---
OA_place: repository
OA_type: green
_id: '20926'
abstract:
- lang: eng
text: Most current machine learning interatomic potentials (MLIPs) rely on short-range
approximations, without explicit treatment of long-range electrostatics. To address
this, we recently developed the Latent Ewald Summation (LES) method, which infers
electrostatic interactions, polarization, and Born effective charges (BECs), just
by learning from energy and force training data. Here, we present LES as a standalone
library, compatible with any short-range MLIP, and demonstrate its integration
with methods such as MACE, NequIP, Allegro, CACE, CHGNet, and UMA. We benchmark
LES-enhanced models on distinct systems, including bulk water, polar dipeptides,
and gold dimer adsorption on defective substrates, and show that LES not only
captures correct electrostatics but also improves accuracy. Additionally, we scale
LES to large and chemically diverse data by training MACELES-OFF on the SPICE
set containing molecules and clusters, making a universal MLIP with electrostatics
for organic systems, including biomolecules. MACELES-OFF is more accurate than
its short-range counterpart (MACE-OFF) trained on the same data set, predicts
dipoles and BECs reliably, and has better descriptions of bulk liquids. By enabling
efficient long-range electrostatics without directly training on electrical properties,
LES paves the way for electrostatic foundation MLIPs.
acknowledgement: Research reported in this publication was supported by the National
Institute Of General Medical Sciences of the National Institutes of Health under
Award Number R35GM159986. The content is solely the responsibility of the authors
and does not necessarily represent the official views of the National Institutes
of Health. D.K. and B.C. acknowledge funding from Toyota Research Institute Synthesis
Advanced Research Challenge. T.J.I., D.S.K. and P.Z. acknowledge funding from BIDMaP
Postdoctoral Fellowship. T.J.I. used resources of the National Energy Research Scientific
Computing Center (NERSC), a Department of Energy Office of Science User Facility
using NERSC award DOEERCAP0031751 ′GenAI@NERSC’. The authors thank Bowen Deng for
valuable discussions on MatGL implementation, and thank Gabor Csanyi for stimulating
discussions.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Dongjin
full_name: Kim, Dongjin
last_name: Kim
- first_name: Xiaoyu
full_name: Wang, Xiaoyu
id: 8dff9c62-32b0-11ee-9fa8-fc73025e10f3
last_name: Wang
- first_name: Santiago
full_name: Vargas, Santiago
last_name: Vargas
- first_name: Peichen
full_name: Zhong, Peichen
last_name: Zhong
- first_name: Daniel S.
full_name: King, Daniel S.
last_name: King
- first_name: Theo Jaffrelot
full_name: Inizan, Theo Jaffrelot
last_name: Inizan
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: Kim D, Wang X, Vargas S, et al. A universal augmentation framework for long-range
electrostatics in machine learning interatomic potentials. Journal of Chemical
Theory and Computation. 2025;21(24):12709-12724. doi:10.1021/acs.jctc.5c01400
apa: Kim, D., Wang, X., Vargas, S., Zhong, P., King, D. S., Inizan, T. J., &
Cheng, B. (2025). A universal augmentation framework for long-range electrostatics
in machine learning interatomic potentials. Journal of Chemical Theory and
Computation. American Chemical Society. https://doi.org/10.1021/acs.jctc.5c01400
chicago: Kim, Dongjin, Xiaoyu Wang, Santiago Vargas, Peichen Zhong, Daniel S. King,
Theo Jaffrelot Inizan, and Bingqing Cheng. “A Universal Augmentation Framework
for Long-Range Electrostatics in Machine Learning Interatomic Potentials.” Journal
of Chemical Theory and Computation. American Chemical Society, 2025. https://doi.org/10.1021/acs.jctc.5c01400.
ieee: D. Kim et al., “A universal augmentation framework for long-range electrostatics
in machine learning interatomic potentials,” Journal of Chemical Theory and
Computation, vol. 21, no. 24. American Chemical Society, pp. 12709–12724,
2025.
ista: Kim D, Wang X, Vargas S, Zhong P, King DS, Inizan TJ, Cheng B. 2025. A universal
augmentation framework for long-range electrostatics in machine learning interatomic
potentials. Journal of Chemical Theory and Computation. 21(24), 12709–12724.
mla: Kim, Dongjin, et al. “A Universal Augmentation Framework for Long-Range Electrostatics
in Machine Learning Interatomic Potentials.” Journal of Chemical Theory and
Computation, vol. 21, no. 24, American Chemical Society, 2025, pp. 12709–24,
doi:10.1021/acs.jctc.5c01400.
short: D. Kim, X. Wang, S. Vargas, P. Zhong, D.S. King, T.J. Inizan, B. Cheng, Journal
of Chemical Theory and Computation 21 (2025) 12709–12724.
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: The training sets, training scripts, and trained potentials
are available at https://github.com/ChengUCB/les_fit. The LES library is publicly
available at https://github.com/ChengUCB/les. The CACE package with the LES implementation
is available at https://github.com/BingqingCheng/cace. The MACE package with the
LES implementation is available at https://github.com/ACEsuit/mace. The NequIP and
Allegro LES extension package is available at https://github.com/ChengUCB/NequIP-LES.
The MatGL package with the LES implementation is available at https://github.com/ChengUCB/matgl.
The UMA package with the LES implementation is available at https://github.com/santi921/fairchem/tree/les_branch.
date_created: 2026-01-04T23:01:33Z
date_published: 2025-12-10T00:00:00Z
date_updated: 2026-08-07T09:35:25Z
day: '10'
department:
- _id: GradSch
- _id: BiCh
doi: 10.1021/acs.jctc.5c01400
external_id:
arxiv:
- '2507.14302'
pmid:
- '41368735 '
fulldoi: https://doi.org/10.1021/acs.jctc.5c01400
intvolume: ' 21'
issue: '24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2507.14302
month: '12'
oa: 1
oa_version: Preprint
page: 12709-12724
pmid: 1
publication: Journal of Chemical Theory and Computation
publication_identifier:
eissn:
- 1549-9626
issn:
- 1549-9618
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: A universal augmentation framework for long-range electrostatics in machine
learning interatomic potentials
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 21
year: '2025'
...
---
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20990'
abstract:
- lang: eng
text: Modeling the response of material and chemical systems to electric fields
remains a longstanding challenge. Machine learning interatomic potentials (MLIPs)
offer an efficient and scalable alternative to quantum mechanical methods, but
do not by themselves incorporate electrical response. Here, we show that polarization
and Born effective charge (BEC) tensors can be directly extracted from long-range
MLIPs within the Latent Ewald Summation (LES) framework, solely by learning from
energy and force data. Using this approach, we predict the infrared spectra of
bulk water under zero or finite external electric fields, ionic conductivities
of high-pressure superionic ice, and the phase transition and hysteresis in ferroelectric
PbTiO3 perovskite. This work thus extends the capability of MLIPs to predict electrical
response –without training on charges or polarization or BECs– and enables accurate
modeling of electric-field-driven processes in diverse systems at scale.
acknowledgement: The authors thank for valuable discussions with Pinchen Xie, David
Limmer, Jeff Neaton, and Greg Voth. The authors thank Sebastien Hamel for providing
the DFT MD trajectories for superionic water, and help clarifying questions related
to the pseudopotentials. The authors thank Federico Grasselli and Stefano Baroni
for providing data and notebooks for computing the conductivity of a molten salt.
This research used the Savio computational cluster resource provided by the Berkeley
Research Computing program at the University of California, Berkeley (supported
by the UC Berkeley Chancellor, Vice Chancellor for Research, and Chief Information
Officer). D.S.K. and P.Z. acknowledge funding from the BIDMaP Postdoctoral Fellowship.
article_number: '384'
article_processing_charge: Yes
article_type: original
author:
- first_name: Peichen
full_name: Zhong, Peichen
last_name: Zhong
- first_name: Dongjin
full_name: Kim, Dongjin
last_name: Kim
- first_name: Daniel S.
full_name: King, Daniel S.
last_name: King
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: Zhong P, Kim D, King DS, Cheng B. Machine learning interatomic potential can
infer electrical response. npj Computational Materials. 2025;11. doi:10.1038/s41524-025-01911-z
apa: Zhong, P., Kim, D., King, D. S., & Cheng, B. (2025). Machine learning interatomic
potential can infer electrical response. Npj Computational Materials. Springer
Nature. https://doi.org/10.1038/s41524-025-01911-z
chicago: Zhong, Peichen, Dongjin Kim, Daniel S. King, and Bingqing Cheng. “Machine
Learning Interatomic Potential Can Infer Electrical Response.” Npj Computational
Materials. Springer Nature, 2025. https://doi.org/10.1038/s41524-025-01911-z.
ieee: P. Zhong, D. Kim, D. S. King, and B. Cheng, “Machine learning interatomic
potential can infer electrical response,” npj Computational Materials,
vol. 11. Springer Nature, 2025.
ista: Zhong P, Kim D, King DS, Cheng B. 2025. Machine learning interatomic potential
can infer electrical response. npj Computational Materials. 11, 384.
mla: Zhong, Peichen, et al. “Machine Learning Interatomic Potential Can Infer Electrical
Response.” Npj Computational Materials, vol. 11, 384, Springer Nature,
2025, doi:10.1038/s41524-025-01911-z.
short: P. Zhong, D. Kim, D.S. King, B. Cheng, Npj Computational Materials 11 (2025).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: The training sets, training scripts, BEC inference scripts,
and trained CACE potentials are available at https://github.com/BingqingCheng/LES-BEC.
date_created: 2026-01-15T12:17:07Z
date_published: 2025-12-29T00:00:00Z
date_updated: 2026-08-07T09:38:09Z
day: '29'
ddc:
- '540'
department:
- _id: BiCh
doi: 10.1038/s41524-025-01911-z
file:
- access_level: open_access
checksum: cc999804ba3bfed809ae46c73869e4e3
content_type: application/pdf
creator: dernst
date_created: 2026-01-20T07:22:04Z
date_updated: 2026-01-20T07:22:04Z
file_id: '21005'
file_name: 2025_npj_Zhong.pdf
file_size: 2686255
relation: main_file
success: 1
file_date_updated: 2026-01-20T07:22:04Z
fulldoi: https://doi.org/10.1038/s41524-025-01911-z
has_accepted_license: '1'
intvolume: ' 11'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: npj Computational Materials
publication_identifier:
eissn:
- 2057-3960
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: no
title: Machine learning interatomic potential can infer electrical response
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 11
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20492'
abstract:
- lang: eng
text: The glassy thermal conductivities observed in crystalline inorganic perovskites
such as Cs3Bi2I6Cl3 are perplexing and lacking theoretical explanations. Here,
we first experimentally measure its thermal transport behavior from 20 to 300 K,
after synthesizing Cs3Bi2I6Cl3 single crystals. Using path-integral molecular
dynamics simulations driven by machine learning potentials, we reveal that Cs3Bi2I6Cl3
has large lattice distortions at low temperatures, which may be related to the
large atomic size mismatch. Employing the Wigner formulation of thermal transport,
we reproduce theexperimental thermal conductivities based on lattice-distorted
structures. This studythus provides a framework for predicting and understanding
glassy thermal transportin materials with strong lattice disorder.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: Z.Z. acknowledges the European Union’s Horizon2020 research and innovation
programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413. We acknowledge
the high-performance computing facilities offered by Institute of Science and Technology
Austria and The University of Hong Kong.
article_processing_charge: No
article_type: original
author:
- first_name: Zezhu
full_name: Zeng, Zezhu
id: 54a2c730-803f-11ed-ab7e-95b29d2680e7
last_name: Zeng
orcid: 0000-0001-5126-4928
- first_name: Zheyong
full_name: Fan, Zheyong
last_name: Fan
- first_name: Michele
full_name: Simoncelli, Michele
last_name: Simoncelli
- first_name: Chen
full_name: Chen, Chen
last_name: Chen
- first_name: Ting
full_name: Liang, Ting
last_name: Liang
- first_name: Yue
full_name: Chen, Yue
last_name: Chen
- first_name: Geoff
full_name: Thornton, Geoff
last_name: Thornton
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: Zeng Z, Fan Z, Simoncelli M, et al. Lattice distortion leads to glassy thermal
transport in crystalline Cs3Bi2I6Cl3. Proceedings of the National Academy of
Sciences. 2025;122(41):e2415664122. doi:10.1073/pnas.2415664122
apa: Zeng, Z., Fan, Z., Simoncelli, M., Chen, C., Liang, T., Chen, Y., … Cheng,
B. (2025). Lattice distortion leads to glassy thermal transport in crystalline
Cs3Bi2I6Cl3. Proceedings of the National Academy of Sciences. National
Academy of Sciences. https://doi.org/10.1073/pnas.2415664122
chicago: Zeng, Zezhu, Zheyong Fan, Michele Simoncelli, Chen Chen, Ting Liang, Yue
Chen, Geoff Thornton, and Bingqing Cheng. “Lattice Distortion Leads to Glassy
Thermal Transport in Crystalline Cs3Bi2I6Cl3.” Proceedings of the National
Academy of Sciences. National Academy of Sciences, 2025. https://doi.org/10.1073/pnas.2415664122.
ieee: Z. Zeng et al., “Lattice distortion leads to glassy thermal transport
in crystalline Cs3Bi2I6Cl3,” Proceedings of the National Academy of Sciences,
vol. 122, no. 41. National Academy of Sciences, p. e2415664122, 2025.
ista: Zeng Z, Fan Z, Simoncelli M, Chen C, Liang T, Chen Y, Thornton G, Cheng B.
2025. Lattice distortion leads to glassy thermal transport in crystalline Cs3Bi2I6Cl3.
Proceedings of the National Academy of Sciences. 122(41), e2415664122.
mla: Zeng, Zezhu, et al. “Lattice Distortion Leads to Glassy Thermal Transport in
Crystalline Cs3Bi2I6Cl3.” Proceedings of the National Academy of Sciences,
vol. 122, no. 41, National Academy of Sciences, 2025, p. e2415664122, doi:10.1073/pnas.2415664122.
short: Z. Zeng, Z. Fan, M. Simoncelli, C. Chen, T. Liang, Y. Chen, G. Thornton,
B. Cheng, Proceedings of the National Academy of Sciences 122 (2025) e2415664122.
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: Primitive Data Types have been deposited in GitHub (Cs3Bi2I6Cl3_heat_conductivity)
(https://github.com/ZengZezhu/Cs3Bi2I6Cl3_heat_conductivity) (74).
date_created: 2025-10-19T22:01:31Z
date_published: 2025-10-14T00:00:00Z
date_updated: 2026-08-07T10:11:03Z
day: '14'
ddc:
- '540'
department:
- _id: BiCh
doi: 10.1073/pnas.2415664122
ec_funded: 1
external_id:
isi:
- '001600415200001'
pmid:
- '41052324'
file:
- access_level: open_access
checksum: 3f9cd0d67ffe9110fb238407671584b7
content_type: application/pdf
creator: dernst
date_created: 2025-10-21T10:02:15Z
date_updated: 2025-10-21T10:02:15Z
file_id: '20513'
file_name: 2025_PNAS_Zeng.pdf
file_size: 12244843
relation: main_file
success: 1
file_date_updated: 2025-10-21T10:02:15Z
fulldoi: https://doi.org/10.1073/pnas.2415664122
has_accepted_license: '1'
intvolume: ' 122'
isi: 1
issue: '41'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '10'
oa: 1
oa_version: Published Version
page: e2415664122
pmid: 1
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/ZengZezhu/Cs3Bi2I6Cl3_heat_conductivity
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Lattice distortion leads to glassy thermal transport in crystalline Cs3Bi2I6Cl3
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 122
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '20011'
abstract:
- lang: eng
text: Heat transport in glasses over a wide temperature range is critical for applications
in gate dielectrics and thermal insulators but remains poorly understood due to
the challenges in modeling vibrational anharmonicity and configurational dynamics
across the glass transition. Recent predictions show an unusual decrease in thermal
conductivity (κ) with temperature in amorphous hafnia (a-HfO2), contrasting with
the typical trend in glasses. Using molecular dynamics with a machine-learning-based
neuroevolution potential, we compute κ of a-HfO2 from 50 K to 2000 K. At low temperatures,
the Wigner transport equation captures both anharmonicity and quantum statistics.
Above 1200 K, atomic diffusion invalidates the quasiparticle picture, and we resort
to the Green–Kubo method to capture convective transport. We further extend the
Wigner transport equation to supercooled a-HfO2, revealing the crucial role of
low-frequency modes in facilitating heat transport. The computed κ, based on both
Green–Kubo and Wigner transport theories, increases continuously with temperature
up to 2000 K.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: We thank Ludovic Berthier for fruitful discussions and Ting Liang
for providing the initial structures of a-SiO2. Z.Z. acknowledges funding from the
European Union’s Horizon 2020 Research and Innovation Programme, under Marie Skłodowska-Curie
grant agreement No. 101034413. The authors also acknowledge the research computing
facilities provided by HPC ISTA and ITS HKU.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Zezhu
full_name: Zeng, Zezhu
id: 54a2c730-803f-11ed-ab7e-95b29d2680e7
last_name: Zeng
orcid: 0000-0001-5126-4928
- first_name: Xia
full_name: Liang, Xia
last_name: Liang
- first_name: Zheyong
full_name: Fan, Zheyong
last_name: Fan
- first_name: Yue
full_name: Chen, Yue
last_name: Chen
- first_name: Michele
full_name: Simoncelli, Michele
last_name: Simoncelli
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: Zeng Z, Liang X, Fan Z, Chen Y, Simoncelli M, Cheng B. Thermal transport of
amorphous hafnia across the glass transition. ACS Materials Letters. 2025:2695-2701.
doi:10.1021/acsmaterialslett.5c00263
apa: Zeng, Z., Liang, X., Fan, Z., Chen, Y., Simoncelli, M., & Cheng, B. (2025).
Thermal transport of amorphous hafnia across the glass transition. ACS Materials
Letters. American Chemical Society. https://doi.org/10.1021/acsmaterialslett.5c00263
chicago: Zeng, Zezhu, Xia Liang, Zheyong Fan, Yue Chen, Michele Simoncelli, and
Bingqing Cheng. “Thermal Transport of Amorphous Hafnia across the Glass Transition.”
ACS Materials Letters. American Chemical Society, 2025. https://doi.org/10.1021/acsmaterialslett.5c00263.
ieee: Z. Zeng, X. Liang, Z. Fan, Y. Chen, M. Simoncelli, and B. Cheng, “Thermal
transport of amorphous hafnia across the glass transition,” ACS Materials Letters.
American Chemical Society, pp. 2695–2701, 2025.
ista: Zeng Z, Liang X, Fan Z, Chen Y, Simoncelli M, Cheng B. 2025. Thermal transport
of amorphous hafnia across the glass transition. ACS Materials Letters., 2695–2701.
mla: Zeng, Zezhu, et al. “Thermal Transport of Amorphous Hafnia across the Glass
Transition.” ACS Materials Letters, American Chemical Society, 2025, pp.
2695–701, doi:10.1021/acsmaterialslett.5c00263.
short: Z. Zeng, X. Liang, Z. Fan, Y. Chen, M. Simoncelli, B. Cheng, ACS Materials
Letters (2025) 2695–2701.
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: All necessary source data files generated for this study
are available in the GitHub repository https://github.com/ZengZezhu/heat-conductivity-a-HfO2.
date_created: 2025-07-13T22:01:24Z
date_published: 2025-06-30T00:00:00Z
date_updated: 2026-08-07T10:06:48Z
day: '30'
ddc:
- '530'
department:
- _id: BiCh
doi: 10.1021/acsmaterialslett.5c00263
ec_funded: 1
external_id:
isi:
- '001520226300001'
file:
- access_level: open_access
checksum: d61e63439ddeaef29e9a2ee0f65c4ec1
content_type: application/pdf
creator: dernst
date_created: 2025-12-30T09:13:06Z
date_updated: 2025-12-30T09:13:06Z
file_id: '20903'
file_name: 2025_ACSMaterialsLetters_Zeng.pdf
file_size: 2402059
relation: main_file
success: 1
file_date_updated: 2025-12-30T09:13:06Z
fulldoi: https://doi.org/10.1021/acsmaterialslett.5c00263
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 2695-2701
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: ACS Materials Letters
publication_identifier:
eissn:
- 2639-4979
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/ZengZezhu/heat-conductivity-a-HfO2
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Thermal transport of amorphous hafnia across the glass transition
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
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short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '19495'
abstract:
- lang: eng
text: Machine learning interatomic potentials (MLIPs) often neglect long-range interactions,
such as electrostatic and dispersion forces. In this work, we introduce a straightforward
and efficient method to account for long-range interactions by learning a hidden
variable from local atomic descriptors and applying an Ewald summation to this
variable. We demonstrate that in systems including charged and polar molecular
dimers, bulk water, and water-vapor interface, standard short-ranged MLIPs can
lead to unphysical predictions even when employing message passing. The long-range
models effectively eliminate these artifacts, with only about twice the computational
cost of short-range MLIPs.
acknowledgement: B. C. thanks David Limmer for providing the water slab dataset, and
Carolin Faller for the NaCl dataset.
article_number: '80'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: Cheng B. Latent Ewald summation for machine learning of long-range interactions.
npj Computational Materials. 2025;11. doi:10.1038/s41524-025-01577-7
apa: Cheng, B. (2025). Latent Ewald summation for machine learning of long-range
interactions. Npj Computational Materials. Springer Nature. https://doi.org/10.1038/s41524-025-01577-7
chicago: Cheng, Bingqing. “Latent Ewald Summation for Machine Learning of Long-Range
Interactions.” Npj Computational Materials. Springer Nature, 2025. https://doi.org/10.1038/s41524-025-01577-7.
ieee: B. Cheng, “Latent Ewald summation for machine learning of long-range interactions,”
npj Computational Materials, vol. 11. Springer Nature, 2025.
ista: Cheng B. 2025. Latent Ewald summation for machine learning of long-range interactions.
npj Computational Materials. 11, 80.
mla: Cheng, Bingqing. “Latent Ewald Summation for Machine Learning of Long-Range
Interactions.” Npj Computational Materials, vol. 11, 80, Springer Nature,
2025, doi:10.1038/s41524-025-01577-7.
short: B. Cheng, Npj Computational Materials 11 (2025).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: The training scripts, trained CACE potentials, and MD input
files are available at https://github.com/BingqingCheng/cace-lr-fit.
date_created: 2025-04-06T22:01:32Z
date_published: 2025-03-26T00:00:00Z
date_updated: 2026-08-07T10:04:17Z
day: '26'
ddc:
- '000'
department:
- _id: BiCh
doi: 10.1038/s41524-025-01577-7
external_id:
arxiv:
- '2408.15165'
isi:
- '001453622900002'
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creator: dernst
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isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: npj Computational Materials
publication_identifier:
eissn:
- 2057-3960
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
researchdata_availability: unclear
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status: public
supplementarymaterial: no
title: Latent Ewald summation for machine learning of long-range interactions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 11
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '20702'
abstract:
- lang: eng
text: Qualitative and quantitative orbital properties such as bonding/antibonding
character, localization, and orbital energies are critical to how chemists understand
reactivity, catalysis, and excited-state behavior. Despite this, representations
of orbitals in deep learning models have been very underdeveloped relative to
representations of molecular geometries and Hamiltonians. Here, we apply state-of-the-art
equivariant deep learning architectures to the task of assigning global labels
to orbitals, namely energies characterizations, given the molecular coefficients
from Hartree–Fock or density functional theory. The architecture we have developed,
the Cartesian Equivariant Orbital Network (CEONET), shows how molecular orbital
coefficients are readily featurized as equivariant node features common to all
graph-based machine-learned potentials. We find that CEONET performs well at predicting
difficult quantitative labels such as the orbital energy and orbital entropy.
Furthermore, we find that the CEONET representation provides an intuitive latent
space for differentiating orbital character for the qualitative assignment of
e.g. bonding or antibonding character. In addition to providing a useful representation
for further integrating deep learning with electronic structure theory, we expect
CEONET to be useful for automatizing and interpreting the results of advanced
electronic structure methods such as complete active space self-consistent field
theory. In particular, the ability of CEONET to infer multireference character
via the orbital entropy paves the way toward the machine-learned selection of
active spaces.
acknowledgement: This work is supported as part of the Catalyst Design for Decarbonization
Center, an Energy Frontier Research Center funded by the U.S. Department of Energy,
Office of Science, Basic Energy Sciences under award no. DE-SC0023383. We thank
the Research Computing Center at the University of Chicago and for access to computational
resources. Additionally, this research used the Savio computational cluster resource
provided by the Berkeley Research Computing program at the University of California
(UC), Berkeley (supported by the UC Berkeley Chancellor, Vice Chancellor for Research,
and Chief Information Officer). Furthermore, we thank Matthew Hennefarth and Matt
Hermes for useful discussions.
article_number: e2510235122
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Daniel S.
full_name: King, Daniel S.
last_name: King
- first_name: Daniel
full_name: Grzenda, Daniel
last_name: Grzenda
- first_name: Ray
full_name: Zhu, Ray
last_name: Zhu
- first_name: Nathaniel
full_name: Hudson, Nathaniel
last_name: Hudson
- first_name: Ian
full_name: Foster, Ian
last_name: Foster
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Laura
full_name: Gagliardi, Laura
last_name: Gagliardi
citation:
ama: King DS, Grzenda D, Zhu R, et al. Cartesian equivariant representations for
learning and understanding molecular orbitals. Proceedings of the National
Academy of Sciences. 2025;122(48). doi:10.1073/pnas.2510235122
apa: King, D. S., Grzenda, D., Zhu, R., Hudson, N., Foster, I., Cheng, B., &
Gagliardi, L. (2025). Cartesian equivariant representations for learning and understanding
molecular orbitals. Proceedings of the National Academy of Sciences. National
Academy of Sciences. https://doi.org/10.1073/pnas.2510235122
chicago: King, Daniel S., Daniel Grzenda, Ray Zhu, Nathaniel Hudson, Ian Foster,
Bingqing Cheng, and Laura Gagliardi. “Cartesian Equivariant Representations for
Learning and Understanding Molecular Orbitals.” Proceedings of the National
Academy of Sciences. National Academy of Sciences, 2025. https://doi.org/10.1073/pnas.2510235122.
ieee: D. S. King et al., “Cartesian equivariant representations for learning
and understanding molecular orbitals,” Proceedings of the National Academy
of Sciences, vol. 122, no. 48. National Academy of Sciences, 2025.
ista: King DS, Grzenda D, Zhu R, Hudson N, Foster I, Cheng B, Gagliardi L. 2025.
Cartesian equivariant representations for learning and understanding molecular
orbitals. Proceedings of the National Academy of Sciences. 122(48), e2510235122.
mla: King, Daniel S., et al. “Cartesian Equivariant Representations for Learning
and Understanding Molecular Orbitals.” Proceedings of the National Academy
of Sciences, vol. 122, no. 48, e2510235122, National Academy of Sciences,
2025, doi:10.1073/pnas.2510235122.
short: D.S. King, D. Grzenda, R. Zhu, N. Hudson, I. Foster, B. Cheng, L. Gagliardi,
Proceedings of the National Academy of Sciences 122 (2025).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: Code has been deposited to https://github.com/GagliardiGroup/CEONet
(83). Data has been deposited to https://doi.org/10.5281/zenodo.16934624 (84).
date_created: 2025-11-30T23:02:06Z
date_published: 2025-12-02T00:00:00Z
date_updated: 2026-08-07T10:27:53Z
day: '02'
ddc:
- '540'
department:
- _id: BiCh
doi: 10.1073/pnas.2510235122
external_id:
pmid:
- '41269783'
file:
- access_level: open_access
checksum: 58051539a884c7a97306fd3afdb539ac
content_type: application/pdf
creator: dernst
date_created: 2025-12-01T08:41:32Z
date_updated: 2025-12-01T08:41:32Z
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file_date_updated: 2025-12-01T08:41:32Z
fulldoi: https://doi.org/10.1073/pnas.2510235122
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intvolume: ' 122'
issue: '48'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: software
url: 'https://github.com/GagliardiGroup/CEONet '
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Cartesian equivariant representations for learning and understanding molecular
orbitals
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: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 122
year: '2025'
...
---
OA_type: closed access
_id: '20704'
abstract:
- lang: eng
text: Generative models have advanced significantly in sampling material systems
with continuous variables, such as atomistic structures. However, their application
to discrete variables, like atom types or spin states, remains underexplored.
In this work, we introduce a discrete flow matching model, tailored for systems
with discrete phase-space coordinates (e.g., the Ising model or a multicomponent
system on a lattice). This approach enables a single model to sample free energy
surfaces over a wide temperature range with minimal training overhead, and the
model generation is scalable to larger lattice sizes than those in the training
set. We demonstrate our approach on the 2D Ising model, showing efficient and
reliable free energy sampling. These results highlight the potential of flow matching
for low-cost, scalable free energy sampling in discrete systems and suggest promising
extensions to alchemical degrees of freedom in crystalline materials. The codebase
developed for this work is openly available at https://github.com/tuoping/alchemicalFES.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: P.T. acknowledges funding from FFG MAGNIFICO and the BIDMaP Postdoctoral
Fellowship. Z.Z. acknowledges funding from the European Union’s Horizon 2020 research
and innovation program under the Marie Skłodowska-Curie grant agreement No. 101034413.
The authors acknowledge the research computing facilities provided by the Institute
of Science and Technology Austria (ISTA), and resources of the National Energy Research
Scientific Computing Center (NERSC), a Department of Energy Office of Science User
Facility using NERSC award DOEERCAP0031751 ’GenAI@NERSC’. P.T. acknowledges valued
discussions with Dr. Daniel King, Dr. Lei Wang, and Dr. Fuzhi Dai.
article_processing_charge: No
article_type: original
author:
- first_name: Ping
full_name: Tuo, Ping
id: 6e5644c0-c180-11ed-a2da-facc4c9f4f09
last_name: Tuo
- first_name: Zezhu
full_name: Zeng, Zezhu
id: 54a2c730-803f-11ed-ab7e-95b29d2680e7
last_name: Zeng
orcid: 0000-0001-5126-4928
- first_name: Jiale
full_name: Chen, Jiale
id: 4d0a9064-1ff6-11ee-9fa6-ec046c604785
last_name: Chen
orcid: 0000-0001-5337-5875
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: Tuo P, Zeng Z, Chen J, Cheng B. Scalable multitemperature free energy sampling
of classical Ising spin states. Journal of Chemical Theory and Computation.
2025;21(22):11427-11435. doi:10.1021/acs.jctc.5c01248
apa: Tuo, P., Zeng, Z., Chen, J., & Cheng, B. (2025). Scalable multitemperature
free energy sampling of classical Ising spin states. Journal of Chemical Theory
and Computation. American Chemical Society. https://doi.org/10.1021/acs.jctc.5c01248
chicago: Tuo, Ping, Zezhu Zeng, Jiale Chen, and Bingqing Cheng. “Scalable Multitemperature
Free Energy Sampling of Classical Ising Spin States.” Journal of Chemical Theory
and Computation. American Chemical Society, 2025. https://doi.org/10.1021/acs.jctc.5c01248.
ieee: P. Tuo, Z. Zeng, J. Chen, and B. Cheng, “Scalable multitemperature free energy
sampling of classical Ising spin states,” Journal of Chemical Theory and Computation,
vol. 21, no. 22. American Chemical Society, pp. 11427–11435, 2025.
ista: Tuo P, Zeng Z, Chen J, Cheng B. 2025. Scalable multitemperature free energy
sampling of classical Ising spin states. Journal of Chemical Theory and Computation.
21(22), 11427–11435.
mla: Tuo, Ping, et al. “Scalable Multitemperature Free Energy Sampling of Classical
Ising Spin States.” Journal of Chemical Theory and Computation, vol. 21,
no. 22, American Chemical Society, 2025, pp. 11427–35, doi:10.1021/acs.jctc.5c01248.
short: P. Tuo, Z. Zeng, J. Chen, B. Cheng, Journal of Chemical Theory and Computation
21 (2025) 11427–11435.
corr_author: '1'
das_tickbox: '0'
date_created: 2025-11-30T23:02:06Z
date_published: 2025-10-31T00:00:00Z
date_updated: 2026-08-07T10:29:06Z
day: '31'
department:
- _id: BiCh
- _id: DaAl
doi: 10.1021/acs.jctc.5c01248
ec_funded: 1
external_id:
isi:
- '001605927900001'
pmid:
- '41172130'
fulldoi: https://doi.org/10.1021/acs.jctc.5c01248
intvolume: ' 21'
isi: 1
issue: '22'
language:
- iso: eng
month: '10'
oa_version: None
page: 11427-11435
pmid: 1
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Journal of Chemical Theory and Computation
publication_identifier:
eissn:
- 1549-9626
issn:
- 1549-9618
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/tuoping/alchemicalFES
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Scalable multitemperature free energy sampling of classical Ising spin states
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 21
year: '2025'
...
---
APC_amount: 3948 EUR
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '19593'
abstract:
- lang: eng
text: Prenatal immune challenges pose significant risks to human embryonic brain
and eye development. However, our knowledge about the safe usage of anti-inflammatory
drugs during pregnancy is still limited. While human induced pluripotent stem
cells (hIPSC)-derived brain organoid models have started to explore functional
consequences upon viral stimulation, these models commonly lack microglia, which
are susceptible to and promote inflammation. Furthermore, microglia are actively
involved in neuronal development. Here, we generate hIPSC-derived microglia precursor
cells and assemble them into retinal organoids. Once the outer plexiform layer
forms, these hIPSC-derived microglia (iMG) fully integrate into the retinal organoids.
Since the ganglion cell survival declines by this time in 3D-retinal organoids,
we adapted the model into 2D and identify that the improved ganglion cell number
significantly decreases only with iMG presence. In parallel, we applied the immunostimulant
POLY(I:C) to mimic a fetal viral infection. While POLY(I:C) exposure alters the
iMG phenotype, it does not hinder their interaction with ganglion cells. Furthermore,
iMG significantly enhance the supernatant’s inflammatory secretome and increase
retinal cell proliferation. Simultaneous exposure with the non-steroidal anti-inflammatory
drug (NSAID) ibuprofen dampens POLY(I:C)-mediated changes of the iMG phenotype
and ameliorates cell proliferation. Remarkably, while POLY(I:C) disrupts neuronal
calcium dynamics independent of iMG, ibuprofen rescues this effect only if iMG
are present. Mechanistically, ibuprofen targets the enzymes cyclooxygenase 1 and
2 (COX1/PTGS1 and COX2/PTGS2) simultaneously, from which iMG mainly express COX1.
Selective COX1 blockage fails to restore the calcium peak amplitude upon POLY(I:C)
stimulation, suggesting ibuprofen’s beneficial effect depends on the presence
and interplay of COX1 and COX2. These findings underscore the importance of microglia
in the context of prenatal immune challenges and provide insight into the mechanisms
by which ibuprofen exerts its protective effects during embryonic development.
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
acknowledgement: We thank the scientific service units at ISTA, specifically the Lab
Support Facility (LSF), the Molecular Biology Services/Virus Services Team, specifically
Flavia Gama Gomes Leite and Mark Andrew Smyth, for the virus production, and the
Imaging and Optics Facility (IOF). We thank all members of the Siegert group and
Marco Benevento for their constant feedback on the project and comments on the manuscript.
A special thanks to Rouven Schulz for input on statistical analysis and sharing
R-scripts, Gloria Colombo for the introduction to cell sorting, Negar Vehdani and
Florianne Schoot Uiterkamp for their support in cell culture. This research was
supported by the Gesellschaft für Forschungsförderung Niederösterreich (grant No.
Sc19-017 to V.H.).
article_number: '98'
article_processing_charge: Yes
article_type: original
author:
- first_name: Verena
full_name: Hübschmann, Verena
id: 32B7C918-F248-11E8-B48F-1D18A9856A87
last_name: Hübschmann
- first_name: Medina
full_name: Korkut, Medina
id: 4B51CE74-F248-11E8-B48F-1D18A9856A87
last_name: Korkut
orcid: 0000-0003-4309-2251
- first_name: Alessandro
full_name: Venturino, Alessandro
id: 41CB84B2-F248-11E8-B48F-1D18A9856A87
last_name: Venturino
orcid: 0000-0003-2356-9403
- first_name: Juan Pablo
full_name: Maya-Arteaga, Juan Pablo
id: c815d433-1f5d-11f0-a875-dad18b1e5924
last_name: Maya-Arteaga
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
citation:
ama: Schmied V, Korkut M, Venturino A, Maya-Arteaga JP, Siegert S. Microglia determine
an immune-challenged environment and facilitate ibuprofen action in human retinal
organoids. Journal of Neuroinflammation. 2025;22(1). doi:10.1186/s12974-025-03366-x
apa: Schmied, V., Korkut, M., Venturino, A., Maya-Arteaga, J. P., & Siegert,
S. (2025). Microglia determine an immune-challenged environment and facilitate
ibuprofen action in human retinal organoids. Journal of Neuroinflammation.
Springer Nature. https://doi.org/10.1186/s12974-025-03366-x
chicago: Schmied, Verena, Medina Korkut, Alessandro Venturino, Juan Pablo Maya-Arteaga,
and Sandra Siegert. “Microglia Determine an Immune-Challenged Environment and
Facilitate Ibuprofen Action in Human Retinal Organoids.” Journal of Neuroinflammation.
Springer Nature, 2025. https://doi.org/10.1186/s12974-025-03366-x.
ieee: V. Schmied, M. Korkut, A. Venturino, J. P. Maya-Arteaga, and S. Siegert, “Microglia
determine an immune-challenged environment and facilitate ibuprofen action in
human retinal organoids,” Journal of Neuroinflammation, vol. 22, no. 1.
Springer Nature, 2025.
ista: Schmied V, Korkut M, Venturino A, Maya-Arteaga JP, Siegert S. 2025. Microglia
determine an immune-challenged environment and facilitate ibuprofen action in
human retinal organoids. Journal of Neuroinflammation. 22(1), 98.
mla: Schmied, Verena, et al. “Microglia Determine an Immune-Challenged Environment
and Facilitate Ibuprofen Action in Human Retinal Organoids.” Journal of Neuroinflammation,
vol. 22, no. 1, 98, Springer Nature, 2025, doi:10.1186/s12974-025-03366-x.
short: V. Schmied, M. Korkut, A. Venturino, J.P. Maya-Arteaga, S. Siegert, Journal
of Neuroinflammation 22 (2025).
corr_author: '1'
date_created: 2025-04-20T22:01:28Z
date_published: 2025-04-03T00:00:00Z
date_updated: 2026-08-12T08:45:16Z
day: '03'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.1186/s12974-025-03366-x
external_id:
isi:
- '001459311800002'
pmid:
- '40181459'
file:
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checksum: dcc355c21ab713e45fda5c61b5fa5299
content_type: application/pdf
creator: dernst
date_created: 2025-04-22T09:46:27Z
date_updated: 2025-04-22T09:46:27Z
file_id: '19607'
file_name: 2025_JourNeuroinflammation_Schmied.pdf
file_size: 4482167
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file_date_updated: 2025-04-22T09:46:27Z
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intvolume: ' 22'
isi: 1
issue: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 9B99D380-BA93-11EA-9121-9846C619BF3A
grant_number: SC19-017
name: How human microglia shape developing neurons during health and inflammation
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Journal of Neuroinflammation
publication_identifier:
eissn:
- 1742-2094
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/pink-skies/
record:
- id: '20074'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Microglia determine an immune-challenged environment and facilitate ibuprofen
action in human retinal organoids
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: 22
year: '2025'
...
---
OA_place: publisher
_id: '20074'
abstract:
- lang: eng
text: "Prenatal immune challenges pose significant risks to human embryonic brain
and eye development. However, we still lack knowledge about the safe usage of
anti-inflammatory drugs during pregnancy. Human induced pluripotent stem cell
(hIPSC)-derived brain organoid models provide a unique opportunity to investigate
neuronal development and have started to explore functional consequences upon
viral infection. However, brain organoids usually lack microglia, the brain-resident
immune cells. They are present in the early human embryonic brain and actively
participate in neuronal circuit development. At the same time, microglia are known
for their immune-sensing properties and will influence viral-mediated effects.
In my thesis, I was interested to study the multifunctional role of human microglia
during retinal development. \r\nIn chapter 1, I characterize the innate occurrence
of IBA1+-microglia-like cells within the retinal organoid differentiation (Bartalska
et al., 2022). Therefore, we differentiate hIPSC using an unguided retinal organoid
differentiation protocol and observe the presence of IBA1+-microglia-like cells
alongside retinal cups between week 3 and 4 in 2.5D culture. However, instead
of infiltrating the neuroectodermal sides, they enrich within non-pigmented, 3D-cystic
compartments that develop in low numbers parallel to 3D-retinal organoids. To
enrich for IBA1+-microglia precursors (preMG), we guided the differentiation with
a low-dosed BMP4 application, which prevents retinal cup development and enhances
microglia and 3D-cysts formation. We characterize the differentiated preMG for
their microglia-like identity and validated their functionality. In parallel,
mass spectrometry identifies the 3D-cysts to express mesenchymal and epithelial
markers. We confirm that comparable 3D-cysts are also the preferential environment
for IBA1+-microglia-like cells within the unguided retinal organoid differentiation.
\r\nIn chapter 2, I investigate how microglia influence retinal development and
whether they contribute to viral-mediated consequences (Schmied et al., 2025).
Here, we assemble preMG, which we have characterized in chapter 1, into 3D-retinal
organoids. Once the outer plexiform layer forms, microglia-like cells (iMG) populate
them and interact with retinal cell types. However, at this developmental stage,
the ganglion cell number decreases in 3D-retinal organoids. Thus, we adapted the
model into 2D which promotes their survival. Integrated iMG engulf ganglion cells
and control their cell number. In parallel, we apply the immunostimulant POLY(I:C)
to mimic a fetal viral infection. Although POLY(I:C) stimulation affects iMG phenotype,
it does not influence their interaction with ganglion cells. Furthermore, iMG
presence significantly contributes to the supernatant’s inflammatory secretome
and increases retinal cell proliferation. Simultaneous exposure to the non-steroidal
anti-inflammatory drug (NSAID) ibuprofen dampens POLY(I:C)-mediated consequences
of the iMG phenotype and ameliorates cell proliferation. Remarkably, while POLY(I:C)
disrupts neuronal calcium dynamics independent of iMG presence, ibuprofen rescues
this effect only in the presence of iMG. Mechanistically, ibuprofen blocks the
enzymes cyclooxygenase 1 and 2 (COX1/ PTGS1 and COX2/ PTGS2) simultaneously, from
which iMG predominantly express COX1. Selective inhibition of COX1 does not restore
the calcium peak amplitude upon POLY(I:C) stimulation, indicating ibuprofen’s
effect depends on the presence and interplay of both, COX1 and COX2. \r\nIn summary,
we characterized the 3D-retinal organoid model for the occurrence of IBA1+-microglia
like cells. As the innately developing IBA1+-cells enrich in mesenchymal over
retinal structures, we optimized a protocol to differentiate IBA1+-microglia precursors.
By combining these two models we generate microglia-assembled retinal organoids.
Our results underscore the importance of microglia during neurodevelopment, in
the context of prenatal immune challenges and provide insight into the mechanisms
by which ibuprofen exerts its protective effects during embryonic development."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Verena
full_name: Hübschmann, Verena
id: 32B7C918-F248-11E8-B48F-1D18A9856A87
last_name: Hübschmann
citation:
ama: Schmied V. Human microglia impact neuronal development in retinal organoids.
2025. doi:10.15479/AT-ISTA-20074
apa: Schmied, V. (2025). Human microglia impact neuronal development in retinal
organoids. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20074
chicago: Schmied, Verena. “Human Microglia Impact Neuronal Development in Retinal
Organoids.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20074.
ieee: V. Schmied, “Human microglia impact neuronal development in retinal organoids,”
Institute of Science and Technology Austria, 2025.
ista: Schmied V. 2025. Human microglia impact neuronal development in retinal organoids.
Institute of Science and Technology Austria.
mla: Schmied, Verena. Human Microglia Impact Neuronal Development in Retinal
Organoids. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20074.
short: V. Schmied, Human Microglia Impact Neuronal Development in Retinal Organoids,
Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-07-24T12:37:22Z
date_published: 2025-07-24T00:00:00Z
date_updated: 2026-08-12T08:45:16Z
day: '24'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: SaSi
doi: 10.15479/AT-ISTA-20074
doi_confirm: '1'
file:
- access_level: closed
checksum: d09f9984002353ad7442358394919bf3
content_type: application/x-zip-compressed
creator: vhuebsch
date_created: 2025-07-30T08:47:53Z
date_updated: 2025-07-30T08:47:53Z
file_id: '20086'
file_name: PhD_Thesis_Schmied.zip
file_size: 43566093
relation: source_file
- access_level: open_access
checksum: 4833690d7283c587f518ba98eeb2c946
content_type: application/pdf
creator: vhuebsch
date_created: 2025-07-30T08:47:46Z
date_updated: 2025-07-30T09:29:09Z
file_id: '20087'
file_name: PhD_Thesis_Schmied.pdf
file_size: 13120922
relation: main_file
file_date_updated: 2025-07-30T09:29:09Z
fulldoi: https://doi.org/10.15479/AT-ISTA-20074
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '151'
project:
- _id: 9B99D380-BA93-11EA-9121-9846C619BF3A
grant_number: SC19-017
name: How human microglia shape developing neurons during health and inflammation
publication_identifier:
isbn:
- 978-3-99078-060-2
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11478'
relation: part_of_dissertation
status: public
- id: '19593'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
title: Human microglia impact neuronal development in retinal organoids
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '19372'
abstract:
- lang: eng
text: We consider the confined Fröhlich polaron and establish an asymptotic series
for the low-energy eigenvalues in negative powers of the coupling constant. The
coefficients of the series are derived through a two-fold perturbation approach,
involving expansions around the electron Pekar minimizer and the excitations of
the quantum field.
acknowledgement: M.B. gratefully acknowledges funding from the ERC Advanced Grant
ERC-AdG CLaQS, grant agreement n. 83478.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Morris
full_name: Brooks, Morris
id: B7ECF9FC-AA38-11E9-AC9A-0930E6697425
last_name: Brooks
orcid: 0000-0002-6249-0928
- first_name: David Johannes
full_name: Mitrouskas, David Johannes
id: cbddacee-2b11-11eb-a02e-a2e14d04e52d
last_name: Mitrouskas
citation:
ama: Brooks M, Mitrouskas DJ. Asymptotic series for low-energy excitations of the
Fröhlich polaron at strong coupling. Probability and Mathematical Physics.
2025;6(1):281-325. doi:10.2140/pmp.2025.6.281
apa: Brooks, M., & Mitrouskas, D. J. (2025). Asymptotic series for low-energy
excitations of the Fröhlich polaron at strong coupling. Probability and Mathematical
Physics. Mathematical Sciences Publishers. https://doi.org/10.2140/pmp.2025.6.281
chicago: Brooks, Morris, and David Johannes Mitrouskas. “Asymptotic Series for Low-Energy
Excitations of the Fröhlich Polaron at Strong Coupling.” Probability and Mathematical
Physics. Mathematical Sciences Publishers, 2025. https://doi.org/10.2140/pmp.2025.6.281.
ieee: M. Brooks and D. J. Mitrouskas, “Asymptotic series for low-energy excitations
of the Fröhlich polaron at strong coupling,” Probability and Mathematical Physics,
vol. 6, no. 1. Mathematical Sciences Publishers, pp. 281–325, 2025.
ista: Brooks M, Mitrouskas DJ. 2025. Asymptotic series for low-energy excitations
of the Fröhlich polaron at strong coupling. Probability and Mathematical Physics.
6(1), 281–325.
mla: Brooks, Morris, and David Johannes Mitrouskas. “Asymptotic Series for Low-Energy
Excitations of the Fröhlich Polaron at Strong Coupling.” Probability and Mathematical
Physics, vol. 6, no. 1, Mathematical Sciences Publishers, 2025, pp. 281–325,
doi:10.2140/pmp.2025.6.281.
short: M. Brooks, D.J. Mitrouskas, Probability and Mathematical Physics 6 (2025)
281–325.
corr_author: '1'
date_created: 2025-03-09T23:01:28Z
date_published: 2025-02-23T00:00:00Z
date_updated: 2026-08-12T08:44:53Z
day: '23'
department:
- _id: RoSe
doi: 10.2140/pmp.2025.6.281
external_id:
arxiv:
- '2306.16373'
fulldoi: https://doi.org/10.2140/pmp.2025.6.281
intvolume: ' 6'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2306.16373
month: '02'
oa: 1
oa_version: Preprint
page: 281-325
publication: Probability and Mathematical Physics
publication_identifier:
eissn:
- 2690-1005
issn:
- 2690-0998
publication_status: published
publisher: Mathematical Sciences Publishers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Asymptotic series for low-energy excitations of the Fröhlich polaron at strong
coupling
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20342'
abstract:
- lang: eng
text: Safety and liveness stand as fundamental concepts in formal languages, playing
a key role in verification. The safety-liveness classification of boolean properties
characterizes whether a given property can be falsified by observing a finite
prefix of an infinite computation trace (always for safety, never for liveness).
In the quantitative setting, properties are arbitrary functions from infinite
words to partially-ordered domains. Extending this paradigm to the quantitative
domain, where properties are arbitrary functions mapping infinite words to partially-ordered
domains, we introduce and study the notions of quantitative safety and liveness.
First, we formally define quantitative safety and liveness, and prove that our
definitions induce conservative quantitative generalizations of both the safety-progress
hierarchy and the safety-liveness decomposition of boolean properties. Consequently,
like their boolean counterparts, quantitative properties can be min-decomposed
into safety and liveness parts, or alternatively, max-decomposed into co-safety
and co-liveness parts. We further establish a connection between quantitative
safety and topological continuity and provide alternative characterizations of
quantitative safety and liveness in terms of their boolean analogs. Second, we
instantiate our framework with the specific classes of quantitative properties
expressed by automata. These quantitative automata contain finitely many states
and rational-valued transition weights, and their common value functions Inf,
Sup, LimInf, LimSup, LimInfAvg, LimSupAvg, and DSum map infinite words into the
totally-ordered domain of real numbers. For all common value functions, we provide
a procedure for deciding whether a given automaton is safe or live, we show how
to construct its safety closure, and we present a min-decomposition into safe
and live automata.
acknowledgement: This work was supported in part by the ERC-2020-AdG 101020093 and
the Israel Science Foundation grant 2410/22. N. Mazzocchi was affiliated with ISTA
when this work was submitted for publication.
article_number: '13149'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Udi
full_name: Boker, Udi
id: 31E297B6-F248-11E8-B48F-1D18A9856A87
last_name: Boker
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Nicolas Adrien
full_name: Mazzocchi, Nicolas Adrien
id: b26baa86-3308-11ec-87b0-8990f34baa85
last_name: Mazzocchi
- first_name: Naci E
full_name: Sarac, Naci E
id: 8C6B42F8-C8E6-11E9-A03A-F2DCE5697425
last_name: Sarac
citation:
ama: Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. Safety and liveness of quantitative
properties and automata. Logical Methods in Computer Science. 2025;21(2).
doi:10.46298/lmcs-21(2:2)2025
apa: Boker, U., Henzinger, T. A., Mazzocchi, N. A., & Sarac, N. E. (2025). Safety
and liveness of quantitative properties and automata. Logical Methods in Computer
Science. EPI Sciences. https://doi.org/10.46298/lmcs-21(2:2)2025
chicago: Boker, Udi, Thomas A Henzinger, Nicolas Adrien Mazzocchi, and Naci E Sarac.
“Safety and Liveness of Quantitative Properties and Automata.” Logical Methods
in Computer Science. EPI Sciences, 2025. https://doi.org/10.46298/lmcs-21(2:2)2025.
ieee: U. Boker, T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Safety and liveness
of quantitative properties and automata,” Logical Methods in Computer Science,
vol. 21, no. 2. EPI Sciences, 2025.
ista: Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. 2025. Safety and liveness of
quantitative properties and automata. Logical Methods in Computer Science. 21(2),
13149.
mla: Boker, Udi, et al. “Safety and Liveness of Quantitative Properties and Automata.”
Logical Methods in Computer Science, vol. 21, no. 2, 13149, EPI Sciences,
2025, doi:10.46298/lmcs-21(2:2)2025.
short: U. Boker, T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, Logical Methods in
Computer Science 21 (2025).
corr_author: '1'
date_created: 2025-09-11T12:17:52Z
date_published: 2025-04-08T00:00:00Z
date_updated: 2026-08-12T08:46:05Z
day: '08'
ddc:
- '000'
department:
- _id: GradSch
- _id: ToHe
doi: 10.46298/lmcs-21(2:2)2025
ec_funded: 1
external_id:
arxiv:
- '2307.06016'
isi:
- '001468887900001'
file:
- access_level: open_access
checksum: 0b4d477bd981379724c35a4de2c176e5
content_type: application/pdf
creator: esarac
date_created: 2025-09-11T12:17:12Z
date_updated: 2025-09-11T12:17:12Z
file_id: '20343'
file_name: 2307.06016.pdf
file_size: 709584
relation: main_file
success: 1
file_date_updated: 2025-09-11T12:17:12Z
fulldoi: https://doi.org/10.46298/lmcs-21(2:2)2025
has_accepted_license: '1'
intvolume: ' 21'
isi: 1
issue: '2'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: Logical Methods in Computer Science
publication_identifier:
eissn:
- 1860-5974
publication_status: published
publisher: EPI Sciences
quality_controlled: '1'
related_material:
record:
- id: '13221'
relation: earlier_version
status: public
- id: '20147'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Safety and liveness of quantitative properties and automata
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: 21
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '19701'
abstract:
- lang: eng
text: 'Living systems are characterized by controlled flows of matter, energy, and
information. While the biophysics community has productively engaged with the
first two, addressing information flows has been more challenging, with some scattered
success in evolutionary theory and a more coherent track record in neuroscience.
Nevertheless, interdisciplinary work of the past two decades at the interface
of biophysics, quantitative biology, and engineering has led to an emerging mathematical
language for describing information flows at the molecular scale. This is where
the central processes of life unfold: from detection and transduction of environmental
signals to the readout or copying of genetic information and the triggering of
adaptive cellular responses. Such processes are coordinated by complex biochemical
reaction networks that operate at room temperature, are out of equilibrium, and
use low copy numbers of diverse molecular species with limited interaction specificity.
Here we review how flows of information through biochemical networks can be formalized
using information-theoretic quantities, quantified from data, and computed within
various modeling frameworks. Optimization of information flows is presented as
a candidate design principle that navigates the relevant time, energy, crosstalk,
and metabolic constraints to predict reliable cellular signaling and gene regulation
architectures built of individually noisy components.'
acknowledgement: G.T. acknowledges the support of the Human Frontiers Science Program
(HFSP), the Austrian Science Fund (FWF 10.55776/P34015, 10.55776/P28844), and the
European Research Council Synergy DYNATRANS (ERC-2023-SyG 101118866) grant. P.R.t.W.
performed his work at the research institute AMOLF and acknowledges support from
the Dutch Research Council (NWO) and funding from the European Research Council
(ERC) under the European Union's Horizon 2020 research and innovation program (grant
agreement 885065).
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Pieter Rein Ten
full_name: Wolde, Pieter Rein Ten
last_name: Wolde
citation:
ama: Tkačik G, Wolde PRT. Information processing in biochemical networks. Annual
Review of Biophysics. 2025;54:249-274. doi:10.1146/annurev-biophys-060524-102720
apa: Tkačik, G., & Wolde, P. R. T. (2025). Information processing in biochemical
networks. Annual Review of Biophysics. Annual Reviews. https://doi.org/10.1146/annurev-biophys-060524-102720
chicago: Tkačik, Gašper, and Pieter Rein Ten Wolde. “Information Processing in Biochemical
Networks.” Annual Review of Biophysics. Annual Reviews, 2025. https://doi.org/10.1146/annurev-biophys-060524-102720.
ieee: G. Tkačik and P. R. T. Wolde, “Information processing in biochemical networks,”
Annual Review of Biophysics, vol. 54. Annual Reviews, pp. 249–274, 2025.
ista: Tkačik G, Wolde PRT. 2025. Information processing in biochemical networks.
Annual Review of Biophysics. 54, 249–274.
mla: Tkačik, Gašper, and Pieter Rein Ten Wolde. “Information Processing in Biochemical
Networks.” Annual Review of Biophysics, vol. 54, Annual Reviews, 2025,
pp. 249–74, doi:10.1146/annurev-biophys-060524-102720.
short: G. Tkačik, P.R.T. Wolde, Annual Review of Biophysics 54 (2025) 249–274.
corr_author: '1'
date_created: 2025-05-18T22:02:50Z
date_published: 2025-05-01T00:00:00Z
date_updated: 2026-08-12T09:25:42Z
day: '01'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1146/annurev-biophys-060524-102720
external_id:
isi:
- '001488641500013'
pmid:
- '39929539'
file:
- access_level: open_access
checksum: 9ab623b2bc45dcd5fdd2c9577ea8ae9f
content_type: application/pdf
creator: dernst
date_created: 2025-05-19T07:55:51Z
date_updated: 2025-05-19T07:55:51Z
file_id: '19710'
file_name: 2025_AnnualReviewBiophysics_Tkacik.pdf
file_size: 317925
relation: main_file
success: 1
file_date_updated: 2025-05-19T07:55:51Z
fulldoi: https://doi.org/10.1146/annurev-biophys-060524-102720
has_accepted_license: '1'
intvolume: ' 54'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 249-274
pmid: 1
project:
- _id: 626c45b5-2b32-11ec-9570-e509828c1ba6
grant_number: P34015
name: Efficient coding with biophysical realism
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
- _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'
- _id: 255008E4-B435-11E9-9278-68D0E5697425
grant_number: RGP0065/2012
name: Information processing and computation in fish groups
publication: Annual Review of Biophysics
publication_identifier:
eissn:
- 1936-1238
publication_status: published
publisher: Annual Reviews
quality_controlled: '1'
scopus_import: '1'
status: public
title: Information processing in biochemical networks
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: 54
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20048'
abstract:
- lang: eng
text: 'During embryonic development, cell behaviors need to be tightly regulated
in time and space. Yet how the temporal and spatial regulations of cell behaviors
are interconnected during embryonic development remains elusive. To address this,
we turned to zebrafish gastrulation, the process whereby dynamic cell behaviors
generate the three principal germ layers of the early embryo. Here, we show that
Hoxb cluster genes are expressed in a temporally collinear manner at the blastoderm
margin, where mesodermal and endodermal (mesendoderm) progenitor cells are specified
and ingress to form mesendoderm/hypoblast. Functional analysis shows that these
Hoxb genes regulate the timing of cell ingression: under- or overexpression of
Hoxb genes perturb the timing of mesendoderm cell ingression and, consequently,
the positioning of these cells along the forming anterior-posterior body axis
after gastrulation. Finally, we found that Hoxb genes control the timing of mesendoderm
ingression by regulating cellular bleb formation and cell surface fluctuations
in the ingressing cells. Collectively, our findings suggest that Hoxb genes interconnect
the temporal and spatial pattern of cell behaviors during zebrafish gastrulation
by controlling cell surface fluctuations.'
acknowledgement: We thank all the Heisenberg lab members for discussions and comments
on the manuscript, and the Bioimaging and Life Science facilities of ISTA for support
with microscopy and fish maintenance, respectively. This study was funded by a Japan
Society for the Promotion of Science (JSPS) Overseas Research Fellowship and a Japan
Science and Technology Agency PRESTO grant (JPMJPR214B) to Y.M. Open Access funding
provided by the Japan Science and Technology Agency. Deposited in PMC for immediate
release.
article_number: dev204261
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Yuuta
full_name: Moriyama, Yuuta
id: addc9b8c-67a0-11f0-b374-a2e094825470
last_name: Moriyama
orcid: 0000-0002-2853-8051
- first_name: Toshiyuki
full_name: Mitsui, Toshiyuki
last_name: Mitsui
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Moriyama Y, Mitsui T, Heisenberg C-PJ. Hoxb genes determine the timing of cell
ingression by regulating cell surface fluctuations during zebrafish gastrulation.
Development. 2025;152(12). doi:10.1242/dev.204261
apa: Moriyama, Y., Mitsui, T., & Heisenberg, C.-P. J. (2025). Hoxb genes determine
the timing of cell ingression by regulating cell surface fluctuations during zebrafish
gastrulation. Development. Company of Biologists. https://doi.org/10.1242/dev.204261
chicago: Moriyama, Yuuta, Toshiyuki Mitsui, and Carl-Philipp J Heisenberg. “Hoxb
Genes Determine the Timing of Cell Ingression by Regulating Cell Surface Fluctuations
during Zebrafish Gastrulation.” Development. Company of Biologists, 2025.
https://doi.org/10.1242/dev.204261.
ieee: Y. Moriyama, T. Mitsui, and C.-P. J. Heisenberg, “Hoxb genes determine the
timing of cell ingression by regulating cell surface fluctuations during zebrafish
gastrulation,” Development, vol. 152, no. 12. Company of Biologists, 2025.
ista: Moriyama Y, Mitsui T, Heisenberg C-PJ. 2025. Hoxb genes determine the timing
of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation.
Development. 152(12), dev204261.
mla: Moriyama, Yuuta, et al. “Hoxb Genes Determine the Timing of Cell Ingression
by Regulating Cell Surface Fluctuations during Zebrafish Gastrulation.” Development,
vol. 152, no. 12, dev204261, Company of Biologists, 2025, doi:10.1242/dev.204261.
short: Y. Moriyama, T. Mitsui, C.-P.J. Heisenberg, Development 152 (2025).
corr_author: '1'
date_created: 2025-07-21T08:10:32Z
date_published: 2025-06-27T00:00:00Z
date_updated: 2026-08-12T10:01:31Z
day: '27'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1242/dev.204261
external_id:
isi:
- '001525252300001'
pmid:
- '40576478'
file:
- access_level: open_access
checksum: 808d8aa28df79d23fb661838d1fdc1be
content_type: application/pdf
creator: dernst
date_created: 2025-07-23T08:43:01Z
date_updated: 2025-07-23T08:43:01Z
file_id: '20070'
file_name: 2025_Development_Moriyama.pdf
file_size: 25935563
relation: main_file
success: 1
file_date_updated: 2025-07-23T08:43:01Z
fulldoi: https://doi.org/10.1242/dev.204261
has_accepted_license: '1'
intvolume: ' 152'
isi: 1
issue: '12'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Development
publication_identifier:
eissn:
- 1477-9129
issn:
- 0950-1991
publication_status: published
publisher: Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Hoxb genes determine the timing of cell ingression by regulating cell surface
fluctuations during zebrafish gastrulation
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: 152
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '21343'
abstract:
- lang: eng
text: "The large sieve is used to estimate the density of quadratic polynomials
Q ∈ Z[x],\r\nsuch that there exists an odd degree polynomial defined over Z which
has resultant ±1 with Q.\r\nGiven a monic polynomial R ∈ Z[x] of odd degree, this
is used to show that for almost all\r\nquadratic polynomials Q ∈ Z[x], there exists
a prime p such that Q and R share a common\r\nroot in Fp. Using recent work of
Landesman, an application to the average size of the odd part\r\nof the class
group of quadratic number fields is also given"
- lang: fre
text: ' Le grand crible est utilisé pour estimer la densité des polynômes quadratiques
Q ∈ Z[x] tels qu’il existe un polynôme de degré impair défini sur Z dont le résultant
avec Q est égal à ±1. Étant donné un polynôme unitaire R ∈ Z[x] de degré impair,
on s’en sert pour montrer que, pour presque tous les polynômes quadratiques Q
∈ Z[x], il existe un nombre premier p tel que Q et R aient une racine commune
dans Fp. En utilisant des travaux récents de Landesman, on obtient également une
application concernant la taille moyenne de la partie impaire du groupe de classe
des corps quadratiques.'
acknowledgement: While working on this paper, the first author was supported by a
FWF grant (DOI 10.55776/P36278).
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: Yik Tung
full_name: Chan, Yik Tung
id: c4c0afc8-9262-11ed-9231-d8b0bc743af1
last_name: Chan
orcid: 0000-0001-8467-4106
citation:
ama: Browning TD, Chan S. Solubility of a resultant equation and applications. Journal
de l’Ecole Polytechnique - Mathematiques. 2025;12:1677-1691. doi:10.5802/jep.320
apa: Browning, T. D., & Chan, S. (2025). Solubility of a resultant equation
and applications. Journal de l’Ecole Polytechnique - Mathematiques. Ecole
Polytechnique. https://doi.org/10.5802/jep.320
chicago: Browning, Timothy D, and Stephanie Chan. “Solubility of a Resultant Equation
and Applications.” Journal de l’Ecole Polytechnique - Mathematiques. Ecole
Polytechnique, 2025. https://doi.org/10.5802/jep.320.
ieee: T. D. Browning and S. Chan, “Solubility of a resultant equation and applications,”
Journal de l’Ecole Polytechnique - Mathematiques, vol. 12. Ecole Polytechnique,
pp. 1677–1691, 2025.
ista: Browning TD, Chan S. 2025. Solubility of a resultant equation and applications.
Journal de l’Ecole Polytechnique - Mathematiques. 12, 1677–1691.
mla: Browning, Timothy D., and Stephanie Chan. “Solubility of a Resultant Equation
and Applications.” Journal de l’Ecole Polytechnique - Mathematiques, vol.
12, Ecole Polytechnique, 2025, pp. 1677–91, doi:10.5802/jep.320.
short: T.D. Browning, S. Chan, Journal de l’Ecole Polytechnique - Mathematiques
12 (2025) 1677–1691.
corr_author: '1'
das_tickbox: '0'
date_created: 2026-02-22T23:01:36Z
date_published: 2025-10-21T00:00:00Z
date_updated: 2026-08-12T11:17:50Z
day: '21'
ddc:
- '510'
department:
- _id: TiBr
doi: 10.5802/jep.320
external_id:
arxiv:
- '2411.09264'
file:
- access_level: open_access
checksum: 828577ea48ac6109d3e9dd1aeddd45c4
content_type: application/pdf
creator: dernst
date_created: 2026-02-24T07:56:34Z
date_updated: 2026-02-24T07:56:34Z
file_id: '21356'
file_name: 2025_JEP_Browning.pdf
file_size: 1003689
relation: main_file
success: 1
file_date_updated: 2026-02-24T07:56:34Z
fulldoi: https://doi.org/10.5802/jep.320
has_accepted_license: '1'
intvolume: ' 12'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 1677-1691
project:
- _id: bd8a4fdc-d553-11ed-ba76-80a0167441a3
grant_number: P36278
name: Rational curves via function field analytic number theory
publication: Journal de l'Ecole Polytechnique - Mathematiques
publication_identifier:
eissn:
- 2270-518X
issn:
- 2429-7100
publication_status: published
publisher: Ecole Polytechnique
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Solubility of a resultant equation and applications
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: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20249'
abstract:
- lang: eng
text: We develop a heuristic for the density of integer points on affine cubic surfaces.
Our heuristic applies to smooth surfaces defined by cubic polynomials that are
log K3, but it can also be adjusted to handle singular cubic surfaces. We compare
our heuristic to Heath-Brown’s prediction for sums of three cubes, as well as
to asymptotic formulae in the literature around Zagier’s work on the Markoff cubic
surface, and work of Baragar and Umeda on further surfaces of Markoff-type. We
also test our heuristic against numerical data for several families of cubic surfaces.
acknowledgement: "The authors owe a debt of thanks to Yonatan Harpaz for asking about
circle method heuristics for log K3 surfaces. His contribution to the resulting
discussion is gratefully acknowledged. Thanks are also due to Andrew Sutherland
for help with numerical data for the equation x^3 + y^3 + z^3 = 1, together with
Alex Gamburd, Amit Ghosh, Peter Sarnak and Matteo Verzobio for their interest in
this paper. Special thanks are due to Victor Wang for helpful conversations about
the circle method heuristics and to the anonymous referee for several useful comments.
While working on this paper, the authors were supported by a FWF grant (DOI 10.55776/P32428),
and the first author was supported by a further FWF grant (DOI 10.55776/P36278)
and a grant from the School of Mathematics at the Institute for Advanced Study in
Princeton.\r\nOpen access funding provided by Institute of Science and Technology
(IST Austria)."
article_number: '81'
article_processing_charge: Yes (via OA deal)
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: Florian Alexander
full_name: Wilsch, Florian Alexander
id: 560601DA-8D36-11E9-A136-7AC1E5697425
last_name: Wilsch
orcid: 0000-0001-7302-8256
citation:
ama: 'Browning TD, Wilsch FA. Integral points on cubic surfaces: heuristics and
numerics. Selecta Mathematica New Series. 2025;31(4). doi:10.1007/s00029-025-01074-1'
apa: 'Browning, T. D., & Wilsch, F. A. (2025). Integral points on cubic surfaces:
heuristics and numerics. Selecta Mathematica New Series. Springer Nature.
https://doi.org/10.1007/s00029-025-01074-1'
chicago: 'Browning, Timothy D, and Florian Alexander Wilsch. “Integral Points on
Cubic Surfaces: Heuristics and Numerics.” Selecta Mathematica New Series.
Springer Nature, 2025. https://doi.org/10.1007/s00029-025-01074-1.'
ieee: 'T. D. Browning and F. A. Wilsch, “Integral points on cubic surfaces: heuristics
and numerics,” Selecta Mathematica New Series, vol. 31, no. 4. Springer
Nature, 2025.'
ista: 'Browning TD, Wilsch FA. 2025. Integral points on cubic surfaces: heuristics
and numerics. Selecta Mathematica New Series. 31(4), 81.'
mla: 'Browning, Timothy D., and Florian Alexander Wilsch. “Integral Points on Cubic
Surfaces: Heuristics and Numerics.” Selecta Mathematica New Series, vol.
31, no. 4, 81, Springer Nature, 2025, doi:10.1007/s00029-025-01074-1.'
short: T.D. Browning, F.A. Wilsch, Selecta Mathematica New Series 31 (2025).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: The data used in Sections 6 and 9 is hosted on the Göttingen
Research Online Data repository [https://doi.org/10.25625/4FLFH8]. The code used
to determine the data in Sections 6.2, 9.1 and 9.2 is found on the second author’s
github page.
date_created: 2025-08-31T22:01:31Z
date_published: 2025-09-01T00:00:00Z
date_updated: 2026-08-12T12:15:32Z
day: '01'
ddc:
- '500'
department:
- _id: TiBr
doi: 10.1007/s00029-025-01074-1
external_id:
arxiv:
- '2407.16315'
isi:
- '001552779800001'
file:
- access_level: open_access
checksum: 89352f1f7e8d2b367ae5f4e9bf9eb1f5
content_type: application/pdf
creator: dernst
date_created: 2025-09-03T06:44:44Z
date_updated: 2025-09-03T06:44:44Z
file_id: '20281'
file_name: 2025_SelectaMathematica_Browning.pdf
file_size: 2484757
relation: main_file
success: 1
file_date_updated: 2025-09-03T06:44:44Z
fulldoi: https://doi.org/10.1007/s00029-025-01074-1
has_accepted_license: '1'
intvolume: ' 31'
isi: 1
issue: '4'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 26AEDAB2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P32428
name: New frontiers of the Manin conjecture
- _id: bd8a4fdc-d553-11ed-ba76-80a0167441a3
grant_number: P36278
name: Rational curves via function field analytic number theory
publication: Selecta Mathematica New Series
publication_identifier:
eissn:
- 1420-9020
issn:
- 1022-1824
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/fwilsch/cubicpts
record:
- id: '22234'
relation: research_data
status: public
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: 'Integral points on cubic surfaces: heuristics and numerics'
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: 31
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20218'
abstract:
- lang: eng
text: Humanity has long sought inspiration from nature to innovate materials and
devices. As science advances, nature-inspired materials are becoming part of our
lives. Animate materials, characterized by their activity, adaptability, and autonomy,
emulate properties of living systems. While only biological materials fully embody
these principles, artificial versions are advancing rapidly, promising transformative
impacts in the circular economy, health and climate resilience within a generation.
This roadmap presents authoritative perspectives on animate materials across different
disciplines and scales, highlighting their interdisciplinary nature and potential
applications in diverse fields including nanotechnology, robotics and the built
environment. It underscores the need for concerted efforts to address shared challenges
such as complexity management, scalability, evolvability, interdisciplinary collaboration,
and ethical and environmental considerations. The framework defined by classifying
materials based on their level of animacy can guide this emerging field to encourage
cooperation and responsible development. By unravelling the mysteries of living
matter and leveraging its principles, we can design materials and systems that
will transform our world in a more sustainable manner.
acknowledgement: "Living Architecture is Funded by the EU Horizon 2020 Future Emerging
Technologies Open programme (2016–2019) Grant Agreement 686585 a consortium of 6
collaborating institutions—Newcastle University, University of Trento, University
of the West of England, Spanish National Research Council, Explora Biotech and Liquifer
Systems Group.\r\n\r\nThe Active Living Infrastructure: Controlled Environment (ALICE)
project is funded by an EU Innovation Award for the development of a bio-digital
‘brick’ prototype, a collaboration between Newcastle University, Translating Nature,
and the University of the West of England (2019–2021) under EU Grant Agreement No.
851246.\r\n\r\nMicrobial Hydroponics: Circular Sustainable Electrobiosynthesis (Mi-Hy)
is Funded by the European Union under Grant Agreement Number 101114746, which is
a collaboration between Beneficiaries, KU Leuven (Belgium), the University of Southampton
(UK), SONY Computer Science Laboratory (France), BioFaction KG (Austria), Spanish
National Research Council (Spain), and Associated Partners, the University of the
West of England (UK) and University of Southampton (UK). Mi-Hy is also supported
through the interdisciplinary KU Leuven Institute for Cultural Heritage (HERKUL)."
article_number: '333501'
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Giorgio
full_name: Volpe, Giorgio
last_name: Volpe
- first_name: Nuno A.M.
full_name: Araújo, Nuno A.M.
last_name: Araújo
- first_name: Maria
full_name: Guix, Maria
last_name: Guix
- first_name: Mark
full_name: Miodownik, Mark
last_name: Miodownik
- first_name: Nicolas
full_name: Martin, Nicolas
last_name: Martin
- first_name: Laura
full_name: Alvarez, Laura
last_name: Alvarez
- first_name: Juliane
full_name: Simmchen, Juliane
last_name: Simmchen
- first_name: Roberto Di
full_name: Leonardo, Roberto Di
last_name: Leonardo
- first_name: Nicola
full_name: Pellicciotta, Nicola
last_name: Pellicciotta
- first_name: Quentin
full_name: Martinet, Quentin
id: b37485a8-d343-11eb-a0e9-df8c484ef8ab
last_name: Martinet
orcid: 0000-0002-2916-6632
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
- first_name: Wai Kit
full_name: Ng, Wai Kit
last_name: Ng
- first_name: Dhruv
full_name: Saxena, Dhruv
last_name: Saxena
- first_name: Riccardo
full_name: Sapienza, Riccardo
last_name: Sapienza
- first_name: Sara
full_name: Nadine, Sara
last_name: Nadine
- first_name: João F.
full_name: Mano, João F.
last_name: Mano
- first_name: Reza
full_name: Mahdavi, Reza
last_name: Mahdavi
- first_name: Caroline
full_name: Beck Adiels, Caroline
last_name: Beck Adiels
- first_name: Joe
full_name: Forth, Joe
last_name: Forth
- first_name: Christian
full_name: Santangelo, Christian
last_name: Santangelo
- first_name: Stefano
full_name: Palagi, Stefano
last_name: Palagi
- first_name: Ji Min
full_name: Seok, Ji Min
last_name: Seok
- first_name: Victoria A.
full_name: Webster-Wood, Victoria A.
last_name: Webster-Wood
- first_name: Shuhong
full_name: Wang, Shuhong
last_name: Wang
- first_name: Lining
full_name: Yao, Lining
last_name: Yao
- first_name: Amirreza
full_name: Aghakhani, Amirreza
last_name: Aghakhani
- first_name: Thomas
full_name: Barois, Thomas
last_name: Barois
- first_name: Hamid
full_name: Kellay, Hamid
last_name: Kellay
- first_name: Corentin
full_name: Coulais, Corentin
last_name: Coulais
- first_name: Martin
full_name: Van Hecke, Martin
last_name: Van Hecke
- first_name: Christopher J.
full_name: Pierce, Christopher J.
last_name: Pierce
- first_name: Tianyu
full_name: Wang, Tianyu
last_name: Wang
- first_name: Baxi
full_name: Chong, Baxi
last_name: Chong
- first_name: Daniel I.
full_name: Goldman, Daniel I.
last_name: Goldman
- first_name: Andreagiovanni
full_name: Reina, Andreagiovanni
last_name: Reina
- first_name: Vito
full_name: Trianni, Vito
last_name: Trianni
- first_name: Giovanni
full_name: Volpe, Giovanni
last_name: Volpe
- first_name: Richard
full_name: Beckett, Richard
last_name: Beckett
- first_name: Sean P.
full_name: Nair, Sean P.
last_name: Nair
- first_name: Rachel
full_name: Armstrong, Rachel
last_name: Armstrong
citation:
ama: 'Volpe G, Araújo NAM, Guix M, et al. Roadmap for animate matter. Journal
of Physics: Condensed Matter. 2025;37(33). doi:10.1088/1361-648X/adebd3'
apa: 'Volpe, G., Araújo, N. A. M., Guix, M., Miodownik, M., Martin, N., Alvarez,
L., … Armstrong, R. (2025). Roadmap for animate matter. Journal of Physics:
Condensed Matter. IOP Publishing. https://doi.org/10.1088/1361-648X/adebd3'
chicago: 'Volpe, Giorgio, Nuno A.M. Araújo, Maria Guix, Mark Miodownik, Nicolas
Martin, Laura Alvarez, Juliane Simmchen, et al. “Roadmap for Animate Matter.”
Journal of Physics: Condensed Matter. IOP Publishing, 2025. https://doi.org/10.1088/1361-648X/adebd3.'
ieee: 'G. Volpe et al., “Roadmap for animate matter,” Journal of Physics:
Condensed Matter, vol. 37, no. 33. IOP Publishing, 2025.'
ista: 'Volpe G, Araújo NAM, Guix M, Miodownik M, Martin N, Alvarez L, Simmchen J,
Leonardo RD, Pellicciotta N, Martinet Q, Palacci JA, Ng WK, Saxena D, Sapienza
R, Nadine S, Mano JF, Mahdavi R, Beck Adiels C, Forth J, Santangelo C, Palagi
S, Seok JM, Webster-Wood VA, Wang S, Yao L, Aghakhani A, Barois T, Kellay H, Coulais
C, Van Hecke M, Pierce CJ, Wang T, Chong B, Goldman DI, Reina A, Trianni V, Volpe
G, Beckett R, Nair SP, Armstrong R. 2025. Roadmap for animate matter. Journal
of Physics: Condensed Matter. 37(33), 333501.'
mla: 'Volpe, Giorgio, et al. “Roadmap for Animate Matter.” Journal of Physics:
Condensed Matter, vol. 37, no. 33, 333501, IOP Publishing, 2025, doi:10.1088/1361-648X/adebd3.'
short: 'G. Volpe, N.A.M. Araújo, M. Guix, M. Miodownik, N. Martin, L. Alvarez, J.
Simmchen, R.D. Leonardo, N. Pellicciotta, Q. Martinet, J.A. Palacci, W.K. Ng,
D. Saxena, R. Sapienza, S. Nadine, J.F. Mano, R. Mahdavi, C. Beck Adiels, J. Forth,
C. Santangelo, S. Palagi, J.M. Seok, V.A. Webster-Wood, S. Wang, L. Yao, A. Aghakhani,
T. Barois, H. Kellay, C. Coulais, M. Van Hecke, C.J. Pierce, T. Wang, B. Chong,
D.I. Goldman, A. Reina, V. Trianni, G. Volpe, R. Beckett, S.P. Nair, R. Armstrong,
Journal of Physics: Condensed Matter 37 (2025).'
date_created: 2025-08-24T22:01:30Z
date_published: 2025-08-18T00:00:00Z
date_updated: 2026-08-12T14:00:12Z
day: '18'
ddc:
- '530'
department:
- _id: JePa
doi: 10.1088/1361-648X/adebd3
external_id:
arxiv:
- '2407.10623'
isi:
- '001550090200001'
file:
- access_level: open_access
checksum: 7309274f78bed785b158bd290337f456
content_type: application/pdf
creator: dernst
date_created: 2025-09-02T07:22:48Z
date_updated: 2025-09-02T07:22:48Z
file_id: '20271'
file_name: 2025_CondensedMatter_Volpe.pdf
file_size: 8997829
relation: main_file
success: 1
file_date_updated: 2025-09-02T07:22:48Z
fulldoi: https://doi.org/10.1088/1361-648X/adebd3
has_accepted_license: '1'
intvolume: ' 37'
isi: 1
issue: '33'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: 'Journal of Physics: Condensed Matter'
publication_identifier:
eissn:
- 1361-648X
issn:
- 0953-8984
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Roadmap for animate matter
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 37
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20453'
abstract:
- lang: eng
text: 'Magnetotropic susceptibility is the thermodynamic coefficient that maps the
curvature of free energy with respect to an applied magnetic field orientation,
providing a means to quantify the magnetic anisotropy of a crystal. In this context,
non-linear magnetic torque behavior has been reported in FePS3, motivating the
investigation of similar non-linear characteristics in its magnetotropic susceptibility.
In this work, we derive the non-linear magnetotropic susceptibility expressions
for FePS3 in both ac*-and bc*-planes using complementary approaches: by taking
the first derivative of torque and through the formal calculation of the magnetotropic
susceptibility. Higher-order terms in the magnetization are included, and the
final equations are obtained by applying symmetry constraints imposed by the C2h
point group of the material. We analyze the behavior of the resulting non-linear
expressions and identify the contributions of each parameter. Our theoretical
results show good agreement with preliminary, unpublished experimental data, offering
meaningful guidance for ongoing and future experimental work.'
acknowledgement: We thank Kimberly A. Modic for her support and discussions regarding
the technique in the context of a project indirectly related to, but distinct from,
the present work. We also thank Brad J. Ramshaw and Arkady Shekhter for scientific
discussions not directly related to this study, but whose insights proved helpful.
We are grateful to Valeska Zambra, Amit Nathwani, Hamza Nasir, and Tayyaba Hussain
for informal discussions on various aspects of the technique, and to Naoya Iwahara
for his thoughtful and constructive feedback. The experimental curve shown in figures
3(b) and 6, from the Thermodynamics of Quantum Materials (TQM) group at ISTA, was
measured by Muhammad Nauman for an unrelated project. We thank Kimberly Modic for
granting access to the laboratory facilities. Je Geun Park provided the crystal
used for that measurement via Younjung Jo, whose contribution we gratefully acknowledge.
Institutional support from the Institute of Science and Technology Austria (ISTA)
is also gratefully acknowledged.
article_number: '405801'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Hamza
full_name: Farooq, Hamza
last_name: Farooq
- first_name: Muhammad
full_name: Nauman, Muhammad
id: 32c21954-2022-11eb-9d5f-af9f93c24e71
last_name: Nauman
orcid: 0000-0002-2111-4846
citation:
ama: 'Farooq H, Nauman M. Non-linear magnetotropic susceptibility in FePS3. Journal
of Physics: Condensed Matter. 2025;37(40). doi:10.1088/1361-648X/ae0913'
apa: 'Farooq, H., & Nauman, M. (2025). Non-linear magnetotropic susceptibility
in FePS3. Journal of Physics: Condensed Matter. IOP Publishing. https://doi.org/10.1088/1361-648X/ae0913'
chicago: 'Farooq, Hamza, and Muhammad Nauman. “Non-Linear Magnetotropic Susceptibility
in FePS3.” Journal of Physics: Condensed Matter. IOP Publishing, 2025.
https://doi.org/10.1088/1361-648X/ae0913.'
ieee: 'H. Farooq and M. Nauman, “Non-linear magnetotropic susceptibility in FePS3,”
Journal of Physics: Condensed Matter, vol. 37, no. 40. IOP Publishing,
2025.'
ista: 'Farooq H, Nauman M. 2025. Non-linear magnetotropic susceptibility in FePS3.
Journal of Physics: Condensed Matter. 37(40), 405801.'
mla: 'Farooq, Hamza, and Muhammad Nauman. “Non-Linear Magnetotropic Susceptibility
in FePS3.” Journal of Physics: Condensed Matter, vol. 37, no. 40, 405801,
IOP Publishing, 2025, doi:10.1088/1361-648X/ae0913.'
short: 'H. Farooq, M. Nauman, Journal of Physics: Condensed Matter 37 (2025).'
corr_author: '1'
date_created: 2025-10-12T22:01:26Z
date_published: 2025-10-06T00:00:00Z
date_updated: 2026-08-12T14:00:34Z
day: '06'
ddc:
- '530'
department:
- _id: KiMo
doi: 10.1088/1361-648X/ae0913
external_id:
isi:
- '001585824100001'
pmid:
- '40967257'
file:
- access_level: open_access
checksum: b182856a5a655496e149afa49ec464f3
content_type: application/pdf
creator: dernst
date_created: 2025-10-13T06:34:15Z
date_updated: 2025-10-13T06:34:15Z
file_id: '20458'
file_name: 2025_JourPhysicsCondMatter_Farooq.pdf
file_size: 1709516
relation: main_file
success: 1
file_date_updated: 2025-10-13T06:34:15Z
fulldoi: https://doi.org/10.1088/1361-648X/ae0913
has_accepted_license: '1'
intvolume: ' 37'
isi: 1
issue: '40'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: 'Journal of Physics: Condensed Matter'
publication_identifier:
eissn:
- 1361-648X
issn:
- 0953-8984
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Non-linear magnetotropic susceptibility in FePS3
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 37
year: '2025'
...
---
OA_type: closed access
_id: '20219'
abstract:
- lang: eng
text: Reproduction is a fundamental biological process, with organisms reproducing
sexually, asexually, and, in some cases, utilizing both modes of reproduction
within the same population. Does the ability to reproduce through a combination
of asexual and sexual modes offer an evolutionary advantage over relying on either
mode alone? Here, we introduce an empirically driven theoretical model to examine
the dynamics and interplay between sexual and asexual reproduction in stick insect
populations. We analyse it using a novel phase transition approach and corroborate
it using published experimental data. We find that the presence of males can either
increase or decrease the overall population size. However, maintaining an optimal
ratio of parthenogenetic to sexual reproduction is crucial for male resilience,
effectively delaying male extinction. Conversely, extreme levels of parthenogenetic
reproduction—whether too high or too low—can lead to male extinction, emphasizing
the need for a balanced number of virgin females to ensure the persistence of
males. Our model also explains male absence in Carausius morosus and persistence
in Extatosoma tiaratum. Our findings provide valuable insights into the interplay
of reproductive strategies and contribute to broader discussions on the transitions
between sexual and asexual reproduction.
acknowledgement: We acknowledge Prof. Uri Alon for introducing us to the topic of
systems biology during the graduate course at the Weizmann Institute of Science,
whose insights and teachings have greatly inspired this work.
article_number: '20250202'
article_processing_charge: No
article_type: original
author:
- first_name: Oran
full_name: Ayalon, Oran
last_name: Ayalon
- first_name: Harikrishnan
full_name: Rajendran, Harikrishnan
id: 876b6b34-8ff4-11ec-97c9-8d95a7aae416
last_name: Rajendran
citation:
ama: Ayalon O, Rajendran H. Interplay of asexual and sexual reproduction in bifunctional
insects. Journal of the Royal Society Interface. 2025;22(229). doi:10.1098/rsif.2025.0202
apa: Ayalon, O., & Rajendran, H. (2025). Interplay of asexual and sexual reproduction
in bifunctional insects. Journal of the Royal Society Interface. Royal
Society. https://doi.org/10.1098/rsif.2025.0202
chicago: Ayalon, Oran, and Harikrishnan Rajendran. “Interplay of Asexual and Sexual
Reproduction in Bifunctional Insects.” Journal of the Royal Society Interface.
Royal Society, 2025. https://doi.org/10.1098/rsif.2025.0202.
ieee: O. Ayalon and H. Rajendran, “Interplay of asexual and sexual reproduction
in bifunctional insects,” Journal of the Royal Society Interface, vol.
22, no. 229. Royal Society, 2025.
ista: Ayalon O, Rajendran H. 2025. Interplay of asexual and sexual reproduction
in bifunctional insects. Journal of the Royal Society Interface. 22(229), 20250202.
mla: Ayalon, Oran, and Harikrishnan Rajendran. “Interplay of Asexual and Sexual
Reproduction in Bifunctional Insects.” Journal of the Royal Society Interface,
vol. 22, no. 229, 20250202, Royal Society, 2025, doi:10.1098/rsif.2025.0202.
short: O. Ayalon, H. Rajendran, Journal of the Royal Society Interface 22 (2025).
corr_author: '1'
date_created: 2025-08-24T22:01:30Z
date_published: 2025-08-13T00:00:00Z
date_updated: 2026-08-12T14:09:20Z
day: '13'
department:
- _id: SyCr
doi: 10.1098/rsif.2025.0202
external_id:
isi:
- '001548084900001'
pmid:
- '40799050'
fulldoi: https://doi.org/10.1098/rsif.2025.0202
intvolume: ' 22'
isi: 1
issue: '229'
language:
- iso: eng
month: '08'
oa_version: None
pmid: 1
publication: Journal of the Royal Society Interface
publication_identifier:
eissn:
- 1742-5662
issn:
- 1742-5689
publication_status: published
publisher: Royal Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Interplay of asexual and sexual reproduction in bifunctional insects
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '19762'
abstract:
- lang: eng
text: The cerebral cortex must contain the appropriate numbers of neurons in each
layer to acquire its proper functional organization. Accordingly, neurogenesis
requires precise regulation along development. Cortical neurons are made either
directly by Radial Glia Cells (RGCs) that self- consume, or indirectly from RGCs
via Intermediate Progenitor Cells (IPCs) and largely preserving the RGC pool.
According to the standing model of cortical development, Direct Neurogenesis predominates
at early stages of development, and progressively shifts to Indirect Neurogenesis,
which predominates at late stages. However, neurogenesis at early stages should
be compatible with RGC amplification, and neurogenesis at late stages needs to
involve RGC consumption, which seems in conflict with the standing model. Here
we studied the modes of neurogenesis along cortical development using multiple
approaches, including birthdating, live imaging and MADM clone labeling. Contrary
to the established dogma, our data show that Indirect Neurogenesis clearly predominates
at early developmental stages, gradually shifting to Direct Neurogenesis at late
stages. These findings challenge the current model of cortical neurogenesis, and
prompt a re-evaluation of previous and ongoing work about the genetic and molecular
mechanisms regulating this process.
acknowledgement: "We thank A. Iñigo for assistance with imaging, and members of the
Borrell and Herrera labs for\r\ninsightful discussions and critical reading of the
manuscript. Funding to our lab members was\r\nprovided by the Spanish Research Agency
(AEI): FPI contract (BES-2016-077737) to L.dV.A., FPI SO contract (SEV-2017-0723-18-1)
to A.E., JdC-Incorporación contract (IJC2020-044653-I) to V.F., and JAE-Intro fellowship
(JAEICU23EX_0071) to I.C., as well as by La Caixa Foundation: La Caixa-Severo Ochoa
fellowship (E-03-2016-0557140) to S.A., INPhINIT-Retaining fellowship (LCF/BQ/DR21/11880012)
to E.F.O., INPhINIT-Incoming fellowship (LCF/BQ/DI22/11940006) to E.N., and Junior
Leader-Retaining grant to A.C. (LCF/BQ/PR23/11980051). Work was supported by grants
from FWF (SFB F78) to S.H.; AEI (PID2021-125618NB-I00) and European Research Council
(101118729) to V.B., who also acknowledges financial support from AEI through the
“Severo Ochoa” Programme for Centers of Excellence in R&D (CEX2021-001165-S)."
article_processing_charge: No
author:
- first_name: Adrián
full_name: Cárdenas, Adrián
last_name: Cárdenas
- first_name: Irem
full_name: Çelik, Irem
last_name: Çelik
- first_name: Alexandre
full_name: Espinós, Alexandre
last_name: Espinós
- first_name: Carmen
full_name: Streicher, Carmen
id: 36BCB99C-F248-11E8-B48F-1D18A9856A87
last_name: Streicher
- first_name: Lara
full_name: López-González, Lara
last_name: López-González
- first_name: Lucia
full_name: del-Valle-Anton, Lucia
last_name: del-Valle-Anton
- first_name: Virginia
full_name: Fernández, Virginia
last_name: Fernández
- first_name: Salma
full_name: Amin, Salma
last_name: Amin
- first_name: Enrico
full_name: Negri, Enrico
last_name: Negri
- first_name: Eduardo Fernández
full_name: Ortuño, Eduardo Fernández
last_name: Ortuño
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Víctor
full_name: Borrell, Víctor
last_name: Borrell
biorxivid: 1
citation:
ama: Cárdenas A, Çelik I, Espinós A, et al. Early indirect neurogenesis transitions
to late direct neurogenesis in mouse cerebral cortex development. bioRxiv.
doi:10.1101/2025.05.22.655488
apa: Cárdenas, A., Çelik, I., Espinós, A., Streicher, C., López-González, L., del-Valle-Anton,
L., … Borrell, V. (n.d.). Early indirect neurogenesis transitions to late direct
neurogenesis in mouse cerebral cortex development. bioRxiv. https://doi.org/10.1101/2025.05.22.655488
chicago: Cárdenas, Adrián, Irem Çelik, Alexandre Espinós, Carmen Streicher, Lara
López-González, Lucia del-Valle-Anton, Virginia Fernández, et al. “Early Indirect
Neurogenesis Transitions to Late Direct Neurogenesis in Mouse Cerebral Cortex
Development.” BioRxiv, n.d. https://doi.org/10.1101/2025.05.22.655488.
ieee: A. Cárdenas et al., “Early indirect neurogenesis transitions to late
direct neurogenesis in mouse cerebral cortex development,” bioRxiv. .
ista: Cárdenas A, Çelik I, Espinós A, Streicher C, López-González L, del-Valle-Anton
L, Fernández V, Amin S, Negri E, Ortuño EF, Hippenmeyer S, Borrell V. Early indirect
neurogenesis transitions to late direct neurogenesis in mouse cerebral cortex
development. bioRxiv, 10.1101/2025.05.22.655488.
mla: Cárdenas, Adrián, et al. “Early Indirect Neurogenesis Transitions to Late Direct
Neurogenesis in Mouse Cerebral Cortex Development.” BioRxiv, doi:10.1101/2025.05.22.655488.
short: A. Cárdenas, I. Çelik, A. Espinós, C. Streicher, L. López-González, L. del-Valle-Anton,
V. Fernández, S. Amin, E. Negri, E.F. Ortuño, S. Hippenmeyer, V. Borrell, BioRxiv
(n.d.).
date_created: 2025-05-29T10:45:55Z
date_published: 2025-05-23T00:00:00Z
date_updated: 2026-08-13T07:18:38Z
day: '23'
department:
- _id: SiHi
doi: 10.1101/2025.05.22.655488
external_id:
biorxivid:
- 10.1101/2025.05.22.655488
fulldoi: https://doi.org/10.1101/2025.05.22.655488
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2025.05.22.655488
month: '05'
oa: 1
oa_version: Preprint
project:
- _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E
grant_number: F7805
name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular
Mechanisms of Neural Stem Cell Lineage Progression
publication: bioRxiv
publication_status: submitted
status: public
title: Early indirect neurogenesis transitions to late direct neurogenesis in mouse
cerebral cortex development
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '19717'
abstract:
- lang: eng
text: Radial glial progenitors (RGPs) generate all projection neurons (PNs) in the
cerebral cortex through incompletely understood processes. Herein, we combine
Mosaic Analysis with Double Markers (MADM)-based clonal analysis at embryonic
days 12.5 and 13.5 with early postnatal callosal tracing to reveal a lineage progression
that challenges the inside-outside model of cortical development and the conventional
view of an invariable sequence of asymmetric neurogenic divisions. Our data demonstrate
that early multipotent RGPs generate all extra-telencephalic (ET) and intra-telencephalic
(IT) PNs across all layers through parallel sublineages and the random specification,
during the earliest neurogenic divisions, of fate-restricted daughter RGPs. While
the neuronal production of the parental multipotent RGPs consists of small ET-PN
or IT-PN outputs, fate-restricted RGPs produce larger translaminar outputs spanning
deep and upper layers of only IT-PNs, the predominant mammalian PN subtype. We
further show that the emergence of IT-PN fate-restricted RGPs also leads to quantitatively
and temporally stereotyped neurogenesis population-wise.
acknowledgement: "We thank M. Caouyette for the plasmid construction for Pou3f1 overexpression;
C. Varela747 Martínez for help with the code for graphical analysis; all members
from the Nieto’s lab for\r\ncomment on the manuscript, specially to F. Martín for
the insightful discussions;J.C. Oliveros\r\nand J.A. García from the computational
service of the CNB for help with the analysis of\r\nRNAseq dataset, C.O. Sorzano
for the help with statistical analysis, and the service of\r\nAdvance Optical Microscopy
of the CNB for their technical advice.\r\nI.V.M holds a fellowship funded by MCICIU
(PRE-2018-083376), the work was funded by\r\nPID2020-112831GB-I00 funded by MCIN/AEI
/10.13039/501100011033.\r\n"
article_processing_charge: No
author:
- first_name: I
full_name: Varela-Martínez, I
last_name: Varela-Martínez
- first_name: Ana
full_name: Villalba Requena, Ana
id: 68cb85a0-39f7-11eb-9559-9aaab4f6a247
last_name: Villalba Requena
orcid: 0000-0002-5615-5277
- first_name: J.
full_name: Garcia-Marqués, J.
last_name: Garcia-Marqués
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: M.
full_name: Nieto, M.
last_name: Nieto
citation:
ama: Varela-Martínez I, Villalba Requena A, Garcia-Marqués J, Hippenmeyer S, Nieto
M. Early emergence of projection-subtype fate-restricted radial glial progenitors
orchestrates neocortical neurogenesis. bioRxiv. doi:10.1101/2025.05.07.652665
apa: Varela-Martínez, I., Villalba Requena, A., Garcia-Marqués, J., Hippenmeyer,
S., & Nieto, M. (n.d.). Early emergence of projection-subtype fate-restricted
radial glial progenitors orchestrates neocortical neurogenesis. bioRxiv.
https://doi.org/10.1101/2025.05.07.652665
chicago: Varela-Martínez, I, Ana Villalba Requena, J. Garcia-Marqués, Simon Hippenmeyer,
and M. Nieto. “Early Emergence of Projection-Subtype Fate-Restricted Radial Glial
Progenitors Orchestrates Neocortical Neurogenesis.” BioRxiv, n.d. https://doi.org/10.1101/2025.05.07.652665.
ieee: I. Varela-Martínez, A. Villalba Requena, J. Garcia-Marqués, S. Hippenmeyer,
and M. Nieto, “Early emergence of projection-subtype fate-restricted radial glial
progenitors orchestrates neocortical neurogenesis,” bioRxiv. .
ista: Varela-Martínez I, Villalba Requena A, Garcia-Marqués J, Hippenmeyer S, Nieto
M. Early emergence of projection-subtype fate-restricted radial glial progenitors
orchestrates neocortical neurogenesis. bioRxiv, 10.1101/2025.05.07.652665.
mla: Varela-Martínez, I., et al. “Early Emergence of Projection-Subtype Fate-Restricted
Radial Glial Progenitors Orchestrates Neocortical Neurogenesis.” BioRxiv,
doi:10.1101/2025.05.07.652665.
short: I. Varela-Martínez, A. Villalba Requena, J. Garcia-Marqués, S. Hippenmeyer,
M. Nieto, BioRxiv (n.d.).
date_created: 2025-05-20T10:19:29Z
date_published: 2025-05-07T00:00:00Z
date_updated: 2026-08-13T07:16:48Z
day: '07'
department:
- _id: SiHi
doi: 10.1101/2025.05.07.652665
fulldoi: https://doi.org/10.1101/2025.05.07.652665
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2025.05.07.652665
month: '05'
oa: 1
oa_version: Preprint
publication: bioRxiv
publication_status: submitted
status: public
title: Early emergence of projection-subtype fate-restricted radial glial progenitors
orchestrates neocortical neurogenesis
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...