| A major goal in molecular biophysics is to understand how biomolecules fold into specific structures to carry out cellular processes to result in a functioning organism. Computational molecular dynamics (MD) simulations can characterize biomolecules at a microscopic level. These indispensable tools use classical mechanical approaches to describe biomolecular dynamics, folding, and binding mechanisms. Although there are many different types of MD simulations, I will focus on two classes of approaches: empirical force field and coarse-grained native structure based ones. In the present thesis, I will discuss recent MD simulation studies of RNA, protein-RNA, and protein-nanoparticle interactions with direct comparisons to experiments whenever possible to validate our approaches. Specifically, I will present the following three projects:;1) Coarse-grained and empirical force field MD simulations of tRNA folding mechanisms.;2) Preliminary development of a coarse-grained protein-RNA MD simulation approach based on well-established protein and RNA folding models.;3) A novel GPU-optimized coarse-grained protein-nanoparticle MD simulation approach for characterizing protein corona formation. |
