
Illinois PHYS 466, Lecture 4: Molecular Dynamics
05 Feb 2009  Online Presentations  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:
...
http://nanohub.org/resources/6239

Nanoparticle and Colloidal Simulations with Molecular Dynamics
05 Dec 2008  Online Presentations  Contributor(s): Steve Plimpton
Modeling nanoparticle or colloidal systems in a molecular dynamics (MD) code requires coarsegraining on several levels to achieve meaningful simulation times for study of rheological and other...
http://nanohub.org/resources/5668

MSE 597G Lecture 4: Interatomic potentials I
14 Nov 2008  Online Presentations  Contributor(s): Alejandro Strachan
Interatomic potentials: pairwise potentials.
http://nanohub.org/resources/5776

MSE 597G Lecture 3: Statistical Mechanics II
14 Nov 2008  Online Presentations  Contributor(s): Alejandro Strachan
Basic physics: statistical mechanics, Algorithms: Integrating the equations of motion.
http://nanohub.org/resources/5775

Running MD on the nanoHUB: The nanoMATERIALS Simulation Toolkit
13 Nov 2008  Online Presentations  Contributor(s): Alejandro Strachan
A quick demostration of the nanoHUB tool: nanoMaterials Simulation Toolkit.
http://nanohub.org/resources/5843

MSE 597G Lecture 5: Interatomic potentials II
13 Nov 2008  Online Presentations  Contributor(s): Alejandro Strachan
Embedded atom model for metals,
Three body terms for semiconductors: StillingerWeber,
Electrostatics and Covalent interactions.
http://nanohub.org/resources/5777

MSE 597G: An Introduction to Molecular Dynamics
13 Nov 2008  Online Presentations  Contributor(s): Alejandro Strachan
http://nanohub.org/resources/5760

MSE 597G Lecture 6: Interatomic potentials III
12 Nov 2008  Online Presentations  Contributor(s): Alejandro Strachan
Reactive force fields,
Parameterization of interatomic potentials
http://nanohub.org/resources/5778

MSE 597G Lecture 7: Advanced Techniques for Molecular Dynamics Simulations
12 Nov 2008  Online Presentations  Contributor(s): Alejandro Strachan
Thermostats and barostats,
Linear methods for energy and force calculations,
Coarse graining or mesodynamics,
Validation and Verification.
http://nanohub.org/resources/5779

MSE 597G Lecture 2: Statistical Mechanics I
11 Nov 2008  Online Presentations  Contributor(s): Alejandro Strachan
Basic physics: statistical mechanics.
http://nanohub.org/resources/5765

MSE 597G Lecture 1: Classical Mechanics
11 Nov 2008  Online Presentations  Contributor(s): Alejandro Strachan
Basic physics: classical mechanics
http://nanohub.org/resources/5507

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...
http://nanohub.org/resources/4726

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...
http://nanohub.org/resources/4717

Dynamics on the Nanoscale: Timedomain ab initio studies of quantum dots, carbon nanotubes and moleculesemiconductor 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...
http://nanohub.org/resources/3951

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...
http://nanohub.org/resources/3678

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...
http://nanohub.org/resources/3677

Lecture 3: simulation details and coarse grain approaches
09 Jan 2008  Online Presentations  Contributor(s): Alejandro Strachan
The last
presentation will describe simulation techniques to simulate materials
under isothermal and isobaric conditions. We will also describe coarse
grain or mesodynamical approaches...
http://nanohub.org/resources/3679

Introduction: molecular dynamics simulations
09 Jan 2008  Online Presentations  Contributor(s): Alejandro Strachan
This short presentation
will describe the idea behind MD simulations and demonstrate its use in
real applications.
http://nanohub.org/resources/3676

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...
http://nanohub.org/resources/3424

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 heterooligomeric integral membrane proteins. These proteins are responsible for most...
http://nanohub.org/resources/2679