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Computational Nanoscience, Homework Assignment 2: Molecular Dynamics Simulation of a Lennard-Jones Liquid
Teaching Materials | 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...
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Computational Nanoscience, Lecture 6: Pair Distribution Function and More on Potentials
Teaching Materials | 13 Feb 2008 | 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 including examples of typical functional forms, relative energy scales, and what to keep in mind when...
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Computational Nanoscience, Lecture 5: A Day of In-Class Simulation: MD of Carbon Nanostructures
Teaching Materials | 13 Feb 2008 | 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 calculating the energy per atom of different fullerenes and nantubes, computing the Young's modulus of a nanotube...
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BioMOCA Suite
Tools | 04 Feb 2008 | Contributor(s):: David Papke, Reza Toghraee, Umberto Ravaioli, Ankit Raj
Simulates ion flow through a channel.
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Computational Nanoscience, Lecture 4: Geometry Optimization and Seeing What You're Doing
Teaching Materials | 13 Feb 2008 | 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 importance of the starting guess and how to find or generate good initial structures. We also briefly...
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Overview of Computational Nanoscience: a UC Berkeley Course
Courses | 01 Feb 2008 | 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 on how to use simulations effectively, intelligently, and cohesively to predict properties that...
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Dynamics on the Nanoscale: Time-domain ab initio studies of quantum dots, carbon nanotubes and molecule-semiconductor interfaces
Online Presentations | 31 Jan 2008 | 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 the excitation, charge, spin, and vibrational dynamics in a variety of novel materials, including...
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Computational Nanoscience, Lecture 2: Introduction to Molecular Dynamics
Teaching Materials | 30 Jan 2008 | 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 considerations such as choice of timestep. A brief discussion of interatomic potentials (the pair potential and...
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Lecture 2: total energy and force calculations
Online Presentations | 14 Jan 2008 | 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 advances like reactive force fields. The key physics of widely used force fields will be described as well...
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Lectures on Molecular Dynamics Modeling of Materials
Courses | 09 Jan 2008 | 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. Recent breakthroughs in methodologies and in first principles-based interatomic potentials significantly...
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Lecture 1: the theory behind molecular dynamics
Online Presentations | 09 Jan 2008 | 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 interpret and analyze its results. The power, range of applicability and limitations of MD will be discussed.
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Lecture 3: simulation details and coarse grain approaches
Online Presentations | 09 Jan 2008 | 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 (where mesoparticles describe groups of atoms) focusing on recent advances in theory that enable...
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Introduction: molecular dynamics simulations
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.
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Nano Heatflow
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.
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Computing the Horribleness of Soft Condensed Matter
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...
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Charge Transfer Across an Energy Transducing Integral Membrane Protein Complex
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...
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Atomistic Modeling of the Mechanical Properties of Nanostructured Materials
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.
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Orientational Dependence of Friction in Polyethylene
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).
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Fouling Mechanisms in Y-shaped Carbon Nanotubes
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...
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Computer Simulation of Nanoparticles, Viruses, and Electrical Power-Generating Bacteria
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...