Learn · Thermodynamics for Biological Systems: Classical and Statistical Aspect
Lecture 74 of 87Week 11
Computer simulations of macromolecules
Prof. G. K. Suraishkumar Prof. Sanjib Senapati · IIT Madras
Credits and licence
- From
- Thermodynamics for Biological Systems: Classical and Statistical Aspect, IIT Madras (at NPTEL)
- Licence
- CC BY-NC-SA, as NPTEL states it. Non-commercial use only.
- Attribution
- NPTEL states: "Distributed under Creative Commons Attribution-ShareAlike / CC BY - NC - SA", beside a BY-NC-SA badge.
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- Tweens profiles and older. How courses are placed
All the lectures
- Introduction and review
- Review contd.
- Need for analysis
- Additional Thermodynamic Functions
- State and Path Variables
- Equations for a Closed System
- Chemical Potential
- Gibbs Duhem equation
- Maxwell's relations
- Inter-relationships between thermodynamic variables contd
- Some useful mathematical manipulations
- Thermodynamic relations for a closed system with 1 mole of pure substance
- Maximum work
- Open systems
- Equations of state - virial equations
- Equations of state - cubic equations
- Volume estimation
- Volume estimation, contd
- Generalized correlations
- Generalized correlations (contd)
- Residual properties
- Residual properties contd.
- Generalized correlations and residual properties
- Fugacity coefficient estimation
- Review of module 3
- Learning aspects
- Chemical potential formulations
- Lewis and Randall rule
- Partial molar properties
- Partial molar property estimation from mixing experiments
- Partial molar property estimation (contd.)
- Activity coefficient from excess property
- Activity coefficient from excess property (contd.)
- Models for activity coefficient in a binary system
- Models for activity coefficient for a binary system (contd.)
- Review of module 4
- Criteria for phase equilibrium
- Phase rule for non-reacting systems
- Clausius Clayperon equation
- Clausius Clayperon equation (contd.)
- Vapour liquid equilibrium
- Vapour-liquid equilibrium (contd.)
- Estimation of fugacity coefficient from P-V-T data at equilibrium
- Liquid-liquid and solid-liquid equilibria
- Review of module 5
- Criteria for bioreaction equilibria
- Phase rule for reacting biosystems
- Equilibrium constants
- Effect of temperature on the equilibrium constants
- Reaction in liquid or solid phases
- Free energy changes for some bioreactions
- Electrolytes
- Review of the classical thermodynamics part
- Introduction to Statistical thermodynamics
- Concepts of macro and microstates
- Thermodynamic probability
- Boltzmann distribution law
- Defining β in Boltzmann distribution law
- Relationship between partition function and thermodynamic quantities
- Partition function of mono atomic gases
- Entropy in terms of probablity
- Gibbs paradox
- Thermodynamic probability for distinguishable particles
- Thermodynamic probability for indistinguishable particles
- Sackur - Tetrode equation
- Partition function and Helmholtz and Gibbs free energy
- Ensemble approach
- Ensemble average, time average, Ergodic hypothesis
- Partition function for classical systems
- Pair potentials for atomic systems
- Potential for molecular systems
- Computer code for LJ potential
- Introduction to computer simulations
- Computer simulations of macromolecules
- MD simulation examples
- Link between theory and experiments
- MD protocol
- Computer simulation tricks
- Understanding force fields
- Idea of Z-matrix
- Basics of MD simulations
- Integration algorithms
- Calculation of Columbic force
- Calculation of LJ force
- Monte Carlo simulations
- Analysis of MD trajectory
- Case study (water)