
Molecular Dynamics Showcase
06 Jul 2013   Contributor(s):: Michael McLennan, ChenYu Li, john stone, Aleksei Aksimentiev, George A. Howlett
View interesting features of a molecular dynamics trajectory file

[Illinois] Physics 550 Biomolecular Physics
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; physical...

Crystalline Cellulose  Atomistic Toolkit
17 Jul 2013   Contributor(s):: Mateo Gómez Zuluaga, Robert J. Moon, Fernando Luis Dri, Pablo Daniel Zavattieri
Crystalline Cellulose  Atomistic Toolkit

Polymatic: A Simulated Polymerization Algorithm
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...

[Illinois] PHYS466 2013 Lecture 4: Molecular Dynamics I
03 Feb 2013   Contributor(s):: David M. Ceperley

[Illinois] Beckman Graduate Seminar: Membrane Sculpting by FBAR Domains Studied by Molecular Dynamics Simulations
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...

[Illinois] CSE Seminar Series: Advances in Firstprinciples Computational Materials Science
20 Nov 2012   Contributor(s):: Elif Ertekin
Title: Advances in firstprinciples computational materials scienceSubtitle: 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 success...

[Illinois] Molecular Dynamics Software (NAMD)
19 Jun 2012   Contributor(s):: Emad Tajkhorshid
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[Illinois] Molecular Dynamics
19 Jun 2012   Contributor(s):: Emad Tajkhorshid
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MD Simulations of Gas Flows in NanoChannels and Interface Thermal Resistance Between Simple Liquids and Solids
30 May 2012   Contributor(s):: Ali Beskok
This talk focuses on our group’s recent research on molecular dynamics simulations of gas flows in nanoscale confined geometries, and interface thermal resistance between simple liquids and solids. Gas flow research demonstrates the importance of wall force field effects that penetrate...

Atomistic Material Science
25 Aug 2011   Contributor(s):: Alejandro Strachan
This course introduces first principles electronic structure calculations of materials properties and the concept of molecular dynamics (MD) simulations of materials focusing on the physics and approximations underlying the simulations and interpretation of their results.

Tutorial 1: Atomistic Material Science  ab initio simulations of materials
25 Aug 2011   Contributor(s):: Alejandro Strachan
This lecture introduces first principles electronic structure calculations of materials properties.It describes the approximations made to the manybody Schrodinger equation in Hartree Fock and Density Functional Theory and numerical approximations used in computer simulations.

Tutorial 2: Atomistic Material Science  Molecular Dynamics simulations of materials
25 Aug 2011   Contributor(s):: Alejandro Strachan
This lecture introduces the concept of molecular dynamics (MD) simulations of materials focusing on the physics and approximations underlying the simulations and interpretation of their results.

2d Ideal Gas Molecular Dynamics
01 Sep 2011   Contributor(s):: Terence Musho, Greg Walker
Simulation of a 2d molecular gas with specified temperature boundary conditions

1D Chain Dispersions
01 Sep 2011   Contributor(s):: Nicholas Roberts, Greg Walker
1D Chain of atoms, bases and layers to produce phonon dispersion

Temperature Accelerated Dynamics
03 May 2011   Contributor(s):: Justin Riley, Markus J. Buehler
Simulate temperature accelerated dynamics

Development of the ReaxFF reactive force fields and applications to combustion, catalysis and material failure
29 Jul 2011   Contributor(s):: Adri van Duin
This lecture will describe how the traditional, nonreactive FFconcept can be extended for application including reactive events by introducing bond order/bond distance concepts. Furthermore, it will address how these reactive force fields can be trained against QMdata, thus greatly enhancing...

nanoMATERIALS nanoscale heat transport
03 Nov 2010   Contributor(s):: KengHua Lin, Sean Sullivan, Mathew Joseph Cherukara, Alejandro Strachan, Tianli Feng, Xiulin Ruan, Bo Qiu
Nonequilibrium MD simulations of heat transport in nanomaterials

MiniMol: Minimal Molecular Simulation Tool
18 Mar 2011   Contributor(s):: Ellad B Tadmor, Ron Earle Miller, Ryan S Elliott
Perform simple molecular dynamics and statics simulations.

Atomic Picture of Plastic Deformation in Metals via Online Molecular Dynamics Simulations
18 Dec 2009   Contributor(s):: Alejandro Strachan
The main goal of this learning module is to introduce students to the atomiclevel processes responsible for plastic deformation in crystalline metals and help them develop a more intuitive understanding of how materials work at molecular scales. The module consists of: i) Two introductory...