---
_id: '13235'
abstract:
- lang: eng
  text: AgSbSe2 is a promising thermoelectric (TE) p-type material for applications
    in the middle-temperature range. AgSbSe2 is characterized by relatively low thermal
    conductivities and high Seebeck coefficients, but its main limitation is moderate
    electrical conductivity. Herein, we detail an efficient and scalable hot-injection
    synthesis route to produce AgSbSe2 nanocrystals (NCs). To increase the carrier
    concentration and improve the electrical conductivity, these NCs are doped with
    Sn2+ on Sb3+ sites. Upon processing, the Sn2+ chemical state is conserved using
    a reducing NaBH4 solution to displace the organic ligand and anneal the material
    under a forming gas flow. The TE properties of the dense materials obtained from
    the consolidation of the NCs using a hot pressing are then characterized. The
    presence of Sn2+ ions replacing Sb3+ significantly increases the charge carrier
    concentration and, consequently, the electrical conductivity. Opportunely, the
    measured Seebeck coefficient varied within a small range upon Sn doping. The excellent
    performance obtained when Sn2+ ions are prevented from oxidation is rationalized
    by modeling the system. Calculated band structures disclosed that Sn doping induces
    convergence of the AgSbSe2 valence bands, accounting for an enhanced electronic
    effective mass. The dramatically enhanced carrier transport leads to a maximized
    power factor for AgSb0.98Sn0.02Se2 of 0.63 mW m–1 K–2 at 640 K. Thermally, phonon
    scattering is significantly enhanced in the NC-based materials, yielding an ultralow
    thermal conductivity of 0.3 W mK–1 at 666 K. Overall, a record-high figure of
    merit (zT) is obtained at 666 K for AgSb0.98Sn0.02Se2 at zT = 1.37, well above
    the values obtained for undoped AgSbSe2, at zT = 0.58 and state-of-art Pb- and
    Te-free materials, which makes AgSb0.98Sn0.02Se2 an excellent p-type candidate
    for medium-temperature TE applications.
acknowledgement: Y.L. acknowledges funding from the National Natural Science Foundation
  of China (NSFC) (Grants No. 22209034), the Innovation and Entrepreneurship Project
  of Overseas Returnees in Anhui Province (Grant No. 2022LCX002). K.H.L. acknowledges
  financial support from the National Natural Science Foundation of China (Grant No.
  22208293). Y.Z. acknowledges support from the SBIR program NanoOhmics. J.L. is grateful
  for the project supported by the Natural Science Foundation of Sichuan (2022NSFSC1229).
  M.I. acknowledges financial support from ISTA and the Werner Siemens Foundation.
article_processing_charge: No
article_type: original
author:
- first_name: Yu
  full_name: Liu, Yu
  id: 2A70014E-F248-11E8-B48F-1D18A9856A87
  last_name: Liu
  orcid: 0000-0001-7313-6740
- first_name: Mingquan
  full_name: Li, Mingquan
  last_name: Li
- first_name: Shanhong
  full_name: Wan, Shanhong
  last_name: Wan
- first_name: Khak Ho
  full_name: Lim, Khak Ho
  last_name: Lim
- first_name: Yu
  full_name: Zhang, Yu
  last_name: Zhang
- first_name: Mengyao
  full_name: Li, Mengyao
  last_name: Li
- first_name: Junshan
  full_name: Li, Junshan
  last_name: Li
- first_name: Maria
  full_name: Ibáñez, Maria
  id: 43C61214-F248-11E8-B48F-1D18A9856A87
  last_name: Ibáñez
  orcid: 0000-0001-5013-2843
- first_name: Min
  full_name: Hong, Min
  last_name: Hong
- first_name: Andreu
  full_name: Cabot, Andreu
  last_name: Cabot
citation:
  ama: 'Liu Y, Li M, Wan S, et al. Surface chemistry and band engineering in AgSbSe₂:
    Toward high thermoelectric performance. <i>ACS Nano</i>. 2023;17(12):11923–11934.
    doi:<a href="https://doi.org/10.1021/acsnano.3c03541">10.1021/acsnano.3c03541</a>'
  apa: 'Liu, Y., Li, M., Wan, S., Lim, K. H., Zhang, Y., Li, M., … Cabot, A. (2023).
    Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric
    performance. <i>ACS Nano</i>. American Chemical Society. <a href="https://doi.org/10.1021/acsnano.3c03541">https://doi.org/10.1021/acsnano.3c03541</a>'
  chicago: 'Liu, Yu, Mingquan Li, Shanhong Wan, Khak Ho Lim, Yu Zhang, Mengyao Li,
    Junshan Li, Maria Ibáñez, Min Hong, and Andreu Cabot. “Surface Chemistry and Band
    Engineering in AgSbSe₂: Toward High Thermoelectric Performance.” <i>ACS Nano</i>.
    American Chemical Society, 2023. <a href="https://doi.org/10.1021/acsnano.3c03541">https://doi.org/10.1021/acsnano.3c03541</a>.'
  ieee: 'Y. Liu <i>et al.</i>, “Surface chemistry and band engineering in AgSbSe₂:
    Toward high thermoelectric performance,” <i>ACS Nano</i>, vol. 17, no. 12. American
    Chemical Society, pp. 11923–11934, 2023.'
  ista: 'Liu Y, Li M, Wan S, Lim KH, Zhang Y, Li M, Li J, Ibáñez M, Hong M, Cabot
    A. 2023. Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric
    performance. ACS Nano. 17(12), 11923–11934.'
  mla: 'Liu, Yu, et al. “Surface Chemistry and Band Engineering in AgSbSe₂: Toward
    High Thermoelectric Performance.” <i>ACS Nano</i>, vol. 17, no. 12, American Chemical
    Society, 2023, pp. 11923–11934, doi:<a href="https://doi.org/10.1021/acsnano.3c03541">10.1021/acsnano.3c03541</a>.'
  short: Y. Liu, M. Li, S. Wan, K.H. Lim, Y. Zhang, M. Li, J. Li, M. Ibáñez, M. Hong,
    A. Cabot, ACS Nano 17 (2023) 11923–11934.
date_created: 2023-07-16T22:01:11Z
date_published: 2023-06-13T00:00:00Z
date_updated: 2025-04-15T06:36:40Z
day: '13'
department:
- _id: MaIb
doi: 10.1021/acsnano.3c03541
external_id:
  isi:
  - '001008564800001'
  pmid:
  - '37310395'
intvolume: '        17'
isi: 1
issue: '12'
language:
- iso: eng
month: '06'
oa_version: None
page: 11923–11934
pmid: 1
project:
- _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A
  name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of
    Semiconductors for Waste Heat Recovery'
publication: ACS Nano
publication_identifier:
  eissn:
  - 1936-086X
  issn:
  - 1936-0851
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric
  performance'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 17
year: '2023'
...
---
_id: '13236'
abstract:
- lang: eng
  text: We present an auction algorithm using multiplicative instead of constant weight
    updates to compute a (1−ε)-approximate maximum weight matching (MWM) in a bipartite
    graph with n vertices and m edges in time O(mε−1log(ε−1)), matching the running
    time of the linear-time approximation algorithm of Duan and Pettie [JACM ’14].
    Our algorithm is very simple and it can be extended to give a dynamic data structure
    that maintains a (1−ε)-approximate maximum weight matching under (1) one-sided
    vertex deletions (with incident edges) and (2) one-sided vertex insertions (with
    incident edges sorted by weight) to the other side. The total time time used is
    O(mε−1log(ε−1)), where m is the sum of the number of initially existing and inserted
    edges.
acknowledgement: The first author thanks to Chandra Chekuri for useful discussions
  about this paper. This project has received funding from the European Research Council
  (ERC) under the European Union’s Horizon 2020 research and innovation programme
  (Grant agreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures
  (MoDynStruct)” and from the Austrian Science Fund (FWF) project “Fast Algorithms
  for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from
  the netidee SCIENCE Stiftung, 2020–2024.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Da Wei
  full_name: Zheng, Da Wei
  last_name: Zheng
- first_name: Monika H
  full_name: Henzinger, Monika H
  id: 540c9bbd-f2de-11ec-812d-d04a5be85630
  last_name: Henzinger
  orcid: 0000-0002-5008-6530
citation:
  ama: 'Zheng DW, Henzinger M. Multiplicative auction algorithm for approximate maximum
    weight bipartite matching. In: <i>International Conference on Integer Programming
    and Combinatorial Optimization</i>. Vol 13904. Springer Nature; 2023:453-465.
    doi:<a href="https://doi.org/10.1007/978-3-031-32726-1_32">10.1007/978-3-031-32726-1_32</a>'
  apa: 'Zheng, D. W., &#38; Henzinger, M. (2023). Multiplicative auction algorithm
    for approximate maximum weight bipartite matching. In <i>International Conference
    on Integer Programming and Combinatorial Optimization</i> (Vol. 13904, pp. 453–465).
    Madison, WI, United States: Springer Nature. <a href="https://doi.org/10.1007/978-3-031-32726-1_32">https://doi.org/10.1007/978-3-031-32726-1_32</a>'
  chicago: Zheng, Da Wei, and Monika Henzinger. “Multiplicative Auction Algorithm
    for Approximate Maximum Weight Bipartite Matching.” In <i>International Conference
    on Integer Programming and Combinatorial Optimization</i>, 13904:453–65. Springer
    Nature, 2023. <a href="https://doi.org/10.1007/978-3-031-32726-1_32">https://doi.org/10.1007/978-3-031-32726-1_32</a>.
  ieee: D. W. Zheng and M. Henzinger, “Multiplicative auction algorithm for approximate
    maximum weight bipartite matching,” in <i>International Conference on Integer
    Programming and Combinatorial Optimization</i>, Madison, WI, United States, 2023,
    vol. 13904, pp. 453–465.
  ista: 'Zheng DW, Henzinger M. 2023. Multiplicative auction algorithm for approximate
    maximum weight bipartite matching. International Conference on Integer Programming
    and Combinatorial Optimization. IPCO: Integer Programming and Combinatorial Optimization,
    LNCS, vol. 13904, 453–465.'
  mla: Zheng, Da Wei, and Monika Henzinger. “Multiplicative Auction Algorithm for Approximate
    Maximum Weight Bipartite Matching.” <i>International Conference on Integer Programming
    and Combinatorial Optimization</i>, vol. 13904, Springer Nature, 2023, pp. 453–65,
    doi:<a href="https://doi.org/10.1007/978-3-031-32726-1_32">10.1007/978-3-031-32726-1_32</a>.
  short: D.W. Zheng, M. Henzinger, in:, International Conference on Integer Programming
    and Combinatorial Optimization, Springer Nature, 2023, pp. 453–465.
conference:
  end_date: 2023-06-23
  location: Madison, WI, United States
  name: 'IPCO: Integer Programming and Combinatorial Optimization'
  start_date: 2023-06-21
date_created: 2023-07-16T22:01:11Z
date_published: 2023-05-22T00:00:00Z
date_updated: 2025-09-09T12:39:59Z
day: '22'
department:
- _id: MoHe
doi: 10.1007/978-3-031-32726-1_32
ec_funded: 1
external_id:
  arxiv:
  - '2301.09217'
  isi:
  - '001281059600032'
intvolume: '     13904'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.48550/arXiv.2301.09217
month: '05'
oa: 1
oa_version: Preprint
page: 453-465
project:
- _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62
  call_identifier: H2020
  grant_number: '101019564'
  name: The design and evaluation of modern fully dynamic data structures
- _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe
  grant_number: P33775
  name: Fast Algorithms for a Reactive Network Layer
publication: International Conference on Integer Programming and Combinatorial Optimization
publication_identifier:
  eissn:
  - 1611-3349
  isbn:
  - '9783031327254'
  issn:
  - 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
  record:
  - id: '15121'
    relation: later_version
    status: public
scopus_import: '1'
status: public
title: Multiplicative auction algorithm for approximate maximum weight bipartite matching
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 13904
year: '2023'
...
---
_id: '13237'
abstract:
- lang: eng
  text: The formation of amyloid fibrils is a general class of protein self-assembly
    behaviour, which is associated with both functional biology and the development
    of a number of disorders, such as Alzheimer and Parkinson diseases. In this Review,
    we discuss how general physical concepts from the study of phase transitions can
    be used to illuminate the fundamental mechanisms of amyloid self-assembly. We
    summarize progress in the efforts to describe the essential biophysical features
    of amyloid self-assembly as a nucleation-and-growth process and discuss how master
    equation approaches can reveal the key molecular pathways underlying this process,
    including the role of secondary nucleation. Additionally, we outline how non-classical
    aspects of aggregate formation involving oligomers or biomolecular condensates
    have emerged, inspiring developments in understanding, modelling and modulating
    complex protein assembly pathways. Finally, we consider how these concepts can
    be applied to kinetics-based drug discovery and therapeutic design to develop
    treatments for protein aggregation diseases.
acknowledgement: The authors acknowledge support from the Institute for the Physics
  of Living Systems, University College London (T.C.T.M.), the Swedish Research Council
  (2015-00143) (S.L.), the European Research Council under the European Union’s Seventh
  Framework Programme (FP7/2007-2013) through the ERC grant PhysProt (agreement no.
  337969) (T.P.J.K.), the BBSRC (T.P.J.K.), the Newman Foundation (T.P.J.K.) and the
  Wellcome Trust Collaborative Award 203249/Z/16/Z (T.P.J.K.). The authors thank C.
  Flandoli for help with illustrations.
article_processing_charge: No
article_type: original
author:
- first_name: Thomas C.T.
  full_name: Michaels, Thomas C.T.
  last_name: Michaels
- first_name: Daoyuan
  full_name: Qian, Daoyuan
  last_name: Qian
- first_name: Anđela
  full_name: Šarić, Anđela
  id: bf63d406-f056-11eb-b41d-f263a6566d8b
  last_name: Šarić
  orcid: 0000-0002-7854-2139
- first_name: Michele
  full_name: Vendruscolo, Michele
  last_name: Vendruscolo
- first_name: Sara
  full_name: Linse, Sara
  last_name: Linse
- first_name: Tuomas P.J.
  full_name: Knowles, Tuomas P.J.
  last_name: Knowles
citation:
  ama: Michaels TCT, Qian D, Šarić A, Vendruscolo M, Linse S, Knowles TPJ. Amyloid
    formation as a protein phase transition. <i>Nature Reviews Physics</i>. 2023;5:379–397.
    doi:<a href="https://doi.org/10.1038/s42254-023-00598-9">10.1038/s42254-023-00598-9</a>
  apa: Michaels, T. C. T., Qian, D., Šarić, A., Vendruscolo, M., Linse, S., &#38;
    Knowles, T. P. J. (2023). Amyloid formation as a protein phase transition. <i>Nature
    Reviews Physics</i>. Springer Nature. <a href="https://doi.org/10.1038/s42254-023-00598-9">https://doi.org/10.1038/s42254-023-00598-9</a>
  chicago: Michaels, Thomas C.T., Daoyuan Qian, Anđela Šarić, Michele Vendruscolo,
    Sara Linse, and Tuomas P.J. Knowles. “Amyloid Formation as a Protein Phase Transition.”
    <i>Nature Reviews Physics</i>. Springer Nature, 2023. <a href="https://doi.org/10.1038/s42254-023-00598-9">https://doi.org/10.1038/s42254-023-00598-9</a>.
  ieee: T. C. T. Michaels, D. Qian, A. Šarić, M. Vendruscolo, S. Linse, and T. P.
    J. Knowles, “Amyloid formation as a protein phase transition,” <i>Nature Reviews
    Physics</i>, vol. 5. Springer Nature, pp. 379–397, 2023.
  ista: Michaels TCT, Qian D, Šarić A, Vendruscolo M, Linse S, Knowles TPJ. 2023.
    Amyloid formation as a protein phase transition. Nature Reviews Physics. 5, 379–397.
  mla: Michaels, Thomas C. T., et al. “Amyloid Formation as a Protein Phase Transition.”
    <i>Nature Reviews Physics</i>, vol. 5, Springer Nature, 2023, pp. 379–397, doi:<a
    href="https://doi.org/10.1038/s42254-023-00598-9">10.1038/s42254-023-00598-9</a>.
  short: T.C.T. Michaels, D. Qian, A. Šarić, M. Vendruscolo, S. Linse, T.P.J. Knowles,
    Nature Reviews Physics 5 (2023) 379–397.
date_created: 2023-07-16T22:01:12Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2023-08-02T06:28:38Z
day: '01'
department:
- _id: AnSa
doi: 10.1038/s42254-023-00598-9
external_id:
  isi:
  - '001017539800001'
intvolume: '         5'
isi: 1
language:
- iso: eng
month: '07'
oa_version: None
page: 379–397
publication: Nature Reviews Physics
publication_identifier:
  eissn:
  - 2522-5820
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Amyloid formation as a protein phase transition
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 5
year: '2023'
...
---
_id: '13251'
abstract:
- lang: eng
  text: A rotating organic cation and a dynamically disordered soft inorganic cage
    are the hallmark features of organic-inorganic lead-halide perovskites. Understanding
    the interplay between these two subsystems is a challenging problem, but it is
    this coupling that is widely conjectured to be responsible for the unique behavior
    of photocarriers in these materials. In this work, we use the fact that the polarizability
    of the organic cation strongly depends on the ambient electrostatic environment
    to put the molecule forward as a sensitive probe of the local crystal fields inside
    the lattice cell. We measure the average polarizability of the C/N–H bond stretching
    mode by means of infrared spectroscopy, which allows us to deduce the character
    of the motion of the cation molecule, find the magnitude of the local crystal
    field, and place an estimate on the strength of the hydrogen bond between the
    hydrogen and halide atoms. Our results pave the way for understanding electric
    fields in lead-halide perovskites using infrared bond spectroscopy.
acknowledgement: "We thank Bingqing Cheng and Hong-Zhou Ye for valuable discussions;
  Y.W.’s work at IST Austria was supported through ISTernship summer internship program
  funded by OeADGmbH; D.L. and Z.A. acknowledge support by IST Austria (ISTA); M.L.
  acknowledges support by the European Research Council (ERC) Starting Grant No. 801770
  (ANGULON).\r\nA.A.Z. and O.M.B. acknowledge support by KAUST."
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Yujing
  full_name: Wei, Yujing
  id: 0c5ff007-2600-11ee-b896-98bd8d663294
  last_name: Wei
  orcid: 0000-0001-8913-9719
- first_name: Artem
  full_name: Volosniev, Artem
  id: 37D278BC-F248-11E8-B48F-1D18A9856A87
  last_name: Volosniev
  orcid: 0000-0003-0393-5525
- first_name: Dusan
  full_name: Lorenc, Dusan
  id: 40D8A3E6-F248-11E8-B48F-1D18A9856A87
  last_name: Lorenc
- first_name: Ayan A.
  full_name: Zhumekenov, Ayan A.
  last_name: Zhumekenov
- first_name: Osman M.
  full_name: Bakr, Osman M.
  last_name: Bakr
- first_name: Mikhail
  full_name: Lemeshko, Mikhail
  id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
  last_name: Lemeshko
  orcid: 0000-0002-6990-7802
- first_name: Zhanybek
  full_name: Alpichshev, Zhanybek
  id: 45E67A2A-F248-11E8-B48F-1D18A9856A87
  last_name: Alpichshev
  orcid: 0000-0002-7183-5203
citation:
  ama: Wei Y, Volosniev A, Lorenc D, et al. Bond polarizability as a probe of local
    crystal fields in hybrid lead-halide perovskites. <i>The Journal of Physical Chemistry
    Letters</i>. 2023;14(27):6309-6314. doi:<a href="https://doi.org/10.1021/acs.jpclett.3c01158">10.1021/acs.jpclett.3c01158</a>
  apa: Wei, Y., Volosniev, A., Lorenc, D., Zhumekenov, A. A., Bakr, O. M., Lemeshko,
    M., &#38; Alpichshev, Z. (2023). Bond polarizability as a probe of local crystal
    fields in hybrid lead-halide perovskites. <i>The Journal of Physical Chemistry
    Letters</i>. American Chemical Society. <a href="https://doi.org/10.1021/acs.jpclett.3c01158">https://doi.org/10.1021/acs.jpclett.3c01158</a>
  chicago: Wei, Yujing, Artem Volosniev, Dusan Lorenc, Ayan A. Zhumekenov, Osman M.
    Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Bond Polarizability as a Probe
    of Local Crystal Fields in Hybrid Lead-Halide Perovskites.” <i>The Journal of
    Physical Chemistry Letters</i>. American Chemical Society, 2023. <a href="https://doi.org/10.1021/acs.jpclett.3c01158">https://doi.org/10.1021/acs.jpclett.3c01158</a>.
  ieee: Y. Wei <i>et al.</i>, “Bond polarizability as a probe of local crystal fields
    in hybrid lead-halide perovskites,” <i>The Journal of Physical Chemistry Letters</i>,
    vol. 14, no. 27. American Chemical Society, pp. 6309–6314, 2023.
  ista: Wei Y, Volosniev A, Lorenc D, Zhumekenov AA, Bakr OM, Lemeshko M, Alpichshev
    Z. 2023. Bond polarizability as a probe of local crystal fields in hybrid lead-halide
    perovskites. The Journal of Physical Chemistry Letters. 14(27), 6309–6314.
  mla: Wei, Yujing, et al. “Bond Polarizability as a Probe of Local Crystal Fields
    in Hybrid Lead-Halide Perovskites.” <i>The Journal of Physical Chemistry Letters</i>,
    vol. 14, no. 27, American Chemical Society, 2023, pp. 6309–14, doi:<a href="https://doi.org/10.1021/acs.jpclett.3c01158">10.1021/acs.jpclett.3c01158</a>.
  short: Y. Wei, A. Volosniev, D. Lorenc, A.A. Zhumekenov, O.M. Bakr, M. Lemeshko,
    Z. Alpichshev, The Journal of Physical Chemistry Letters 14 (2023) 6309–6314.
corr_author: '1'
date_created: 2023-07-18T11:13:17Z
date_published: 2023-07-05T00:00:00Z
date_updated: 2025-04-23T13:01:50Z
day: '05'
ddc:
- '530'
department:
- _id: MiLe
- _id: ZhAl
doi: 10.1021/acs.jpclett.3c01158
ec_funded: 1
external_id:
  arxiv:
  - '2304.14198'
  isi:
  - '001022811500001'
  pmid:
  - '37405449'
file:
- access_level: open_access
  checksum: c0c040063f06a51b9c463adc504f1a23
  content_type: application/pdf
  creator: dernst
  date_created: 2023-07-19T06:55:39Z
  date_updated: 2023-07-19T06:55:39Z
  file_id: '13253'
  file_name: 2023_JourPhysChemistry_Wei.pdf
  file_size: 2121252
  relation: main_file
  success: 1
file_date_updated: 2023-07-19T06:55:39Z
has_accepted_license: '1'
intvolume: '        14'
isi: 1
issue: '27'
keyword:
- General Materials Science
- Physical and Theoretical Chemistry
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 6309-6314
pmid: 1
project:
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '801770'
  name: 'Angulon: physics and applications of a new quasiparticle'
publication: The Journal of Physical Chemistry Letters
publication_identifier:
  eissn:
  - 1948-7185
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bond polarizability as a probe of local crystal fields in hybrid lead-halide
  perovskites
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2023'
...
---
_id: '13256'
abstract:
- lang: eng
  text: The El Niño-Southern Oscillation (ENSO) and the Indian summer monsoon (ISM,
    or monsoon) are two giants of tropical climate. Here we assess the future evolution
    of the ENSO-monsoon teleconnection in climate simulations with idealized forcing
    of CO2 increment at a rate of 1% year-1 starting from a present-day condition
    (367 p.p.m.) until quadrupling. We find a monotonous weakening of the ENSO-monsoon
    teleconnection with the increase in CO2. Increased co-occurrences of El Niño and
    positive Indian Ocean Dipoles (pIODs) in a warmer climate weaken the teleconnection.
    Co-occurrences of El Niño and pIOD are attributable to mean sea surface temperature
    (SST) warming that resembles a pIOD-type warming pattern in the Indian Ocean and
    an El Niño-type warming in the Pacific. Since ENSO is a critical precursor of
    the strength of the Indian monsoon, a weakening of this relation may mean a less
    predictable Indian monsoon in a warmer climate.
acknowledgement: This work was supported by National Research Foundation of Korea
  (NRF) grants funded by the Korean government (MSIT) (NRF-2018R1A5A1024958, RS-2023-00208000).
  Model simulation and data transfer were supported by the National Supercomputing
  Center with supercomputing resources including technical support (KSC-2019-CHA-0005),
  the National Center for Meteorological Supercomputer of the Korea Meteorological
  Administration (KMA), and by the Korea Research Environment Open NETwork (KREONET),
  respectively. We sincerely thank Dr. Jongsoo Shin of Pohang University of Science
  and Technology, Pohang, South Korea for the model simulations.
article_number: '82'
article_processing_charge: Yes
article_type: original
author:
- first_name: Bidyut B
  full_name: Goswami, Bidyut B
  id: 3a4ac09c-6d61-11ec-bf66-884cde66b64b
  last_name: Goswami
- first_name: Soon Il
  full_name: An, Soon Il
  last_name: An
citation:
  ama: GOSWAMI BB, An SI. An assessment of the ENSO-monsoon teleconnection in a warming
    climate. <i>npj Climate and Atmospheric Science</i>. 2023;6. doi:<a href="https://doi.org/10.1038/s41612-023-00411-5">10.1038/s41612-023-00411-5</a>
  apa: GOSWAMI, B. B., &#38; An, S. I. (2023). An assessment of the ENSO-monsoon teleconnection
    in a warming climate. <i>Npj Climate and Atmospheric Science</i>. Springer Nature.
    <a href="https://doi.org/10.1038/s41612-023-00411-5">https://doi.org/10.1038/s41612-023-00411-5</a>
  chicago: GOSWAMI, BIDYUT B, and Soon Il An. “An Assessment of the ENSO-Monsoon Teleconnection
    in a Warming Climate.” <i>Npj Climate and Atmospheric Science</i>. Springer Nature,
    2023. <a href="https://doi.org/10.1038/s41612-023-00411-5">https://doi.org/10.1038/s41612-023-00411-5</a>.
  ieee: B. B. GOSWAMI and S. I. An, “An assessment of the ENSO-monsoon teleconnection
    in a warming climate,” <i>npj Climate and Atmospheric Science</i>, vol. 6. Springer
    Nature, 2023.
  ista: GOSWAMI BB, An SI. 2023. An assessment of the ENSO-monsoon teleconnection
    in a warming climate. npj Climate and Atmospheric Science. 6, 82.
  mla: GOSWAMI, BIDYUT B., and Soon Il An. “An Assessment of the ENSO-Monsoon Teleconnection
    in a Warming Climate.” <i>Npj Climate and Atmospheric Science</i>, vol. 6, 82,
    Springer Nature, 2023, doi:<a href="https://doi.org/10.1038/s41612-023-00411-5">10.1038/s41612-023-00411-5</a>.
  short: B.B. GOSWAMI, S.I. An, Npj Climate and Atmospheric Science 6 (2023).
date_created: 2023-07-23T22:01:10Z
date_published: 2023-07-08T00:00:00Z
date_updated: 2023-08-02T06:38:07Z
day: '08'
ddc:
- '550'
department:
- _id: CaMu
doi: 10.1038/s41612-023-00411-5
external_id:
  isi:
  - '001024920300002'
file:
- access_level: open_access
  checksum: e9967d436a83b8ffcc6f58782e1f7500
  content_type: application/pdf
  creator: dernst
  date_created: 2023-07-31T08:00:01Z
  date_updated: 2023-07-31T08:00:01Z
  file_id: '13326'
  file_name: 2023_npjclimate_Goswami.pdf
  file_size: 1750712
  relation: main_file
  success: 1
file_date_updated: 2023-07-31T08:00:01Z
has_accepted_license: '1'
intvolume: '         6'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: npj Climate and Atmospheric Science
publication_identifier:
  eissn:
  - 2397-3722
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: An assessment of the ENSO-monsoon teleconnection in a warming climate
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 6
year: '2023'
...
---
_id: '13257'
abstract:
- lang: eng
  text: The magnetotropic susceptibility is the thermodynamic coefficient associated
    with the rotational anisotropy of the free energy in an external magnetic field
    and is closely related to the magnetic susceptibility. It emerges naturally in
    frequency-shift measurements of oscillating mechanical cantilevers, which are
    becoming an increasingly important tool in the quantitative study of the thermodynamics
    of modern condensed-matter systems. Here we discuss the basic properties of the
    magnetotropic susceptibility as they relate to the experimental aspects of frequency-shift
    measurements, as well as to the interpretation of those experiments in terms of
    the intrinsic properties of the system under study.
acknowledgement: "We thank Aharon Kapitulnik, Philip Moll, and Andreas Rydh for illuminating
  discussions. The work at the Los Alamos National Laboratory is supported by National
  Science Foundation Cooperative Agreements No. DMR-1157490 and No. DMR-1644779, the
  state of Florida, and the U.S. Department of Energy. A.S. acknowledges support from
  the DOE/BES Science of 100T grant. B.J.R. acknowledges funding from the National
  Science Foundation under Grant No.\r\nDMR-1752784."
article_number: '035111'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: A.
  full_name: Shekhter, A.
  last_name: Shekhter
- first_name: R. D.
  full_name: Mcdonald, R. D.
  last_name: Mcdonald
- first_name: B. J.
  full_name: Ramshaw, B. J.
  last_name: Ramshaw
- first_name: Kimberly A
  full_name: Modic, Kimberly A
  id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425
  last_name: Modic
  orcid: 0000-0001-9760-3147
citation:
  ama: Shekhter A, Mcdonald RD, Ramshaw BJ, Modic KA. Magnetotropic susceptibility.
    <i>Physical Review B</i>. 2023;108(3). doi:<a href="https://doi.org/10.1103/PhysRevB.108.035111">10.1103/PhysRevB.108.035111</a>
  apa: Shekhter, A., Mcdonald, R. D., Ramshaw, B. J., &#38; Modic, K. A. (2023). Magnetotropic
    susceptibility. <i>Physical Review B</i>. American Physical Society. <a href="https://doi.org/10.1103/PhysRevB.108.035111">https://doi.org/10.1103/PhysRevB.108.035111</a>
  chicago: Shekhter, A., R. D. Mcdonald, B. J. Ramshaw, and Kimberly A Modic. “Magnetotropic
    Susceptibility.” <i>Physical Review B</i>. American Physical Society, 2023. <a
    href="https://doi.org/10.1103/PhysRevB.108.035111">https://doi.org/10.1103/PhysRevB.108.035111</a>.
  ieee: A. Shekhter, R. D. Mcdonald, B. J. Ramshaw, and K. A. Modic, “Magnetotropic
    susceptibility,” <i>Physical Review B</i>, vol. 108, no. 3. American Physical
    Society, 2023.
  ista: Shekhter A, Mcdonald RD, Ramshaw BJ, Modic KA. 2023. Magnetotropic susceptibility.
    Physical Review B. 108(3), 035111.
  mla: Shekhter, A., et al. “Magnetotropic Susceptibility.” <i>Physical Review B</i>,
    vol. 108, no. 3, 035111, American Physical Society, 2023, doi:<a href="https://doi.org/10.1103/PhysRevB.108.035111">10.1103/PhysRevB.108.035111</a>.
  short: A. Shekhter, R.D. Mcdonald, B.J. Ramshaw, K.A. Modic, Physical Review B 108
    (2023).
date_created: 2023-07-23T22:01:10Z
date_published: 2023-07-15T00:00:00Z
date_updated: 2023-12-13T11:58:57Z
day: '15'
department:
- _id: KiMo
doi: 10.1103/PhysRevB.108.035111
external_id:
  arxiv:
  - '2208.10038'
  isi:
  - '001062708600002'
intvolume: '       108'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.48550/arXiv.2208.10038
month: '07'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
  eissn:
  - 2469-9969
  issn:
  - 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Magnetotropic susceptibility
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2023'
...
---
_id: '13258'
abstract:
- lang: eng
  text: Many human interactions feature the characteristics of social dilemmas where
    individual actions have consequences for the group and the environment. The feedback
    between behavior and environment can be studied with the framework of stochastic
    games. In stochastic games, the state of the environment can change, depending
    on the choices made by group members. Past work suggests that such feedback can
    reinforce cooperative behaviors. In particular, cooperation can evolve in stochastic
    games even if it is infeasible in each separate repeated game. In stochastic games,
    participants have an interest in conditioning their strategies on the state of
    the environment. Yet in many applications, precise information about the state
    could be scarce. Here, we study how the availability of information (or lack thereof)
    shapes evolution of cooperation. Already for simple examples of two state games
    we find surprising effects. In some cases, cooperation is only possible if there
    is precise information about the state of the environment. In other cases, cooperation
    is most abundant when there is no information about the state of the environment.
    We systematically analyze all stochastic games of a given complexity class, to
    determine when receiving information about the environment is better, neutral,
    or worse for evolution of cooperation.
acknowledgement: 'This work was supported by the European Research Council CoG 863818
  (ForM-SMArt) (to K.C.), the European Research Council Starting Grant 850529: E-DIRECT
  (to C.H.), the European Union’s Horizon 2020 research and innovation program under
  the Marie Sklodowska-Curie Grant Agreement #754411 and the French Agence Nationale
  de la Recherche (under the Investissement d’Avenir programme, ANR-17-EURE-0010)
  (to M.K.).'
article_number: '4153'
article_processing_charge: Yes
article_type: original
author:
- first_name: Maria
  full_name: Kleshnina, Maria
  id: 4E21749C-F248-11E8-B48F-1D18A9856A87
  last_name: Kleshnina
- first_name: Christian
  full_name: Hilbe, Christian
  id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
  last_name: Hilbe
  orcid: 0000-0001-5116-955X
- first_name: Stepan
  full_name: Simsa, Stepan
  id: 409d615c-2f95-11ee-b934-90a352102c1e
  last_name: Simsa
  orcid: 0000-0001-6687-1210
- first_name: Krishnendu
  full_name: Chatterjee, Krishnendu
  id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
  last_name: Chatterjee
  orcid: 0000-0002-4561-241X
- first_name: Martin A.
  full_name: Nowak, Martin A.
  last_name: Nowak
citation:
  ama: Kleshnina M, Hilbe C, Simsa S, Chatterjee K, Nowak MA. The effect of environmental
    information on evolution of cooperation in stochastic games. <i>Nature Communications</i>.
    2023;14. doi:<a href="https://doi.org/10.1038/s41467-023-39625-9">10.1038/s41467-023-39625-9</a>
  apa: Kleshnina, M., Hilbe, C., Simsa, S., Chatterjee, K., &#38; Nowak, M. A. (2023).
    The effect of environmental information on evolution of cooperation in stochastic
    games. <i>Nature Communications</i>. Springer Nature. <a href="https://doi.org/10.1038/s41467-023-39625-9">https://doi.org/10.1038/s41467-023-39625-9</a>
  chicago: Kleshnina, Maria, Christian Hilbe, Stepan Simsa, Krishnendu Chatterjee,
    and Martin A. Nowak. “The Effect of Environmental Information on Evolution of
    Cooperation in Stochastic Games.” <i>Nature Communications</i>. Springer Nature,
    2023. <a href="https://doi.org/10.1038/s41467-023-39625-9">https://doi.org/10.1038/s41467-023-39625-9</a>.
  ieee: M. Kleshnina, C. Hilbe, S. Simsa, K. Chatterjee, and M. A. Nowak, “The effect
    of environmental information on evolution of cooperation in stochastic games,”
    <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.
  ista: Kleshnina M, Hilbe C, Simsa S, Chatterjee K, Nowak MA. 2023. The effect of
    environmental information on evolution of cooperation in stochastic games. Nature
    Communications. 14, 4153.
  mla: Kleshnina, Maria, et al. “The Effect of Environmental Information on Evolution
    of Cooperation in Stochastic Games.” <i>Nature Communications</i>, vol. 14, 4153,
    Springer Nature, 2023, doi:<a href="https://doi.org/10.1038/s41467-023-39625-9">10.1038/s41467-023-39625-9</a>.
  short: M. Kleshnina, C. Hilbe, S. Simsa, K. Chatterjee, M.A. Nowak, Nature Communications
    14 (2023).
corr_author: '1'
date_created: 2023-07-23T22:01:11Z
date_published: 2023-07-12T00:00:00Z
date_updated: 2025-04-14T07:43:55Z
day: '12'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1038/s41467-023-39625-9
ec_funded: 1
external_id:
  isi:
  - '001029450400031'
  pmid:
  - '37438341'
file:
- access_level: open_access
  checksum: 5aceefdfe76686267b93ae4fe81899f1
  content_type: application/pdf
  creator: dernst
  date_created: 2023-07-31T11:32:36Z
  date_updated: 2023-07-31T11:32:36Z
  file_id: '13337'
  file_name: 2023_NatureComm_Kleshnina.pdf
  file_size: 1601682
  relation: main_file
  success: 1
file_date_updated: 2023-07-31T11:32:36Z
has_accepted_license: '1'
intvolume: '        14'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
  call_identifier: H2020
  grant_number: '863818'
  name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 260C2330-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '754411'
  name: ISTplus - Postdoctoral Fellowships
publication: Nature Communications
publication_identifier:
  eissn:
  - 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
  record:
  - id: '13336'
    relation: research_data
    status: public
scopus_import: '1'
status: public
title: The effect of environmental information on evolution of cooperation in stochastic
  games
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2023'
...
---
_id: '13259'
abstract:
- lang: eng
  text: Plants can regenerate their bodies via de novo establishment of shoot apical
    meristems (SAMs) from pluripotent callus. Only a small fraction of callus cells
    is eventually specified into SAMs but the molecular mechanisms underlying fate
    specification remain obscure. The expression of WUSCHEL (WUS) is an early hallmark
    of SAM fate acquisition. Here, we show that a WUS paralog, WUSCHEL-RELATED HOMEOBOX
    13 (WOX13), negatively regulates SAM formation from callus in Arabidopsis thaliana.
    WOX13 promotes non-meristematic cell fate via transcriptional repression of WUS
    and other SAM regulators and activation of cell wall modifiers. Our Quartz-Seq2–based
    single cell transcriptome revealed that WOX13 plays key roles in determining cellular
    identity of callus cell population. We propose that reciprocal inhibition between
    WUS and WOX13 mediates critical cell fate determination in pluripotent cell population,
    which has a major impact on regeneration efficiency.
acknowledgement: Wethank Y.Iwayama, K.Ohtawa, K.Fukumoto,andN. Mataga (RIKENRRD) for
  technical assistance in Quartz-Seq2analyses; M. Mouri(RIKENCSRS)for technical support
  with plasmid construction and transactivation assay; Y. Ikeda (NAIST) for technical
  support with tissue culture; and A. Furuta for technical support in bulk RNA-seq
  analysis. We also thank the Single-cell Omics Laboratory for technical consultation
  in scRNA-seq analyses, the members of the Laboratory for Bioinformatics Research
  at the RIKEN Center for Biosystems Dynamics Research, and A. Matsushima and T. Ichikawa
  for IT infrastructure management. This work was supported by JSPS KAKENHI(17K15146,19H05670,20K06712,20H04894,20H05431,and
  22H04713 to M.I. and 20H03284 and 20H05911 to K.S.), by the JST FOREST Program (JPMJFR214H
  to M.I.), by The Naito Foundation to M.I.; by Takeda Science Foundation to M.I,and
  by the Shiseido Female Researcher Science Grant to M.I. This work was partially
  supported by RIKENE pigenome Control Program, Medical Research Center Initiative
  for High Depth Omics, and JST CREST(JPMJCR16G3and JPMJCR1926)to I.N.
article_processing_charge: Yes
article_type: original
author:
- first_name: Nao
  full_name: Ogura, Nao
  last_name: Ogura
- first_name: Yohei
  full_name: Sasagawa, Yohei
  last_name: Sasagawa
- first_name: Tasuku
  full_name: Ito, Tasuku
  id: d5a17a4a-e534-11eb-93ec-91fa2aa9bd57
  last_name: Ito
  orcid: 0000-0002-2482-9089
- first_name: Toshiaki
  full_name: Tameshige, Toshiaki
  last_name: Tameshige
- first_name: Satomi
  full_name: Kawai, Satomi
  last_name: Kawai
- first_name: Masaki
  full_name: Sano, Masaki
  last_name: Sano
- first_name: Yuki
  full_name: Doll, Yuki
  last_name: Doll
- first_name: Akira
  full_name: Iwase, Akira
  last_name: Iwase
- first_name: Ayako
  full_name: Kawamura, Ayako
  last_name: Kawamura
- first_name: Takamasa
  full_name: Suzuki, Takamasa
  last_name: Suzuki
- first_name: Itoshi
  full_name: Nikaido, Itoshi
  last_name: Nikaido
- first_name: Keiko
  full_name: Sugimoto, Keiko
  last_name: Sugimoto
- first_name: Momoko
  full_name: Ikeuchi, Momoko
  last_name: Ikeuchi
citation:
  ama: Ogura N, Sasagawa Y, Ito T, et al. WUSCHEL-RELATED HOMEOBOX 13 suppresses de
    novo shoot regeneration via cell fate control of pluripotent callus. <i>Science
    Advances</i>. 2023;9(27):eadg6983. doi:<a href="https://doi.org/10.1126/sciadv.adg6983">10.1126/sciadv.adg6983</a>
  apa: Ogura, N., Sasagawa, Y., Ito, T., Tameshige, T., Kawai, S., Sano, M., … Ikeuchi,
    M. (2023). WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via
    cell fate control of pluripotent callus. <i>Science Advances</i>. American Association
    for the Advancement of Science. <a href="https://doi.org/10.1126/sciadv.adg6983">https://doi.org/10.1126/sciadv.adg6983</a>
  chicago: Ogura, Nao, Yohei Sasagawa, Tasuku Ito, Toshiaki Tameshige, Satomi Kawai,
    Masaki Sano, Yuki Doll, et al. “WUSCHEL-RELATED HOMEOBOX 13 Suppresses de Novo
    Shoot Regeneration via Cell Fate Control of Pluripotent Callus.” <i>Science Advances</i>.
    American Association for the Advancement of Science, 2023. <a href="https://doi.org/10.1126/sciadv.adg6983">https://doi.org/10.1126/sciadv.adg6983</a>.
  ieee: N. Ogura <i>et al.</i>, “WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot
    regeneration via cell fate control of pluripotent callus,” <i>Science Advances</i>,
    vol. 9, no. 27. American Association for the Advancement of Science, p. eadg6983,
    2023.
  ista: Ogura N, Sasagawa Y, Ito T, Tameshige T, Kawai S, Sano M, Doll Y, Iwase A,
    Kawamura A, Suzuki T, Nikaido I, Sugimoto K, Ikeuchi M. 2023. WUSCHEL-RELATED
    HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent
    callus. Science Advances. 9(27), eadg6983.
  mla: Ogura, Nao, et al. “WUSCHEL-RELATED HOMEOBOX 13 Suppresses de Novo Shoot Regeneration
    via Cell Fate Control of Pluripotent Callus.” <i>Science Advances</i>, vol. 9,
    no. 27, American Association for the Advancement of Science, 2023, p. eadg6983,
    doi:<a href="https://doi.org/10.1126/sciadv.adg6983">10.1126/sciadv.adg6983</a>.
  short: N. Ogura, Y. Sasagawa, T. Ito, T. Tameshige, S. Kawai, M. Sano, Y. Doll,
    A. Iwase, A. Kawamura, T. Suzuki, I. Nikaido, K. Sugimoto, M. Ikeuchi, Science
    Advances 9 (2023) eadg6983.
date_created: 2023-07-23T22:01:11Z
date_published: 2023-07-07T00:00:00Z
date_updated: 2023-12-13T11:59:29Z
day: '07'
ddc:
- '580'
doi: 10.1126/sciadv.adg6983
external_id:
  isi:
  - '001030983100012'
  pmid:
  - '37418524'
file:
- access_level: open_access
  checksum: f59217e1083767777318b5d0cc5e141d
  content_type: application/pdf
  creator: dernst
  date_created: 2023-08-01T06:40:35Z
  date_updated: 2023-08-01T06:40:35Z
  file_id: '13338'
  file_name: 2023_ScienceAdvance_Ogura.pdf
  file_size: 1759993
  relation: main_file
  success: 1
file_date_updated: 2023-08-01T06:40:35Z
has_accepted_license: '1'
intvolume: '         9'
isi: 1
issue: '27'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: eadg6983
pmid: 1
publication: Science Advances
publication_identifier:
  eissn:
  - 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell
  fate control of pluripotent callus
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: 9
year: '2023'
...
---
_id: '13260'
abstract:
- lang: eng
  text: Experimental evolution studies are powerful approaches to examine the evolutionary
    history of lab populations. Such studies have shed light on how selection changes
    phenotypes and genotypes. Most of these studies have not examined the time course
    of adaptation under sexual selection manipulation, by resequencing the populations’
    genomes at multiple time points. Here, we analyze allele frequency trajectories
    in Drosophila pseudoobscura where we altered their sexual selection regime for
    200 generations and sequenced pooled populations at 5 time points. The intensity
    of sexual selection was either relaxed in monogamous populations (M) or elevated
    in polyandrous lines (E). We present a comprehensive study of how selection alters
    population genetics parameters at the chromosome and gene level. We investigate
    differences in the effective population size—Ne—between the treatments, and perform
    a genome-wide scan to identify signatures of selection from the time-series data.
    We found genomic signatures of adaptation to both regimes in D. pseudoobscura.
    There are more significant variants in E lines as expected from stronger sexual
    selection. However, we found that the response on the X chromosome was substantial
    in both treatments, more pronounced in E and restricted to the more recently sex-linked
    chromosome arm XR in M. In the first generations of experimental evolution, we
    estimate Ne to be lower on the X in E lines, which might indicate a swift adaptive
    response at the onset of selection. Additionally, the third chromosome was affected
    by elevated polyandry whereby its distal end harbors a region showing a strong
    signal of adaptive evolution especially in E lines.
acknowledgement: This work was supported by the Vienna Science and Technology Fund
  (WWTF)(10.47379/MA16061). C.K. received funding from the Royal Society (RG170315)
  and the Carnegie Trust (RIG007474). M.G.R. and R.R.S. have been supported by NERC
  (UK) grants NE/I014632/1 and NE/V001566/1. Bioinformatics analyses were performed
  on the computer cluster at the University of St Andrews Bioinformatics Unit, which
  is funded by Wellcome Trust ISSF awards 105621/Z/14/Z. Complementary data parsing
  was carried out with the computational resources provided by the Research/Scientific
  Computing teams at The James Hutton Institute and the National Institute of Agricultural
  Botany (NIAB)—UK’s Crop Diversity Bioinformatics HPC, BBSRC grant BB/S019669/1.
  We are thankful to Paris Veltsos and R. Axel W. Wiberg for useful discussions about
  the project as well as providing us with the resequencing data they had produced
  as a result of previous work on this experiment. We are especially grateful to Tanya
  Sneddon for her help with the DNA extraction process and shipping.
article_number: evad113
article_processing_charge: Yes
article_type: original
author:
- first_name: Carolina
  full_name: De Castro Barbosa Rodrigues Barata, Carolina
  id: 20565186-803f-11ed-ab7e-96a4ff7694ef
  last_name: De Castro Barbosa Rodrigues Barata
  orcid: 0000-0003-1945-2245
- first_name: Rhonda R.
  full_name: Snook, Rhonda R.
  last_name: Snook
- first_name: Michael G.
  full_name: Ritchie, Michael G.
  last_name: Ritchie
- first_name: Carolin
  full_name: Kosiol, Carolin
  last_name: Kosiol
citation:
  ama: 'de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. Selection
    on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila
    pseudoobscura. <i>Genome biology and evolution</i>. 2023;15(7). doi:<a href="https://doi.org/10.1093/gbe/evad113">10.1093/gbe/evad113</a>'
  apa: 'de Castro Barbosa Rodrigues Barata, C., Snook, R. R., Ritchie, M. G., &#38;
    Kosiol, C. (2023). Selection on the fly: Short-term adaptation to an altered sexual
    selection regime in Drosophila pseudoobscura. <i>Genome Biology and Evolution</i>.
    Oxford University Press. <a href="https://doi.org/10.1093/gbe/evad113">https://doi.org/10.1093/gbe/evad113</a>'
  chicago: 'Castro Barbosa Rodrigues Barata, Carolina de, Rhonda R. Snook, Michael
    G. Ritchie, and Carolin Kosiol. “Selection on the Fly: Short-Term Adaptation to
    an Altered Sexual Selection Regime in Drosophila Pseudoobscura.” <i>Genome Biology
    and Evolution</i>. Oxford University Press, 2023. <a href="https://doi.org/10.1093/gbe/evad113">https://doi.org/10.1093/gbe/evad113</a>.'
  ieee: 'C. de Castro Barbosa Rodrigues Barata, R. R. Snook, M. G. Ritchie, and C.
    Kosiol, “Selection on the fly: Short-term adaptation to an altered sexual selection
    regime in Drosophila pseudoobscura,” <i>Genome biology and evolution</i>, vol.
    15, no. 7. Oxford University Press, 2023.'
  ista: 'de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. 2023.
    Selection on the fly: Short-term adaptation to an altered sexual selection regime
    in Drosophila pseudoobscura. Genome biology and evolution. 15(7), evad113.'
  mla: 'de Castro Barbosa Rodrigues Barata, Carolina, et al. “Selection on the Fly:
    Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila Pseudoobscura.”
    <i>Genome Biology and Evolution</i>, vol. 15, no. 7, evad113, Oxford University
    Press, 2023, doi:<a href="https://doi.org/10.1093/gbe/evad113">10.1093/gbe/evad113</a>.'
  short: C. de Castro Barbosa Rodrigues Barata, R.R. Snook, M.G. Ritchie, C. Kosiol,
    Genome Biology and Evolution 15 (2023).
corr_author: '1'
date_created: 2023-07-23T22:01:11Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2025-05-14T11:08:37Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/gbe/evad113
external_id:
  isi:
  - '001023444700003'
  pmid:
  - '37341535'
file:
- access_level: open_access
  checksum: 70de3c4878de6efe00dc56de2df8812f
  content_type: application/pdf
  creator: dernst
  date_created: 2023-08-01T06:58:34Z
  date_updated: 2023-08-01T06:58:34Z
  file_id: '13339'
  file_name: 2023_GBE_Barata.pdf
  file_size: 2382587
  relation: main_file
  success: 1
file_date_updated: 2023-08-01T06:58:34Z
has_accepted_license: '1'
intvolume: '        15'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome biology and evolution
publication_identifier:
  eissn:
  - 1759-6653
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
  link:
  - relation: software
    url: https://github.com/carolbarata/dpseudo-n-beyond
scopus_import: '1'
status: public
title: 'Selection on the fly: Short-term adaptation to an altered sexual selection
  regime in Drosophila pseudoobscura'
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: 15
year: '2023'
...
---
_id: '13261'
abstract:
- lang: eng
  text: Chromosomes in the eukaryotic nucleus are highly compacted. However, for many
    functional processes, including transcription initiation, the pairwise motion
    of distal chromosomal elements such as enhancers and promoters is essential and
    necessitates dynamic fluidity. Here, we used a live-imaging assay to simultaneously
    measure the positions of pairs of enhancers and promoters and their transcriptional
    output while systematically varying the genomic separation between these two DNA
    loci. Our analysis reveals the coexistence of a compact globular organization
    and fast subdiffusive dynamics. These combined features cause an anomalous scaling
    of polymer relaxation times with genomic separation leading to long-ranged correlations.
    Thus, encounter times of DNA loci are much less dependent on genomic distance
    than predicted by existing polymer models, with potential consequences for eukaryotic
    gene expression.
acknowledgement: This work was supported in part by the U.S. National Science Foundation,
  the Center for the Physics of Biological Function (grant PHY-1734030), and the National
  Institutes of Health (grants R01GM097275, U01DA047730, and U01DK127429). D.B.B.
  was supported by the NOMIS Foundation as a fellow and by an EMBO postdoctoral fellowship
  (ALTF 343-2022). H.C. was supported by a Charles H. Revson Biomedical Science Fellowship.
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: Hongtao
  full_name: Chen, Hongtao
  last_name: Chen
- first_name: Lev
  full_name: Barinov, Lev
  last_name: Barinov
- first_name: Benjamin
  full_name: Zoller, Benjamin
  last_name: Zoller
- first_name: Thomas
  full_name: Gregor, Thomas
  last_name: Gregor
citation:
  ama: Brückner D, Chen H, Barinov L, Zoller B, Gregor T. Stochastic motion and transcriptional
    dynamics of pairs of distal DNA loci on a compacted chromosome. <i>Science</i>.
    2023;380(6652):1357-1362. doi:<a href="https://doi.org/10.1126/science.adf5568">10.1126/science.adf5568</a>
  apa: Brückner, D., Chen, H., Barinov, L., Zoller, B., &#38; Gregor, T. (2023). Stochastic
    motion and transcriptional dynamics of pairs of distal DNA loci on a compacted
    chromosome. <i>Science</i>. American Association for the Advancement of Science.
    <a href="https://doi.org/10.1126/science.adf5568">https://doi.org/10.1126/science.adf5568</a>
  chicago: Brückner, David, Hongtao Chen, Lev Barinov, Benjamin Zoller, and Thomas
    Gregor. “Stochastic Motion and Transcriptional Dynamics of Pairs of Distal DNA
    Loci on a Compacted Chromosome.” <i>Science</i>. American Association for the
    Advancement of Science, 2023. <a href="https://doi.org/10.1126/science.adf5568">https://doi.org/10.1126/science.adf5568</a>.
  ieee: D. Brückner, H. Chen, L. Barinov, B. Zoller, and T. Gregor, “Stochastic motion
    and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome,”
    <i>Science</i>, vol. 380, no. 6652. American Association for the Advancement of
    Science, pp. 1357–1362, 2023.
  ista: Brückner D, Chen H, Barinov L, Zoller B, Gregor T. 2023. Stochastic motion
    and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome.
    Science. 380(6652), 1357–1362.
  mla: Brückner, David, et al. “Stochastic Motion and Transcriptional Dynamics of
    Pairs of Distal DNA Loci on a Compacted Chromosome.” <i>Science</i>, vol. 380,
    no. 6652, American Association for the Advancement of Science, 2023, pp. 1357–62,
    doi:<a href="https://doi.org/10.1126/science.adf5568">10.1126/science.adf5568</a>.
  short: D. Brückner, H. Chen, L. Barinov, B. Zoller, T. Gregor, Science 380 (2023)
    1357–1362.
date_created: 2023-07-23T22:01:12Z
date_published: 2023-06-29T00:00:00Z
date_updated: 2025-04-14T08:55:54Z
day: '29'
department:
- _id: EdHa
doi: 10.1126/science.adf5568
external_id:
  isi:
  - '001106405600028'
intvolume: '       380'
isi: 1
issue: '6652'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1126/science.adf5568
month: '06'
oa: 1
oa_version: Preprint
page: 1357-1362
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
publication: Science
publication_identifier:
  eissn:
  - 1095-9203
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Stochastic motion and transcriptional dynamics of pairs of distal DNA loci
  on a compacted chromosome
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 380
year: '2023'
...
---
_id: '13262'
abstract:
- lang: eng
  text: 'Determining the degree of inherent parallelism in classical sequential algorithms
    and leveraging it for fast parallel execution is a key topic in parallel computing,
    and detailed analyses are known for a wide range of classical algorithms. In this
    paper, we perform the first such analysis for the fundamental Union-Find problem,
    in which we are given a graph as a sequence of edges, and must maintain its connectivity
    structure under edge additions. We prove that classic sequential algorithms for
    this problem are well-parallelizable under reasonable assumptions, addressing
    a conjecture by [Blelloch, 2017]. More precisely, we show via a new potential
    argument that, under uniform random edge ordering, parallel union-find operations
    are unlikely to interfere: T concurrent threads processing the graph in parallel
    will encounter memory contention O(T2 · log |V| · log |E|) times in expectation,
    where |E| and |V| are the number of edges and nodes in the graph, respectively.
    We leverage this result to design a new parallel Union-Find algorithm that is
    both internally deterministic, i.e., its results are guaranteed to match those
    of a sequential execution, but also work-efficient and scalable, as long as the
    number of threads T is O(|E|1 over 3 - ε), for an arbitrarily small constant ε
    > 0, which holds for most large real-world graphs. We present lower bounds which
    show that our analysis is close to optimal, and experimental results suggesting
    that the performance cost of internal determinism is limited.'
article_processing_charge: Yes (via OA deal)
arxiv: 1
author:
- first_name: Alexander
  full_name: Fedorov, Alexander
  id: 2e711909-896a-11ed-bdf8-eb0f5a2984c6
  last_name: Fedorov
- first_name: Diba
  full_name: Hashemi, Diba
  id: ed9595ea-2f8f-11ee-ba95-d2b546540783
  last_name: Hashemi
- first_name: Giorgi
  full_name: Nadiradze, Giorgi
  id: 3279A00C-F248-11E8-B48F-1D18A9856A87
  last_name: Nadiradze
  orcid: 0000-0001-5634-0731
- first_name: Dan-Adrian
  full_name: Alistarh, Dan-Adrian
  id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
  last_name: Alistarh
  orcid: 0000-0003-3650-940X
citation:
  ama: 'Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. Provably-efficient and internally-deterministic
    parallel Union-Find. In: <i>Proceedings of the 35th ACM Symposium on Parallelism
    in Algorithms and Architectures</i>. Association for Computing Machinery; 2023:261-271.
    doi:<a href="https://doi.org/10.1145/3558481.3591082">10.1145/3558481.3591082</a>'
  apa: 'Fedorov, A., Hashemi, D., Nadiradze, G., &#38; Alistarh, D.-A. (2023). Provably-efficient
    and internally-deterministic parallel Union-Find. In <i>Proceedings of the 35th
    ACM Symposium on Parallelism in Algorithms and Architectures</i> (pp. 261–271).
    Orlando, FL, United States: Association for Computing Machinery. <a href="https://doi.org/10.1145/3558481.3591082">https://doi.org/10.1145/3558481.3591082</a>'
  chicago: Fedorov, Alexander, Diba Hashemi, Giorgi Nadiradze, and Dan-Adrian Alistarh.
    “Provably-Efficient and Internally-Deterministic Parallel Union-Find.” In <i>Proceedings
    of the 35th ACM Symposium on Parallelism in Algorithms and Architectures</i>,
    261–71. Association for Computing Machinery, 2023. <a href="https://doi.org/10.1145/3558481.3591082">https://doi.org/10.1145/3558481.3591082</a>.
  ieee: A. Fedorov, D. Hashemi, G. Nadiradze, and D.-A. Alistarh, “Provably-efficient
    and internally-deterministic parallel Union-Find,” in <i>Proceedings of the 35th
    ACM Symposium on Parallelism in Algorithms and Architectures</i>, Orlando, FL,
    United States, 2023, pp. 261–271.
  ista: 'Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. 2023. Provably-efficient
    and internally-deterministic parallel Union-Find. Proceedings of the 35th ACM
    Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism
    in Algorithms and Architectures, 261–271.'
  mla: Fedorov, Alexander, et al. “Provably-Efficient and Internally-Deterministic
    Parallel Union-Find.” <i>Proceedings of the 35th ACM Symposium on Parallelism
    in Algorithms and Architectures</i>, Association for Computing Machinery, 2023,
    pp. 261–71, doi:<a href="https://doi.org/10.1145/3558481.3591082">10.1145/3558481.3591082</a>.
  short: A. Fedorov, D. Hashemi, G. Nadiradze, D.-A. Alistarh, in:, Proceedings of
    the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Association
    for Computing Machinery, 2023, pp. 261–271.
conference:
  end_date: 2023-06-19
  location: Orlando, FL, United States
  name: 'SPAA: Symposium on Parallelism in Algorithms and Architectures'
  start_date: 2023-06-17
corr_author: '1'
date_created: 2023-07-23T22:01:12Z
date_published: 2023-06-17T00:00:00Z
date_updated: 2025-09-09T12:43:18Z
day: '17'
ddc:
- '000'
department:
- _id: DaAl
- _id: GradSch
doi: 10.1145/3558481.3591082
external_id:
  arxiv:
  - '2304.09331'
  isi:
  - '001108889000024'
file:
- access_level: open_access
  checksum: 72e312aabf0c5248c99b5cd3a88e4c88
  content_type: application/pdf
  creator: dernst
  date_created: 2023-07-31T10:53:08Z
  date_updated: 2023-07-31T10:53:08Z
  file_id: '13334'
  file_name: 2023_SPAA_Fedorov.pdf
  file_size: 2087937
  relation: main_file
  success: 1
file_date_updated: 2023-07-31T10:53:08Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 261-271
publication: Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and
  Architectures
publication_identifier:
  isbn:
  - '9781450395458'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Provably-efficient and internally-deterministic parallel Union-Find
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2023'
...
---
_id: '13263'
abstract:
- lang: eng
  text: "Motivation: Boolean networks are simple but efficient mathematical formalism
    for modelling complex biological systems. However, having only two levels of activation
    is sometimes not enough to fully capture the dynamics of real-world biological
    systems. Hence, the need for multi-valued networks (MVNs), a generalization of
    Boolean networks. Despite the importance of MVNs for modelling biological systems,
    only limited progress has been made on developing theories, analysis methods,
    and tools that can support them. In particular, the recent use of trap spaces
    in Boolean networks made a great impact on the field of systems biology, but there
    has been no similar concept defined and studied for MVNs to date.\r\n\r\nResults:
    In this work, we generalize the concept of trap spaces in Boolean networks to
    that in MVNs. We then develop the theory and the analysis methods for trap spaces
    in MVNs. In particular, we implement all proposed methods in a Python package
    called trapmvn. Not only showing the applicability of our approach via a realistic
    case study, we also evaluate the time efficiency of the method on a large collection
    of real-world models. The experimental results confirm the time efficiency, which
    we believe enables more accurate analysis on larger and more complex multi-valued
    models."
acknowledgement: This work was supported by L’Institut Carnot STAR, Marseille, France,
  and by the European Union’s Horizon 2020 research and innovation programme under
  the Marie Skłodowska-Curie Grant Agreement No. [101034413].
article_processing_charge: Yes
article_type: original
author:
- first_name: Van Giang
  full_name: Trinh, Van Giang
  last_name: Trinh
- first_name: Belaid
  full_name: Benhamou, Belaid
  last_name: Benhamou
- first_name: Thomas A
  full_name: Henzinger, Thomas A
  id: 40876CD8-F248-11E8-B48F-1D18A9856A87
  last_name: Henzinger
  orcid: 0000-0002-2985-7724
- first_name: Samuel
  full_name: Pastva, Samuel
  id: 07c5ea74-f61c-11ec-a664-aa7c5d957b2b
  last_name: Pastva
  orcid: 0000-0003-1993-0331
citation:
  ama: 'Trinh VG, Benhamou B, Henzinger TA, Pastva S. Trap spaces of multi-valued
    networks: Definition, computation, and applications. <i>Bioinformatics</i>. 2023;39(Supplement_1):i513-i522.
    doi:<a href="https://doi.org/10.1093/bioinformatics/btad262">10.1093/bioinformatics/btad262</a>'
  apa: 'Trinh, V. G., Benhamou, B., Henzinger, T. A., &#38; Pastva, S. (2023). Trap
    spaces of multi-valued networks: Definition, computation, and applications. <i>Bioinformatics</i>.
    Oxford University Press. <a href="https://doi.org/10.1093/bioinformatics/btad262">https://doi.org/10.1093/bioinformatics/btad262</a>'
  chicago: 'Trinh, Van Giang, Belaid Benhamou, Thomas A Henzinger, and Samuel Pastva.
    “Trap Spaces of Multi-Valued Networks: Definition, Computation, and Applications.”
    <i>Bioinformatics</i>. Oxford University Press, 2023. <a href="https://doi.org/10.1093/bioinformatics/btad262">https://doi.org/10.1093/bioinformatics/btad262</a>.'
  ieee: 'V. G. Trinh, B. Benhamou, T. A. Henzinger, and S. Pastva, “Trap spaces of
    multi-valued networks: Definition, computation, and applications,” <i>Bioinformatics</i>,
    vol. 39, no. Supplement_1. Oxford University Press, pp. i513–i522, 2023.'
  ista: 'Trinh VG, Benhamou B, Henzinger TA, Pastva S. 2023. Trap spaces of multi-valued
    networks: Definition, computation, and applications. Bioinformatics. 39(Supplement_1),
    i513–i522.'
  mla: 'Trinh, Van Giang, et al. “Trap Spaces of Multi-Valued Networks: Definition,
    Computation, and Applications.” <i>Bioinformatics</i>, vol. 39, no. Supplement_1,
    Oxford University Press, 2023, pp. i513–22, doi:<a href="https://doi.org/10.1093/bioinformatics/btad262">10.1093/bioinformatics/btad262</a>.'
  short: V.G. Trinh, B. Benhamou, T.A. Henzinger, S. Pastva, Bioinformatics 39 (2023)
    i513–i522.
corr_author: '1'
date_created: 2023-07-23T22:01:12Z
date_published: 2023-06-30T00:00:00Z
date_updated: 2025-05-14T11:07:28Z
day: '30'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1093/bioinformatics/btad262
ec_funded: 1
external_id:
  isi:
  - '001027457000060'
  pmid:
  - '37387165'
file:
- access_level: open_access
  checksum: ba3abe1171df1958413b7c7f957f5486
  content_type: application/pdf
  creator: dernst
  date_created: 2023-07-31T11:09:05Z
  date_updated: 2023-07-31T11:09:05Z
  file_id: '13335'
  file_name: 2023_Bioinformatics_Trinh.pdf
  file_size: 641736
  relation: main_file
  success: 1
file_date_updated: 2023-07-31T11:09:05Z
has_accepted_license: '1'
intvolume: '        39'
isi: 1
issue: Supplement_1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: i513-i522
pmid: 1
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
  call_identifier: H2020
  grant_number: '101034413'
  name: 'IST-BRIDGE: International postdoctoral program'
publication: Bioinformatics
publication_identifier:
  eissn:
  - 1367-4811
  issn:
  - 1367-4803
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
  link:
  - relation: software
    url: https://github.com/giang-trinh/trap-mvn
scopus_import: '1'
status: public
title: 'Trap spaces of multi-valued networks: Definition, computation, and applications'
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 39
year: '2023'
...
---
_id: '13265'
abstract:
- lang: eng
  text: In this study, we propose a computational framework for optimizing the continuity
    of the toolpath in fabricating surface models on an extrusion-based 3D printer.
    Toolpath continuity is a critical issue that influences both the quality and the
    efficiency of extrusion-based fabrication. Transfer moves lead to rough and bumpy
    surfaces, where this phenomenon worsens for materials with large viscosity, like
    clay. The effects of continuity on the surface models are even more severe in
    terms of the quality of the surface and the stability of the model. We introduce
    a criterion called the one–path patch (OPP) to represent a patch on the surface
    of the shell that can be traversed along one path by considering the constraints
    on fabrication. We study the properties of the OPPs and their merging operations
    to propose a bottom-up OPP merging procedure to decompose the given shell surface
    into a minimal number of OPPs, and to generate the “as-continuous-as-possible”
    (ACAP) toolpath. Furthermore, we augment the path planning algorithm with a curved-layer
    printing scheme that reduces staircase defects and improves the continuity of
    the toolpath by connecting multiple segments. We evaluated the ACAP algorithm
    on ceramic and thermoplastic materials, and the results showed that it improves
    the fabrication of surface models in terms of both efficiency and surface quality.
acknowledgement: 'This work was supported in part by grants from the NSFC (61972232),
  Science and Technology Program of Shenzhen, China (CJGJZD20200617102202007). '
article_number: '26'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Fanchao
  full_name: Zhong, Fanchao
  last_name: Zhong
- first_name: Yonglai
  full_name: Xu, Yonglai
  last_name: Xu
- first_name: Haisen
  full_name: Zhao, Haisen
  id: fb7f793a-80d1-11eb-8869-d56e5b2a8ff4
  last_name: Zhao
  orcid: 0000-0002-6389-1045
- first_name: Lin
  full_name: Lu, Lin
  last_name: Lu
citation:
  ama: Zhong F, Xu Y, Zhao H, Lu L. As-Continuous-As-Possible extrusion-based fabrication
    of surface models. <i>ACM Transactions on Graphics</i>. 2023;42(3). doi:<a href="https://doi.org/10.1145/3575859">10.1145/3575859</a>
  apa: Zhong, F., Xu, Y., Zhao, H., &#38; Lu, L. (2023). As-Continuous-As-Possible
    extrusion-based fabrication of surface models. <i>ACM Transactions on Graphics</i>.
    Association for Computing Machinery. <a href="https://doi.org/10.1145/3575859">https://doi.org/10.1145/3575859</a>
  chicago: Zhong, Fanchao, Yonglai Xu, Haisen Zhao, and Lin Lu. “As-Continuous-As-Possible
    Extrusion-Based Fabrication of Surface Models.” <i>ACM Transactions on Graphics</i>.
    Association for Computing Machinery, 2023. <a href="https://doi.org/10.1145/3575859">https://doi.org/10.1145/3575859</a>.
  ieee: F. Zhong, Y. Xu, H. Zhao, and L. Lu, “As-Continuous-As-Possible extrusion-based
    fabrication of surface models,” <i>ACM Transactions on Graphics</i>, vol. 42,
    no. 3. Association for Computing Machinery, 2023.
  ista: Zhong F, Xu Y, Zhao H, Lu L. 2023. As-Continuous-As-Possible extrusion-based
    fabrication of surface models. ACM Transactions on Graphics. 42(3), 26.
  mla: Zhong, Fanchao, et al. “As-Continuous-As-Possible Extrusion-Based Fabrication
    of Surface Models.” <i>ACM Transactions on Graphics</i>, vol. 42, no. 3, 26, Association
    for Computing Machinery, 2023, doi:<a href="https://doi.org/10.1145/3575859">10.1145/3575859</a>.
  short: F. Zhong, Y. Xu, H. Zhao, L. Lu, ACM Transactions on Graphics 42 (2023).
date_created: 2023-07-23T22:01:13Z
date_published: 2023-03-17T00:00:00Z
date_updated: 2023-12-13T11:34:59Z
day: '17'
department:
- _id: BeBi
doi: 10.1145/3575859
external_id:
  arxiv:
  - '2201.02374'
  isi:
  - '001018739600002'
intvolume: '        42'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.48550/arXiv.2201.02374
month: '03'
oa: 1
oa_version: Preprint
publication: ACM Transactions on Graphics
publication_identifier:
  eissn:
  - 1557-7368
  issn:
  - 0730-0301
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: As-Continuous-As-Possible extrusion-based fabrication of surface models
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2023'
...
---
_id: '13266'
abstract:
- lang: eng
  text: The 3′,5′-cyclic adenosine monophosphate (cAMP) is a versatile second messenger
    in many mammalian signaling pathways. However, its role in plants remains not
    well-recognized. Recent discovery of adenylate cyclase (AC) activity for transport
    inhibitor response 1/auxin-signaling F-box proteins (TIR1/AFB) auxin receptors
    and the demonstration of its importance for canonical auxin signaling put plant
    cAMP research back into spotlight. This insight briefly summarizes the well-established
    cAMP signaling pathways in mammalian cells and describes the turbulent and controversial
    history of plant cAMP research highlighting the major progress and the unresolved
    points. We also briefly review the current paradigm of auxin signaling to provide
    a background for the discussion on the AC activity of TIR1/AFB auxin receptors
    and its potential role in transcriptional auxin signaling as well as impact of
    these discoveries on plant cAMP research in general.
acknowledgement: 'We gratefully acknowledge our brave colleagues, whose excellent
  efforts kept the plant cAMP research going in the last two decades. The authors
  were financially supported by the Austrian Science Fund (FWF): I 6123 and P 37051-B.'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Linlin
  full_name: Qi, Linlin
  id: 44B04502-A9ED-11E9-B6FC-583AE6697425
  last_name: Qi
  orcid: 0000-0001-5187-8401
- first_name: Jiří
  full_name: Friml, Jiří
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
citation:
  ama: Qi L, Friml J. Tale of cAMP as a second messenger in auxin signaling and beyond.
    <i>New Phytologist</i>. 2023;240(2):489-495. doi:<a href="https://doi.org/10.1111/nph.19123">10.1111/nph.19123</a>
  apa: Qi, L., &#38; Friml, J. (2023). Tale of cAMP as a second messenger in auxin
    signaling and beyond. <i>New Phytologist</i>. Wiley. <a href="https://doi.org/10.1111/nph.19123">https://doi.org/10.1111/nph.19123</a>
  chicago: Qi, Linlin, and Jiří Friml. “Tale of CAMP as a Second Messenger in Auxin
    Signaling and Beyond.” <i>New Phytologist</i>. Wiley, 2023. <a href="https://doi.org/10.1111/nph.19123">https://doi.org/10.1111/nph.19123</a>.
  ieee: L. Qi and J. Friml, “Tale of cAMP as a second messenger in auxin signaling
    and beyond,” <i>New Phytologist</i>, vol. 240, no. 2. Wiley, pp. 489–495, 2023.
  ista: Qi L, Friml J. 2023. Tale of cAMP as a second messenger in auxin signaling
    and beyond. New Phytologist. 240(2), 489–495.
  mla: Qi, Linlin, and Jiří Friml. “Tale of CAMP as a Second Messenger in Auxin Signaling
    and Beyond.” <i>New Phytologist</i>, vol. 240, no. 2, Wiley, 2023, pp. 489–95,
    doi:<a href="https://doi.org/10.1111/nph.19123">10.1111/nph.19123</a>.
  short: L. Qi, J. Friml, New Phytologist 240 (2023) 489–495.
corr_author: '1'
date_created: 2023-07-23T22:01:13Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2024-10-22T12:50:00Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1111/nph.19123
external_id:
  isi:
  - '001026321500001'
  pmid:
  - '37434303'
file:
- access_level: open_access
  checksum: 6d9bbd45b8e7bb3ceee2586d447bacb2
  content_type: application/pdf
  creator: dernst
  date_created: 2024-01-29T11:21:43Z
  date_updated: 2024-01-29T11:21:43Z
  file_id: '14898'
  file_name: 2023_NewPhytologist_Qi.pdf
  file_size: 974464
  relation: main_file
  success: 1
file_date_updated: 2024-01-29T11:21:43Z
has_accepted_license: '1'
intvolume: '       240'
isi: 1
issue: '2'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 489-495
pmid: 1
project:
- _id: bd76d395-d553-11ed-ba76-f678c14f9033
  grant_number: I06123
  name: Peptide receptors for auxin canalization in Arabidopsis
- _id: 7bcece63-9f16-11ee-852c-ae94e099eeb6
  grant_number: P37051
  name: Guanylate cyclase activity of TIR1/AFBs auxin receptors
publication: New Phytologist
publication_identifier:
  eissn:
  - 1469-8137
  issn:
  - 0028-646X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tale of cAMP as a second messenger in auxin signaling and beyond
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: 240
year: '2023'
...
---
_id: '13268'
abstract:
- lang: eng
  text: We give a simple argument to prove Nagai’s conjecture for type II degenerations
    of compact hyperkähler manifolds and cohomology classes of middle degree. Under
    an additional assumption, the techniques yield the conjecture in arbitrary degree.
    This would complete the proof of Nagai’s conjecture in general, as it was proved
    already for type I degenerations by Kollár, Laza, Saccà, and Voisin [10] and independently
    by Soldatenkov [18], while it is immediate for type III degenerations. Our arguments
    are close in spirit to a recent paper by Harder [8] proving similar results for
    the restrictive class of good degenerations.
acknowledgement: The first author is supported by the ERC Synergy Grant HyperK. The
  second author is supported by the Max Planck Institute for Mathematics and the Institute
  of Science and Technology Austria. This project has received funding from the European
  Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie
  grant agreement No 101034413.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: D.
  full_name: Huybrechts, D.
  last_name: Huybrechts
- first_name: Mirko
  full_name: Mauri, Mirko
  id: 2cf70c34-09c1-11ed-bd8d-c34fac206130
  last_name: Mauri
citation:
  ama: Huybrechts D, Mauri M. On type II degenerations of hyperkähler manifolds. <i>Mathematical
    Research Letters</i>. 2023;30(1):125-141. doi:<a href="https://doi.org/10.4310/mrl.2023.v30.n1.a6">10.4310/mrl.2023.v30.n1.a6</a>
  apa: Huybrechts, D., &#38; Mauri, M. (2023). On type II degenerations of hyperkähler
    manifolds. <i>Mathematical Research Letters</i>. International Press. <a href="https://doi.org/10.4310/mrl.2023.v30.n1.a6">https://doi.org/10.4310/mrl.2023.v30.n1.a6</a>
  chicago: Huybrechts, D., and Mirko Mauri. “On Type II Degenerations of Hyperkähler
    Manifolds.” <i>Mathematical Research Letters</i>. International Press, 2023. <a
    href="https://doi.org/10.4310/mrl.2023.v30.n1.a6">https://doi.org/10.4310/mrl.2023.v30.n1.a6</a>.
  ieee: D. Huybrechts and M. Mauri, “On type II degenerations of hyperkähler manifolds,”
    <i>Mathematical Research Letters</i>, vol. 30, no. 1. International Press, pp.
    125–141, 2023.
  ista: Huybrechts D, Mauri M. 2023. On type II degenerations of hyperkähler manifolds.
    Mathematical Research Letters. 30(1), 125–141.
  mla: Huybrechts, D., and Mirko Mauri. “On Type II Degenerations of Hyperkähler Manifolds.”
    <i>Mathematical Research Letters</i>, vol. 30, no. 1, International Press, 2023,
    pp. 125–41, doi:<a href="https://doi.org/10.4310/mrl.2023.v30.n1.a6">10.4310/mrl.2023.v30.n1.a6</a>.
  short: D. Huybrechts, M. Mauri, Mathematical Research Letters 30 (2023) 125–141.
corr_author: '1'
date_created: 2023-07-23T22:01:14Z
date_published: 2023-06-21T00:00:00Z
date_updated: 2025-04-14T07:54:52Z
day: '21'
department:
- _id: TaHa
doi: 10.4310/mrl.2023.v30.n1.a6
ec_funded: 1
external_id:
  arxiv:
  - '2108.01587'
  isi:
  - '001027656000006'
intvolume: '        30'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.48550/arXiv.2108.01587
month: '06'
oa: 1
oa_version: Preprint
page: 125-141
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
  call_identifier: H2020
  grant_number: '101034413'
  name: 'IST-BRIDGE: International postdoctoral program'
publication: Mathematical Research Letters
publication_identifier:
  eissn:
  - 1945-001X
  issn:
  - 1073-2780
publication_status: published
publisher: International Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: On type II degenerations of hyperkähler manifolds
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2023'
...
---
_id: '13269'
abstract:
- lang: eng
  text: This paper is a collection of results on combinatorial properties of codes
    for the Z-channel . A Z-channel with error fraction τ takes as input a length-
    n binary codeword and injects in an adversarial manner up to n τ asymmetric errors,
    i.e., errors that only zero out bits but do not flip 0’s to 1’s. It is known that
    the largest ( L - 1)-list-decodable code for the Z-channel with error fraction
    τ has exponential size (in n ) if τ is less than a critical value that we call
    the ( L - 1)- list-decoding Plotkin point and has constant size if τ is larger
    than the threshold. The ( L -1)-list-decoding Plotkin point is known to be L -1/L-1
    – L -L/ L-1 , which equals 1/4 for unique-decoding with L -1 = 1. In this paper,
    we derive various results for the size of the largest codes above and below the
    list-decoding Plotkin point. In particular, we show that the largest ( L -1)-list-decodable
    code ε-above the Plotkin point, for any given sufficiently small positive constant
    ε > 0, has size Θ L (ε -3/2 ) for any L - 1 ≥ 1. We also devise upper and lower
    bounds on the exponential size of codes below the list-decoding Plotkin point.
acknowledgement: "Nikita Polyanskii’s research was conducted in part during October
  2020 - December 2021 with the Technical University of Munich and the Skolkovo Institute
  of Science and Technology. His work was supported by the German Research Foundation
  (Deutsche Forschungsgemeinschaft, DFG) under Grant No. WA3907/1-1 and the Russian
  Foundation for Basic Research (RFBR)\r\nunder Grant No. 20-01-00559.\r\nYihan Zhang
  is supported by funding from the European Union’s Horizon 2020 research and innovation
  programme under grant agreement No 682203-ERC-[Inf-Speed-Tradeoff]."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Nikita
  full_name: Polyanskii, Nikita
  last_name: Polyanskii
- first_name: Yihan
  full_name: Zhang, Yihan
  id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c
  last_name: Zhang
  orcid: 0000-0002-6465-6258
citation:
  ama: Polyanskii N, Zhang Y. Codes for the Z-channel. <i>IEEE Transactions on Information
    Theory</i>. 2023;69(10):6340-6357. doi:<a href="https://doi.org/10.1109/TIT.2023.3292219">10.1109/TIT.2023.3292219</a>
  apa: Polyanskii, N., &#38; Zhang, Y. (2023). Codes for the Z-channel. <i>IEEE Transactions
    on Information Theory</i>. Institute of Electrical and Electronics Engineers.
    <a href="https://doi.org/10.1109/TIT.2023.3292219">https://doi.org/10.1109/TIT.2023.3292219</a>
  chicago: Polyanskii, Nikita, and Yihan Zhang. “Codes for the Z-Channel.” <i>IEEE
    Transactions on Information Theory</i>. Institute of Electrical and Electronics
    Engineers, 2023. <a href="https://doi.org/10.1109/TIT.2023.3292219">https://doi.org/10.1109/TIT.2023.3292219</a>.
  ieee: N. Polyanskii and Y. Zhang, “Codes for the Z-channel,” <i>IEEE Transactions
    on Information Theory</i>, vol. 69, no. 10. Institute of Electrical and Electronics
    Engineers, pp. 6340–6357, 2023.
  ista: Polyanskii N, Zhang Y. 2023. Codes for the Z-channel. IEEE Transactions on
    Information Theory. 69(10), 6340–6357.
  mla: Polyanskii, Nikita, and Yihan Zhang. “Codes for the Z-Channel.” <i>IEEE Transactions
    on Information Theory</i>, vol. 69, no. 10, Institute of Electrical and Electronics
    Engineers, 2023, pp. 6340–57, doi:<a href="https://doi.org/10.1109/TIT.2023.3292219">10.1109/TIT.2023.3292219</a>.
  short: N. Polyanskii, Y. Zhang, IEEE Transactions on Information Theory 69 (2023)
    6340–6357.
corr_author: '1'
date_created: 2023-07-23T22:01:14Z
date_published: 2023-07-04T00:00:00Z
date_updated: 2024-10-09T21:06:01Z
day: '04'
department:
- _id: MaMo
doi: 10.1109/TIT.2023.3292219
external_id:
  arxiv:
  - '2105.01427'
  isi:
  - '001069680100011'
intvolume: '        69'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.48550/arXiv.2105.01427
month: '07'
oa: 1
oa_version: Preprint
page: 6340-6357
publication: IEEE Transactions on Information Theory
publication_identifier:
  eissn:
  - 1557-9654
  issn:
  - 0018-9448
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Codes for the Z-channel
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 69
year: '2023'
...
---
_id: '13270'
abstract:
- lang: eng
  text: "Consider a geodesic triangle on a surface of constant curvature and subdivide
    it recursively into four triangles by joining the midpoints of its edges. We show
    the existence of a uniform δ>0\r\n such that, at any step of the subdivision,
    all the triangle angles lie in the interval (δ,π−δ)\r\n. Additionally, we exhibit
    stabilising behaviours for both angles and lengths as this subdivision progresses."
acknowledgement: Open access funding provided by the Institute of Science and Technology
  (IST Austria).
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Florestan R
  full_name: Brunck, Florestan R
  id: 6ab6e556-f394-11eb-9cf6-9dfb78f00d8d
  last_name: Brunck
citation:
  ama: Brunck FR. Iterated medial triangle subdivision in surfaces of constant curvature.
    <i>Discrete and Computational Geometry</i>. 2023;70(3):1059-1089. doi:<a href="https://doi.org/10.1007/s00454-023-00500-5">10.1007/s00454-023-00500-5</a>
  apa: Brunck, F. R. (2023). Iterated medial triangle subdivision in surfaces of constant
    curvature. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href="https://doi.org/10.1007/s00454-023-00500-5">https://doi.org/10.1007/s00454-023-00500-5</a>
  chicago: Brunck, Florestan R. “Iterated Medial Triangle Subdivision in Surfaces
    of Constant Curvature.” <i>Discrete and Computational Geometry</i>. Springer Nature,
    2023. <a href="https://doi.org/10.1007/s00454-023-00500-5">https://doi.org/10.1007/s00454-023-00500-5</a>.
  ieee: F. R. Brunck, “Iterated medial triangle subdivision in surfaces of constant
    curvature,” <i>Discrete and Computational Geometry</i>, vol. 70, no. 3. Springer
    Nature, pp. 1059–1089, 2023.
  ista: Brunck FR. 2023. Iterated medial triangle subdivision in surfaces of constant
    curvature. Discrete and Computational Geometry. 70(3), 1059–1089.
  mla: Brunck, Florestan R. “Iterated Medial Triangle Subdivision in Surfaces of Constant
    Curvature.” <i>Discrete and Computational Geometry</i>, vol. 70, no. 3, Springer
    Nature, 2023, pp. 1059–89, doi:<a href="https://doi.org/10.1007/s00454-023-00500-5">10.1007/s00454-023-00500-5</a>.
  short: F.R. Brunck, Discrete and Computational Geometry 70 (2023) 1059–1089.
corr_author: '1'
date_created: 2023-07-23T22:01:14Z
date_published: 2023-07-05T00:00:00Z
date_updated: 2024-10-09T21:06:01Z
day: '05'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.1007/s00454-023-00500-5
external_id:
  arxiv:
  - '2107.04112'
  isi:
  - '001023742800003'
file:
- access_level: open_access
  checksum: 865e68daafdd4edcfc280172ec50f5ea
  content_type: application/pdf
  creator: dernst
  date_created: 2024-01-29T11:15:22Z
  date_updated: 2024-01-29T11:15:22Z
  file_id: '14897'
  file_name: 2023_DiscreteComputGeometry_Brunck.pdf
  file_size: 1466020
  relation: main_file
  success: 1
file_date_updated: 2024-01-29T11:15:22Z
has_accepted_license: '1'
intvolume: '        70'
isi: 1
issue: '3'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 1059-1089
publication: Discrete and Computational Geometry
publication_identifier:
  eissn:
  - 1432-0444
  issn:
  - 0179-5376
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Iterated medial triangle subdivision in surfaces of constant curvature
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: 70
year: '2023'
...
---
_id: '13275'
abstract:
- lang: eng
  text: We introduce a generic and accessible implementation of an exact diagonalization
    method for studying few-fermion models. Our aim is to provide a testbed for the
    newcomers to the field as well as a stepping stone for trying out novel optimizations
    and approximations. This userguide consists of a description of the algorithm,
    and several examples in varying orders of sophistication. In particular, we exemplify
    our routine using an effective-interaction approach that fixes the low-energy
    physics. We benchmark this approach against the existing data, and show that it
    is able to deliver state-of-the-art numerical results at a significantly reduced
    computational cost.
article_processing_charge: No
author:
- first_name: Lukas
  full_name: Rammelmüller, Lukas
  last_name: Rammelmüller
- first_name: David
  full_name: Huber, David
  last_name: Huber
- first_name: Artem
  full_name: Volosniev, Artem
  id: 37D278BC-F248-11E8-B48F-1D18A9856A87
  last_name: Volosniev
  orcid: 0000-0003-0393-5525
citation:
  ama: Rammelmüller L, Huber D, Volosniev A. Codebase release 1.0 for FermiFCI. 2023.
    doi:<a href="https://doi.org/10.21468/scipostphyscodeb.12-r1.0">10.21468/scipostphyscodeb.12-r1.0</a>
  apa: Rammelmüller, L., Huber, D., &#38; Volosniev, A. (2023). Codebase release 1.0
    for FermiFCI. SciPost Foundation. <a href="https://doi.org/10.21468/scipostphyscodeb.12-r1.0">https://doi.org/10.21468/scipostphyscodeb.12-r1.0</a>
  chicago: Rammelmüller, Lukas, David Huber, and Artem Volosniev. “Codebase Release
    1.0 for FermiFCI.” SciPost Foundation, 2023. <a href="https://doi.org/10.21468/scipostphyscodeb.12-r1.0">https://doi.org/10.21468/scipostphyscodeb.12-r1.0</a>.
  ieee: L. Rammelmüller, D. Huber, and A. Volosniev, “Codebase release 1.0 for FermiFCI.”
    SciPost Foundation, 2023.
  ista: Rammelmüller L, Huber D, Volosniev A. 2023. Codebase release 1.0 for FermiFCI,
    SciPost Foundation, <a href="https://doi.org/10.21468/scipostphyscodeb.12-r1.0">10.21468/scipostphyscodeb.12-r1.0</a>.
  mla: Rammelmüller, Lukas, et al. <i>Codebase Release 1.0 for FermiFCI</i>. SciPost
    Foundation, 2023, doi:<a href="https://doi.org/10.21468/scipostphyscodeb.12-r1.0">10.21468/scipostphyscodeb.12-r1.0</a>.
  short: L. Rammelmüller, D. Huber, A. Volosniev, (2023).
corr_author: '1'
date_created: 2023-07-24T10:46:23Z
date_published: 2023-04-19T00:00:00Z
date_updated: 2025-04-15T06:54:44Z
day: '19'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.21468/scipostphyscodeb.12-r1.0
ec_funded: 1
main_file_link:
- open_access: '1'
  url: https://doi.org/10.21468/SciPostPhysCodeb.12-r1.0
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '754411'
  name: ISTplus - Postdoctoral Fellowships
publisher: SciPost Foundation
related_material:
  record:
  - id: '13276'
    relation: used_in_publication
    status: public
status: public
title: Codebase release 1.0 for FermiFCI
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13276'
abstract:
- lang: eng
  text: <jats:p>We introduce a generic and accessible implementation of an exact diagonalization
    method for studying few-fermion models. Our aim is to provide a testbed for the
    newcomers to the field as well as a stepping stone for trying out novel optimizations
    and approximations. This userguide consists of a description of the algorithm,
    and several examples in varying orders of sophistication. In particular, we exemplify
    our routine using an effective-interaction approach that fixes the low-energy
    physics. We benchmark this approach against the existing data, and show that it
    is able to deliver state-of-the-art numerical results at a significantly reduced
    computational cost.</jats:p>
acknowledgement: "We acknowledge fruitful discussions with Hans-Werner Hammer and
  thank Gerhard Zürn and\r\nPietro Massignan for sending us their data. We thank Fabian
  Brauneis for beta-testing the\r\nprovided code-package, and comments on the manuscript.\r\nL.R.
  is supported by FP7/ERC Consolidator Grant QSIMCORR, No.\r\n771891, and the Deutsche
  Forschungsgemeinschaft (DFG, German Research Foundation) under\r\nGermany’s Excellence
  Strategy –EXC–2111–390814868. A.G.V. acknowledges support\r\nby European Union’s
  Horizon 2020 research and innovation programme under the Marie\r\nSkłodowska-Curie
  Grant Agreement No. 754411."
article_number: '12'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Lukas
  full_name: Rammelmüller, Lukas
  last_name: Rammelmüller
- first_name: David
  full_name: Huber, David
  last_name: Huber
- first_name: Artem
  full_name: Volosniev, Artem
  id: 37D278BC-F248-11E8-B48F-1D18A9856A87
  last_name: Volosniev
  orcid: 0000-0003-0393-5525
citation:
  ama: Rammelmüller L, Huber D, Volosniev A. A modular implementation of an effective
    interaction approach for harmonically trapped fermions in 1D. <i>SciPost Physics
    Codebases</i>. 2023. doi:<a href="https://doi.org/10.21468/scipostphyscodeb.12">10.21468/scipostphyscodeb.12</a>
  apa: Rammelmüller, L., Huber, D., &#38; Volosniev, A. (2023). A modular implementation
    of an effective interaction approach for harmonically trapped fermions in 1D.
    <i>SciPost Physics Codebases</i>. SciPost Foundation. <a href="https://doi.org/10.21468/scipostphyscodeb.12">https://doi.org/10.21468/scipostphyscodeb.12</a>
  chicago: Rammelmüller, Lukas, David Huber, and Artem Volosniev. “A Modular Implementation
    of an Effective Interaction Approach for Harmonically Trapped Fermions in 1D.”
    <i>SciPost Physics Codebases</i>. SciPost Foundation, 2023. <a href="https://doi.org/10.21468/scipostphyscodeb.12">https://doi.org/10.21468/scipostphyscodeb.12</a>.
  ieee: L. Rammelmüller, D. Huber, and A. Volosniev, “A modular implementation of
    an effective interaction approach for harmonically trapped fermions in 1D,” <i>SciPost
    Physics Codebases</i>. SciPost Foundation, 2023.
  ista: Rammelmüller L, Huber D, Volosniev A. 2023. A modular implementation of an
    effective interaction approach for harmonically trapped fermions in 1D. SciPost
    Physics Codebases., 12.
  mla: Rammelmüller, Lukas, et al. “A Modular Implementation of an Effective Interaction
    Approach for Harmonically Trapped Fermions in 1D.” <i>SciPost Physics Codebases</i>,
    12, SciPost Foundation, 2023, doi:<a href="https://doi.org/10.21468/scipostphyscodeb.12">10.21468/scipostphyscodeb.12</a>.
  short: L. Rammelmüller, D. Huber, A. Volosniev, SciPost Physics Codebases (2023).
corr_author: '1'
date_created: 2023-07-24T10:47:15Z
date_published: 2023-04-19T00:00:00Z
date_updated: 2025-04-15T06:54:44Z
day: '19'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.21468/scipostphyscodeb.12
ec_funded: 1
external_id:
  arxiv:
  - '2202.04603'
file:
- access_level: open_access
  checksum: f583a70fe915d2208c803f5afb426daa
  content_type: application/pdf
  creator: dernst
  date_created: 2023-07-31T09:09:23Z
  date_updated: 2023-07-31T09:09:23Z
  file_id: '13330'
  file_name: 2023_SciPostPhysCodebase_Rammelmueller.pdf
  file_size: 551418
  relation: main_file
  success: 1
file_date_updated: 2023-07-31T09:09:23Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '754411'
  name: ISTplus - Postdoctoral Fellowships
publication: SciPost Physics Codebases
publication_identifier:
  issn:
  - 2949-804X
publication_status: published
publisher: SciPost Foundation
quality_controlled: '1'
related_material:
  record:
  - id: '13275'
    relation: research_data
    status: public
status: public
title: A modular implementation of an effective interaction approach for harmonically
  trapped fermions in 1D
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13277'
abstract:
- lang: eng
  text: Recent experimental advances have inspired the development of theoretical
    tools to describe the non-equilibrium dynamics of quantum systems. Among them
    an exact representation of quantum spin systems in terms of classical stochastic
    processes has been proposed. Here we provide first steps towards the extension
    of this stochastic approach to bosonic systems by considering the one-dimensional
    quantum quartic oscillator. We show how to exactly parameterize the time evolution
    of this prototypical model via the dynamics of a set of classical variables. We
    interpret these variables as stochastic processes, which allows us to propose
    a novel way to numerically simulate the time evolution of the system. We benchmark
    our findings by considering analytically solvable limits and providing alternative
    derivations of known results.
acknowledgement: 'S. De Nicola acknowledges funding from the Institute of Science
  and Technology Austria (ISTA), and from the European Union’s Horizon 2020 research
  and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411.
  S. De Nicola also acknowledges funding from the EPSRC Center for Doctoral Training
  in Cross-Disciplinary Approaches to NonEquilibrium Systems (CANES) under Grant EP/L015854/1. '
article_number: '029'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Gennaro
  full_name: Tucci, Gennaro
  last_name: Tucci
- first_name: Stefano
  full_name: De Nicola, Stefano
  id: 42832B76-F248-11E8-B48F-1D18A9856A87
  last_name: De Nicola
  orcid: 0000-0002-4842-6671
- first_name: Sascha
  full_name: Wald, Sascha
  last_name: Wald
- first_name: Andrea
  full_name: Gambassi, Andrea
  last_name: Gambassi
citation:
  ama: Tucci G, De Nicola S, Wald S, Gambassi A. Stochastic representation of the
    quantum quartic oscillator. <i>SciPost Physics Core</i>. 2023;6(2). doi:<a href="https://doi.org/10.21468/scipostphyscore.6.2.029">10.21468/scipostphyscore.6.2.029</a>
  apa: Tucci, G., De Nicola, S., Wald, S., &#38; Gambassi, A. (2023). Stochastic representation
    of the quantum quartic oscillator. <i>SciPost Physics Core</i>. SciPost Foundation.
    <a href="https://doi.org/10.21468/scipostphyscore.6.2.029">https://doi.org/10.21468/scipostphyscore.6.2.029</a>
  chicago: Tucci, Gennaro, Stefano De Nicola, Sascha Wald, and Andrea Gambassi. “Stochastic
    Representation of the Quantum Quartic Oscillator.” <i>SciPost Physics Core</i>.
    SciPost Foundation, 2023. <a href="https://doi.org/10.21468/scipostphyscore.6.2.029">https://doi.org/10.21468/scipostphyscore.6.2.029</a>.
  ieee: G. Tucci, S. De Nicola, S. Wald, and A. Gambassi, “Stochastic representation
    of the quantum quartic oscillator,” <i>SciPost Physics Core</i>, vol. 6, no. 2.
    SciPost Foundation, 2023.
  ista: Tucci G, De Nicola S, Wald S, Gambassi A. 2023. Stochastic representation
    of the quantum quartic oscillator. SciPost Physics Core. 6(2), 029.
  mla: Tucci, Gennaro, et al. “Stochastic Representation of the Quantum Quartic Oscillator.”
    <i>SciPost Physics Core</i>, vol. 6, no. 2, 029, SciPost Foundation, 2023, doi:<a
    href="https://doi.org/10.21468/scipostphyscore.6.2.029">10.21468/scipostphyscore.6.2.029</a>.
  short: G. Tucci, S. De Nicola, S. Wald, A. Gambassi, SciPost Physics Core 6 (2023).
corr_author: '1'
date_created: 2023-07-24T10:47:46Z
date_published: 2023-04-14T00:00:00Z
date_updated: 2025-04-14T07:43:56Z
day: '14'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.21468/scipostphyscore.6.2.029
ec_funded: 1
external_id:
  arxiv:
  - '2211.01923'
file:
- access_level: open_access
  checksum: b472bc82108747eda5d52adf9e2ac7f3
  content_type: application/pdf
  creator: dernst
  date_created: 2023-07-31T09:02:27Z
  date_updated: 2023-07-31T09:02:27Z
  file_id: '13329'
  file_name: 2023_SciPostPhysCore_Tucci.pdf
  file_size: 523236
  relation: main_file
  success: 1
file_date_updated: 2023-07-31T09:02:27Z
has_accepted_license: '1'
intvolume: '         6'
issue: '2'
keyword:
- Statistical and Nonlinear Physics
- Atomic and Molecular Physics
- and Optics
- Nuclear and High Energy Physics
- Condensed Matter Physics
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '754411'
  name: ISTplus - Postdoctoral Fellowships
publication: SciPost Physics Core
publication_identifier:
  issn:
  - 2666-9366
publication_status: published
publisher: SciPost Foundation
quality_controlled: '1'
scopus_import: '1'
status: public
title: Stochastic representation of the quantum quartic oscillator
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: 6
year: '2023'
...
