
Forces That Govern Life: On the Way to Understanding Intermolecular Interactions
20 Jul 2017   Contributor(s):: Lyudmila V. Slipchenko
This talk will overview our recent work on the Effective Fragment Potential (EFP) method. EFP is a model potential designed for describing noncovalent interactions. The absence of fitted parameters and a natural partitioning of the interaction energy into Coulomb, polarization, dispersion, and...

Molecular Modeling and Electronic Structure Calculations
01 May 2017   Contributor(s):: George C. Schatz, Baudilio Tejerina, Shelby Hatch, Jennifer Roden
This is a purely computational project that is concerned with using the nanoHUB tool QCLab to create and optimize molecules, and to study their spectroscopic and structural properties. The molecules studied are generally small molecules of interest to atmospheric chemistry, however the tool can...

Atomistic Simulations of Materials Chemistry: From Nanoelectronics to Energetics
07 Apr 2015   Contributor(s):: Alejandro Strachan
Presentation slides with embedded videos are available for download. Please see the Support Docs tab.

[Illinois] PHYS466 2013: Atomic Scale Simulations
06 Feb 2013   Contributor(s):: David M. Ceperley
Application of Monte Carlo and Molecular Dynamics techniques in primarily classical simulations to understand and predict properties of microscopic systems in materials science, physics, biology, and chemistry. Numerical algorithms, connections between simulation results and real properties of...

Chemistry of Transition Metal Alloy Nanoparticles with Desired Phase Properties
20 Jun 2011   Contributor(s):: Lichang Wang
In this presentation, I will discuss the results of two alloy nanoparticles, PtAu and PtVFe. I will also present the synergetic results of unraveling PtVFe nanoparticles by coupling computational chemistry with experimental work.

ABINIT: FirstTime User Guide
09 Jun 2009   Contributor(s):: Benjamin P Haley
This firsttime user guide provides an introduction to using ABINIT on nanoHUB. We include a very brief summary of Density Functional Theory along with a tour of the Rappture interface. We discuss the default simulation (what happens if you don't change any inputs, and just hit "simulate") as...

Energy and Nanoscience A More Perfect Union
29 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...

Facio
25 May 2008   Contributor(s):: Masahiko Suenaga
Facio is a 3Dgraphics program for molecular modeling and visualization of quantum chemical calculations(GAMESS and Gaussian).It is a GUI for FMO (Fragment MO) calculation. Selected features include:(1) From a PDB file, create GAMESS/FMO input with 4 mouse clicks.(2) Manual fragmentation for the...

Northwestern University Initiative for Teaching Nanoscience
12 Aug 2008   Contributor(s):: Baudilio Tejerina
This package allows users to study and analyze of molecular properties using various electronic structure methods.

Theoretical Electron Density Visualizer
01 Jul 2008   Contributor(s):: Baudilio Tejerina
TEDVis calculates and displays 3D maps of molecular ED and its derivatives from the wave function.

Ionic Selectivity in Channels: complex biology created by the balance of simple physics
05 Jun 2008   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 control the movement of electric charge and current across biological membranes and so play a role in...

Dynamics of Quantum Fluids: Path integral and Semiclassical Methods
21 May 2008   Contributor(s):: Nancy Makri
The interplay of manybody nonlinear interactions and quantum mechanical effects such as zeropoint motion or identical particle exchange symmetries lead to intriguing phenomena in lowtemperature fluids, some of which remain poorly understood. Recent advances in theory and methodology have...

Computational Nanoscience, Lecture 20: Quantum Monte Carlo, part I
15 May 2008   Contributor(s):: Elif Ertekin, Jeffrey C Grossman
This lecture provides and introduction to Quantum Monte Carlo methods. We review the concept of electron correlation and introduce Variational Monte Carlo methods as an approach to going beyond the mean field approximation. We describe briefly the SlaterJastrow expansion of the wavefunction,...

Computational Nanoscience, Lecture 21: Quantum Monte Carlo, part II
15 May 2008   Contributor(s):: Jeffrey C Grossman, Elif Ertekin
This is our second lecture in a series on Quantum Monte Carlo methods. We describe the Diffusion Monte Carlo approach here, in which the approximation to the solution is not restricted by choice of a functional form for the wavefunction. The DMC approach is explained, and the fixed node...

Computational Nanoscience, PopQuiz
15 May 2008   Contributor(s):: Elif Ertekin, Jeffrey C Grossman
This quiz summarizes the most important concepts which have covered in class so far related to Molecular Dynamics, Classical Monte Carlo Methods, and Quantum Mechanical Methods.University of California, Berkeley

Computational Nanoscience, PopQuiz Solutions
15 May 2008   Contributor(s):: Elif Ertekin, Jeffrey C Grossman
The solutions to the popquiz are given in this handout.University of California, Berkeley

UV/Vis Spectra simulator
04 Mar 2008   Contributor(s):: Baudilio Tejerina
This tool computes molecular electronic spectra.

Calculating Resonances Using a Complex Absorbing Potential
13 Mar 2008   Contributor(s):: Robin Santra
The Siegert (or Gamow) wave function associated with a resonance state is exponentially divergent at large distances from the scattering target. A complex absorbing potential (CAP) provides a computationally simple and efficient technique for calculating the complex Siegert energy of a resonance...

CNDO/INDO
09 Oct 2007   Contributor(s):: Baudilio Tejerina, Jeff Reimers
Semiempirical Molecular Orbital calculations.

Computational Nanoscience, Lecture 4: Geometry Optimization and Seeing What You're Doing
13 Feb 2008   Contributor(s):: Jeffrey C Grossman, Elif Ertekin
In this lecture, we discuss various methods for finding the ground state structure of a given system by minimizing its energy. Derivative and nonderivative methods are discussed, as well as the importance of the starting guess and how to find or generate good initial structures. We also briefly...