Biological macromolecules such as proteins, DNAs, and lipids, perform diverse functions in the cell that are the foundations of life processes. These complex mechanisms are a result of finely balanced thermodynamic forces governing both inter- and intramolecular interactions, as well as kinetic processes that occur over a vast range of time and length scales. Understanding the fundamental driving forces of biomolecular functions, and how they can be altered to tune cellular mechanisms, is therefore a central problem in modern biophysics research. In this talk, Wereszczynski will discuss work in our group that utilizes molecular dynamics simulations to explore these processes at atomic-scale resolution. First, he will focus on simulations aimed at understanding the physical mechanisms underpinning gene expression and epigenetic regulation. Second, he will discuss how we can use enhanced sampling simulations in conjunction with small angle X-ray scattering experiments and Bayesian inference to rigorously determine a minimal ensemble of states of flexible biomolecular complexes.