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Crack Propagation Simulation
Tools | 06 Aug 2014 | Contributor(s):: hojin kim, Nilofer Rajpurkar, Benjamin P Haley, Alejandro Strachan
Simulate crack propagations through materials under applied loads.
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Homework assignment: learning about elastic constants via molecular dynamics simulations
Teaching Materials | 17 Feb 2015 | Contributor(s):: Alejandro Strachan, David Ray Johnson
In this homework assignment students will use molecular dynamics to compute the elastic constants of metals using an embedded atom model to describe atomic interactions. They will deform a single crystal along different directions and obtain c11, c12 and c44 elastic constants from the...
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Melting via molecular dynamics simulations
Teaching Materials | 10 Mar 2015 | Contributor(s):: Alejandro Strachan
In this assignment you will use MD simulations to study melting in metals using the nanoMATERIALS simulation tool in nanoHUB. You will build a supercell and heat it up to study its melting. You can visualize the atomic configuration as the temperature is increased and after melting. From the...
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LAMMPS
Tools | 27 Mar 2014 | Contributor(s):: Benjamin P Haley
Run LAMMPS by uploading a data file and command script.
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IMA 2013 UQ: Bayesian Calibration of Molecular Dynamics Simulations for Composite Materials Properties
Online Presentations | 10 Feb 2014 | Contributor(s):: Paul N. Patrone
In this talk, I discuss ongoing research whose goal is to determine, via Bayesian inference, an ensemble of inputs that represents a class of commercially important amine-cured epoxies. We construct an analytical approximation (i.e. a surrogate or emulator) of the simulations, treating the input...
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IMA 2013 UQ: DFT-based Thermal Properties: Three Levels of Error Management
Online Presentations | 10 Feb 2014 | Contributor(s):: Kurt Lejaeghere
It is often computationally expensive to predict finite-temperature properties of a crystal from density-functional theory (DFT). The temperature-dependent thermal expansion coefficient α, for example, is calculated from the phonon spectrum, and the melting temperature Tm can only be obtained...
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Designing meaningful MD simulations: The lithiation of Silicon
Presentation Materials | 25 Mar 2014 | Contributor(s):: Maria C Rincon, hojin kim, David Guzman, Alejandro Strachan
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Molecular Dynamics Showcase
Tools | 06 Jul 2013 | Contributor(s):: Michael McLennan, Chen-Yu Li, john stone, Aleksei Aksimentiev, George A. Howlett
View interesting features of a molecular dynamics trajectory file
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[Illinois] Physics 550 Biomolecular Physics
Courses | 03 Sep 2013 | Contributor(s):: Klaus Schulten, Taekjip Ha
Physical concepts governing the structure and function of biological macromolecules; general properties, spatial structure, energy levels, dynamics and functions, and relation to other complex physical systems such as glasses; recent research in biomolecular physics;...
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Crystalline Cellulose - Atomistic Toolkit
Tools | 17 Jul 2013 | Contributor(s):: Mateo Gómez Zuluaga, Robert J. Moon, Fernando Luis Dri, Pablo Daniel Zavattieri
Crystalline Cellulose - Atomistic Toolkit
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[Illinois] Molecular and Multiscale Simulation Summer School
Series | 08 May 2013 | Contributor(s):: NanoBio Node
This Summer School will train students in molecular simulation and simulation at multiple time and length scales. Instruction will be provided on quantum Monte Carlo simulation, molecular dynamics, coarse-grained simulations, and multiscale simulations with opportunities for hands-on experience...
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Polymatic: A Simulated Polymerization Algorithm
Downloads | 13 Mar 2013 | Contributor(s):: Lauren Abbott, Coray Colina
Polymatic is a set of codes for structure generation of amorphous polymers by a simulated polymerization algorithm. The main task of Polymatic is to perform polymerization steps within a system based on a number of defined bonding criteria. It works in conjunction with a simulation package to...
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[Illinois] PHYS466 2013 Lecture 4: Molecular Dynamics I
Online Presentations | 03 Feb 2013 | Contributor(s):: David M. Ceperley
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[Illinois] Coarse-grained Simulation of Ion Channels
Online Presentations | 29 Dec 2012 | Contributor(s):: Umberto Ravaioli
This Summer School will train students in molecular simulation and simulation at multiple time and length scales. Instruction will be provided on quantum Monte Carlo simulation, molecular dynamics, coarse-grained simulations, and multiscale simulations with opportunities for hands-on experience...
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[Illinois] Beckman Graduate Seminar: Membrane Sculpting by F-BAR Domains Studied by Molecular Dynamics Simulations
Online Presentations | 17 Dec 2012 | Contributor(s):: Hang Yu
Interplay between cellular membranes and their peripheral proteins drives many processes in eukaryotic cells. Proteins of the Bin/Amphiphysin/Rvs (BAR) domain family, in particular, play a role in cellular morphogenesis, for example curving planar membranes into tubular membranes. However, it is...
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[Illinois] CSE Seminar Series: Advances in First-principles Computational Materials Science
Online Presentations | 20 Nov 2012 | Contributor(s):: Elif Ertekin
Title: Advances in first-principles computational materials science Subtitle: Things we can calculate now, that we couldn't when I was in grad school. The capability to rationally design new materials with tailored properties and functionality on a computer remains a grand challenge whose...
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Two-temperature Non-equilibrium Molecular Dynamics Simulator
Tools | 26 Jul 2012 | Contributor(s):: Yan Wang, Xin Jin, Xiulin Ruan
Simulate electron-phonon coupled thermal transport across metal-nonmetal interface
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[Illinois] Molecular Dynamics Software (NAMD)
Online Presentations | 19 Jun 2012 | Contributor(s):: Emad Tajkhorshid
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[Illinois] Coarse-grained / Multiscale Simulation Software (NAMD)
Online Presentations | 19 Jun 2012 | Contributor(s):: Emad Tajkhorshid
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[Illinois] Molecular Dynamics
Online Presentations | 19 Jun 2012 | Contributor(s):: Emad Tajkhorshid
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