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MSE 597G Lecture 7: Advanced Techniques for Molecular Dynamics Simulations
0.0 out of 5 stars
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.
MSE 597G Lecture 2: Statistical Mechanics I
11 Nov 2008 | Online Presentations | Contributor(s): Alejandro Strachan
Basic physics: statistical mechanics.
MSE 597G Lecture 1: Classical Mechanics
Basic physics: classical mechanics
Ionic Selectivity in Channels: complex biology created by the balance of simple physics
3.5 out of 5 stars
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...
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...
Dynamics on the Nanoscale: Time-domain ab initio studies of quantum dots, carbon nanotubes and molecule-semiconductor 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...
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
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...
Lecture 3: simulation details and coarse grain approaches
presentation will describe simulation techniques to simulate materials
under isothermal and isobaric conditions. We will also describe coarse
grain or mesodynamical approaches...
Introduction: molecular dynamics simulations
This short presentation
will describe the idea behind MD simulations and demonstrate its use in
Computing the Horribleness of Soft Condensed Matter
5.0 out of 5 stars
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...
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...
Atomistic Modeling of the Mechanical Properties of Nanostructured Materials
23 Apr 2007 | Online Presentations | 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...
Orientational Dependence of Friction in Polyethylene
16 Apr 2007 | Online Presentations | 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...
Fouling Mechanisms in Y-shaped Carbon Nanotubes
04 Apr 2007 | Online Presentations | 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...
Computer Simulation of Nanoparticles, Viruses, and Electrical Power-Generating Bacteria
20 Mar 2007 | Online Presentations | 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....
Materials strength: does size matter? nanoMATERIALS simulation toolkit tutorial
01 Feb 2007 | Online Presentations | Contributor(s): Alejandro Strachan
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...
Potassium Channels: Conduction, Selectivity, Blockage, Inactivation, and Gating
05 Nov 2006 | Online Presentations | Contributor(s): Benoit Roux, NCN SLC@Northwestern
The determination of the structure of the KcsA K+ channel from
Streptomyces lividan has made it possible to investigate the function
of a biological channel at the atomic level. Because of its...
20 Aug 2005 | Online Presentations | Contributor(s): Susan Sinnott
Structure and Ion Permeation of the Gramicidin Channel using Molecular Dynamics
12 Apr 2004 | Online Presentations | Contributor(s): Toby Allen
Molecular dynamics (MD) has become an essential tool for obtaining microscopic insight into biological function. The gramicidin channel as an excellent benchmark system for this purpose. Using...