Physical Constraints on Biological Function at the Molecular Scale

FOCUS · A27 · ID: 2154445

Presentations

  • Typicality in high-dimensional gene regulation out of equilibrium

    ORAL

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    Publication: An earlier preprint underlying some of this work is available at https://www.biorxiv.org/content/10.1101/2023.04.11.536490v1 ; more recent findings supporting this presentation are under preparation by the same authors.

    Presenters

    • Gabriel L Salmon

      Caltech

    Authors

    • Gabriel L Salmon

      Caltech

    • Sara D Mahdavi

      Caltech

    • Patill Daghlian

      Caltech

    • Hernan G Garcia

      University of California, Berkeley

    • Rob Phillips

      Caltech

    View abstract →

  • Universal thermodynamic bounds on symmetry breaking in living systems: from error correction to pattern formation

    ORAL

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    Publication: Liang, Shiling, Paolo De Los Rios, and Daniel Maria Busiello. "Universal thermodynamic bounds on symmetry breaking in biochemical systems." arXiv preprint arXiv:2212.12074 (2022).

    Presenters

    • Shiling Liang

      École Polytechnique Fédérale de Lausanne (EPFL)

    Authors

    • Shiling Liang

      École Polytechnique Fédérale de Lausanne (EPFL)

    • Paolo De Los Rios

      École Polytechnique Fédérale de Lausanne (EPFL)

    • Daniel Maria Busiello

      Max Planck Institute for the Physics of Complex Systems

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  • Signatures of energy dissipation in bacterial chemotaxis signaling pathways

    ORAL

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    Publication: "A nonequilibrium allostericmodel for receptor-kinase complexes: The role of energy dissipation in chemotaxis signaling", David Hathcock, Qiwei Yu, Bernardo A. Mello, Divya N. Amind, Gerald L. Hazelbauer, and Yuhai Tu, PNAS, 120 (42), e2303115120, 2023. https://doi.org/10.1073/pnas.2303115120

    Presenters

    • Yuhai Tu

      IBM T. J. Watson Research Center

    Authors

    • Yuhai Tu

      IBM T. J. Watson Research Center

    • David Hathcock

      IBM TJ Watson Research Center

    • Qiwei Yu

      Princeton University

    View abstract →

  • A minimal scenario for the origin of non-equilibrium order

    ORAL

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    Presenters

    • Riccardo Ravasio

      University of Chicago

    Authors

    • Riccardo Ravasio

      University of Chicago

    • Kabir B Husain

      University of Chicago

    • Constantine G Evans

      Maynooth University

    • Rob Phillips

      Caltech

    • Marco Ribezzi-Crivellari

      Quantum-SI

    • Jack W Szostak

      University of Chicago

    • Arvind Murugan

      University of Chicago

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  • In there any speed-accuracy tradeoff for various non-cognate species in nucleotide substrate incorporation and selection of RNA polymerase elongation?

    ORAL

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    Publication: [1] Jin Yu*. Efficient fidelity control by stepwise nucleotide selection in polymerase elongation. Molecular Based Mathematical Biology, 2, 141-160, 2014

    [2] Chunhong Long, Chao E, Lin-Tai Da, and Jin Yu*. Determining selection free energetics from nucleotide pre-insertion to insertion in viral T7 RNA polymerase transcription fidelity control. Nucleic Acids Research 47(9), 4721-4735, 2019

    [3] Moises E Romero, Chunhong Long, Daniel La Rocco, Anusha M Keerthi, Dajun Xu, and Jin Yu*. Probing remdesivir nucleotide analogue insertion to SARS-CoV-2 RNA dependent RNA polymerase in viral replication. Molecular Systems Design & Engineering, 2021, 6, 888 – 902

    [4] Moises E Romero, Shannon J McElhenney and Jin Yu*. Trapping non-cognate nucleotide upon initial binding for replication fidelity control in SARS-CoV-2 RNA dependent RNA polymerase bioRxiv 2023.09.01.555996

    Presenters

    • Jin Yu

      University of California-Irvine

    Authors

    • Jin Yu

      University of California-Irvine

    View abstract →

  • Diffusion of Nanoparticles in a Potential Energy Well

    ORAL

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    Presenters

    • Ho Tin Cheung

      The Hong Kong University of Science and Technology

    Authors

    • Ho Tin Cheung

      The Hong Kong University of Science and Technology

    • Hyokeun Park

      The Hong Kong University of Science and Technology

    • K.Y. Michael Wong

      Hong Kong University of Science and Technology

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  • Tradeoffs in concentration sensing in dynamic environments

    ORAL

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    Publication: Arxiv preprint: https://arxiv.org/abs/2310.00062

    Presenters

    • Brian A Camley

      Johns Hopkins University, Department of Physics & Astronomy and Biophysics, Johns Hopkins University, Baltimore, MD.

    Authors

    • Brian A Camley

      Johns Hopkins University, Department of Physics & Astronomy and Biophysics, Johns Hopkins University, Baltimore, MD.

    • Aparajita Kashyap

      Johns Hopkins University

    • Wei Wang

      Johns Hopkins University

    View abstract →