
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
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

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

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

Computational Nanoscience, Lecture 5: A Day of InClass Simulation: MD of Carbon Nanostructures
13 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
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

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
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

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

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

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

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

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

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

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

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

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 heterooligomeric integral membrane proteins. These proteins are responsible for most...
http://nanohub.org/resources/2679