
Atomic Picture of Plastic Deformation in Metals: Prelab Lecture
24 Jan 2010  Online Presentations  Contributor(s): Alejandro Strachan
This lecture provides a detailed description of the activities the students will perform in the lab. We present a tutorial with step by step instructions on how to run MD simulations using the...
http://nanohub.org/resources/8043

Atomic Picture of Plastic Deformation in Metals: Lab Assignment Handout
19 Jan 2010  Teaching Materials  Contributor(s): Alejandro Strachan
In this lab students will perform online molecular dynamics (MD) simulations of metallic nanowires deformed uniaxially and analyze the results...
http://nanohub.org/resources/8140

Lecture 10: Non Equilibrium MD
05 Jan 2010  Presentation Materials  Contributor(s): Ashlie Martini
Topics:
Calculating transport coefficient
Shear flow
Perturbation methods
http://nanohub.org/resources/8125

Lecture 9: Dynamic Properties
05 Jan 2010  Presentation Materials  Contributor(s): Ashlie Martini
Topics:
Time correlation functions
Einstein relations
GreenKubo relations
http://nanohub.org/resources/8124

Lecture 8: Static Properties
05 Jan 2010  Presentation Materials  Contributor(s): Ashlie Martini
Topics:
Thermodynamic properties
Entropic properties
Static structure
http://nanohub.org/resources/8123

Lecture 7: Initialization and Equilibrium
05 Jan 2010  Presentation Materials  Contributor(s): Ashlie Martini
Topics:
Initial positions
Initial velocities
Evaluating equilibrium
http://nanohub.org/resources/8122

Lecture 6: Neighbor Lists
05 Jan 2010  Presentation Materials  Contributor(s): Ashlie Martini
Topics:
Saving simulation time
Verlet lists
Cell lists
http://nanohub.org/resources/8121

Lecture 5: Boundary Conditions
05 Jan 2010  Presentation Materials  Contributor(s): Ashlie Martini
Topics:
Fixed boundaries
Periodic boundary conditions
Minimum image distance
http://nanohub.org/resources/8120

Lecture 4: Temperature Control
05 Jan 2010  Presentation Materials  Contributor(s): Ashlie Martini
Topics:
Velocity scaling
Heat bath/reservoir
Stochastic methods
http://nanohub.org/resources/8119

Lecture 3: Integration Algorithms
05 Jan 2010  Presentation Materials  Contributor(s): Ashlie Martini
Topics:
General guidelines
Verlet algorithm
Predictorcorrector methods
http://nanohub.org/resources/8118

Lecture 2: Potential Energy Functions
05 Jan 2010  Presentation Materials  Contributor(s): Ashlie Martini
Topics:
Pair potentials
Coulomb interactions
Embedded atom model
Intramolecular interactions (bond, angle, torsion)
http://nanohub.org/resources/8117

Lecture 1: Basic Concepts
05 Jan 2010  Presentation Materials  Contributor(s): Ashlie Martini
Topics:
What is MD
Newton’s law
Basic concepts and terminology
http://nanohub.org/resources/7795

Short Course on Molecular Dynamics Simulation
13 Oct 2009  Courses  Contributor(s): Ashlie Martini
This set of ten presentations accompanied a graduate level course on Molecular Dynamics simulation. The specific objective of the course (and the presentations) is to provide:
1. Awareness of...
http://nanohub.org/resources/7570

MIT Tools for Energy Conversion and Storage
12 Oct 2009  Tools  Contributor(s): Jeffrey C Grossman, JooHyoung Lee, Varadharajan Srinivasan, Alexander S McLeod, Lucas Wagner
AtomicScale Simulation Tools to Explore Energy Conversion and Storage Materials
http://nanohub.org/resources/nanoenergytools

Energy and Nanoscience A More Perfect Union
29 Mar 2009  Online Presentations  Contributor(s): Mark A. 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,...
http://nanohub.org/resources/6554

Illinois Center for Cellular Mechanics: Discovery through the Computational Microscope
11 Feb 2009  Online Presentations  Contributor(s): Klaus Schulten
Computational Microscope
Allatom molecular dynamics simulations have become increasingly popular as a tool
to investigate protein function and dynamics. However, researchers are...
http://nanohub.org/resources/6253

Illinois PHYS 466, Lecture 4: Molecular Dynamics
05 Feb 2009  Online Presentations  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:
...
http://nanohub.org/resources/6239

Nanoparticle and Colloidal Simulations with Molecular Dynamics
05 Dec 2008  Online Presentations  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...
http://nanohub.org/resources/5668

MSE 597G Lecture 4: Interatomic potentials I
14 Nov 2008  Online Presentations  Contributor(s): Alejandro Strachan
Interatomic potentials: pairwise potentials.
http://nanohub.org/resources/5776

MSE 597G Lecture 3: Statistical Mechanics II
14 Nov 2008  Online Presentations  Contributor(s): Alejandro Strachan
Basic physics: statistical mechanics, Algorithms: Integrating the equations of motion.
http://nanohub.org/resources/5775