
Polymer Modeler
28 Jun 2010  Tools  Contributor(s): Benjamin P Haley, Nate Wilson, Chunyu Li, Andrea Arguelles, Eugenio Jaramillo, Alejandro Strachan
Build thermoplastic polymer chains and run LAMMPS to relax the chains and study mechanical properties
http://nanohub.org/resources/polymod

Francisco Murphy
Studying biochemistry and molecular biology Want to do a master
http://nanohub.org/members/45284

Ripples and Warping of Graphene: A Theoretical Study
08 Jun 2010  Online Presentations  Contributor(s): Umesh V. Waghmare
We use firstprinciples density functional theory based analysis to understand formation of ripples in graphene and related 2D materials. For an infinite graphene, we show that ripples are linked...
http://nanohub.org/resources/9010

Atomic StickSlip
09 Nov 2009  Tools  Contributor(s): Ashlie Martini, Jianguo Wu
Molecular dynamics simulation of atomic stickslip friction
http://nanohub.org/resources/stickslip

Learning Module: Atomic Picture of Plastic Deformation in Metals
The main goal of this learning module is to introduce students to the atomiclevel processes responsible for plastic deformation in crystalline metals and help them develop a more intuitive...
http://nanohub.org/wiki/LearningModulePlasticityMD

Atomic Picture of Plastic Deformation in Metals: Overview Lecture
24 Jan 2010  Online Presentations  Contributor(s): Alejandro Strachan
The lecture describes the objectives of the learning module and provides the necessary background for the activities. We briefly discuss the following topics:
mechanical response of macroscopic...
http://nanohub.org/resources/8038

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
13 Sep 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