Project Title: Influenza Virulence and Transmissibility through the Computational Microscope
My work embraces a multiscale computational protocol that exploits different methods (Molecular Dynamics, Brownian Dynamics), analyses algorithms (Markov state model, PCA) and modeling tools for crossing the spatial scales (from molecular to subcellular / cellular) and exploring events occurring in different temporal scales. I will apply this computational approach to build a model of the entire influenza A (H1N1) virion, with all the surface components revealed and treated for the first time at atomic-level of detail. Unprecedented all-atom simulations of this realistic ~160 million-atoms model will serve to shed light on the Influenza A virus biology, virulence and transmissibility, with a particular emphasis on the role played by the glycans exposed by the neuraminidase and hemagglutinin glycoproteins.
Mentors: Dr. Rommie Amaro, UC San Diego; Dr. Ian Wilson, TSRI
Project Title: The ZO-1 Regulation of Cardicac Perinexus Structure and Electrophysiology
The goal of this project is to obtain detailed transmitting electron microscope imaging of the perinexus together with super high-resolution localization of ion channels in order to reconstruct a 3D computational geometry. This geometry would then be used to access ephaptic coupling in a diffusion based finite element model, and experimental predictions would be validated with optical voltage mapping in ex-vivo mouse hearts. The geometry would be made publicly available for other researchers who wish to build on the work proposed here.
Mentors: Drs. Andrew McCulloch, Mark Ellisman and Robert Ross, UC San Diego