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MSE 597G Lecture 7: Advanced Techniques for Molecular Dynamics Simulations
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12 Nov 2008 | | 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 | | 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
05 Jun 2008 | | 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 control the movement of electric charge and current across biological membranes and so play a role in biology...
BNC Annual Research Review: An Introduction to PRISM and MEMS Simulation
04 Jun 2008 | | 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 upcoming year.
Dynamics on the Nanoscale: Time-domain ab initio studies of quantum dots, carbon nanotubes and molecule-semiconductor interfaces
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...
Lecture 2: total energy and force calculations
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...
Lecture 1: the theory behind molecular dynamics
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.
Lecture 3: simulation details and coarse grain approaches
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...
Introduction: molecular dynamics simulations
This short presentation will describe the idea behind MD simulations and demonstrate its use in real applications.
Computing the Horribleness of Soft Condensed Matter
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...
Charge Transfer Across an Energy Transducing Integral Membrane Protein Complex
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...
Atomistic Modeling of the Mechanical Properties of Nanostructured Materials
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.
Orientational Dependence of Friction in Polyethylene
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).
Fouling Mechanisms in Y-shaped Carbon Nanotubes
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...
Computer Simulation of Nanoparticles, Viruses, and Electrical Power-Generating Bacteria
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...
Materials strength: does size matter? nanoMATERIALS simulation toolkit tutorial
01 Feb 2007 | | 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 new phenomena that arises in nanoscale and nanostructured materials and result in their unique...
Potassium Channels: Conduction, Selectivity, Blockage, Inactivation, and Gating
03 Nov 2006 | | Contributor(s):: Benoit Roux, NCN at Northwestern University
The determination of the structure of the KcsA K+ channel fromStreptomyces lividan has made it possible to investigate the functionof a biological channel at the atomic level. Because of its structuralsimilarity with eukaryotic K-channels, investigations of KcsA areexpected to help understand a...
15 Jun 2004 | | Contributor(s):: Susan Sinnott
Structure and Ion Permeation of the Gramicidin Channel using Molecular Dynamics
12 Apr 2004 | | 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 extensive MD simulations with explicit solvent and membrane, we determine the backbone structure and...