---
_id: '17546'
abstract:
- lang: eng
  text: We show that gas disks around the components of an orbiting binary system
    (so-called minidisks) may be susceptible to a resonant instability that causes
    the minidisks to become significantly eccentric. Eccentricity is injected by,
    and also induces, regular impacts between the minidisks at roughly the orbital
    period of the binary. Such eccentric minidisks are seen in vertically integrated,
    two-dimensional simulations of a circular, equal-mass binary accreting from a
    circumbinary gas disk with a Γ-law equation of state. Minidisk eccentricity is
    suppressed by the use of an isothermal equation of state. However, the instability
    still operates and can be revealed in a minimal disk-binary simulation by removing
    the circumbinary disk and feeding the minidisks from the component positions.
    Minidisk eccentricity is also suppressed when the gravitational softening length
    is large (≳4% of the binary semimajor axis), suggesting that its absence could
    be an artifact of widely adopted numerical approximations; a follow-up study in
    three dimensions with well-resolved, geometrically thin minidisks (aspect ratios
    ≲0.02) may be needed to assess whether eccentric minidisks can occur in real astrophysical
    environments. If they can, the electromagnetic signature may be important for
    discriminating between binary and single black hole scenarios for quasiperiodic
    oscillations in active galactic nuclei; in turn, this might aid in targeted searches
    with pulsar timing arrays for individual supermassive black hole binary sources
    of low-frequency gravitational waves.
article_number: '76'
article_processing_charge: No
article_type: original
author:
- first_name: John Ryan
  full_name: Westernacher-Schneider, John Ryan
  last_name: Westernacher-Schneider
- first_name: Jonathan
  full_name: Zrake, Jonathan
  last_name: Zrake
- first_name: Andrew
  full_name: MacFadyen, Andrew
  last_name: MacFadyen
- first_name: Zoltán
  full_name: Haiman, Zoltán
  id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36
  last_name: Haiman
citation:
  ama: Westernacher-Schneider JR, Zrake J, MacFadyen A, Haiman Z. Eccentric minidisks
    in accreting binaries. <i>The Astrophysical Journal</i>. 2024;962(1). doi:<a href="https://doi.org/10.3847/1538-4357/ad1a17">10.3847/1538-4357/ad1a17</a>
  apa: Westernacher-Schneider, J. R., Zrake, J., MacFadyen, A., &#38; Haiman, Z. (2024).
    Eccentric minidisks in accreting binaries. <i>The Astrophysical Journal</i>. American
    Astronomical Society. <a href="https://doi.org/10.3847/1538-4357/ad1a17">https://doi.org/10.3847/1538-4357/ad1a17</a>
  chicago: Westernacher-Schneider, John Ryan, Jonathan Zrake, Andrew MacFadyen, and
    Zoltán Haiman. “Eccentric Minidisks in Accreting Binaries.” <i>The Astrophysical
    Journal</i>. American Astronomical Society, 2024. <a href="https://doi.org/10.3847/1538-4357/ad1a17">https://doi.org/10.3847/1538-4357/ad1a17</a>.
  ieee: J. R. Westernacher-Schneider, J. Zrake, A. MacFadyen, and Z. Haiman, “Eccentric
    minidisks in accreting binaries,” <i>The Astrophysical Journal</i>, vol. 962,
    no. 1. American Astronomical Society, 2024.
  ista: Westernacher-Schneider JR, Zrake J, MacFadyen A, Haiman Z. 2024. Eccentric
    minidisks in accreting binaries. The Astrophysical Journal. 962(1), 76.
  mla: Westernacher-Schneider, John Ryan, et al. “Eccentric Minidisks in Accreting
    Binaries.” <i>The Astrophysical Journal</i>, vol. 962, no. 1, 76, American Astronomical
    Society, 2024, doi:<a href="https://doi.org/10.3847/1538-4357/ad1a17">10.3847/1538-4357/ad1a17</a>.
  short: J.R. Westernacher-Schneider, J. Zrake, A. MacFadyen, Z. Haiman, The Astrophysical
    Journal 962 (2024).
date_created: 2024-09-05T10:06:09Z
date_published: 2024-02-08T00:00:00Z
date_updated: 2024-09-18T09:16:14Z
day: '08'
doi: 10.3847/1538-4357/ad1a17
extern: '1'
fulldoi: https://doi.org/10.3847/1538-4357/ad1a17
intvolume: '       962'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.3847/1538-4357/ad1a17
month: '02'
oa: 1
oa_version: Published Version
publication: The Astrophysical Journal
publication_identifier:
  issn:
  - 0004-637X
  - 1538-4357
publication_status: published
publisher: American Astronomical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Eccentric minidisks in accreting binaries
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 962
year: '2024'
...
---
_id: '17590'
abstract:
- lang: eng
  text: Close encounters between stellar-mass black holes (BHs) and stars occur frequently
    in dense star clusters and in the disks of active galactic nuclei. Recent studies
    have shown that in highly eccentric close encounters, the star can be tidally
    disrupted by the BH in a microtidal disruption event (microTDE), resulting in
    rapid mass accretion and possibly bright electromagnetic signatures. Here we consider
    a scenario in which the star might approach the stellar-mass BH in a gradual,
    nearly circular inspiral, under the influence of dynamical friction in a circum-binary
    gas disk or three-body interactions in a star cluster. We perform hydrodynamics
    simulations of this scenario using the smoothed particle hydrodynamics code PHANTOM.
    We find that under certain circumstances (for initial eccentricity e0 ≳ 0.4 and
    penetration factor β = 1, or e0 < 0.4 and β ≲ 0.67), the mass of the star is slowly
    stripped away by the BH. We call this gradual tidal disruption a "tidal-peeling
    event." Additionally, we discover that some low-eccentricity microTDEs (e0 < 0.4
    and β = 1) are a new form of fast luminous transients similar to parabolic microTDEs.
    Depending on the initial distance and eccentricity of the encounter, these low-eccentricity
    microTDEs might exhibit significant accretion rates and orbital evolution distinct
    from those of a typical (eccentric) microTDE.
article_number: '149'
article_processing_charge: No
article_type: original
author:
- first_name: Chengcheng
  full_name: Xin, Chengcheng
  last_name: Xin
- first_name: Zoltán
  full_name: Haiman, Zoltán
  id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36
  last_name: Haiman
- first_name: Rosalba
  full_name: Perna, Rosalba
  last_name: Perna
- first_name: Yihan
  full_name: Wang, Yihan
  last_name: Wang
- first_name: Taeho
  full_name: Ryu, Taeho
  last_name: Ryu
citation:
  ama: 'Xin C, Haiman Z, Perna R, Wang Y, Ryu T. “Tidal Peeling Events”: Low-eccentricity
    tidal disruption of a star by a stellar-mass black hole. <i>The Astrophysical
    Journal</i>. 2024;961(2). doi:<a href="https://doi.org/10.3847/1538-4357/ad11d3">10.3847/1538-4357/ad11d3</a>'
  apa: 'Xin, C., Haiman, Z., Perna, R., Wang, Y., &#38; Ryu, T. (2024). “Tidal Peeling
    Events”: Low-eccentricity tidal disruption of a star by a stellar-mass black hole.
    <i>The Astrophysical Journal</i>. American Astronomical Society. <a href="https://doi.org/10.3847/1538-4357/ad11d3">https://doi.org/10.3847/1538-4357/ad11d3</a>'
  chicago: 'Xin, Chengcheng, Zoltán Haiman, Rosalba Perna, Yihan Wang, and Taeho Ryu.
    “‘Tidal Peeling Events’: Low-Eccentricity Tidal Disruption of a Star by a Stellar-Mass
    Black Hole.” <i>The Astrophysical Journal</i>. American Astronomical Society,
    2024. <a href="https://doi.org/10.3847/1538-4357/ad11d3">https://doi.org/10.3847/1538-4357/ad11d3</a>.'
  ieee: 'C. Xin, Z. Haiman, R. Perna, Y. Wang, and T. Ryu, “‘Tidal Peeling Events’:
    Low-eccentricity tidal disruption of a star by a stellar-mass black hole,” <i>The
    Astrophysical Journal</i>, vol. 961, no. 2. American Astronomical Society, 2024.'
  ista: 'Xin C, Haiman Z, Perna R, Wang Y, Ryu T. 2024. “Tidal Peeling Events”: Low-eccentricity
    tidal disruption of a star by a stellar-mass black hole. The Astrophysical Journal.
    961(2), 149.'
  mla: 'Xin, Chengcheng, et al. “‘Tidal Peeling Events’: Low-Eccentricity Tidal Disruption
    of a Star by a Stellar-Mass Black Hole.” <i>The Astrophysical Journal</i>, vol.
    961, no. 2, 149, American Astronomical Society, 2024, doi:<a href="https://doi.org/10.3847/1538-4357/ad11d3">10.3847/1538-4357/ad11d3</a>.'
  short: C. Xin, Z. Haiman, R. Perna, Y. Wang, T. Ryu, The Astrophysical Journal 961
    (2024).
date_created: 2024-09-05T12:36:41Z
date_published: 2024-01-22T00:00:00Z
date_updated: 2024-09-19T12:21:53Z
day: '22'
doi: 10.3847/1538-4357/ad11d3
extern: '1'
fulldoi: https://doi.org/10.3847/1538-4357/ad11d3
intvolume: '       961'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.3847/1538-4357/ad11d3
month: '01'
oa: 1
oa_version: Published Version
publication: The Astrophysical Journal
publication_identifier:
  issn:
  - 0004-637X
  - 1538-4357
publication_status: published
publisher: American Astronomical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: '“Tidal Peeling Events”: Low-eccentricity tidal disruption of a star by a stellar-mass
  black hole'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 961
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '17852'
abstract:
- lang: eng
  text: Metal-metal contacts, though not yet widely realized, may provide exciting
    opportunities to serve as tunable and functional interfaces in single-molecule
    devices. One of the simplest components which might facilitate such binding interactions
    is the ferrocene group. Notably, direct bonds between the ferrocene iron center
    and metals such as Pd or Co have been demonstrated in molecular complexes comprising
    coordinating ligands attached to the cyclopentadienyl rings. Here, we demonstrate
    that ferrocene-based single-molecule devices with Fe-Au interfacial contact geometries
    form at room temperature in the absence of supporting coordinating ligands. Applying
    a photoredox reaction, we propose that ferrocene only functions effectively as
    a contact group when oxidized, binding to gold through a formal Fe<jats:sup>3+</jats:sup>
    center. This observation is further supported by a series of control measurements
    and density functional theory calculations. Our findings extend the scope of junction
    contact chemistries beyond those involving main group elements, lay the foundation
    for light switchable ferrocene-based single-molecule devices, and highlight new
    potential mechanistic function(s) of unsubstituted ferrocenium groups in synthetic
    processes.
article_number: '1439'
article_processing_charge: Yes
article_type: original
author:
- first_name: Woojung
  full_name: Lee, Woojung
  last_name: Lee
- first_name: Liang
  full_name: Li, Liang
  last_name: Li
- first_name: María
  full_name: Camarasa-Gómez, María
  last_name: Camarasa-Gómez
- first_name: Daniel
  full_name: Hernangómez-Pérez, Daniel
  last_name: Hernangómez-Pérez
- first_name: Xavier
  full_name: Roy, Xavier
  last_name: Roy
- first_name: Ferdinand
  full_name: Evers, Ferdinand
  last_name: Evers
- first_name: Michael S.
  full_name: Inkpen, Michael S.
  last_name: Inkpen
- first_name: Latha
  full_name: Venkataraman, Latha
  id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf
  last_name: Venkataraman
  orcid: 0000-0002-6957-6089
citation:
  ama: Lee W, Li L, Camarasa-Gómez M, et al. Photooxidation driven formation of Fe-Au
    linked ferrocene-based single-molecule junctions. <i>Nature Communications</i>.
    2024;15. doi:<a href="https://doi.org/10.1038/s41467-024-45707-z">10.1038/s41467-024-45707-z</a>
  apa: Lee, W., Li, L., Camarasa-Gómez, M., Hernangómez-Pérez, D., Roy, X., Evers,
    F., … Venkataraman, L. (2024). Photooxidation driven formation of Fe-Au linked
    ferrocene-based single-molecule junctions. <i>Nature Communications</i>. Springer
    Nature. <a href="https://doi.org/10.1038/s41467-024-45707-z">https://doi.org/10.1038/s41467-024-45707-z</a>
  chicago: Lee, Woojung, Liang Li, María Camarasa-Gómez, Daniel Hernangómez-Pérez,
    Xavier Roy, Ferdinand Evers, Michael S. Inkpen, and Latha Venkataraman. “Photooxidation
    Driven Formation of Fe-Au Linked Ferrocene-Based Single-Molecule Junctions.” <i>Nature
    Communications</i>. Springer Nature, 2024. <a href="https://doi.org/10.1038/s41467-024-45707-z">https://doi.org/10.1038/s41467-024-45707-z</a>.
  ieee: W. Lee <i>et al.</i>, “Photooxidation driven formation of Fe-Au linked ferrocene-based
    single-molecule junctions,” <i>Nature Communications</i>, vol. 15. Springer Nature,
    2024.
  ista: Lee W, Li L, Camarasa-Gómez M, Hernangómez-Pérez D, Roy X, Evers F, Inkpen
    MS, Venkataraman L. 2024. Photooxidation driven formation of Fe-Au linked ferrocene-based
    single-molecule junctions. Nature Communications. 15, 1439.
  mla: Lee, Woojung, et al. “Photooxidation Driven Formation of Fe-Au Linked Ferrocene-Based
    Single-Molecule Junctions.” <i>Nature Communications</i>, vol. 15, 1439, Springer
    Nature, 2024, doi:<a href="https://doi.org/10.1038/s41467-024-45707-z">10.1038/s41467-024-45707-z</a>.
  short: W. Lee, L. Li, M. Camarasa-Gómez, D. Hernangómez-Pérez, X. Roy, F. Evers,
    M.S. Inkpen, L. Venkataraman, Nature Communications 15 (2024).
date_created: 2024-09-06T12:38:44Z
date_published: 2024-02-16T00:00:00Z
date_updated: 2024-11-18T10:47:10Z
day: '16'
doi: 10.1038/s41467-024-45707-z
extern: '1'
external_id:
  pmid:
  - '38365892'
fulldoi: https://doi.org/10.1038/s41467-024-45707-z
intvolume: '        15'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1038/s41467-024-45707-z
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
  issn:
  - 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Photooxidation driven formation of Fe-Au linked ferrocene-based single-molecule
  junctions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2024'
...
---
OA_type: closed access
_id: '17853'
abstract:
- lang: eng
  text: Single-molecule one-dimensional topological insulator (1D TI) is a class of
    molecular wires that exhibit increasing conductance with wire length. This unique
    trend is due to the coupling between the two low-lying topological edge states
    of 1D TIs described by the Su–Schrieffer–Heeger model. In principle, this quantum
    phenomenon within 1D TIs can be utilized to achieve long-range gating in molecular
    conductors. Here, we study electron transport through a single-edge state of doubly
    oxidized oligophenylene bis(triarylamine) to understand the effect of the edge
    state coupling on conductance. We find that conductance is elevated by approximately
    1 order of magnitude compared to a control molecule with the same conductance
    pathway. Density function theory calculations further support that the increase
    in conductance is due to the interaction between the edge states of 1D TIs. This
    work demonstrates a new gating paradigm in molecular electronics, while also providing
    a deeper understanding of how edge states interact and affect electron transport
    within 1D TIs.
article_processing_charge: No
article_type: original
author:
- first_name: Liang
  full_name: Li, Liang
  last_name: Li
- first_name: Shayan
  full_name: Louie, Shayan
  last_name: Louie
- first_name: Nicholas M.
  full_name: Orchanian, Nicholas M.
  last_name: Orchanian
- first_name: Colin
  full_name: Nuckolls, Colin
  last_name: Nuckolls
- first_name: Latha
  full_name: Venkataraman, Latha
  id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf
  last_name: Venkataraman
  orcid: 0000-0002-6957-6089
citation:
  ama: Li L, Louie S, Orchanian NM, Nuckolls C, Venkataraman L. Long-range gating
    in single-molecule one-dimensional topological insulators. <i>Journal of the American
    Chemical Society</i>. 2024;146(24):16920-16925. doi:<a href="https://doi.org/10.1021/jacs.4c05699">10.1021/jacs.4c05699</a>
  apa: Li, L., Louie, S., Orchanian, N. M., Nuckolls, C., &#38; Venkataraman, L. (2024).
    Long-range gating in single-molecule one-dimensional topological insulators. <i>Journal
    of the American Chemical Society</i>. American Chemical Society. <a href="https://doi.org/10.1021/jacs.4c05699">https://doi.org/10.1021/jacs.4c05699</a>
  chicago: Li, Liang, Shayan Louie, Nicholas M. Orchanian, Colin Nuckolls, and Latha
    Venkataraman. “Long-Range Gating in Single-Molecule One-Dimensional Topological
    Insulators.” <i>Journal of the American Chemical Society</i>. American Chemical
    Society, 2024. <a href="https://doi.org/10.1021/jacs.4c05699">https://doi.org/10.1021/jacs.4c05699</a>.
  ieee: L. Li, S. Louie, N. M. Orchanian, C. Nuckolls, and L. Venkataraman, “Long-range
    gating in single-molecule one-dimensional topological insulators,” <i>Journal
    of the American Chemical Society</i>, vol. 146, no. 24. American Chemical Society,
    pp. 16920–16925, 2024.
  ista: Li L, Louie S, Orchanian NM, Nuckolls C, Venkataraman L. 2024. Long-range
    gating in single-molecule one-dimensional topological insulators. Journal of the
    American Chemical Society. 146(24), 16920–16925.
  mla: Li, Liang, et al. “Long-Range Gating in Single-Molecule One-Dimensional Topological
    Insulators.” <i>Journal of the American Chemical Society</i>, vol. 146, no. 24,
    American Chemical Society, 2024, pp. 16920–25, doi:<a href="https://doi.org/10.1021/jacs.4c05699">10.1021/jacs.4c05699</a>.
  short: L. Li, S. Louie, N.M. Orchanian, C. Nuckolls, L. Venkataraman, Journal of
    the American Chemical Society 146 (2024) 16920–16925.
date_created: 2024-09-06T12:40:17Z
date_published: 2024-06-24T00:00:00Z
date_updated: 2024-11-18T10:51:21Z
day: '24'
doi: 10.1021/jacs.4c05699
extern: '1'
external_id:
  pmid:
  - '38832840'
fulldoi: https://doi.org/10.1021/jacs.4c05699
intvolume: '       146'
issue: '24'
language:
- iso: eng
month: '06'
oa_version: None
page: 16920-16925
pmid: 1
publication: Journal of the American Chemical Society
publication_identifier:
  eissn:
  - 1520-5126
  issn:
  - 0002-7863
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Long-range gating in single-molecule one-dimensional topological insulators
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 146
year: '2024'
...
---
OA_type: closed access
_id: '17854'
abstract:
- lang: eng
  text: As social media platforms continue to grow in popularity, there is an increasing
    need for science outreach teams to bring STEM content to the virtual landscape.
    Here, we highlight the use of short-form videos on our TikTok channel─@IvyLeagueScience─as
    a new way to approach science outreach. Through a combination of content production
    and data analytics, we were able to build an online platform with >150k followers,
    3.6 million likes, and 18 million views. By bringing science to social media,
    we engage with students across the world, allowing them to experience science-based
    content. In this case study, we hope to encourage other scientific outreach teams
    to employ social media as a means of increasing visibility of scientists and STEM
    careers.
article_processing_charge: No
article_type: original
author:
- first_name: Claudia R.
  full_name: Prindle, Claudia R.
  last_name: Prindle
- first_name: Nicholas M.
  full_name: Orchanian, Nicholas M.
  last_name: Orchanian
- first_name: Latha
  full_name: Venkataraman, Latha
  id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf
  last_name: Venkataraman
  orcid: 0000-0002-6957-6089
- first_name: Colin
  full_name: Nuckolls, Colin
  last_name: Nuckolls
citation:
  ama: Prindle CR, Orchanian NM, Venkataraman L, Nuckolls C. Short-form videos as
    an emerging social media tool for STEM edutainment. <i>Journal of Chemical Education</i>.
    2024;101(3):1319-1324. doi:<a href="https://doi.org/10.1021/acs.jchemed.3c01185">10.1021/acs.jchemed.3c01185</a>
  apa: Prindle, C. R., Orchanian, N. M., Venkataraman, L., &#38; Nuckolls, C. (2024).
    Short-form videos as an emerging social media tool for STEM edutainment. <i>Journal
    of Chemical Education</i>. American Chemical Society. <a href="https://doi.org/10.1021/acs.jchemed.3c01185">https://doi.org/10.1021/acs.jchemed.3c01185</a>
  chicago: Prindle, Claudia R., Nicholas M. Orchanian, Latha Venkataraman, and Colin
    Nuckolls. “Short-Form Videos as an Emerging Social Media Tool for STEM Edutainment.”
    <i>Journal of Chemical Education</i>. American Chemical Society, 2024. <a href="https://doi.org/10.1021/acs.jchemed.3c01185">https://doi.org/10.1021/acs.jchemed.3c01185</a>.
  ieee: C. R. Prindle, N. M. Orchanian, L. Venkataraman, and C. Nuckolls, “Short-form
    videos as an emerging social media tool for STEM edutainment,” <i>Journal of Chemical
    Education</i>, vol. 101, no. 3. American Chemical Society, pp. 1319–1324, 2024.
  ista: Prindle CR, Orchanian NM, Venkataraman L, Nuckolls C. 2024. Short-form videos
    as an emerging social media tool for STEM edutainment. Journal of Chemical Education.
    101(3), 1319–1324.
  mla: Prindle, Claudia R., et al. “Short-Form Videos as an Emerging Social Media
    Tool for STEM Edutainment.” <i>Journal of Chemical Education</i>, vol. 101, no.
    3, American Chemical Society, 2024, pp. 1319–24, doi:<a href="https://doi.org/10.1021/acs.jchemed.3c01185">10.1021/acs.jchemed.3c01185</a>.
  short: C.R. Prindle, N.M. Orchanian, L. Venkataraman, C. Nuckolls, Journal of Chemical
    Education 101 (2024) 1319–1324.
date_created: 2024-09-06T12:43:20Z
date_published: 2024-02-14T00:00:00Z
date_updated: 2024-11-18T10:55:30Z
day: '14'
doi: 10.1021/acs.jchemed.3c01185
extern: '1'
fulldoi: https://doi.org/10.1021/acs.jchemed.3c01185
intvolume: '       101'
issue: '3'
language:
- iso: eng
month: '02'
oa_version: None
page: 1319-1324
publication: Journal of Chemical Education
publication_identifier:
  eissn:
  - 1938-1328
  issn:
  - 0021-9584
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Short-form videos as an emerging social media tool for STEM edutainment
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 101
year: '2024'
...
---
_id: '17855'
abstract:
- lang: eng
  text: Biased metal–molecule–metal junctions emit light through electroluminescence,
    a phenomenon at the intersection of molecular electronics and nanoplasmonics.
    This can occur when the junction plasmon mode is excited by inelastic electron
    current fluctuations. Here, we simultaneously measure the conductance and electroluminescence
    intensity from single-molecule junctions with time resolution in a solution environment
    at room temperature. We use current versus bias data to determine the molecular
    junction transport parameters and then relate these to the expected current shot
    noise. We find that the electroluminescence signal accurately matches the theoretical
    prediction of shot-noise-driven emission in a large fraction of the molecular
    junctions studied. This introduces a novel experimental method for qualitatively
    estimating finite-frequency shot noise in single-molecule junctions under ambient
    conditions. We further demonstrate that electroluminescence can be used to obtain
    the level alignment of the frontier orbital dominating transport in the molecular
    junction.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Angela L.
  full_name: Paoletta, Angela L.
  last_name: Paoletta
- first_name: Latha
  full_name: Venkataraman, Latha
  id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf
  last_name: Venkataraman
  orcid: 0000-0002-6957-6089
citation:
  ama: Paoletta AL, Venkataraman L. Determining transmission characteristics from
    shot-noise-driven electroluminescence in single-molecule junctions. <i>Nano Letters</i>.
    2024;24(6):1931-1935. doi:<a href="https://doi.org/10.1021/acs.nanolett.3c04207">10.1021/acs.nanolett.3c04207</a>
  apa: Paoletta, A. L., &#38; Venkataraman, L. (2024). Determining transmission characteristics
    from shot-noise-driven electroluminescence in single-molecule junctions. <i>Nano
    Letters</i>. American Chemical Society. <a href="https://doi.org/10.1021/acs.nanolett.3c04207">https://doi.org/10.1021/acs.nanolett.3c04207</a>
  chicago: Paoletta, Angela L., and Latha Venkataraman. “Determining Transmission
    Characteristics from Shot-Noise-Driven Electroluminescence in Single-Molecule
    Junctions.” <i>Nano Letters</i>. American Chemical Society, 2024. <a href="https://doi.org/10.1021/acs.nanolett.3c04207">https://doi.org/10.1021/acs.nanolett.3c04207</a>.
  ieee: A. L. Paoletta and L. Venkataraman, “Determining transmission characteristics
    from shot-noise-driven electroluminescence in single-molecule junctions,” <i>Nano
    Letters</i>, vol. 24, no. 6. American Chemical Society, pp. 1931–1935, 2024.
  ista: Paoletta AL, Venkataraman L. 2024. Determining transmission characteristics
    from shot-noise-driven electroluminescence in single-molecule junctions. Nano
    Letters. 24(6), 1931–1935.
  mla: Paoletta, Angela L., and Latha Venkataraman. “Determining Transmission Characteristics
    from Shot-Noise-Driven Electroluminescence in Single-Molecule Junctions.” <i>Nano
    Letters</i>, vol. 24, no. 6, American Chemical Society, 2024, pp. 1931–35, doi:<a
    href="https://doi.org/10.1021/acs.nanolett.3c04207">10.1021/acs.nanolett.3c04207</a>.
  short: A.L. Paoletta, L. Venkataraman, Nano Letters 24 (2024) 1931–1935.
date_created: 2024-09-06T12:44:24Z
date_published: 2024-02-05T00:00:00Z
date_updated: 2024-11-18T10:58:19Z
day: '05'
doi: 10.1021/acs.nanolett.3c04207
extern: '1'
external_id:
  pmid:
  - '38315038'
fulldoi: https://doi.org/10.1021/acs.nanolett.3c04207
intvolume: '        24'
issue: '6'
language:
- iso: eng
month: '02'
oa_version: None
page: 1931-1935
pmid: 1
publication: Nano Letters
publication_identifier:
  issn:
  - 1530-6984
  - 1530-6992
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Determining transmission characteristics from shot-noise-driven electroluminescence
  in single-molecule junctions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2024'
...
---
_id: '17856'
abstract:
- lang: eng
  text: The successful incorporation of molecules as active circuit elements relies
    on the ability to tune their electronic properties through chemical design. A
    synthetic strategy that has been used to manipulate and gate circuit conductance
    involves attaching a pendant substituent along the molecular conduction pathway.
    However, such a chemical gate has not yet been shown to significantly modify conductance.
    Here, we report a novel series of triarylmethylium and triangulenium carbocations
    gated by different substituents coupled to the delocalized conducting orbitals
    on the molecular backbone through a Fano resonance. By changing the pendant substituents
    to modulate the position of the Fano resonance and its coupling to the conducting
    orbitals, we can regulate the junction conductance by a remarkable factor of 450.
    This work thus provides a new design principle to enable effective chemical gating
    of single-molecule devices toward effective molecular transistors.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Claudia R.
  full_name: Prindle, Claudia R.
  last_name: Prindle
- first_name: Wanzhuo
  full_name: Shi, Wanzhuo
  last_name: Shi
- first_name: Liang
  full_name: Li, Liang
  last_name: Li
- first_name: Jesper
  full_name: Dahl Jensen, Jesper
  last_name: Dahl Jensen
- first_name: Bo W.
  full_name: Laursen, Bo W.
  last_name: Laursen
- first_name: Michael L.
  full_name: Steigerwald, Michael L.
  last_name: Steigerwald
- first_name: Colin
  full_name: Nuckolls, Colin
  last_name: Nuckolls
- first_name: Latha
  full_name: Venkataraman, Latha
  id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf
  last_name: Venkataraman
  orcid: 0000-0002-6957-6089
citation:
  ama: Prindle CR, Shi W, Li L, et al. Effective gating in single-molecule junctions
    through fano resonances. <i>Journal of the American Chemical Society</i>. 2024;146(6):3646-3650.
    doi:<a href="https://doi.org/10.1021/jacs.3c14226">10.1021/jacs.3c14226</a>
  apa: Prindle, C. R., Shi, W., Li, L., Dahl Jensen, J., Laursen, B. W., Steigerwald,
    M. L., … Venkataraman, L. (2024). Effective gating in single-molecule junctions
    through fano resonances. <i>Journal of the American Chemical Society</i>. American
    Chemical Society. <a href="https://doi.org/10.1021/jacs.3c14226">https://doi.org/10.1021/jacs.3c14226</a>
  chicago: Prindle, Claudia R., Wanzhuo Shi, Liang Li, Jesper Dahl Jensen, Bo W. Laursen,
    Michael L. Steigerwald, Colin Nuckolls, and Latha Venkataraman. “Effective Gating
    in Single-Molecule Junctions through Fano Resonances.” <i>Journal of the American
    Chemical Society</i>. American Chemical Society, 2024. <a href="https://doi.org/10.1021/jacs.3c14226">https://doi.org/10.1021/jacs.3c14226</a>.
  ieee: C. R. Prindle <i>et al.</i>, “Effective gating in single-molecule junctions
    through fano resonances,” <i>Journal of the American Chemical Society</i>, vol.
    146, no. 6. American Chemical Society, pp. 3646–3650, 2024.
  ista: Prindle CR, Shi W, Li L, Dahl Jensen J, Laursen BW, Steigerwald ML, Nuckolls
    C, Venkataraman L. 2024. Effective gating in single-molecule junctions through
    fano resonances. Journal of the American Chemical Society. 146(6), 3646–3650.
  mla: Prindle, Claudia R., et al. “Effective Gating in Single-Molecule Junctions
    through Fano Resonances.” <i>Journal of the American Chemical Society</i>, vol.
    146, no. 6, American Chemical Society, 2024, pp. 3646–50, doi:<a href="https://doi.org/10.1021/jacs.3c14226">10.1021/jacs.3c14226</a>.
  short: C.R. Prindle, W. Shi, L. Li, J. Dahl Jensen, B.W. Laursen, M.L. Steigerwald,
    C. Nuckolls, L. Venkataraman, Journal of the American Chemical Society 146 (2024)
    3646–3650.
date_created: 2024-09-06T12:45:11Z
date_published: 2024-01-31T00:00:00Z
date_updated: 2024-11-18T11:02:24Z
day: '31'
doi: 10.1021/jacs.3c14226
extern: '1'
external_id:
  pmid:
  - '38293735'
fulldoi: https://doi.org/10.1021/jacs.3c14226
intvolume: '       146'
issue: '6'
language:
- iso: eng
month: '01'
oa_version: None
page: 3646-3650
pmid: 1
publication: Journal of the American Chemical Society
publication_identifier:
  eissn:
  - 1520-5126
  issn:
  - 0002-7863
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Effective gating in single-molecule junctions through fano resonances
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 146
year: '2024'
...
---
OA_type: closed access
_id: '17857'
abstract:
- lang: eng
  text: Gold–dithiol molecular junctions have been studied both experimentally and
    theoretically. However, the nature of the gold–thiolate bond as it relates to
    the solvent has seldom been investigated. It is known that solvents can impact
    the electronic structure of single-molecule junctions, but the correlation between
    the solvent and dithiol-linked single-molecule junction conductance is not well
    understood. We study molecular junctions formed with thiol-terminated phenylenes
    from both 1-chloronaphthalene and 1-bromonaphthalene solutions. We find that the
    most probable conductance and the distribution of conductances are both affected
    by the solvent. First-principles calculations show that junction conductance depends
    on the binding configurations (adatom, atop, and bridge) of the thiolate on the
    Au surface, as has been shown previously. More importantly, we find that brominated
    solvents can restrict the binding of thiols to specific Au sites. This mechanism
    offers new insight into the effects of the solvent environment on covalent bonding
    in molecular junctions.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Johnson
  full_name: Dalmieda, Johnson
  last_name: Dalmieda
- first_name: Wanzhuo
  full_name: Shi, Wanzhuo
  last_name: Shi
- first_name: Liang
  full_name: Li, Liang
  last_name: Li
- first_name: Latha
  full_name: Venkataraman, Latha
  id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf
  last_name: Venkataraman
  orcid: 0000-0002-6957-6089
citation:
  ama: Dalmieda J, Shi W, Li L, Venkataraman L. Solvent-mediated modulation of the
    Au–S bond in dithiol molecular junctions. <i>Nano Letters</i>. 2024;24(2):703-707.
    doi:<a href="https://doi.org/10.1021/acs.nanolett.3c04058">10.1021/acs.nanolett.3c04058</a>
  apa: Dalmieda, J., Shi, W., Li, L., &#38; Venkataraman, L. (2024). Solvent-mediated
    modulation of the Au–S bond in dithiol molecular junctions. <i>Nano Letters</i>.
    American Chemical Society. <a href="https://doi.org/10.1021/acs.nanolett.3c04058">https://doi.org/10.1021/acs.nanolett.3c04058</a>
  chicago: Dalmieda, Johnson, Wanzhuo Shi, Liang Li, and Latha Venkataraman. “Solvent-Mediated
    Modulation of the Au–S Bond in Dithiol Molecular Junctions.” <i>Nano Letters</i>.
    American Chemical Society, 2024. <a href="https://doi.org/10.1021/acs.nanolett.3c04058">https://doi.org/10.1021/acs.nanolett.3c04058</a>.
  ieee: J. Dalmieda, W. Shi, L. Li, and L. Venkataraman, “Solvent-mediated modulation
    of the Au–S bond in dithiol molecular junctions,” <i>Nano Letters</i>, vol. 24,
    no. 2. American Chemical Society, pp. 703–707, 2024.
  ista: Dalmieda J, Shi W, Li L, Venkataraman L. 2024. Solvent-mediated modulation
    of the Au–S bond in dithiol molecular junctions. Nano Letters. 24(2), 703–707.
  mla: Dalmieda, Johnson, et al. “Solvent-Mediated Modulation of the Au–S Bond in
    Dithiol Molecular Junctions.” <i>Nano Letters</i>, vol. 24, no. 2, American Chemical
    Society, 2024, pp. 703–07, doi:<a href="https://doi.org/10.1021/acs.nanolett.3c04058">10.1021/acs.nanolett.3c04058</a>.
  short: J. Dalmieda, W. Shi, L. Li, L. Venkataraman, Nano Letters 24 (2024) 703–707.
date_created: 2024-09-06T12:46:39Z
date_published: 2024-01-04T00:00:00Z
date_updated: 2024-11-19T12:50:27Z
day: '04'
doi: 10.1021/acs.nanolett.3c04058
extern: '1'
external_id:
  pmid:
  - '38175934'
fulldoi: https://doi.org/10.1021/acs.nanolett.3c04058
intvolume: '        24'
issue: '2'
language:
- iso: eng
month: '01'
oa_version: None
page: 703-707
pmid: 1
publication: Nano Letters
publication_identifier:
  eissn:
  - 1530-6992
  issn:
  - 1530-6984
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Solvent-mediated modulation of the Au–S bond in dithiol molecular junctions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2024'
...
---
OA_type: closed access
_id: '17859'
abstract:
- lang: eng
  text: The electrostatic environment around nanoscale molecular junctions modulates
    charge transport; solvents alter this environment. Methods to directly probe solvent
    effects require correlating measurements of the local electrostatic environment
    with charge transport across the metal–molecule–metal junction. Here, we measure
    the conductance and current–voltage characteristics of molecular wires using a
    scanning tunneling microscope–break junction (STM-BJ) setup in two commonly used
    solvents. Our results show that the solvent environment induces shifts in molecular
    conductance, which we quantify, but more importantly we find that the solvent
    also impacts the magnitude of current rectification in molecular junctions. By
    incorporating electrochemical impedance spectroscopy into the STM-BJ setup, we
    measure the capacitance of the dipole layer formed at the metal–solvent interface
    and show that rectification can be correlated with solvent capacitance. These
    results provide a method of quantifying the impact of the solvent environment
    and a path toward improved environmental control of molecular devices.
article_processing_charge: No
article_type: original
author:
- first_name: Wanzhuo
  full_name: Shi, Wanzhuo
  last_name: Shi
- first_name: Julia E.
  full_name: Greenwald, Julia E.
  last_name: Greenwald
- first_name: Latha
  full_name: Venkataraman, Latha
  id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf
  last_name: Venkataraman
  orcid: 0000-0002-6957-6089
citation:
  ama: Shi W, Greenwald JE, Venkataraman L. Impact of solvent electrostatic environment
    on molecular junctions probed via electrochemical impedance spectroscopy. <i>Nano
    Letters</i>. 2024;24(30):9283-9288. doi:<a href="https://doi.org/10.1021/acs.nanolett.4c02103">10.1021/acs.nanolett.4c02103</a>
  apa: Shi, W., Greenwald, J. E., &#38; Venkataraman, L. (2024). Impact of solvent
    electrostatic environment on molecular junctions probed via electrochemical impedance
    spectroscopy. <i>Nano Letters</i>. American Chemical Society. <a href="https://doi.org/10.1021/acs.nanolett.4c02103">https://doi.org/10.1021/acs.nanolett.4c02103</a>
  chicago: Shi, Wanzhuo, Julia E. Greenwald, and Latha Venkataraman. “Impact of Solvent
    Electrostatic Environment on Molecular Junctions Probed via Electrochemical Impedance
    Spectroscopy.” <i>Nano Letters</i>. American Chemical Society, 2024. <a href="https://doi.org/10.1021/acs.nanolett.4c02103">https://doi.org/10.1021/acs.nanolett.4c02103</a>.
  ieee: W. Shi, J. E. Greenwald, and L. Venkataraman, “Impact of solvent electrostatic
    environment on molecular junctions probed via electrochemical impedance spectroscopy,”
    <i>Nano Letters</i>, vol. 24, no. 30. American Chemical Society, pp. 9283–9288,
    2024.
  ista: Shi W, Greenwald JE, Venkataraman L. 2024. Impact of solvent electrostatic
    environment on molecular junctions probed via electrochemical impedance spectroscopy.
    Nano Letters. 24(30), 9283–9288.
  mla: Shi, Wanzhuo, et al. “Impact of Solvent Electrostatic Environment on Molecular
    Junctions Probed via Electrochemical Impedance Spectroscopy.” <i>Nano Letters</i>,
    vol. 24, no. 30, American Chemical Society, 2024, pp. 9283–88, doi:<a href="https://doi.org/10.1021/acs.nanolett.4c02103">10.1021/acs.nanolett.4c02103</a>.
  short: W. Shi, J.E. Greenwald, L. Venkataraman, Nano Letters 24 (2024) 9283–9288.
date_created: 2024-09-06T12:48:34Z
date_published: 2024-07-18T00:00:00Z
date_updated: 2024-11-20T15:24:37Z
day: '18'
doi: 10.1021/acs.nanolett.4c02103
extern: '1'
external_id:
  pmid:
  - '39023006'
fulldoi: https://doi.org/10.1021/acs.nanolett.4c02103
intvolume: '        24'
issue: '30'
language:
- iso: eng
month: '07'
oa_version: None
page: 9283-9288
pmid: 1
publication: Nano Letters
publication_identifier:
  eissn:
  - 1530-6992
  issn:
  - 1530-6984
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Impact of solvent electrostatic environment on molecular junctions probed via
  electrochemical impedance spectroscopy
type: journal_article
user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d
volume: 24
year: '2024'
...
---
_id: '18153'
abstract:
- lang: eng
  text: Attention supports decision making by selecting the features that are relevant
    for decisions. Selective enhancement of the relevant features and inhibition of
    distractors has been proposed as potential neural mechanisms driving this selection
    process. Yet, how attention operates when relevance cannot be directly determined,
    and the attention signal needs to be internally constructed is less understood.
    Here we recorded from populations of neurons in the anterior cingulate cortex
    (ACC) of mice in an attention-shifting task where relevance of stimulus modalities
    changed across blocks of trials. In contrast with V1 recordings, decoding of the
    irrelevant modality gradually declined in ACC after an initial transient. Our
    analytical proof and a recurrent neural network model of the task revealed mutually
    inhibiting connections that produced context-gated suppression as observed in
    mice. Using this RNN model we predicted a correlation between contextual modulation
    of individual neurons and their stimulus drive, which we confirmed in ACC but
    not in V1.
article_number: '5559'
article_processing_charge: Yes
article_type: original
author:
- first_name: Márton Albert
  full_name: Hajnal, Márton Albert
  last_name: Hajnal
- first_name: Duy
  full_name: Tran, Duy
  last_name: Tran
- first_name: Zsombor
  full_name: Szabó, Zsombor
  id: 47757b1e-3f56-11ef-9908-8ddefb4d05eb
  last_name: Szabó
  orcid: 0009-0003-8524-4994
- first_name: Andrea
  full_name: Albert, Andrea
  last_name: Albert
- first_name: Karen
  full_name: Safaryan, Karen
  last_name: Safaryan
- first_name: Michael
  full_name: Einstein, Michael
  last_name: Einstein
- first_name: Mauricio
  full_name: Vallejo Martelo, Mauricio
  last_name: Vallejo Martelo
- first_name: Pierre-Olivier
  full_name: Polack, Pierre-Olivier
  last_name: Polack
- first_name: Peyman
  full_name: Golshani, Peyman
  last_name: Golshani
- first_name: Gergő
  full_name: Orbán, Gergő
  last_name: Orbán
citation:
  ama: Hajnal MA, Tran D, Szabó Z, et al. Shifts in attention drive context-dependent
    subspace encoding in anterior cingulate cortex in mice during decision making.
    <i>Nature Communications</i>. 2024;15. doi:<a href="https://doi.org/10.1038/s41467-024-49845-2">10.1038/s41467-024-49845-2</a>
  apa: Hajnal, M. A., Tran, D., Szabó, Z., Albert, A., Safaryan, K., Einstein, M.,
    … Orbán, G. (2024). Shifts in attention drive context-dependent subspace encoding
    in anterior cingulate cortex in mice during decision making. <i>Nature Communications</i>.
    Springer Nature. <a href="https://doi.org/10.1038/s41467-024-49845-2">https://doi.org/10.1038/s41467-024-49845-2</a>
  chicago: Hajnal, Márton Albert, Duy Tran, Zsombor Szabó, Andrea Albert, Karen Safaryan,
    Michael Einstein, Mauricio Vallejo Martelo, Pierre-Olivier Polack, Peyman Golshani,
    and Gergő Orbán. “Shifts in Attention Drive Context-Dependent Subspace Encoding
    in Anterior Cingulate Cortex in Mice during Decision Making.” <i>Nature Communications</i>.
    Springer Nature, 2024. <a href="https://doi.org/10.1038/s41467-024-49845-2">https://doi.org/10.1038/s41467-024-49845-2</a>.
  ieee: M. A. Hajnal <i>et al.</i>, “Shifts in attention drive context-dependent subspace
    encoding in anterior cingulate cortex in mice during decision making,” <i>Nature
    Communications</i>, vol. 15. Springer Nature, 2024.
  ista: Hajnal MA, Tran D, Szabó Z, Albert A, Safaryan K, Einstein M, Vallejo Martelo
    M, Polack P-O, Golshani P, Orbán G. 2024. Shifts in attention drive context-dependent
    subspace encoding in anterior cingulate cortex in mice during decision making.
    Nature Communications. 15, 5559.
  mla: Hajnal, Márton Albert, et al. “Shifts in Attention Drive Context-Dependent
    Subspace Encoding in Anterior Cingulate Cortex in Mice during Decision Making.”
    <i>Nature Communications</i>, vol. 15, 5559, Springer Nature, 2024, doi:<a href="https://doi.org/10.1038/s41467-024-49845-2">10.1038/s41467-024-49845-2</a>.
  short: M.A. Hajnal, D. Tran, Z. Szabó, A. Albert, K. Safaryan, M. Einstein, M. Vallejo
    Martelo, P.-O. Polack, P. Golshani, G. Orbán, Nature Communications 15 (2024).
date_created: 2024-09-28T06:59:03Z
date_published: 2024-07-02T00:00:00Z
date_updated: 2024-10-01T07:14:56Z
day: '02'
ddc:
- '570'
doi: 10.1038/s41467-024-49845-2
extern: '1'
external_id:
  pmid:
  - '37873364'
file:
- access_level: open_access
  checksum: 22caa17a6691884c66c650c61227e903
  content_type: application/pdf
  creator: dernst
  date_created: 2024-10-01T07:13:36Z
  date_updated: 2024-10-01T07:13:36Z
  file_id: '18163'
  file_name: 2024_NatureComm_Hajnal.pdf
  file_size: 4346510
  relation: main_file
  success: 1
file_date_updated: 2024-10-01T07:13:36Z
fulldoi: https://doi.org/10.1038/s41467-024-49845-2
has_accepted_license: '1'
intvolume: '        15'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
  issn:
  - 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Shifts in attention drive context-dependent subspace encoding in anterior cingulate
  cortex in mice during decision making
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: '2024'
...
---
OA_type: closed access
_id: '18167'
abstract:
- lang: eng
  text: 'Holdase chaperones are essential in the mitochondrial membrane-protein biogenesis
    as they stabilize preproteins and keep them in an import-competent state as they
    travel through the aqueous cytosol and intermembrane space. The small TIM chaperones
    of the mitochondrial intermembrane space function within a fine balance of client
    promiscuity and high affinity binding, while being also able to release their
    client proteins without significant energy barrier to the downstream insertases/translocases.
    The tendency of the preproteins to aggregate and the dynamic nature of the preprotein—chaperone
    complexes makes the preparation of these complexes challenging. Here we present
    two optimized methods for complex formation of highly hydrophobic precursor proteins
    and chaperones: a pull-down approach and an in-vitro translation strategy. In
    the former, attaching the client protein to an affinity resin keeps the individual
    client protein copies apart from each other and decreases the client self-aggregation
    probability, thereby favouring complex formation. In the latter approach, a purified
    chaperone, added to the cell-free protein synthesis, captures the nascent precursor
    protein. The choice of method will depend on the desired client-chaperone complex
    amount, or the need for specific labeling scheme.'
article_processing_charge: No
author:
- first_name: Undina
  full_name: Guillerm, Undina
  id: bb74f472-ae54-11eb-9835-bc9c22fb1183
  last_name: Guillerm
- first_name: Iva
  full_name: Sučec, Iva
  last_name: Sučec
- first_name: Paul
  full_name: Schanda, Paul
  id: 7B541462-FAF6-11E9-A490-E8DFE5697425
  last_name: Schanda
  orcid: 0000-0002-9350-7606
citation:
  ama: 'Guillerm U, Sučec I, Schanda P. Generation of TIM chaperone substrate complexes.
    In: <i>Methods in Enzymology</i>. Vol 707. Elsevier; 2024:391-422. doi:<a href="https://doi.org/10.1016/bs.mie.2024.07.051">10.1016/bs.mie.2024.07.051</a>'
  apa: Guillerm, U., Sučec, I., &#38; Schanda, P. (2024). Generation of TIM chaperone
    substrate complexes. In <i>Methods in Enzymology</i> (Vol. 707, pp. 391–422).
    Elsevier. <a href="https://doi.org/10.1016/bs.mie.2024.07.051">https://doi.org/10.1016/bs.mie.2024.07.051</a>
  chicago: Guillerm, Undina, Iva Sučec, and Paul Schanda. “Generation of TIM Chaperone
    Substrate Complexes.” In <i>Methods in Enzymology</i>, 707:391–422. Elsevier,
    2024. <a href="https://doi.org/10.1016/bs.mie.2024.07.051">https://doi.org/10.1016/bs.mie.2024.07.051</a>.
  ieee: U. Guillerm, I. Sučec, and P. Schanda, “Generation of TIM chaperone substrate
    complexes,” in <i>Methods in Enzymology</i>, vol. 707, Elsevier, 2024, pp. 391–422.
  ista: 'Guillerm U, Sučec I, Schanda P. 2024.Generation of TIM chaperone substrate
    complexes. In: Methods in Enzymology. vol. 707, 391–422.'
  mla: Guillerm, Undina, et al. “Generation of TIM Chaperone Substrate Complexes.”
    <i>Methods in Enzymology</i>, vol. 707, Elsevier, 2024, pp. 391–422, doi:<a href="https://doi.org/10.1016/bs.mie.2024.07.051">10.1016/bs.mie.2024.07.051</a>.
  short: U. Guillerm, I. Sučec, P. Schanda, in:, Methods in Enzymology, Elsevier,
    2024, pp. 391–422.
corr_author: '1'
date_created: 2024-10-01T10:58:27Z
date_published: 2024-09-13T00:00:00Z
date_updated: 2025-10-22T06:40:54Z
day: '13'
department:
- _id: PaSc
doi: 10.1016/bs.mie.2024.07.051
external_id:
  pmid:
  - '39488384'
fulldoi: https://doi.org/10.1016/bs.mie.2024.07.051
intvolume: '       707'
language:
- iso: eng
month: '09'
oa_version: None
page: 391-422
pmid: 1
publication: Methods in Enzymology
publication_identifier:
  issn:
  - 0076-6879
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Generation of TIM chaperone substrate complexes
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 707
year: '2024'
...
---
_id: '18187'
abstract:
- lang: eng
  text: Quasicrystals are ordered but not periodic, which makes them fascinating objects
    at the interface between order and disorder. Experiments with ultracold atoms
    zoom in on this interface by driving a quasicrystal and exploring its fractal
    properties.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Julian
  full_name: Leonard, Julian
  id: b75b3f45-7995-11ef-9bfd-9a9cd02c3577
  last_name: Leonard
  orcid: 0000-0003-3696-6870
citation:
  ama: Leonard J. A kicked quasicrystal. <i>Nature Physics</i>. 2024;20(3):351-352.
    doi:<a href="https://doi.org/10.1038/s41567-023-02357-0">10.1038/s41567-023-02357-0</a>
  apa: Leonard, J. (2024). A kicked quasicrystal. <i>Nature Physics</i>. Springer
    Nature. <a href="https://doi.org/10.1038/s41567-023-02357-0">https://doi.org/10.1038/s41567-023-02357-0</a>
  chicago: Leonard, Julian. “A Kicked Quasicrystal.” <i>Nature Physics</i>. Springer
    Nature, 2024. <a href="https://doi.org/10.1038/s41567-023-02357-0">https://doi.org/10.1038/s41567-023-02357-0</a>.
  ieee: J. Leonard, “A kicked quasicrystal,” <i>Nature Physics</i>, vol. 20, no. 3.
    Springer Nature, pp. 351–352, 2024.
  ista: Leonard J. 2024. A kicked quasicrystal. Nature Physics. 20(3), 351–352.
  mla: Leonard, Julian. “A Kicked Quasicrystal.” <i>Nature Physics</i>, vol. 20, no.
    3, Springer Nature, 2024, pp. 351–52, doi:<a href="https://doi.org/10.1038/s41567-023-02357-0">10.1038/s41567-023-02357-0</a>.
  short: J. Leonard, Nature Physics 20 (2024) 351–352.
date_created: 2024-10-07T11:45:17Z
date_published: 2024-01-19T00:00:00Z
date_updated: 2024-10-14T07:54:20Z
day: '19'
doi: 10.1038/s41567-023-02357-0
extern: '1'
fulldoi: https://doi.org/10.1038/s41567-023-02357-0
intvolume: '        20'
issue: '3'
language:
- iso: eng
month: '01'
oa_version: None
page: 351-352
publication: Nature Physics
publication_identifier:
  eissn:
  - 1745-2481
  issn:
  - 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A kicked quasicrystal
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2024'
...
---
_id: '18188'
abstract:
- lang: eng
  text: New generations of ultracold-atom experiments are continually raising the
    demand for efficient solutions to optimal control problems. Here, we apply Bayesian
    optimization to improve a state-preparation protocol recently implemented in an
    ultracold-atom system to realize a two-particle fractional quantum Hall state.
    Compared to manual ramp design, we demonstrate the superior performance of our
    optimization approach in a numerical simulation – resulting in a protocol that
    is 10x faster at the same fidelity, even when taking into account experimentally
    realistic levels of disorder in the system. We extensively analyze and discuss
    questions of robustness and the relationship between numerical simulation and
    experimental realization, and how to make the best use of the surrogate model
    trained during optimization. We find that numerical simulation can be expected
    to substantially reduce the number of experiments that need to be performed with
    even the most basic transfer learning techniques. The proposed protocol and workflow
    will pave the way toward the realization of more complex many-body quantum states
    in experiments.
article_number: '1388'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Tizian
  full_name: Blatz, Tizian
  last_name: Blatz
- first_name: Joyce
  full_name: Kwan, Joyce
  last_name: Kwan
- first_name: Julian
  full_name: Leonard, Julian
  id: b75b3f45-7995-11ef-9bfd-9a9cd02c3577
  last_name: Leonard
- first_name: Annabelle
  full_name: Bohrdt, Annabelle
  last_name: Bohrdt
citation:
  ama: Blatz T, Kwan J, Leonard J, Bohrdt A. Bayesian optimization for robust state
    preparation in quantum many-body systems. <i>Quantum</i>. 2024;8. doi:<a href="https://doi.org/10.22331/q-2024-06-27-1388">10.22331/q-2024-06-27-1388</a>
  apa: Blatz, T., Kwan, J., Leonard, J., &#38; Bohrdt, A. (2024). Bayesian optimization
    for robust state preparation in quantum many-body systems. <i>Quantum</i>. Verein
    zur Förderung des Open Access Publizierens in den Quantenwissenschaften. <a href="https://doi.org/10.22331/q-2024-06-27-1388">https://doi.org/10.22331/q-2024-06-27-1388</a>
  chicago: Blatz, Tizian, Joyce Kwan, Julian Leonard, and Annabelle Bohrdt. “Bayesian
    Optimization for Robust State Preparation in Quantum Many-Body Systems.” <i>Quantum</i>.
    Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften,
    2024. <a href="https://doi.org/10.22331/q-2024-06-27-1388">https://doi.org/10.22331/q-2024-06-27-1388</a>.
  ieee: T. Blatz, J. Kwan, J. Leonard, and A. Bohrdt, “Bayesian optimization for robust
    state preparation in quantum many-body systems,” <i>Quantum</i>, vol. 8. Verein
    zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2024.
  ista: Blatz T, Kwan J, Leonard J, Bohrdt A. 2024. Bayesian optimization for robust
    state preparation in quantum many-body systems. Quantum. 8, 1388.
  mla: Blatz, Tizian, et al. “Bayesian Optimization for Robust State Preparation in
    Quantum Many-Body Systems.” <i>Quantum</i>, vol. 8, 1388, Verein zur Förderung
    des Open Access Publizierens in den Quantenwissenschaften, 2024, doi:<a href="https://doi.org/10.22331/q-2024-06-27-1388">10.22331/q-2024-06-27-1388</a>.
  short: T. Blatz, J. Kwan, J. Leonard, A. Bohrdt, Quantum 8 (2024).
date_created: 2024-10-07T11:45:56Z
date_published: 2024-06-27T00:00:00Z
date_updated: 2024-10-08T11:15:55Z
day: '27'
doi: 10.22331/q-2024-06-27-1388
extern: '1'
external_id:
  arxiv:
  - '2312.09253'
fulldoi: https://doi.org/10.22331/q-2024-06-27-1388
intvolume: '         8'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.22331/q-2024-06-27-1388
month: '06'
oa: 1
oa_version: Published Version
publication: Quantum
publication_identifier:
  issn:
  - 2521-327X
publication_status: published
publisher: Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bayesian optimization for robust state preparation in quantum many-body systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2024'
...
---
_id: '18202'
abstract:
- lang: eng
  text: "We report on adiabatic state preparation in the one-dimensional quantum Ising\r\nmodel
    using ultracold bosons in a tilted optical lattice. We prepare many-body\r\nground
    states of controllable system sizes and observe enhanced fluctuations\r\naround
    the transition between paramagnetic and antiferromagnetic states,\r\nmarking the
    precursor of quantum critical behavior. Furthermore, we find\r\nevidence for superpositions
    of domain walls and study their effect on the\r\nmany-body ground state by measuring
    the populations of each spin configuration\r\nacross the transition. These results
    shed new light on the effect of boundary\r\nconditions in finite-size quantum
    systems."
article_number: '2404.07481'
article_processing_charge: No
arxiv: 1
author:
- first_name: Sooshin
  full_name: Kim, Sooshin
  last_name: Kim
- first_name: Alexander
  full_name: Lukin, Alexander
  last_name: Lukin
- first_name: Matthew
  full_name: Rispoli, Matthew
  last_name: Rispoli
- first_name: M. Eric
  full_name: Tai, M. Eric
  last_name: Tai
- first_name: Adam M.
  full_name: Kaufman, Adam M.
  last_name: Kaufman
- first_name: Perrin
  full_name: Segura, Perrin
  last_name: Segura
- first_name: Yanfei
  full_name: Li, Yanfei
  last_name: Li
- first_name: Joyce
  full_name: Kwan, Joyce
  last_name: Kwan
- first_name: Julian
  full_name: Leonard, Julian
  id: b75b3f45-7995-11ef-9bfd-9a9cd02c3577
  last_name: Leonard
- first_name: Brice Bakkali-Hassani
  full_name: Brice Bakkali-Hassani, Brice Bakkali-Hassani
  last_name: Brice Bakkali-Hassani
- first_name: Markus
  full_name: Greiner, Markus
  last_name: Greiner
citation:
  ama: Kim S, Lukin A, Rispoli M, et al. Adiabatic state preparation in a quantum
    Ising spin chain. <i>arXiv</i>. doi:<a href="https://doi.org/10.48550/arXiv.2404.07481">10.48550/arXiv.2404.07481</a>
  apa: Kim, S., Lukin, A., Rispoli, M., Tai, M. E., Kaufman, A. M., Segura, P., …
    Greiner, M. (n.d.). Adiabatic state preparation in a quantum Ising spin chain.
    <i>arXiv</i>. <a href="https://doi.org/10.48550/arXiv.2404.07481">https://doi.org/10.48550/arXiv.2404.07481</a>
  chicago: Kim, Sooshin, Alexander Lukin, Matthew Rispoli, M. Eric Tai, Adam M. Kaufman,
    Perrin Segura, Yanfei Li, et al. “Adiabatic State Preparation in a Quantum Ising
    Spin Chain.” <i>ArXiv</i>, n.d. <a href="https://doi.org/10.48550/arXiv.2404.07481">https://doi.org/10.48550/arXiv.2404.07481</a>.
  ieee: S. Kim <i>et al.</i>, “Adiabatic state preparation in a quantum Ising spin
    chain,” <i>arXiv</i>. .
  ista: Kim S, Lukin A, Rispoli M, Tai ME, Kaufman AM, Segura P, Li Y, Kwan J, Leonard
    J, Brice Bakkali-Hassani BB-H, Greiner M. Adiabatic state preparation in a quantum
    Ising spin chain. arXiv, 2404.07481.
  mla: Kim, Sooshin, et al. “Adiabatic State Preparation in a Quantum Ising Spin Chain.”
    <i>ArXiv</i>, 2404.07481, doi:<a href="https://doi.org/10.48550/arXiv.2404.07481">10.48550/arXiv.2404.07481</a>.
  short: S. Kim, A. Lukin, M. Rispoli, M.E. Tai, A.M. Kaufman, P. Segura, Y. Li, J.
    Kwan, J. Leonard, B.B.-H. Brice Bakkali-Hassani, M. Greiner, ArXiv (n.d.).
date_created: 2024-10-08T11:25:52Z
date_published: 2024-04-11T00:00:00Z
date_updated: 2024-10-08T11:28:26Z
day: '11'
doi: 10.48550/arXiv.2404.07481
extern: '1'
external_id:
  arxiv:
  - '2404.07481'
fulldoi: https://doi.org/10.48550/arXiv.2404.07481
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.48550/arXiv.2404.07481
month: '04'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: Adiabatic state preparation in a quantum Ising spin chain
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
_id: '18203'
abstract:
- lang: eng
  text: Protein Data Bank (PDB) files list the relative spatial location of atoms
    in a protein structure as the final output of the process of fitting and refining
    to experimentally determined electron density measurements. Where experimental
    evidence exists for multiple conformations, atoms are modelled in alternate locations.
    Programs reading PDB files commonly ignore these alternate conformations by default
    leaving users oblivious to the presence of alternate conformations in the structures
    they analyze. This has led to underappreciation of their prevalence, under characterisation
    of their features and limited the accessibility to this high-resolution data representing
    structural ensembles. We have trawled PDB files to extract structural features
    of residues with alternately located atoms. The output includes the distance between
    alternate conformations and identifies the location of these segments within the
    protein chain and in proximity of all other atoms within a defined radius. This
    dataset should be of use in efforts to predict multiple structures from a single
    sequence and support studies investigating protein flexibility and the association
    with protein function.
article_number: '783'
article_processing_charge: No
article_type: original
author:
- first_name: Aviv A.
  full_name: Rosenberg, Aviv A.
  last_name: Rosenberg
- first_name: Ailie
  full_name: Marx, Ailie
  last_name: Marx
- first_name: Alexander
  full_name: Bronstein, Alexander
  id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
  last_name: Bronstein
  orcid: 0000-0001-9699-8730
citation:
  ama: Rosenberg AA, Marx A, Bronstein AM. A dataset of alternately located segments
    in protein crystal structures. <i>Scientific Data</i>. 2024;11. doi:<a href="https://doi.org/10.1038/s41597-024-03595-4">10.1038/s41597-024-03595-4</a>
  apa: Rosenberg, A. A., Marx, A., &#38; Bronstein, A. M. (2024). A dataset of alternately
    located segments in protein crystal structures. <i>Scientific Data</i>. Springer
    Nature. <a href="https://doi.org/10.1038/s41597-024-03595-4">https://doi.org/10.1038/s41597-024-03595-4</a>
  chicago: Rosenberg, Aviv A., Ailie Marx, and Alex M. Bronstein. “A Dataset of Alternately
    Located Segments in Protein Crystal Structures.” <i>Scientific Data</i>. Springer
    Nature, 2024. <a href="https://doi.org/10.1038/s41597-024-03595-4">https://doi.org/10.1038/s41597-024-03595-4</a>.
  ieee: A. A. Rosenberg, A. Marx, and A. M. Bronstein, “A dataset of alternately located
    segments in protein crystal structures,” <i>Scientific Data</i>, vol. 11. Springer
    Nature, 2024.
  ista: Rosenberg AA, Marx A, Bronstein AM. 2024. A dataset of alternately located
    segments in protein crystal structures. Scientific Data. 11, 783.
  mla: Rosenberg, Aviv A., et al. “A Dataset of Alternately Located Segments in Protein
    Crystal Structures.” <i>Scientific Data</i>, vol. 11, 783, Springer Nature, 2024,
    doi:<a href="https://doi.org/10.1038/s41597-024-03595-4">10.1038/s41597-024-03595-4</a>.
  short: A.A. Rosenberg, A. Marx, A.M. Bronstein, Scientific Data 11 (2024).
date_created: 2024-10-08T11:50:30Z
date_published: 2024-07-17T00:00:00Z
date_updated: 2024-10-09T10:08:08Z
day: '17'
doi: 10.1038/s41597-024-03595-4
extern: '1'
external_id:
  pmid:
  - '39019896'
fulldoi: https://doi.org/10.1038/s41597-024-03595-4
has_accepted_license: '1'
intvolume: '        11'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1038/s41597-024-03595-4
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Scientific Data
publication_identifier:
  issn:
  - 2052-4463
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A dataset of alternately located segments in protein crystal structures
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: 11
year: '2024'
...
---
_id: '18204'
abstract:
- lang: eng
  text: 'Non-linear dynamical systems describe numerous real-world phenomena, ranging
    from the weather, to financial markets and disease progression. Individual systems
    may share substantial common information, for example patients’ anatomy. Lately,
    deep-learning has emerged as a leading method for data-driven modeling of non-linear
    dynamical systems. Yet, despite recent breakthroughs, prior works largely ignored
    the existence of shared information between different systems. However, such cases
    are quite common, for example, in medicine: we may wish to have a patient-specific
    model for some disease, but the data collected from a single patient is usually
    too small to train a deep-learning model. Hence, we must properly utilize data
    gathered from other patients. Here, we explicitly consider such cases by jointly
    modeling multiple systems. We show that the current single-system models consistently
    fail when trying to learn simultaneously from multiple systems. We suggest a framework
    for jointly approximating the Koopman operators of multiple systems, while intrinsically
    exploiting common information. We demonstrate how we can adapt to a new system
    using order-of-magnitude less new data and show the superiority of our model over
    competing methods, in terms of both forecasting ability and statistical fidelity,
    across chaotic, cardiac, and climate systems.'
article_number: '141'
article_processing_charge: Yes
article_type: original
author:
- first_name: Yonatan
  full_name: Elul, Yonatan
  last_name: Elul
- first_name: Eyal
  full_name: Rozenberg, Eyal
  last_name: Rozenberg
- first_name: Amit
  full_name: Boyarski, Amit
  last_name: Boyarski
- first_name: Yael
  full_name: Yaniv, Yael
  last_name: Yaniv
- first_name: Assaf
  full_name: Schuster, Assaf
  last_name: Schuster
- first_name: Alexander
  full_name: Bronstein, Alexander
  id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
  last_name: Bronstein
  orcid: 0000-0001-9699-8730
citation:
  ama: Elul Y, Rozenberg E, Boyarski A, Yaniv Y, Schuster A, Bronstein AM. Data-driven
    modeling of interrelated dynamical systems. <i>Communications Physics</i>. 2024;7.
    doi:<a href="https://doi.org/10.1038/s42005-024-01626-5">10.1038/s42005-024-01626-5</a>
  apa: Elul, Y., Rozenberg, E., Boyarski, A., Yaniv, Y., Schuster, A., &#38; Bronstein,
    A. M. (2024). Data-driven modeling of interrelated dynamical systems. <i>Communications
    Physics</i>. Springer Nature. <a href="https://doi.org/10.1038/s42005-024-01626-5">https://doi.org/10.1038/s42005-024-01626-5</a>
  chicago: Elul, Yonatan, Eyal Rozenberg, Amit Boyarski, Yael Yaniv, Assaf Schuster,
    and Alex M. Bronstein. “Data-Driven Modeling of Interrelated Dynamical Systems.”
    <i>Communications Physics</i>. Springer Nature, 2024. <a href="https://doi.org/10.1038/s42005-024-01626-5">https://doi.org/10.1038/s42005-024-01626-5</a>.
  ieee: Y. Elul, E. Rozenberg, A. Boyarski, Y. Yaniv, A. Schuster, and A. M. Bronstein,
    “Data-driven modeling of interrelated dynamical systems,” <i>Communications Physics</i>,
    vol. 7. Springer Nature, 2024.
  ista: Elul Y, Rozenberg E, Boyarski A, Yaniv Y, Schuster A, Bronstein AM. 2024.
    Data-driven modeling of interrelated dynamical systems. Communications Physics.
    7, 141.
  mla: Elul, Yonatan, et al. “Data-Driven Modeling of Interrelated Dynamical Systems.”
    <i>Communications Physics</i>, vol. 7, 141, Springer Nature, 2024, doi:<a href="https://doi.org/10.1038/s42005-024-01626-5">10.1038/s42005-024-01626-5</a>.
  short: Y. Elul, E. Rozenberg, A. Boyarski, Y. Yaniv, A. Schuster, A.M. Bronstein,
    Communications Physics 7 (2024).
date_created: 2024-10-08T12:45:35Z
date_published: 2024-05-01T00:00:00Z
date_updated: 2024-10-09T10:12:11Z
day: '01'
doi: 10.1038/s42005-024-01626-5
extern: '1'
fulldoi: https://doi.org/10.1038/s42005-024-01626-5
intvolume: '         7'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1038/s42005-024-01626-5
month: '05'
oa: 1
oa_version: Published Version
publication: Communications Physics
publication_identifier:
  issn:
  - 2399-3650
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Data-driven modeling of interrelated dynamical systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2024'
...
---
_id: '18205'
abstract:
- lang: eng
  text: We explore numerically an unsupervised, physics-informed, deep learning-based
    reconstruction technique for time-resolved imaging by multiplexed ptychography.
    In our method, the untrained deep learning model replaces the iterative algorithm’s
    update step, yielding superior reconstructions of multiple dynamic object frames
    compared to conventional methodologies. More precisely, we demonstrate improvements
    in image quality and resolution, while reducing sensitivity to the number of recorded
    frames, the mutual orthogonality of different probe modes, overlap between neighboring
    probe beams and the cutoff frequency of the ptychographic microscope – properties
    that are generally of paramount importance for ptychographic reconstruction algorithms.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Omri
  full_name: Wengrowicz, Omri
  last_name: Wengrowicz
- first_name: Alexander
  full_name: Bronstein, Alexander
  id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
  last_name: Bronstein
  orcid: 0000-0001-9699-8730
- first_name: Oren
  full_name: Cohen, Oren
  last_name: Cohen
citation:
  ama: Wengrowicz O, Bronstein AM, Cohen O. Unsupervised physics-informed deep learning-based
    reconstruction for time-resolved imaging by multiplexed ptychography. <i>Optics
    Express</i>. 2024;32(6):8791-8803. doi:<a href="https://doi.org/10.1364/oe.515445">10.1364/oe.515445</a>
  apa: Wengrowicz, O., Bronstein, A. M., &#38; Cohen, O. (2024). Unsupervised physics-informed
    deep learning-based reconstruction for time-resolved imaging by multiplexed ptychography.
    <i>Optics Express</i>. Optica Publishing Group. <a href="https://doi.org/10.1364/oe.515445">https://doi.org/10.1364/oe.515445</a>
  chicago: Wengrowicz, Omri, Alex M. Bronstein, and Oren Cohen. “Unsupervised Physics-Informed
    Deep Learning-Based Reconstruction for Time-Resolved Imaging by Multiplexed Ptychography.”
    <i>Optics Express</i>. Optica Publishing Group, 2024. <a href="https://doi.org/10.1364/oe.515445">https://doi.org/10.1364/oe.515445</a>.
  ieee: O. Wengrowicz, A. M. Bronstein, and O. Cohen, “Unsupervised physics-informed
    deep learning-based reconstruction for time-resolved imaging by multiplexed ptychography,”
    <i>Optics Express</i>, vol. 32, no. 6. Optica Publishing Group, pp. 8791–8803,
    2024.
  ista: Wengrowicz O, Bronstein AM, Cohen O. 2024. Unsupervised physics-informed deep
    learning-based reconstruction for time-resolved imaging by multiplexed ptychography.
    Optics Express. 32(6), 8791–8803.
  mla: Wengrowicz, Omri, et al. “Unsupervised Physics-Informed Deep Learning-Based
    Reconstruction for Time-Resolved Imaging by Multiplexed Ptychography.” <i>Optics
    Express</i>, vol. 32, no. 6, Optica Publishing Group, 2024, pp. 8791–803, doi:<a
    href="https://doi.org/10.1364/oe.515445">10.1364/oe.515445</a>.
  short: O. Wengrowicz, A.M. Bronstein, O. Cohen, Optics Express 32 (2024) 8791–8803.
date_created: 2024-10-08T12:46:01Z
date_published: 2024-03-11T00:00:00Z
date_updated: 2024-10-09T10:26:44Z
day: '11'
doi: 10.1364/oe.515445
extern: '1'
external_id:
  pmid:
  - '38571128'
fulldoi: https://doi.org/10.1364/oe.515445
intvolume: '        32'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1364/OE.515445
month: '03'
oa: 1
oa_version: Published Version
page: 8791-8803
pmid: 1
publication: Optics Express
publication_identifier:
  issn:
  - 1094-4087
publication_status: published
publisher: Optica Publishing Group
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unsupervised physics-informed deep learning-based reconstruction for time-resolved
  imaging by multiplexed ptychography
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2024'
...
---
_id: '18206'
abstract:
- lang: eng
  text: In the context of in vitro fertilization (IVF), selecting embryos for transfer
    is critical in determining pregnancy outcomes, with implantation as the essential
    first milestone for a successful pregnancy. This study introduces the Bonna algorithm,
    an advanced deep-learning framework engineered to predict embryo implantation
    probabilities. The algorithm employs a sophisticated integration of machine-learning
    techniques, utilizing MobileNetV2 for pixel and context embedding, a custom Pix2Pix
    model for precise segmentation, and a Vision Transformer for additional depth
    in embedding. MobileNetV2 was chosen for its robust feature extraction capabilities,
    focusing on textures and edges. The custom Pix2Pix model is adapted for precise
    segmentation of significant biological features such as the zona pellucida and
    blastocyst cavity. The Vision Transformer adds a global perspective, capturing
    complex patterns not apparent in local image segments. Tested on a dataset of
    images of human blastocysts collected from Ukraine, Israel, and Spain, the Bonna
    algorithm was rigorously validated through 10-fold cross-validation to ensure
    its robustness and reliability. It demonstrates superior performance with a mean
    area under the receiver operating characteristic curve (AUC) of 0.754, significantly
    outperforming existing models. The study not only advances predictive accuracy
    in embryo selection but also highlights the algorithm’s clinical applicability
    due to reliable confidence reporting.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Gilad
  full_name: Rave, Gilad
  last_name: Rave
- first_name: Daniel E.
  full_name: Fordham, Daniel E.
  last_name: Fordham
- first_name: Alexander
  full_name: Bronstein, Alexander
  id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
  last_name: Bronstein
  orcid: 0000-0001-9699-8730
- first_name: David H.
  full_name: Silver, David H.
  last_name: Silver
citation:
  ama: 'Rave G, Fordham DE, Bronstein AM, Silver DH. Enhancing predictive accuracy
    in embryo implantation: The Bonna algorithm and its clinical implications. In:
    <i>First International Conference on Artificial Intelligence in Healthcare</i>.
    Vol 14976. Springer Nature; 2024:160-171. doi:<a href="https://doi.org/10.1007/978-3-031-67285-9_12">10.1007/978-3-031-67285-9_12</a>'
  apa: 'Rave, G., Fordham, D. E., Bronstein, A. M., &#38; Silver, D. H. (2024). Enhancing
    predictive accuracy in embryo implantation: The Bonna algorithm and its clinical
    implications. In <i>First International Conference on Artificial Intelligence
    in Healthcare</i> (Vol. 14976, pp. 160–171). Swansea, United Kingdom: Springer
    Nature. <a href="https://doi.org/10.1007/978-3-031-67285-9_12">https://doi.org/10.1007/978-3-031-67285-9_12</a>'
  chicago: 'Rave, Gilad, Daniel E. Fordham, Alex M. Bronstein, and David H. Silver.
    “Enhancing Predictive Accuracy in Embryo Implantation: The Bonna Algorithm and Its
    Clinical Implications.” In <i>First International Conference on Artificial Intelligence
    in Healthcare</i>, 14976:160–71. Springer Nature, 2024. <a href="https://doi.org/10.1007/978-3-031-67285-9_12">https://doi.org/10.1007/978-3-031-67285-9_12</a>.'
  ieee: 'G. Rave, D. E. Fordham, A. M. Bronstein, and D. H. Silver, “Enhancing predictive
    accuracy in embryo implantation: The Bonna algorithm and its clinical implications,”
    in <i>First International Conference on Artificial Intelligence in Healthcare</i>,
    Swansea, United Kingdom, 2024, vol. 14976, pp. 160–171.'
  ista: 'Rave G, Fordham DE, Bronstein AM, Silver DH. 2024. Enhancing predictive accuracy
    in embryo implantation: The Bonna algorithm and its clinical implications. First
    International Conference on Artificial Intelligence in Healthcare. AIiH: Artificial
    Intelligence in Healthcare, LNCS, vol. 14976, 160–171.'
  mla: 'Rave, Gilad, et al. “Enhancing Predictive Accuracy in Embryo Implantation:
    The Bonna Algorithm and Its Clinical Implications.” <i>First International Conference
    on Artificial Intelligence in Healthcare</i>, vol. 14976, Springer Nature, 2024,
    pp. 160–71, doi:<a href="https://doi.org/10.1007/978-3-031-67285-9_12">10.1007/978-3-031-67285-9_12</a>.'
  short: G. Rave, D.E. Fordham, A.M. Bronstein, D.H. Silver, in:, First International
    Conference on Artificial Intelligence in Healthcare, Springer Nature, 2024, pp.
    160–171.
conference:
  end_date: 2024-09-06
  location: Swansea, United Kingdom
  name: 'AIiH: Artificial Intelligence in Healthcare'
  start_date: 2024-09-04
date_created: 2024-10-08T12:46:23Z
date_published: 2024-08-15T00:00:00Z
date_updated: 2024-10-09T10:33:39Z
day: '15'
doi: 10.1007/978-3-031-67285-9_12
extern: '1'
fulldoi: https://doi.org/10.1007/978-3-031-67285-9_12
intvolume: '     14976'
language:
- iso: eng
month: '08'
oa_version: None
page: 160-171
publication: First International Conference on Artificial Intelligence in Healthcare
publication_identifier:
  eisbn:
  - '9783031672859'
  eissn:
  - 1611-3349
  isbn:
  - '9783031672842'
  issn:
  - 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Enhancing predictive accuracy in embryo implantation: The Bonna algorithm
  and its clinical implications'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14976
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '22065'
abstract:
- lang: eng
  text: The Benjamin–Ono equation is shown to be well-posed, both on the line and
    on the circle, in the Sobolev spaces H^s for s > -1/2. The proof rests on a new
    gauge transformation and benefits from our introduction of a modified Lax pair
    representation of the full hierarchy. As we will show, these developments yield
    important additional dividends beyond well-posedness, including (i) the unification
    of the diverse approaches to polynomial conservation laws; (ii) a generalization
    of Gérard’s explicit formula to the full hierarchy; and (iii) new virial-type
    identities covering all equations in the hierarchy.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Rowan
  full_name: Killip, Rowan
  last_name: Killip
- first_name: Thierry
  full_name: Laurens, Thierry
  last_name: Laurens
- first_name: Monica
  full_name: Visan, Monica
  id: 056daca0-b8d1-11f0-964f-f91054abf8ca
  last_name: Visan
citation:
  ama: Killip R, Laurens T, Vişan M. Sharp well-posedness for the Benjamin–Ono equation.
    <i>Inventiones mathematicae</i>. 2024;236(3):999-1054. doi:<a href="https://doi.org/10.1007/s00222-024-01250-8">10.1007/s00222-024-01250-8</a>
  apa: Killip, R., Laurens, T., &#38; Vişan, M. (2024). Sharp well-posedness for the
    Benjamin–Ono equation. <i>Inventiones Mathematicae</i>. Springer Nature. <a href="https://doi.org/10.1007/s00222-024-01250-8">https://doi.org/10.1007/s00222-024-01250-8</a>
  chicago: Killip, Rowan, Thierry Laurens, and Monica Vişan. “Sharp Well-Posedness
    for the Benjamin–Ono Equation.” <i>Inventiones Mathematicae</i>. Springer Nature,
    2024. <a href="https://doi.org/10.1007/s00222-024-01250-8">https://doi.org/10.1007/s00222-024-01250-8</a>.
  ieee: R. Killip, T. Laurens, and M. Vişan, “Sharp well-posedness for the Benjamin–Ono
    equation,” <i>Inventiones mathematicae</i>, vol. 236, no. 3. Springer Nature,
    pp. 999–1054, 2024.
  ista: Killip R, Laurens T, Vişan M. 2024. Sharp well-posedness for the Benjamin–Ono
    equation. Inventiones mathematicae. 236(3), 999–1054.
  mla: Killip, Rowan, et al. “Sharp Well-Posedness for the Benjamin–Ono Equation.”
    <i>Inventiones Mathematicae</i>, vol. 236, no. 3, Springer Nature, 2024, pp. 999–1054,
    doi:<a href="https://doi.org/10.1007/s00222-024-01250-8">10.1007/s00222-024-01250-8</a>.
  short: R. Killip, T. Laurens, M. Vişan, Inventiones Mathematicae 236 (2024) 999–1054.
das_tickbox: '1'
date_created: 2026-06-19T08:13:06Z
date_published: 2024-06-01T00:00:00Z
date_updated: 2026-06-30T07:11:40Z
day: '01'
doi: 10.1007/s00222-024-01250-8
extern: '1'
external_id:
  arxiv:
  - '2304.00124'
fulldoi: https://doi.org/10.1007/s00222-024-01250-8
intvolume: '       236'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.48550/arXiv.2304.00124
month: '06'
oa: 1
oa_version: Preprint
page: 999-1054
publication: Inventiones mathematicae
publication_identifier:
  eissn:
  - 1432-1297
  issn:
  - 0020-9910
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sharp well-posedness for the Benjamin–Ono equation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 236
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '22062'
abstract:
- lang: eng
  text: We prove that the derivative nonlinear Schrödinger equation in one space dimension
    is globally well-posed on the line in L^2 (R), which is the scaling-critical space
    for this equation.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Benjamin
  full_name: Harrop-Griffiths, Benjamin
  last_name: Harrop-Griffiths
- first_name: Rowan
  full_name: Killip, Rowan
  last_name: Killip
- first_name: Maria
  full_name: Ntekoume, Maria
  last_name: Ntekoume
- first_name: Monica
  full_name: Visan, Monica
  id: 056daca0-b8d1-11f0-964f-f91054abf8ca
  last_name: Visan
citation:
  ama: Harrop-Griffiths B, Killip R, Ntekoume M, Vişan M. Global well-posedness for
    the derivative nonlinear Schrödinger equation in L^2(R). <i>Journal of the European
    Mathematical Society</i>. 2024;28(2):843-924. doi:<a href="https://doi.org/10.4171/jems/1490">10.4171/jems/1490</a>
  apa: Harrop-Griffiths, B., Killip, R., Ntekoume, M., &#38; Vişan, M. (2024). Global
    well-posedness for the derivative nonlinear Schrödinger equation in L^2(R). <i>Journal
    of the European Mathematical Society</i>. EMS Press. <a href="https://doi.org/10.4171/jems/1490">https://doi.org/10.4171/jems/1490</a>
  chicago: Harrop-Griffiths, Benjamin, Rowan Killip, Maria Ntekoume, and Monica Vişan.
    “Global Well-Posedness for the Derivative Nonlinear Schrödinger Equation in L^2(R).”
    <i>Journal of the European Mathematical Society</i>. EMS Press, 2024. <a href="https://doi.org/10.4171/jems/1490">https://doi.org/10.4171/jems/1490</a>.
  ieee: B. Harrop-Griffiths, R. Killip, M. Ntekoume, and M. Vişan, “Global well-posedness
    for the derivative nonlinear Schrödinger equation in L^2(R),” <i>Journal of the
    European Mathematical Society</i>, vol. 28, no. 2. EMS Press, pp. 843–924, 2024.
  ista: Harrop-Griffiths B, Killip R, Ntekoume M, Vişan M. 2024. Global well-posedness
    for the derivative nonlinear Schrödinger equation in L^2(R). Journal of the European
    Mathematical Society. 28(2), 843–924.
  mla: Harrop-Griffiths, Benjamin, et al. “Global Well-Posedness for the Derivative
    Nonlinear Schrödinger Equation in L^2(R).” <i>Journal of the European Mathematical
    Society</i>, vol. 28, no. 2, EMS Press, 2024, pp. 843–924, doi:<a href="https://doi.org/10.4171/jems/1490">10.4171/jems/1490</a>.
  short: B. Harrop-Griffiths, R. Killip, M. Ntekoume, M. Vişan, Journal of the European
    Mathematical Society 28 (2024) 843–924.
date_created: 2026-06-19T08:11:46Z
date_published: 2024-06-26T00:00:00Z
date_updated: 2026-06-30T07:04:07Z
day: '26'
doi: 10.4171/jems/1490
extern: '1'
external_id:
  arxiv:
  - '2204.12548'
fulldoi: https://doi.org/10.4171/jems/1490
intvolume: '        28'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.48550/arXiv.2204.12548
mathsc:
- 35Q55
month: '06'
oa: 1
oa_version: Preprint
page: 843-924
publication: Journal of the European Mathematical Society
publication_identifier:
  eissn:
  - 1435-9863
  issn:
  - 1435-9855
publication_status: published
publisher: EMS Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Global well-posedness for the derivative nonlinear Schrödinger equation in
  L^2(R)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 28
year: '2024'
...
