Tags: molecular dynamics (MD)

More tags

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.

All Categories (281-300 of 310)

  1. Introduction: molecular dynamics simulations

    0.0 out of 5 stars 

    Online Presentations | 09 Jan 2008 | Contributor(s):: Alejandro Strachan

    This short presentation will describe the idea behind MD simulations and demonstrate its use in real applications.

  2. Nano Heatflow

    0.0 out of 5 stars 

    Tools | 25 Sep 2007 | Contributor(s):: Joe Ringgenberg, P. Alex Greaney, daniel richards, Jeffrey C Grossman, Jeffrey B. Neaton, Justin Riley

    Study the transfer of energy between the vibrational modes of a carbon nanotube.

  3. Computing the Horribleness of Soft Condensed Matter

    5.0 out of 5 stars 

    Online Presentations | 19 Oct 2007 | Contributor(s):: Eric Jakobsson

    A great triumph of computer simulations 40 years ago was to make the liquid state of matter understandable in terms of physical interactions between individual molecules. Prior to the first simulations of liquid argon and liquid water in the 1960's, there was no quantitatively rigorous molecular...

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

    0.0 out of 5 stars 

    Online Presentations | 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...

  5. Atomistic Modeling of the Mechanical Properties of Nanostructured Materials

    0.0 out of 5 stars 

    Online Presentations | 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.

  6. Orientational Dependence of Friction in Polyethylene

    0.0 out of 5 stars 

    Online Presentations | 16 Apr 2007 | Contributor(s):: SeongJun Heo

    The frictional properties of polyethylene polymer are investigated by using classical molecular dynamics simulations. Especially, the sliding orientational effect is considered in this study. The results of polyethylene are also compared to those of polytetrafluoroethylene(PTFE).

  7. Fouling Mechanisms in Y-shaped Carbon Nanotubes

    0.0 out of 5 stars 

    Online Presentations | 04 Apr 2007 | Contributor(s):: Jason Myers, SeongJun Heo, Susan Sinnott

    In the modern pharmaceutical and chemical industries, solutions of extremely high purity are needed. Current filtration methods are reaching the limits of their abilities, so new filters must be developed. One possible filter is a Y-shaped carbon nanotube (Y-tube). By changing the sizes of the...

  8. Computer Simulation of Nanoparticles, Viruses, and Electrical Power-Generating Bacteria

    0.0 out of 5 stars 

    Online Presentations | 20 Mar 2007 | Contributor(s):: Peter J. Ortoleva

    Models of cells and nanometer-scale biosystems are presented that clarify their physico-chemical characteristics and allow for computer- aided design of therapeutic and nanotechnical devices. Multiscale techniques are used to obtain rigorous, coarse-grained equations for the migration and...

  9. Materials strength: does size matter? nanoMATERIALS simulation toolkit tutorial

    5.0 out of 5 stars 

    Online Presentations | 01 Feb 2007 | Contributor(s):: Alejandro Strachan

    Molecular dynamics (MD) is a powerful technique to characterize the fundamental, atomic-level processes that govern materials behavior and is playing an important role in our understanding of the new phenomena that arises in nanoscale and nanostructured materials and result in their unique...

  10. Podolskaya I. Natalie

    https://nanohub.org/members/17814

  11. Potassium Channels: Conduction, Selectivity, Blockage, Inactivation, and Gating

    0.0 out of 5 stars 

    Online Presentations | 03 Nov 2006 | Contributor(s):: Benoit Roux, NCN at Northwestern University

    The determination of the structure of the KcsA K+ channel fromStreptomyces lividan has made it possible to investigate the functionof a biological channel at the atomic level. Because of its structuralsimilarity with eukaryotic K-channels, investigations of KcsA areexpected to help understand a...

  12. REBO

    4.0 out of 5 stars 

    Tools | 24 Jul 2006 | Contributor(s):: Wen-Dung Hsu, SeongJun Heo, jing xu, Susan Sinnott

    Reactive Empirical Bond-Order (REBO) potential is a many-body expression optimized for modeling covalently bonded materials, such as carbon and silicon, in large-scale atomistic simulations

  13. Micelle

    0.0 out of 5 stars 

    Tools | 24 Jul 2006 | Contributor(s):: Kunal Shah, Patrick Chiu, jing xu, Susan Sinnott

    Parallel Molecular Dynamics (MD) code that models surfactant structures in water and at liquid/solid interfaces.

  14. Molecular Workbench: An Interface to the Molecular World

    5.0 out of 5 stars 

    Downloads | 25 Jun 2006 | Contributor(s):: Charles Xie

    The Molecular Workbench software is a free, open-source modeling and authoring program specifically designed for use in science education. Powered by a set of real-time molecular simulation engines that compute and visualize the motion of particles interacting through force fields, in both 2D and...

  15. nano-Materials Simulation Toolkit

    5.0 out of 5 stars 

    Tools | 08 Aug 2006 | Contributor(s):: Alejandro Strachan, Amritanshu Palaria, Ya Zhou, Janam Jhaveri

    Molecular Dynamics simulations of nano-materials

  16. Nanofluidics

    0.0 out of 5 stars 

    Online Presentations | 15 Jun 2004 | Contributor(s):: Susan Sinnott

    Nanofluidics

  17. REBO Nanofluidics Exercise

    0.0 out of 5 stars 

    Teaching Materials | 10 May 2006 | Contributor(s):: Susan Sinnott, Hetal Patel

    Nanofluidics exercise showing the variation of energy and position of methane and butane molecules flowing through an opened carbon nanotube as the system temperature and the length of the nanotube are varied.

  18. Structure and Ion Permeation of the Gramicidin Channel using Molecular Dynamics

    0.0 out of 5 stars 

    Online Presentations | 12 Apr 2004 | Contributor(s):: Toby Allen

    Molecular dynamics (MD) has become an essential tool for obtaining microscopic insight into biological function. The gramicidin channel as an excellent benchmark system for this purpose. Using extensive MD simulations with explicit solvent and membrane, we determine the backbone structure and...

  19. Atomic Simulation Environment developers

    Groups

    The development team for the Atomic Simulation Environment (ASE) and related tools, based at DTU Physics, the Technical University of Denmark.  

    https://nanohub.org/groups/asedevel

  20. Atomistic view of materials

    Groups

    This group is for instructors and students of the Atomistic View of Materials Class.

    https://nanohub.org/groups/atoms2materials