1 Advanced Thermodynamics and Molecular Simulations
2 Lecture 01-Introduction to the course
3 Lecture 02: Molecular basis of energy and entropy
4 Lecture 03: Probability and probability distributions
5 Lecture 04: Probability distributions and thermodynamic equilibrium
6 Lecture 05: Energy distribution in molecular systems
7 Lecture 06: First and second law of thermodynamics
8 Lecture 07- Reversible and irreversible processes; third law; legendre transformation...
9 Lecture 08- Thermodynamic functions for multi-component systems; chemical potential...
10 Lecture 09-Extensive and intensive variables; gibbs duhem relation; euler theorem; maxwell relations
11 Lecture 10- Discrete and continuous probabilities; stirling approximation
12 Lecture 11- Binomial distribution approaches gaussian distribution for large n...
13 Lecture 12- Solution of drunkard walk; lagrange multipliers
14 Lecture 13: Energy distribution in molecular system revisited
15 Lecture 14: Canonical ensemble: most probable distribution, partition function
16 Lecture 15: Definition of temperature; third law of thermodynamics
17 Lecture 16: Canonical ensemble: Helmholtz free energy, averages and fluctuations, specific heat
18 Lecture 17: Partition function of a dense gas; grand canonical ensemble: partition function
19 Lecture 18: Computing properties in grand canonical ensemble
20 Lecture 19: Isothermal isobaric ensemble
21 Lecture 20: Summary of thermodynamic ensembles; partition function of an ideal gas
22 Lecture 21: Mixing and phase separation, phase equilibrium of a multiphase multicomponent system
23 Lecture 22: Pure component phase diagram; Solution thermodynamics: Helmholtz free energy density
24 Lecture 23: Characterizing mixing and phase separation using Helmholtz free energy density
25 Lecture 24: Common tangent construction, definition of binodal, spinodal, and critical point
26 Lecture 25: Osmotic pressure and chemical potential
27 Lecture 26: Lattice model of liquid solutions I
28 Lecture 27: Lattice model of liquid solutions II
29 Lecture 28: Lattice model of liquid solutions III
30 Lecture 29: Critical review of Lattice model, theoretical basis of molecular dynamics simulation
31 Lecture 30: Theoretical basis of molecular dynamics simulation
32 Lecture 31: Interaction energy and force field
33 Lecture 32: Liouiville theorem; theoretical basis of Monte Carlo simulation
34 Lecture 33: Introduction to Monte Carlo simulation method
35 Lecture 34: Markov chain algorithm, condition for equilibrium and detailed balance
36 Lecture 35: Metropolis algorithm, periodic boundary condition
37 Lecture 36: Numerical implementation of Monte Carlo simulation: python examples I
38 Lecture 37: Numerical implementation of Monte Carlo simulation: python examples II
39 Lecture 38: Numerical implementation of Monte Carlo simulation: python examples III
40 Lecture 39: Numerical implementation of Monte Carlo simulation: python examples IV
41 Lecture 40: Numerical implementation of Monte Carlo simulation: python examples V
42 Lecture 41: Particle simulations: comparison with quantum chemical and continuum simulations
43 Lecture 42: Pair potentials
44 Lecture 43: Saving CPU time: short range and long range interactions
45 Lecture 44: Bonded and nonbonded interactions, force fields
46 Lecture 45: Practical aspects of molecular simulations
47 lecture 46: Numerical implementation of MD; thermostat and barostat
48 Lecture 47: MD simulations - efficiency and parallelization, sampling and averaging
49 Lecture 48: MD simulations - analysis of simulation trajectories (continued), case studies I
50 Lecture 49: MD simulations - case studies II
51 Lecture 50: MD simulations - case studies III
52 Lecture 51: Free energies and phase behavior; extension of canonical ensemble monte carlo...
53 Lecture 52: Extension of canonical ensemble monte carlo to other ensembles (continued)
54 Lecture 53: Monte carlo in gibbs ensemble and semi-grand canonical ensemble...
55 Lecture 54: Thermodynamic integration (continued); widom's particle insertion...
56 Lecture 55: Multiple histogram method; umbrella sampling; thermodynamic cycle...
57 Lecture 56:Tackling time scale issues (continued); nonequilibrium molecular dynamics...
58 Lecture 57: Multiparticle collision dynamics; lattice boltzmann method; coarse-graining
59 Lecture 58: Case studies
60 Lecture 59: Simulations of chemical reactions using kinetic monte carlo simulations
61 Lecture 60: Reactive force fields; ab initio molecular dynamics and other advanced methods ...