Tags: molecular dynamics (MD)

Description

Molecular dynamics is a form of computer simulation in which atoms and molecules are allowed to interact for a period of time by approximations of known physics, giving a view of the motion of the particles. This kind of simulation is frequently used in the study of proteins and biomolecules, as well as in materials science. More information on Molecular dynamics can be found here.

Resources (121-140 of 197)

  1. Atomic Picture of Plastic Deformation in Metals via Online Molecular Dynamics Simulations

    Courses | 01 Jun 2011 | Contributor(s):: Alejandro Strachan

    The main goal of this learning module is to introduce students to the atomic-level processes responsible for plastic deformation in crystalline metals and help them develop a more intuitive understanding of how materials work at molecular scales. The module consists of: i) Two introductory...

  2. Additional Tutorials on Selected Topics in Nanotechnology

    Workshops | 29 Mar 2011 | Contributor(s):: Gerhard Klimeck, Umesh V. Waghmare, Timothy S Fisher, N. S. Vidhyadhiraja

    Select tutorials in nanotechnology, a part of the 2010 NCN@Purdue Summer School: Electronics from the Bottom Up.

  3. Stretching simulation of an alpha-helical protein domain

    Tools | 10 Jan 2011 | Contributor(s):: Markus Buehler, Justin Riley, Joo-Hyoung Lee, Jeffrey C Grossman

    Uses steered molecular dynamics (SMD) to apply a tensile load to the ends of a molecule (such as an alpha-helical protein domain)

  4. OPV: Time Domain Ab Initio Studies of Organic-Inorganic Composites for Solar Cells

    Online Presentations | 21 Jan 2011 | Contributor(s):: Oleg Prezhdo

    This presentation was part of the "Organic Photovoltaics: Experiment and Theory" workshop at the 2010 Users' Meeting of the Molecular Foundry and the National Center for Electron Microscopy, both DOE-funded Research Centers at Lawrence Berkeley National Laboratory.

  5. ME 597A Lecture 13: Uncertainty Quantification of Molecular Dynamics Simulations

    Online Presentations | 31 Jan 2011 | Contributor(s):: Alejandro Strachan

    Guest lecturer: Alejandro Strachan. 

  6. 2010 NCN@Purdue Summer School: Electronics from the Bottom Up

    Workshops | 20 Apr 2010

    Electronics from the Bottom Up seeks to bring a new perspective to electronic devices – one that is designed to help realize the opportunities that nanotechnology presents.

  7. MOLpull: A tool for molecular free energy reconstruction along a pulling coordinate

    Tools | 24 Aug 2010 | Contributor(s):: Lisa Felberg, Ignacio Franco, Martin McCullagh, Mark Ratner, George C. Schatz, Marcelo Carignano

    Estimates the force required for stretching a molecule and determines the potential of mean force along the extension coordinate.

  8. Addressing Molecular Dynamics Time-scale Issues to Study Atomic-scale Friction

    Online Presentations | 12 Oct 2010 | Contributor(s):: Ashlie Martini

    This presentation will include an introduction to several accelerated molecular dynamics methods. However, particular focus will be given to parallel replica (ParRep) dynamics in which atomistic simulations are run parallel in time to extend their total duration. The ParRep method is based on the...

  9. Tutorial 3: Materials Simulation by First-Principles Density Functional Theory

    Courses | 14 Sep 2010 | Contributor(s):: Umesh V. Waghmare

    This two-part lecture will provide an introduction to first-principles density functional theory based methods for simulation of materials, with a focus on determination of interatomic force constants and vibrational spectra of nano- structures and extended periodic materials.

  10. Tutorial 3b: Materials Simulation by First-Principles Density Functional Theory II

    Online Presentations | 09 Sep 2010 | Contributor(s):: Umesh V. Waghmare

  11. Polymer Modeler

    Tools | 28 Jun 2010 | 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

  12. Ripples and Warping of Graphene: A Theoretical Study

    Online Presentations | 19 May 2010 | Contributor(s):: Umesh V. Waghmare

    We use first-principles density functional theory based analysis to understand formation of ripples in graphene and related 2-D materials. For an infinite graphene, we show that ripples are linked with a low energy branch of phonons that exhibits quadratic dispersion at long wave-lengths. Many...

  13. Atomic Stick-Slip

    Tools | 09 Nov 2009 | Contributor(s):: Ashlie Martini, Jianguo Wu

    Molecular dynamics simulation of atomic stick-slip friction

  14. Atomic Picture of Plastic Deformation in Metals: Overview Lecture

    Online Presentations | 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...

  15. Atomic Picture of Plastic Deformation in Metals: Prelab Lecture

    Online Presentations | 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...

  16. Atomic Picture of Plastic Deformation in Metals: Lab Assignment Handout

    Teaching Materials | 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...

  17. Lecture 10: Non Equilibrium MD

    Presentation Materials | 05 Jan 2010 | Contributor(s):: Ashlie Martini

    Topics:Calculating transport coefficientShear flowPerturbation methods

  18. Lecture 9: Dynamic Properties

    Presentation Materials | 05 Jan 2010 | Contributor(s):: Ashlie Martini

    Topics:Time correlation functionsEinstein relationsGreen-Kubo relations

  19. Lecture 8: Static Properties

    Presentation Materials | 05 Jan 2010 | Contributor(s):: Ashlie Martini

    Topics:Thermodynamic propertiesEntropic propertiesStatic structure

  20. Lecture 7: Initialization and Equilibrium

    Presentation Materials | 05 Jan 2010 | Contributor(s):: Ashlie Martini

    Topics:Initial positionsInitial velocitiesEvaluating equilibrium