Pande lab, Departments of Chemistry and of Structural Biology, Stanford University

Many of the wonders associated with biomolecules rests in their functionality, but before they can carry out any function, many of these molecules must accomplish another amazing feat: them must first assemble themselves. Moreover, these molecules must build complex structures quickly and reliably.

Our main research interests revolve around the related questions of how do these processes work, how did these processes evolve, and how can we mimic these processes in de novo deigned biological and synthetic biomimetic systems? In particular, we are interested in the specific aspects of self assembly pathways, which often requires both an understanding of the thermodynamic forces as well as the specific atomic and molecular design involved.

Computer simulation is particularly well suited to address these questions, as it naturally lends itself to thermodynamic, kinetic, and atomic level structural details. However, the two primary challenges in this field are (1) to describe phenomena which occurs on time scales (i.e. tens of microseconds to milliseconds) which is currently out of reach of typical all-atom simulations (but reachable with our methodology), and (2) to draw some understanding out of the overwhelming sea of data which results. Therefore, our work also involves developing methods for tackling these seemingly intractable computational problems, both in terms of novel simulation and analysis techniques as well as new computer hardware paradigms for carrying out these calculations.