Saravana Prakash Thirumuruganandham

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Vibrational excitations of low-frequency collective modes are essential for functionally important conformational transitions in proteins. We carried out an analysis of the low-frequency modes in the G protein coupled receptors (GPCR) family of cone opsins based on both normal-mode analysis and molecular dynamics (MD) simulations. Power spectra obtained by(More)
Using molecular dynamics simulation, we compare two cases of ultrafast heating of a small water droplet containing a solvated protein (echistatin). If the water temperature after irradiation is above the critical temperature, explosive boiling liberates the protein within some 10 ps of its hydration shell, while its temperature remains relatively low. By(More)
Using molecular dynamics simulation, we study the evaporation of water molecules off partially solvated ubiquitin. The evaporation and cooling rates are determined for a molecule at the initial temperature of 300 K. The cooling rate is found to be around 3 K/ns, and decreases with water temperature in the course of the evaporation. The conformation changes(More)
Vibrational spectra of proteins potentially give insight into biologically significant molecular motion and the proportions of different types of secondary structure. Vibrational spectra can be calculated either from normal modes obtained by diagonalizing the mass-weighted Hessian or from the time autocorrelation function derived from molecular dynamics(More)
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