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Molecular Dynamics Of Nucleic Acids, Proteins, And Their Complexes: From Atomistic And Coarse-Grained Descriptions To New Methodologies, Parth Chaturvedi

Open Access Theses & Dissertations

Computational modeling of biological macromolecules through molecular dynamics (MD) simulations is becoming increasingly useful to interpret the experimental results and guide the future experiments. Over the last decade, MD simulations have become much more powerful and accessible due to advancements in fields of structural biology, computer science and integrated chip design. In this Thesis, I utilize different MD simulation techniques to model interaction of and antiviral mechanisms. Within the framework of nucleic acid modelling, we describe first dynamics of small circular single stranded nucleic acids and highlight key dynamical differences of backbone behavior in solution between DNA and RNA and …