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WFU Physics Colloquium

TITLE: Molecular Dynamic Simulation of Bio-Molecular Dynamics, Folding, and Assembly

SPEAKER: Rongzhong Li

Ph. D. Presentation
Mentor: Professor Samuel Cho

TIME: Tuesday April 28, 2015 at 1:00 PM

PLACE: Room 107 Olin Physical Laboratory

All interested persons are cordially invited to attend.


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 three 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 w simulation approach for characterizing protein corona formation.

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