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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.
Atomic Picture of Plastic Deformation in Metals: Lab Assignment Handout
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19 Jan 2010 | Teaching Materials | Contributor(s): Alejandro Strachan
In this lab students will perform online molecular dynamics (MD) simulations of metallic nanowires deformed uniaxially and analyze the results...
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 …
Computational Nanoscience, Homework Assignment 2: Molecular Dynamics Simulation of a Lennard-Jones Liquid
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 identical …
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 including …
Computational Nanoscience, Lecture 5: A Day of In-Class Simulation: MD of Carbon Nanostructures
In this lecture we carry out simulations in-class, with guidance from the instructors. We use the LAMMPS tool (within the nanoHUB simulation toolkit for this course). Examples include calculating …
Computational Nanoscience, Lecture 4: Geometry Optimization and Seeing What You're Doing
In this lecture, we discuss various methods for finding the ground state structure of a given system by minimizing its energy. Derivative and non-derivative methods are discussed, as well as the …
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 considerations …
REBO Nanofluidics Exercise
10 May 2006 | Teaching Materials | 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 …
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