Subject Code: PH6L001	Subject Name: Atomistic Simulations in Physics	L-T-P: 2-0-2	Credit: 4
Pre-requisite(s): Nil
Text Books/Reference Books: Text book: Berend Smit and Daan Frenkel, Understanding Molecular Simulation: From Algorithms to Applications, Elsevier Martin, R. Electronic Structure: Basic Theory and Practical Methods. Cambridge, UK: Cambridge University Press D. C. Rapaport, The Art of Molecular Dynamics Simulation, Cambridge University Press Reference books: Allen M. P. and Tildesley D. J. Computer Simulation of Liquids, Clarendon Press, Oxford. SB Santra, P Ray , Computational Statistical Physics: Hindustan Book Agency D.C. Rapaport. The Art of Molecular Dynamics Simulation. Cambridge University Press, M. Kalos and P. A. Whitlock. Monte Carlo Methods. John Wiley & Sons, New York, 1986. D. Eisenberg and D. Crothers. Physical Chemistry with Applications to Life Science. Benjamin Cummings, Menlo Park, California, David Sholl and Jan Steckel Density Functional Theory: A Practical Introduction, John Wiley & Sons

Subject Code: PH6L001

Subject Name: Atomistic Simulations in Physics

L-T-P: 2-0-2

Credit: 4

Pre-requisite(s): Nil

Text Books/Reference Books:

Text book:

Berend Smit and Daan Frenkel, Understanding Molecular Simulation: From Algorithms to Applications, Elsevier
Martin, R. Electronic Structure: Basic Theory and Practical Methods. Cambridge, UK: Cambridge University Press
D. C. Rapaport, The Art of Molecular Dynamics Simulation, Cambridge University Press

Reference books:

Allen M. P. and Tildesley D. J. Computer Simulation of Liquids, Clarendon Press, Oxford.
SB Santra, P Ray , Computational Statistical Physics: Hindustan Book Agency
D.C. Rapaport. The Art of Molecular Dynamics Simulation. Cambridge University Press,
M. Kalos and P. A. Whitlock. Monte Carlo Methods. John Wiley & Sons, New York, 1986.
D. Eisenberg and D. Crothers. Physical Chemistry with Applications to Life Science. Benjamin Cummings, Menlo Park, California,
David Sholl and Jan Steckel Density Functional Theory: A Practical Introduction, John Wiley & Sons

Syllabus:

Classical Simulations: A broad overview of simulation methods operating on length scales from the atomistic to the continuum scale, General theory of atomistic simulations, Monte Carlo Simulations, classical molecular dynamics (MD) simulations MD integration algorithms for different thermodynamic ensembles (NVE, NVT, NPT), various integration schemes, periodic boundary conditions, long-range interactions, Ewald Summations, empirical force-fields, Event-driven techniques, applications to nano and biological systems, Protein, DNA and cell-membrane simulations

Quantum Simulations: Hartree-Fock theory, algebraic formulation of density functional theory (DFT), Hohenberg-Kohn DFT, Kohn-Sham DFT, The Exchange-Correlation Energy, Energy optimization, electronic structure, the density of states, application of DFTs for nanomaterials.

Mini projects based on contemporary research topics: such as Protein binding with different surfaces and molecules, stability of various lipid membranes under different physical conditions, sequence-dependent properties of DNA/RNA oligomers