Tags: molecular dynamics

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 (1-20 of 127)

  1. 1-D Chain Dispersions

    01 Sep 2011 | | Contributor(s):: Nicholas Roberts, Greg Walker

    1-D Chain of atoms, bases and layers to produce phonon dispersion

  2. 2010 NCN@Purdue Summer School: Electronics from the Bottom Up

    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.

  3. 2d Ideal Gas Molecular Dynamics

    01 Sep 2011 | | Contributor(s):: Terence Musho, Greg Walker

    Simulation of a 2d molecular gas with specified temperature boundary conditions

  4. Additional Tutorials on Selected Topics in Nanotechnology

    23 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.

  5. 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...

  6. Applying Machine Learning to Computational Chemistry: Can We Predict Molecular Properties Faster without Compromising Accuracy?

    26 Jul 2017 | | Contributor(s):: Hanjing Xu, Pradeep Kumar Gurunathan

    Non-covalent interactions are crucial in analyzing protein folding and structure, function of DNA and RNA, structures of molecular crystals and aggregates, and many other processes in the fields of biology and chemistry. However, it is time and resource consuming to calculate such interactions...

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

    18 Dec 2009 | | 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...

  8. 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...

  9. 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 tests molecular dynamics simulations of materialsmechanical...

  10. 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...

  11. Atomic Stick-Slip

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

    Molecular dynamics simulation of atomic stick-slip friction

  12. Atomistic Material Science

    25 Aug 2011 | | Contributor(s):: Alejandro Strachan

    This course introduces first principles electronic structure calculations of materials properties and the concept of molecular dynamics (MD) simulations of materials focusing on the physics and approximations underlying the simulations and interpretation of their results.

  13. Atomistic Modeling of the Mechanical Properties of Nanostructured Materials

    16 Apr 2007 | | Contributor(s):: SeongJun Heo, Susan Sinnott

    The mechanical properties of carbon nanotubes are studied by using classical molecular dynamics simulations. Especially, the effects of filling, temperature, and functionalization on CNT's tensional and twisting properties are considered in this study.

  14. Atomistic Modeling: Past, Present, and Future, MGI, ICME, etc.

    03 Nov 2015 | | Contributor(s):: Paul Saxe

    I will present a perspective on atomistic modeling — tools using quantum methods such as DFT, as well as molecular dynamics and Monte Carlo methods based on forcefields — over the past 30 years or so. While we are all caught up in the present, it is important to remember and realize...

  15. Atomistic Polymer Workflow Notebook

    19 Oct 2017 | | Contributor(s):: Benjamin P Haley

    Run PolymerModeler and nuSIMM tools to create atomistic polymer systems

  16. BioMOCA Suite

    04 Feb 2008 | | Contributor(s):: David Papke, Reza Toghraee, Umberto Ravaioli, Ankit Raj

    Simulates ion flow through a channel.

  17. BNC Annual Research Review: An Introduction to PRISM and MEMS Simulation

    04 Jun 2008 | | Contributor(s):: Jayathi Murthy

    This presentation is part of a collection of presentations describing the projects, people, and capabilities enhanced by research performed in the Birck Center, and a look at plans for the upcoming year.

  18. Charge Transfer Across an Energy Transducing Integral Membrane Protein Complex

    31 May 2007 | | Contributor(s):: William A. Cramer

    The cytochrome bc complexes of the mitochondrial respiratory and photosynthetic electron transport chains are hetero-oligomeric integral membrane proteins. These proteins are responsible for most of the energy transduction and transport activities across biological membranes. Such complexes...

  19. Coarse Graining of Crystalline Cellulose

    29 Jul 2016 | | Contributor(s):: Kuo Tian, Mehdi Shishehbor, Pablo Daniel Zavattieri

    Bio-inspired Crystalline Nano-Cellulose coarse graining toolkit

  20. Computational Nanoscience, Homework Assignment 2: Molecular Dynamics Simulation of a Lennard-Jones Liquid

    14 Feb 2008 | | Contributor(s):: Elif Ertekin, Jeffrey C Grossman

    The purpose of this assignment is to perform a full molecular dynamics simulation based on the Verlet algorithm to calculate various properties of a simple liquid, modeled as an ensemble of identical classical particles interacting via the Lennard-Jones potential.This assignment is to be...