HITS-SIMPLAIX Joint Colloquium Rommie Amaro: Multiscale Computational Microscopy for In Situ Molecular Dynamics

By Rommie Amaro,

Endowed Chair, Distinguished Professorship in Theoretical and Computational Chemistry, Department of Molecular Biology, UC San Diego, USA

Advances in multiscale computational microscopy are transforming our ability to visualize and understand biomolecular systems in their native contexts. In this talk, I will highlight recent progress in in situ molecular dynamics (MD), where data-integrated simulations reveal how cellular environments reshape protein structure, cryptic site accessibility, and viral vulnerability. By bridging many different kinds of biological datasets and large-scale physics-based modeling, we can now construct mesoscale digital twins of enveloped viruses and respiratory aerosols at unprecedented resolution, from individual glycoprotein motions to billion-atom droplets. These simulations uncover how crowded, chemically complex microenvironments modulate diffusion, aggregation, and interactions among mucins, albumin, viral spike proteins, and lipids—yielding new insights into airborne infectivity and viral resilience. Together, these efforts illustrate the power of in situ MD to reveal the hidden dynamics governing pathogens, proteins, and their environments, opening new avenues for therapeutic design and predictive biological modeling.

Biography

For a full CV, please click here.

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