---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '22620'
abstract:
- lang: eng
text: Development depends on precise shaping of molecular gradients, but how natural
selection acts to establish precision is unknown. Here, we analyze genes that
control differences in the gradient of yellow flower color between two varieties
of snapdragon (Antirrhinum). We show that these differences depend, in part, on
cis-regulatory variation in the pigment biosynthetic gene, FLAVIA (FLA). FLA interacts
multiplicatively with three other loci, one of which is a trans-acting regulator
of FLA, to further shape the yellow gradient. All the loci exhibit clines at a
hybrid zone, with widths that correlate with phenotypic effect, showing how selection
can hone gradient shape with remarkable precision by acting on cis and trans variation
at multiple loci.
acknowledgement: We thank C. Taylor for plant care, N. Barton for sharing SNP data
and useful comments, H. Tavares for useful discussions and bioinformatics, M. Couchman
for field and data archiving, T. Li for help with photography and phenotyping, J.
Chan for help with ImageJ analyses, and X. Rebocho for organization of field experiments.
This work was supported by Biotechnology and Biological Sciences Research Council
grants BB/S009256/1 (to E.C.), BB/G009325/1 (to E.C.), BBS/E/JI/230002C (to E.C.),
and BBS/E/J/000PR9773 (to E.C.); Biotechnology Biological Sciences Research Council
Norwich Research Park Biosciences Doctoral Training Partnership grant BB/M011216/1
(to D.R.); and Natural Science Foundation of China grant 32030007 (to Y.X.)
article_processing_charge: Yes
article_type: original
author:
- first_name: Desmond
full_name: Bradley, Desmond
last_name: Bradley
- first_name: Louis
full_name: Boell, Louis
last_name: Boell
- first_name: Daniel
full_name: Richardson, Daniel
last_name: Richardson
- first_name: Lucy
full_name: Copsey, Lucy
last_name: Copsey
- first_name: Annabel
full_name: Whibley, Annabel
last_name: Whibley
- first_name: Ting
full_name: Xu, Ting
last_name: Xu
- first_name: Yu’E
full_name: Zhang, Yu’E
last_name: Zhang
- first_name: Yongbiao
full_name: Xue, Yongbiao
last_name: Xue
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Enrico
full_name: Coen, Enrico
last_name: Coen
citation:
ama: Bradley D, Boell L, Richardson D, et al. Shaping of developmental gradients
through selection on multiple loci in Antirrhinum. Science Advances. 2026;12(29):1-11.
doi:10.1126/sciadv.adx2011
apa: Bradley, D., Boell, L., Richardson, D., Copsey, L., Whibley, A., Xu, T., …
Coen, E. (2026). Shaping of developmental gradients through selection on multiple
loci in Antirrhinum. Science Advances. AAAS. https://doi.org/10.1126/sciadv.adx2011
chicago: Bradley, Desmond, Louis Boell, Daniel Richardson, Lucy Copsey, Annabel
Whibley, Ting Xu, Yu’E Zhang, Yongbiao Xue, David Field, and Enrico Coen. “Shaping
of Developmental Gradients through Selection on Multiple Loci in Antirrhinum.”
Science Advances. AAAS, 2026. https://doi.org/10.1126/sciadv.adx2011.
ieee: D. Bradley et al., “Shaping of developmental gradients through selection
on multiple loci in Antirrhinum,” Science Advances, vol. 12, no. 29. AAAS,
pp. 1–11, 2026.
ista: Bradley D, Boell L, Richardson D, Copsey L, Whibley A, Xu T, Zhang Y, Xue
Y, Field D, Coen E. 2026. Shaping of developmental gradients through selection
on multiple loci in Antirrhinum. Science Advances. 12(29), 1–11.
mla: Bradley, Desmond, et al. “Shaping of Developmental Gradients through Selection
on Multiple Loci in Antirrhinum.” Science Advances, vol. 12, no. 29, AAAS,
2026, pp. 1–11, doi:10.1126/sciadv.adx2011.
short: D. Bradley, L. Boell, D. Richardson, L. Copsey, A. Whibley, T. Xu, Y. Zhang,
Y. Xue, D. Field, E. Coen, Science Advances 12 (2026) 1–11.
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: All data and code needed to evaluate and reproduce the
results in the paper are present in the paper and/or the Supplementary Materials.
All materials generated in this study are described in Materials and Methods and
are available on request from E.C. (enrico.coen@jic.ac.uk).
date_created: 2026-08-02T22:01:53Z
date_published: 2026-07-17T00:00:00Z
date_updated: 2026-08-03T09:52:37Z
day: '17'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1126/sciadv.adx2011
external_id:
pmid:
- '42467783'
file:
- access_level: open_access
checksum: f9155dc2d9273e43c0caf78dffa96864
content_type: application/pdf
creator: dernst
date_created: 2026-08-03T09:44:40Z
date_updated: 2026-08-03T09:44:40Z
file_id: '22635'
file_name: 2026_ScienceAdv_Bradley.pdf
file_size: 916329
relation: main_file
success: 1
file_date_updated: 2026-08-03T09:44:40Z
fulldoi: https://doi.org/10.1126/sciadv.adx2011
has_accepted_license: '1'
intvolume: ' 12'
issue: '29'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 1-11
pmid: 1
publication: Science Advances
publication_identifier:
eissn:
- 2375-2548
publication_status: published
publisher: AAAS
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Shaping of developmental gradients through selection on multiple loci in Antirrhinum
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: 12
year: '2026'
...
---
OA_place: repository
OA_type: green
_id: '22619'
abstract:
- lang: eng
text: Planar germanium is currently the only semiconducting platform where high-coherence
spin qubits and proximity-induced superconductivity have each been demonstrated.
Recent research into spin qubits in Ge/SiGe heterostructures has focused on increasing
the thickness of the SiGe capping layer, reporting improvements in the electrostatic
noise levels. Meanwhile, heterostructures with thinner capping layers remain rather
unexplored, despite the potential advantages for proximity-induced superconductivity.
Here, we study a Ge/SiGe heterostructure with a thin SiGe cap d - 4nm and investigate
its viability to host low-noise quantum dots. To keep the thermal budget compatible
with superconducting layers, low-temperature oxide deposition processes were developed
and implemented for the gate dielectrics. The charge noise level of the fabricated
devices is estimated to be 1.8 +- 1.0 μeV/ square HZ, comparable to devices
fabricated on shallow heterostructures ( d - 20nm) with high-temperature deposited
oxides. Low charge noise levels, together with the straightforward integration
of superconductors, make this heterostructure an attractive platform for prototyping
hybrid semiconducting–superconducting devices.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
acknowledgement: 'We sincerely thank Nick van Loo, Greg Mazur, Dhananjay Joshi, and
Srijit Goswami for their inputs on low-temperature HfOx deposition; Matias Urdampilleta
and Daniel Jirovec for discussions; and Kristen Léonard for the careful reading
of the manuscript. This research was supported by the Scientific Service Units of
ISTA through resources provided by the Miba Machine Shop and the Nanofabrication
facility. The authors acknowledge support from the NOMIS Foundation; the European
Innovation Council Pathfinder Grant No. 101115315 (QuKiT); the FWF Projects with
DOI:10.55776/F86, DOI:10.55776/PAT7682124, and DOI:10.55776/P36507; and the HE-MSCA-PF
project with DOI:10.3030/101150858. ICN2 is supported by the Severo Ochoa Program
from Spanish MCIN/AEI (Grant No.: CEX2021-001214-S) and is funded by the CERCA Program/Generalitat
de Catalunya. ICN2 acknowledges funding from Generalitat de Catalunya (No. 2021SGR00457).
We acknowledge support from the CSIC Interdisciplinary Thematic Platform (PTI+)
on Quantum Technologies (PTI-QTEP+).'
article_number: '033505'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Maksim
full_name: Borovkov, Maksim
id: 1fd0975f-8b61-11ed-b69e-d149334f28c5
last_name: Borovkov
- first_name: Yona A
full_name: Schell, Yona A
id: fe39122d-06bb-11ec-a33b-9e22b40e40a5
last_name: Schell
- first_name: Dina
full_name: Sokolova, Dina
id: 2d2d62f8-72f0-11ef-b75a-8ec3e8a60032
last_name: Sokolova
- first_name: Kevin Etienne Robert
full_name: Roux, Kevin Etienne Robert
id: 53f93ea2-803f-11ed-ab7e-b283135794ef
last_name: Roux
- first_name: Paul
full_name: Falthansl-Scheinecker, Paul
id: 85b43b21-15b2-11ec-abd3-e2c252cc2285
last_name: Falthansl-Scheinecker
- first_name: Giorgio
full_name: Fabris, Giorgio
id: 298cf6f3-1ff6-11ee-9fa6-d94cfa0b3352
last_name: Fabris
- first_name: Devashish C
full_name: Shah, Devashish C
id: de191434-4e7e-11ef-bf4b-9a056fc19fc3
last_name: Shah
orcid: 0009-0007-5829-7707
- first_name: Jaime
full_name: Saez Mollejo, Jaime
id: e0390f72-f6e0-11ea-865d-862393336714
last_name: Saez Mollejo
- first_name: Rodolfo
full_name: Previdi, Rodolfo
id: bc4ea1dc-00ce-11ec-8a4e-b325ca8b9876
last_name: Previdi
- first_name: Inas
full_name: Taha, Inas
last_name: Taha
- first_name: Aziz
full_name: Genç, Aziz
last_name: Genç
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Stefano
full_name: Calcaterra, Stefano
last_name: Calcaterra
- first_name: Afonso De Cerdeira
full_name: Oliveira, Afonso De Cerdeira
last_name: Oliveira
- first_name: Daniel
full_name: Chrastina, Daniel
last_name: Chrastina
- first_name: Giovanni
full_name: Isella, Giovanni
last_name: Isella
- first_name: Anton
full_name: Bubis, Anton
id: 1f6212b5-f795-11ec-9c0c-de4780302890
last_name: Bubis
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
citation:
ama: Borovkov M, Schell YA, Sokolova D, et al. Low-noise quantum dots in ultra-shallow
Ge/SiGe heterostructures for prototyping hybrid semiconducting–superconducting
devices. Applied Physics Letters. 2026;129(3). doi:10.1063/5.0333142
apa: Borovkov, M., Schell, Y. A., Sokolova, D., Roux, K. E. R., Falthansl-Scheinecker,
P., Fabris, G., … Katsaros, G. (2026). Low-noise quantum dots in ultra-shallow
Ge/SiGe heterostructures for prototyping hybrid semiconducting–superconducting
devices. Applied Physics Letters. AIP Publishing. https://doi.org/10.1063/5.0333142
chicago: Borovkov, Maksim, Yona A Schell, Dina Sokolova, Kevin Etienne Robert Roux,
Paul Falthansl-Scheinecker, Giorgio Fabris, Devashish C Shah, et al. “Low-Noise
Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid
Semiconducting–Superconducting Devices.” Applied Physics Letters. AIP Publishing,
2026. https://doi.org/10.1063/5.0333142.
ieee: M. Borovkov et al., “Low-noise quantum dots in ultra-shallow Ge/SiGe
heterostructures for prototyping hybrid semiconducting–superconducting devices,”
Applied Physics Letters, vol. 129, no. 3. AIP Publishing, 2026.
ista: Borovkov M, Schell YA, Sokolova D, Roux KER, Falthansl-Scheinecker P, Fabris
G, Shah DC, Saez Mollejo J, Previdi R, Taha I, Genç A, Arbiol J, Calcaterra S,
Oliveira ADC, Chrastina D, Isella G, Bubis A, Katsaros G. 2026. Low-noise quantum
dots in ultra-shallow Ge/SiGe heterostructures for prototyping hybrid semiconducting–superconducting
devices. Applied Physics Letters. 129(3), 033505.
mla: Borovkov, Maksim, et al. “Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures
for Prototyping Hybrid Semiconducting–Superconducting Devices.” Applied Physics
Letters, vol. 129, no. 3, 033505, AIP Publishing, 2026, doi:10.1063/5.0333142.
short: M. Borovkov, Y.A. Schell, D. Sokolova, K.E.R. Roux, P. Falthansl-Scheinecker,
G. Fabris, D.C. Shah, J. Saez Mollejo, R. Previdi, I. Taha, A. Genç, J. Arbiol,
S. Calcaterra, A.D.C. Oliveira, D. Chrastina, G. Isella, A. Bubis, G. Katsaros,
Applied Physics Letters 129 (2026).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: The data that support the findings of this study are openly
available in Institute of Science and Technology repository at http://doi.org/10.15479/AT-ISTA-22242,
Ref. 50.
date_created: 2026-08-02T22:01:53Z
date_published: 2026-07-20T00:00:00Z
date_updated: 2026-08-03T11:08:39Z
day: '20'
department:
- _id: GeKa
- _id: GradSch
- _id: NanoFab
doi: 10.1063/5.0333142
external_id:
arxiv:
- '2602.21363'
fulldoi: https://doi.org/10.1063/5.0333142
intvolume: ' 129'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2602.21363
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: bdc2ca30-d553-11ed-ba76-cf164a5bb811
grant_number: '101115315'
name: Quantum bits with Kitaev Transmons
- _id: 34a66131-11ca-11ed-8bc3-a31681c6b03e
grant_number: F8606
name: 'Center for Correlated Quantum Materials and Solid State Quantum Systems:
Conventional and unconventional topological superconductors'
- _id: 5b9e579c-ab3d-11f0-914f-88754c5b5a3f
grant_number: PAT 7682124
name: Superconducting spin qubits in planar Ge
- _id: bd8bd29e-d553-11ed-ba76-f0070d4b237a
grant_number: P36507
name: Merging spin and superconducting qubits in planar Ge
- _id: 8ea8abf7-16d5-11f0-9cad-c41e56ec8bb3
grant_number: '101150858'
name: Realization and Manipulation of a Planar hybrid superconducting Andreev spin
qubit in Germanium
publication: Applied Physics Letters
publication_identifier:
eissn:
- 1077-3118
issn:
- 0003-6951
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
related_material:
record:
- id: '22242'
relation: research_data
status: public
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Low-noise quantum dots in ultra-shallow Ge/SiGe heterostructures for prototyping
hybrid semiconducting–superconducting devices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 129
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '22618'
abstract:
- lang: eng
text: "We use a function field version of the circle method to prove that a positive
proportion of elements in \U0001D53D\U0001D45E[\U0001D461] are representable
as a sum of three cubes of minimal degree from \U0001D53D\U0001D45E[\U0001D461],
assuming a suitable form of the Ratios Conjecture and that char(\U0001D53D\U0001D45E)
>3. The analogue of this conjecture for quadratic Dirichlet L-functions is known
for large fixed q, via recent developments in homological stability."
acknowledgement: While working on this paper the first two authors were supported
by FWF grant (DOI 10.55776/P36278) and the third author was supported by the European
Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie
Grant Agreement No. 101034413, and by the National Science and Technology Council
Project Grant 114-2115-M-001-010-MY2.
article_number: e112
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Jakob
full_name: Glas, Jakob
id: d6423cba-dc74-11ea-a0a7-ee61689ff5fb
last_name: Glas
- first_name: Victor
full_name: Wang, Victor
id: 76096395-aea4-11ed-a680-ab8ebbd3f1b9
last_name: Wang
orcid: 0000-0002-0704-7026
citation:
ama: Browning TD, Glas J, Wang V. Sums of three cubes over a function field. Forum
of Mathematics Sigma. 2026;14. doi:10.1017/fms.2026.10259
apa: Browning, T. D., Glas, J., & Wang, V. (2026). Sums of three cubes over
a function field. Forum of Mathematics Sigma. Cambridge University Press.
https://doi.org/10.1017/fms.2026.10259
chicago: Browning, Timothy D, Jakob Glas, and Victor Wang. “Sums of Three Cubes
over a Function Field.” Forum of Mathematics Sigma. Cambridge University
Press, 2026. https://doi.org/10.1017/fms.2026.10259.
ieee: T. D. Browning, J. Glas, and V. Wang, “Sums of three cubes over a function
field,” Forum of Mathematics Sigma, vol. 14. Cambridge University Press,
2026.
ista: Browning TD, Glas J, Wang V. 2026. Sums of three cubes over a function field.
Forum of Mathematics Sigma. 14, e112.
mla: Browning, Timothy D., et al. “Sums of Three Cubes over a Function Field.” Forum
of Mathematics Sigma, vol. 14, e112, Cambridge University Press, 2026, doi:10.1017/fms.2026.10259.
short: T.D. Browning, J. Glas, V. Wang, Forum of Mathematics Sigma 14 (2026).
corr_author: '1'
das_tickbox: '0'
date_created: 2026-08-02T22:01:52Z
date_published: 2026-07-22T00:00:00Z
date_updated: 2026-08-03T12:13:59Z
day: '22'
ddc:
- '500'
department:
- _id: TiBr
- _id: GradSch
doi: 10.1017/fms.2026.10259
ec_funded: 1
external_id:
arxiv:
- '2402.07146'
file:
- access_level: open_access
checksum: e92a762e03f832bdca8c106a9a88ef9b
content_type: application/pdf
creator: dernst
date_created: 2026-08-03T12:12:03Z
date_updated: 2026-08-03T12:12:03Z
file_id: '22636'
file_name: 2026_ForumMathematics_Browning.pdf
file_size: 810718
relation: main_file
success: 1
file_date_updated: 2026-08-03T12:12:03Z
fulldoi: https://doi.org/10.1017/fms.2026.10259
has_accepted_license: '1'
intvolume: ' 14'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: bd8a4fdc-d553-11ed-ba76-80a0167441a3
grant_number: P36278
name: Rational curves via function field analytic number theory
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Forum of Mathematics Sigma
publication_identifier:
eissn:
- 2050-5094
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Sums of three cubes over a function field
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: 14
year: '2026'
...
---
OA_place: repository
_id: '22242'
abstract:
- lang: eng
text: This deposit contains the data and analysis code accompanying the publication
"Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping
Hybrid Semiconducting–Superconducting Devices" (Borovkov et al.). The deposit
includes the raw transport and current-noise measurements of three gate-defined
quantum-dot devices as QCodes SQLite databases, the master table of the charge-noise
(flank-method) analysis with the pointers linking every analyzed PSD trace to
the raw data, the toy-model noise simulation datasets behind the supplementary
figures, the archived analysis figures (PSD fits and lever-arm extractions), and
the Python code reproducing the full analysis and all figures. The code is also
maintained at https://github.com/ISTA-Nanoelectronics/noise_paper_public; instructions
are provided in the README files.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
article_processing_charge: No
author:
- first_name: Maksim
full_name: Borovkov, Maksim
id: 1fd0975f-8b61-11ed-b69e-d149334f28c5
last_name: Borovkov
citation:
ama: Borovkov M. Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures
for Prototyping Hybrid Semiconducting-Superconducting Devices. 2026. doi:10.15479/AT-ISTA-22242
apa: Borovkov, M. (2026). Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures
for Prototyping Hybrid Semiconducting-Superconducting Devices. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT-ISTA-22242
chicago: Borovkov, Maksim. “Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures
for Prototyping Hybrid Semiconducting-Superconducting Devices.” Institute of Science
and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22242.
ieee: M. Borovkov, “Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures
for Prototyping Hybrid Semiconducting-Superconducting Devices.” Institute of Science
and Technology Austria, 2026.
ista: Borovkov M. 2026. Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures
for Prototyping Hybrid Semiconducting-Superconducting Devices, Institute of Science
and Technology Austria, 10.15479/AT-ISTA-22242.
mla: Borovkov, Maksim. Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures
for Prototyping Hybrid Semiconducting-Superconducting Devices. Institute of
Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22242.
short: M. Borovkov, (2026).
contributor:
- contributor_type: contact_person
first_name: Maksim
id: 1fd0975f-8b61-11ed-b69e-d149334f28c5
last_name: Borovkov
corr_author: '1'
date_created: 2026-07-04T17:32:27Z
date_published: 2026-07-04T00:00:00Z
date_updated: 2026-08-03T11:08:38Z
day: '04'
ddc:
- '530'
department:
- _id: GradSch
- _id: GeKa
doi: 10.15479/AT-ISTA-22242
doi_confirm: '1'
file:
- access_level: open_access
checksum: 2a1ea297e01a7a202a6b144d69a46eef
content_type: application/x-zip-compressed
creator: mborovko
date_created: 2026-07-04T17:28:49Z
date_updated: 2026-07-04T17:28:49Z
file_id: '22243'
file_name: noise_paper_public_deposit.zip
file_size: 3082596099
relation: main_file
success: 1
file_date_updated: 2026-07-04T17:28:49Z
fulldoi: https://doi.org/10.15479/AT-ISTA-22242
has_accepted_license: '1'
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: bdc2ca30-d553-11ed-ba76-cf164a5bb811
grant_number: '101115315'
name: Quantum bits with Kitaev Transmons
- _id: 34a66131-11ca-11ed-8bc3-a31681c6b03e
grant_number: F8606
name: 'Center for Correlated Quantum Materials and Solid State Quantum Systems:
Conventional and unconventional topological superconductors'
- _id: bd8bd29e-d553-11ed-ba76-f0070d4b237a
grant_number: P36507
name: Merging spin and superconducting qubits in planar Ge
- _id: 8ea8abf7-16d5-11f0-9cad-c41e56ec8bb3
grant_number: '101150858'
name: Realization and Manipulation of a Planar hybrid superconducting Andreev spin
qubit in Germanium
- _id: 5b9e579c-ab3d-11f0-914f-88754c5b5a3f
grant_number: PAT 7682124
name: Superconducting spin qubits in planar Ge
publisher: Institute of Science and Technology Austria
related_material:
link:
- relation: research_data
url: https://github.com/ISTA-Nanoelectronics/noise_paper_public
record:
- id: '22619'
relation: used_in_publication
status: public
status: public
title: Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping
Hybrid Semiconducting-Superconducting Devices
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data
user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '22449'
abstract:
- lang: eng
text: Transpiration (T) connects water, energy, and carbon cycles within ecosystems.
While T has often been reported to increase with soil warming, underlying reasons
remain poorly understood. Here, using a mechanistic ecohydrological model, T&C‐BG,
we simulated T responses to soil warming at 30 sites spanning various biomes and
climates. Consistent with observations, the numerical model reproduces negative,
insignificant, and predominantly positive T responses under soil warming. Numerical
results show that soil warming generally increases T for sites with a small Bowen
ratio. The main mechanisms leading to positive T responses to soil warming are
complex changes in energy partitioning with modifications of canopy surface temperature
and aerodynamic, stomatal, and leaf boundary layer conductance. However, soil
warming can also affect phenology, which might result in either increased or decreased
T. Our findings shed light on how T changes with warmer soil and help interpret
outcomes of warming experiments.
article_number: e2025GL120046
article_processing_charge: No
article_type: letter_note
author:
- first_name: Zhaoyang
full_name: Luo, Zhaoyang
last_name: Luo
- first_name: Jianning
full_name: Ren, Jianning
last_name: Ren
- first_name: Qi
full_name: Zhuang, Qi
last_name: Zhuang
- first_name: Simone
full_name: Fatichi, Simone
id: cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6
last_name: Fatichi
citation:
ama: 'Luo Z, Ren J, Zhuang Q, Fatichi S. Transpiration changes with soil warming:
Insights from a mechanistic model. Geophysical Research Letters. 2026;53(8).
doi:10.1029/2025gl120046'
apa: 'Luo, Z., Ren, J., Zhuang, Q., & Fatichi, S. (2026). Transpiration changes
with soil warming: Insights from a mechanistic model. Geophysical Research
Letters. American Geophysical Union. https://doi.org/10.1029/2025gl120046'
chicago: 'Luo, Zhaoyang, Jianning Ren, Qi Zhuang, and Simone Fatichi. “Transpiration
Changes with Soil Warming: Insights from a Mechanistic Model.” Geophysical
Research Letters. American Geophysical Union, 2026. https://doi.org/10.1029/2025gl120046.'
ieee: 'Z. Luo, J. Ren, Q. Zhuang, and S. Fatichi, “Transpiration changes with soil
warming: Insights from a mechanistic model,” Geophysical Research Letters,
vol. 53, no. 8. American Geophysical Union, 2026.'
ista: 'Luo Z, Ren J, Zhuang Q, Fatichi S. 2026. Transpiration changes with soil
warming: Insights from a mechanistic model. Geophysical Research Letters. 53(8),
e2025GL120046.'
mla: 'Luo, Zhaoyang, et al. “Transpiration Changes with Soil Warming: Insights from
a Mechanistic Model.” Geophysical Research Letters, vol. 53, no. 8, e2025GL120046,
American Geophysical Union, 2026, doi:10.1029/2025gl120046.'
short: Z. Luo, J. Ren, Q. Zhuang, S. Fatichi, Geophysical Research Letters 53 (2026).
das_tickbox: '1'
date_created: 2026-07-27T12:30:23Z
date_published: 2026-04-28T00:00:00Z
date_updated: 2026-08-03T13:37:39Z
day: '28'
ddc:
- '550'
doi: 10.1029/2025gl120046
extern: '1'
fulldoi: https://doi.org/10.1029/2025gl120046
has_accepted_license: '1'
intvolume: ' 53'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.1029/2025GL120046'
month: '04'
oa: 1
oa_version: Published Version
publication: Geophysical Research Letters
publication_identifier:
eissn:
- 1944-8007
issn:
- 0094-8276
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Transpiration changes with soil warming: Insights from a mechanistic model'
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: 53
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '22480'
abstract:
- lang: eng
text: "Background:\r\nThe spatial distribution of tree canopies influences ecological
functions and residents’ exposure to green spaces. Although several studies have
examined green space configuration at neighborhood scales, evidence on tree canopy
configuration at the municipal scale, an operational unit for urban planning,
remains limited.\r\nMethods:\r\nWe conducted a nationwide ecological study of
2,136 Swiss municipalities. Tree canopy coverage (PLAND), aggregation (AI, reflecting
how tightly green patches are grouped together), patch density (PD, a measure
of fragmentation), and area-weighted mean shape index (SHAPE_AM, a measure of
shape complexity) were derived from 1-m canopy maps within municipality-specific
populated areas. Natural-cause, cardiovascular, and cancer mortality (2017–2019)
were obtained from the Swiss National Cohort. Fully adjusted negative binomial
regression models estimated associations between canopy metric and mortality for
each IQR increase in the metrics.\r\nResults:\r\nHolding configuration constant,
each IQR increase in canopy coverage (∼18%) was associated with a 3.6% [B: −0.036;
95% CI: −0.078 – 0.005] reduction in cardiovascular mortality. Higher aggregation
corresponded to a 4.3% [B: 0.043; 95% CI: 0.026–0.061], an 8.9% [B: 0.089; 95%
CI: 0.059–0.119], and a 2.1% [B: 0.021; 95% CI: 0–0.042] higher number of natural-cause,
cardiovascular, and cancer deaths respectively. Higher fragmentation was associated
with a 3.3% [B: 0.033; 95% CI: 0.016–0.050], a 4.9% [B: 0.049; 95% CI: 0.020–0.078],
and a 2.2% [B: 0.022; 95% CI: 0.001–0.043] increase in these causes respectively.
No meaningful associations were observed between shape complexity and any mortality
outcomes. Associations for aggregation and fragmentation were generally stronger
in highly urbanized municipalities.\r\nConclusions:\r\nAt the municipal scale,
mortality was lower where tree canopy was distributed across several moderately
sized, spatially balanced patches rather than highly aggregated or highly fragmented
structures. These findings suggest that urban greening strategies should optimize
its spatial configuration to maximize health benefits."
article_number: '110188'
article_processing_charge: No
article_type: original
author:
- first_name: Dengkai
full_name: Chi, Dengkai
last_name: Chi
- first_name: Gabriele
full_name: Manoli, Gabriele
last_name: Manoli
- first_name: Jun
full_name: Yang, Jun
last_name: Yang
- first_name: Daniel
full_name: Richards, Daniel
last_name: Richards
- first_name: Amy
full_name: Hahs, Amy
last_name: Hahs
- first_name: Brenda
full_name: Lin, Brenda
last_name: Lin
- first_name: Mark J.
full_name: McDonnell, Mark J.
last_name: McDonnell
- first_name: Ye
full_name: Zhang, Ye
last_name: Zhang
- first_name: Yue
full_name: Zhu, Yue
last_name: Zhu
- first_name: Yeshan
full_name: Qiu, Yeshan
last_name: Qiu
- first_name: Jing
full_name: Wang, Jing
last_name: Wang
- first_name: Xing
full_name: Zheng, Xing
last_name: Zheng
- first_name: Paolo
full_name: Burlando, Paolo
last_name: Burlando
- first_name: Simone
full_name: Fatichi, Simone
id: cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6
last_name: Fatichi
- first_name: Puay Yok
full_name: Tan, Puay Yok
last_name: Tan
citation:
ama: 'Chi D, Manoli G, Yang J, et al. Tree canopy configuration and Swiss adult
mortality at the municipal level: A nationwide ecological study. Environment
International. 2026;209. doi:10.1016/j.envint.2026.110188'
apa: 'Chi, D., Manoli, G., Yang, J., Richards, D., Hahs, A., Lin, B., … Tan, P.
Y. (2026). Tree canopy configuration and Swiss adult mortality at the municipal
level: A nationwide ecological study. Environment International. Elsevier.
https://doi.org/10.1016/j.envint.2026.110188'
chicago: 'Chi, Dengkai, Gabriele Manoli, Jun Yang, Daniel Richards, Amy Hahs, Brenda
Lin, Mark J. McDonnell, et al. “Tree Canopy Configuration and Swiss Adult Mortality
at the Municipal Level: A Nationwide Ecological Study.” Environment International.
Elsevier, 2026. https://doi.org/10.1016/j.envint.2026.110188.'
ieee: 'D. Chi et al., “Tree canopy configuration and Swiss adult mortality
at the municipal level: A nationwide ecological study,” Environment International,
vol. 209. Elsevier, 2026.'
ista: 'Chi D, Manoli G, Yang J, Richards D, Hahs A, Lin B, McDonnell MJ, Zhang Y,
Zhu Y, Qiu Y, Wang J, Zheng X, Burlando P, Fatichi S, Tan PY. 2026. Tree canopy
configuration and Swiss adult mortality at the municipal level: A nationwide ecological
study. Environment International. 209, 110188.'
mla: 'Chi, Dengkai, et al. “Tree Canopy Configuration and Swiss Adult Mortality
at the Municipal Level: A Nationwide Ecological Study.” Environment International,
vol. 209, 110188, Elsevier, 2026, doi:10.1016/j.envint.2026.110188.'
short: D. Chi, G. Manoli, J. Yang, D. Richards, A. Hahs, B. Lin, M.J. McDonnell,
Y. Zhang, Y. Zhu, Y. Qiu, J. Wang, X. Zheng, P. Burlando, S. Fatichi, P.Y. Tan,
Environment International 209 (2026).
das_tickbox: '1'
date_created: 2026-07-27T12:30:23Z
date_published: 2026-03-01T00:00:00Z
date_updated: 2026-08-03T14:17:29Z
day: '01'
ddc:
- '550'
doi: 10.1016/j.envint.2026.110188
extern: '1'
external_id:
pmid:
- '41812348'
fulldoi: https://doi.org/10.1016/j.envint.2026.110188
has_accepted_license: '1'
intvolume: ' 209'
keyword:
- Aggregation
- Fragmentation
- Green space exposure
- Green space morphology
- Green space structure
- Landscape metrics
- Shape complexity
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.envint.2026.110188
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Environment International
publication_identifier:
eissn:
- 1873-6750
issn:
- 0160-4120
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Tree canopy configuration and Swiss adult mortality at the municipal level:
A nationwide ecological study'
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: 209
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '22645'
abstract:
- lang: eng
text: Nanocrystal superlattices are commonly formed by changing concentration, solvent
conditions, or particle surface chemistry. Although effective, these approaches
alter multiple contributions to the interparticle potential simultaneously, making
it difficult to isolate the interactions responsible for ordering or to control
assembly in chemically complex environments. Here, we show that oligomeric species
present in a nanocrystal reaction medium drive superlattice formation through
a depletion mechanism. Using PbTe nanocrystals as a model system, we identify
Pb–oleate oligomers in the crude reaction mixture, characterize their solution
structure, and quantify their contribution to the interparticle potential, establishing
depletion as the dominant short-range interaction governing spontaneous body-centered
cubic superlattice formation. We then confirm the depletion origin of ordering
by showing that varying depletant concentration predictably shifts the order–disorder
boundary and produces a thermally reversible transition between dispersed and
ordered states ─ behavior that is inconsistent with van der Waals or ligand-mediated
mechanisms but is a direct consequence of depletion control. Having established
and validated the mechanism, we demonstrate that the same depletion framework
can be deliberately activated in purified dispersions and transferred across nanocrystal
systems of different composition and shape, including anisotropic and binary assemblies.
These results establish precursor-derived depletion as a general and chemically
grounded mechanism for nanocrystal superlattice formation, and show that collective
ordering can be programmed through the surrounding medium rather than through
particle surface modification.
acknowledged_ssus:
- _id: EM-Fac
- _id: NMR
- _id: LifeSc
acknowledgement: ISTA and the Werner Siemens Foundation financially supported this
work. The Scientific Service Units (SSU) of ISTA supported this research through
resources provided by the Electron Microscopy Facility (EMF), NMR Facility, and
the Lab Support Facility (LSF). M.E. acknowledges financial support from Deutsche
Forschungsgemeinschaft through Collaborative Research Centre 1411. We thank Dr.
Tommaso Constanzo and Tobias Kleinhanns for assistance with high-quality electron
microscope image acquisition, Dr. Jeonghyun Park for providing NCs, Dr. Mariano
Calcabrini for assistance with the NMR study, and Prof. Jonathan De Roo for fruitful
discussions. This work benefited from the use of the SasView application, originally
developed under NSF award DMR-0520547. SasView contains code developed with funding
from the European Union’s Horizon 2020 research and innovation program under the
SINE2020 project, grant agreement No. 654000.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Seungho
full_name: Lee, Seungho
id: BB243B88-D767-11E9-B658-BC13E6697425
last_name: Lee
orcid: 0000-0002-6962-8598
- first_name: Daniel
full_name: Balazs, Daniel
id: 302BADF6-85FC-11EA-9E3B-B9493DDC885E
last_name: Balazs
orcid: 0000-0001-7597-043X
- first_name: Aiswarya
full_name: Rayaroth Puthiyaveettil, Aiswarya
id: 8aceb01b-8972-11ed-ae7b-d5fe53775add
last_name: Rayaroth Puthiyaveettil
- first_name: Sharona
full_name: Horta, Sharona
id: 03a7e858-01b1-11ec-8b71-99ae6c4a05bc
last_name: Horta
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Michael
full_name: Engel, Michael
last_name: Engel
- first_name: Ihor
full_name: Cherniukh, Ihor
id: d03b62b2-5976-11ef-a8d7-9525504b7895
last_name: Cherniukh
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
citation:
ama: Lee S, Balazs D, Rayaroth Puthiyaveettil A, et al. Reaction medium asan architect
of nanocrystal superlattices. Journal of the AmericanChemical Society.
2026;148(29):31245-31252. doi:10.1021/jacs.6c07859
apa: Lee, S., Balazs, D., Rayaroth Puthiyaveettil, A., Horta, S., Goodrich, C. P.,
Engel, M., … Ibáñez, M. (2026). Reaction medium asan architect of nanocrystal
superlattices. Journal of the AmericanChemical Society. American Chemical
Society. https://doi.org/10.1021/jacs.6c07859
chicago: Lee, Seungho, Daniel Balazs, Aiswarya Rayaroth Puthiyaveettil, Sharona
Horta, Carl Peter Goodrich, Michael Engel, Ihor Cherniukh, and Maria Ibáñez. “Reaction
Medium Asan Architect of Nanocrystal Superlattices.” Journal of the AmericanChemical
Society. American Chemical Society, 2026. https://doi.org/10.1021/jacs.6c07859.
ieee: S. Lee et al., “Reaction medium asan architect of nanocrystal superlattices,”
Journal of the AmericanChemical Society, vol. 148, no. 29. American Chemical
Society, pp. 31245–31252, 2026.
ista: Lee S, Balazs D, Rayaroth Puthiyaveettil A, Horta S, Goodrich CP, Engel M,
Cherniukh I, Ibáñez M. 2026. Reaction medium asan architect of nanocrystal superlattices.
Journal of the AmericanChemical Society. 148(29), 31245–31252.
mla: Lee, Seungho, et al. “Reaction Medium Asan Architect of Nanocrystal Superlattices.”
Journal of the AmericanChemical Society, vol. 148, no. 29, American Chemical
Society, 2026, pp. 31245–52, doi:10.1021/jacs.6c07859.
short: S. Lee, D. Balazs, A. Rayaroth Puthiyaveettil, S. Horta, C.P. Goodrich, M.
Engel, I. Cherniukh, M. Ibáñez, Journal of the AmericanChemical Society 148 (2026)
31245–31252.
corr_author: '1'
das_tickbox: '0'
date_created: 2026-08-04T06:29:31Z
date_published: 2026-07-15T00:00:00Z
date_updated: 2026-08-04T06:47:13Z
day: '15'
ddc:
- '540'
department:
- _id: MaIb
- _id: LifeSc
- _id: GradSch
- _id: CaGo
doi: 10.1021/jacs.6c07859
external_id:
pmid:
- '42532904'
file:
- access_level: open_access
checksum: 063314ae5ac4225ebd4436aa8707d113
content_type: application/pdf
creator: dernst
date_created: 2026-08-04T06:40:17Z
date_updated: 2026-08-04T06:40:17Z
file_id: '22646'
file_name: 2026_JACS_Lee.pdf
file_size: 6564594
relation: main_file
success: 1
file_date_updated: 2026-08-04T06:40:17Z
fulldoi: https://doi.org/10.1021/jacs.6c07859
has_accepted_license: '1'
intvolume: ' 148'
issue: '29'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 31245-31252
pmid: 1
project:
- _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A
name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of
Semiconductors for Waste Heat Recovery'
publication: Journal of the AmericanChemical Society
publication_identifier:
eissn:
- 1520-5126
issn:
- 0002-7863
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Reaction medium asan architect of nanocrystal superlattices
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: 148
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '22642'
abstract:
- lang: eng
text: Continuously operating atom-light interfaces represent a key prerequisite
for steady-state quantum sensors and efficient quantum processors. Here, we demonstrate
continuous accumulation of sub-Doppler-cooled atoms in a shallow intracavity dipole
trap, realizing this regime. The key ingredient is a light-shift manipulation
that creates spatially varying cooling parameters, enabling efficient capture
and accumulation of atoms within a cavity mode. Demonstrated with rubidium atoms,
a continuous flux from a source cell is funneled through the magneto-optical trap
into the cavity mode, where the atoms are cooled and maintained below 10µK in
steady state without time-sequenced operation. We characterize the resulting continuously
maintained ensemble of millions of atoms and its collective coupling to the cavity
field, establishing a route toward continuously operated cavity-QED systems and
long-duration atomic and hybrid quantum sensors.
acknowledgement: "The authors thank Vyacheslav Li for his earlier contributions to
the development of the setup utilized in this work.\r\nThis work was supported by
the Institute of Science and Technology Austria (ISTA); E.G. was supported by the
European Research Council under Grant No. 101087907 (ERC CoG\r\nQuHAMP)."
article_number: '023302'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Edward-Fulbright
full_name: Gheorghita, Edward-Fulbright
id: e664a051-133f-11ed-8f02-a05999ad0822
last_name: Gheorghita
- first_name: Sebastian
full_name: Wald, Sebastian
id: 133F200A-B015-11E9-AD41-0EDAE5697425
last_name: Wald
orcid: 0000-0002-5869-1604
- first_name: Andrea
full_name: Pupić, Andrea
id: ef9c50a4-5335-11ef-8b9b-8ce03e6380ed
last_name: Pupić
- first_name: Onur
full_name: Hosten, Onur
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
citation:
ama: Gheorghita E-F, Wald S, Pupić A, Hosten O. Continuous accumulation of cold
atoms in an optical cavity. Physical Review A. 2026;114(2). doi:10.1103/71f2-sq4p
apa: Gheorghita, E.-F., Wald, S., Pupić, A., & Hosten, O. (2026). Continuous
accumulation of cold atoms in an optical cavity. Physical Review A. American
Physical Society. https://doi.org/10.1103/71f2-sq4p
chicago: Gheorghita, Edward-Fulbright, Sebastian Wald, Andrea Pupić, and Onur Hosten.
“Continuous Accumulation of Cold Atoms in an Optical Cavity.” Physical Review
A. American Physical Society, 2026. https://doi.org/10.1103/71f2-sq4p.
ieee: E.-F. Gheorghita, S. Wald, A. Pupić, and O. Hosten, “Continuous accumulation
of cold atoms in an optical cavity,” Physical Review A, vol. 114, no. 2.
American Physical Society, 2026.
ista: Gheorghita E-F, Wald S, Pupić A, Hosten O. 2026. Continuous accumulation of
cold atoms in an optical cavity. Physical Review A. 114(2), 023302.
mla: Gheorghita, Edward-Fulbright, et al. “Continuous Accumulation of Cold Atoms
in an Optical Cavity.” Physical Review A, vol. 114, no. 2, 023302, American
Physical Society, 2026, doi:10.1103/71f2-sq4p.
short: E.-F. Gheorghita, S. Wald, A. Pupić, O. Hosten, Physical Review A 114 (2026).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: "There are no publicly available research data or software\r\nsupporting
this manuscript. Requests for further information\r\nor data should be sent to the
authors."
date_created: 2026-08-04T05:58:23Z
date_published: 2026-08-03T00:00:00Z
date_updated: 2026-08-04T06:07:20Z
day: '03'
ddc:
- '530'
department:
- _id: OnHo
- _id: GradSch
doi: 10.1103/71f2-sq4p
external_id:
arxiv:
- '2512.14528'
file:
- access_level: open_access
checksum: fdecc394b734b56e1b3b151a816bbe14
content_type: application/pdf
creator: dernst
date_created: 2026-08-04T06:03:14Z
date_updated: 2026-08-04T06:03:14Z
file_id: '22643'
file_name: 2026_PhysicalReviewA_Gheorghita.pdf
file_size: 959463
relation: main_file
success: 1
file_date_updated: 2026-08-04T06:03:14Z
fulldoi: https://doi.org/10.1103/71f2-sq4p
has_accepted_license: '1'
intvolume: ' 114'
issue: '2'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: bdb2a702-d553-11ed-ba76-f12e3e5a3bc6
grant_number: '101087907'
name: 'A quantum hybrid of atoms and milligram-scale pendulums: towards gravitational
quantum mechanics'
publication: Physical Review A
publication_identifier:
eissn:
- 2469-9934
issn:
- 2469-9926
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
researchdata_availability: upon request
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Continuous accumulation of cold atoms in an optical cavity
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: 114
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
_id: '22647'
abstract:
- lang: eng
text: "Within the plant endomembrane system, the vesicle coat protein clathrin localizes
to the plasma membrane (PM) and the trans-Golgi Network/early endosome (TGN/EE).
While the role of clathrin in endocytosis at the PM is well established, its function
at TGN/EE, presumably in late secretion (trafficking from the TGN/EE to the cell
surface) or en route to the vacuole, is debated. Similarly debated are potential
homeostatic mechanisms balancing the trafficking routes, especially endocytosis
and late secretion.\r\nWe address these questions in Arabidopsis thaliana using
conditional silencing of CLATHRIN HEAVY CHAIN (CHC), conditional overexpression
of the clathrin uncoating factor AUXILIN-LIKE1, and secretory mutants.\r\nCHC
silencing interferes with trafficking of cargoes destined for the apoplast and
the PM, supporting a function of clathrin in late secretion. The secretory cargoes
become abnormally rerouted from the TGN/EE to the vacuole. Unlike CHC silencing,
overexpression of AUXILIN-LIKE1 selectively inhibits clathrin-mediated endocytosis
while secretion continues normally at early points of induction. Conversely, secretory
mutants exhibit a reduced PM recruitment of clathrin, and variably, of the TPLATE
endocytic component.\r\nTogether, our data show a role of clathrin in secretion
and suggest secretion as a fundamental trafficking process to which endocytosis
is adjusted by a weak homeostatic mechanism."
acknowledgement: 'The authors wish to acknowledge Dr. Paweł Baster for cloning PIN1-GFP-2/pDONR221,
Ms. Aline Monzer and Dr. Mingyue Li for help with CHC protein level evaluation,
Dr. Michał Rychłowski for help with confocal microscopy, Prof. Ari Pekka Mähönen
for sharing the p1R4-pUBQ10:XVE plasmid, and Prof. Ying Gu for sharing seeds of
the sec5 mutant. M.A. would like to thank Dr. Xixi Zhang and Prof. Sebastian Bednarek
for inspiring discussions. This work was supported by the Taif University Researchers
Supporting Project, TURSP-HC2022/02 to JF and SA and Austrian Science Fund (FWF):
I 3630-B25 to JF. Open Access funding provided by Institute of Science and Technology
Austria.'
article_number: nph.71454
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Maciek
full_name: Adamowski, Maciek
id: 45F536D2-F248-11E8-B48F-1D18A9856A87
last_name: Adamowski
orcid: 0000-0001-6463-5257
- first_name: Adam
full_name: Gackowski, Adam
last_name: Gackowski
- first_name: Ivana
full_name: Matijevic, Ivana
id: 83c17ce3-15b2-11ec-abd3-f486545870bd
last_name: Matijevic
- first_name: Saqer S.
full_name: Alotaibi, Saqer S.
last_name: Alotaibi
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Adamowski M, Gackowski A, Matijevic I, Alotaibi SS, Friml J. The role of clathrin
in post‐Golgi secretion in plant cells. New Phytologist. 2026. doi:10.1111/nph.71454
apa: Adamowski, M., Gackowski, A., Matijevic, I., Alotaibi, S. S., & Friml,
J. (2026). The role of clathrin in post‐Golgi secretion in plant cells. New
Phytologist. Wiley. https://doi.org/10.1111/nph.71454
chicago: Adamowski, Maciek, Adam Gackowski, Ivana Matijevic, Saqer S. Alotaibi,
and Jiří Friml. “The Role of Clathrin in Post‐Golgi Secretion in Plant Cells.”
New Phytologist. Wiley, 2026. https://doi.org/10.1111/nph.71454.
ieee: M. Adamowski, A. Gackowski, I. Matijevic, S. S. Alotaibi, and J. Friml, “The
role of clathrin in post‐Golgi secretion in plant cells,” New Phytologist.
Wiley, 2026.
ista: Adamowski M, Gackowski A, Matijevic I, Alotaibi SS, Friml J. 2026. The role
of clathrin in post‐Golgi secretion in plant cells. New Phytologist., nph. 71454.
mla: Adamowski, Maciek, et al. “The Role of Clathrin in Post‐Golgi Secretion in
Plant Cells.” New Phytologist, nph. 71454, Wiley, 2026, doi:10.1111/nph.71454.
short: M. Adamowski, A. Gackowski, I. Matijevic, S.S. Alotaibi, J. Friml, New Phytologist
(2026).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: 'Original data associated with this study have been deposited
in Dataset S1. The accession nos. of A. thaliana genes used in this study are as
follows: CHC1 (AT3G11130), CHC2 (AT3G08530), CLC2 (AT2G40060), TPLATE (AT3G01780),
AP2A1 (AT5G22770), DRP1C (AT1G14830), GNOM-LIKE1 (AT5G39500), BEN3/BIG2 (AT3G60860),
TMK4 (AT3G23750), PIN1 (AT1G73590), AUXILIN-LIKE1 (AT4G12780), AP1M2 (AT1G60780),
ECHIDNA (AT1G09330), SEC5A (AT1G76850), SEC5B (AT1G21170), TUB2 (AT5G62690), and
PP2AA3 (AT1G13320).'
date_created: 2026-08-04T06:48:41Z
date_published: 2026-07-20T00:00:00Z
date_updated: 2026-08-04T07:58:27Z
day: '20'
department:
- _id: JiFr
- _id: MaLo
- _id: GradSch
doi: 10.1111/nph.71454
external_id:
pmid:
- '42477503'
fulldoi: https://doi.org/10.1111/nph.71454
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/nph.71454
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
publication: New Phytologist
publication_identifier:
eissn:
- 1469-8137
issn:
- 0028-646X
publication_status: epub_ahead
publisher: Wiley
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: The role of clathrin in post‐Golgi secretion in plant cells
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '22639'
abstract:
- lang: eng
text: We present an abstract Dyson expansion for perturbations that are merely relatively
form-bounded, and apply it to the polaron problem. For a large class of polaron-type
models, including the Fröhlich and Nelson models, we prove that the vacuum expectation
value of the heat semi-group is a completely monotone function of the square of
the total momentum. Consequently, the ground-state energy is a concave function
of the square of the momentum, a result recently proved for the Fröhlich model
in [14] using a probabilistic approach via Wiener integrals.
acknowledgement: Open access funding provided by Institute of Science and Technology
(IST Austria).
article_number: '87'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Davide
full_name: Desio, Davide
id: ea10a57b-23f6-11ef-9085-80d8596d52ef
last_name: Desio
orcid: 0000-0001-9840-3809
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Desio D, Seiringer R. Dyson expansion for form-bounded perturbations and applications
to the polaron problem. Letters in Mathematical Physics. 2026;116(4). doi:10.1007/s11005-026-02107-2
apa: Desio, D., & Seiringer, R. (2026). Dyson expansion for form-bounded perturbations
and applications to the polaron problem. Letters in Mathematical Physics.
Springer Nature. https://doi.org/10.1007/s11005-026-02107-2
chicago: Desio, Davide, and Robert Seiringer. “Dyson Expansion for Form-Bounded
Perturbations and Applications to the Polaron Problem.” Letters in Mathematical
Physics. Springer Nature, 2026. https://doi.org/10.1007/s11005-026-02107-2.
ieee: D. Desio and R. Seiringer, “Dyson expansion for form-bounded perturbations
and applications to the polaron problem,” Letters in Mathematical Physics,
vol. 116, no. 4. Springer Nature, 2026.
ista: Desio D, Seiringer R. 2026. Dyson expansion for form-bounded perturbations
and applications to the polaron problem. Letters in Mathematical Physics. 116(4),
87.
mla: Desio, Davide, and Robert Seiringer. “Dyson Expansion for Form-Bounded Perturbations
and Applications to the Polaron Problem.” Letters in Mathematical Physics,
vol. 116, no. 4, 87, Springer Nature, 2026, doi:10.1007/s11005-026-02107-2.
short: D. Desio, R. Seiringer, Letters in Mathematical Physics 116 (2026).
corr_author: '1'
das_tickbox: '0'
date_created: 2026-08-03T13:21:14Z
date_published: 2026-07-17T00:00:00Z
date_updated: 2026-08-04T05:57:21Z
day: '17'
ddc:
- '510'
department:
- _id: RoSe
- _id: GradSch
doi: 10.1007/s11005-026-02107-2
external_id:
arxiv:
- '2512.13443'
file:
- access_level: open_access
checksum: 1b90ff7da16b9604d6fe2c6281493456
content_type: application/pdf
creator: dernst
date_created: 2026-08-04T05:55:58Z
date_updated: 2026-08-04T05:55:58Z
file_id: '22641'
file_name: 2026_LettersMathPhysics_Desio.pdf
file_size: 371840
relation: main_file
success: 1
file_date_updated: 2026-08-04T05:55:58Z
fulldoi: https://doi.org/10.1007/s11005-026-02107-2
has_accepted_license: '1'
intvolume: ' 116'
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Letters in Mathematical Physics
publication_identifier:
issn:
- 1573-0530
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Dyson expansion for form-bounded perturbations and applications to the polaron
problem
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: 116
year: '2026'
...
---
OA_type: closed access
_id: '22638'
abstract:
- lang: eng
text: The one-bond proton-carbon coupling constant (1JCH) is an insightful probe
of carbohydrate configuration. Equatorial and axial protons at the C1 position
typically exhibit distinct 1JCH values, enabling NMR measurements to distinguish
α- and β-configurations in carbohydrates. In principle, such measurements could
provide insights into carbohydrates in the cell walls of intact microbes. However,
traditionally, these measurements are performed by solution NMR with carbohydrates
that were extracted, solubilized and fractionated, leaving the biological relevance
of the measurements uncertain. Here, we demonstrate that 1H-detected solid-state
NMR with fast magic-angle spinning allows quantitative measurements of 1JCH couplings
for mobile capsular polysaccharides, directly on submilligram amounts of pathogenic
cells. Our approach is demonstrated on intact cells of the pathogenic yeast Cryptococcus
neoformans. High-resolution proton-detected spectra enabled the determination
of coupling constants for five mobile polysaccharide units of the cryptococcal
capsule, revealing their native configurations and confirming previous solution
NMR-based anomeric configuration assignments.
acknowledgement: We thank the ANR (ANR-16-CE11-0020-02 to A. Loquet and V.A. and ANR-21-CE17-0032
to V.A.) as well as the Swiss National Science Foundation for early postdoc mobility
project P2EZP2_184258 to A. Lends. This work has benefited from the Biophysical
and Structural Chemistry Platform at Institut Européen de Chimie et Biologie IECB,
Centre National de la Recherche Scientifique CNRS Unité d’Appui et de Recherche
UAR 3033, INSERM US001, and the CNRS (IR-RMN FR3050 and Infranalytics FR2054).
article_processing_charge: No
article_type: original
author:
- first_name: Alons
full_name: Lends, Alons
last_name: Lends
- first_name: Gaelle
full_name: Lamon, Gaelle
last_name: Lamon
- first_name: Alicia
full_name: Vallet, Alicia
last_name: Vallet
- first_name: Axelle
full_name: Grélard, Axelle
last_name: Grélard
- first_name: Estelle
full_name: Morvan, Estelle
last_name: Morvan
- first_name: Vishukumar
full_name: Aimanianda, Vishukumar
last_name: Aimanianda
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Antoine
full_name: Loquet, Antoine
last_name: Loquet
citation:
ama: Lends A, Lamon G, Vallet A, et al. On-cell detection of polysaccharide one-bond1Jch
couplings by proton-detected solid-state NMR. Journal of the American Chemical
Society. 2026;148(27):28037-28042. doi:10.1021/jacs.6c06064
apa: Lends, A., Lamon, G., Vallet, A., Grélard, A., Morvan, E., Aimanianda, V.,
… Loquet, A. (2026). On-cell detection of polysaccharide one-bond1Jch couplings
by proton-detected solid-state NMR. Journal of the American Chemical Society.
American Chemical Society. https://doi.org/10.1021/jacs.6c06064
chicago: Lends, Alons, Gaelle Lamon, Alicia Vallet, Axelle Grélard, Estelle Morvan,
Vishukumar Aimanianda, Paul Schanda, and Antoine Loquet. “On-Cell Detection of
Polysaccharide One-Bond1Jch Couplings by Proton-Detected Solid-State NMR.” Journal
of the American Chemical Society. American Chemical Society, 2026. https://doi.org/10.1021/jacs.6c06064.
ieee: A. Lends et al., “On-cell detection of polysaccharide one-bond1Jch
couplings by proton-detected solid-state NMR,” Journal of the American Chemical
Society, vol. 148, no. 27. American Chemical Society, pp. 28037–28042, 2026.
ista: Lends A, Lamon G, Vallet A, Grélard A, Morvan E, Aimanianda V, Schanda P,
Loquet A. 2026. On-cell detection of polysaccharide one-bond1Jch couplings by
proton-detected solid-state NMR. Journal of the American Chemical Society. 148(27),
28037–28042.
mla: Lends, Alons, et al. “On-Cell Detection of Polysaccharide One-Bond1Jch Couplings
by Proton-Detected Solid-State NMR.” Journal of the American Chemical Society,
vol. 148, no. 27, American Chemical Society, 2026, pp. 28037–42, doi:10.1021/jacs.6c06064.
short: A. Lends, G. Lamon, A. Vallet, A. Grélard, E. Morvan, V. Aimanianda, P. Schanda,
A. Loquet, Journal of the American Chemical Society 148 (2026) 28037–28042.
das_tickbox: '0'
date_created: 2026-08-03T13:20:41Z
date_published: 2026-06-15T00:00:00Z
date_updated: 2026-08-04T05:52:13Z
day: '15'
department:
- _id: PaSc
doi: 10.1021/jacs.6c06064
external_id:
pmid:
- '42377973'
fulldoi: https://doi.org/10.1021/jacs.6c06064
intvolume: ' 148'
issue: '27'
language:
- iso: eng
month: '06'
oa_version: None
page: 28037-28042
pmid: 1
publication: Journal of the American Chemical Society
publication_identifier:
eissn:
- 1520-5126
issn:
- 0002-7863
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: yes
title: On-cell detection of polysaccharide one-bond1Jch couplings by proton-detected
solid-state NMR
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 148
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '22644'
abstract:
- lang: eng
text: "We analyze the average behavior of various arithmetic functions at the values
of degree \U0001D451 binary forms ordered by height, with probability 1. This
approach yields averaged versions of the Chowla conjecture and the Bateman–Horn
conjecture for random binary forms. Furthermore, we show that the rational Hasse
principle holds for almost all Châtelet varieties defined by a fixed norm form
of degree \U0001D452 and by varying binary forms of fixed degree \U0001D451, provided
\U0001D452 divides \U0001D451. This proves an average version of a conjecture
of Colliot-Thélène."
acknowledgement: I am deeply grateful to my advisor Tim Browning for suggesting this
problem and for the many valuable discussions that shaped this work. I would also
like to thank Efthymios Sofos, Matteo Verzobio, and Shuntaro Yamagishi for discussions
and insights that contributed to this paper. I am also very grateful to the anonymous
referee for their careful reading and for the considerable effort they put into
improving the manuscript.
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Yijie
full_name: Diao, Yijie
id: 7b7eb4ca-eb2c-11ec-b98b-accec0b20c3b
last_name: Diao
orcid: 0000-0002-4989-5330
citation:
ama: Diao Y. Liouville function, von Mangoldt function, and norm forms at random
binary forms. Glasgow Mathematical Journal. 2026:1-34. doi:10.1017/s0017089526101074
apa: Diao, Y. (2026). Liouville function, von Mangoldt function, and norm forms
at random binary forms. Glasgow Mathematical Journal. Cambridge University
Press. https://doi.org/10.1017/s0017089526101074
chicago: Diao, Yijie. “Liouville Function, von Mangoldt Function, and Norm Forms
at Random Binary Forms.” Glasgow Mathematical Journal. Cambridge University
Press, 2026. https://doi.org/10.1017/s0017089526101074.
ieee: Y. Diao, “Liouville function, von Mangoldt function, and norm forms at random
binary forms,” Glasgow Mathematical Journal. Cambridge University Press,
pp. 1–34, 2026.
ista: Diao Y. 2026. Liouville function, von Mangoldt function, and norm forms at
random binary forms. Glasgow Mathematical Journal., 1–34.
mla: Diao, Yijie. “Liouville Function, von Mangoldt Function, and Norm Forms at
Random Binary Forms.” Glasgow Mathematical Journal, Cambridge University
Press, 2026, pp. 1–34, doi:10.1017/s0017089526101074.
short: Y. Diao, Glasgow Mathematical Journal (2026) 1–34.
corr_author: '1'
das_tickbox: '0'
date_created: 2026-08-04T06:15:04Z
date_published: 2026-07-21T00:00:00Z
date_updated: 2026-08-04T06:28:01Z
day: '21'
ddc:
- '500'
department:
- _id: TiBr
- _id: GradSch
doi: 10.1017/s0017089526101074
external_id:
arxiv:
- '2506.18065'
fulldoi: https://doi.org/10.1017/s0017089526101074
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1017/S0017089526101074
mathsc:
- 11N32
- 11N37
- 11D57
- 11G35
month: '07'
oa: 1
oa_version: Published Version
page: 1-34
publication: Glasgow Mathematical Journal
publication_identifier:
eissn:
- 1469-509X
issn:
- 0017-0895
publication_status: epub_ahead
publisher: Cambridge University Press
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Liouville function, von Mangoldt function, and norm forms at random binary
forms
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
year: '2026'
...
---
OA_place: publisher
OA_type: gold
_id: '21923'
abstract:
- lang: eng
text: "The appearance of simulated natural phenomena heavily depends on the way
surfaces are textured. However, applying texture maps to dynamic deformable surfaces
presents a significant challenge, due to ever-shifting differences in length scales
involved. When these surfaces move and advect the texture along with them, their
final appearance degrades as deformed regions dramatically distort their texture
map. Modifications to the texture directly at the pixel level in response to the
deformation may introduce ghosting artifacts and look unnatural. In the real world,
the appearance of surface details on a deforming material changes through the
interplay of physical processes such as rupturing, exposure of internal structure,
or wrinkling. Motivated by these behaviors, in this work we explore how physical
principles can guide the texturing methods based on the measure of surface deformation.\r\nWe
present two novel wave-based procedural texturing algorithms which reproduce common
physical properties like advection and self-similarity, enabling the plausible
animation of deforming objects with extreme texture map distortions. Our algorithms
are fully procedural, require no actual physics simulation, and store no state
or history of deformation besides the input UV map, making them highly parallelizable
on the GPU and efficient enough for real-time applications. We show the versatility
of the method by animating physical phenomena with extreme deformations such as
flowing lava, stretching putty and outpouring sludge."
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "We thank the anonymous reviewers for their helpful comments, the
members of the Visual Computing Group at ISTA for their feedback. We also thank
Jonathan Gagnon for their help with running the Lapped Textures codes and SideFX
for the Houdini Education software licenses.\r\nImages in Fig. 2 by Kisoulou and
Vultured on Unsplash, Michal Jarmoluk and Public Domain Pictures from Pixabay and
Hawai‘i Volcanoes NPS on flickr. This research was supported by the Scientific Service
Units (SSU) of ISTA through resources provided by Scientific Computing and was funded
in part by the European Union (ERC-2021-COG 101045083 CoDiNA)."
article_number: '154'
article_processing_charge: Yes
article_type: original
author:
- first_name: Aleksei
full_name: Kalinov, Aleksei
id: 44b7120e-eb97-11eb-a6c2-e1557aa81d02
last_name: Kalinov
orcid: 0000-0003-2189-3904
- first_name: Mickaël
full_name: Ly, Mickaël
id: 6340d7f0-b48d-11eb-b10d-b7487e71d9f1
last_name: Ly
- first_name: Christian
full_name: Hafner, Christian
id: 400429CC-F248-11E8-B48F-1D18A9856A87
last_name: Hafner
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Kalinov A, Ly M, Hafner C, Wojtan C. Physics-inspired procedural texturing
of extremely deformable surfaces. ACM Transactions on Graphics. 2026;45(4).
doi:10.1145/3811353
apa: 'Kalinov, A., Ly, M., Hafner, C., & Wojtan, C. (2026). Physics-inspired
procedural texturing of extremely deformable surfaces. ACM Transactions on
Graphics. Los Angeles, CA, United States: Association for Computing Machinery.
https://doi.org/10.1145/3811353'
chicago: Kalinov, Aleksei, Mickaël Ly, Christian Hafner, and Chris Wojtan. “Physics-Inspired
Procedural Texturing of Extremely Deformable Surfaces.” ACM Transactions on
Graphics. Association for Computing Machinery, 2026. https://doi.org/10.1145/3811353.
ieee: A. Kalinov, M. Ly, C. Hafner, and C. Wojtan, “Physics-inspired procedural
texturing of extremely deformable surfaces,” ACM Transactions on Graphics,
vol. 45, no. 4. Association for Computing Machinery, 2026.
ista: Kalinov A, Ly M, Hafner C, Wojtan C. 2026. Physics-inspired procedural texturing
of extremely deformable surfaces. ACM Transactions on Graphics. 45(4), 154.
mla: Kalinov, Aleksei, et al. “Physics-Inspired Procedural Texturing of Extremely
Deformable Surfaces.” ACM Transactions on Graphics, vol. 45, no. 4, 154,
Association for Computing Machinery, 2026, doi:10.1145/3811353.
short: A. Kalinov, M. Ly, C. Hafner, C. Wojtan, ACM Transactions on Graphics 45
(2026).
conference:
end_date: 2026-07-23
location: Los Angeles, CA, United States
name: 'SIGGRAPH: International Conference and Exhibition on Computer Graphics and
Interactive Techniques'
start_date: 2026-07-19
corr_author: '1'
das_tickbox: '0'
date_created: 2026-05-29T13:25:16Z
date_published: 2026-07-01T00:00:00Z
date_updated: 2026-08-04T09:07:44Z
day: '01'
ddc:
- '006'
department:
- _id: GradSch
- _id: ChWo
doi: 10.1145/3811353
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intvolume: ' 45'
issue: '4'
keyword:
- Procedural animation
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088
grant_number: '101045083'
name: Computational Discovery of Numerical Algorithms for Animation and Simulation
of Natural Phenomena
publication: ACM Transactions on Graphics
publication_identifier:
issn:
- 0730-0301
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/infinite-deformation-and-shape-computation/
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Physics-inspired procedural texturing of extremely deformable 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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 45
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
_id: '22363'
abstract:
- lang: eng
text: Eukaryotic gene regulation relies on stochastic yet controlled promoter switching,
in which genes transition between transcriptionally active and inactive states.
Despite the molecular complexity of this process, recent studies have revealed
a surprising invariance of the “switching correlation time” (TC)—the characteristic
decay time of the autocorrelation function of promoter activity fluctuations—across
gene expression levels in multiple genes and organisms. A biophysically plausible
explanation for this invariance has so far been lacking. Here, we show that this
empirical constraint imposes stringent requirements on minimal yet realistic models
of transcriptional regulation. Specifically, reproducing TC–invariance requires
regulatory architectures with at least four internal states and nonequilibrium
dynamics that break detailed balance. Using Bayesian inference on Drosophila gap
gene expression data, we demonstrate that such models i) quantitatively reproduce
the observed TC–invariance, ii) remain robust to parameter perturbations, and
iii) maximize information transmission from transcription factor concentration
to gene expression. Remarkably, the TC-invariant modulation strategy we identify
as optimal closely parallels contemporary control-theoretic results on the modulation
of stochastic switching systems. Taken together, our results suggest that eukaryotic
transcriptional regulation operates in a nonequilibrium regime to balance precision,
reaction-rate limitations, and energy dissipation, thereby achieving near-optimal
information transmission under fundamental physical constraints.
acknowledgement: This work was supported by the French NationalResearch Agency (ANR-20-CE12-0028
“ChroDynE” and ANR-23-CE13-0021“GastruCyp” and ANR-10 LABX-73 “Revive;” all T.G.),
and by funding from theEuropean Research Council (ERC-2023-SyG, “Dynatrans,” 101118866,
T.G. andG.T.). This work was also supported in part by the U.S. NSF, through the
Centerfor the Physics of Biological Function (PHY-1734030, T.G.), and by NIH GrantsR01GM097275,
U01DA047730, and U01DK127429 (T.G.)
article_number: e2524855123
article_processing_charge: Yes
article_type: original
author:
- first_name: Benjamin
full_name: Zoller, Benjamin
last_name: Zoller
- first_name: Alexis
full_name: Benichou, Alexis
id: 3a67230c-5fc0-11ef-a673-de9a2ffadafe
last_name: Benichou
- first_name: Thomas
full_name: Gregor, Thomas
last_name: Gregor
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Zoller B, Benichou A, Gregor T, Tkačik G. Invariant nonequilibrium dynamics
in gene regulation optimize information flow. Proceedings of the National Academy
of Sciences of the United States of America. 2026;123(28). doi:10.1073/pnas.2524855123
apa: Zoller, B., Benichou, A., Gregor, T., & Tkačik, G. (2026). Invariant nonequilibrium
dynamics in gene regulation optimize information flow. Proceedings of the National
Academy of Sciences of the United States of America. National Academy of Sciences.
https://doi.org/10.1073/pnas.2524855123
chicago: Zoller, Benjamin, Alexis Benichou, Thomas Gregor, and Gašper Tkačik. “Invariant
Nonequilibrium Dynamics in Gene Regulation Optimize Information Flow.” Proceedings
of the National Academy of Sciences of the United States of America. National
Academy of Sciences, 2026. https://doi.org/10.1073/pnas.2524855123.
ieee: B. Zoller, A. Benichou, T. Gregor, and G. Tkačik, “Invariant nonequilibrium
dynamics in gene regulation optimize information flow,” Proceedings of the
National Academy of Sciences of the United States of America, vol. 123, no.
28. National Academy of Sciences, 2026.
ista: Zoller B, Benichou A, Gregor T, Tkačik G. 2026. Invariant nonequilibrium dynamics
in gene regulation optimize information flow. Proceedings of the National Academy
of Sciences of the United States of America. 123(28), e2524855123.
mla: Zoller, Benjamin, et al. “Invariant Nonequilibrium Dynamics in Gene Regulation
Optimize Information Flow.” Proceedings of the National Academy of Sciences
of the United States of America, vol. 123, no. 28, e2524855123, National Academy
of Sciences, 2026, doi:10.1073/pnas.2524855123.
short: B. Zoller, A. Benichou, T. Gregor, G. Tkačik, Proceedings of the National
Academy of Sciences of the United States of America 123 (2026).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: Software code data have been deposited in Institute Pasteur
GitHub (https://gitlab.pasteur.fr/tglab/invariantpromoterdynamicspaper) (51).
date_created: 2026-07-19T22:01:46Z
date_published: 2026-07-14T00:00:00Z
date_updated: 2026-08-04T09:21:10Z
day: '14'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1073/pnas.2524855123
external_id:
pmid:
- '42406962'
file:
- access_level: open_access
checksum: f4d82dd706ff1629db68d71190288350
content_type: application/pdf
creator: dernst
date_created: 2026-07-20T13:12:47Z
date_updated: 2026-07-20T13:12:47Z
file_id: '22376'
file_name: 2026_PNAS_Zoller.pdf
file_size: 24580098
relation: main_file
success: 1
file_date_updated: 2026-07-20T13:12:47Z
fulldoi: https://doi.org/10.1073/pnas.2524855123
has_accepted_license: '1'
intvolume: ' 123'
issue: '28'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 7bfe6a29-9f16-11ee-852c-c0da5e2045d9
grant_number: '101118866'
name: 'Transcription in 4D: the dynamic interplay between chromatin architecture
and gene expression in developing pseudo-embryos'
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/the-art-of-proper-flickering/
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Invariant nonequilibrium dynamics in gene regulation optimize information flow
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 123
year: '2026'
...
---
OA_type: closed access
_id: '22315'
abstract:
- lang: eng
text: Plant tropisms enable roots to navigate complex soils by responding to directional
environmental cues. Biological decay, although central to nutrient cycling, also
creates microbially active and potentially hostile niches. In this work, we identified
“saprotropism,” a previously unrecognized growth response that enables roots to
actively bend away from decaying plant-derived matter. Fungal-driven microbial
decomposition released organic acids and formed stable pH gradients in surrounding
soil, allowing roots to pinpoint decay without direct contact. Root epidermal
cells sensed this acidic gradient through the root meristem growth factor peptide-receptor
module, converting external pH asymmetry into asymmetric abscisic acid (ABA) distribution.
ABA asymmetry drove microtubule reorganization, which was decoded into decay-avoidant
root bending. Together, these findings establish microbial decay–derived chemical
gradients as an instructive signal for root navigation and expand the framework
of microbe-soil-plant communication.
acknowledgement: 'We are grateful to H. Guo and L. Liu (Department of Biology, Southern
University of Science and Technology) for providing the rgf1/2/3, rgi1/2/3/4, tpst-1,
and pepr1/2 lines. We thank K.-h. Liu (College of Life Science, Northwest A&F University)
for generously providing the ABA biosensor nlsABACUS2-400n. We also thank J. Li
and J. Chang (School of Life Sciences, Lanzhou University) for providing the ahk2-5/cre1-2,
ahp1/2/3, arr16/arr17, and pTCSn::GFP lines. Our thanks further extend to D. Qian,
also from the School of Life Sciences at Lanzhou University, for sharing Arabidopsis
line pTUB6::mCherry-TUB6. We are grateful to Y. Zhao (CAS Center for Excellence
in Molecular Plant Sciences, Chinese Academy of Sciences) for providing nced3/5,
snrk2.2/2.3/2.6, and pyl duodecuple mutants. We also acknowledge the Teaching and
Research Core Facility at the College of Life Sciences, Northwest A&F University,
particularly N. Fan, for their invaluable technical assistance. We also thank Life
Science Research Core Services (LSRCS), Northwest A&F University, for helping with
characterization, including CLSM (X. Liu). Fundamental and Interdisciplinary Disciplines
Breakthrough Plan of the Ministry of Education of China JYB2025XDXM706 (Y.Z.); Qin
Chuangyuan High-level Innovation and Entrepreneurship Talent Program QCYRCXM-2022-237
(Y.Z.); Fundamental Research Funds for the Central Universities K20200168 (Y.Z.);
National Natural Science Foundation of China 32570375 (Y.Z.); National Natural Science
Foundation of China 32400699 (A.Z.); European Research Council (ERC, CYNIPS) 101142681
(J.F.); Austrian Science Fund (FWF): P 37051-B (J.F.).'
article_number: eadw6568
article_processing_charge: No
article_type: original
author:
- first_name: Zhulatai
full_name: Bao, Zhulatai
last_name: Bao
- first_name: Huihui
full_name: Wang, Huihui
last_name: Wang
- first_name: Ai
full_name: Zhang, Ai
last_name: Zhang
- first_name: Ruxi
full_name: Gao, Ruxi
last_name: Gao
- first_name: Wen
full_name: Gu, Wen
last_name: Gu
- first_name: Ni
full_name: Fan, Ni
last_name: Fan
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Yuzhou
full_name: Zhang, Yuzhou
last_name: Zhang
citation:
ama: Bao Z, Wang H, Zhang A, et al. Roots navigate around decay regions by sensing
local pH gradients. Science. 2026;393(6807). doi:10.1126/science.adw6568
apa: Bao, Z., Wang, H., Zhang, A., Gao, R., Gu, W., Fan, N., … Zhang, Y. (2026).
Roots navigate around decay regions by sensing local pH gradients. Science.
American Association for the Advancement of Science. https://doi.org/10.1126/science.adw6568
chicago: Bao, Zhulatai, Huihui Wang, Ai Zhang, Ruxi Gao, Wen Gu, Ni Fan, Jiří Friml,
and Yuzhou Zhang. “Roots Navigate around Decay Regions by Sensing Local PH Gradients.”
Science. American Association for the Advancement of Science, 2026. https://doi.org/10.1126/science.adw6568.
ieee: Z. Bao et al., “Roots navigate around decay regions by sensing local
pH gradients,” Science, vol. 393, no. 6807. American Association for the
Advancement of Science, 2026.
ista: Bao Z, Wang H, Zhang A, Gao R, Gu W, Fan N, Friml J, Zhang Y. 2026. Roots
navigate around decay regions by sensing local pH gradients. Science. 393(6807),
eadw6568.
mla: Bao, Zhulatai, et al. “Roots Navigate around Decay Regions by Sensing Local
PH Gradients.” Science, vol. 393, no. 6807, eadw6568, American Association
for the Advancement of Science, 2026, doi:10.1126/science.adw6568.
short: Z. Bao, H. Wang, A. Zhang, R. Gao, W. Gu, N. Fan, J. Friml, Y. Zhang, Science
393 (2026).
das_tickbox: '1'
dataavailabilitystatement: All data are available in the manuscript or the supplementary
materials. The raw RNA-seq data have been deposited in the NCBI Gene Expression
Omnibus (GEO) under accession number GSE315473. Microbiome sequencing data have
been deposited in the Sequence Read Archive (SRA) under BioProject number PRJNA1397137.
Materials are available upon request from the corresponding author.
date_created: 2026-07-13T14:57:10Z
date_published: 2026-07-09T00:00:00Z
date_updated: 2026-08-04T09:22:49Z
day: '09'
department:
- _id: JiFr
doi: 10.1126/science.adw6568
external_id:
pmid:
- '42424472'
fulldoi: https://doi.org/10.1126/science.adw6568
intvolume: ' 393'
issue: '6807'
language:
- iso: eng
month: '07'
oa_version: None
pmid: 1
project:
- _id: 8f347782-16d5-11f0-9cad-8c19706ee739
grant_number: '101142681'
name: Cyclic nucleotides as second messengers in plants
- _id: 7bcece63-9f16-11ee-852c-ae94e099eeb6
grant_number: P37051
name: Guanylate cyclase activity of TIR1/AFBs auxin receptors
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/roots-steer-clear-of-plant-rot/
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Roots navigate around decay regions by sensing local pH gradients
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 393
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '22295'
abstract:
- lang: eng
text: 'Despite the functional diversity of over 100 causal genes1,2,3, phenotypic
convergence across models may reveal common neurobiological processes in autism
spectrum disorder (ASD). Here we profiled 251 samples from 11 monogenic mouse
models of ASD using single-nucleus multi-omic sequencing across three developmental
stages, both sexes and two brain regions. Despite genetic heterogeneity, ASD-linked
mutations converged on perturbations of the radial glial cell lineage. These alterations
reflect a transient developmental delay rather than lasting lineage misspecification
and resolve by postnatal stages. Molecularly, the largest transcriptional differences
emerged in neurons at early postnatal stages. These changes included downregulation
of synaptic and ion channel-related genes, consistent with homeostatic adaptation
or delayed maturation. Network analysis showed molecular convergence across models
within each developmental stage, suggesting that diverse mutations linked to ASD
impinge on common, stage-specific processes. Convergence becomes less pronounced
by postnatal day 14, highlighting the dynamic nature of ASD-associated changes.
Cross-genotype heterogeneity is superimposed on stage-specific effects. Electrophysiology
corroborated this pattern: mutants generally showed altered neuronal excitability
and synaptic properties with model-specific nuances. Our study also highlighted
sex-specific gene expression alterations, with female mice often displaying larger
effect sizes than male mice. Together, our findings provide a comprehensive view
of developmental cellular and molecular dynamics across models of ASD.'
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: We thank F. Freeman, V. Voronin and M. Ladron de Guevara for technical
assistance; A. Stichelberger and S. Liegenfeld for the management of our animal
colony; M. Schunn, C. Gold and the Preclinical Facility team for technical assistance;
C. Jansen and the Scientific Computing Facility for bioinformatics support and technical
assistance; the Biomedical Sequencing Facility at CeMM for assistance with next-generation
sequencing; and J. Lin and T. Krausgruber in the laboratory of C. Bock for support
with flow cytometry; J. Kirchner for illustrating the multi-omics approach depicted
in Fig. 1; and all members of the laboratory of G.N. for their support and discussions.
This study was supported by the Scientific Service Units of ISTA through resources
provided by the Imaging & Optics Facility and the Laboratory Support Facility. Bulk
RNA-seq was performed by the Next Generation Sequencing Facility at Vienna BioCenter
Core Facilities, member of the Vienna BioCenter. This work was supported by a European
Research Council Consolidator Grant (PR1028ERC02), by SFARI (PR1028SIM02) and by
the Austrian Science Fund (PE1028W1232 and PR1028FG1803) to G.N. Open access funding
provided by Institute of Science and Technology (IST Austria).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Lena A
full_name: Schwarz, Lena A
id: 29A8453C-F248-11E8-B48F-1D18A9856A87
last_name: Schwarz
- first_name: Christoph
full_name: Dotter, Christoph
id: 4C66542E-F248-11E8-B48F-1D18A9856A87
last_name: Dotter
orcid: 0000-0002-9033-9096
- first_name: Sergey
full_name: Isaev, Sergey
last_name: Isaev
- first_name: Michela
full_name: Lisi, Michela
id: 39383c1b-d3eb-11ef-8d6c-c8cdf4e10c8c
last_name: Lisi
- first_name: Daniel
full_name: Malzl, Daniel
last_name: Malzl
- first_name: Christoph
full_name: Büschl, Christoph
id: 2a8c054c-0913-11ee-9159-f8ef515809ed
last_name: Büschl
- first_name: Sabrina
full_name: Ladstätter, Sabrina
last_name: Ladstätter
- first_name: Bárbara
full_name: Oliveira, Bárbara
id: 3B03AA1A-F248-11E8-B48F-1D18A9856A87
last_name: Oliveira
- first_name: Matteo
full_name: Barel, Matteo
id: 8959927b-2236-11ed-bd6e-ea83d94ade0e
last_name: Barel
- first_name: Bernadette
full_name: Basilico, Bernadette
id: 36035796-5ACA-11E9-A75E-7AF2E5697425
last_name: Basilico
orcid: 0000-0003-1843-3173
- first_name: Chaitanya
full_name: Chintaluri, Chaitanya
id: BA06AFEE-A4BA-11EA-AE5C-14673DDC885E
last_name: Chintaluri
orcid: 0000-0003-4252-1608
- first_name: Sarah
full_name: Gorkiewicz, Sarah
id: f141a35d-15a9-11ec-9fb2-fef6becc7b6f
last_name: Gorkiewicz
- first_name: Mohammad
full_name: Goudarzi, Mohammad
id: 3384113A-F248-11E8-B48F-1D18A9856A87
last_name: Goudarzi
- first_name: Tereza
full_name: Belinova, Tereza
id: 0bf89b6a-d28b-11eb-8bd6-f43768e4d368
last_name: Belinova
- first_name: Stephan
full_name: Reichl, Stephan
last_name: Reichl
- first_name: Gintarė
full_name: Sendžikaitė, Gintarė
id: dd6d52f2-c50d-11eb-9548-bcf0ff82b344
last_name: Sendžikaitė
- first_name: Satish
full_name: Arcot Jayaram, Satish
id: b0bbee33-09f7-11eb-909c-8b358058d28a
last_name: Arcot Jayaram
orcid: 0000-0002-2479-2669
- first_name: Peter
full_name: Koppensteiner, Peter
id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87
last_name: Koppensteiner
orcid: 0000-0002-3509-1948
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: Jörg
full_name: Menche, Jörg
last_name: Menche
- first_name: Igor
full_name: Adameyko, Igor
last_name: Adameyko
- first_name: Peter Vasili
full_name: Kharchenko, Peter Vasili
id: 0095641e-7eb7-11f1-8665-aec51a2ab5e0
last_name: Kharchenko
- first_name: Christoph
full_name: Bock, Christoph
last_name: Bock
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Schwarz LA, Dotter C, Isaev S, et al. Cortical development dynamics across
autism spectrum disorder mouse models. Nature. 2026. doi:10.1038/s41586-026-10679-1
apa: Schwarz, L. A., Dotter, C., Isaev, S., Lisi, M., Malzl, D., Büschl, C., … Novarino,
G. (2026). Cortical development dynamics across autism spectrum disorder mouse
models. Nature. Springer Nature. https://doi.org/10.1038/s41586-026-10679-1
chicago: Schwarz, Lena A, Christoph Dotter, Sergey Isaev, Michela Lisi, Daniel Malzl,
Christoph Büschl, Sabrina Ladstätter, et al. “Cortical Development Dynamics across
Autism Spectrum Disorder Mouse Models.” Nature. Springer Nature, 2026.
https://doi.org/10.1038/s41586-026-10679-1.
ieee: L. A. Schwarz et al., “Cortical development dynamics across autism
spectrum disorder mouse models,” Nature. Springer Nature, 2026.
ista: Schwarz LA, Dotter C, Isaev S, Lisi M, Malzl D, Büschl C, Ladstätter S, Oliveira
B, Barel M, Basilico B, Chintaluri C, Gorkiewicz S, Goudarzi M, Belinova T, Reichl
S, Sendžikaitė G, Arcot Jayaram S, Koppensteiner P, Sommer CM, Vogels TP, Menche
J, Adameyko I, Kharchenko PV, Bock C, Novarino G. 2026. Cortical development dynamics
across autism spectrum disorder mouse models. Nature.
mla: Schwarz, Lena A., et al. “Cortical Development Dynamics across Autism Spectrum
Disorder Mouse Models.” Nature, Springer Nature, 2026, doi:10.1038/s41586-026-10679-1.
short: L.A. Schwarz, C. Dotter, S. Isaev, M. Lisi, D. Malzl, C. Büschl, S. Ladstätter,
B. Oliveira, M. Barel, B. Basilico, C. Chintaluri, S. Gorkiewicz, M. Goudarzi,
T. Belinova, S. Reichl, G. Sendžikaitė, S. Arcot Jayaram, P. Koppensteiner, C.M.
Sommer, T.P. Vogels, J. Menche, I. Adameyko, P.V. Kharchenko, C. Bock, G. Novarino,
Nature (2026).
corr_author: '1'
dataavailabilitystatement: Single-nucleus multiomics data are available from the Gene
Expression Omnibus (GSE328363). The mm10 reference genome was used for the alignment
(refdata-cellranger-arc-mm10-2020-A-2.0.0, obtained from https://cf.10xgenomics.com/supp/cell-arc/refdata-cellranger-arc-mm10-2020-A-2.0.0.tar.gz).
Single-cell data can be accessed and visualized through a CELLxGENE database (https://adameykolab.hifo.meduniwien.ac.at/cellxgene_public/filecrawl/.2026_Nature_Schwarz).
Source data are provided with this paper. Scripts and analyses that support the
main findings of this study are accessible in a GitHub repository (https://git.ista.ac.at/research-sofware/mouseome).
date_created: 2026-07-13T09:47:21Z
date_published: 2026-06-17T00:00:00Z
date_updated: 2026-08-04T09:29:55Z
day: '17'
ddc:
- '570'
department:
- _id: AnKi
- _id: GaNo
- _id: TiVo
- _id: ScienComp
- _id: GradSch
- _id: Bio
- _id: PreCl
doi: 10.1038/s41586-026-10679-1
external_id:
pmid:
- '42310454'
fulldoi: https://doi.org/10.1038/s41586-026-10679-1
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
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url: https://doi.org/10.1038/s41586-026-10679-1
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 34ba8964-11ca-11ed-8bc3-e15864e7e9a6
grant_number: '101044865'
name: Toward an understanding of the brain interstitial system and the extracellular
proteome in health and autism spectrum disorders
- _id: 9B91375C-BA93-11EA-9121-9846C619BF3A
grant_number: '707964'
name: Critical windows and reversibility of ASD associated with mutations in chromatin
remodelers
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232
name: Molecular Drug Targets
- _id: ebb38b5d-77a9-11ec-83b8-a42e08120a88
grant_number: FG1803 49015
name: Neurobiology of anxiety in autism spectrum disorders
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/patterns-in-genetic-chaos/
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Cortical development dynamics across autism spectrum disorder mouse models
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
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '22268'
abstract:
- lang: eng
text: AlphaFold3 predicts highly accurate protein structures from sequence but tends
to collapse to a single dominant conformation, even when the underlying structure
is inherently heterogeneous. Moreover, its predictions are oblivious to experimental
conditions that can alter local sequence conformation. In this work, we show that
AlphaFold3 can be guided to match data obtained by nuclear magnetic resonance
(NMR) spectroscopy, X-ray crystallography and cryogenic electron microscopy (cryo-EM)
experiments and combinations thereof. Our approach can also incorporate data that
explicitly report on dynamics, such as site-resolved order parameters. We demonstrate
that this methodology generates compact structural ensembles whose ensemble-averaged
observables agree with experiment, with fewer distance restraint violations than
traditionally resolved NMR structures and with unmodeled alternate conformations
uncovered in electron density. This methodology paves the way for experimentally
aware predictive models that generate structural ensembles consistent with the
measurements, potentially over multiple modalities, and that can be further refined
toward thermodynamically grounded ensembles by incorporating energetics.
acknowledgement: A. Marx acknowledges the financial support of the Helmsley Fellowships
Program for Sustainability and Health. A.M.B. and P.S. are supported by the Institute
of Science and Technology Austria Internal Project Call grant Generative Protein
NMR. S.V. was supported in part by funding from the Eric and Wendy Schmidt Center
at the Broad Institute of MIT and Harvard. Open access funding provided by Institute
of Science and Technology (IST Austria).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Sai A
full_name: Maddipatla, Sai A
id: e957f5e5-91c9-11f0-a95f-e090f66ecb4d
last_name: Maddipatla
- first_name: Nadav E
full_name: Sellam, Nadav E
id: ef280fe0-91c9-11f0-a95f-8dea3f5bc513
last_name: Sellam
- first_name: Meital I
full_name: Bojan, Meital I
id: 11d88cf5-91ca-11f0-a95f-edf9f08f47b7
last_name: Bojan
- first_name: Vova
full_name: Masalitin, Vova
id: ff7958eb-91c9-11f0-a95f-f3bf65828cf6
last_name: Masalitin
- first_name: Sanketh
full_name: Vedula, Sanketh
last_name: Vedula
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Ailie
full_name: Marx, Ailie
last_name: Marx
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
citation:
ama: Maddipatla SA, Sellam NE, Bojan MI, et al. Experiment-guided AlphaFold3 resolves
measurement-consistent protein ensembles. Nature Biotechnology. 2026. doi:10.1038/s41587-026-03166-5
apa: Maddipatla, S. A., Sellam, N. E., Bojan, M. I., Masalitin, V., Vedula, S.,
Schanda, P., … Bronstein, A. M. (2026). Experiment-guided AlphaFold3 resolves
measurement-consistent protein ensembles. Nature Biotechnology. Springer
Nature. https://doi.org/10.1038/s41587-026-03166-5
chicago: Maddipatla, Sai A, Nadav E Sellam, Meital I Bojan, Vova Masalitin, Sanketh
Vedula, Paul Schanda, Ailie Marx, and Alex M. Bronstein. “Experiment-Guided AlphaFold3
Resolves Measurement-Consistent Protein Ensembles.” Nature Biotechnology.
Springer Nature, 2026. https://doi.org/10.1038/s41587-026-03166-5.
ieee: S. A. Maddipatla et al., “Experiment-guided AlphaFold3 resolves measurement-consistent
protein ensembles,” Nature Biotechnology. Springer Nature, 2026.
ista: Maddipatla SA, Sellam NE, Bojan MI, Masalitin V, Vedula S, Schanda P, Marx
A, Bronstein AM. 2026. Experiment-guided AlphaFold3 resolves measurement-consistent
protein ensembles. Nature Biotechnology.
mla: Maddipatla, Sai A., et al. “Experiment-Guided AlphaFold3 Resolves Measurement-Consistent
Protein Ensembles.” Nature Biotechnology, Springer Nature, 2026, doi:10.1038/s41587-026-03166-5.
short: S.A. Maddipatla, N.E. Sellam, M.I. Bojan, V. Masalitin, S. Vedula, P. Schanda,
A. Marx, A.M. Bronstein, Nature Biotechnology (2026).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: All structures and metrics reported in this paper are openly
available on Harvard Dataverse - https://doi.org/10.7910/DVN/PLYUHN. All code is
openly available on GitHub (https://github.com/sai-advaith/guided_alphafold); the
version used for this paper (version 0.9.1) is permanently archived on Zenodo https://doi.org/10.5281/zenodo.17307005
date_created: 2026-07-12T22:02:19Z
date_published: 2026-06-29T00:00:00Z
date_updated: 2026-08-04T09:25:18Z
day: '29'
ddc:
- '570'
department:
- _id: PaSc
- _id: AlBr
- _id: GradSch
doi: 10.1038/s41587-026-03166-5
external_id:
pmid:
- '42374114'
fulldoi: https://doi.org/10.1038/s41587-026-03166-5
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41587-026-03166-5
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Biotechnology
publication_identifier:
eissn:
- 1546-1696
issn:
- 1087-0156
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/toward-experiment-guided-alphafold/
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Experiment-guided AlphaFold3 resolves measurement-consistent protein ensembles
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
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '21987'
abstract:
- lang: eng
text: 'We introduce JODIE, a genetic joint modeling approach that estimates how
DNA loci influence human traits by partitioning genetic effects into four components:
direct effects (from a child’s alleles), indirect maternal and paternal effects
(from parents’ alleles), and parent-of-origin (PofO) effects (dependent on parental
transmission of alleles), while uniquely accounting for assortative mating. We
analyze 30,000 child-mother-father trios from the Estonian Biobank and the Norwegian
Mother, Father, and Child Cohort, focusing on height, body mass index, and childhood
educational test scores. We find direct effects to be the largest contributor
to trait variation, but combined, indirect parental and PofO effects are similarly
substantial. We support our results by within-family genome-wide association testing
and identify 276 independently associated DNA regions with a complex interplay
between direct, indirect, and PofO effects. By joint modeling, we show that direct,
indirect, and PofO effects collectively shape human phenotypic variation across
loci genome-wide.'
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "We thank Zoltan Kutalik, Peter Visscher, and members of the Robinson
group at ISTA for their comments, which improved this manuscript. This work was
funded by an SNSF Eccellenza Grant to M.R.R. (PCEGP3-181181) and by core funding
from the Institute of Science and Technology Austria.\r\nThe Norwegian Mother, Father,
and Child Cohort Study is supported by the Norwegian Ministry of Health and Care
Services and the Ministry of Education and Research. We are grateful to all the
participating families in Norway who take part in this on-going cohort study. We
thank the Norwegian Institute of Public Health (NIPH) for generating high-quality
genomic data. The research is part of the HARVEST collaboration, supported by the
Research Council of Norway (#229624). We also thank the NORMENT Center for providing
genotype data, funded by the Research Council of Norway (#223273), South East Norway
Health Authorities, and Stiftelsen Kristian Gerhard Jebsen, and in collaboration
with deCODE Genetics. We further thank the Center for Diabetes Research, the University
of Bergen for providing genotype data funded by the ERC AdG project SELECTionPREDISPOSED,
Stiftelsen Kristian Gerhard Jebsen, Trond Mohn Foundation, the Research Council
of Norway, the Novo Nordisk Foundation, the University of Bergen, and the Western
Norway Health Authorities. The MoBa work was performed on the TSD (Tjeneste for
Sensitive Data) facilities, owned by the University of Oslo, operated and developed
by the TSD service group at the University of Oslo, IT Department (USIT, tsd-drift@usit.uio.no).
E.Y. is supported by the European Union (grant numbers 101045526 and 101073237)
and the Research Council of Norway (grant numbers 336078, 288083, and 331640).\r\nWe
would like to acknowledge the participants and investigators of the Generation Scotland
Cohort study. Generation Scotland received core support from the Chief Scientist
Office of the Scottish Government Health Directorates (CZD/16/6) and the Scottish
Funding Council (HR03006). Genotyping and methylation typing of the GS:SFHS samples
was carried out by the Genetics Core Laboratory at the Wellcome Trust Clinical Research
Facility, Edinburgh, Scotland and was funded by the Medical Research Council UK
and the Wellcome Trust (Wellcome Trust Strategic Award “STratifying Resilience and
Depression Longitudinally” [STRADL] ref. 104036/Z/14/Z).\r\nWe would like to thank
and acknowledge the participants and investigators of the Estonian Biobank (EstBB)
study. The research was conducted using the Estonian Center of Genomics/Roadmap
II funded by the Estonian Research Council (project number TT17).\r\nNorwegian analyses
were performed on resources provided by Sigma2 - the National Infrastructure for
High-Performance Computing and Data Storage in Norway. Estonian Data analysis was
carried out in the High-Performance Computing Center cloud provided by University
of Tartu. Analysis of the Generation Scotland data and the summary statistics obtained
from the other analyses was conducted at IST Austria and is supported by the Scientific
Service Units (SSU) of IST Austria through resources provided by Scientific Computing
(SciComp)."
article_number: '101277'
article_processing_charge: Yes
article_type: original
author:
- first_name: Ilse
full_name: Krätschmer, Ilse
id: 30d4014e-7753-11eb-b44b-db6d61112e73
last_name: Krätschmer
orcid: 0000-0002-5636-9259
- first_name: Laura
full_name: Hegemann, Laura
last_name: Hegemann
- first_name: Robin J.
full_name: Hofmeister, Robin J.
last_name: Hofmeister
- first_name: Elizabeth C.
full_name: Corfield, Elizabeth C.
last_name: Corfield
- first_name: Mahdi
full_name: Mahmoudi, Mahdi
last_name: Mahmoudi
- first_name: Olivier
full_name: Delaneau, Olivier
last_name: Delaneau
- first_name: Ole A.
full_name: Andreassen, Ole A.
last_name: Andreassen
- first_name: Archie
full_name: Campbell, Archie
last_name: Campbell
- first_name: Caroline
full_name: Hayward, Caroline
last_name: Hayward
- first_name: Riccardo E.
full_name: Marioni, Riccardo E.
last_name: Marioni
- first_name: Eivind
full_name: Ystrom, Eivind
last_name: Ystrom
- first_name: Alexandra
full_name: Havdahl, Alexandra
last_name: Havdahl
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
citation:
ama: Krätschmer I, Hegemann L, Hofmeister RJ, et al. Separating direct, indirect,
and parent-of-origin genetic effects in the human population. Cell Genomics.
2026;6(7). doi:10.1016/j.xgen.2026.101277
apa: Krätschmer, I., Hegemann, L., Hofmeister, R. J., Corfield, E. C., Mahmoudi,
M., Delaneau, O., … Robinson, M. R. (2026). Separating direct, indirect, and parent-of-origin
genetic effects in the human population. Cell Genomics. Elsevier. https://doi.org/10.1016/j.xgen.2026.101277
chicago: Krätschmer, Ilse, Laura Hegemann, Robin J. Hofmeister, Elizabeth C. Corfield,
Mahdi Mahmoudi, Olivier Delaneau, Ole A. Andreassen, et al. “Separating Direct,
Indirect, and Parent-of-Origin Genetic Effects in the Human Population.” Cell
Genomics. Elsevier, 2026. https://doi.org/10.1016/j.xgen.2026.101277.
ieee: I. Krätschmer et al., “Separating direct, indirect, and parent-of-origin
genetic effects in the human population,” Cell Genomics, vol. 6, no. 7.
Elsevier, 2026.
ista: Krätschmer I, Hegemann L, Hofmeister RJ, Corfield EC, Mahmoudi M, Delaneau
O, Andreassen OA, Campbell A, Hayward C, Marioni RE, Ystrom E, Havdahl A, Robinson
MR. 2026. Separating direct, indirect, and parent-of-origin genetic effects in
the human population. Cell Genomics. 6(7), 101277.
mla: Krätschmer, Ilse, et al. “Separating Direct, Indirect, and Parent-of-Origin
Genetic Effects in the Human Population.” Cell Genomics, vol. 6, no. 7,
101277, Elsevier, 2026, doi:10.1016/j.xgen.2026.101277.
short: I. Krätschmer, L. Hegemann, R.J. Hofmeister, E.C. Corfield, M. Mahmoudi,
O. Delaneau, O.A. Andreassen, A. Campbell, C. Hayward, R.E. Marioni, E. Ystrom,
A. Havdahl, M.R. Robinson, Cell Genomics 6 (2026).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: "Information on how to access the MoBaPsychGen post-imputation
QC data are available here: https://www.fhi.no/en/me/the-psychgen-centre-for-genetic-epidemiology-and-mental-health/access-to-genetic-data-after-quality-control-by-the-mobapsychgen-pipeline-v/.\r\nEstonian
Biobank data (https://genomics.ut.ee/en/content/estonian-biobank) were used in this
project. For access to be granted to the Estonian Biobank genotypic and corresponding
phenotypic data, a preliminary application must be presented to the oversight committee,
who must first approve the project. Ethics permission must then be obtained from
the Estonian Committee on Bioethics and Human Research. Finally, a full project
must be submitted and approved by the Estonian Biobank.\r\nAccess to the Generation
Scotland data is available with appropriate permission from the Generation Scotland
Access Committee. Applications should be made to access@generationscotland.org (https://genscot.ed.ac.uk/).\r\nThe
code for JODIE developed in this work is open source and is publicly available on
zenodo (https://doi.org/10.5281/zenodo.19593928) and GitHub (https://github.com/medical-genomics-group/JODIE).\r\nHaplotype
Reference Consortium Release 1.1 data (https://ega-archive.org/datasets/EGAD00001002729)
are available by application to a Data Access Committee (DAC) of the Wellcome Trust
Sanger Institute.\r\nThe Common Metabolic Diseases Atlas can be accessed here: https://cmdga.org."
date_created: 2026-06-10T07:39:08Z
date_published: 2026-07-08T00:00:00Z
date_updated: 2026-08-04T09:34:08Z
day: '08'
ddc:
- '570'
department:
- _id: MaRo
doi: 10.1016/j.xgen.2026.101277
external_id:
pmid:
- '40909755'
file:
- access_level: open_access
checksum: f896b510480d2d4e4a7fd46c2e2761f4
content_type: application/pdf
creator: dernst
date_created: 2026-07-28T07:24:50Z
date_updated: 2026-07-28T07:24:50Z
file_id: '22597'
file_name: 2026_CellGenomics_Kraetschmer.pdf
file_size: 3679297
relation: main_file
success: 1
file_date_updated: 2026-07-28T07:24:50Z
fulldoi: https://doi.org/10.1016/j.xgen.2026.101277
has_accepted_license: '1'
intvolume: ' 6'
issue: '7'
keyword:
- direct genetic effects
- DGE
- indirect genetic effects
- IGE
- parent-of-origin effects
- phenotypic variation
- assortative mating
- within-family GWAS
- MoBa
- EstBB
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 9B8D11D6-BA93-11EA-9121-9846C619BF3A
grant_number: PCEGP3_181181
name: Improving estimation and prediction of common complex disease risk
publication: Cell Genomics
publication_identifier:
eissn:
- 2666-979X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/human-traits-beyond-inherited-genes/
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Separating direct, indirect, and parent-of-origin genetic effects in the human
population
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 6
year: '2026'
...
---
OA_place: publisher
_id: '22334'
abstract:
- lang: eng
text: "Characterizing protein dynamics at the atomic level is essential for our
understanding of biological mechanisms. Whether it is to facilitate metabolite
transport, catalyze reactions, transmit signals, or regulate metabolism – proteins
are constantly in motion and sample multiple conformational states to fulfill
their function. Nuclear magnetic resonance (NMR) spectroscopy is particularly
well suited to elucidate the dynamics of biomolecules on their complex free-energy
landscape. In particular, solid-state magic-angle spinning (MAS) NMR enables the
study of large molecular assemblies, protein crystals, or insoluble proteins at
atomic resolution without an inherent molecular size limitation. MAS NMR experiments
to probe protein dynamics are extremely versatile and sensitive to motional timescales
from picoseconds to seconds. Over the past decades, technological advances, developments
in experimental design, and new isotope-labeling approaches have further expanded
the possibilities of this technique and significantly improved the accuracy of
the determined motional parameters.\r\nFunctionally important sites of proteins
often contain aromatic residues. Their side-chain motions have therefore long
served as valuable indicators of mechanistically relevant dynamics in NMR studies.
In this thesis, site-specifically labeled aromatic residues act as sensitive reporters
for MAS NMR studies of protein dynamics. The first part addresses how different
environments impact side-chain motion by probing ring flips of phenylalanines
and tyrosines in crystalline proteins and amyloid fibrils. It provides important
insights for the analysis of dynamics obtained in non-native protein environments
and emphasizes the complex factors that determine the timescale of internal dynamics.
In the second part, the focus shifts towards methodological questions regarding
the investigation of protein dynamics by 19F MAS NMR. The fluorine nucleus exhibits
promising characteristics for NMR studies but also presents significant challenges,
which is why the full methodological potential of 19F MAS NMR has not been fully
realized yet. This work demonstrates that paramagnetic doping can considerably
reduce the measurement time and improve the sensitivity of fluorinated samples.
Finally, 19F MAS NMR is evaluated as a tool for studying protein side-chain dynamics
on the example of tryptophans. The results illustrate the challenges in analyzing
such experiments and lay the foundation for further development of 19F MAS NMR
relaxation studies.\r\nTaken together, this thesis highlights the potential of
combining specific isotope labeling, MAS NMR, and complementary methods such as
crystallography and computational simulations to elucidate internal protein dynamics.
The further development of such integrative approaches will be crucial to improving
our understanding of complex mechanisms and protein function.\r\n"
acknowledged_ssus:
- _id: LifeSc
- _id: NMR
acknowledgement: "During the work on this thesis, I was the recipient of a DOC Fellowship
of the Austrian\r\nAcademy of Sciences at the Institute of Science and Technology
Austria (grant no. PR10660EAW01)."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Lea Marie
full_name: Becker, Lea Marie
id: 36336939-eb97-11eb-a6c2-c83f1214ca79
last_name: Becker
orcid: 0000-0002-6401-5151
citation:
ama: Becker LM. Exploring protein dynamics using specific labeling approaches for
solid-state MAS NMR. 2026. doi:10.15479/AT-ISTA-22334
apa: Becker, L. M. (2026). Exploring protein dynamics using specific labeling
approaches for solid-state MAS NMR. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT-ISTA-22334
chicago: Becker, Lea Marie. “Exploring Protein Dynamics Using Specific Labeling
Approaches for Solid-State MAS NMR.” Institute of Science and Technology Austria,
2026. https://doi.org/10.15479/AT-ISTA-22334.
ieee: L. M. Becker, “Exploring protein dynamics using specific labeling approaches
for solid-state MAS NMR,” Institute of Science and Technology Austria, 2026.
ista: Becker LM. 2026. Exploring protein dynamics using specific labeling approaches
for solid-state MAS NMR. Institute of Science and Technology Austria.
mla: Becker, Lea Marie. Exploring Protein Dynamics Using Specific Labeling Approaches
for Solid-State MAS NMR. Institute of Science and Technology Austria, 2026,
doi:10.15479/AT-ISTA-22334.
short: L.M. Becker, Exploring Protein Dynamics Using Specific Labeling Approaches
for Solid-State MAS NMR, Institute of Science and Technology Austria, 2026.
corr_author: '1'
das_tickbox: '1'
date_created: 2026-07-14T08:08:51Z
date_published: 2026-07-13T00:00:00Z
date_updated: 2026-08-04T09:32:45Z
day: '13'
ddc:
- '572'
degree_awarded: PhD
department:
- _id: GradSch
- _id: PaSc
doi: 10.15479/AT-ISTA-22334
doi_confirm: '1'
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fulldoi: https://doi.org/10.15479/AT-ISTA-22334
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language:
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month: '07'
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grant_number: '26777'
name: Exploring protein dynamics by solid-state MAS NMR through specific labeling
approaches
publication_identifier:
isbn:
- 978-3-99078-084-8
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
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relation: part_of_dissertation
status: public
- id: '22105'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
title: Exploring protein dynamics using specific labeling approaches for solid-state
MAS NMR
tmp:
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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: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2026'
...
---
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abstract:
- lang: eng
text: Protein conformational energy landscapes are shaped not only by intramolecular
interactions but also by their environment. In protein crystals and protein–protein
complexes, intermolecular contacts alter this energy landscape, but the exact
nature of this alteration is difficult to decipher. Understanding how the crystal
lattice affects protein dynamics is crucial for crystallography-based studies
of motion, yet its influence on collective motions remains unclear. Aromatic ring
flips in the hydrophobic core represent sensitive probes of such dynamics. Here,
we compare the kinetics of aromatic ring flips in the protein GB1 in crystals,
in complex with its binding partner IgG, and in solution, combining advanced isotope
labelling with quantitative NMR methods. We show that rings in the core flip nearly
a thousand times less frequently in crystals than in solution. Enhanced-sampling
molecular dynamics simulations, based on a crystal structure of a GB1 variant
reported in this work, reproduce these elevated barriers and reveal how the crystal
restrains motions.
acknowledged_ssus:
- _id: NMR
- _id: LifeSc
acknowledgement: We thank N. R. Skrynnikov and O. O. Lebedenko (St. Petersburg) for
insightful discussions and for performing exploratory MD simulations. We are grateful
to T. Schubeis (Lyon) for advice on GB1 crystallization and R. Schmid for initial
crystallization trials. We thank C. Mueller-Dieckmann for assistance with room-temperature
X-ray crystallography data collection on beamline ID30B at the ESRF, which is acknowledged
for providing beamtime through its In-House Research programme. We thank S. Falkner
for assistance with constructing the structural model of the IgG:GB1 complex. We
thank J. Lewandowski for providing feedback on the paper and granting access to
backbone relaxation data of IgG:GB1T2Q and GB1T2Q microcrystals. This research was
supported by the Scientific Service Units (SSU) of the Institute of Science and
Technology Austria (ISTA) through resources provided by the Nuclear Magnetic Resonance
and the Lab Support Facilities. We thank P. Rovó and M. V. Falcón for excellent
support of the NMR facility. L.M.B. is recipient of a DOC fellowship of the Austrian
Academy of Sciences at the Institute of Science and Technology Austria (grant number
PR10660EAW01). C.C. acknowledges the European Research Council (grant project 101097272
‘MilliInMicro’) and the Métropole du Grand Nancy (grant project ‘ARC’). BM07-FIP2
is supported by the French ANR PIA3 (France 2030) EquipEx+ project MAGNIFIX under
grant agreement ANR-21-ESRE-0011.Open access funding provided by Institute of Science
and Technology (IST Austria).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Lea Marie
full_name: Becker, Lea Marie
id: 36336939-eb97-11eb-a6c2-c83f1214ca79
last_name: Becker
orcid: 0000-0002-6401-5151
- first_name: Haohao
full_name: Fu, Haohao
last_name: Fu
- first_name: Benjamin
full_name: Tatman, Benjamin
id: 71cda2f3-e604-11ee-a1df-da10587eda3f
last_name: Tatman
- first_name: Matthias
full_name: Dreydoppel, Matthias
last_name: Dreydoppel
- first_name: Anna
full_name: Kapitonova, Anna
id: 9fb2a840-89e1-11ee-a8b7-cc5c7ba62471
last_name: Kapitonova
- first_name: Daniel
full_name: Balazs, Daniel
id: 302BADF6-85FC-11EA-9E3B-B9493DDC885E
last_name: Balazs
orcid: 0000-0001-7597-043X
- first_name: Ulrich
full_name: Weininger, Ulrich
last_name: Weininger
- first_name: Sylvain
full_name: Engilberge, Sylvain
last_name: Engilberge
- first_name: Christophe
full_name: Chipot, Christophe
last_name: Chipot
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Becker LM, Fu H, Tatman B, et al. Aromatic ring flips reveal reshaping of protein
dynamics in crystals and complexes. Nature Chemistry. 2026;18:1221-1230.
doi:10.1038/s41557-026-02155-0
apa: Becker, L. M., Fu, H., Tatman, B., Dreydoppel, M., Kapitonova, A., Balazs,
D., … Schanda, P. (2026). Aromatic ring flips reveal reshaping of protein dynamics
in crystals and complexes. Nature Chemistry. Springer Nature. https://doi.org/10.1038/s41557-026-02155-0
chicago: Becker, Lea Marie, Haohao Fu, Benjamin Tatman, Matthias Dreydoppel, Anna
Kapitonova, Daniel Balazs, Ulrich Weininger, Sylvain Engilberge, Christophe Chipot,
and Paul Schanda. “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in
Crystals and Complexes.” Nature Chemistry. Springer Nature, 2026. https://doi.org/10.1038/s41557-026-02155-0.
ieee: L. M. Becker et al., “Aromatic ring flips reveal reshaping of protein
dynamics in crystals and complexes,” Nature Chemistry, vol. 18. Springer
Nature, pp. 1221–1230, 2026.
ista: Becker LM, Fu H, Tatman B, Dreydoppel M, Kapitonova A, Balazs D, Weininger
U, Engilberge S, Chipot C, Schanda P. 2026. Aromatic ring flips reveal reshaping
of protein dynamics in crystals and complexes. Nature Chemistry. 18, 1221–1230.
mla: Becker, Lea Marie, et al. “Aromatic Ring Flips Reveal Reshaping of Protein
Dynamics in Crystals and Complexes.” Nature Chemistry, vol. 18, Springer
Nature, 2026, pp. 1221–30, doi:10.1038/s41557-026-02155-0.
short: L.M. Becker, H. Fu, B. Tatman, M. Dreydoppel, A. Kapitonova, D. Balazs, U.
Weininger, S. Engilberge, C. Chipot, P. Schanda, Nature Chemistry 18 (2026) 1221–1230.
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: The cryo and room-temperature crystal structures of GB1QDD
are deposited at the PDB under the access codes 9I2I and 9T8Z, respectively. The
solid-state NMR backbone assignment of GB1QDD is deposited at the BMRB under the
access code 53330. NMR spectra, analysis scripts and raw data are publicly available
at the ISTA research explorer (https://doi.org/10.15479/AT-ISTA-20641)120. Files
to reproduce the enhanced-sampling MD simulations are publicly available at the
ISTA research explorer (https://doi.org/10.15479/AT-ISTA-21145)121.
date_created: 2026-06-21T22:03:01Z
date_published: 2026-07-01T00:00:00Z
date_updated: 2026-08-04T09:32:45Z
day: '01'
ddc:
- '540'
department:
- _id: PaSc
- _id: LifeSc
doi: 10.1038/s41557-026-02155-0
external_id:
pmid:
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creator: dernst
date_created: 2026-07-28T06:58:35Z
date_updated: 2026-07-28T06:58:35Z
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fulldoi: https://doi.org/10.1038/s41557-026-02155-0
has_accepted_license: '1'
intvolume: ' 18'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 1221-1230
pmid: 1
project:
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grant_number: '26777'
name: Exploring protein dynamics by solid-state MAS NMR through specific labeling
approaches
publication: Nature Chemistry
publication_identifier:
eissn:
- '17554349'
issn:
- '17554330'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
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- description: News on ISTA website
relation: research_data
url: https://ista.ac.at/en/news/how-proteins-breathe/
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researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Aromatic ring flips reveal reshaping of protein dynamics in crystals and complexes
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: 18
year: '2026'
...