---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18820'
abstract:
- lang: eng
  text: 'Feature selection is essential in the analysis of molecular systems and many
    other fields, but several uncertainties remain: What is the optimal number of
    features for a simplified, interpretable model that retains essential information?
    How should features with different units be aligned, and how should their relative
    importance be weighted? Here, we introduce the Differentiable Information Imbalance
    (DII), an automated method to rank information content between sets of features.
    Using distances in a ground truth feature space, DII identifies a low-dimensional
    subset of features that best preserves these relationships. Each feature is scaled
    by a weight, which is optimized by minimizing the DII through gradient descent.
    This allows simultaneously performing unit alignment and relative importance scaling,
    while preserving interpretability. DII can also produce sparse solutions and determine
    the optimal size of the reduced feature space. We demonstrate the usefulness of
    this approach on two benchmark molecular problems: (1) identifying collective
    variables that describe conformations of a biomolecule, and (2) selecting features
    for training a machine-learning force field. These results show the potential
    of DII in addressing feature selection challenges and optimizing dimensionality
    in various applications. The method is available in the Python library DADApy.'
acknowledgement: The authors thank Dr. Matteo Carli for providing the CLN025 replica
  exchange MD trajectory and Matteo Allione for the fruitful discussions connected
  with the idea of the linear scaling estimator. This work was partially funded by
  NextGenerationEU through the Italian National Centre for HPC, Big Data, and Quantum
  Computing (Grant No. CN00000013 received by A.L.). A.L. also acknowledges financial
  support by the region Friuli Venezia Giulia (project F53C22001770002 received by
  A.L.).
article_number: '270'
article_processing_charge: Yes
article_type: original
author:
- first_name: Romina
  full_name: Wild, Romina
  last_name: Wild
- first_name: Felix
  full_name: Wodaczek, Felix
  id: 8b4b6a9f-32b0-11ee-9fa8-bbe85e26258e
  last_name: Wodaczek
  orcid: 0009-0000-1457-795X
- first_name: Vittorio
  full_name: Del Tatto, Vittorio
  last_name: Del Tatto
- first_name: Bingqing
  full_name: Cheng, Bingqing
  id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
  last_name: Cheng
  orcid: 0000-0002-3584-9632
- first_name: Alessandro
  full_name: Laio, Alessandro
  last_name: Laio
citation:
  ama: Wild R, Wodaczek F, Del Tatto V, Cheng B, Laio A. Automatic feature selection
    and weighting in molecular systems using Differentiable Information Imbalance.
    <i>Nature Communications</i>. 2025;16. doi:<a href="https://doi.org/10.1038/s41467-024-55449-7">10.1038/s41467-024-55449-7</a>
  apa: Wild, R., Wodaczek, F., Del Tatto, V., Cheng, B., &#38; Laio, A. (2025). Automatic
    feature selection and weighting in molecular systems using Differentiable Information
    Imbalance. <i>Nature Communications</i>. Springer Nature. <a href="https://doi.org/10.1038/s41467-024-55449-7">https://doi.org/10.1038/s41467-024-55449-7</a>
  chicago: Wild, Romina, Felix Wodaczek, Vittorio Del Tatto, Bingqing Cheng, and Alessandro
    Laio. “Automatic Feature Selection and Weighting in Molecular Systems Using Differentiable
    Information Imbalance.” <i>Nature Communications</i>. Springer Nature, 2025. <a
    href="https://doi.org/10.1038/s41467-024-55449-7">https://doi.org/10.1038/s41467-024-55449-7</a>.
  ieee: R. Wild, F. Wodaczek, V. Del Tatto, B. Cheng, and A. Laio, “Automatic feature
    selection and weighting in molecular systems using Differentiable Information
    Imbalance,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025.
  ista: Wild R, Wodaczek F, Del Tatto V, Cheng B, Laio A. 2025. Automatic feature
    selection and weighting in molecular systems using Differentiable Information
    Imbalance. Nature Communications. 16, 270.
  mla: Wild, Romina, et al. “Automatic Feature Selection and Weighting in Molecular
    Systems Using Differentiable Information Imbalance.” <i>Nature Communications</i>,
    vol. 16, 270, Springer Nature, 2025, doi:<a href="https://doi.org/10.1038/s41467-024-55449-7">10.1038/s41467-024-55449-7</a>.
  short: R. Wild, F. Wodaczek, V. Del Tatto, B. Cheng, A. Laio, Nature Communications
    16 (2025).
date_created: 2025-01-12T23:04:00Z
date_published: 2025-01-02T00:00:00Z
date_updated: 2025-02-27T12:41:25Z
day: '02'
ddc:
- '570'
department:
- _id: AnSa
- _id: BiCh
doi: 10.1038/s41467-024-55449-7
external_id:
  isi:
  - '001389959100009'
  pmid:
  - '39747013'
file:
- access_level: open_access
  checksum: b3d0f3568d9a87c494cf231a5324029a
  content_type: application/pdf
  creator: dernst
  date_created: 2025-01-14T06:59:25Z
  date_updated: 2025-01-14T06:59:25Z
  file_id: '18846'
  file_name: 2025_NatureComm_Wild.pdf
  file_size: 1216738
  relation: main_file
  success: 1
file_date_updated: 2025-01-14T06:59:25Z
has_accepted_license: '1'
intvolume: '        16'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
  eissn:
  - 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Automatic feature selection and weighting in molecular systems using Differentiable
  Information Imbalance
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '18821'
abstract:
- lang: eng
  text: 'Even though the one-dimensional contact interaction requires no regularization,
    renormalization methods have been shown to improve the convergence of numerical
    calculations considerably. In this work, we compare and contrast these methods:
    “the running coupling constant” where the two-body ground-state energy is used
    as a renormalization condition, and two effective interaction approaches that
    include information about the ground as well as excited states. In particular,
    we calculate the energies and densities of few-fermion systems in a harmonic oscillator
    with the configuration-interaction method and compare the results based upon renormalized
    and bare interactions. We find that the use of the running coupling constant instead
    of the bare interaction improves convergence significantly. A comparison with
    an effective interaction, which is designed to reproduce the relative part of
    the energy spectrum of two particles, showed a similar improvement. The effective
    interaction provides an additional improvement if the center-of-mass excitations
    are included in the construction. Finally, we discuss the transformation of observables
    alongside the renormalization of the potential, and demonstrate that this might
    be an essential ingredient for accurate numerical calculations.'
acknowledgement: We thank J. Cremon and J. Bjerlin for earlier contributions to the
  configuration-interaction calculations used in this work (see Refs. [49,50]). F.B.
  and S.M.R. acknowledge helpful discussions with Carl Heintze, Sandra Brandstetter,
  and Lila Chergui. We further want to thank Lila Chergui for helpful comments on
  the paper. This research was financially supported by the Knut and Alice Wallenberg
  Foundation (Grant No. KAW 2018.0217) and the Swedish Research Council (Grant No.
  2022-03654 VR).
article_number: '013303'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Fabian
  full_name: Brauneis, Fabian
  last_name: Brauneis
- first_name: Hans Werner
  full_name: Hammer, Hans Werner
  last_name: Hammer
- first_name: Stephanie M.
  full_name: Reimann, Stephanie M.
  last_name: Reimann
- first_name: Artem
  full_name: Volosniev, Artem
  id: 37D278BC-F248-11E8-B48F-1D18A9856A87
  last_name: Volosniev
  orcid: 0000-0003-0393-5525
citation:
  ama: Brauneis F, Hammer HW, Reimann SM, Volosniev A. Comparison of renormalized
    interactions using one-dimensional few-body systems as a testbed. <i>Physical
    Review A</i>. 2025;111(1). doi:<a href="https://doi.org/10.1103/PhysRevA.111.013303">10.1103/PhysRevA.111.013303</a>
  apa: Brauneis, F., Hammer, H. W., Reimann, S. M., &#38; Volosniev, A. (2025). Comparison
    of renormalized interactions using one-dimensional few-body systems as a testbed.
    <i>Physical Review A</i>. American Physical Society. <a href="https://doi.org/10.1103/PhysRevA.111.013303">https://doi.org/10.1103/PhysRevA.111.013303</a>
  chicago: Brauneis, Fabian, Hans Werner Hammer, Stephanie M. Reimann, and Artem Volosniev.
    “Comparison of Renormalized Interactions Using One-Dimensional Few-Body Systems
    as a Testbed.” <i>Physical Review A</i>. American Physical Society, 2025. <a href="https://doi.org/10.1103/PhysRevA.111.013303">https://doi.org/10.1103/PhysRevA.111.013303</a>.
  ieee: F. Brauneis, H. W. Hammer, S. M. Reimann, and A. Volosniev, “Comparison of
    renormalized interactions using one-dimensional few-body systems as a testbed,”
    <i>Physical Review A</i>, vol. 111, no. 1. American Physical Society, 2025.
  ista: Brauneis F, Hammer HW, Reimann SM, Volosniev A. 2025. Comparison of renormalized
    interactions using one-dimensional few-body systems as a testbed. Physical Review
    A. 111(1), 013303.
  mla: Brauneis, Fabian, et al. “Comparison of Renormalized Interactions Using One-Dimensional
    Few-Body Systems as a Testbed.” <i>Physical Review A</i>, vol. 111, no. 1, 013303,
    American Physical Society, 2025, doi:<a href="https://doi.org/10.1103/PhysRevA.111.013303">10.1103/PhysRevA.111.013303</a>.
  short: F. Brauneis, H.W. Hammer, S.M. Reimann, A. Volosniev, Physical Review A 111
    (2025).
date_created: 2025-01-12T23:04:00Z
date_published: 2025-01-03T00:00:00Z
date_updated: 2025-02-27T12:41:58Z
day: '03'
department:
- _id: MiLe
doi: 10.1103/PhysRevA.111.013303
external_id:
  arxiv:
  - '2408.10052'
  isi:
  - '001398791400004'
intvolume: '       111'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: ' https://doi.org/10.48550/arXiv.2408.10052'
month: '01'
oa: 1
oa_version: Preprint
publication: Physical Review A
publication_identifier:
  eissn:
  - 2469-9934
  issn:
  - 2469-9926
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Comparison of renormalized interactions using one-dimensional few-body systems
  as a testbed
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 111
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18822'
abstract:
- lang: eng
  text: Let N(X) be the number of integral zeros (mathematical equation). Works of
    Hooley and Heath-Brown imply (mathematical equation), if one assumes automorphy
    and grand Riemann hypothesis for certain Hasse–Weil L-functions. Assuming instead
    a natural large sieve inequality, we recover the same bound on N(X). This is part
    of a more general statement, for diagonal cubic forms in (mathematical equation)
    variables, where we allow approximations to Hasse–Weil L-functions.
acknowledgement: I thank Peter Sarnak for suggesting projects that ultimately led
  to the present paper. I also thank him for many encouraging discussions, helpful
  comments, and references. Thanks also to Tim Browning, Trevor Wooley, and Nina Zubrilina
  for helpful comments, and to Levent Alpöge and Will Sawin for some interesting old
  discussions. I thank Yang Liu, Evan O'Dorney, Ashwin Sah, and Mark Sellke for conversations
  illuminating the combinatorics of an older, counting version of the present Lemma
  4.9. Finally, special thanks are due to the editors and referees for their patience
  and help with the exposition. This work was partially supported by NSF Grant DMS-1802211,
  and the European Union's Horizon 2020 research and innovation program under the
  Marie Skłodowska-Curie Grant Agreement No. 101034413.
article_number: e70008
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Victor
  full_name: Wang, Victor
  id: 76096395-aea4-11ed-a680-ab8ebbd3f1b9
  last_name: Wang
  orcid: 0000-0002-0704-7026
citation:
  ama: Wang V. Diagonal cubic forms and the large sieve. <i>Mathematika</i>. 2025;71(1).
    doi:<a href="https://doi.org/10.1112/mtk.70008">10.1112/mtk.70008</a>
  apa: Wang, V. (2025). Diagonal cubic forms and the large sieve. <i>Mathematika</i>.
    London Mathematical Society. <a href="https://doi.org/10.1112/mtk.70008">https://doi.org/10.1112/mtk.70008</a>
  chicago: Wang, Victor. “Diagonal Cubic Forms and the Large Sieve.” <i>Mathematika</i>.
    London Mathematical Society, 2025. <a href="https://doi.org/10.1112/mtk.70008">https://doi.org/10.1112/mtk.70008</a>.
  ieee: V. Wang, “Diagonal cubic forms and the large sieve,” <i>Mathematika</i>, vol.
    71, no. 1. London Mathematical Society, 2025.
  ista: Wang V. 2025. Diagonal cubic forms and the large sieve. Mathematika. 71(1),
    e70008.
  mla: Wang, Victor. “Diagonal Cubic Forms and the Large Sieve.” <i>Mathematika</i>,
    vol. 71, no. 1, e70008, London Mathematical Society, 2025, doi:<a href="https://doi.org/10.1112/mtk.70008">10.1112/mtk.70008</a>.
  short: V. Wang, Mathematika 71 (2025).
corr_author: '1'
date_created: 2025-01-12T23:04:01Z
date_published: 2025-01-02T00:00:00Z
date_updated: 2025-04-14T07:54:56Z
day: '02'
ddc:
- '510'
department:
- _id: TiBr
doi: 10.1112/mtk.70008
ec_funded: 1
external_id:
  isi:
  - '001388255500001'
file:
- access_level: open_access
  checksum: 700a8596b4bffce2320d074120962c22
  content_type: application/pdf
  creator: dernst
  date_created: 2025-01-14T06:52:09Z
  date_updated: 2025-01-14T06:52:09Z
  file_id: '18845'
  file_name: 2025_Mathematika_Wang.pdf
  file_size: 309893
  relation: main_file
  success: 1
file_date_updated: 2025-01-14T06:52:09Z
has_accepted_license: '1'
intvolume: '        71'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
  call_identifier: H2020
  grant_number: '101034413'
  name: 'IST-BRIDGE: International postdoctoral program'
publication: Mathematika
publication_identifier:
  eissn:
  - 2041-7942
  issn:
  - 0025-5793
publication_status: published
publisher: London Mathematical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Diagonal cubic forms and the large sieve
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: 71
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18823'
article_number: kiae651
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Dechang
  full_name: Cao, Dechang
  last_name: Cao
- first_name: Joke G
  full_name: De Jaeger-Braet, Joke G
  id: 26bd38d3-c59a-11ee-a1af-d7a988cafcc5
  last_name: De Jaeger-Braet
citation:
  ama: 'Cao D, De Jaeger-Braet JG. Memory of maternal temperatures: DNA methylation
    alterations across generations. <i>Plant Physiology</i>. 2025;197(1). doi:<a href="https://doi.org/10.1093/plphys/kiae651">10.1093/plphys/kiae651</a>'
  apa: 'Cao, D., &#38; De Jaeger-Braet, J. G. (2025). Memory of maternal temperatures:
    DNA methylation alterations across generations. <i>Plant Physiology</i>. Oxford
    University Press. <a href="https://doi.org/10.1093/plphys/kiae651">https://doi.org/10.1093/plphys/kiae651</a>'
  chicago: 'Cao, Dechang, and Joke G De Jaeger-Braet. “Memory of Maternal Temperatures:
    DNA Methylation Alterations across Generations.” <i>Plant Physiology</i>. Oxford
    University Press, 2025. <a href="https://doi.org/10.1093/plphys/kiae651">https://doi.org/10.1093/plphys/kiae651</a>.'
  ieee: 'D. Cao and J. G. De Jaeger-Braet, “Memory of maternal temperatures: DNA methylation
    alterations across generations,” <i>Plant Physiology</i>, vol. 197, no. 1. Oxford
    University Press, 2025.'
  ista: 'Cao D, De Jaeger-Braet JG. 2025. Memory of maternal temperatures: DNA methylation
    alterations across generations. Plant Physiology. 197(1), kiae651.'
  mla: 'Cao, Dechang, and Joke G. De Jaeger-Braet. “Memory of Maternal Temperatures:
    DNA Methylation Alterations across Generations.” <i>Plant Physiology</i>, vol.
    197, no. 1, kiae651, Oxford University Press, 2025, doi:<a href="https://doi.org/10.1093/plphys/kiae651">10.1093/plphys/kiae651</a>.'
  short: D. Cao, J.G. De Jaeger-Braet, Plant Physiology 197 (2025).
corr_author: '1'
date_created: 2025-01-12T23:04:02Z
date_published: 2025-01-01T00:00:00Z
date_updated: 2025-07-15T08:18:19Z
day: '01'
ddc:
- '580'
department:
- _id: XiFe
doi: 10.1093/plphys/kiae651
external_id:
  isi:
  - '001382979900001'
  pmid:
  - '39691053'
file:
- access_level: open_access
  checksum: a9b2a12d7bc6174f27e28413e9c77a9c
  content_type: application/pdf
  creator: dernst
  date_created: 2025-07-15T08:17:25Z
  date_updated: 2025-07-15T08:17:25Z
  file_id: '20023'
  file_name: 2025_PlantPhysiology_Cao.pdf
  file_size: 1214018
  relation: main_file
  success: 1
file_date_updated: 2025-07-15T08:17:25Z
has_accepted_license: '1'
intvolume: '       197'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Plant Physiology
publication_identifier:
  eissn:
  - 1532-2548
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Memory of maternal temperatures: DNA methylation alterations across generations'
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: 197
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18848'
abstract:
- lang: eng
  text: Type II CRISPR endonucleases are widely used programmable genome editing tools.
    Recently, CRISPR-Cas systems with highly compact nucleases have been discovered,
    including Cas9d (a type II-D nuclease). Here, we report the cryo-EM structures
    of a Cas9d nuclease (747 amino acids in length) in multiple functional states,
    revealing a stepwise process of DNA targeting involving a conformational switch
    in a REC2 domain insertion. Our structures provide insights into the intricately
    folded guide RNA which acts as a structural scaffold to anchor small, flexible
    protein domains for DNA recognition. The sgRNA can be truncated by up to ~25%
    yet still retain activity in vivo. Using ancestral sequence reconstruction, we
    generated compact nucleases capable of efficient genome editing in mammalian cells.
    Collectively, our results provide mechanistic insights into the evolution and
    DNA targeting of diverse type II CRISPR-Cas systems, providing a blueprint for
    future re-engineering of minimal RNA-guided DNA endonucleases.
acknowledgement: We would like to thank M. Ocampo Camacho and M.F. Canedo Ocampo for
  assistance with the figures. We thank M. Hooper for assistance developing the GFP
  assay and operating the CE machine for in vitro cleavage analysis. We thank E. Schwartz
  and A. Brilot for expert cryo-EM support in the Sauer Structural Biology Laboratory
  at UT Austin. This work was funded, in part, by a sponsored research agreement with
  Metagenomi, Inc. (to D.W.T), a Welch Foundation Research Grant F-1938 (to D.W.T),
  and the Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation Medical Research
  Grant (to D.W.T), and a grant from the National Institute of Allergy and Infectious
  Diseases (NIAID 1R01AI110577 to K.A.J.).
article_number: '457'
article_processing_charge: Yes
article_type: original
author:
- first_name: Rodrigo Fregoso
  full_name: Ocampo, Rodrigo Fregoso
  last_name: Ocampo
- first_name: Jack Peter Kelly
  full_name: Bravo, Jack Peter Kelly
  id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e
  last_name: Bravo
  orcid: 0000-0003-0456-0753
- first_name: Tyler L.
  full_name: Dangerfield, Tyler L.
  last_name: Dangerfield
- first_name: Isabel
  full_name: Nocedal, Isabel
  last_name: Nocedal
- first_name: Samatar A.
  full_name: Jirde, Samatar A.
  last_name: Jirde
- first_name: Lisa M.
  full_name: Alexander, Lisa M.
  last_name: Alexander
- first_name: Nicole C.
  full_name: Thomas, Nicole C.
  last_name: Thomas
- first_name: Anjali
  full_name: Das, Anjali
  last_name: Das
- first_name: Sarah
  full_name: Nielson, Sarah
  last_name: Nielson
- first_name: Kenneth A.
  full_name: Johnson, Kenneth A.
  last_name: Johnson
- first_name: Christopher T.
  full_name: Brown, Christopher T.
  last_name: Brown
- first_name: Cristina N.
  full_name: Butterfield, Cristina N.
  last_name: Butterfield
- first_name: Daniela S.A.
  full_name: Goltsman, Daniela S.A.
  last_name: Goltsman
- first_name: David W.
  full_name: Taylor, David W.
  last_name: Taylor
citation:
  ama: Ocampo RF, Bravo JPK, Dangerfield TL, et al. DNA targeting by compact Cas9d
    and its resurrected ancestor. <i>Nature Communications</i>. 2025;16. doi:<a href="https://doi.org/10.1038/s41467-024-55573-4">10.1038/s41467-024-55573-4</a>
  apa: Ocampo, R. F., Bravo, J. P. K., Dangerfield, T. L., Nocedal, I., Jirde, S.
    A., Alexander, L. M., … Taylor, D. W. (2025). DNA targeting by compact Cas9d and
    its resurrected ancestor. <i>Nature Communications</i>. Springer Nature. <a href="https://doi.org/10.1038/s41467-024-55573-4">https://doi.org/10.1038/s41467-024-55573-4</a>
  chicago: Ocampo, Rodrigo Fregoso, Jack Peter Kelly Bravo, Tyler L. Dangerfield,
    Isabel Nocedal, Samatar A. Jirde, Lisa M. Alexander, Nicole C. Thomas, et al.
    “DNA Targeting by Compact Cas9d and Its Resurrected Ancestor.” <i>Nature Communications</i>.
    Springer Nature, 2025. <a href="https://doi.org/10.1038/s41467-024-55573-4">https://doi.org/10.1038/s41467-024-55573-4</a>.
  ieee: R. F. Ocampo <i>et al.</i>, “DNA targeting by compact Cas9d and its resurrected
    ancestor,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025.
  ista: Ocampo RF, Bravo JPK, Dangerfield TL, Nocedal I, Jirde SA, Alexander LM, Thomas
    NC, Das A, Nielson S, Johnson KA, Brown CT, Butterfield CN, Goltsman DSA, Taylor
    DW. 2025. DNA targeting by compact Cas9d and its resurrected ancestor. Nature
    Communications. 16, 457.
  mla: Ocampo, Rodrigo Fregoso, et al. “DNA Targeting by Compact Cas9d and Its Resurrected
    Ancestor.” <i>Nature Communications</i>, vol. 16, 457, Springer Nature, 2025,
    doi:<a href="https://doi.org/10.1038/s41467-024-55573-4">10.1038/s41467-024-55573-4</a>.
  short: R.F. Ocampo, J.P.K. Bravo, T.L. Dangerfield, I. Nocedal, S.A. Jirde, L.M.
    Alexander, N.C. Thomas, A. Das, S. Nielson, K.A. Johnson, C.T. Brown, C.N. Butterfield,
    D.S.A. Goltsman, D.W. Taylor, Nature Communications 16 (2025).
date_created: 2025-01-19T23:01:50Z
date_published: 2025-01-07T00:00:00Z
date_updated: 2025-07-03T11:58:22Z
day: '07'
ddc:
- '570'
department:
- _id: JaBr
doi: 10.1038/s41467-024-55573-4
external_id:
  pmid:
  - '39774105'
file:
- access_level: open_access
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  creator: dernst
  date_created: 2025-01-22T14:35:22Z
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oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
  eissn:
  - 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA targeting by compact Cas9d and its resurrected ancestor
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: 16
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18849'
abstract:
- lang: eng
  text: Many biological systems operate near the physical limits to their performance,
    suggesting that aspects of their behavior and underlying mechanisms could be derived
    from optimization principles. However, such principles have often been applied
    only in simplified models. Here, we explore a detailed mechanistic model of the
    gap gene network in the Drosophila embryo, optimizing its 50+ parameters to maximize
    the information that gene expression levels provide about nuclear positions. This
    optimization is conducted under realistic constraints, such as limits on the number
    of available molecules. Remarkably, the optimal networks we derive closely match
    the architecture and spatial gene expression profiles observed in the real organism.
    Our framework quantifies the tradeoffs involved in maximizing functional performance
    and allows for the exploration of alternative network configurations, addressing
    the question of which features are necessary and which are contingent. Our results
    suggest that multiple solutions to the optimization problem might exist across
    closely related organisms, offering insights into the evolution of gene regulatory
    networks.
acknowledgement: We thank Nicholas H. Barton for his comments on the manuscript, Benjamin
  Zoller for helpful discussions, and Aleksandra Walczak and Curtis Callan for early
  collaborations that shaped this work. Special thanks to Eric F. Wieschaus for many
  persistently inspiring conversations. This work was supported in part by the Human
  Frontiers Science Program; the Austrian Science Fund (FWF P28844); by the European
  Research Council grant DynaTrans (101118866); by U.S. NSF, through the Center for
  the Physics of Biological Function (PHY–1734030); by NIH Grants R01GM097275, U01DA047730,
  and U01DK127429; by the John Simon Guggenheim Memorial Foundation; and by the LOEWE
  priority program “Center for Multiscale Modeling in Life Sciences” (CMMS), sponsored
  by the Hessian Ministry for Science and Research, Arts and Culture (HMWK).
article_number: e2402925121
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Thomas R
  full_name: Sokolowski, Thomas R
  id: 3E999752-F248-11E8-B48F-1D18A9856A87
  last_name: Sokolowski
  orcid: 0000-0002-1287-3779
- first_name: Thomas
  full_name: Gregor, Thomas
  last_name: Gregor
- first_name: William
  full_name: Bialek, William
  last_name: Bialek
- first_name: Gašper
  full_name: Tkačik, Gašper
  id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
  last_name: Tkačik
  orcid: 0000-0002-6699-1455
citation:
  ama: Sokolowski TR, Gregor T, Bialek W, Tkačik G. Deriving a genetic regulatory
    network from an optimization principle. <i>Proceedings of the National Academy
    of Sciences</i>. 2025;122(1). doi:<a href="https://doi.org/10.1073/pnas.2402925121">10.1073/pnas.2402925121</a>
  apa: Sokolowski, T. R., Gregor, T., Bialek, W., &#38; Tkačik, G. (2025). Deriving
    a genetic regulatory network from an optimization principle. <i>Proceedings of
    the National Academy of Sciences</i>. National Academy of Sciences. <a href="https://doi.org/10.1073/pnas.2402925121">https://doi.org/10.1073/pnas.2402925121</a>
  chicago: Sokolowski, Thomas R, Thomas Gregor, William Bialek, and Gašper Tkačik.
    “Deriving a Genetic Regulatory Network from an Optimization Principle.” <i>Proceedings
    of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a
    href="https://doi.org/10.1073/pnas.2402925121">https://doi.org/10.1073/pnas.2402925121</a>.
  ieee: T. R. Sokolowski, T. Gregor, W. Bialek, and G. Tkačik, “Deriving a genetic
    regulatory network from an optimization principle,” <i>Proceedings of the National
    Academy of Sciences</i>, vol. 122, no. 1. National Academy of Sciences, 2025.
  ista: Sokolowski TR, Gregor T, Bialek W, Tkačik G. 2025. Deriving a genetic regulatory
    network from an optimization principle. Proceedings of the National Academy of
    Sciences. 122(1), e2402925121.
  mla: Sokolowski, Thomas R., et al. “Deriving a Genetic Regulatory Network from an
    Optimization Principle.” <i>Proceedings of the National Academy of Sciences</i>,
    vol. 122, no. 1, e2402925121, National Academy of Sciences, 2025, doi:<a href="https://doi.org/10.1073/pnas.2402925121">10.1073/pnas.2402925121</a>.
  short: T.R. Sokolowski, T. Gregor, W. Bialek, G. Tkačik, Proceedings of the National
    Academy of Sciences 122 (2025).
corr_author: '1'
date_created: 2025-01-19T23:01:50Z
date_published: 2025-01-07T00:00:00Z
date_updated: 2026-02-16T12:26:51Z
day: '07'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1073/pnas.2402925121
external_id:
  isi:
  - '001392772400001'
  pmid:
  - '39752518'
file:
- access_level: open_access
  checksum: 8dbfc7d495413340225ebfae69b0cf9a
  content_type: application/pdf
  creator: dernst
  date_created: 2025-01-20T10:10:04Z
  date_updated: 2025-01-20T10:10:04Z
  file_id: '18862'
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file_date_updated: 2025-01-20T10:10:04Z
has_accepted_license: '1'
intvolume: '       122'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _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: 2665AAFE-B435-11E9-9278-68D0E5697425
  grant_number: RGP0034/2018
  name: Can evolution minimize spurious signaling crosstalk to reach optimal performance?
publication: Proceedings of the National Academy of Sciences
publication_identifier:
  eissn:
  - 1091-6490
  issn:
  - 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Deriving a genetic regulatory network from an optimization principle
tmp:
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  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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 122
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18851'
abstract:
- lang: eng
  text: 'We present volume-limited samples of cataclysmic variables (CVs) and AM CVn
    binaries jointly selected from SRG/eROSITA eRASS1 and Gaia DR3 using an X-ray
    + optical color–color diagram (the "X-ray Main Sequence"). This tool identifies
    all CV subtypes, including magnetic and low-accretion rate systems, in contrast
    to most previous surveys. We find 23 CVs, 3 of which are AM CVns, out to 150 pc
    in the Western Galactic Hemisphere. Our 150 pc sample is spectroscopically verified
    and complete down to LX = 1.3 × 1029 erg s−1 in the 0.2–2.3 keV band, and we also
    present CV candidates out to 300 pc and 1000 pc. We discovered two previously
    unknown systems in our 150 pc sample: the third nearest AM CVn and a magnetic
    period bouncer. We find the mean LX of CVs to be 〈LX〉 ≈ 4.6 × 1030 erg s−1, in
    contrast to previous surveys which yielded 〈LX〉 ∼ 1031−1032 erg s−1. We construct
    X-ray luminosity functions that, for the first time, flatten out at LX ∼ 1030
    erg s−1. We infer average number, mass, and luminosity densities of ρN,CV = (3.7
    ± 0.7) × 10−6pc−3, (math formular), and (math formular), respectively, in the
    solar neighborhood. Our uniform selection method also allows us to place meaningful
    estimates on the space density of AM CVns, ρN,AM CVn = (5.5 ± 3.7) × 10−7 pc−3.
    Magnetic CVs and period bouncers make up 35% and 25% of our sample, respectively.
    This work, through a novel discovery technique, shows that the observed number
    densities of CVs and AM CVns, as well as the fraction of period bouncers, are
    still in tension with population synthesis estimates.'
acknowledgement: "We thank Roman Krivonos for insightful feedback, Kevin Burdge, Dovi
  Poznanski, and Jim Fuller for useful discussions, and Sunny Wong for providing AM
  CVn evolutionary models. A.C.R. acknowledges support from an NSF Graduate Fellowship.\r\n\r\nA.C.R.
  thanks the LSST-DA Data Science Fellowship Program, which is funded by LSST-DA,
  the Brinson Foundation, and the Moore Foundation; his participation in the program
  has benefited this work. RLO is a Research Fellow of the Brazilian institution CNPq
  (PQ-315632/2023-2).\r\n\r\nThis work is based on data from eROSITA, the soft X-ray
  instrument aboard SRG, a joint Russian-German science mission supported by the Russian
  Space Agency (Roskosmos), in the interests of the Russian Academy of Sciences represented
  by its Space Research Institute (IKI), and the Deutsches Zentrum für Luft- und Raumfahrt
  (DLR). The SRG spacecraft was built by Lavochkin Association (NPOL) and its subcontractors,
  and is operated by NPOL with support from the Max Planck Institute for Extraterrestrial
  Physics (MPE). The development and construction of the eROSITA X-ray instrument
  was led by MPE, with contributions from the Dr. Karl Remeis Observatory Bamberg
  & ECAP (FAU Erlangen-Nuernberg), the University of Hamburg Observatory, the Leibniz
  Institute for Astrophysics Potsdam (AIP), and the Institute for Astronomy and Astrophysics
  of the University of Tübingen, with the support of DLR and the Max Planck Society.
  The Argelander Institute for Astronomy of the University of Bonn and the Ludwig
  Maximilians Universität Munich also participated in the science preparation for
  eROSITA.\r\n\r\nThis work presents results from the European Space Agency (ESA)
  space mission Gaia. Gaia data are being processed by the Gaia Data Processing and
  Analysis Consortium (DPAC). Funding for the DPAC is provided by national institutions,
  in particular the institutions participating in the Gaia MultiLateral Agreement
  (MLA). The Gaia mission website is https://www.cosmos.esa.int/gaia. The Gaia archive
  website is https://archives.esac.esa.int/gaia.\r\n\r\nSome of the data presented
  herein were obtained at Keck Observatory, which is a private 501(c)3 non-profit
  organization operated as a scientific partnership among the California Institute
  of Technology, the University of California, and the National Aeronautics and Space
  Administration. The Observatory was made possible by the generous financial support
  of the W. M. Keck Foundation. The authors wish to recognize and acknowledge the
  very significant cultural role and reverence that the summit of Maunakea has always
  had within the Native Hawaiian community. We are most fortunate to have the opportunity
  to conduct observations from this mountain. We are also grateful to the staff of
  Palomar Observatory and that of Lick Observatory for their assistance in carrying
  out observations used in this work.\r\n\r\nBased on observations obtained with the
  Samuel Oschin Telescope 48 inch and the 60 inch Telescope at the Palomar Observatory
  as part of the Zwicky Transient Facility project. ZTF is supported by the National
  Science Foundation under grants No. AST-1440341 and AST-2034437 and a collaboration
  including current partners Caltech, IPAC, the Weizmann Institute of Science, the
  Oskar Klein Center at Stockholm University, the University of Maryland, Deutsches
  Elektronen-Synchrotron and Humboldt University, the TANGO Consortium of Taiwan,
  the University of Wisconsin at Milwaukee, Trinity College Dublin, Lawrence Livermore
  National Laboratories, IN2P3, University of Warwick, Ruhr University Bochum, Northwestern
  University and former partners the University of Washington, Los Alamos National
  Laboratories, and Lawrence Berkeley National Laboratories. Operations are conducted
  by COO, IPAC, and UW.\r\n\r\nSoftware: used: Python and the following libraries:
  matplotlib (Hunter 2007), scipy (Virtanen et al. 2020), astropy (Astropy Collaboration
  et al. 2013), numpy (van der Walt et al. 2011). PypeIt (Prochaska et al. 2020),
  lpipe (Perley 2019), and Tool for OPerations on Catalogues And Tables (TOPCAT) (Taylor
  2005)."
article_number: '014201'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Antonio C.
  full_name: Rodriguez, Antonio C.
  last_name: Rodriguez
- first_name: Kareem
  full_name: El-Badry, Kareem
  last_name: El-Badry
- first_name: Valery
  full_name: Suleimanov, Valery
  last_name: Suleimanov
- first_name: Anna F.
  full_name: Pala, Anna F.
  last_name: Pala
- first_name: Shrinivas R.
  full_name: Kulkarni, Shrinivas R.
  last_name: Kulkarni
- first_name: Boris
  full_name: Gaensicke, Boris
  last_name: Gaensicke
- first_name: Kaya
  full_name: Mori, Kaya
  last_name: Mori
- first_name: R. Michael
  full_name: Rich, R. Michael
  last_name: Rich
- first_name: Arnab
  full_name: Sarkar, Arnab
  last_name: Sarkar
- first_name: Tong
  full_name: Bao, Tong
  last_name: Bao
- first_name: Raimundo Lopes
  full_name: De Oliveira, Raimundo Lopes
  last_name: De Oliveira
- first_name: Gavin
  full_name: Ramsay, Gavin
  last_name: Ramsay
- first_name: Paula
  full_name: Szkody, Paula
  last_name: Szkody
- first_name: Matthew
  full_name: Graham, Matthew
  last_name: Graham
- first_name: Thomas A.
  full_name: Prince, Thomas A.
  last_name: Prince
- first_name: Ilaria
  full_name: Caiazzo, Ilaria
  id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d
  last_name: Caiazzo
  orcid: 0000-0002-4770-5388
- first_name: Zachary P.
  full_name: Vanderbosch, Zachary P.
  last_name: Vanderbosch
- first_name: Jan Van
  full_name: Roestel, Jan Van
  last_name: Roestel
- first_name: Kaustav K.
  full_name: Das, Kaustav K.
  last_name: Das
- first_name: Yu Jing
  full_name: Qin, Yu Jing
  last_name: Qin
- first_name: Mansi M.
  full_name: Kasliwal, Mansi M.
  last_name: Kasliwal
- first_name: Avery
  full_name: Wold, Avery
  last_name: Wold
- first_name: Steven L.
  full_name: Groom, Steven L.
  last_name: Groom
- first_name: Daniel
  full_name: Reiley, Daniel
  last_name: Reiley
- first_name: Reed
  full_name: Riddle, Reed
  last_name: Riddle
citation:
  ama: 'Rodriguez AC, El-Badry K, Suleimanov V, et al. Cataclysmic variables and AM
    CVn binaries in SRG/eROSITA + Gaia: Volume limited samples, X-ray luminosity functions,
    and space densities. <i>Publications of the Astronomical Society of the Pacific</i>.
    2025;137(1). doi:<a href="https://doi.org/10.1088/1538-3873/ada185">10.1088/1538-3873/ada185</a>'
  apa: 'Rodriguez, A. C., El-Badry, K., Suleimanov, V., Pala, A. F., Kulkarni, S.
    R., Gaensicke, B., … Riddle, R. (2025). Cataclysmic variables and AM CVn binaries
    in SRG/eROSITA + Gaia: Volume limited samples, X-ray luminosity functions, and
    space densities. <i>Publications of the Astronomical Society of the Pacific</i>.
    IOP Publishing. <a href="https://doi.org/10.1088/1538-3873/ada185">https://doi.org/10.1088/1538-3873/ada185</a>'
  chicago: 'Rodriguez, Antonio C., Kareem El-Badry, Valery Suleimanov, Anna F. Pala,
    Shrinivas R. Kulkarni, Boris Gaensicke, Kaya Mori, et al. “Cataclysmic Variables
    and AM CVn Binaries in SRG/EROSITA + Gaia: Volume Limited Samples, X-Ray Luminosity
    Functions, and Space Densities.” <i>Publications of the Astronomical Society of
    the Pacific</i>. IOP Publishing, 2025. <a href="https://doi.org/10.1088/1538-3873/ada185">https://doi.org/10.1088/1538-3873/ada185</a>.'
  ieee: 'A. C. Rodriguez <i>et al.</i>, “Cataclysmic variables and AM CVn binaries
    in SRG/eROSITA + Gaia: Volume limited samples, X-ray luminosity functions, and
    space densities,” <i>Publications of the Astronomical Society of the Pacific</i>,
    vol. 137, no. 1. IOP Publishing, 2025.'
  ista: 'Rodriguez AC, El-Badry K, Suleimanov V, Pala AF, Kulkarni SR, Gaensicke B,
    Mori K, Rich RM, Sarkar A, Bao T, De Oliveira RL, Ramsay G, Szkody P, Graham M,
    Prince TA, Caiazzo I, Vanderbosch ZP, Roestel JV, Das KK, Qin YJ, Kasliwal MM,
    Wold A, Groom SL, Reiley D, Riddle R. 2025. Cataclysmic variables and AM CVn binaries
    in SRG/eROSITA + Gaia: Volume limited samples, X-ray luminosity functions, and
    space densities. Publications of the Astronomical Society of the Pacific. 137(1),
    014201.'
  mla: 'Rodriguez, Antonio C., et al. “Cataclysmic Variables and AM CVn Binaries in
    SRG/EROSITA + Gaia: Volume Limited Samples, X-Ray Luminosity Functions, and Space
    Densities.” <i>Publications of the Astronomical Society of the Pacific</i>, vol.
    137, no. 1, 014201, IOP Publishing, 2025, doi:<a href="https://doi.org/10.1088/1538-3873/ada185">10.1088/1538-3873/ada185</a>.'
  short: A.C. Rodriguez, K. El-Badry, V. Suleimanov, A.F. Pala, S.R. Kulkarni, B.
    Gaensicke, K. Mori, R.M. Rich, A. Sarkar, T. Bao, R.L. De Oliveira, G. Ramsay,
    P. Szkody, M. Graham, T.A. Prince, I. Caiazzo, Z.P. Vanderbosch, J.V. Roestel,
    K.K. Das, Y.J. Qin, M.M. Kasliwal, A. Wold, S.L. Groom, D. Reiley, R. Riddle,
    Publications of the Astronomical Society of the Pacific 137 (2025).
date_created: 2025-01-19T23:01:51Z
date_published: 2025-01-01T00:00:00Z
date_updated: 2025-02-27T12:46:32Z
day: '01'
ddc:
- '520'
department:
- _id: IlCa
doi: 10.1088/1538-3873/ada185
external_id:
  arxiv:
  - '2408.16053'
  isi:
  - '001393204700001'
file:
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  creator: dernst
  date_created: 2025-01-20T09:52:34Z
  date_updated: 2025-01-20T09:52:34Z
  file_id: '18860'
  file_name: 2025_PASP_Rodriguez.pdf
  file_size: 5155631
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file_date_updated: 2025-01-20T09:52:34Z
has_accepted_license: '1'
intvolume: '       137'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Publications of the Astronomical Society of the Pacific
publication_identifier:
  issn:
  - 0004-6280
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Cataclysmic variables and AM CVn binaries in SRG/eROSITA + Gaia: Volume limited
  samples, X-ray luminosity functions, and space densities'
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
  name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
  short: CC BY (3.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 137
year: '2025'
...
---
OA_place: publisher
OA_type: diamond
_id: '18852'
abstract:
- lang: eng
  text: 'Recent observations have found a growing number of hypervelocity stars with
    speeds of ≈1500 − 2500 km s−1 that could have only been produced through thermonuclear
    supernovae in white dwarf binaries. Most of the observed hypervelocity runaways
    in this class display a surprising inflated structure: their current radii are
    roughly an order of magnitude greater than they would have been as white dwarfs
    filling their Roche lobe. While many simulations exist studying the dynamical
    phase leading to supernova detonation in these systems, no detailed calculations
    of the long-term structure of the runaways have yet been performed. We used an
    existing AREPO hydrodynamical simulation of a supernova in a white dwarf binary
    as a starting point for the evolution of these stars with the one-dimensional
    stellar evolution code MESA. We show that the supernova shock is not energetic
    enough to inflate the white dwarf over timescales longer than a few thousand years,
    significantly shorter than the 105 − 6 year lifetimes inferred for observed hypervelocity
    runaways. Although they experience a shock from a supernova less than ≈0.02 R⊙
    away, our models do not experience significant interior heating, and all contract
    back to radii of around 0.01 R⊙ within about 104 years. Explaining the observed
    inflated states requires either an additional source of significant heating or
    some other physics that is not yet accounted for in the subsequent evolution.'
acknowledgement: 'This project was originally started as part of the Kavli Summer
  Program which took place in the Max Planck Institute for Astrophysics in Garching
  in July 2023, supported by the Kavli Foundation. We are grateful to Stephen Justham,
  Selma de Mink, and Jim Fuller for enriching discussions. We would like to thank
  the anonymous referee for their helpful report. A.B. was supported by the Deutsche
  Forschungsgemeinschaft (DFG) through grant GE2506/18-1. K.J.S. was supported by
  NASA through the Astrophysics Theory Program (80NSSC20K0544) and by NASA/ESA Hubble
  Space Telescope programs #15871 and #15918. W.E.K. was supported by NSF Grants OAC-2311323,
  AST-2206523, and NASA/ESA HST-AR-Theory HSTAR-16613.002-A. K.E. was supported in
  part by HST-GO-17441.001-A. AB and ASR would like to thank Rob Farmer for his support
  with PyMESA.'
article_number: A114
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Aakash
  full_name: Bhat, Aakash
  last_name: Bhat
- first_name: Evan B.
  full_name: Bauer, Evan B.
  last_name: Bauer
- first_name: Rüdiger
  full_name: Pakmor, Rüdiger
  last_name: Pakmor
- first_name: Ken J.
  full_name: Shen, Ken J.
  last_name: Shen
- first_name: Ilaria
  full_name: Caiazzo, Ilaria
  id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d
  last_name: Caiazzo
  orcid: 0000-0002-4770-5388
- first_name: Abinaya Swaruba
  full_name: Rajamuthukumar, Abinaya Swaruba
  last_name: Rajamuthukumar
- first_name: Kareem
  full_name: El-Badry, Kareem
  last_name: El-Badry
- first_name: Wolfgang E.
  full_name: Kerzendorf, Wolfgang E.
  last_name: Kerzendorf
citation:
  ama: Bhat A, Bauer EB, Pakmor R, et al. Supernova shocks cannot explain the inflated
    state of hypervelocity runaways from white dwarf binaries. <i>Astronomy &#38;
    Astrophysics</i>. 2025;693(1). doi:<a href="https://doi.org/10.1051/0004-6361/202451371">10.1051/0004-6361/202451371</a>
  apa: Bhat, A., Bauer, E. B., Pakmor, R., Shen, K. J., Caiazzo, I., Rajamuthukumar,
    A. S., … Kerzendorf, W. E. (2025). Supernova shocks cannot explain the inflated
    state of hypervelocity runaways from white dwarf binaries. <i>Astronomy &#38;
    Astrophysics</i>. EDP Sciences. <a href="https://doi.org/10.1051/0004-6361/202451371">https://doi.org/10.1051/0004-6361/202451371</a>
  chicago: Bhat, Aakash, Evan B. Bauer, Rüdiger Pakmor, Ken J. Shen, Ilaria Caiazzo,
    Abinaya Swaruba Rajamuthukumar, Kareem El-Badry, and Wolfgang E. Kerzendorf. “Supernova
    Shocks Cannot Explain the Inflated State of Hypervelocity Runaways from White
    Dwarf Binaries.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2025. <a href="https://doi.org/10.1051/0004-6361/202451371">https://doi.org/10.1051/0004-6361/202451371</a>.
  ieee: A. Bhat <i>et al.</i>, “Supernova shocks cannot explain the inflated state
    of hypervelocity runaways from white dwarf binaries,” <i>Astronomy &#38; Astrophysics</i>,
    vol. 693, no. 1. EDP Sciences, 2025.
  ista: Bhat A, Bauer EB, Pakmor R, Shen KJ, Caiazzo I, Rajamuthukumar AS, El-Badry
    K, Kerzendorf WE. 2025. Supernova shocks cannot explain the inflated state of
    hypervelocity runaways from white dwarf binaries. Astronomy &#38; Astrophysics.
    693(1), A114.
  mla: Bhat, Aakash, et al. “Supernova Shocks Cannot Explain the Inflated State of
    Hypervelocity Runaways from White Dwarf Binaries.” <i>Astronomy &#38; Astrophysics</i>,
    vol. 693, no. 1, A114, EDP Sciences, 2025, doi:<a href="https://doi.org/10.1051/0004-6361/202451371">10.1051/0004-6361/202451371</a>.
  short: A. Bhat, E.B. Bauer, R. Pakmor, K.J. Shen, I. Caiazzo, A.S. Rajamuthukumar,
    K. El-Badry, W.E. Kerzendorf, Astronomy &#38; Astrophysics 693 (2025).
date_created: 2025-01-19T23:01:51Z
date_published: 2025-01-07T00:00:00Z
date_updated: 2026-02-16T12:08:05Z
day: '07'
ddc:
- '520'
department:
- _id: IlCa
doi: 10.1051/0004-6361/202451371
external_id:
  arxiv:
  - '2407.03424'
  isi:
  - '001406577300001'
file:
- access_level: open_access
  checksum: e532b9c8123c29cfb0ee758e6d00453c
  content_type: application/pdf
  creator: dernst
  date_created: 2025-01-20T09:57:00Z
  date_updated: 2025-01-20T09:57:00Z
  file_id: '18861'
  file_name: 2025_AstronomyAstrophysics_Bhat.pdf
  file_size: 1692527
  relation: main_file
  success: 1
file_date_updated: 2025-01-20T09:57:00Z
has_accepted_license: '1'
intvolume: '       693'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Astronomy & Astrophysics
publication_identifier:
  eissn:
  - 1432-0746
  issn:
  - 0004-6361
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Supernova shocks cannot explain the inflated state of hypervelocity runaways
  from white dwarf binaries
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: 693
year: '2025'
...
---
OA_type: closed access
_id: '18853'
abstract:
- lang: eng
  text: Electrolyte additives are extensively validated effective in mitigating dendrite
    growth and parasitic reactions in aqueous zinc-ion batteries (AZIBs). Nonetheless,
    the mechanisms by which additives influence the formation and characteristics
    of the inorganic solid–electrolyte interphase (SEI) are not yet fully elucidated.
    Herein, we investigate how Zn(CF3COO)2 additives influence solvation structure
    and elucidate the mechanism by which these additives promote the dual reduction
    of anions. Through cryo-transmission electron microscopy analysis, we identified
    the SEI as a highly amorphous ZnS/ZnF2 phase. This amorphous hybrid SEI demonstrates
    exceptional stability, mechanical robustness, and high Zn2+ conductivity, effectively
    mitigating parasitic reactions and enhancing Zn plating/stripping reversibility.
    Even under elevated current densities, the Zn anode exhibits ultra-stable longevity
    and ultra-high reversibility. This study provides a comprehensive understanding
    of the intrinsic mechanisms governing solvation structure modulation that lead
    to the formation of amorphous hybrid SEI, underscoring their efficacy in enhancing
    the performance and durability of AZIBs.
acknowledged_ssus:
- _id: EM-Fac
- _id: NanoFab
acknowledgement: The authors acknowledge financial support from the Joint Fund of
  Henan Province Science and Technology R&D Program (235200810097) and the Generalitat
  de Catalunya (2021SGR01581). This research was supported by the Scientific Service
  Units (SSU) of ISTA Austria through resources provided by the Electron Microscopy
  Facility (EMF) and the Nanofabrication Facility (NFF). G. Z. and J. L. thank the
  China Scholarship Council (CSC) for the scholarship support.
article_processing_charge: No
article_type: original
author:
- first_name: Guifang
  full_name: Zeng, Guifang
  last_name: Zeng
- first_name: Qing
  full_name: Sun, Qing
  last_name: Sun
- first_name: Sharona
  full_name: Horta, Sharona
  id: 03a7e858-01b1-11ec-8b71-99ae6c4a05bc
  last_name: Horta
- first_name: Paulina R.
  full_name: Martínez-Alanis, Paulina R.
  last_name: Martínez-Alanis
- first_name: Peng
  full_name: Wu, Peng
  last_name: Wu
- first_name: Jing
  full_name: Li, Jing
  last_name: Li
- first_name: Shang
  full_name: Wang, Shang
  last_name: Wang
- first_name: Maria
  full_name: Ibáñez, Maria
  id: 43C61214-F248-11E8-B48F-1D18A9856A87
  last_name: Ibáñez
  orcid: 0000-0001-5013-2843
- first_name: Yanhong
  full_name: Tian, Yanhong
  last_name: Tian
- first_name: Lijie
  full_name: Ci, Lijie
  last_name: Ci
- first_name: Andreu
  full_name: Cabot, Andreu
  last_name: Cabot
citation:
  ama: Zeng G, Sun Q, Horta S, et al. Modulating the solvation structure to enhance
    amorphous solid electrolyte interface formation for ultra-stable aqueous zinc
    anode. <i>Energy and Environmental Science</i>. 2025;18(4):1683-1695. doi:<a href="https://doi.org/10.1039/d4ee03750b">10.1039/d4ee03750b</a>
  apa: Zeng, G., Sun, Q., Horta, S., Martínez-Alanis, P. R., Wu, P., Li, J., … Cabot,
    A. (2025). Modulating the solvation structure to enhance amorphous solid electrolyte
    interface formation for ultra-stable aqueous zinc anode. <i>Energy and Environmental
    Science</i>. Royal Society of Chemistry. <a href="https://doi.org/10.1039/d4ee03750b">https://doi.org/10.1039/d4ee03750b</a>
  chicago: Zeng, Guifang, Qing Sun, Sharona Horta, Paulina R. Martínez-Alanis, Peng
    Wu, Jing Li, Shang Wang, et al. “Modulating the Solvation Structure to Enhance
    Amorphous Solid Electrolyte Interface Formation for Ultra-Stable Aqueous Zinc
    Anode.” <i>Energy and Environmental Science</i>. Royal Society of Chemistry, 2025.
    <a href="https://doi.org/10.1039/d4ee03750b">https://doi.org/10.1039/d4ee03750b</a>.
  ieee: G. Zeng <i>et al.</i>, “Modulating the solvation structure to enhance amorphous
    solid electrolyte interface formation for ultra-stable aqueous zinc anode,” <i>Energy
    and Environmental Science</i>, vol. 18, no. 4. Royal Society of Chemistry, pp.
    1683–1695, 2025.
  ista: Zeng G, Sun Q, Horta S, Martínez-Alanis PR, Wu P, Li J, Wang S, Ibáñez M,
    Tian Y, Ci L, Cabot A. 2025. Modulating the solvation structure to enhance amorphous
    solid electrolyte interface formation for ultra-stable aqueous zinc anode. Energy
    and Environmental Science. 18(4), 1683–1695.
  mla: Zeng, Guifang, et al. “Modulating the Solvation Structure to Enhance Amorphous
    Solid Electrolyte Interface Formation for Ultra-Stable Aqueous Zinc Anode.” <i>Energy
    and Environmental Science</i>, vol. 18, no. 4, Royal Society of Chemistry, 2025,
    pp. 1683–95, doi:<a href="https://doi.org/10.1039/d4ee03750b">10.1039/d4ee03750b</a>.
  short: G. Zeng, Q. Sun, S. Horta, P.R. Martínez-Alanis, P. Wu, J. Li, S. Wang, M.
    Ibáñez, Y. Tian, L. Ci, A. Cabot, Energy and Environmental Science 18 (2025) 1683–1695.
date_created: 2025-01-19T23:01:52Z
date_published: 2025-02-21T00:00:00Z
date_updated: 2025-07-10T11:51:27Z
day: '21'
department:
- _id: MaIb
doi: 10.1039/d4ee03750b
external_id:
  isi:
  - '001389898000001'
intvolume: '        18'
isi: 1
issue: '4'
language:
- iso: eng
month: '02'
oa_version: None
page: 1683-1695
publication: Energy and Environmental Science
publication_identifier:
  eissn:
  - 1754-5706
  issn:
  - 1754-5692
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Modulating the solvation structure to enhance amorphous solid electrolyte interface
  formation for ultra-stable aqueous zinc anode
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2025'
...
---
OA_place: publisher
OA_type: diamond
_id: '18854'
abstract:
- lang: eng
  text: "Context. One of the surprising early findings with JWST has been the discovery
    of a strong “roll-over” or a softening of the absorption edge of Lyα in a large
    number of galaxies at z ≳ 6, in addition to systematic offsets from photometric
    redshift estimates and fundamental galaxy scaling relations. This has been interpreted
    as strong cumulative damped Lyα absorption (DLA) wings from high column densities
    of neutral atomic hydrogen (H I), signifying major gas accretion events in the
    formation of these galaxies.\r\nAims. To explore this new phenomenon systematically,
    we assembled the JWST/NIRSpec PRImordial gas Mass AssembLy (PRIMAL) legacy survey
    of 584 galaxies at z = 5.0 − 13.4, designed to study the physical properties and
    gas in and around galaxies during the reionization epoch.\r\nMethods. We characterized
    this benchmark sample in full and spectroscopically derived the galaxy redshifts,
    metallicities, star formation rates, and ultraviolet (UV) slopes. We defined a
    new diagnostic, the Lyα damping parameter DLyα, to measure and quantify the net
    effect of Lyα emission strength, the H I fraction in the intergalactic medium,
    or the local H I column density for each source. The JWST-PRIMAL survey is based
    on the spectroscopic DAWN JWST Archive (DJA-Spec). We describe DJA-Spec in this
    paper, detailing the reduction methods, the post-processing steps, and basic analysis
    tools. All the software, reduced spectra, and spectroscopically derived quantities
    and catalogs are made publicly available in dedicated repositories.\r\nResults.
    We find that the fraction of galaxies showing strong integrated DLAs with NHI > 1021 cm−2
    only increases slightly from ≈60% at z ≈ 6 up to ≈65 − 90% at z > 8. Similarly,
    the prevalence and prominence of Lyα emission is found to increase with decreasing
    redshift, in qualitative agreement with previous observational results. Strong
    Lyα emitters (LAEs) are predominantly found to be associated with low-metallicity
    and UV faint galaxies. By contrast, strong DLAs are observed in galaxies with
    a variety of intrinsic physical properties, but predominantly at high redshifts
    and low metallicities.\r\nConclusions. Our results indicate that strong DLAs likely
    reflect a particular early assembly phase of reionization-era galaxies, at which
    point they are largely dominated by pristine H I gas accretion. At z = 8 − 10,
    this gas gradually cools and forms into stars that ionize their local surroundings,
    forming large ionized bubbles and producing strong observed Lyα emission at z < 8."
acknowledgement: 'We would like to thank the referee for a detailed and constructive
  report, greatly improving the presentation of the results in this work. We would
  like to thank Peter Jakobsen for his vision and heroic endeavor in optimally designing
  the JWST/NIRSpec instrument and some of its first on-sky observations and for enlightening
  discussions about the intricacies of the NIRSpec data. Further, we would like to
  thank John Chisholm for helpful clarifications and discussions related to the escape
  fraction of ionizing photons and Aayush Saxena for enlightening conversations on
  the escape and absorption of Lyman-α photons. This work has received funding from
  the Swiss State Secretariat for Education, Research and Innovation (SERI) under
  contract number MB22.00072. The Cosmic Dawn Center (DAWN) is funded by the Danish
  National Research Foundation under grant DNRF140. The data products presented herein
  were retrieved from the DAWN JWST Archive (DJA). DJA is an initiative of the Cosmic
  Dawn Center, which is funded by the Danish National Research Foundation under grant
  DNRF140. P.D. acknowledge support from the NWO grant 016.VIDI.189.162 (“ODIN") and
  warmly thanks the European Commission’s and University of Groningen’s CO-FUND Rosalind
  Franklin program. Support from the ERC Advanced Grant INTERSTELLAR H2020/740120
  is kindly acknowledged (A.F.). S.G. acknowledges financial support from the Villum
  Young Investigator grants 37440 and 13160 and the Cosmic Dawn Center. M.K. was supported
  by the ANID BASAL project FB210003. G.E.M. acknowledges financial support from the
  Villum Young Investigator grants 37440 and 13160 and the Cosmic Dawn Center. J.W.
  acknowledges support from the Science and Technology Facilities Council (STFC),
  by the ERC through Advanced Grant 695671 “QUENCH”, by the UKRI Frontier Research
  grant RISEandFALL. Support for this work was provided by NASA through the NASA Hubble
  Fellowship grant HST-HF2-51515.001-A awarded by the Space Telescope Science Institute,
  which is operated by the Association of Universities for Research in Astronomy,
  Incorporated, under NASA contract NAS5-26555. F.C. acknowledges support from a UKRI
  Frontier Research Guarantee Grant (PI Cullen; grant reference EP/X021025/1). J.H.W.
  acknowledges support by NSF grant AST-2108020 and NASA grants 80NSSC20K0520 and
  80NSSC21K1053. NRT acknowledges support through STFC consolidated grant ST/W000857/1.
  M.J.H. is supported by the Swedish Research Council, VetenskapsrÅdet, and is fellow
  of the Knut & Alice Wallenberg foundation. This work is based in part on observations
  made with the NASA/ESA/CSA James Webb Space Telescope. The data were obtained from
  the Mikulski Archive for Space Telescopes (MAST) at the Space Telescope Science
  Institute, which is operated by the Association of Universities for Research in
  Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. Software: This work made
  use of and acknowledge the following software: NumPy (Harris et al. 2020), Matplotlib
  (Hunter 2007), LMfit (Newville et al. 2014), SciPy (Virtanen et al. 2020), grizli
  (Brammer 2023a), Astrodrizzle (Gonzaga et al. 2012), and MsaExp (v0.3; Brammer 2023b).'
article_number: A60
article_processing_charge: No
article_type: original
author:
- first_name: K. E.
  full_name: Heintz, K. E.
  last_name: Heintz
- first_name: G. B.
  full_name: Brammer, G. B.
  last_name: Brammer
- first_name: D.
  full_name: Watson, D.
  last_name: Watson
- first_name: P. A.
  full_name: Oesch, P. A.
  last_name: Oesch
- first_name: L. C.
  full_name: Keating, L. C.
  last_name: Keating
- first_name: M. J.
  full_name: Hayes, M. J.
  last_name: Hayes
- first_name: Unknown
  full_name: Abdurro'Uf, Unknown
  last_name: Abdurro'Uf
- first_name: K. Z.
  full_name: Arellano-Córdova, K. Z.
  last_name: Arellano-Córdova
- first_name: A. C.
  full_name: Carnall, A. C.
  last_name: Carnall
- first_name: C. R.
  full_name: Christiansen, C. R.
  last_name: Christiansen
- first_name: F.
  full_name: Cullen, F.
  last_name: Cullen
- first_name: R.
  full_name: Davé, R.
  last_name: Davé
- first_name: P.
  full_name: Dayal, P.
  last_name: Dayal
- first_name: A.
  full_name: Ferrara, A.
  last_name: Ferrara
- first_name: K.
  full_name: Finlator, K.
  last_name: Finlator
- first_name: J. P.U.
  full_name: Fynbo, J. P.U.
  last_name: Fynbo
- first_name: S. R.
  full_name: Flury, S. R.
  last_name: Flury
- first_name: V.
  full_name: Gelli, V.
  last_name: Gelli
- first_name: S.
  full_name: Gillman, S.
  last_name: Gillman
- first_name: R.
  full_name: Gottumukkala, R.
  last_name: Gottumukkala
- first_name: K.
  full_name: Gould, K.
  last_name: Gould
- first_name: T. R.
  full_name: Greve, T. R.
  last_name: Greve
- first_name: S. E.
  full_name: Hardin, S. E.
  last_name: Hardin
- first_name: T. Y.Y.
  full_name: Hsiao, T. Y.Y.
  last_name: Hsiao
- first_name: A.
  full_name: Hutter, A.
  last_name: Hutter
- first_name: P.
  full_name: Jakobsson, P.
  last_name: Jakobsson
- first_name: M.
  full_name: Killi, M.
  last_name: Killi
- first_name: N.
  full_name: Khosravaninezhad, N.
  last_name: Khosravaninezhad
- first_name: P.
  full_name: Laursen, P.
  last_name: Laursen
- first_name: M. M.
  full_name: Lee, M. M.
  last_name: Lee
- first_name: G. E.
  full_name: Magdis, G. E.
  last_name: Magdis
- first_name: Jorryt J
  full_name: Matthee, Jorryt J
  id: 7439a258-f3c0-11ec-9501-9df22fe06720
  last_name: Matthee
  orcid: 0000-0003-2871-127X
- first_name: R. P.
  full_name: Naidu, R. P.
  last_name: Naidu
- first_name: D.
  full_name: Narayanan, D.
  last_name: Narayanan
- first_name: C.
  full_name: Pollock, C.
  last_name: Pollock
- first_name: M. K.M.
  full_name: Prescott, M. K.M.
  last_name: Prescott
- first_name: V.
  full_name: Rusakov, V.
  last_name: Rusakov
- first_name: M.
  full_name: Shuntov, M.
  last_name: Shuntov
- first_name: A.
  full_name: Sneppen, A.
  last_name: Sneppen
- first_name: R.
  full_name: Smit, R.
  last_name: Smit
- first_name: N. R.
  full_name: Tanvir, N. R.
  last_name: Tanvir
- first_name: C.
  full_name: Terp, C.
  last_name: Terp
- first_name: S.
  full_name: Toft, S.
  last_name: Toft
- first_name: F.
  full_name: Valentino, F.
  last_name: Valentino
- first_name: A. P.
  full_name: Vijayan, A. P.
  last_name: Vijayan
- first_name: J. R.
  full_name: Weaver, J. R.
  last_name: Weaver
- first_name: J. H.
  full_name: Wise, J. H.
  last_name: Wise
- first_name: J.
  full_name: Witstok, J.
  last_name: Witstok
citation:
  ama: 'Heintz KE, Brammer GB, Watson D, et al. The JWST-PRIMAL archival survey: A
    JWST/NIRSpec reference sample for the physical properties and Lyman-α absorption
    and emission of ∼600 galaxies at z = 5.0-13.4. <i>Astronomy &#38; Astrophysics</i>.
    2025;693. doi:<a href="https://doi.org/10.1051/0004-6361/202450243">10.1051/0004-6361/202450243</a>'
  apa: 'Heintz, K. E., Brammer, G. B., Watson, D., Oesch, P. A., Keating, L. C., Hayes,
    M. J., … Witstok, J. (2025). The JWST-PRIMAL archival survey: A JWST/NIRSpec reference
    sample for the physical properties and Lyman-α absorption and emission of ∼600
    galaxies at z = 5.0-13.4. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a
    href="https://doi.org/10.1051/0004-6361/202450243">https://doi.org/10.1051/0004-6361/202450243</a>'
  chicago: 'Heintz, K. E., G. B. Brammer, D. Watson, P. A. Oesch, L. C. Keating, M.
    J. Hayes, Unknown Abdurro’Uf, et al. “The JWST-PRIMAL Archival Survey: A JWST/NIRSpec
    Reference Sample for the Physical Properties and Lyman-α Absorption and Emission
    of ∼600 Galaxies at z = 5.0-13.4.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences,
    2025. <a href="https://doi.org/10.1051/0004-6361/202450243">https://doi.org/10.1051/0004-6361/202450243</a>.'
  ieee: 'K. E. Heintz <i>et al.</i>, “The JWST-PRIMAL archival survey: A JWST/NIRSpec
    reference sample for the physical properties and Lyman-α absorption and emission
    of ∼600 galaxies at z = 5.0-13.4,” <i>Astronomy &#38; Astrophysics</i>, vol. 693.
    EDP Sciences, 2025.'
  ista: 'Heintz KE, Brammer GB, Watson D, Oesch PA, Keating LC, Hayes MJ, Abdurro’Uf
    U, Arellano-Córdova KZ, Carnall AC, Christiansen CR, Cullen F, Davé R, Dayal P,
    Ferrara A, Finlator K, Fynbo JPU, Flury SR, Gelli V, Gillman S, Gottumukkala R,
    Gould K, Greve TR, Hardin SE, Hsiao TYY, Hutter A, Jakobsson P, Killi M, Khosravaninezhad
    N, Laursen P, Lee MM, Magdis GE, Matthee JJ, Naidu RP, Narayanan D, Pollock C,
    Prescott MKM, Rusakov V, Shuntov M, Sneppen A, Smit R, Tanvir NR, Terp C, Toft
    S, Valentino F, Vijayan AP, Weaver JR, Wise JH, Witstok J. 2025. The JWST-PRIMAL
    archival survey: A JWST/NIRSpec reference sample for the physical properties and
    Lyman-α absorption and emission of ∼600 galaxies at z = 5.0-13.4. Astronomy &#38;
    Astrophysics. 693, A60.'
  mla: 'Heintz, K. E., et al. “The JWST-PRIMAL Archival Survey: A JWST/NIRSpec Reference
    Sample for the Physical Properties and Lyman-α Absorption and Emission of ∼600
    Galaxies at z = 5.0-13.4.” <i>Astronomy &#38; Astrophysics</i>, vol. 693, A60,
    EDP Sciences, 2025, doi:<a href="https://doi.org/10.1051/0004-6361/202450243">10.1051/0004-6361/202450243</a>.'
  short: K.E. Heintz, G.B. Brammer, D. Watson, P.A. Oesch, L.C. Keating, M.J. Hayes,
    U. Abdurro’Uf, K.Z. Arellano-Córdova, A.C. Carnall, C.R. Christiansen, F. Cullen,
    R. Davé, P. Dayal, A. Ferrara, K. Finlator, J.P.U. Fynbo, S.R. Flury, V. Gelli,
    S. Gillman, R. Gottumukkala, K. Gould, T.R. Greve, S.E. Hardin, T.Y.Y. Hsiao,
    A. Hutter, P. Jakobsson, M. Killi, N. Khosravaninezhad, P. Laursen, M.M. Lee,
    G.E. Magdis, J.J. Matthee, R.P. Naidu, D. Narayanan, C. Pollock, M.K.M. Prescott,
    V. Rusakov, M. Shuntov, A. Sneppen, R. Smit, N.R. Tanvir, C. Terp, S. Toft, F.
    Valentino, A.P. Vijayan, J.R. Weaver, J.H. Wise, J. Witstok, Astronomy &#38; Astrophysics
    693 (2025).
date_created: 2025-01-19T23:01:52Z
date_published: 2025-01-06T00:00:00Z
date_updated: 2026-02-16T12:07:37Z
day: '06'
ddc:
- '520'
department:
- _id: JoMa
doi: 10.1051/0004-6361/202450243
external_id:
  isi:
  - '001390856800001'
file:
- access_level: open_access
  checksum: 67a791080ade9bfb449d249de2af7456
  content_type: application/pdf
  creator: dernst
  date_created: 2025-01-20T09:17:33Z
  date_updated: 2025-01-20T09:17:33Z
  file_id: '18858'
  file_name: 2025_AstronomyAstrophysics_Heintz.pdf
  file_size: 4513466
  relation: main_file
  success: 1
file_date_updated: 2025-01-20T09:17:33Z
has_accepted_license: '1'
intvolume: '       693'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Astronomy & Astrophysics
publication_identifier:
  eissn:
  - 1432-0746
  issn:
  - 0004-6361
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The JWST-PRIMAL archival survey: A JWST/NIRSpec reference sample for the physical
  properties and Lyman-α absorption and emission of ∼600 galaxies at z = 5.0-13.4'
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: 693
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '18855'
abstract:
- lang: eng
  text: "A central problem in computational statistics is to convert a procedure for
    sampling combinatorial objects into a procedure for counting those objects, and
    vice versa. We consider sampling problems which come from Gibbs distributions,
    which are families of probability distributions over a discrete space Ω with probability
    mass function of the form μ^Ω_β(ω) ∝ e^{β H(ω)} for β in an interval [β_min, β_max]
    and H(ω) ∈ {0} ∪ [1, n]. Two important parameters are the partition function,
    which is the normalization factor Z(β) = ∑_{ω ∈ Ω} e^{β H(ω)}, and the vector
    of pre-image counts c_x=|H^-1(x)|.\r\nWe develop black-box sampling algorithms
    to estimate the counts roughly Õ(n²/ε²) samples for integer-valued distributions
    and Õ(q/ε²) samples for general distributions, where q = (log Z(β_max))/Z(β_min)
    \ (ignoring some second-order terms and parameters). We show this is optimal up
    to logarithmic factors. We illustrate with improved algorithms for counting connected
    subgraphs, independent sets, and perfect matchings. As a key subroutine, we estimate
    all values of the partition function using Õ(n²/ε²) samples for integer-valued
    distributions and Õ(q/ε²) samples for general distributions. This improves over
    a prior algorithm of Huber (2015) which computes a single point estimate Z(β_max)
    and which uses a slightly larger amount of samples. We show matching lower bounds,
    demonstrating this complexity is optimal as a function of n and q up to logarithmic
    terms."
acknowledgement: "We thank Heng Guo for helpful explanations of algorithms for sampling
  connected subgraphs and matchings, and Maksym Serbyn for bringing to our attention
  the WL algorithm and its use in physics.\r\nThis is an extended version, which includes
  work under the same name from ICALP 2023, as well as the earlier work [22] appearing
  in COLT 2018.\r\nV. Kolmogorov was supported by the European Research Council under
  the European Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement
  no 616160"
article_number: '3'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: David G.
  full_name: Harris, David G.
  last_name: Harris
- first_name: Vladimir
  full_name: Kolmogorov, Vladimir
  id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
  last_name: Kolmogorov
citation:
  ama: Harris DG, Kolmogorov V. Parameter estimation for Gibbs distributions. <i>ACM
    Transactions on Algorithms</i>. 2025;21(1). doi:<a href="https://doi.org/10.1145/3685676">10.1145/3685676</a>
  apa: Harris, D. G., &#38; Kolmogorov, V. (2025). Parameter estimation for Gibbs
    distributions. <i>ACM Transactions on Algorithms</i>. Association for Computing
    Machinery. <a href="https://doi.org/10.1145/3685676">https://doi.org/10.1145/3685676</a>
  chicago: Harris, David G., and Vladimir Kolmogorov. “Parameter Estimation for Gibbs
    Distributions.” <i>ACM Transactions on Algorithms</i>. Association for Computing
    Machinery, 2025. <a href="https://doi.org/10.1145/3685676">https://doi.org/10.1145/3685676</a>.
  ieee: D. G. Harris and V. Kolmogorov, “Parameter estimation for Gibbs distributions,”
    <i>ACM Transactions on Algorithms</i>, vol. 21, no. 1. Association for Computing
    Machinery, 2025.
  ista: Harris DG, Kolmogorov V. 2025. Parameter estimation for Gibbs distributions.
    ACM Transactions on Algorithms. 21(1), 3.
  mla: Harris, David G., and Vladimir Kolmogorov. “Parameter Estimation for Gibbs
    Distributions.” <i>ACM Transactions on Algorithms</i>, vol. 21, no. 1, 3, Association
    for Computing Machinery, 2025, doi:<a href="https://doi.org/10.1145/3685676">10.1145/3685676</a>.
  short: D.G. Harris, V. Kolmogorov, ACM Transactions on Algorithms 21 (2025).
corr_author: '1'
date_created: 2025-01-19T23:01:52Z
date_published: 2025-01-01T00:00:00Z
date_updated: 2025-07-10T11:50:44Z
day: '01'
department:
- _id: VlKo
doi: 10.1145/3685676
ec_funded: 1
external_id:
  arxiv:
  - '2007.10824'
  isi:
  - '001399998600008'
intvolume: '        21'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.48550/arXiv.2007.10824
month: '01'
oa: 1
oa_version: Preprint
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '616160'
  name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: ACM Transactions on Algorithms
publication_identifier:
  eissn:
  - 1549-6333
  issn:
  - 1549-6325
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
  record:
  - id: '14084'
    relation: earlier_version
    status: public
scopus_import: '1'
status: public
title: Parameter estimation for Gibbs distributions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2025'
...
---
OA_place: publisher
OA_type: diamond
_id: '18866'
abstract:
- lang: eng
  text: Using JWST Near Infrared Camera (NIRCam) images of the globular cluster 47,Tucanæ,
    (or NGC,104), taken at two epochs just 7 months apart, we derived proper-motion
    membership down to F322W2 ∼ 27. We identified an intriguing feature at the very
    low-mass end of the main sequence, around ∼ 0.08,M_⋅, at magnitudes F322W2 ∼ 24
    and m_ F150W2 ∼ 25. This feature, dubbed 'kink', is characterized by a prominent
    discontinuity in the slope of the main sequence. A similar discontinuity is seen
    in theoretical isochrones with oxygen-poor chemistries, related to the rapid onset
    of absorption. We therefore hypothesize that the cluster hosts disproportionately
    more oxygen-poor stars near the bottom of the main sequence compared to the upper
    main sequence and the red giant branch. Our results show no strong or conclusive
    evidence of a rise in the brown dwarf luminosity function at faint magnitudes,
    in contrast to previous findings likely affected by faint red background galaxies.
    In our analysis, we accounted for this contamination by using proper motion membership.
acknowledgement: We dedicate this paper to the memory of our colleague Prof. Harvey
  Richer (⋆ April 1944 —† 13 November 2023), a highly accomplished astronomer and
  expert in stellar populations and in particular within globular clusters, who passed
  away during this project. Harvey grew up in Montreal and was at least the second
  star man to graduate from his high school, having been preceded by William Shatner
  by more than a decade. He worked at the University of British Columbia for most
  of his career, and his focus was the late stages of stellar evolution, in particular
  carbon stars and white dwarfs. We thank the referee for his valuable suggestions
  and comments, which helped improve the paper, as well as for his prompt revision.
article_number: A68
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: M.
  full_name: Scalco, M.
  last_name: Scalco
- first_name: R.
  full_name: Gerasimov, R.
  last_name: Gerasimov
- first_name: L. R.
  full_name: Bedin, L. R.
  last_name: Bedin
- first_name: E.
  full_name: Vesperini, E.
  last_name: Vesperini
- first_name: M.
  full_name: Correnti, M.
  last_name: Correnti
- first_name: D.
  full_name: Nardiello, D.
  last_name: Nardiello
- first_name: A.
  full_name: Burgasser, A.
  last_name: Burgasser
- first_name: H.
  full_name: Richer, H.
  last_name: Richer
- first_name: Ilaria
  full_name: Caiazzo, Ilaria
  id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d
  last_name: Caiazzo
  orcid: 0000-0002-4770-5388
- first_name: J.
  full_name: Heyl, J.
  last_name: Heyl
- first_name: M.
  full_name: Libralato, M.
  last_name: Libralato
- first_name: J.
  full_name: Anderson, J.
  last_name: Anderson
- first_name: M.
  full_name: Griggio, M.
  last_name: Griggio
citation:
  ama: Scalco M, Gerasimov R, Bedin LR, et al. JWST photometry and astrometry of 47
    Tucanae. Discontinuity in the stellar sequence at the star--brown dwarf transition.
    <i>Astronomy &#38; Astrophysics</i>. 2025;694. doi:<a href="https://doi.org/10.1051/0004-6361/202452907">10.1051/0004-6361/202452907</a>
  apa: Scalco, M., Gerasimov, R., Bedin, L. R., Vesperini, E., Correnti, M., Nardiello,
    D., … Griggio, M. (2025). JWST photometry and astrometry of 47 Tucanae. Discontinuity
    in the stellar sequence at the star--brown dwarf transition. <i>Astronomy &#38;
    Astrophysics</i>. EDP Sciences. <a href="https://doi.org/10.1051/0004-6361/202452907">https://doi.org/10.1051/0004-6361/202452907</a>
  chicago: Scalco, M., R. Gerasimov, L. R. Bedin, E. Vesperini, M. Correnti, D. Nardiello,
    A. Burgasser, et al. “JWST Photometry and Astrometry of 47 Tucanae. Discontinuity
    in the Stellar Sequence at the Star--Brown Dwarf Transition.” <i>Astronomy &#38;
    Astrophysics</i>. EDP Sciences, 2025. <a href="https://doi.org/10.1051/0004-6361/202452907">https://doi.org/10.1051/0004-6361/202452907</a>.
  ieee: M. Scalco <i>et al.</i>, “JWST photometry and astrometry of 47 Tucanae. Discontinuity
    in the stellar sequence at the star--brown dwarf transition,” <i>Astronomy &#38;
    Astrophysics</i>, vol. 694. EDP Sciences, 2025.
  ista: Scalco M, Gerasimov R, Bedin LR, Vesperini E, Correnti M, Nardiello D, Burgasser
    A, Richer H, Caiazzo I, Heyl J, Libralato M, Anderson J, Griggio M. 2025. JWST
    photometry and astrometry of 47 Tucanae. Discontinuity in the stellar sequence
    at the star--brown dwarf transition. Astronomy &#38; Astrophysics. 694, A68.
  mla: Scalco, M., et al. “JWST Photometry and Astrometry of 47 Tucanae. Discontinuity
    in the Stellar Sequence at the Star--Brown Dwarf Transition.” <i>Astronomy &#38;
    Astrophysics</i>, vol. 694, A68, EDP Sciences, 2025, doi:<a href="https://doi.org/10.1051/0004-6361/202452907">10.1051/0004-6361/202452907</a>.
  short: M. Scalco, R. Gerasimov, L.R. Bedin, E. Vesperini, M. Correnti, D. Nardiello,
    A. Burgasser, H. Richer, I. Caiazzo, J. Heyl, M. Libralato, J. Anderson, M. Griggio,
    Astronomy &#38; Astrophysics 694 (2025).
date_created: 2025-01-21T15:29:36Z
date_published: 2025-02-04T00:00:00Z
date_updated: 2025-07-10T11:51:28Z
day: '04'
ddc:
- '520'
department:
- _id: IlCa
doi: 10.1051/0004-6361/202452907
external_id:
  arxiv:
  - '2501.04446'
  isi:
  - '001414753300007'
file:
- access_level: open_access
  checksum: db765ce222df60a1e7c19da1968906a8
  content_type: application/pdf
  creator: dernst
  date_created: 2025-04-16T07:13:31Z
  date_updated: 2025-04-16T07:13:31Z
  file_id: '19569'
  file_name: 2025_AstronomyAstrophysics_Scalco.pdf
  file_size: 18080704
  relation: main_file
  success: 1
file_date_updated: 2025-04-16T07:13:31Z
has_accepted_license: '1'
intvolume: '       694'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: Astronomy & Astrophysics
publication_identifier:
  eissn:
  - 1432-0746
  issn:
  - 0004-6361
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: JWST photometry and astrometry of 47 Tucanae. Discontinuity in the stellar
  sequence at the star--brown dwarf transition
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: 694
year: '2025'
...
---
OA_type: closed access
_id: '18878'
abstract:
- lang: eng
  text: Thermoelectric (TE) materials, with the ability to convert heat into electrical
    energy, can generate micro-electrical fields at electronic interfaces with biological
    systems, making them applicable in electric-catalyzing as nanozymes, and modulate
    the infected microenvironment of skin wounds. Thereby, by harnessing temperature
    differences in vitro or in vivo, TE nanomaterials can provide antimicrobial reactive
    oxygen species (ROS) by catalyzing redox reactions, thereby accelerating wound
    healing by suppressing infection. However, despite their promising potential,
    there is still a lack of comprehensive understanding of the antimicrobial mechanisms,
    biocompatibility, and practical applications of TE nanomaterials in wound healing,
    as this is a newly-emerged sub-area of energy-related biomedical applications.
    This review aims to address this gap by highlighting the emerging progress of
    TE materials in wound healing, clarifying their mechanism and advances, emphasizing
    their potential challenges for commercialization and clinical use, and proposing
    novel design strategies of TE nanomaterials for effective antibacterial performance.
acknowledgement: This work was financially supported by the Sichuan Science and Technology
  Program (Nos. 2023ZYD0064 and 2023YFG0220), the Fundamental Research Funds for the
  Central Universities (No. YJ202242), and the Research Funding from West China School/Hospital
  of Stomatology, Sichuan University (No. QDJF2022–2).
article_processing_charge: No
article_type: review
author:
- first_name: Shiyu
  full_name: Jia, Shiyu
  last_name: Jia
- first_name: Cai
  full_name: Qi, Cai
  last_name: Qi
- first_name: Shengduo
  full_name: Xu, Shengduo
  id: 12ab8624-4c8a-11ec-9e11-e1ac2438f22f
  last_name: Xu
- first_name: Lei
  full_name: Yang, Lei
  last_name: Yang
- first_name: Qiang
  full_name: Sun, Qiang
  last_name: Sun
citation:
  ama: Jia S, Qi C, Xu S, Yang L, Sun Q. Advancements of thermoelectric nanomaterials
    in ROS-mediated broad-spectrum antibacterial therapies for wound healing. <i>Journal
    of Materials Science and Technology</i>. 2025;225(08):212-226. doi:<a href="https://doi.org/10.1016/j.jmst.2024.11.039">10.1016/j.jmst.2024.11.039</a>
  apa: Jia, S., Qi, C., Xu, S., Yang, L., &#38; Sun, Q. (2025). Advancements of thermoelectric
    nanomaterials in ROS-mediated broad-spectrum antibacterial therapies for wound
    healing. <i>Journal of Materials Science and Technology</i>. Elsevier. <a href="https://doi.org/10.1016/j.jmst.2024.11.039">https://doi.org/10.1016/j.jmst.2024.11.039</a>
  chicago: Jia, Shiyu, Cai Qi, Shengduo Xu, Lei Yang, and Qiang Sun. “Advancements
    of Thermoelectric Nanomaterials in ROS-Mediated Broad-Spectrum Antibacterial Therapies
    for Wound Healing.” <i>Journal of Materials Science and Technology</i>. Elsevier,
    2025. <a href="https://doi.org/10.1016/j.jmst.2024.11.039">https://doi.org/10.1016/j.jmst.2024.11.039</a>.
  ieee: S. Jia, C. Qi, S. Xu, L. Yang, and Q. Sun, “Advancements of thermoelectric
    nanomaterials in ROS-mediated broad-spectrum antibacterial therapies for wound
    healing,” <i>Journal of Materials Science and Technology</i>, vol. 225, no. 08.
    Elsevier, pp. 212–226, 2025.
  ista: Jia S, Qi C, Xu S, Yang L, Sun Q. 2025. Advancements of thermoelectric nanomaterials
    in ROS-mediated broad-spectrum antibacterial therapies for wound healing. Journal
    of Materials Science and Technology. 225(08), 212–226.
  mla: Jia, Shiyu, et al. “Advancements of Thermoelectric Nanomaterials in ROS-Mediated
    Broad-Spectrum Antibacterial Therapies for Wound Healing.” <i>Journal of Materials
    Science and Technology</i>, vol. 225, no. 08, Elsevier, 2025, pp. 212–26, doi:<a
    href="https://doi.org/10.1016/j.jmst.2024.11.039">10.1016/j.jmst.2024.11.039</a>.
  short: S. Jia, C. Qi, S. Xu, L. Yang, Q. Sun, Journal of Materials Science and Technology
    225 (2025) 212–226.
date_created: 2025-01-26T23:01:49Z
date_published: 2025-08-01T00:00:00Z
date_updated: 2025-12-30T07:19:04Z
day: '01'
department:
- _id: MaIb
doi: 10.1016/j.jmst.2024.11.039
external_id:
  isi:
  - '001407204300001'
intvolume: '       225'
isi: 1
issue: '08'
language:
- iso: eng
month: '08'
oa_version: None
page: 212-226
publication: Journal of Materials Science and Technology
publication_identifier:
  issn:
  - 1005-0302
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Advancements of thermoelectric nanomaterials in ROS-mediated broad-spectrum
  antibacterial therapies for wound healing
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 225
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '18880'
abstract:
- lang: eng
  text: In this paper, we provide a rate of convergence for a version of the Carathéodory
    convergence for the multiple SLE model with a Dyson Brownian motion driver towards
    its hydrodynamic limit, for β=1 and β=2. The results are obtained by combining
    techniques from the field of Schramm–Loewner Evolutions with modern techniques
    from random matrices. Our approach shows how one can apply modern tools used in
    the proof of universality in random matrix theory to the field of Schramm–Loewner
    Evolutions.
article_number: '2450028'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Andrew J
  full_name: Campbell, Andrew J
  id: 582b06a9-1f1c-11ee-b076-82ffce00dde4
  last_name: Campbell
- first_name: Kyle
  full_name: Luh, Kyle
  last_name: Luh
- first_name: Vlad
  full_name: Margarint, Vlad
  last_name: Margarint
citation:
  ama: 'Campbell AJ, Luh K, Margarint V. Rate of convergence in multiple SLE using
    random matrix theory. <i>Random Matrices: Theory and Application</i>. 2025;14(1).
    doi:<a href="https://doi.org/10.1142/S201032632450028X">10.1142/S201032632450028X</a>'
  apa: 'Campbell, A. J., Luh, K., &#38; Margarint, V. (2025). Rate of convergence
    in multiple SLE using random matrix theory. <i>Random Matrices: Theory and Application</i>.
    World Scientific Publishing. <a href="https://doi.org/10.1142/S201032632450028X">https://doi.org/10.1142/S201032632450028X</a>'
  chicago: 'Campbell, Andrew J, Kyle Luh, and Vlad Margarint. “Rate of Convergence
    in Multiple SLE Using Random Matrix Theory.” <i>Random Matrices: Theory and Application</i>.
    World Scientific Publishing, 2025. <a href="https://doi.org/10.1142/S201032632450028X">https://doi.org/10.1142/S201032632450028X</a>.'
  ieee: 'A. J. Campbell, K. Luh, and V. Margarint, “Rate of convergence in multiple
    SLE using random matrix theory,” <i>Random Matrices: Theory and Application</i>,
    vol. 14, no. 1. World Scientific Publishing, 2025.'
  ista: 'Campbell AJ, Luh K, Margarint V. 2025. Rate of convergence in multiple SLE
    using random matrix theory. Random Matrices: Theory and Application. 14(1), 2450028.'
  mla: 'Campbell, Andrew J., et al. “Rate of Convergence in Multiple SLE Using Random
    Matrix Theory.” <i>Random Matrices: Theory and Application</i>, vol. 14, no. 1,
    2450028, World Scientific Publishing, 2025, doi:<a href="https://doi.org/10.1142/S201032632450028X">10.1142/S201032632450028X</a>.'
  short: 'A.J. Campbell, K. Luh, V. Margarint, Random Matrices: Theory and Application
    14 (2025).'
date_created: 2025-01-26T23:01:49Z
date_published: 2025-01-01T00:00:00Z
date_updated: 2025-07-10T11:51:29Z
day: '01'
department:
- _id: LaEr
doi: 10.1142/S201032632450028X
external_id:
  arxiv:
  - '2301.04722'
  isi:
  - '001397136000001'
intvolume: '        14'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.48550/arXiv.2301.04722
month: '01'
oa: 1
oa_version: Preprint
publication: 'Random Matrices: Theory and Application'
publication_identifier:
  eissn:
  - 2010-3271
  issn:
  - 2010-3263
publication_status: published
publisher: World Scientific Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Rate of convergence in multiple SLE using random matrix theory
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18881'
abstract:
- lang: eng
  text: The determination of the intrinsic properties of solid active material candidates
    is essential for their performance optimization. However, macroscopic electrodes
    and related analytical techniques show challenges concerning the number of additional
    influencing parameters. We explore recessed microelectrodes (rME) as a platform
    that allows for a binder-free investigation of Prussian Blue analogues (PBA),
    a family of promising battery materials. The enhanced diffusion using microelectrochemical
    tools is indispensable to assess the intrinsic material performance, overcoming
    the limitation of cation diffusion from the electrolyte to the solid interface
    during (dis)charging cycles and allowing the investigation of limiting steps in
    the coupled ion-electron transfer process. The intrinsic electrochemical performance
    of PBAs was studied in a three-electrode configuration by means of cyclic voltammetry
    and galvanostatic (dis)charging in aqueous Na+-containing electrolyte. We extended
    the evaluation to the role of the electrolyte on the performance of cathodic and
    anodic processes of a Mn-based PBA. Ex-situ and operando chemical characterization
    were coupled to support the microelectrochemical results.
acknowledgement: The authors acknowledge funding from the European Union's Horizon
  Europe research and innovation programme – European Innovation Council (EIC) under
  the grant agreement 101046742 (MeBattery), the European Research Council (ERC) under
  the European Union's Horizon 2020 research and innovation programme (CasCat [833408]),
  and the Spanish Government (Ministerio de Ciencia e Innovación, Grants PID2021-124974OB-C22).
  The authors thank Martin Trautmann (RUB) and Prof. Dr. Daniel Grasseschi (Federal
  University of Rio de Janeiro – UFRJ) for support concerning ICP-MS and Raman measurements,
  respectively. Open Access funding enabled and organized by Projekt DEAL.
article_number: e202400743
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Nomnotho
  full_name: Jiyane, Nomnotho
  last_name: Jiyane
- first_name: Carla
  full_name: Santana Santos, Carla
  last_name: Santana Santos
- first_name: Igor
  full_name: Echevarria Poza, Igor
  id: fbae1d3b-8142-11ed-8927-a8cf34feb495
  last_name: Echevarria Poza
- first_name: Mario
  full_name: Palacios Corella, Mario
  id: 452e82c6-803f-11ed-ab7e-ca0439e73a5d
  last_name: Palacios Corella
- first_name: Muhammad Adib
  full_name: Abdillah Mahbub, Muhammad Adib
  last_name: Abdillah Mahbub
- first_name: Gimena
  full_name: Marin-Tajadura, Gimena
  last_name: Marin-Tajadura
- first_name: Thomas
  full_name: Quast, Thomas
  last_name: Quast
- first_name: Maria
  full_name: Ibáñez, Maria
  id: 43C61214-F248-11E8-B48F-1D18A9856A87
  last_name: Ibáñez
  orcid: 0000-0001-5013-2843
- first_name: Edgar
  full_name: Ventosa, Edgar
  last_name: Ventosa
- first_name: Wolfgang
  full_name: Schuhmann, Wolfgang
  last_name: Schuhmann
citation:
  ama: Jiyane N, Santana Santos C, Echevarria Poza I, et al. Recessed microelectrodes
    as a platform to investigate the intrinsic redox process of Prussian blue analogs
    for energy storage application. <i>Batteries &#38; Supercaps</i>. 2025;8(3). doi:<a
    href="https://doi.org/10.1002/batt.202400743">10.1002/batt.202400743</a>
  apa: Jiyane, N., Santana Santos, C., Echevarria Poza, I., Palacios Corella, M.,
    Abdillah Mahbub, M. A., Marin-Tajadura, G., … Schuhmann, W. (2025). Recessed microelectrodes
    as a platform to investigate the intrinsic redox process of Prussian blue analogs
    for energy storage application. <i>Batteries &#38; Supercaps</i>. Wiley. <a href="https://doi.org/10.1002/batt.202400743">https://doi.org/10.1002/batt.202400743</a>
  chicago: Jiyane, Nomnotho, Carla Santana Santos, Igor Echevarria Poza, Mario Palacios
    Corella, Muhammad Adib Abdillah Mahbub, Gimena Marin-Tajadura, Thomas Quast, Maria
    Ibáñez, Edgar Ventosa, and Wolfgang Schuhmann. “Recessed Microelectrodes as a
    Platform to Investigate the Intrinsic Redox Process of Prussian Blue Analogs for
    Energy Storage Application.” <i>Batteries &#38; Supercaps</i>. Wiley, 2025. <a
    href="https://doi.org/10.1002/batt.202400743">https://doi.org/10.1002/batt.202400743</a>.
  ieee: N. Jiyane <i>et al.</i>, “Recessed microelectrodes as a platform to investigate
    the intrinsic redox process of Prussian blue analogs for energy storage application,”
    <i>Batteries &#38; Supercaps</i>, vol. 8, no. 3. Wiley, 2025.
  ista: Jiyane N, Santana Santos C, Echevarria Poza I, Palacios Corella M, Abdillah
    Mahbub MA, Marin-Tajadura G, Quast T, Ibáñez M, Ventosa E, Schuhmann W. 2025.
    Recessed microelectrodes as a platform to investigate the intrinsic redox process
    of Prussian blue analogs for energy storage application. Batteries &#38; Supercaps.
    8(3), e202400743.
  mla: Jiyane, Nomnotho, et al. “Recessed Microelectrodes as a Platform to Investigate
    the Intrinsic Redox Process of Prussian Blue Analogs for Energy Storage Application.”
    <i>Batteries &#38; Supercaps</i>, vol. 8, no. 3, e202400743, Wiley, 2025, doi:<a
    href="https://doi.org/10.1002/batt.202400743">10.1002/batt.202400743</a>.
  short: N. Jiyane, C. Santana Santos, I. Echevarria Poza, M. Palacios Corella, M.A.
    Abdillah Mahbub, G. Marin-Tajadura, T. Quast, M. Ibáñez, E. Ventosa, W. Schuhmann,
    Batteries &#38; Supercaps 8 (2025).
date_created: 2025-01-26T23:01:50Z
date_published: 2025-03-01T00:00:00Z
date_updated: 2026-02-16T12:15:59Z
day: '01'
ddc:
- '540'
department:
- _id: MaIb
doi: 10.1002/batt.202400743
external_id:
  isi:
  - '001402369200001'
file:
- access_level: open_access
  checksum: a9ebdb25c43dc2823cc8a1ba9154d914
  content_type: application/pdf
  creator: dernst
  date_created: 2025-04-16T06:47:09Z
  date_updated: 2025-04-16T06:47:09Z
  file_id: '19568'
  file_name: 2025_Batteries_Jiyane.pdf
  file_size: 1251786
  relation: main_file
  success: 1
file_date_updated: 2025-04-16T06:47:09Z
has_accepted_license: '1'
intvolume: '         8'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: Batteries & Supercaps
publication_identifier:
  eissn:
  - 2566-6223
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Recessed microelectrodes as a platform to investigate the intrinsic redox process
  of Prussian blue analogs for energy storage application
tmp:
  image: /images/cc_by_nc.png
  legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
  short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2025'
...
---
OA_type: closed access
_id: '18882'
abstract:
- lang: eng
  text: Ternary liquid-like thermoelectric materials have garnered significant attention
    due to their ultra-low lattice thermal conductivity. Among these, Ag8SnSe6 stands
    out for its exceptionally low sound velocity and thermal conductivity. However,
    the inherent poor electrical conductivity and suboptimal thermoelectric properties
    of Ag8SnSe6 necessitate further improvement. Here, a novel approach is initiated
    to enhance the thermoelectric properties of Ag8SnSe6 by combining low-dimensionalization
    with intrinsic doping. For the first time, this work successfully synthesizes
    single-phase Ag8SnSe6 nanocrystals, ≈10 nm in size, with the correct phase and
    composition using a robust and reliable colloidal method. This approach represents
    a significant improvement over previous reports on this material. Reducing the
    crystal domains of Ag8SnSe6 to the nanoscale induces quantum confinement effects,
    increasing the density of states near the Fermi surface. It also introduces additional
    grain boundaries, which lower the lattice thermal conductivity and simplify structural
    design. Moreover, incorporating small amounts of Sn nanopowder into the Ag8SnSe6
    nanocrystals before consolidation further enhances the thermoelectric performance.
    Sn acts as a donor dopant, increasing the electronic concentration while at the
    same time improving their mobility by reducing interface barriers, thus significantly
    improving the material transport properties. Additionally, the presence of Sn
    leads to the formation of point defects, dislocations, and secondary phases, which
    increase phonon scattering and further reduce the thermal conductivity. Through
    this synergistic optimization, the figure of merit  shows a significant increase
    across a wide temperature range. Overall, a strategy is presented for the controlled
    preparation of Ag8SnSe6 nanocrystals, the decoupling of their electrical and thermal
    transport, and the practical application of this material to thermoelectric single-leg
    modules.
acknowledgement: X.Z. and M.L. contributed equally to this work. This work was supported
  by the National Key R&D Program of China (No. 2024YFE0105200). Also supported by
  the China Postdoctoral Science Foundation under Grant Number 2023M743151. M.J. acknowledges
  funding from the China Postdoctoral Science Foundation (No. 2023M743221). A.C. thanks
  the support from the projects ENE2016-77798-C4-3-R and NANOGEN (PID2020-116093RB-C43),
  funded by MCIN/ AEI/10.13039/501100011033/ and by “ERDF A way of making Europe”,
  by the “European Union”.
article_number: '2421449'
article_processing_charge: No
article_type: original
author:
- first_name: Xueke
  full_name: Zhao, Xueke
  last_name: Zhao
- first_name: Mengyao
  full_name: Li, Mengyao
  last_name: Li
- first_name: Mochen
  full_name: Jia, Mochen
  last_name: Jia
- first_name: Christine
  full_name: Fiedler, Christine
  id: bd3fceba-dc74-11ea-a0a7-c17f71817366
  last_name: Fiedler
- first_name: Bingfei
  full_name: Nan, Bingfei
  last_name: 'Nan'
- first_name: Dongwen
  full_name: Yang, Dongwen
  last_name: Yang
- first_name: Lei
  full_name: Li, Lei
  last_name: Li
- first_name: Zicheng
  full_name: Yuan, Zicheng
  last_name: Yuan
- first_name: Hongzhang
  full_name: Song, Hongzhang
  last_name: Song
- first_name: Yu
  full_name: Liu, Yu
  id: 2A70014E-F248-11E8-B48F-1D18A9856A87
  last_name: Liu
  orcid: 0000-0001-7313-6740
- first_name: Maria
  full_name: Ibáñez, Maria
  id: 43C61214-F248-11E8-B48F-1D18A9856A87
  last_name: Ibáñez
  orcid: 0000-0001-5013-2843
- first_name: Ziyu
  full_name: Wang, Ziyu
  last_name: Wang
- first_name: Chongxin
  full_name: Shan, Chongxin
  last_name: Shan
- first_name: Andreu
  full_name: Cabot, Andreu
  last_name: Cabot
citation:
  ama: Zhao X, Li M, Jia M, et al. Low-dimensional structure modulation in Ag8SnSe6
    for enhanced thermoelectric performance. <i>Advanced Functional Materials</i>.
    2025;35(24). doi:<a href="https://doi.org/10.1002/adfm.202421449">10.1002/adfm.202421449</a>
  apa: Zhao, X., Li, M., Jia, M., Fiedler, C., Nan, B., Yang, D., … Cabot, A. (2025).
    Low-dimensional structure modulation in Ag8SnSe6 for enhanced thermoelectric performance.
    <i>Advanced Functional Materials</i>. Wiley. <a href="https://doi.org/10.1002/adfm.202421449">https://doi.org/10.1002/adfm.202421449</a>
  chicago: Zhao, Xueke, Mengyao Li, Mochen Jia, Christine Fiedler, Bingfei Nan, Dongwen
    Yang, Lei Li, et al. “Low-Dimensional Structure Modulation in Ag8SnSe6 for Enhanced
    Thermoelectric Performance.” <i>Advanced Functional Materials</i>. Wiley, 2025.
    <a href="https://doi.org/10.1002/adfm.202421449">https://doi.org/10.1002/adfm.202421449</a>.
  ieee: X. Zhao <i>et al.</i>, “Low-dimensional structure modulation in Ag8SnSe6 for
    enhanced thermoelectric performance,” <i>Advanced Functional Materials</i>, vol.
    35, no. 24. Wiley, 2025.
  ista: Zhao X, Li M, Jia M, Fiedler C, Nan B, Yang D, Li L, Yuan Z, Song H, Liu Y,
    Ibáñez M, Wang Z, Shan C, Cabot A. 2025. Low-dimensional structure modulation
    in Ag8SnSe6 for enhanced thermoelectric performance. Advanced Functional Materials.
    35(24), 2421449.
  mla: Zhao, Xueke, et al. “Low-Dimensional Structure Modulation in Ag8SnSe6 for Enhanced
    Thermoelectric Performance.” <i>Advanced Functional Materials</i>, vol. 35, no.
    24, 2421449, Wiley, 2025, doi:<a href="https://doi.org/10.1002/adfm.202421449">10.1002/adfm.202421449</a>.
  short: X. Zhao, M. Li, M. Jia, C. Fiedler, B. Nan, D. Yang, L. Li, Z. Yuan, H. Song,
    Y. Liu, M. Ibáñez, Z. Wang, C. Shan, A. Cabot, Advanced Functional Materials 35
    (2025).
date_created: 2025-01-26T23:01:50Z
date_published: 2025-06-19T00:00:00Z
date_updated: 2025-12-30T07:17:39Z
day: '19'
department:
- _id: MaIb
- _id: GradSch
doi: 10.1002/adfm.202421449
external_id:
  isi:
  - '001398067000001'
intvolume: '        35'
isi: 1
issue: '24'
language:
- iso: eng
month: '06'
oa_version: None
publication: Advanced Functional Materials
publication_identifier:
  eissn:
  - 1616-3028
  issn:
  - 1616-301X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Low-dimensional structure modulation in Ag8SnSe6 for enhanced thermoelectric
  performance
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18936'
abstract:
- lang: eng
  text: A major obstacle to predictive understanding of evolution stems from the complexity
    of biological systems, which prevents detailed characterization of key evolutionary
    properties. Here, we highlight some of the major sources of complexity that arise
    when relating molecular mechanisms to their evolutionary consequences and ask
    whether accounting for every mechanistic detail is important to accurately predict
    evolutionary outcomes. To do this, we developed a mechanistic model of a bacterial
    promoter regulated by 2 proteins, allowing us to connect any promoter genotype
    to 6 phenotypes that capture the dynamics of gene expression following an environmental
    switch. Accounting for the mechanisms that govern how this system works enabled
    us to provide an in-depth picture of how regulated bacterial promoters might evolve.
    More importantly, we used the model to explore which factors that contribute to
    the complexity of this system are essential for understanding its evolution, and
    which can be simplified without information loss. We found that several key evolutionary
    properties—the distribution of phenotypic and fitness effects of mutations, the
    evolutionary trajectories during selection for regulation—can be accurately captured
    without accounting for all, or even most, parameters of the system. Our findings
    point to the need for a mechanistic approach to studying evolution, as it enables
    tackling biological complexity and in doing so improves the ability to predict
    evolutionary outcomes.
acknowledgement: "The authors thank Nick Barton, Stepan Denisov, Claudia Igler, Srdjan
  Sarikas, Anna Staron, and the anonymous reviewers for useful comments and discussions
  that helped improve our work.\r\nFunding for this work was provided by the Wellcome
  Trust–Royal Society Sir Henry Dale Fellowship (216779/Z/19/Z) and the Royal Society
  Research Grant (RG\\R2\\232522) to M.L."
article_number: iyae191
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Rok
  full_name: Grah, Rok
  id: 483E70DE-F248-11E8-B48F-1D18A9856A87
  last_name: Grah
  orcid: 0000-0003-2539-3560
- first_name: Calin C
  full_name: Guet, Calin C
  id: 47F8433E-F248-11E8-B48F-1D18A9856A87
  last_name: Guet
  orcid: 0000-0001-6220-2052
- first_name: Gašper
  full_name: Tkačik, Gašper
  id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
  last_name: Tkačik
  orcid: 0000-0002-6699-1455
- first_name: Mato
  full_name: Lagator, Mato
  id: 345D25EC-F248-11E8-B48F-1D18A9856A87
  last_name: Lagator
citation:
  ama: 'Grah R, Guet CC, Tkačik G, Lagator M. Linking molecular mechanisms to their
    evolutionary consequences: a primer. <i>Genetics</i>. 2025;229(2). doi:<a href="https://doi.org/10.1093/genetics/iyae191">10.1093/genetics/iyae191</a>'
  apa: 'Grah, R., Guet, C. C., Tkačik, G., &#38; Lagator, M. (2025). Linking molecular
    mechanisms to their evolutionary consequences: a primer. <i>Genetics</i>. Oxford
    University Press. <a href="https://doi.org/10.1093/genetics/iyae191">https://doi.org/10.1093/genetics/iyae191</a>'
  chicago: 'Grah, Rok, Calin C Guet, Gašper Tkačik, and Mato Lagator. “Linking Molecular
    Mechanisms to Their Evolutionary Consequences: A Primer.” <i>Genetics</i>. Oxford
    University Press, 2025. <a href="https://doi.org/10.1093/genetics/iyae191">https://doi.org/10.1093/genetics/iyae191</a>.'
  ieee: 'R. Grah, C. C. Guet, G. Tkačik, and M. Lagator, “Linking molecular mechanisms
    to their evolutionary consequences: a primer,” <i>Genetics</i>, vol. 229, no.
    2. Oxford University Press, 2025.'
  ista: 'Grah R, Guet CC, Tkačik G, Lagator M. 2025. Linking molecular mechanisms
    to their evolutionary consequences: a primer. Genetics. 229(2), iyae191.'
  mla: 'Grah, Rok, et al. “Linking Molecular Mechanisms to Their Evolutionary Consequences:
    A Primer.” <i>Genetics</i>, vol. 229, no. 2, iyae191, Oxford University Press,
    2025, doi:<a href="https://doi.org/10.1093/genetics/iyae191">10.1093/genetics/iyae191</a>.'
  short: R. Grah, C.C. Guet, G. Tkačik, M. Lagator, Genetics 229 (2025).
corr_author: '1'
date_created: 2025-01-29T08:21:35Z
date_published: 2025-02-01T00:00:00Z
date_updated: 2025-05-19T14:08:02Z
day: '01'
ddc:
- '570'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1093/genetics/iyae191
external_id:
  isi:
  - '001379194200001'
  pmid:
  - '39601269'
file:
- access_level: open_access
  checksum: f730e416795969449ef49d97b82ac494
  content_type: application/pdf
  creator: dernst
  date_created: 2025-04-16T09:41:04Z
  date_updated: 2025-04-16T09:41:04Z
  file_id: '19580'
  file_name: 2025_Genetics_Grah.pdf
  file_size: 1511688
  relation: main_file
  success: 1
file_date_updated: 2025-04-16T09:41:04Z
has_accepted_license: '1'
intvolume: '       229'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genetics
publication_identifier:
  eissn:
  - 1943-2631
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Linking molecular mechanisms to their evolutionary consequences: a primer'
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: 229
year: '2025'
...
---
OA_type: closed access
_id: '18960'
abstract:
- lang: eng
  text: The importance of physical forces in the morphogenesis, homeostatic function,
    and pathological dysfunction of multicellular tissues is being increasingly characterized,
    both theoretically and experimentally. Analogies between biological systems and
    inert materials such as foams, gels, and liquid crystals have provided striking
    insights into the core design principles underlying multicellular organization.
    However, these connections can seem surprising given that a key feature of multicellular
    systems is their ability to constantly consume energy, providing an active origin
    for the forces that they produce. Key emerging questions are, therefore, to understand
    whether and how this activity grants tissues novel properties that do not have
    counterparts in classical materials, as well as their consequences for biological
    function. Here, we review recent discoveries at the intersection of active matter
    and tissue biology, with an emphasis on how modeling and experiments can be combined
    to understand the dynamics of multicellular systems. These approaches suggest
    that a number of key biological tissue-scale phenomena, such as morphogenetic
    shape changes, collective migration, or fate decisions, share unifying design
    principles that can be described by physical models of tissue active matter.
acknowledgement: We thank Fridtjof Brauns, Anna Kicheva, and Carl-Philipp Heisenberg
  for a critical reading of the manuscript and Claudia Flandoli for the artwork in
  the figures. D.B.B. was supported by the NOMIS foundation as a NOMIS Fellow and
  by an EMBO Postdoctoral Fellowship (ALTF 343-2022). This work received funding from
  the European Research Council (ERC) under the European Union\u2019s Horizon 2020
  Research and Innovation Programme Grant Agreement no. 851288.
article_number: a041653
article_processing_charge: No
article_type: original
author:
- first_name: David
  full_name: Brückner, David
  id: e1e86031-6537-11eb-953a-f7ab92be508d
  last_name: Brückner
  orcid: 0000-0001-7205-2975
- first_name: Edouard B
  full_name: Hannezo, Edouard B
  id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
  last_name: Hannezo
  orcid: 0000-0001-6005-1561
citation:
  ama: 'Brückner D, Hannezo EB. Tissue active matter: Integrating mechanics and signaling
    into dynamical models. <i>Cold Spring Harbor Perspectives in Biology</i>. 2025;17(4).
    doi:<a href="https://doi.org/10.1101/cshperspect.a041653">10.1101/cshperspect.a041653</a>'
  apa: 'Brückner, D., &#38; Hannezo, E. B. (2025). Tissue active matter: Integrating
    mechanics and signaling into dynamical models. <i>Cold Spring Harbor Perspectives
    in Biology</i>. Cold Spring Harbor Laboratory Press. <a href="https://doi.org/10.1101/cshperspect.a041653">https://doi.org/10.1101/cshperspect.a041653</a>'
  chicago: 'Brückner, David, and Edouard B Hannezo. “Tissue Active Matter: Integrating
    Mechanics and Signaling into Dynamical Models.” <i>Cold Spring Harbor Perspectives
    in Biology</i>. Cold Spring Harbor Laboratory Press, 2025. <a href="https://doi.org/10.1101/cshperspect.a041653">https://doi.org/10.1101/cshperspect.a041653</a>.'
  ieee: 'D. Brückner and E. B. Hannezo, “Tissue active matter: Integrating mechanics
    and signaling into dynamical models,” <i>Cold Spring Harbor Perspectives in Biology</i>,
    vol. 17, no. 4. Cold Spring Harbor Laboratory Press, 2025.'
  ista: 'Brückner D, Hannezo EB. 2025. Tissue active matter: Integrating mechanics
    and signaling into dynamical models. Cold Spring Harbor Perspectives in Biology.
    17(4), a041653.'
  mla: 'Brückner, David, and Edouard B. Hannezo. “Tissue Active Matter: Integrating
    Mechanics and Signaling into Dynamical Models.” <i>Cold Spring Harbor Perspectives
    in Biology</i>, vol. 17, no. 4, a041653, Cold Spring Harbor Laboratory Press,
    2025, doi:<a href="https://doi.org/10.1101/cshperspect.a041653">10.1101/cshperspect.a041653</a>.'
  short: D. Brückner, E.B. Hannezo, Cold Spring Harbor Perspectives in Biology 17
    (2025).
corr_author: '1'
date_created: 2025-01-29T13:33:47Z
date_published: 2025-04-01T00:00:00Z
date_updated: 2025-12-30T07:08:34Z
day: '01'
department:
- _id: EdHa
doi: 10.1101/cshperspect.a041653
ec_funded: 1
external_id:
  isi:
  - '001456660400001'
  pmid:
  - '38951023'
intvolume: '        17'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa_version: None
pmid: 1
project:
- _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b
  grant_number: ALTF 343-2022
  name: A mechano-chemical theory for stem cell fate decisions in organoid development
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
  call_identifier: H2020
  grant_number: '851288'
  name: Design Principles of Branching Morphogenesis
publication: Cold Spring Harbor Perspectives in Biology
publication_identifier:
  issn:
  - 1943-0264
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Tissue active matter: Integrating mechanics and signaling into dynamical models'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '18984'
abstract:
- lang: eng
  text: Although planets have been found orbiting binary systems, whether they can
    survive binary interactions is debated. While the tightest-orbit binaries should
    host the most dynamically stable and long-lived circumbinary planetary systems,
    they are also the systems that are expected to experience mass transfer, common
    envelope evolution, or stellar mergers. In this study, we explore the effect of
    stable non-conservative mass transfer on the dynamical evolution of circumbinary
    planets. We present a new script that seamlessly integrates binary evolution data
    from the 1D binary stellar evolution code MESA into the N-body simulation code
    REBOUND. This integration framework enables a comprehensive examination of the
    dynamical evolution of circumbinary planets orbiting mass-transferring binaries,
    while simultaneously accounting for the detailed stellar structure evolution.
    In addition, we introduce a recalibration method to mitigate numerical errors
    from updates of binary properties during the system's dynamical evolution. We
    construct a reference binary model in which a 2.21M⊙ star loses its hydrogen-rich
    envelope through non-conservative mass transfer to the 1.76M⊙ companion star,
    creating a 0.38M⊙ subdwarf. We find the tightest stable orbital separation for
    circumbinary planets to be ≃2.5 times the binary separation after mass transfer.
    Accounting for tides by using the interior stellar structure, we find that tidal
    effects become apparent after the rapid mass transfer phase and start to fade
    away during the latter stage of the slow mass transfer phase. Our research provides
    a new framework for exploring circumbinary planet dynamics in interacting binary
    systems.
acknowledgement: We thank the participants of the 2023 Kavli Summer Program in Astrophysics,
  hosted by the Max Planck Institute for Astrophysics and funded by the Kavli Foundation.
  In particular, Holly Preece, Selma de Mink, and Stephen Justham for their feedback
  and comments on our work. ZX acknowledges support from the China Scholarship Council
  (CSC). ST acknowledges the funding from the European Union’s Horizon 2020 research
  and innovation programme under the Marie Skłodowska-Curie grant agreement No. 101034413.
  AAT acknowledges support from the Horizon Europe research and innovation programmes
  under the Marie Skłodowska-Curie grant agreement no. 101103134.
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Zepei
  full_name: Xing, Zepei
  last_name: Xing
- first_name: Santiago
  full_name: Torres Rodriguez, Santiago
  id: a8df4360-4328-11ee-8f1a-e502d0c83fc2
  last_name: Torres Rodriguez
  orcid: 0000-0002-3150-8988
- first_name: Ylva Louise Linsdotter
  full_name: Götberg, Ylva Louise Linsdotter
  id: d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d
  last_name: Götberg
  orcid: 0000-0002-6960-6911
- first_name: Alessandro A.
  full_name: Trani, Alessandro A.
  last_name: Trani
- first_name: Valeriya
  full_name: Korol, Valeriya
  last_name: Korol
- first_name: Jorge
  full_name: Cuadra, Jorge
  last_name: Cuadra
citation:
  ama: 'Xing Z, Torres Rodriguez S, Götberg YLL, Trani AA, Korol V, Cuadra J. Combining
    REBOUND and MESA: Dynamical evolution of planets orbiting interacting binaries.
    <i>Monthly Notices of the Royal Astronomical Society</i>. 2025;537(1):285-292.
    doi:<a href="https://doi.org/10.1093/mnras/stae2820">10.1093/mnras/stae2820</a>'
  apa: 'Xing, Z., Torres Rodriguez, S., Götberg, Y. L. L., Trani, A. A., Korol, V.,
    &#38; Cuadra, J. (2025). Combining REBOUND and MESA: Dynamical evolution of planets
    orbiting interacting binaries. <i>Monthly Notices of the Royal Astronomical Society</i>.
    Oxford University Press. <a href="https://doi.org/10.1093/mnras/stae2820">https://doi.org/10.1093/mnras/stae2820</a>'
  chicago: 'Xing, Zepei, Santiago Torres Rodriguez, Ylva Louise Linsdotter Götberg,
    Alessandro A. Trani, Valeriya Korol, and Jorge Cuadra. “Combining REBOUND and
    MESA: Dynamical Evolution of Planets Orbiting Interacting Binaries.” <i>Monthly
    Notices of the Royal Astronomical Society</i>. Oxford University Press, 2025.
    <a href="https://doi.org/10.1093/mnras/stae2820">https://doi.org/10.1093/mnras/stae2820</a>.'
  ieee: 'Z. Xing, S. Torres Rodriguez, Y. L. L. Götberg, A. A. Trani, V. Korol, and
    J. Cuadra, “Combining REBOUND and MESA: Dynamical evolution of planets orbiting
    interacting binaries,” <i>Monthly Notices of the Royal Astronomical Society</i>,
    vol. 537, no. 1. Oxford University Press, pp. 285–292, 2025.'
  ista: 'Xing Z, Torres Rodriguez S, Götberg YLL, Trani AA, Korol V, Cuadra J. 2025.
    Combining REBOUND and MESA: Dynamical evolution of planets orbiting interacting
    binaries. Monthly Notices of the Royal Astronomical Society. 537(1), 285–292.'
  mla: 'Xing, Zepei, et al. “Combining REBOUND and MESA: Dynamical Evolution of Planets
    Orbiting Interacting Binaries.” <i>Monthly Notices of the Royal Astronomical Society</i>,
    vol. 537, no. 1, Oxford University Press, 2025, pp. 285–92, doi:<a href="https://doi.org/10.1093/mnras/stae2820">10.1093/mnras/stae2820</a>.'
  short: Z. Xing, S. Torres Rodriguez, Y.L.L. Götberg, A.A. Trani, V. Korol, J. Cuadra,
    Monthly Notices of the Royal Astronomical Society 537 (2025) 285–292.
date_created: 2025-02-02T23:01:53Z
date_published: 2025-02-01T00:00:00Z
date_updated: 2025-12-30T07:25:37Z
day: '01'
ddc:
- '520'
department:
- _id: YlGo
- _id: LiBu
doi: 10.1093/mnras/stae2820
ec_funded: 1
external_id:
  arxiv:
  - '2410.19695'
  isi:
  - '001400731500001'
file:
- access_level: open_access
  checksum: 49fb4fe69f487d36169ccea60acbeccc
  content_type: application/pdf
  creator: dernst
  date_created: 2025-12-30T07:24:34Z
  date_updated: 2025-12-30T07:24:34Z
  file_id: '20881'
  file_name: 2025_MonthlyNoticesRAS_Xing.pdf
  file_size: 2974244
  relation: main_file
  success: 1
file_date_updated: 2025-12-30T07:24:34Z
has_accepted_license: '1'
intvolume: '       537'
isi: 1
issue: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 285-292
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
  call_identifier: H2020
  grant_number: '101034413'
  name: 'IST-BRIDGE: International postdoctoral program'
publication: Monthly Notices of the Royal Astronomical Society
publication_identifier:
  eissn:
  - 1365-2966
  issn:
  - 0035-8711
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Combining REBOUND and MESA: Dynamical evolution of planets orbiting interacting
  binaries'
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: 537
year: '2025'
...
---
OA_type: closed access
_id: '18985'
abstract:
- lang: eng
  text: Persistent multiyear drought (MYD) events pose a growing threat to nature
    and humans in a changing climate. We identified and inventoried global MYDs by
    detecting spatiotemporally contiguous climatic anomalies, showing that MYDs have
    become drier, hotter, and led to increasingly diminished vegetation greenness.
    The global terrestrial land affected by MYDs has increased at a rate of 49,279
    ± 14,771 square kilometers per year from 1980 to 2018. Temperate grasslands have
    exhibited the greatest declines in vegetation greenness during MYDs, whereas boreal
    and tropical forests have had comparably minor responses. With MYDs becoming more
    common, this global quantitative inventory of the occurrence, severity, trend,
    and impact of MYDs provides an important benchmark for facilitating more effective
    and collaborative preparedness toward mitigation of and adaptation to such extreme
    events.
acknowledgement: This study received support from the Extremes Research Program funded
  by the Swiss Federal Institute for Forest, Snow and Landscape Research (WSL) within
  the EMERGE project of the Extremes program.
article_processing_charge: No
article_type: original
author:
- first_name: Liangzhi
  full_name: Chen, Liangzhi
  last_name: Chen
- first_name: Philipp
  full_name: Brun, Philipp
  last_name: Brun
- first_name: Pascal
  full_name: Buri, Pascal
  id: 317987aa-9421-11ee-ac5a-b941b041abba
  last_name: Buri
- first_name: Simone
  full_name: Fatichi, Simone
  last_name: Fatichi
- first_name: Arthur
  full_name: Gessler, Arthur
  last_name: Gessler
- first_name: Michael
  full_name: Mccarthy, Michael
  id: 22a2674a-61ce-11ee-94b5-d18813baf16f
  last_name: Mccarthy
- first_name: Francesca
  full_name: Pellicciotti, Francesca
  id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
  last_name: Pellicciotti
  orcid: 0000-0002-5554-8087
- first_name: Benjamin
  full_name: Stocker, Benjamin
  last_name: Stocker
- first_name: Dirk Nikolaus
  full_name: Karger, Dirk Nikolaus
  last_name: Karger
citation:
  ama: Chen L, Brun P, Buri P, et al. Global increase in the occurrence and impact
    of multiyear droughts. <i>Science</i>. 2025;387(6731):278-284. doi:<a href="https://doi.org/10.1126/science.ado4245">10.1126/science.ado4245</a>
  apa: Chen, L., Brun, P., Buri, P., Fatichi, S., Gessler, A., McCarthy, M., … Karger,
    D. N. (2025). Global increase in the occurrence and impact of multiyear droughts.
    <i>Science</i>. AAAS. <a href="https://doi.org/10.1126/science.ado4245">https://doi.org/10.1126/science.ado4245</a>
  chicago: Chen, Liangzhi, Philipp Brun, Pascal Buri, Simone Fatichi, Arthur Gessler,
    Michael McCarthy, Francesca Pellicciotti, Benjamin Stocker, and Dirk Nikolaus
    Karger. “Global Increase in the Occurrence and Impact of Multiyear Droughts.”
    <i>Science</i>. AAAS, 2025. <a href="https://doi.org/10.1126/science.ado4245">https://doi.org/10.1126/science.ado4245</a>.
  ieee: L. Chen <i>et al.</i>, “Global increase in the occurrence and impact of multiyear
    droughts,” <i>Science</i>, vol. 387, no. 6731. AAAS, pp. 278–284, 2025.
  ista: Chen L, Brun P, Buri P, Fatichi S, Gessler A, McCarthy M, Pellicciotti F,
    Stocker B, Karger DN. 2025. Global increase in the occurrence and impact of multiyear
    droughts. Science. 387(6731), 278–284.
  mla: Chen, Liangzhi, et al. “Global Increase in the Occurrence and Impact of Multiyear
    Droughts.” <i>Science</i>, vol. 387, no. 6731, AAAS, 2025, pp. 278–84, doi:<a
    href="https://doi.org/10.1126/science.ado4245">10.1126/science.ado4245</a>.
  short: L. Chen, P. Brun, P. Buri, S. Fatichi, A. Gessler, M. McCarthy, F. Pellicciotti,
    B. Stocker, D.N. Karger, Science 387 (2025) 278–284.
date_created: 2025-02-02T23:01:54Z
date_published: 2025-01-17T00:00:00Z
date_updated: 2025-09-30T10:24:34Z
day: '17'
department:
- _id: FrPe
doi: 10.1126/science.ado4245
external_id:
  isi:
  - '001491931700027'
  pmid:
  - '39818908'
intvolume: '       387'
isi: 1
issue: '6731'
language:
- iso: eng
month: '01'
oa_version: None
page: 278-284
pmid: 1
publication: Science
publication_identifier:
  eissn:
  - 1095-9203
publication_status: published
publisher: AAAS
quality_controlled: '1'
scopus_import: '1'
status: public
title: Global increase in the occurrence and impact of multiyear droughts
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 387
year: '2025'
...
