Running MD on the nanoHUB: The nano-MATERIALS Simulation Toolkit

13 Nov 2008 | Online Presentations | Contributor(s): Alejandro Strachan

A quick demostration of the nanoHUB tool: nano-Materials Simulation Toolkit.

https://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: Stillinger-Weber, Electrostatics and Covalent interactions.

https://nanohub.org/resources/5777

MSE 597G: An Introduction to Molecular Dynamics

13 Nov 2008 | Online Presentations | Contributor(s): Alejandro Strachan

https://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

https://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.

https://nanohub.org/resources/5779

MSE 597G Lecture 2: Statistical Mechanics I

11 Nov 2008 | Online Presentations | Contributor(s): Alejandro Strachan

Basic physics: statistical mechanics.

https://nanohub.org/resources/5765

MSE 597G Lecture 1: Classical Mechanics

11 Nov 2008 | Online Presentations | Contributor(s): Alejandro Strachan

Basic physics: classical mechanics.

https://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 …

https://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 upcoming …

https://nanohub.org/resources/4717

Dynamics on the Nanoscale: Time-domain ab initio studies of quantum dots, carbon nanotubes and molecule-semiconductor 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 …

https://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 …

https://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 …

https://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 (where …

https://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.

https://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 …

https://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 hetero-oligomeric integral membrane proteins. These proteins are responsible for most of …

https://nanohub.org/resources/2679

Atomistic Modeling of the Mechanical Properties of Nanostructured Materials

16 Apr 2007 | Online Presentations | 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 …

https://nanohub.org/resources/2604

Orientational Dependence of Friction in Polyethylene

16 Apr 2007 | Online Presentations | Contributor(s): SeongJun Heo

The frictional properties of polyethylene polymer are investigated by using classical molecular dynamics simulations. Especially, the sliding orientational effect is considered in this study. The …

https://nanohub.org/resources/2601

Fouling Mechanisms in Y-shaped Carbon Nanotubes

04 Apr 2007 | Online Presentations | Contributor(s): Jason Myers, 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 …

https://nanohub.org/resources/2582

Computer Simulation of Nanoparticles, Viruses, and Electrical Power-Generating Bacteria

20 Mar 2007 | Online Presentations | Contributor(s): Peter J. Ortoleva

Models of cells and nanometer-scale biosystems are presented that clarify their physico-chemical characteristics and allow for computer- aided design of therapeutic and nanotechnical devices. …

https://nanohub.org/resources/2485