Multiscale Modeling and Molecular Assemblies

Presentations

• Molecular Origin of Aging in Biomolecular Condensate

  ORAL

  March 7, 2024, 4:00 PM – March 7, 2024, 4:12 PM

  Presenters

  • Subhadip Biswas

    Iowa State University

  Authors

  • Subhadip Biswas

    Iowa State University

  • Davit Potoyan

    Iowa State University

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• PTM-Psi: A Python Package to Facilitate the Computational Investigation of Post-Translational Modification on Protein Structures and Their Impacts on Dynamics and Functions

  ORAL

  March 7, 2024, 4:12 PM – March 7, 2024, 4:24 PM

  Publication: Submitted manuscript

  Presenters

  • Margaret S Cheung

    Pacific Northwest National Laboratory

  Authors

  • Margaret S Cheung

    Pacific Northwest National Laboratory

  • Daniel Rodriguez

    Pacific Northwest National Laboratory (PNNL), Pacific Northwest National Laboratory

  • Hoshin Kim

    Pacific Northwest National Laboratory

  • Natalie Sadler

    Pacific Northwest National Laboratory

  • Xiaolu Li

    Pacific Northwest National Laboratory

  • Pavlo Bohutskyi

    Pacific Northwest National Laboratory

  • Marat Valiev

    Pacific Northwest National Laboratory

  • Weijun Qian

    Pacific Northwest National Laboratory

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• Experiment and simulations reveal residue details for how target binding tunes calmodulin's calcium binding properties

  ORAL

  March 7, 2024, 4:24 PM – March 7, 2024, 4:36 PM

  Publication: https://pubs.acs.org/doi/10.1021/acs.jpcb.2c08734

  Presenters

  • Jules Berlin Nde Kengne

    University of Washington

  Authors

  • Jules Berlin Nde Kengne

    University of Washington

  • Pengzhi Zhang

    Center for Bioinformatics and Computational Biology, Houston Methodist Research Institute

  • Neal Waxham

    3Department of Neurobiology and Anatomy, University of Texas Health Science Center

  • Margaret S Cheung

    Pacific Northwest National Laboratory

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• Modeling the Global Dynamics of the Tropomyosin-Actin Molecular Switch that Governs Cardiac Cell Contraction

  ORAL

  March 7, 2024, 4:36 PM – March 7, 2024, 4:48 PM

  Presenters

  • Harshita Pajarla

    Yale University

  Authors

  • Harshita Pajarla

    Yale University

  • Stuart G Campbell

    Yale University

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• Molecular mechanisms of thermal sensing by TRP ion channels

  ORAL · Invited

  March 7, 2024, 4:48 PM – March 7, 2024, 5:24 PM

  Presenters

  • Davit Potoyan

    Iowa State University

  Authors

  • Davit Potoyan

    Iowa State University

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• Insights into Alzheimer's risk factors through waste protein transport modeling

  ORAL

  March 7, 2024, 5:24 PM – March 7, 2024, 5:36 PM

  Publication: Watkins, Mukherjee, and Tithof. "Dynamics of waste proteins in brain tissue: Numerical insights into Alzheimer's risk factors." Phys. Rev. E. Under Review, October 2023.

  Presenters

  • Lily Watkins

    University of Minnesota Twin Cities

  Authors

  • Lily Watkins

    University of Minnesota Twin Cities

  • Saikat Mukherjee

    Iowa State University

  • Jeff Tithof

    University of Minnesota

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• Understanding the physical processes behind DNA-DNA proximity ligation assays

  ORAL

  March 7, 2024, 5:36 PM – March 7, 2024, 5:48 PM

  Presenters

  • Bernardo J Zubillaga Herrera

    Northeastern University

  Authors

  • Bernardo J Zubillaga Herrera

    Northeastern University

  • Amit Das

    IIT Delhi, Indian Institute of Technology Delhi (IIT)

  • Linden Burack

    Northeastern University

  • Ailun Wang

    Northeastern University

  • Michele Di Pierro

    Northeastern University

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• Simulation-based inference for non-parametric statistical comparison of biomolecule dynamics

  ORAL

  March 7, 2024, 5:48 PM – March 7, 2024, 6:00 PM

  Publication: 1. Verdier, H. et al. Learning physical properties of anomalous random walks using graph neural networks. J. Phys. Math. Theor. 54, 234001 (2021).
  2. Muñoz-Gil, G. et al. Objective comparison of methods to decode anomalous diffusion. Nat. Commun. 12, 6253 (2021).
  3. Verdier, H., Laurent, F., Cassé, A., Vestergaard, C. L. & Masson, J.-B. Variational inference of fractional Brownian motion with linear computational complexity. Phys. Rev. E 106, 055311 (2022).
  4. Blanc, T. et al. Towards Human in the Loop Analysis of Complex Point Clouds: Advanced Visualizations, Quantifications, and Communication Features in Virtual Reality. Front. Bioinforma. 1, (2022).
  5. Verdier, H. et al. Simulation-based inference for non-parametric statistical comparison of biomolecule dynamics. PLOS Comput. Biol. 19, e1010088 (2023).

  Presenters

  • jean-baptiste masson

    institut pasteur - CNRS - Universite paris cite - INRIA

  Authors

  • jean-baptiste masson

    institut pasteur - CNRS - Universite paris cite - INRIA

  • hippolyte verdier

    institut pasteur - CNRS - Universite paris cite - INRIA

  • christian L vestergaard

    institut pasteur - CNRS - Universite paris cite - INRIA

  • françois Laurent

    institut pasteur - CNRS - Universite paris cite - INRIA

  • christian Specht

    Diseases and Hormones of the Nervous System (DHNS), Inserm U1195, Universite Paris-Saclay, Paris, France

  • alhassan cassé

    Histopathology and Bio-Imaging Group, Sanofi, R&D, Vitry-Sur-Seine, France

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• Statistical physics of biological aging

  ORAL

  March 7, 2024, 6:00 PM – March 7, 2024, 6:12 PM

  Presenters

  • Steffen Rulands

    LMU Munich

  Authors

  • Steffen Rulands

    LMU Munich

  • Aida Hashtroud

    LMU Munich

  • Matteo Ciarchi

    LMU Munich

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• Thermodynamics of morphological transitions in growing membranes

  ORAL

  March 7, 2024, 6:12 PM – March 7, 2024, 6:24 PM

  Presenters

  • Jordan L Shivers

    University of Chicago

  Authors

  • Jordan L Shivers

    University of Chicago

  • Michael Nguyen

    University of Chicago

  • Aaron R Dinner

    University of Chicago

  • Suriyanarayanan Vaikuntanathan

    University of Chicago

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• Deciphering the interface laws of Turing foams

  ORAL

  March 7, 2024, 6:24 PM – March 7, 2024, 6:36 PM

  Publication: Weyer, H., Roth, T. & Frey, E. Deciphering the interface laws of Turing foams (in preparation);
  Roth, T., Weyer, H. & Frey, E. Interface dynamics of two-component mass-conserving reaction-diffusion systems (in preparation).

  Presenters

  • Henrik Weyer

    Ludwig-Maximilians-Universität (LMU Munich)

  Authors

  • Henrik Weyer

    Ludwig-Maximilians-Universität (LMU Munich)

  • Tobias Roth

    Ludwig-Maximilians-Universität (LMU Munich)

  • Erwin A Frey

    Ludwig Maximilian University of Munich, Ludwig-Maximilians-Universität (LMU Munich)

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• Unraveling the Structure of Cofilin Oligomers: Insights into Actomyosin Network regulation through Coarse-Grained Molecular Dynamics

  ORAL

  March 7, 2024, 6:36 PM – March 7, 2024, 6:48 PM

  Presenters

  • Chengxuan Li

    University of Washington

  Authors

  • Chengxuan Li

    University of Washington

  • Tingyi Wei

    National Chung Cheng University

  • Min-Yeh Tsai

    Tamkang Univ

  • Margaret Cheung

    Pacific Northwest National Laboratory/University of Washingt

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• Microscopic origins of the viscosity of RNA-peptides condensates

  ORAL

  March 7, 2024, 6:48 PM – March 7, 2024, 7:00 PM

  Presenters

  • Sean Yang

    Iowa State University

  Authors

  • Sean Yang

    Iowa State University

  • Davit Potoyan

    Iowa State University

  View abstract →