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Molecular dynamics is a form of computer simulation in which atoms and molecules are allowed to interact for a period of time by approximations of known physics, giving a view of the motion of the particles. This kind of simulation is frequently used in the study of proteins and biomolecules, as well as in materials science. More information on Molecular dynamics can be found here.
Running MD on the nanoHUB: The nano-MATERIALS Simulation Toolkit
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13 Nov 2008 | Online Presentations | Contributor(s): Alejandro Strachan
A quick demostration of the nanoHUB tool: nano-Materials Simulation Toolkit.
MSE 597G Lecture 5: Interatomic potentials II
Embedded atom model for metals, Three body terms for semiconductors: Stillinger-Weber, Electrostatics and Covalent interactions.
MSE 597G: An Introduction to Molecular Dynamics
MSE 597G Lecture 6: Interatomic potentials III
12 Nov 2008 | Online Presentations | Contributor(s): Alejandro Strachan
Reactive force fields, Parameterization of interatomic potentials
MSE 597G Lecture 7: Advanced Techniques for Molecular Dynamics Simulations
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
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 upcoming …
Dynamics on the Nanoscale: Time-domain ab initio studies of quantum dots, carbon nanotubes and molecule-semiconductor 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 …
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 …
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
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 …
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 | 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 of …
Atomistic Modeling of the Mechanical Properties of Nanostructured Materials
16 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 tensional …
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. …
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