| Studying the nucleic acids and their interactions with proteins is a challenging problem in the area of biophysics and biochemistry. A wealth of knowledge about the structural dynamics of biological molecules has been provided using single molecule manipulation techniques in the last few decades. However, these experiments may only report a limited number of config- urational observables about the system of interest. Thus, it is important that experimental studies are complemented by molecular dynamics (MD) simulations that reveal atomistic details on the fluctuations and conformational changes of biomolecules. Here, I presented applications on the systems of nucleic acids-deoxyribonucleic acid (DNA), ribonucleic acid (RNA) and DNA/typeII topoisomerase protein complex- by using several molecular dynam- ics simulation techniques to investigate their dynamics, structures and thermodynamics. Additionally, a new method in which Langevin dynamics are altered by the introduction of a combined normal mode-string (NM-S) minimum energy path was introduced a new com- putational method to study conformational kinetics in a variety of biological systems that undergo rare transitions between important conformational states. |
