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Tags: molecular dynamics

Resources

Tools

Online Presentations

  • 10.0 Ranking Strachan: Materials strength: does size ...

    Materials strength: does size matter? nanoMATERIALS simulation toolkit tutorial

    Type Online Presentations
    Contributor(s) Alejandro Strachan
    Date 01 Feb. 2007
    Avg. Rating 5.0 out of 5 stars  (2)
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    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 ...

  • 8.9 Ranking Strachan: Introduction: molecular dynamics ...

    Introduction: molecular dynamics simulations

    Type Online Presentations
    Contributor(s) Alejandro Strachan
    Date 09 Jan. 2008
    Avg. Rating 0.0 out of 5 stars  (0)
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    This short presentation will describe the idea behind MD simulations and demonstrate its use in real applications.

  • 8.5 Ranking Ortoleva: Computer Simulation of ...

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

    Type Online Presentations
    Contributor(s) Peter J. Ortoleva
    Date 20 Mar. 2007
    Avg. Rating 0.0 out of 5 stars  (0)
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    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 ...

  • 8.2 Ranking Strachan: Lecture 2: total energy and force ...

    Lecture 2: total energy and force calculations

    Type Online Presentations
    Contributor(s) Alejandro Strachan
    Date 14 Jan. 2008
    Avg. Rating 0.0 out of 5 stars  (0)
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    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 advances like reactive force fields. The key physics of widely used force fields will be described ...

  • 8.2 Ranking Strachan: Lecture 1: the theory behind ...

    Lecture 1: the theory behind molecular dynamics

    Type Online Presentations
    Contributor(s) Alejandro Strachan
    Date 09 Jan. 2008
    Avg. Rating 0.0 out of 5 stars  (0)
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    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 interpret and analyze its results. The power, range of applicability and limitations of MD will be ...

  • 7.7 Ranking Strachan: Lecture 3: simulation details and ...

    Lecture 3: simulation details and coarse grain approaches

    Type Online Presentations
    Contributor(s) Alejandro Strachan
    Date 09 Jan. 2008
    Avg. Rating 0.0 out of 5 stars  (0)
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    The last presentation will describe simulation techniques to simulate materials under isothermal and isobaric conditions. We will also describe coarse grain or mesodynamical approaches (where mesoparticles describe groups of atoms) focusing on recent advances in theory that enable ...

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Courses

  • 9.2 Ranking Grossman: Overview of Computational ...

    Overview of Computational Nanoscience: a UC Berkeley Course

    Type Courses
    Contributor(s) Jeffrey C Grossman, Elif Ertekin
    Date 01 Feb. 2008
    Avg. Rating 5.0 out of 5 stars  (3)
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    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 on how to use simulations effectively, intelligently, and cohesively to predict properties that occur ...

  • 6.1 Ranking Strachan: Lectures on Molecular Dynamics ...

    Lectures on Molecular Dynamics Modeling of Materials

    Type Courses
    Contributor(s) Alejandro Strachan
    Date 09 Jan. 2008
    Avg. Rating 0.0 out of 5 stars  (0)
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    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. Recent breakthroughs in methodologies and in first principles-based interatomic potentials significantly ...

Teaching Materials

  • 10.0 Ranking Grossman: Computational Nanoscience, Lecture ...

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

    Type Teaching Materials
    Contributor(s) Jeffrey C Grossman, Elif Ertekin
    Date 13 Feb. 2008
    Avg. Rating 5.0 out of 5 stars  (1)
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    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 importance of the starting guess and how to find or generate good initial structures. We also briefly ...

  • 10.0 Ranking Grossman: Computational Nanoscience, Lecture ...

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

    Type Teaching Materials
    Contributor(s) Jeffrey C Grossman, Elif Ertekin
    Date 15 Feb. 2008
    Avg. Rating 5.0 out of 5 stars  (1)
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    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 calculating the energy per atom of different fullerenes and nantubes, computing the Young's modulus of a nanotube ...

  • 10.0 Ranking Grossman: Computational Nanoscience, Lecture ...

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

    Type Teaching Materials
    Contributor(s) Jeffrey C Grossman, Elif Ertekin
    Date 15 Feb. 2008
    Avg. Rating 5.0 out of 5 stars  (1)
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    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 including examples of typical functional forms, relative energy scales, and what to keep in mind when ...

  • 10.0 Ranking Ertekin: Computational Nanoscience, ...

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

    Type Teaching Materials
    Contributor(s) Elif Ertekin, Jeffrey C Grossman
    Date 15 Feb. 2008
    Avg. Rating 5.0 out of 5 stars  (1)
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    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 completed following lectures 5 and 6 using the "LAMMPS" program in the Berkeley Computational Nanoscience ...

  • 9.5 Ranking Ertekin: Computational Nanoscience, ...

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

    Type Teaching Materials
    Contributor(s) Elif Ertekin, Jeffrey C Grossman
    Date 15 Feb. 2008
    Avg. Rating 0.0 out of 5 stars  (0)
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    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 ...

  • 0.0 Ranking Sinnott: REBO Nanofluidics Exercise

    REBO Nanofluidics Exercise

    Type Teaching Materials
    Contributor(s) Susan Sinnott, Hetal Patel
    Date 09 Jun. 2004
    Avg. Rating 0.0 out of 5 stars  (0)
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    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.

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Downloads

  • 10.0 Ranking Xie: Molecular Workbench: An Interface ...

    Molecular Workbench: An Interface to the Molecular World

    Type Downloads
    Contributor(s) Charles Xie
    Date 31 Aug. 2006
    Avg. Rating 5.0 out of 5 stars  (2)
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    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 ...

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