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Biophysical and biochemical structural properties of proteins and nucleic acids, and lipid membranes. The relation between structural properties and sequence information. Overview of experimental and theoretical (e.g., threading, homology modelling, etc.) methods for structure determination and prediction. Introduction to molecular dynamics (MD) molecular modelling methods. Force fields for protein simulations. Explicit and implicit models for water. Simulations of membranes, membrane proteins. MD methods for various statistical ensembles. Free energy calculations and protein dynamical transitions. Analyzing conformational changes from classical MD simulations. Replica Exchange Molecular Dynamics (REMD). Analyzing conformational changes from REMD simulations. Introduction to coarse-grained models of proteins and nanomaterial-membrane/protein interactions.
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