Biological Physics II - Organization and Dynamics

Presentations

• ProtSCAPE: Mapping the landscape of protein conformations in molecular dynamics

  ORAL

  March 19, 2025, 2:30 PM – March 19, 2025, 2:42 PM

  Publication: Siddharth Viswanath*, Dhananjay Bhaskar*, David R Johnson, Joao Felipe Rocha, Egbert Castro, Jackson D Grady, Alex T Grigas, Michael Perlmutter, Corey O'Hern, Smita Krishnaswamy. ProtSCAPE: Mapping the landscape of protein conformation in molecular dynamics. Molecular Machine Learning Conference (2024)

  Presenters

  • Dhananjay Bhaskar

    • Yale University

  Authors

  • Dhananjay Bhaskar

    • Yale University

  • Siddharth Viswanath

    • Yale University

  • David R Johnson

    • Boise State University

  • Joao F Rocha

    • Yale University

  • Egbert Castro

    • Yale University

  • Jackson D Grady

    • Yale University

  • Alex T Grigas

    • Yale University

  • Michael A Perlmutter

    • Boise State University

  • Corey S O'Hern

    • Yale University

  • Smita Krishnaswamy

    • Yale University

  View abstract →

• Mesoscale properties of protein clusters determine the size and nature of liquid-liquid phase separation (LLPS)

  ORAL

  March 19, 2025, 2:42 PM – March 19, 2025, 2:54 PM

  Publication: 1. Mesoscale properties of protein clusters determine the size and nature of liquid-liquid phase separation (LLPS) - submitted
  2. Core-shell model of the clusters of CPEB4 isoforms preceding liquid-liquid phase separation - Biophys. J. , 2023

  Presenters

  • Gonen Golani

    • University of Haifa

  Authors

  • Samuel A Safran

    • Weizmann Institute of Science

  • Gonen Golani

    • University of Haifa

  • Anthony A Hyman

    • Max Planck Institute of Cell Biology and Genetics

  • Daniella Goldfarb

    • Weizmann Institute of Science

  • Manas Seal

    • Weizmann Institute of Science

  • Mrityunjoy Kar

    • Institute of Biofunctional Polymer Materials, Leibniz Institute of Polymer Research

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• Abstract Withdrawn

  ORAL · Withdrawn

  March 19, 2025, 2:54 PM – March 19, 2025, 3:06 PM

  View abstract →

• Modeling and Experimental Insights into the Structure and Dynamics of Lipid Nanoparticles

  ORAL

  March 19, 2025, 3:06 PM – March 19, 2025, 3:18 PM

  Presenters

  • Gulsah Gul

    • Koc University

  Authors

  • Gulsah Gul

    • Koc University

  • Erkan Senses

    • Koc University

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• A mechanical model for the coordination of septum formation and cell splitting in Staphylococcus aureus

  ORAL

  March 19, 2025, 3:18 PM – March 19, 2025, 3:30 PM

  Publication: Local decrease in cell wall stress as a possible trigger for cell splitting in Staphylococcus aureus - publication in preparation
  Sheila Hoshyaripour, Marco Mauri, David Owen, Abimbola F. Adedeji Olulana, Jamie K. Hobbs, Simon J. Foster and Rosalind J. Allen

  Presenters

  • Rosalind J Allen

    • University of Jena

  Authors

  • Rosalind J Allen

    • University of Jena

  • Sheila Hoshyaripour

    • University Jena

  • Marco Mauri

    • University Jena

  • David Owen

    • University of Sheffield

  • Abimbola Feyisara Olulana

    • University of Sheffield

  • Jamie K. Hobbs

    • University of Sheffield

  • Simon J Foster

    • University of Sheffield

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• Mathematical modeling of the frozen zone dynamics in hydrogel and biological tissue

  ORAL

  March 19, 2025, 3:30 PM – March 19, 2025, 3:42 PM

  Publication: O. V. Ivakhnenko, O. F. Todrin, V. Yu. Globa, M. O. Chyzh, G. O. Kovalov, S. N. Shevchenko, bioRxiv:2024.10.19.619201 (2024)

  Presenters

  • Oleh Ivakhnenko

    • B. Verkin ILTPE of NASU
    • B. Verkin ILTPE, Ukraine, and RIKEN, Japan

  Authors

  • Oleh Ivakhnenko

    • B. Verkin ILTPE of NASU
    • B. Verkin ILTPE, Ukraine, and RIKEN, Japan

  • Artem Ryzhov

    • B. Verkin ILTPE of NASU
    • B. Verkin ILTPE

  • Sergey N Shevchenko

    • B. Verkin ILTPE of NASU
    • B. Verkin ILTPE
    • Kharkov University

  View abstract →

• Abstract Withdrawn

  ORAL · Withdrawn

  March 19, 2025, 3:42 PM – March 19, 2025, 3:54 PM

  View abstract →

• A Novel Method for UV Thin-Film Backside Development for Ordered DNA Fragmentation

  ORAL

  March 19, 2025, 3:54 PM – March 19, 2025, 4:06 PM

  Publication: [1] Righini, M., Costa, J., & Zhou, W. (2021). DNA bridges: A novel platform for single-molecule sequencing and other DNA-protein interaction applications. PloS one, 16(11), e0260428. https://doi.org/10.1371/journal.pone.0260428
  [2] Li, N., Jin, K., Bai, Y., Fu, H., Liu, L., & Liu, B. (2020). Tn5 Transposase Applied in Genomics Research. International journal of molecular sciences, 21(21), 8329. https://doi.org/10.3390/ijms21218329

  Presenters

  • Kevin Zhang

    • North Hunterdon High School

  Authors

  • Kevin Zhang

    • North Hunterdon High School

  • Stella Song

    • Phillips Exeter Academy

  • Elena Mingorance

    • South Side High School

  • Kevin Lee

    • The Albany Academies

  • Aditi Kiran

    • BASIS Independent Fremont

  • Alice Hu

    • King High School

  • Danielle Liu

    • University of Pennsylvania

  • Patrick Lewis

    • State Univ of NY - Stony Brook

  • Navya Gautam

    • Duke University

  • Jonathan C Sokolov

    • State Univ of NY - Stony Brook

  • Miriam Rafailovich

    • Stony Brook University, The State University of New York
    • Stony Brook University
    • State Univ of NY - Stony Brook

  View abstract →

• Femtosecond Three-Dimensional Imaging of Single-Protein with Hard X-ray Laser

  ORAL

  March 19, 2025, 4:06 PM – March 19, 2025, 4:18 PM

  Publication: 1. P.L. Xavier et al. Femtosecond Three-Dimensional Imaging of Single-Protein with Hard X-ray Laser. (to be submitted) (in preparation)

  Presenters

  • Paul Lourdu Xavier

    • Center for Free-Electron Laser Science, DESY/Max-Planck Institute for the Structure and Dynamics of Matter/European XFEL

  Authors

  • Paul Lourdu Xavier

    • Center for Free-Electron Laser Science, DESY/Max-Planck Institute for the Structure and Dynamics of Matter/European XFEL

  • Andrew J Morgan

    • University of Melbourne

  • Johan Bielecki

    • European XFEL

  • Richard Bean

    • European XFEL

  • Chufeng Li

    • Center for Free-Electron Laser Science, DESY

  • Wenhui Zhang

    • Center for Free-Electron Laser Science, DESY

  • Jungcheng E

    • European XFEL

  • Mansi Butola

    • Center for Free-Electron Laser Science, DESY

  • Amit K Samanta

    • Center for Free-Electron Laser Science, DESY

  • Jochen Kuepper

    • Center for Free-Electron Laser Science, DESY

  • Maia Azubel

    • Stanford University

  • David A Bushnell

    • Stanford University

  • Sébastien Boutet

    • SLAC National Accelerator Laboratory

  • Roger D Kornberg

    • Stanford University

  • David Baker

    • Institute for Protein Design, University of Washington
    • University of Washington

  • Neil King

    • Institute for Protein Design, University of Washington

  • Sergey Ovchinnikov

    • Massachusetts Institute of Technology

  • Erin C Yang

    • Institute for Protein Design, University of Washington

  • Shunzhi Wang

    • Institute for Protein Design, University of Washington

  • Richard Kirian

    • Arizona State University

  • Filipe Maia

    • Uppsala University

  • Duane Loh

    • National University of Singapore
    • Department of Physics, Department of Biological Sciences, and NUS Centre for Bioimaging Sciences, National University of Singapore

  • Saša Bajt

    • Center for Free-Electron Laser Science, DESY

  • Henry N Chapman

    • Center for Free-Electron Laser Science, DESY

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• Abstract Withdrawn

  ORAL · Withdrawn

  March 19, 2025, 4:18 PM – March 19, 2025, 4:30 PM

  View abstract →