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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...
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Materials strength: does size matter? nanoMATERIALS simulation toolkit tutorial
Online Presentations | 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...
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Potassium Channels: Conduction, Selectivity, Blockage, Inactivation, and Gating
Online Presentations | 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...
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REBO
Tools | 24 Jul 2006 | Contributor(s):: Wen-Dung Hsu, SeongJun Heo, jing xu, Susan Sinnott
Reactive Empirical Bond-Order (REBO) potential is a many-body expression optimized for modeling covalently bonded materials, such as carbon and silicon, in large-scale atomistic simulations
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Micelle
Tools | 24 Jul 2006 | Contributor(s):: Kunal Shah, Patrick Chiu, jing xu, Susan Sinnott
Parallel Molecular Dynamics (MD) code that models surfactant structures in water and at liquid/solid interfaces.
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Molecular Workbench: An Interface to the Molecular World
Downloads | 25 Jun 2006 | Contributor(s):: Charles Xie
The Molecular Workbench software is a free, open-source modeling and authoring program specifically designed for use in science education. Powered by a set of real-time molecular simulation engines that compute and visualize the motion of particles interacting through force fields, in both 2D and...
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nano-Materials Simulation Toolkit
Tools | 08 Aug 2006 | Contributor(s):: Alejandro Strachan, Amritanshu Palaria, Ya Zhou, Janam Jhaveri
Molecular Dynamics simulations of nano-materials
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Nanofluidics
Online Presentations | 15 Jun 2004 | Contributor(s):: Susan Sinnott
Nanofluidics
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REBO Nanofluidics Exercise
Teaching Materials | 10 May 2006 | Contributor(s):: Susan Sinnott, Hetal Patel
Nanofluidics exercise showing the variation of energy and position of methane and butane molecules flowing through an opened carbon nanotube as the system temperature and the length of the nanotube are varied.
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Structure and Ion Permeation of the Gramicidin Channel using Molecular Dynamics
Online Presentations | 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...