
Addressing Molecular Dynamics Timescale Issues to Study Atomicscale Friction
12 Oct 2010   Contributor(s):: Ashlie Martini
This presentation will include an introduction to several accelerated molecular dynamics methods. However, particular focus will be given to parallel replica (ParRep) dynamics in which atomistic simulations are run parallel in time to extend their total duration. The ParRep method is based on...

Atomic Picture of Plastic Deformation in Metals: Overview Lecture
24 Jan 2010   Contributor(s):: Alejandro Strachan
The lecture describes the objectives of the learning module and provides the necessary background for the activities. We briefly discuss the following topics:mechanical response of macroscopic polycrystalline metals during tensile tests molecular dynamics simulations of materialsmechanical...

Atomic Picture of Plastic Deformation in Metals: Prelab Lecture
24 Jan 2010   Contributor(s):: Alejandro Strachan
This lecture provides a detailed description of the activities the students will perform in the lab. We present a tutorial with step by step instructions on how to run MD simulations using the nanoMaterials Simulation Toolkit.This lecture is part of the learning module Atomic Picture of Plastic...

Atomistic Modeling of the Mechanical Properties of Nanostructured Materials
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.

Atomistic Modeling: Past, Present, and Future, MGI, ICME, etc.
03 Nov 2015   Contributor(s):: Paul Saxe
I will present a perspective on atomistic modeling — tools using quantum methods such as DFT, as well as molecular dynamics and Monte Carlo methods based on forcefields — over the past 30 years or so. While we are all caught up in the present, it is important to remember and realize...

BNC Annual Research Review: An Introduction to PRISM and MEMS Simulation
04 Jun 2008   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 year.

Charge Transfer Across an Energy Transducing Integral Membrane Protein Complex
31 May 2007   Contributor(s):: William A. Cramer
The cytochrome bc complexes of the mitochondrial respiratory and photosynthetic electron transport chains are heterooligomeric integral membrane proteins. These proteins are responsible for most of the energy transduction and transport activities across biological membranes. Such complexes...

Computer Simulation of Nanoparticles, Viruses, and Electrical PowerGenerating Bacteria
20 Mar 2007 
Models of cells and nanometerscale biosystems are presented that clarify their physicochemical characteristics and allow for computer aided design of therapeutic and nanotechnical devices. Multiscale techniques are used to obtain rigorous, coarsegrained equations for the migration and...

Computing the Horribleness of Soft Condensed Matter
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...

Development of the ReaxFF reactive force fields and applications to combustion, catalysis and material failure
12 Sep 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...

Dynamics on the Nanoscale: Timedomain ab initio studies of quantum dots, carbon nanotubes and moleculesemiconductor interfaces
31 Jan 2008   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 the excitation, charge, spin, and vibrational dynamics in a variety of novel materials, including...

Energy and Nanoscience A More Perfect Union
27 Mar 2009   Contributor(s):: Mark Ratner
Huge problems of energy and sustainability confront the science/engineering community, mankind, and our planet. The energy problem comes in many dimensions, including supply, demand, conservation, transportation, and storage. This overview will stress the nature of these problems, and offer a...

Fouling Mechanisms in Yshaped Carbon Nanotubes
04 Apr 2007   Contributor(s):: Jason, 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 Yshaped carbon nanotube (Ytube). By changing the sizes of the...

Illinois Center for Cellular Mechanics: Discovery through the Computational Microscope
09 Feb 2009   Contributor(s):: Klaus Schulten
Computational MicroscopeAllatom molecular dynamics simulations have become increasingly popular as a toolto investigate protein function and dynamics. However, researchers are usuallyconcerned about the short time scales covered by simulations, the apparentimpossibility to model large and...

Illinois PHYS 466, Lecture 4: Molecular Dynamics
05 Feb 2009   Contributor(s):: David M. Ceperley
Molecular Dynamics What to choose in an integrator The Verlet algorithm Boundary Conditions in Space and time Reading assignment: Frenkel and Smit Chapter 4 Content: Characteristics of simulations The Verlet Algorithm Higher Order Methods? Quote from Berendsen Longterm stability of Verlet...

IMA 2013 UQ: Bayesian Calibration of Molecular Dynamics Simulations for Composite Materials Properties
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 aminecured epoxies. We construct an analytical approximation (i.e. a surrogate or emulator) of the simulations, treating the input...

IMA 2013 UQ: DFTbased Thermal Properties: Three Levels of Error Management
10 Feb 2014   Contributor(s):: Kurt Lejaeghere
It is often computationally expensive to predict finitetemperature properties of a crystal from densityfunctional theory (DFT). The temperaturedependent thermal expansion coefficient α, for example, is calculated from the phonon spectrum, and the melting temperature Tm can only be obtained...

Introduction to Molecular Dynamics
27 Aug 2015   Contributor(s):: Alejandro Strachan

Introduction to Molecular Dynamics
06 Apr 2015   Contributor(s):: Alejandro Strachan
This short presentation will describe the idea behind MD simulations and demonstrate its use in real applications.

Introduction: molecular dynamics simulations
09 Jan 2008   Contributor(s):: Alejandro Strachan
This short presentation will describe the idea behind MD simulations and demonstrate its use in real applications.