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Illinois PHYS 466, Lecture 11: Importance Sampling
20 Mar 2009 | Contributor(s):: David M. Ceperley
Importance samplingToday We will talk about the third option: Importance sampling and correlated samplingContent: Importance Sampling Finding Optimal p*(x) for Sampling Example of importance sampling What are allowed values of a? What does infinite variance look like? General Approach to...
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Illinois PHYS 466, Lecture 12: Random Walks
30 Mar 2009 | Contributor(s):: David M. Ceperley
Random Walks Today we will discuss Markov chains (random walks), detailed balance and transition rules. These methods were introduced by Metropolis et al. in 1953 who applied it to a hard sphere liquid. It is one of the most powerful and used algorithmsContent: Equation of State Calculations by...
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Illinois PHYS 466, Lecture 13: Brownian Dynamics
08 Apr 2009 | Contributor(s):: David M. Ceperley
Brownian DynamicsLet’s explore the connection between Brownian motion and Metropolis Monte Carlo. Why? Connection with smart MC Introduce the idea of kinetic Monte Carlo Get rid of solvent degrees of freedom and have much longer time steps.Content: Local Markov process General Form of Evolution...
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Illinois PHYS 466, Lecture 14: Neighbor Tables, Long-Range Potentials, Ewald Sums
22 Apr 2009 | Contributor(s):: David M. Ceperley, Omar N Sobh
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Illinois PHYS 466, Lecture 15: Constraints
22 Apr 2009 | | Contributor(s):: David M. Ceperley, Omar N Sobh
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Illinois PHYS 466, Lecture 16: Free Energies from Simulations
28 Apr 2009 | | Contributor(s):: David M. Ceperley, Omar N Sobh
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Illinois PHYS 466, Lecture 17: Simulation of Polymers
30 Apr 2009 | | Contributor(s):: David M. Ceperley, Omar N Sobh
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Illinois PHYS 466, Lecture 18: Kinetic Monte Carlo (KMC)
04 May 2009 | | Contributor(s):: David M. Ceperley, Omar N Sobh
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Illinois PHYS 466, Lecture 19: The Ising Model
01 Jun 2009 | | Contributor(s):: David M. Ceperley, Omar N Sobh
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Illinois PHYS 466, Lecture 1: Introduction
28 Jan 2009 | | Contributor(s):: David M. Ceperley
Introduction to Simulation Content: Why do simulations? Moore's law Two Simulation Modes Dirac, 1929 Challenges of Simulation: Physical and mathematical underpinnings Complexity Estimation of Computer Time and Size Challenges of Simulation: Multi-scale computational materials research Short...
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Illinois PHYS 466, Lecture 3: Basics of Statistical Mechanics
31 Jan 2009 | | Contributor(s):: David M. Ceperley
Basics of Statistical Mechanics Review of ensembles Microcanonical, canonical, Maxwell-Boltzmann Constant pressure, temperature, volume,… Thermodynamic limit Ergodicity (see online notes also) Reading assignment: Frenkel and Smit pgs. 1-22.Content: The Fundamentals according to Newton “Molecular...
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Illinois PHYS 466, Lecture 4: Molecular Dynamics
05 Feb 2009 | | Contributor(s):: David M. Ceperley
Molecular Dynamics What to choose in an integrator The Verlet algorithm Boundary Conditions in Space and time Reading assignment: Frenkel and Smit Chapter 4 Content: Characteristics of simulations The Verlet Algorithm Higher Order Methods? Quote from Berendsen Long-term stability of Verlet...
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Illinois PHYS 466, Lecture 5: Interatomic Potentials
17 Feb 2009 | | Contributor(s):: David M. Ceperley
Interatomic Potentials Before we can start a simulation, we need the model! Interaction between atoms and molecules is determined by quantum mechanics But we don’t know V(R)!Content: The electronic-structure problem Born-Oppenheimer (1927) Approximation Semi-empirical potentials Atom-Atom...
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Illinois PHYS 466, Lecture 6: Scalar Properties and Static Correlations
27 Feb 2009 | | Contributor(s):: David M. Ceperley
Scalar Properties, Static Correlations and Order ParametersWhat do we get out of a simulation? Static properties: pressure, specific heat, etc. Density Pair correlations in real space and Fourier space Order parameters and broken symmetry: How to tell a liquid from a solid Dynamical properties...
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Illinois PHYS 466, Lecture 7: Dynamical Correlations & Transport Coefficients
27 Feb 2009 | | Contributor(s):: David M. Ceperley
Dynamical correlations and transport coefficientsDynamics is why we do molecular dynamics! Perturbation theory Linear-response theory Diffusion constants, velocity-velocity auto correlation fct. Transport coefficients Diffusion: Particle flux Viscosity: Stress tensor Heat transport: energy...
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Illinois PHYS 466, Lecture 8: Temperature and Pressure Controls
03 Mar 2009 | | Contributor(s):: David M. Ceperley
Temperature and Pressure ControlsContent: Constant Temperature MD Quench method Brownian dynamics/Anderson thermostat Nose-Hoover thermostat (FS 6.1.2) Nose-Hoover thermodynamics Effect of thermostat Comparison of Thermostats Constant pressure or constant volume Constant Pressure (FS 6.2)...
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Illinois Phys550 Molecular Biophysics
25 Jan 2010 | | Contributor(s):: Klaus Schulten
Physical concepts governing the structure and function of biological macromolecules; general properties, spatial structure, energy levels, dynamics and functions, and relation to other complex physical systems such as glasses; recent research in biomolecular physics; physical techniques and...
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Illinois Phys550 Molecular Biophysics Lecture 10: Interaction of Radiation with Molecules
02 Mar 2010 | | Contributor(s):: Klaus Schulten
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Illinois Phys550 Molecular Biophysics Lecture 11: Two Photon Processes
03 Mar 2010 | | Contributor(s):: Klaus Schulten
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Illinois Phys550 Molecular Biophysics Lecture 12: Radiation Processes Light Scattering
08 Mar 2010 | | Contributor(s):: Klaus Schulten