Unit 1 Introduction to Statistical Mechanics

• Concept of Macro-state and Microstate- Thermodynamic Ensembles- Boltzman distribution- Introduction to Quantum Mechanics and Molecular Mechanics
• Integration of Newton's laws of Motion
• Intermolecular forces in biological systems
• Stabilizing forces in proteins
• lipids and nucleic acids. 20 Program Name: Bachelor of Engineering Level: UG Branch: Biotechnology Subject Code: BE05004061 Subject Name: Biophysics

Unit 2 Basic concepts of molecular structure

15 lecture hours

• bond length
• bond angle
• torsion angle and non-covalent interactions – Molecular structure and internal energy – Energy minimization of small molecules – Types of energy minimization- Empirical representation of molecular energies –Use of force fields and the molecular mechanics method –Discussion of global energy minimum –Molecular visualization tools

Unit 3 Simulation Techniques

20 lecture hours

• Stochastic and Deterministic simulations Molecular Dynamics and Monte Carlo simulation- Definition & Types Model Building- Velocity Verlet and Leap-frog algorithms
• Periodic Boundary conditions
• generating ab initio and template-based models Applications of Molecular Dynamics Simulations