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Ripples and Warping of Graphene: A Theoretical Study
08 Jun 2010 | | Contributor(s):: Umesh V. Waghmare
We use first-principles density functional theory based analysis to understand formation of ripples in graphene and related 2-D materials. For an infinite graphene, we show that ripples are linked with a low energy branch of phonons that exhibits quadratic dispersion at long wave-lengths. Many...
Running MD on the nanoHUB: The nano-MATERIALS Simulation Toolkit
out of 5 stars
13 Nov 2008 | | Contributor(s):: Alejandro Strachan
A quick demostration of the nanoHUB tool: nano-Materials Simulation Toolkit.
Short Course on Molecular Dynamics Simulation
13 Oct 2009 | | Contributor(s):: Ashlie Martini
This set of ten presentations accompanied a graduate level course on Molecular Dynamics simulation. The specific objective of the course (and the presentations) is to provide:1. Awareness of the opportunities and limitations of Molecular Dynamics as a tool for scientific and engineering...
Structural Analysis for Molecular Dynamics Trajectories
03 Mar 2019 | | Contributor(s):: Nicholas J Finan, Saaketh Desai, Sam Reeve, Alejandro Strachan
This tool reads in LAMMPS trajectories and performs the following analysis: Radial Distribution Function (RDF), X-Ray Diffraction (XRD), Vibrational Density of States, and (More to Come!). By default the tool requires trajectory files to be input by the user however there are some...
Structure and Ion Permeation of the Gramicidin Channel using Molecular Dynamics
12 Apr 2004 | | Contributor(s):: Toby Allen
Molecular dynamics (MD) has become an essential tool for obtaining microscopic insight into biological function. The gramicidin channel as an excellent benchmark system for this purpose. Using extensive MD simulations with explicit solvent and membrane, we determine the backbone structure and...
Structure-Force Field Generator for Molecular Dynamics Simulations
01 Aug 2017 | | Contributor(s):: Carlos Miguel Patiño, Lorena Alzate-Vargas, Alejandro Strachan
Atomistic and molecular simulations have become an important research field due to the progress made in computer performance and the necessity of new and improved materials. Despite this, first principle simulations of large molecules are still not possible because the high computational time and...
Temperature Accelerated Dynamics
03 May 2011 | | Contributor(s):: Justin Riley, Markus J. Buehler
Simulate temperature accelerated dynamics
23 May 2017 | | Contributor(s):: Luca Bergamasco, Matteo Fasano, Eliodoro Chiavazzo, Pietro Asinari, Annalisa Cardellini, Matteo Morciano
Compute thermal conductivity of single-walled carbon nano-tubes via NEMD method
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 many-body 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
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.
Tutorial 3: Materials Simulation by First-Principles Density Functional Theory
14 Sep 2010 | | Contributor(s):: Umesh V. Waghmare
This two-part lecture will provide an introduction to first-principles density functional theory based methods for simulation of materials, with a focus on determination of interatomic force constants and vibrational spectra of nano- structures and extended periodic materials.
Tutorial 3b: Materials Simulation by First-Principles Density Functional Theory II
09 Sep 2010 | | Contributor(s):: Umesh V. Waghmare
Vacancy Formation Energy with MD
03 May 2017 | | Contributor(s):: Sam Reeve, Alejandro Strachan
Calculate vacancy formation energy with molecular dynamics and various atomic interaction models
[Illinois] Beckman Graduate Seminar: Membrane Sculpting by F-BAR 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 First-principles Computational Materials Science
20 Nov 2012 | | Contributor(s):: Elif Ertekin
Title: Advances in first-principles 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
19 Jun 2012 | | Contributor(s):: Emad Tajkhorshid
[Illinois] Molecular Dynamics Software (NAMD)
[Illinois] PHYS466 2013 Lecture 4: Molecular Dynamics I
03 Feb 2013 | | Contributor(s):: David M. Ceperley
[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...