_name: Coulais
- first_name: Martin
full_name: Van Hecke, Martin
last_name: Van Hecke
- first_name: Christopher J.
full_name: Pierce, Christopher J.
last_name: Pierce
- first_name: Tianyu
full_name: Wang, Tianyu
last_name: Wang
- first_name: Baxi
full_name: Chong, Baxi
last_name: Chong
- first_name: Daniel I.
full_name: Goldman, Daniel I.
last_name: Goldman
- first_name: Andreagiovanni
full_name: Reina, Andreagiovanni
last_name: Reina
- first_name: Vito
full_name: Trianni, Vito
last_name: Trianni
- first_name: Giovanni
full_name: Volpe, Giovanni
last_name: Volpe
- first_name: Richard
full_name: Beckett, Richard
last_name: Beckett
- first_name: Sean P.
full_name: Nair, Sean P.
last_name: Nair
- first_name: Rachel
full_name: Armstrong, Rachel
last_name: Armstrong
citation:
ama: 'Volpe G, Araújo NAM, Guix M, et al. Roadmap for animate matter. Journal
of Physics: Condensed Matter. 2025;37(33). doi:10.1088/1361-648X/adebd3'
apa: 'Volpe, G., Araújo, N. A. M., Guix, M., Miodownik, M., Martin, N., Alvarez,
L., … Armstrong, R. (2025). Roadmap for animate matter. Journal of Physics:
Condensed Matter. IOP Publishing. https://doi.org/10.1088/1361-648X/adebd3'
chicago: 'Volpe, Giorgio, Nuno A.M. Araújo, Maria Guix, Mark Miodownik, Nicolas
Martin, Laura Alvarez, Juliane Simmchen, et al. “Roadmap for Animate Matter.”
Journal of Physics: Condensed Matter. IOP Publishing, 2025. https://doi.org/10.1088/1361-648X/adebd3.'
ieee: 'G. Volpe et al., “Roadmap for animate matter,” Journal of Physics:
Condensed Matter, vol. 37, no. 33. IOP Publishing, 2025.'
ista: 'Volpe G, Araújo NAM, Guix M, Miodownik M, Martin N, Alvarez L, Simmchen J,
Leonardo RD, Pellicciotta N, Martinet Q, Palacci JA, Ng WK, Saxena D, Sapienza
R, Nadine S, Mano JF, Mahdavi R, Beck Adiels C, Forth J, Santangelo C, Palagi
S, Seok JM, Webster-Wood VA, Wang S, Yao L, Aghakhani A, Barois T, Kellay H, Coulais
C, Van Hecke M, Pierce CJ, Wang T, Chong B, Goldman DI, Reina A, Trianni V, Volpe
G, Beckett R, Nair SP, Armstrong R. 2025. Roadmap for animate matter. Journal
of Physics: Condensed Matter. 37(33), 333501.'
mla: 'Volpe, Giorgio, et al. “Roadmap for Animate Matter.” Journal of Physics:
Condensed Matter, vol. 37, no. 33, 333501, IOP Publishing, 2025, doi:10.1088/1361-648X/adebd3.'
short: 'G. Volpe, N.A.M. Araújo, M. Guix, M. Miodownik, N. Martin, L. Alvarez, J.
Simmchen, R.D. Leonardo, N. Pellicciotta, Q. Martinet, J.A. Palacci, W.K. Ng,
D. Saxena, R. Sapienza, S. Nadine, J.F. Mano, R. Mahdavi, C. Beck Adiels, J. Forth,
C. Santangelo, S. Palagi, J.M. Seok, V.A. Webster-Wood, S. Wang, L. Yao, A. Aghakhani,
T. Barois, H. Kellay, C. Coulais, M. Van Hecke, C.J. Pierce, T. Wang, B. Chong,
D.I. Goldman, A. Reina, V. Trianni, G. Volpe, R. Beckett, S.P. Nair, R. Armstrong,
Journal of Physics: Condensed Matter 37 (2025).'
date_created: 2025-08-24T22:01:30Z
date_published: 2025-08-18T00:00:00Z
date_updated: 2026-08-12T14:00:12Z
day: '18'
ddc:
- '530'
department:
- _id: JePa
doi: 10.1088/1361-648X/adebd3
external_id:
arxiv:
- '2407.10623'
isi:
- '001550090200001'
file:
- access_level: open_access
checksum: 7309274f78bed785b158bd290337f456
content_type: application/pdf
creator: dernst
date_created: 2025-09-02T07:22:48Z
date_updated: 2025-09-02T07:22:48Z
file_id: '20271'
file_name: 2025_CondensedMatter_Volpe.pdf
file_size: 8997829
relation: main_file
success: 1
file_date_updated: 2025-09-02T07:22:48Z
has_accepted_license: '1'
intvolume: ' 37'
isi: 1
issue: '33'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: 'Journal of Physics: Condensed Matter'
publication_identifier:
eissn:
- 1361-648X
issn:
- 0953-8984
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Roadmap for animate matter
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: 37
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20453'
abstract:
- lang: eng
text: 'Magnetotropic susceptibility is the thermodynamic coefficient that maps the
curvature of free energy with respect to an applied magnetic field orientation,
providing a means to quantify the magnetic anisotropy of a crystal. In this context,
non-linear magnetic torque behavior has been reported in FePS3, motivating the
investigation of similar non-linear characteristics in its magnetotropic susceptibility.
In this work, we derive the non-linear magnetotropic susceptibility expressions
for FePS3 in both ac*-and bc*-planes using complementary approaches: by taking
the first derivative of torque and through the formal calculation of the magnetotropic
susceptibility. Higher-order terms in the magnetization are included, and the
final equations are obtained by applying symmetry constraints imposed by the C2h
point group of the material. We analyze the behavior of the resulting non-linear
expressions and identify the contributions of each parameter. Our theoretical
results show good agreement with preliminary, unpublished experimental data, offering
meaningful guidance for ongoing and future experimental work.'
acknowledgement: We thank Kimberly A. Modic for her support and discussions regarding
the technique in the context of a project indirectly related to, but distinct from,
the present work. We also thank Brad J. Ramshaw and Arkady Shekhter for scientific
discussions not directly related to this study, but whose insights proved helpful.
We are grateful to Valeska Zambra, Amit Nathwani, Hamza Nasir, and Tayyaba Hussain
for informal discussions on various aspects of the technique, and to Naoya Iwahara
for his thoughtful and constructive feedback. The experimental curve shown in figures
3(b) and 6, from the Thermodynamics of Quantum Materials (TQM) group at ISTA, was
measured by Muhammad Nauman for an unrelated project. We thank Kimberly Modic for
granting access to the laboratory facilities. Je Geun Park provided the crystal
used for that measurement via Younjung Jo, whose contribution we gratefully acknowledge.
Institutional support from the Institute of Science and Technology Austria (ISTA)
is also gratefully acknowledged.
article_number: '405801'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Hamza
full_name: Farooq, Hamza
last_name: Farooq
- first_name: Muhammad
full_name: Nauman, Muhammad
id: 32c21954-2022-11eb-9d5f-af9f93c24e71
last_name: Nauman
orcid: 0000-0002-2111-4846
citation:
ama: 'Farooq H, Nauman M. Non-linear magnetotropic susceptibility in FePS3. Journal
of Physics: Condensed Matter. 2025;37(40). doi:10.1088/1361-648X/ae0913'
apa: 'Farooq, H., & Nauman, M. (2025). Non-linear magnetotropic susceptibility
in FePS3. Journal of Physics: Condensed Matter. IOP Publishing. https://doi.org/10.1088/1361-648X/ae0913'
chicago: 'Farooq, Hamza, and Muhammad Nauman. “Non-Linear Magnetotropic Susceptibility
in FePS3.” Journal of Physics: Condensed Matter. IOP Publishing, 2025.
https://doi.org/10.1088/1361-648X/ae0913.'
ieee: 'H. Farooq and M. Nauman, “Non-linear magnetotropic susceptibility in FePS3,”
Journal of Physics: Condensed Matter, vol. 37, no. 40. IOP Publishing,
2025.'
ista: 'Farooq H, Nauman M. 2025. Non-linear magnetotropic susceptibility in FePS3.
Journal of Physics: Condensed Matter. 37(40), 405801.'
mla: 'Farooq, Hamza, and Muhammad Nauman. “Non-Linear Magnetotropic Susceptibility
in FePS3.” Journal of Physics: Condensed Matter, vol. 37, no. 40, 405801,
IOP Publishing, 2025, doi:10.1088/1361-648X/ae0913.'
short: 'H. Farooq, M. Nauman, Journal of Physics: Condensed Matter 37 (2025).'
corr_author: '1'
date_created: 2025-10-12T22:01:26Z
date_published: 2025-10-06T00:00:00Z
date_updated: 2026-08-12T14:00:34Z
day: '06'
ddc:
- '530'
department:
- _id: KiMo
doi: 10.1088/1361-648X/ae0913
external_id:
isi:
- '001585824100001'
pmid:
- '40967257'
file:
- access_level: open_access
checksum: b182856a5a655496e149afa49ec464f3
content_type: application/pdf
creator: dernst
date_created: 2025-10-13T06:34:15Z
date_updated: 2025-10-13T06:34:15Z
file_id: '20458'
file_name: 2025_JourPhysicsCondMatter_Farooq.pdf
file_size: 1709516
relation: main_file
success: 1
file_date_updated: 2025-10-13T06:34:15Z
has_accepted_license: '1'
intvolume: ' 37'
isi: 1
issue: '40'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: 'Journal of Physics: Condensed Matter'
publication_identifier:
eissn:
- 1361-648X
issn:
- 0953-8984
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Non-linear magnetotropic susceptibility in FePS3
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: 37
year: '2025'
...
---
OA_type: closed access
_id: '20219'
abstract:
- lang: eng
text: Reproduction is a fundamental biological process, with organisms reproducing
sexually, asexually, and, in some cases, utilizing both modes of reproduction
within the same population. Does the ability to reproduce through a combination
of asexual and sexual modes offer an evolutionary advantage over relying on either
mode alone? Here, we introduce an empirically driven theoretical model to examine
the dynamics and interplay between sexual and asexual reproduction in stick insect
populations. We analyse it using a novel phase transition approach and corroborate
it using published experimental data. We find that the presence of males can either
increase or decrease the overall population size. However, maintaining an optimal
ratio of parthenogenetic to sexual reproduction is crucial for male resilience,
effectively delaying male extinction. Conversely, extreme levels of parthenogenetic
reproduction—whether too high or too low—can lead to male extinction, emphasizing
the need for a balanced number of virgin females to ensure the persistence of
males. Our model also explains male absence in Carausius morosus and persistence
in Extatosoma tiaratum. Our findings provide valuable insights into the interplay
of reproductive strategies and contribute to broader discussions on the transitions
between sexual and asexual reproduction.
acknowledgement: We acknowledge Prof. Uri Alon for introducing us to the topic of
systems biology during the graduate course at the Weizmann Institute of Science,
whose insights and teachings have greatly inspired this work.
article_number: '20250202'
article_processing_charge: No
article_type: original
author:
- first_name: Oran
full_name: Ayalon, Oran
last_name: Ayalon
- first_name: Harikrishnan
full_name: Rajendran, Harikrishnan
id: 876b6b34-8ff4-11ec-97c9-8d95a7aae416
last_name: Rajendran
citation:
ama: Ayalon O, Rajendran H. Interplay of asexual and sexual reproduction in bifunctional
insects. Journal of the Royal Society Interface. 2025;22(229). doi:10.1098/rsif.2025.0202
apa: Ayalon, O., & Rajendran, H. (2025). Interplay of asexual and sexual reproduction
in bifunctional insects. Journal of the Royal Society Interface. Royal
Society. https://doi.org/10.1098/rsif.2025.0202
chicago: Ayalon, Oran, and Harikrishnan Rajendran. “Interplay of Asexual and Sexual
Reproduction in Bifunctional Insects.” Journal of the Royal Society Interface.
Royal Society, 2025. https://doi.org/10.1098/rsif.2025.0202.
ieee: O. Ayalon and H. Rajendran, “Interplay of asexual and sexual reproduction
in bifunctional insects,” Journal of the Royal Society Interface, vol.
22, no. 229. Royal Society, 2025.
ista: Ayalon O, Rajendran H. 2025. Interplay of asexual and sexual reproduction
in bifunctional insects. Journal of the Royal Society Interface. 22(229), 20250202.
mla: Ayalon, Oran, and Harikrishnan Rajendran. “Interplay of Asexual and Sexual
Reproduction in Bifunctional Insects.” Journal of the Royal Society Interface,
vol. 22, no. 229, 20250202, Royal Society, 2025, doi:10.1098/rsif.2025.0202.
short: O. Ayalon, H. Rajendran, Journal of the Royal Society Interface 22 (2025).
corr_author: '1'
date_created: 2025-08-24T22:01:30Z
date_published: 2025-08-13T00:00:00Z
date_updated: 2026-08-12T14:09:20Z
day: '13'
department:
- _id: SyCr
doi: 10.1098/rsif.2025.0202
external_id:
isi:
- '001548084900001'
pmid:
- '40799050'
intvolume: ' 22'
isi: 1
issue: '229'
language:
- iso: eng
month: '08'
oa_version: None
pmid: 1
publication: Journal of the Royal Society Interface
publication_identifier:
eissn:
- 1742-5662
issn:
- 1742-5689
publication_status: published
publisher: Royal Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Interplay of asexual and sexual reproduction in bifunctional insects
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '19762'
abstract:
- lang: eng
text: The cerebral cortex must contain the appropriate numbers of neurons in each
layer to acquire its proper functional organization. Accordingly, neurogenesis
requires precise regulation along development. Cortical neurons are made either
directly by Radial Glia Cells (RGCs) that self- consume, or indirectly from RGCs
via Intermediate Progenitor Cells (IPCs) and largely preserving the RGC pool.
According to the standing model of cortical development, Direct Neurogenesis predominates
at early stages of development, and progressively shifts to Indirect Neurogenesis,
which predominates at late stages. However, neurogenesis at early stages should
be compatible with RGC amplification, and neurogenesis at late stages needs to
involve RGC consumption, which seems in conflict with the standing model. Here
we studied the modes of neurogenesis along cortical development using multiple
approaches, including birthdating, live imaging and MADM clone labeling. Contrary
to the established dogma, our data show that Indirect Neurogenesis clearly predominates
at early developmental stages, gradually shifting to Direct Neurogenesis at late
stages. These findings challenge the current model of cortical neurogenesis, and
prompt a re-evaluation of previous and ongoing work about the genetic and molecular
mechanisms regulating this process.
acknowledgement: "We thank A. Iñigo for assistance with imaging, and members of the
Borrell and Herrera labs for\r\ninsightful discussions and critical reading of the
manuscript. Funding to our lab members was\r\nprovided by the Spanish Research Agency
(AEI): FPI contract (BES-2016-077737) to L.dV.A., FPI SO contract (SEV-2017-0723-18-1)
to A.E., JdC-Incorporación contract (IJC2020-044653-I) to V.F., and JAE-Intro fellowship
(JAEICU23EX_0071) to I.C., as well as by La Caixa Foundation: La Caixa-Severo Ochoa
fellowship (E-03-2016-0557140) to S.A., INPhINIT-Retaining fellowship (LCF/BQ/DR21/11880012)
to E.F.O., INPhINIT-Incoming fellowship (LCF/BQ/DI22/11940006) to E.N., and Junior
Leader-Retaining grant to A.C. (LCF/BQ/PR23/11980051). Work was supported by grants
from FWF (SFB F78) to S.H.; AEI (PID2021-125618NB-I00) and European Research Council
(101118729) to V.B., who also acknowledges financial support from AEI through the
“Severo Ochoa” Programme for Centers of Excellence in R&D (CEX2021-001165-S)."
article_processing_charge: No
author:
- first_name: Adrián
full_name: Cárdenas, Adrián
last_name: Cárdenas
- first_name: Irem
full_name: Çelik, Irem
last_name: Çelik
- first_name: Alexandre
full_name: Espinós, Alexandre
last_name: Espinós
- first_name: Carmen
full_name: Streicher, Carmen
id: 36BCB99C-F248-11E8-B48F-1D18A9856A87
last_name: Streicher
- first_name: Lara
full_name: López-González, Lara
last_name: López-González
- first_name: Lucia
full_name: del-Valle-Anton, Lucia
last_name: del-Valle-Anton
- first_name: Virginia
full_name: Fernández, Virginia
last_name: Fernández
- first_name: Salma
full_name: Amin, Salma
last_name: Amin
- first_name: Enrico
full_name: Negri, Enrico
last_name: Negri
- first_name: Eduardo Fernández
full_name: Ortuño, Eduardo Fernández
last_name: Ortuño
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Víctor
full_name: Borrell, Víctor
last_name: Borrell
biorxivid: 1
citation:
ama: Cárdenas A, Çelik I, Espinós A, et al. Early indirect neurogenesis transitions
to late direct neurogenesis in mouse cerebral cortex development. bioRxiv.
doi:10.1101/2025.05.22.655488
apa: Cárdenas, A., Çelik, I., Espinós, A., Streicher, C., López-González, L., del-Valle-Anton,
L., … Borrell, V. (n.d.). Early indirect neurogenesis transitions to late direct
neurogenesis in mouse cerebral cortex development. bioRxiv. https://doi.org/10.1101/2025.05.22.655488
chicago: Cárdenas, Adrián, Irem Çelik, Alexandre Espinós, Carmen Streicher, Lara
López-González, Lucia del-Valle-Anton, Virginia Fernández, et al. “Early Indirect
Neurogenesis Transitions to Late Direct Neurogenesis in Mouse Cerebral Cortex
Development.” BioRxiv, n.d. https://doi.org/10.1101/2025.05.22.655488.
ieee: A. Cárdenas et al., “Early indirect neurogenesis transitions to late
direct neurogenesis in mouse cerebral cortex development,” bioRxiv. .
ista: Cárdenas A, Çelik I, Espinós A, Streicher C, López-González L, del-Valle-Anton
L, Fernández V, Amin S, Negri E, Ortuño EF, Hippenmeyer S, Borrell V. Early indirect
neurogenesis transitions to late direct neurogenesis in mouse cerebral cortex
development. bioRxiv, 10.1101/2025.05.22.655488.
mla: Cárdenas, Adrián, et al. “Early Indirect Neurogenesis Transitions to Late Direct
Neurogenesis in Mouse Cerebral Cortex Development.” BioRxiv, doi:10.1101/2025.05.22.655488.
short: A. Cárdenas, I. Çelik, A. Espinós, C. Streicher, L. López-González, L. del-Valle-Anton,
V. Fernández, S. Amin, E. Negri, E.F. Ortuño, S. Hippenmeyer, V. Borrell, BioRxiv
(n.d.).
date_created: 2025-05-29T10:45:55Z
date_published: 2025-05-23T00:00:00Z
date_updated: 2026-08-13T07:18:38Z
day: '23'
department:
- _id: SiHi
doi: 10.1101/2025.05.22.655488
external_id:
biorxivid:
- 10.1101/2025.05.22.655488
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2025.05.22.655488
month: '05'
oa: 1
oa_version: Preprint
project:
- _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E
grant_number: F7805
name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular
Mechanisms of Neural Stem Cell Lineage Progression
publication: bioRxiv
publication_status: submitted
status: public
title: Early indirect neurogenesis transitions to late direct neurogenesis in mouse
cerebral cortex development
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '19717'
abstract:
- lang: eng
text: Radial glial progenitors (RGPs) generate all projection neurons (PNs) in the
cerebral cortex through incompletely understood processes. Herein, we combine
Mosaic Analysis with Double Markers (MADM)-based clonal analysis at embryonic
days 12.5 and 13.5 with early postnatal callosal tracing to reveal a lineage progression
that challenges the inside-outside model of cortical development and the conventional
view of an invariable sequence of asymmetric neurogenic divisions. Our data demonstrate
that early multipotent RGPs generate all extra-telencephalic (ET) and intra-telencephalic
(IT) PNs across all layers through parallel sublineages and the random specification,
during the earliest neurogenic divisions, of fate-restricted daughter RGPs. While
the neuronal production of the parental multipotent RGPs consists of small ET-PN
or IT-PN outputs, fate-restricted RGPs produce larger translaminar outputs spanning
deep and upper layers of only IT-PNs, the predominant mammalian PN subtype. We
further show that the emergence of IT-PN fate-restricted RGPs also leads to quantitatively
and temporally stereotyped neurogenesis population-wise.
acknowledgement: "We thank M. Caouyette for the plasmid construction for Pou3f1 overexpression;
C. Varela747 Martínez for help with the code for graphical analysis; all members
from the Nieto’s lab for\r\ncomment on the manuscript, specially to F. Martín for
the insightful discussions;J.C. Oliveros\r\nand J.A. García from the computational
service of the CNB for help with the analysis of\r\nRNAseq dataset, C.O. Sorzano
for the help with statistical analysis, and the service of\r\nAdvance Optical Microscopy
of the CNB for their technical advice.\r\nI.V.M holds a fellowship funded by MCICIU
(PRE-2018-083376), the work was funded by\r\nPID2020-112831GB-I00 funded by MCIN/AEI
/10.13039/501100011033.\r\n"
article_processing_charge: No
author:
- first_name: I
full_name: Varela-Martínez, I
last_name: Varela-Martínez
- first_name: Ana
full_name: Villalba Requena, Ana
id: 68cb85a0-39f7-11eb-9559-9aaab4f6a247
last_name: Villalba Requena
orcid: 0000-0002-5615-5277
- first_name: J.
full_name: Garcia-Marqués, J.
last_name: Garcia-Marqués
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: M.
full_name: Nieto, M.
last_name: Nieto
citation:
ama: Varela-Martínez I, Villalba Requena A, Garcia-Marqués J, Hippenmeyer S, Nieto
M. Early emergence of projection-subtype fate-restricted radial glial progenitors
orchestrates neocortical neurogenesis. bioRxiv. doi:10.1101/2025.05.07.652665
apa: Varela-Martínez, I., Villalba Requena, A., Garcia-Marqués, J., Hippenmeyer,
S., & Nieto, M. (n.d.). Early emergence of projection-subtype fate-restricted
radial glial progenitors orchestrates neocortical neurogenesis. bioRxiv.
https://doi.org/10.1101/2025.05.07.652665
chicago: Varela-Martínez, I, Ana Villalba Requena, J. Garcia-Marqués, Simon Hippenmeyer,
and M. Nieto. “Early Emergence of Projection-Subtype Fate-Restricted Radial Glial
Progenitors Orchestrates Neocortical Neurogenesis.” BioRxiv, n.d. https://doi.org/10.1101/2025.05.07.652665.
ieee: I. Varela-Martínez, A. Villalba Requena, J. Garcia-Marqués, S. Hippenmeyer,
and M. Nieto, “Early emergence of projection-subtype fate-restricted radial glial
progenitors orchestrates neocortical neurogenesis,” bioRxiv. .
ista: Varela-Martínez I, Villalba Requena A, Garcia-Marqués J, Hippenmeyer S, Nieto
M. Early emergence of projection-subtype fate-restricted radial glial progenitors
orchestrates neocortical neurogenesis. bioRxiv, 10.1101/2025.05.07.652665.
mla: Varela-Martínez, I., et al. “Early Emergence of Projection-Subtype Fate-Restricted
Radial Glial Progenitors Orchestrates Neocortical Neurogenesis.” BioRxiv,
doi:10.1101/2025.05.07.652665.
short: I. Varela-Martínez, A. Villalba Requena, J. Garcia-Marqués, S. Hippenmeyer,
M. Nieto, BioRxiv (n.d.).
date_created: 2025-05-20T10:19:29Z
date_published: 2025-05-07T00:00:00Z
date_updated: 2026-08-13T07:16:48Z
day: '07'
department:
- _id: SiHi
doi: 10.1101/2025.05.07.652665
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2025.05.07.652665
month: '05'
oa: 1
oa_version: Preprint
publication: bioRxiv
publication_status: submitted
status: public
title: Early emergence of projection-subtype fate-restricted radial glial progenitors
orchestrates neocortical neurogenesis
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '19674'
abstract:
- lang: eng
text: 'When examined through the lens of their residual streams, a puzzling property
emerges in transformer networks: residual contributions (e.g., attention heads)
sometimes specialize in specific tasks or input attributes. In this paper, we
analyze this phenomenon in vision transformers, focusing on the spectral geometry
of residuals, and explore its implications for modality alignment in vision-language
models. First, we link it to the intrinsically low-dimensional structure of visual
head representations, zooming into their principal components and showing that
they encode specialized roles across a wide variety of input data distributions.
Then, we analyze the effect of head specialization in multimodal models, focusing
on how improved alignment between text and specialized heads impacts zero-shot
classification performance. This specialization-performance link consistently
holds across diverse pre-training data, network sizes, and objectives, demonstrating
a powerful new mechanism for boosting zero-shot classification through targeted
alignment. Ultimately, we translate these insights into actionable terms by introducing
ResiDual, a technique for spectral alignment of the residual stream. Much like
panning for gold, it lets the noise from irrelevant unit principal components
(i.e., attributes) wash away to amplify task-relevant ones. Remarkably, this dual
perspective on modality alignment yields fine-tuning level performance on different
data distributions while modelling an extremely interpretable and parameter-efficient
transformation, as we extensively show on 70 pre-trained network-dataset combinations
(7 models, 10 datasets).'
acknowledgement: "The authors gratefully acknowledge Volkan Cevher for an insightful
discussion about sparse recovery algorithms, Alex Smola for valuable feedback on
the experiments, and Marco Baroni for an engaging conversation on the phenomenon
of head specialization in NLP.\r\n"
article_number: '2411.00246'
article_processing_charge: No
arxiv: 1
author:
- first_name: Lorenzo
full_name: Basile, Lorenzo
last_name: Basile
- first_name: Valentino
full_name: Maiorca, Valentino
last_name: Maiorca
- first_name: Luca
full_name: Bortolussi, Luca
last_name: Bortolussi
- first_name: Emanuele
full_name: Rodolà, Emanuele
last_name: Rodolà
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
citation:
ama: Basile L, Maiorca V, Bortolussi L, Rodolà E, Locatello F. ResiDual transformer
alignment with spectral decomposition. arXiv. doi:10.48550/arXiv.2411.00246
apa: Basile, L., Maiorca, V., Bortolussi, L., Rodolà, E., & Locatello, F. (n.d.).
ResiDual transformer alignment with spectral decomposition. arXiv. https://doi.org/10.48550/arXiv.2411.00246
chicago: Basile, Lorenzo, Valentino Maiorca, Luca Bortolussi, Emanuele Rodolà, and
Francesco Locatello. “ResiDual Transformer Alignment with Spectral Decomposition.”
ArXiv, n.d. https://doi.org/10.48550/arXiv.2411.00246.
ieee: L. Basile, V. Maiorca, L. Bortolussi, E. Rodolà, and F. Locatello, “ResiDual
transformer alignment with spectral decomposition,” arXiv. .
ista: Basile L, Maiorca V, Bortolussi L, Rodolà E, Locatello F. ResiDual transformer
alignment with spectral decomposition. arXiv, 2411.00246.
mla: Basile, Lorenzo, et al. “ResiDual Transformer Alignment with Spectral Decomposition.”
ArXiv, 2411.00246, doi:10.48550/arXiv.2411.00246.
short: L. Basile, V. Maiorca, L. Bortolussi, E. Rodolà, F. Locatello, ArXiv (n.d.).
date_created: 2025-05-11T22:02:41Z
date_published: 2025-04-14T00:00:00Z
date_updated: 2026-08-13T07:33:41Z
day: '14'
ddc:
- '000'
department:
- _id: FrLo
doi: 10.48550/arXiv.2411.00246
external_id:
arxiv:
- '2411.00246'
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2411.00246
month: '04'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: ResiDual transformer alignment with spectral decomposition
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: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_place: publisher
_id: '20167'
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: "This work was supported by EMBO (ALTF 302-2019 to Niko Amin-Wetzel),
the FWF\r\n(ESPRIT PR1054E140 to Niko Amin-Wetzel), the European Research Council\r\n(Advanced
Grant 269058 to Mario de Bono) and Wellcome (209504/A/17/Z\r\nInvestigator Award
to Mario de Bono). "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Hanna
full_name: Schön, Hanna
id: C8E17EDC-D7AA-11E9-B7B7-45ECE5697425
last_name: Schön
citation:
ama: Schön H. The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding
GPCRs. 2025. doi:10.15479/AT-ISTA-20167
apa: Schön, H. (2025). The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs
encoding GPCRs. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20167
chicago: Schön, Hanna. “The ER Complex SUTU-7/MACO-1 Regulates the Fate of MRNAs
Encoding GPCRs.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20167.
ieee: H. Schön, “The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding
GPCRs,” Institute of Science and Technology Austria, 2025.
ista: Schön H. 2025. The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding
GPCRs. Institute of Science and Technology Austria.
mla: Schön, Hanna. The ER Complex SUTU-7/MACO-1 Regulates the Fate of MRNAs Encoding
GPCRs. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20167.
short: H. Schön, The ER Complex SUTU-7/MACO-1 Regulates the Fate of MRNAs Encoding
GPCRs, Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-08-13T11:13:13Z
date_published: 2025-08-13T00:00:00Z
date_updated: 2026-08-13T13:05:37Z
day: '13'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MaDe
doi: 10.15479/AT-ISTA-20167
doi_confirm: '1'
file:
- access_level: closed
checksum: b40c74404b8d9593802dabf57bfdf10f
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: hschoen
date_created: 2025-09-08T14:33:50Z
date_updated: 2025-09-09T08:57:04Z
file_id: '20311'
file_name: 2025_Schoen_Hanna_Thesis.docx
file_size: 78812587
relation: source_file
- access_level: closed
checksum: 16abc3ff66396ce2457fe07ffa8bed90
content_type: application/pdf
creator: hschoen
date_created: 2025-09-11T14:20:59Z
date_updated: 2026-08-13T13:05:36Z
embargo: 2027-03-15
embargo_to: open_access
file_id: '20347'
file_name: 2025_Schoen_Hanna_Thesis.pdf
file_size: 9667057
relation: main_file
file_date_updated: 2026-08-13T13:05:36Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa_version: Published Version
page: '171'
project:
- _id: 23870BE8-32DE-11EA-91FC-C7463DDC885E
grant_number: 209504/A/17/Z
name: Molecular mechanisms of neural circuit function
- _id: 23813290-32DE-11EA-91FC-C7463DDC885E
grant_number: ALTF 302-2019
name: Control of gene expression at the endoplasmic reticulum
publication_identifier:
isbn:
- 978-3-99078-061-9
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
title: The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs
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_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20538'
abstract:
- lang: eng
text: In this study, we describe an integrated approach for methyl group assignment
comprising precursor-based selective methyl group labeling, a novel pulse sequence
for methyl to backbone coherence transfer and chemical shift predictions using
UCBShift 2.0. The utility of this novel α-ketoacid isotopologue is shown by the
adaptation of an HMBC-HMQC pulse sequence that simultaneously connects geminal
methyl groups of leucine and valine residues to each other and to the protein
backbone. By additional 13C,2H-labeling of residues other than valine and leucine
residues of the protein, important chemical shift information about neighboring
residues (following valine and leucine residues) can be achieved. Thus, different
valine and leucine residues in a protein can be characterized as a specific chemical
shift vector. Frequency matching with predicted chemical shifts via UCBShift 2.0
using experimental data taken from a subset of the BMRB database revealed a correct
assignment performance of about 90%. With applications to proteins of 60.2 kDa
and 134 kDa (4 × 33.5 kDa) in size, we demonstrate that the approach provides
valuable information even for very large proteins.
acknowledged_ssus:
- _id: NMR
- _id: LifeSc
acknowledgement: A.L.P and G.T were funded by the “New Ideas” program by Vienna Doctoral
School in Chemistry. S.K. was funded by the Austrian Science Fund FWF P35098-B.
This work was supported financially by the Austrian Science Fund (FWF, grant numbers
I06223 and I5812-B, “AlloSpace”). This research was supported by the Scientific
Service Units (SSU) of Institute of Science and Technology Austria (ISTA) through
resources provided by the Nuclear Magnetic Resonance Facility and the Lab Support
Facility (LSF). We thank Celina Sailer for assistance with the analysis of the NMR
spectrum of HsTom70.
article_number: '169465'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Sonja
full_name: Knödlstorfer, Sonja
last_name: Knödlstorfer
- first_name: Giorgia
full_name: Toscano, Giorgia
id: 334a5e40-8747-11f0-b671-ba1f5154b4b4
last_name: Toscano
- first_name: Aleksandra L.
full_name: Ptaszek, Aleksandra L.
last_name: Ptaszek
- first_name: Georg
full_name: Kontaxis, Georg
last_name: Kontaxis
- first_name: Federico
full_name: Napoli, Federico
id: d42e08e7-f4fc-11eb-af0a-d71e26138f1b
last_name: Napoli
orcid: 0000-0002-9043-136X
- first_name: Jakob
full_name: Schneider, Jakob
id: 64368429-eb97-11eb-a6c2-c980b1f44415
last_name: Schneider
- first_name: Katharina
full_name: Maier, Katharina
last_name: Maier
- first_name: Anna
full_name: Kapitonova, Anna
id: 9fb2a840-89e1-11ee-a8b7-cc5c7ba62471
last_name: Kapitonova
- first_name: Roman J.
full_name: Lichtenecker, Roman J.
last_name: Lichtenecker
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Robert
full_name: Konrat, Robert
last_name: Konrat
citation:
ama: Knödlstorfer S, Toscano G, Ptaszek AL, et al. A novel HMBC-CC-HMQC NMR strategy
for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with
UCBShift 2.0. Journal of Molecular Biology. 2025;437(23). doi:10.1016/j.jmb.2025.169465
apa: Knödlstorfer, S., Toscano, G., Ptaszek, A. L., Kontaxis, G., Napoli, F., Schneider,
J., … Konrat, R. (2025). A novel HMBC-CC-HMQC NMR strategy for methyl assignment
using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0. Journal
of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2025.169465
chicago: Knödlstorfer, Sonja, Giorgia Toscano, Aleksandra L. Ptaszek, Georg Kontaxis,
Federico Napoli, Jakob Schneider, Katharina Maier, et al. “A Novel HMBC-CC-HMQC
NMR Strategy for Methyl Assignment Using Triple-13C-Labeled α-Ketoisovalerate
Integrated with UCBShift 2.0.” Journal of Molecular Biology. Elsevier,
2025. https://doi.org/10.1016/j.jmb.2025.169465.
ieee: S. Knödlstorfer et al., “A novel HMBC-CC-HMQC NMR strategy for methyl
assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift
2.0,” Journal of Molecular Biology, vol. 437, no. 23. Elsevier, 2025.
ista: Knödlstorfer S, Toscano G, Ptaszek AL, Kontaxis G, Napoli F, Schneider J,
Maier K, Kapitonova A, Lichtenecker RJ, Schanda P, Konrat R. 2025. A novel HMBC-CC-HMQC
NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate
integrated with UCBShift 2.0. Journal of Molecular Biology. 437(23), 169465.
mla: Knödlstorfer, Sonja, et al. “A Novel HMBC-CC-HMQC NMR Strategy for Methyl Assignment
Using Triple-13C-Labeled α-Ketoisovalerate Integrated with UCBShift 2.0.” Journal
of Molecular Biology, vol. 437, no. 23, 169465, Elsevier, 2025, doi:10.1016/j.jmb.2025.169465.
short: S. Knödlstorfer, G. Toscano, A.L. Ptaszek, G. Kontaxis, F. Napoli, J. Schneider,
K. Maier, A. Kapitonova, R.J. Lichtenecker, P. Schanda, R. Konrat, Journal of
Molecular Biology 437 (2025).
date_created: 2025-10-26T23:01:35Z
date_published: 2025-12-01T00:00:00Z
date_updated: 2026-08-13T14:19:02Z
day: '01'
ddc:
- '540'
department:
- _id: PaSc
- _id: GradSch
doi: 10.1016/j.jmb.2025.169465
external_id:
pmid:
- '41016549'
file:
- access_level: open_access
checksum: feb92f9c79032c261165f4ca573f444a
content_type: application/pdf
creator: dernst
date_created: 2025-12-30T10:29:08Z
date_updated: 2025-12-30T10:29:08Z
file_id: '20915'
file_name: 2025_JourMolecularBiology_Knoedlstorfer.pdf
file_size: 3076611
relation: main_file
success: 1
file_date_updated: 2025-12-30T10:29:08Z
has_accepted_license: '1'
intvolume: ' 437'
issue: '23'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: bdb9578d-d553-11ed-ba76-ed5d39fce6f0
grant_number: I06223
name: Structure and mechanism of the mitochondrial MIM insertase
- _id: eb9c82eb-77a9-11ec-83b8-aadd536561cf
grant_number: I05812
name: AlloSpace. The emergence and mechanisms of allostery
publication: Journal of Molecular Biology
publication_identifier:
eissn:
- 1089-8638
issn:
- 0022-2836
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled
α-ketoisovalerate integrated with UCBShift 2.0
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: 437
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20258'
abstract:
- lang: eng
text: The specific introduction of ^1H-^13C or ^1H-^15N moieties into otherwise
deuterated proteins holds great potential for high-resolution solution and magic-angle
spinning (MAS) NMR studies of protein structure and dynamics. Arginine residues
play key roles for example at active sites of enzymes. Taking advantage of a chemically
synthesized Arg with a ^13C-^1H2 group in an otherwise deuterated backbone, we
demonstrate here the usefulness of proton-detected MAS NMR approaches to probe
arginine dynamics. In experiments with crystalline ubiquitin and the 134 kDa tetrameric
enzyme malate dehydrogenase we detected a wide range of motions, from sites that
are rigid on time scales of at least tens of milliseconds to residues undergoing
predominantly nanosecond motions. Spin-relaxation and dipolar-coupling measurements
enabled quantitative determination of these dynamics. We observed microsecond
dynamics of residue Arg54 in crystalline ubiquitin, whose backbone is known to
sample different β-turn conformations on this time scale. The labeling scheme
and experiments presented here expand the toolkit for high-resolution proton-detected
MAS NMR.
acknowledged_ssus:
- _id: NMR
- _id: LifeSc
acknowledgement: This work was supported financially by the Austrian Science Fund
(FWF, Grant No. I5812-B, “AlloSpace”). This research was supported by the Scientific
Service Units (SSU) of Institute of Science and Technology Austria (ISTA) through
resources provided by the Nuclear Magnetic Resonance Facility and the Lab Support
Facility (LSF). We thank Petra Rovò and Margarita Valhondo Falcón for excellent
support of the NMR facility.
article_number: '169379'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Darja
full_name: Rohden, Darja
id: 81dc668a-19fa-11f0-bf31-d56534059ef3
last_name: Rohden
- first_name: Federico
full_name: Napoli, Federico
id: d42e08e7-f4fc-11eb-af0a-d71e26138f1b
last_name: Napoli
orcid: 0000-0002-9043-136X
- first_name: Anna
full_name: Kapitonova, Anna
id: 9fb2a840-89e1-11ee-a8b7-cc5c7ba62471
last_name: Kapitonova
- first_name: Benjamin
full_name: Tatman, Benjamin
id: 71cda2f3-e604-11ee-a1df-da10587eda3f
last_name: Tatman
- first_name: Roman J.
full_name: Lichtenecker, Roman J.
last_name: Lichtenecker
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Rohden D, Napoli F, Kapitonova A, Tatman B, Lichtenecker RJ, Schanda P. Arginine
dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme.
Journal of Molecular Biology. 2025;437(23). doi:10.1016/j.jmb.2025.169379
apa: Rohden, D., Napoli, F., Kapitonova, A., Tatman, B., Lichtenecker, R. J., &
Schanda, P. (2025). Arginine dynamics probed by magic-angle spinning NMR with
a specific isotope-labeling scheme. Journal of Molecular Biology. Elsevier.
https://doi.org/10.1016/j.jmb.2025.169379
chicago: Rohden, Darja, Federico Napoli, Anna Kapitonova, Benjamin Tatman, Roman
J. Lichtenecker, and Paul Schanda. “Arginine Dynamics Probed by Magic-Angle Spinning
NMR with a Specific Isotope-Labeling Scheme.” Journal of Molecular Biology.
Elsevier, 2025. https://doi.org/10.1016/j.jmb.2025.169379.
ieee: D. Rohden, F. Napoli, A. Kapitonova, B. Tatman, R. J. Lichtenecker, and P.
Schanda, “Arginine dynamics probed by magic-angle spinning NMR with a specific
isotope-labeling scheme,” Journal of Molecular Biology, vol. 437, no. 23.
Elsevier, 2025.
ista: Rohden D, Napoli F, Kapitonova A, Tatman B, Lichtenecker RJ, Schanda P. 2025.
Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling
scheme. Journal of Molecular Biology. 437(23), 169379.
mla: Rohden, Darja, et al. “Arginine Dynamics Probed by Magic-Angle Spinning NMR
with a Specific Isotope-Labeling Scheme.” Journal of Molecular Biology,
vol. 437, no. 23, 169379, Elsevier, 2025, doi:10.1016/j.jmb.2025.169379.
short: D. Rohden, F. Napoli, A. Kapitonova, B. Tatman, R.J. Lichtenecker, P. Schanda,
Journal of Molecular Biology 437 (2025).
corr_author: '1'
date_created: 2025-08-31T22:01:33Z
date_published: 2025-12-01T00:00:00Z
date_updated: 2026-08-13T14:19:01Z
day: '01'
ddc:
- '540'
department:
- _id: PaSc
doi: 10.1016/j.jmb.2025.169379
external_id:
isi:
- '001618289100020'
file:
- access_level: open_access
checksum: 90d50594d8ea9860ac5da41297992847
content_type: application/pdf
creator: dernst
date_created: 2025-12-29T14:51:40Z
date_updated: 2025-12-29T14:51:40Z
file_id: '20876'
file_name: 2025_JourMolecularBiology_Rohden.pdf
file_size: 2270555
relation: main_file
success: 1
file_date_updated: 2025-12-29T14:51:40Z
has_accepted_license: '1'
intvolume: ' 437'
isi: 1
issue: '23'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: eb9c82eb-77a9-11ec-83b8-aadd536561cf
grant_number: I05812
name: AlloSpace. The emergence and mechanisms of allostery
publication: Journal of Molecular Biology
publication_identifier:
eissn:
- 1089-8638
issn:
- 0022-2836
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '19956'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling
scheme
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: 437
year: '2025'
...
---
_id: '19956'
abstract:
- lang: eng
text: The specific introduction of 1H-13C or 1H-15N moieties into otherwise deuterated
proteins holds great potential for high-resolution solution and magic-angle spinning
(MAS) NMR studies of protein structure and dynamics. Arginine residues play key
roles for example at active sites of enzymes. Taking advantage of a chemically
synthesized Arg with a 13C-1H2 group in an otherwise deuterated backbone, we demonstrate
here the usefulness of proton-detected arginine MAS NMR approaches to probe arginine
dynamics. In experiments on crystalline ubiquitin and the 134 kDa tetrameric enzyme
malate dehydrogenase we detected a wide range of motions, from sites that are
rigid on time scales of at least tens of milliseconds to residues undergoing predominantly
nanosecond motions. Spin-relaxation and dipolar-coupling measurements enabled
quantitative determination of these dynamics. We observed microsecond dynamics
of residue Arg54 in crystalline ubiquitin, whose backbone is known to sample different
β-turn conformations on this time scale. The labeling scheme and experiments presented
here expand the toolkit for high-resolution proton-detected MAS NMR
acknowledged_ssus:
- _id: NMR
- _id: LifeSc
article_processing_charge: No
author:
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Schanda P. Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific
Isotope-Labeling Scheme. 2025. doi:10.15479/AT-ISTA-19956
apa: Schanda, P. (2025). Arginine Dynamics Probed by Magic-Angle Spinning NMR with
a Specific Isotope-Labeling Scheme. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT-ISTA-19956
chicago: Schanda, Paul. “Arginine Dynamics Probed by Magic-Angle Spinning NMR with
a Specific Isotope-Labeling Scheme.” Institute of Science and Technology Austria,
2025. https://doi.org/10.15479/AT-ISTA-19956.
ieee: P. Schanda, “Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific
Isotope-Labeling Scheme.” Institute of Science and Technology Austria, 2025.
ista: Schanda P. 2025. Arginine Dynamics Probed by Magic-Angle Spinning NMR with
a Specific Isotope-Labeling Scheme, Institute of Science and Technology Austria,
10.15479/AT-ISTA-19956.
mla: Schanda, Paul. Arginine Dynamics Probed by Magic-Angle Spinning NMR with
a Specific Isotope-Labeling Scheme. Institute of Science and Technology Austria,
2025, doi:10.15479/AT-ISTA-19956.
short: P. Schanda, (2025).
contributor:
- contributor_type: researcher
first_name: Darja
last_name: Rohden
- contributor_type: researcher
first_name: Federico
last_name: Napoli
- contributor_type: researcher
first_name: Ben
last_name: Tatman
- contributor_type: researcher
first_name: Paul
last_name: Schanda
corr_author: '1'
date_created: 2025-07-03T04:21:37Z
date_published: 2025-07-03T00:00:00Z
date_updated: 2026-08-13T14:19:01Z
day: '03'
ddc:
- '572'
department:
- _id: PaSc
doi: 10.15479/AT-ISTA-19956
file:
- access_level: open_access
checksum: a2ef61aa9fb5313c7d426913eb0482c0
content_type: application/octet-stream
creator: pschanda
date_created: 2025-07-03T10:30:14Z
date_updated: 2025-07-03T10:30:14Z
file_id: '19960'
file_name: README
file_size: 1160
relation: main_file
success: 1
- access_level: open_access
checksum: 8fb77b96d0fcc95c9903005652207a8c
content_type: application/zip
creator: pschanda
date_created: 2025-07-03T10:30:55Z
date_updated: 2025-07-03T10:30:55Z
file_id: '19961'
file_name: data_Arg_MASNMR_Rohden.zip
file_size: 128597184
relation: main_file
success: 1
- access_level: open_access
checksum: a60cc16d20b089c4bef94040a99cfba5
content_type: application/x-xz
creator: pschanda
date_created: 2025-08-14T07:06:58Z
date_updated: 2025-08-14T07:06:58Z
file_id: '20172'
file_name: 20240903_ubi_DN_Argd1C13_2D_spectra.tar.xz
file_size: 4766564
relation: main_file
success: 1
file_date_updated: 2025-08-14T07:06:58Z
has_accepted_license: '1'
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: eb9c82eb-77a9-11ec-83b8-aadd536561cf
grant_number: I05812
name: AlloSpace. The emergence and mechanisms of allostery
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '20258'
relation: used_in_publication
status: public
status: public
title: Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling
Scheme
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: research_data
user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d
year: '2025'
...
---
OA_place: publisher
_id: '19395'
abstract:
- lang: eng
text: "Plant growth and development rely significantly on phytohormones, with auxin
serving as a master regulator, orchestrating processes from embryogenesis to organogenesis,
vascular patterning, and environmental adaptation. Since its conceptual proposition
by Charles Darwin in 1880 as an endogenous chemical signal influencing phototropism
in grass, auxin has captivated scientists seeking to understand how such a small
molecule exerts a profound influence on plant development.\r\nOne particularly
fascinating aspect of auxin function is its ability to self-organize its transport.
Through a feedback mechanism between auxin perception and directional transport—primarily
mediated by PIN auxin transporters—auxin establishes narrow transport channels.
This phenomenon, known as auxin canalization, is fundamental to vascular formation,
regeneration, and other key developmental processes. Despite advances in our understanding,
driven by experimental studies and computational models, auxin canalization remains
an enigma, with many unanswered questions.\r\nLike other hormones, auxin functions
through intricate signaling pathways. It operates through at least two distinct
signaling mechanisms: the well-characterized canonical pathway and the less understood
non-canonical pathway. While significant progress has been made in elucidating
the canonical pathway, the non-canonical mechanisms remain less defined and require
further investigation.\r\nIn this study, we revisit the non-canonical auxin signaling
pathway mediated by the cell-surface complex Auxin Binding Protein 1-Transmembrane
Kinase 1 (ABP1-TMK1), with a particular focus on its downstream phosphorylation
events. We reveal that this auxin-mediated phosphorylation is conserved across
the green lineage, underscoring its fundamental role in plant development. We
explore key phosphorylation targets, particularly PIN2, which is essential for
root gravitropism. To further understand TMK1’s role in diverse developmental
processes, we identified and investigated its interactors as potential co-receptors
or regulatory components within its signaling network.\r\nGiven the previously
established role of ABP1-TMK1 in auxin canalization, we sought to further investigate
this process and identified several TMK1 interactors also involved in this intricate
mechanism.\r\nThese findings provide new insights into the complex regulation
of auxin canalization, highlighting a broader and more interconnected signaling
framework than previously understood."
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
acknowledgement: I would like to acknowledge the facilities at ISTA, particularly
LSF, IOF, and, of course, the plant facility, for providing the necessary resources
for my research.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Aline
full_name: Monzer, Aline
id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425
last_name: Monzer
citation:
ama: 'Monzer A. Cell-surface auxin signaling: Linking molecular pathways to plant
development. 2025. doi:10.15479/AT-ISTA-19395'
apa: 'Monzer, A. (2025). Cell-surface auxin signaling: Linking molecular pathways
to plant development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19395'
chicago: 'Monzer, Aline. “Cell-Surface Auxin Signaling: Linking Molecular Pathways
to Plant Development.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19395.'
ieee: 'A. Monzer, “Cell-surface auxin signaling: Linking molecular pathways to plant
development,” Institute of Science and Technology Austria, 2025.'
ista: 'Monzer A. 2025. Cell-surface auxin signaling: Linking molecular pathways
to plant development. Institute of Science and Technology Austria.'
mla: 'Monzer, Aline. Cell-Surface Auxin Signaling: Linking Molecular Pathways
to Plant Development. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19395.'
short: 'A. Monzer, Cell-Surface Auxin Signaling: Linking Molecular Pathways to Plant
Development, Institute of Science and Technology Austria, 2025.'
corr_author: '1'
date_created: 2025-03-12T14:25:42Z
date_published: 2025-03-13T00:00:00Z
date_updated: 2026-08-14T09:33:46Z
day: '13'
ddc:
- '580'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JiFr
doi: 10.15479/AT-ISTA-19395
doi_confirm: '1'
file:
- access_level: open_access
checksum: 9a3dd03bb4ec6b9907a325c3c4e8a1d7
content_type: application/pdf
creator: amonzer
date_created: 2025-03-12T14:14:49Z
date_updated: 2025-03-12T14:14:49Z
file_id: '19396'
file_name: Final Thesis Aline Monzer.pdf
file_size: 13119670
relation: main_file
success: 1
- access_level: closed
checksum: a353ce1ee2eabce37bca35499e76dbf1
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: amonzer
date_created: 2025-03-12T14:15:19Z
date_updated: 2025-04-01T07:55:27Z
file_id: '19397'
file_name: Thesis Aline.docx
file_size: 13774837
relation: source_file
file_date_updated: 2025-04-01T07:55:27Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '160'
publication_identifier:
eisbn:
- 978-3-99078-054-1
eissn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '12291'
relation: part_of_dissertation
status: public
- id: '14826'
relation: part_of_dissertation
status: public
- id: '19399'
relation: part_of_dissertation
status: public
- id: '19398'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
title: 'Cell-surface auxin signaling: Linking molecular pathways to plant development'
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2025'
...
---
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:
- id: '20656'
relation: later_version
status: public
- id: '20364'
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
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:
record:
- id: '22716'
relation: later_version
status: public
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:
- access_level: open_access
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:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.16415061
month: '07'
oa: 1
oa_version: None
publisher: Repository
related_material:
record:
- id: '20452'
relation: used_in_publication
status: public
status: public
title: 'BingqingCheng/cace-lr-fit: V0'
type: research_data_reference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
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'
- '004'
degree_awarded: PhD
department:
- _id: GradSch
- _id: BjHo
doi: 10.15479/AT-ISTA-19684
doi_confirm: '1'
file:
- access_level: open_access
checksum: 0e452642b79f13633f1595bde71a67e3
content_type: application/pdf
creator: gyalniz
date_created: 2025-05-12T15:13:28Z
date_updated: 2025-05-12T15:13:28Z
file_id: '19685'
file_name: Gökhan Yalnız - PhD thesis.pdf
file_size: 20058169
relation: main_file
success: 1
- access_level: open_access
checksum: 921099d76adab2df784ce12ce41cfb22
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).'
file_id: '19686'
file_name: Movie 2A.1.mp4
file_size: 37763743
relation: supplementary_material
title: Chapter 2 - Movie 2A.1
- access_level: open_access
checksum: 0ae5ac7d9896003c0c4207dd746808dc
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
relation: supplementary_material
title: Chapter 3 - Movie 3A.1
- access_level: open_access
checksum: ef8d270e066c1a9c3cb5ae46acf945e6
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'
file_name: Movie 3A.2.mp4
file_size: 7043169
relation: supplementary_material
title: Chapter 3 - Movie 3A.2
- access_level: open_access
checksum: 7ed871f428100d6827ac9b0e8ca8e985
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).'
file_id: '19689'
file_name: Movie 3A.3.mp4
file_size: 7748659
relation: supplementary_material
title: Chapter 3 - Movie 3A.3
- access_level: open_access
checksum: dd5a252e1da00c8f303588e22e2baeef
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).'
file_id: '19690'
file_name: Movie 3A.4.mp4
file_size: 5873052
relation: supplementary_material
title: Chapter 3 - Movie 3A.4
- access_level: open_access
checksum: 5ac58b86810698db28cbfc28f351ff70
content_type: video/mp4
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.
file_id: '19691'
file_name: Movie 4A.1.mp4
file_size: 9209327
relation: supplementary_material
title: Chapter 4 - Movie 4A.1
- access_level: open_access
checksum: ac877f1e1ef39439911bf37cb1793b8e
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
- access_level: open_access
checksum: fd17eabb70129ceaa414e40924d1d2fe
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'
file_name: Movie 5A.2.mp4
file_size: 3990352
relation: supplementary_material
title: Chapter 5 - Movie 5A.2
- access_level: open_access
checksum: 32f904497ab0bbee38f0788d96b91454
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.
file_id: '19694'
file_name: Movie 5A.3.mp4
file_size: 5171009
relation: supplementary_material
title: Chapter 5 - Movie 5A.3
- access_level: closed
checksum: f313261b9bb12dfb943fead8318954c6
content_type: application/x-zip-compressed
creator: gyalniz
date_created: 2025-05-12T15:27:10Z
date_updated: 2025-05-12T15:43:28Z
file_id: '19695'
file_name: Gökhan Yalnız - PhD thesis.zip
file_size: 18991996
relation: source_file
file_date_updated: 2025-05-12T15:43:28Z
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'
...