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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 (61-80 of 93)

  1. Ionic Selectivity in Channels: complex biology created by the balance of simple physics

    05 Jun 2008 | Online Presentations | Contributor(s): Bob Eisenberg

    An important class of biological molecules—proteins called ionic channels—conduct ions (like Na+ , K+ , Ca2+ , and Cl− ) through a narrow tunnel of fixed charge (‘doping’). Ionic channels...

    http://nanohub.org/resources/4726

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

    04 Jun 2008 | Online Presentations | 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...

    http://nanohub.org/resources/4717

  3. MD Simulation

    31 Mar 2008 | Tools | Contributor(s): Sanket S Mahajan, Ganesh Subbarayan, Xufeng Wang

    Code to perform Molecular Dynamics (MD) Simulations

    http://nanohub.org/resources/mdsim

  4. Computational Nanoscience, Homework Assignment 3: Molecular Dynamics Simulation of Carbon Nanotubes

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

    The purpose of this assignment is to perform molecular dynamics simulations to calculate various properties of carbon nanotubes using LAMMPS and Tersoff potentials. This assignment is to be...

    http://nanohub.org/resources/4054

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

    14 Feb 2008 | Teaching Materials | 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...

    http://nanohub.org/resources/4052

  6. Computational Nanoscience, Lecture 6: Pair Distribution Function and More on Potentials

    13 Feb 2008 | Teaching Materials | Contributor(s): Jeffrey C Grossman, Elif Ertekin

    In this lecture we remind ourselves what a pair distribution function is, how to compute it, and why it is so important in simulations. Then, we revisit potentials and go into more detail...

    http://nanohub.org/resources/4039

  7. Computational Nanoscience, Lecture 5: A Day of In-Class Simulation: MD of Carbon Nanostructures

    13 Feb 2008 | Teaching Materials | Contributor(s): Jeffrey C Grossman, Elif Ertekin

    In this lecture we carry out simulations in-class, with guidance from the instructors. We use the LAMMPS tool (within the nanoHUB simulation toolkit for this course). Examples include...

    http://nanohub.org/resources/4037

  8. BioMOCA Suite

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

    Simulates ion flow through a channel.

    http://nanohub.org/resources/BMCsuite

  9. Computational Nanoscience, Lecture 4: Geometry Optimization and Seeing What You're Doing

    13 Feb 2008 | Teaching Materials | Contributor(s): Jeffrey C Grossman, Elif Ertekin

    In this lecture, we discuss various methods for finding the ground state structure of a given system by minimizing its energy. Derivative and non-derivative methods are discussed, as well as the...

    http://nanohub.org/resources/4035

  10. Overview of Computational Nanoscience: a UC Berkeley Course

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

    This course will provide students with the fundamentals of computational problem-solving techniques that are used to understand and predict properties of nanoscale systems. Emphasis will be placed...

    http://nanohub.org/resources/3944

  11. Dynamics on the Nanoscale: Time-domain ab initio studies of quantum dots, carbon nanotubes and molecule-semiconductor interfaces

    31 Jan 2008 | Online Presentations | Contributor(s): Oleg Prezhdo

    Device miniaturization requires an understanding of the dynamical response of materials on the nanometer scale. A great deal of experimental and theoretical work has been devoted to characterizing...

    http://nanohub.org/resources/3951

  12. Computational Nanoscience, Lecture 2: Introduction to Molecular Dynamics

    30 Jan 2008 | Teaching Materials | Contributor(s): Jeffrey C Grossman, Elif Ertekin

    In this lecture, we present and introduction to classical molecular dynamics. Approaches to integrating the equations of motion (Verlet and other) are discussed, along with practical...

    http://nanohub.org/resources/3940

  13. Lecture 2: total energy and force calculations

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

    This lecture will describe the various models used to describe the interactions between atoms in a wide range of materials including metals, ceramics and soft materials as well as new recent...

    http://nanohub.org/resources/3678

  14. Lectures on Molecular Dynamics Modeling of Materials

    09 Jan 2008 | Courses | Contributor(s): Alejandro Strachan

    Molecular dynamics simulations are playing an increasingly important role in many areas of science and engineering, from biology and pharmacy to nanoelectronics and structural materials....

    http://nanohub.org/resources/3675

  15. Lecture 1: the theory behind molecular dynamics

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

    The first lecture will provide a brief description of classical mechanics and statistical mechanics necessary to understand the physics and approximations behind MD and how to correctly...

    http://nanohub.org/resources/3677

  16. Lecture 3: simulation details and coarse grain approaches

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

    The last presentation will describe simulation techniques to simulate materials under isothermal and isobaric conditions. We will also describe coarse grain or mesodynamical approaches...

    http://nanohub.org/resources/3679

  17. Introduction: molecular dynamics simulations

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

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

    http://nanohub.org/resources/3676

  18. Nano Heatflow

    25 Sep 2007 | Tools | 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.

    http://nanohub.org/resources/nanoheatflow

  19. Computing the Horribleness of Soft Condensed Matter

    19 Oct 2007 | Online Presentations | 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...

    http://nanohub.org/resources/3424

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

    31 May 2007 | Online Presentations | 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...

    http://nanohub.org/resources/2679

nanoHUB.org, a resource for nanoscience and nanotechnology, is supported by the National Science Foundation and other funding agencies. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.