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About
Chapters
Schedule (Spring 2025)
Stats
Probability theory
Random variables
Diffusion
Entropy and Information
Thermodynamics
Review of thermodynamics principles
Thermodynamic Potentials
Ensembles
Intro to Statistical Ensembles
Ensembles in phase-space
Open Systems
Summary of Ensembles
Phase transitions
Phase transitions: a birds eye view
Monte Carlo and “the power of randomness”
Ising models and Metropolis algorithm
Mean Field
Fluids
Statistical mechanics of fluids
Molecular Dynamics
MD/MC simulations of fluids
Tutorials
Python
Python3
NumPy
Plotting
Tutorial: Building Python Classes
Numpy lab
Numpy and Probabilities
Numpy Lab: Sinc Function
Numpy Lab: Linear Functions
Tutorial: Numpy simultions of 1D gas
Tutorial: Numpy simultions of 2D gas
Random Walks
Random walk simulations
The Inverse Transform of RVs
Change of variables with automatic differentiation (autodiff)
Conformations of Random Polymer Chains
Langevin Equation for Brownian Motion and Mean Square Displacement (MSD)
Application of ensembles
Free energy and protein folding
Two-state system
Mass action law
Simulating Ising models
Markov Chains
Other Methods for sampling Ising models
Non-boltzman (enhanced) sampling ideas
Simulating Fluids
Molecular dynamics simulations with OpenMM
Double Well potential using OpenMM
Create Structure and Topology objects
Simulating Ethane
TIP3P/TIP4P Water Model Simulation in OpenMM
Simulating Alanine dipeptide
Simulating solvated protein
Final Projects
Final Project: Simulating Ising Spin Relaxation with Glauber Dynamics
Final Project: Metastability and Nucleation in the 2D Ising Model
Final Project: Simulating Chemical Reactions with Langevin Dynamics
Final Project: Phase Separation in Binary Lennard-Jones Mixtures
Final Project: Sequence-Dependent Structure in Lennard-Jones Polymers Using OpenMM
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Application of ensembles
Application of ensembles
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