Title:  Building the lens of a computational microscope
Abstract:  One of the grand challenges for molecular dynamics (MD) simulations is sampling kinetic properties (e.g., rate constants, continuous pathways) efficiently in a computationally tractable period. Thus, researchers have developed “enhanced sampling methods” to efficiently sample thermodynamic and/or kinetic properties from MD simulations, but more development is needed for sampling kinetic properties. I will first introduce the motivation and an application where enhanced sampling methods were crucial for its findings (i.e., the activation mechanism of the SARS-CoV-2 spike protein). Then I will discuss my efforts in developing methods that can sample kinetic properties more efficiently than conventional methods (i.e., Gaussian accelerated molecular dynamics-weighted ensemble method (GaMD-WE) and the concurrent adaptive sampling algorithm (CAS)) and future directions.