Details of CH4114 (Autumn 2023)
| Level: 4 | Type: Theory | Credits: 4.0 |
| Course Code | Course Name | Instructor(s) |
|---|---|---|
| CH4114 | Simulation of Biological and Chemical Systems | Neelanjana Sengupta |
| Preamble |
|---|
| Preamble: This course will introduce concepts and methods underlying molecular dynamics
simulations of multi-component (bio)molecular systems. It should equip one with skills for designing meaningful simulations, data analysis and benchmarking with experimental observations. The course will involve a simulation project in the latter half (*). * The total number of participants will be limited. |
| Syllabus |
|---|
| 1. Introduction to Molecular Simulations
a. History of development b. Bottoms-up approach: the Computational Microscope 2. Statistical mechanics background a. Microscopic and macroscopic parameters b. Phase space and Ensembles c. Equilibrium and ergodicity 3. The MD engine a. Empirical potentials: the Force Field b. Many-body equations of motion; numerical solutions c. Thermodynamic control: thermostats and barostats d. Periodic boundary conditions; attaining the thermodynamic limit 4. Standard analysis toolbox a. Static vs. dynamic quantities b. Structural analysis 5. Transitions in free energy landscapes a. Local and global minima; transition states b. Collective variables; enhanced sampling 6. Project: a. System setup and simulation b. Identification of equilibrium c. Data analysis |
| Prerequisite |
|---|
| Basic understanding of thermodynamics and biomolecular structure. Working knowledge of Linux
Suitability: Senior BS-MS students; IPhD students; Research Scholar from both DCS and DBS |
| References |
|---|
| References:
1. Computer Simulations of Liquids, M.P Allen and D.J Tildesley (Oxford) 2. Understanding Molecular Simulation: D. Frenkel and B. Smit (Elsevier) 3. The Art of Molecular Dynamics Simulations: D. C. Rapaport (Cambridge) 4. Additional material will be provided |
Course Credit Options
| Sl. No. | Programme | Semester No | Course Choice |
|---|---|---|---|
| 1 | IP | 1 | Not Allowed |
| 2 | IP | 3 | Not Allowed |
| 3 | IP | 5 | Not Allowed |
| 4 | MP | 1 | Not Allowed |
| 5 | MP | 3 | Elective |
| 6 | MR | 1 | Not Allowed |
| 7 | MR | 3 | Not Allowed |
| 8 | MS | 3 | Not Allowed |
| 9 | MS | 5 | Not Allowed |
| 10 | MS | 7 | Elective |
| 11 | MS | 9 | Elective |
| 12 | RS | 1 | Elective |
| 13 | RS | 2 | Elective |