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Atomic Stick-Slip
09 Nov 2009 | | Contributor(s):: Ashlie Martini, Jianguo Wu
Molecular dynamics simulation of atomic stick-slip friction
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Atomic Picture of Plastic Deformation in Metals: Overview Lecture
18 Dec 2009 | | 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 polycrystalline metals during tensile testsmolecular dynamics simulations of materialsmechanical...
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Atomic Picture of Plastic Deformation in Metals: Prelab Lecture
18 Dec 2009 | | 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 nano-Materials Simulation Toolkit. This lecture is part of the learning module Atomic Picture of Plastic...
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Atomic Picture of Plastic Deformation in Metals: Lab Assignment Handout
19 Jan 2010 | | Contributor(s):: Alejandro Strachan
In this lab students will perform online molecular dynamics (MD) simulations of metallic nanowires deformed uniaxially and analyze the results...
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Lecture 10: Non Equilibrium MD
05 Jan 2010 | | Contributor(s):: Ashlie Martini
Topics:Calculating transport coefficientShear flowPerturbation methods
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Lecture 9: Dynamic Properties
05 Jan 2010 | | Contributor(s):: Ashlie Martini
Topics:Time correlation functionsEinstein relationsGreen-Kubo relations
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Lecture 8: Static Properties
05 Jan 2010 | | Contributor(s):: Ashlie Martini
Topics:Thermodynamic propertiesEntropic propertiesStatic structure
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Lecture 7: Initialization and Equilibrium
05 Jan 2010 | | Contributor(s):: Ashlie Martini
Topics:Initial positionsInitial velocitiesEvaluating equilibrium
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Lecture 6: Neighbor Lists
05 Jan 2010 | | Contributor(s):: Ashlie Martini
Topics:Saving simulation timeVerlet listsCell lists
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Lecture 5: Boundary Conditions
05 Jan 2010 | | Contributor(s):: Ashlie Martini
Topics:Fixed boundariesPeriodic boundary conditionsMinimum image distance
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Lecture 4: Temperature Control
05 Jan 2010 | | Contributor(s):: Ashlie Martini
Topics:Velocity scalingHeat bath/reservoirStochastic methods
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Lecture 3: Integration Algorithms
05 Jan 2010 | | Contributor(s):: Ashlie Martini
Topics:General guidelinesVerlet algorithmPredictor-corrector methods
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Lecture 2: Potential Energy Functions
05 Jan 2010 | | Contributor(s):: Ashlie Martini
Topics:Pair potentialsCoulomb interactionsEmbedded atom modelIntra-molecular interactions (bond, angle, torsion)
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Lecture 1: Basic Concepts
13 Nov 2009 | | Contributor(s):: Ashlie Martini
Topics:What is MDNewton’s lawBasic concepts and terminology
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Short Course on Molecular Dynamics Simulation
11 Oct 2009 | | 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 the opportunities and limitations of Molecular Dynamics as a tool for scientific and engineering...
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MIT Tools for Energy Conversion and Storage
13 Sep 2009 | | Contributor(s):: Jeffrey C Grossman, Joo-Hyoung Lee, Varadharajan Srinivasan, Alexander S McLeod, Lucas Wagner
Atomic-Scale Simulation Tools to Explore Energy Conversion and Storage Materials
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Energy and Nanoscience A More Perfect Union
27 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 few...
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Illinois Center for Cellular Mechanics: Discovery through the Computational Microscope
09 Feb 2009 | | Contributor(s):: Klaus Schulten
Computational MicroscopeAll-atom 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...
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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 MatSE485/Phys466/CSE485 - Atomic-Scale Simulation
27 Jan 2009 | | Contributor(s):: David M. Ceperley
THE OBJECTIVE is to learn and apply fundamental techniques used in (primarily classical) simulations in order to help understand and predict properties of microscopic systems in materials science, physics, chemistry, and biology. THE EMPHASIS will be on connections between the simulation...