Tags: molecular dynamics


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.

Online Presentations (21-40 of 60)

  1. Tutorial 1: Atomistic Material Science - ab initio simulations of materials

    03 Nov 2011 | | Contributor(s):: Alejandro Strachan

    This lecture introduces first principles electronic structure calculations of materials properties.It describes the approximations made to the many-body Schrodinger equation in Hartree Fock and Density Functional Theory and numerical approximations used in computer simulations.

  2. Tutorial 2: Atomistic Material Science - Molecular Dynamics simulations of materials

    03 Nov 2011 | | Contributor(s):: Alejandro Strachan

    This lecture introduces the concept of molecular dynamics (MD) simulations of materials focusing on the physics and approximations underlying the simulations and interpretation of their results.

  3. Development of the ReaxFF reactive force fields and applications to combustion, catalysis and material failure

    12 Sep 2011 | | Contributor(s):: Adri van Duin

    This lecture will describe how the traditional, non-reactive FF-concept can be extended for application including reactive events by introducing bond order/bond distance concepts. Furthermore, it will address how these reactive force fields can be trained against QM-data, thus greatly enhancing...

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

    31 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

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

    Guest lecturer: Alejandro Strachan. 

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

    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...

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

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

  8. Ripples and Warping of Graphene: A Theoretical Study

    08 Jun 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...

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

    24 Jan 2010 | | 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 tests molecular dynamics simulations of materialsmechanical...

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

    24 Jan 2010 | | 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...

  11. 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...

  12. Illinois Center for Cellular Mechanics: Discovery through the Computational Microscope

    11 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...

  13. 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...

  14. 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 coarse-graining 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...

  15. MSE 597G Lecture 4: Interatomic potentials I

    14 Nov 2008 | | Contributor(s):: Alejandro Strachan

    Interatomic potentials: pairwise potentials.

  16. MSE 597G Lecture 3: Statistical Mechanics II

    14 Nov 2008 | | Contributor(s):: Alejandro Strachan

    Basic physics: statistical mechanics, Algorithms: Integrating the equations of motion.

  17. Running MD on the nanoHUB: The nano-MATERIALS Simulation Toolkit

    13 Nov 2008 | | Contributor(s):: Alejandro Strachan

    A quick demostration of the nanoHUB tool: nano-Materials Simulation Toolkit.

  18. MSE 597G Lecture 5: Interatomic potentials II

    13 Nov 2008 | | Contributor(s):: Alejandro Strachan

    Embedded atom model for metals,Three body terms for semiconductors: Stillinger-Weber,Electrostatics and Covalent interactions.

  19. MSE 597G: An Introduction to Molecular Dynamics

    13 Nov 2008 | | Contributor(s):: Alejandro Strachan

  20. MSE 597G Lecture 6: Interatomic potentials III

    12 Nov 2008 | | Contributor(s):: Alejandro Strachan

    Reactive force fields,Parameterization of interatomic potentials