
Energy and Nanoscience A More Perfect Union
29 Mar 2009   Contributor(s):: Mark Ratner
Huge problems of energy and sustainability confront the science/engineering community, mankind, and our planet. The energy problem comes in many dimensions, including supply, demand, conservation, transportation, and storage. This overview will stress the nature of these problems, and offer a...

Illinois Center for Cellular Mechanics: Discovery through the Computational Microscope
11 Feb 2009   Contributor(s):: Klaus Schulten
Computational MicroscopeAllatom molecular dynamics simulations have become increasingly popular as a toolto investigate protein function and dynamics. However, researchers are usuallyconcerned about the short time scales covered by simulations, the apparentimpossibility to model large and...

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 Longterm stability of Verlet...

Nanoparticle and Colloidal Simulations with Molecular Dynamics
05 Dec 2008   Contributor(s):: Steve Plimpton
Modeling nanoparticle or colloidal systems in a molecular dynamics (MD) code requires coarsegraining on several levels to achieve meaningful simulation times for study of rheological and other manufacturing properties. These include treating colloids as single particles, moving from explicit to...

MSE 597G Lecture 4: Interatomic potentials I
14 Nov 2008   Contributor(s):: Alejandro Strachan
Interatomic potentials: pairwise potentials.

MSE 597G Lecture 3: Statistical Mechanics II
14 Nov 2008   Contributor(s):: Alejandro Strachan
Basic physics: statistical mechanics, Algorithms: Integrating the equations of motion.

MSE 597G An Introduction to Molecular Dynamics
13 Nov 2008   Contributor(s):: Alejandro Strachan
The goal of this short course is to provide an introduction to the theory and algorithms behind MD simulations, describe some of the most exciting recent developments in the field and exemplify with a few applications applications. The series also includes a tutorial on the nanoMATERIALS...

Running MD on the nanoHUB: The nanoMATERIALS Simulation Toolkit
13 Nov 2008   Contributor(s):: Alejandro Strachan
A quick demostration of the nanoHUB tool: nanoMaterials Simulation Toolkit.

MSE 597G Lecture 5: Interatomic potentials II
13 Nov 2008   Contributor(s):: Alejandro Strachan
Embedded atom model for metals,Three body terms for semiconductors: StillingerWeber,Electrostatics and Covalent interactions.

MSE 597G: An Introduction to Molecular Dynamics
13 Nov 2008   Contributor(s):: Alejandro Strachan

MSE 597G Lecture 6: Interatomic potentials III
12 Nov 2008   Contributor(s):: Alejandro Strachan
Reactive force fields,Parameterization of interatomic potentials

MSE 597G Lecture 7: Advanced Techniques for Molecular Dynamics Simulations
12 Nov 2008   Contributor(s):: Alejandro Strachan
Thermostats and barostats,Linear methods for energy and force calculations,Coarse graining or mesodynamics,Validation and Verification.

MSE 597G Lecture 2: Statistical Mechanics I
11 Nov 2008   Contributor(s):: Alejandro Strachan
Basic physics: statistical mechanics.

MSE 597G Lecture 1: Classical Mechanics
11 Nov 2008   Contributor(s):: Alejandro Strachan
Basic physics: classical mechanics

Ionic Selectivity in Channels: complex biology created by the balance of simple physics
05 Jun 2008   Contributor(s):: Bob Eisenberg
An important class of biological molecules—proteins called ionic channels—conduct ions (like Na+ , K+ , Ca2+ , and Cl− ) through a narrow tunnel of fixed charge (‘doping’). Ionic channels control the movement of electric charge and current across biological membranes and so play a role in...

BNC Annual Research Review: An Introduction to PRISM and MEMS Simulation
04 Jun 2008   Contributor(s):: Jayathi Murthy
This presentation is part of a collection of presentations describing the projects, people, and capabilities enhanced by research performed in the Birck Center, and a look at plans for the upcoming year.

MD Simulation
31 Mar 2008   Contributor(s):: Sanket S Mahajan, Ganesh Subbarayan, Xufeng Wang
Code to perform Molecular Dynamics (MD) Simulations

Computational Nanoscience, Homework Assignment 3: Molecular Dynamics Simulation of Carbon Nanotubes
14 Feb 2008   Contributor(s):: Elif Ertekin, Jeffrey C Grossman
The purpose of this assignment is to perform molecular dynamics simulations to calculate various properties of carbon nanotubes using LAMMPS and Tersoff potentials.This assignment is to be completed following lectures 5 and 6 using the "LAMMPS" program in the Berkeley Computational Nanoscience...

Computational Nanoscience, Homework Assignment 2: Molecular Dynamics Simulation of a LennardJones Liquid
14 Feb 2008   Contributor(s):: Elif Ertekin, Jeffrey C Grossman
The purpose of this assignment is to perform a full molecular dynamics simulation based on the Verlet algorithm to calculate various properties of a simple liquid, modeled as an ensemble of identical classical particles interacting via the LennardJones potential.This assignment is to be...

Computational Nanoscience, Lecture 6: Pair Distribution Function and More on Potentials
13 Feb 2008   Contributor(s):: Jeffrey C Grossman, Elif Ertekin
In this lecture we remind ourselves what a pair distribution function is, how to compute it, and why it is so important in simulations. Then, we revisit potentials and go into more detail including examples of typical functional forms, relative energy scales, and what to keep in mind when...