
MSE 597G An Introduction to Molecular Dynamics
13 Nov 2008  Courses  Contributor(s): Alejandro Strachan
The goal of this short course is to provide an introduction to the theory and algorithms behind MD simulations, describe some of the most exciting recent developments in the field and exemplify...
http://nanohub.org/resources/5838

Running MD on the nanoHUB: The nanoMATERIALS Simulation Toolkit
13 Nov 2008  Online Presentations  Contributor(s): Alejandro Strachan
A quick demostration of the nanoHUB tool: nanoMaterials Simulation Toolkit.
http://nanohub.org/resources/5843

MSE 597G Lecture 5: Interatomic potentials II
13 Nov 2008  Online Presentations  Contributor(s): Alejandro Strachan
Embedded atom model for metals,
Three body terms for semiconductors: StillingerWeber,
Electrostatics and Covalent interactions.
http://nanohub.org/resources/5777

MSE 597G: An Introduction to Molecular Dynamics
13 Nov 2008  Online Presentations  Contributor(s): Alejandro Strachan
http://nanohub.org/resources/5760

MSE 597G Lecture 6: Interatomic potentials III
12 Nov 2008  Online Presentations  Contributor(s): Alejandro Strachan
Reactive force fields,
Parameterization of interatomic potentials
http://nanohub.org/resources/5778

MSE 597G Lecture 7: Advanced Techniques for Molecular Dynamics Simulations
12 Nov 2008  Online Presentations  Contributor(s): Alejandro Strachan
Thermostats and barostats,
Linear methods for energy and force calculations,
Coarse graining or mesodynamics,
Validation and Verification.
http://nanohub.org/resources/5779

MSE 597G Lecture 2: Statistical Mechanics I
11 Nov 2008  Online Presentations  Contributor(s): Alejandro Strachan
Basic physics: statistical mechanics.
http://nanohub.org/resources/5765

MSE 597G Lecture 1: Classical Mechanics
11 Nov 2008  Online Presentations  Contributor(s): Alejandro Strachan
Basic physics: classical mechanics
http://nanohub.org/resources/5507

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

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

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

Computational Nanoscience, Homework Assignment 3: Molecular Dynamics Simulation of Carbon Nanotubes
15 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

Computational Nanoscience, Homework Assignment 2: Molecular Dynamics Simulation of a LennardJones Liquid
15 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

Computational Nanoscience, Lecture 6: Pair Distribution Function and More on Potentials
15 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

Computational Nanoscience, Lecture 5: A Day of InClass Simulation: MD of Carbon Nanostructures
15 Feb 2008  Teaching Materials  Contributor(s): Jeffrey C Grossman, Elif Ertekin
In this lecture we carry out simulations inclass, 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

BioMOCA Suite
14 Feb 2008  Tools  Contributor(s): David Papke, Reza Toghraee, Umberto Ravaioli, Ankit Raj
Simulates ion flow through a channel.
http://nanohub.org/resources/BMCsuite

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 nonderivative methods are discussed, as well as the...
http://nanohub.org/resources/4035

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 problemsolving techniques that are used to understand and predict properties of nanoscale systems. Emphasis will be placed...
http://nanohub.org/resources/3944

Dynamics on the Nanoscale: Timedomain ab initio studies of quantum dots, carbon nanotubes and moleculesemiconductor interfaces
01 Feb 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

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