
Stretching simulation of an alphahelical protein domain
10 Jan 2011  Tools  Contributor(s): Markus Buehler, Justin Riley, JooHyoung Lee, Jeffrey C Grossman
Uses steered molecular dynamics (SMD) to apply a tensile load to the ends of a molecule (such as an alphahelical protein domain)

Crack Propagation Lab
06 Dec 2010  Tools  Contributor(s): Markus Buehler, Justin Riley, JooHyoung Lee, Jeffrey C Grossman
Models supersonic crack propagation in a 2D triangular lattice

Nanowire Tensile Deformation Lab
17 Aug 2010  Tools  Contributor(s): Markus Buehler, Justin Riley, JooHyoung Lee, Jeffrey C Grossman
Simulates tensile deformation of a copper nanowire

Stretching Simulation of FCC Crystal
18 Nov 2010  Tools  Contributor(s): Markus Buehler, Justin Riley, JooHyoung Lee, Jeffrey C Grossman
This tool simulates a continuous expansion of an FCC crystal while measuring the energy, stresses, etc

Amorphous Silicon Generator
21 Oct 2010  Tools  Contributor(s): Eric Carl Johlin, Lucas Wagner, Jeffrey C Grossman, Justin Riley, David Strubbe
aSi:H Generator

Nano*High: Nature's Nasty Nanomachines: How Viruses Work, and How We Can Stop Them
25 Sep 2010  Online Presentations  Contributor(s): Carolyn R. Bertozzi
The birth and growth of nanotechnology is only a few decades old, whereas Nature has been building nanomachines for millennia. Viruses are marvels of natural nanoengineering, but can pose a problem for human health. To combat these nanomachines, scientists are turning to recent developments in nanotechnology to prevent infection and cure disease.

Nano*High: Xrays, Lasers, and Molecular Movies
25 Sep 2010  Online Presentations  Contributor(s): Roger W. Falcone
Xray imaging is an excellent method to make visible what would normally be invisible  who hasn't had an Xray at the doctor or dentist's office before? At the Lawrence Berkeley National Lab, the Advanced Light Source is a gigantic Xray imaging machine. Dr. Roger Falcone discusses Xray tomography, is a method that uses these Xrays to produce threedimensional images and movies of the smallest ...

Nanostructured Optoelectronics Toolbox
19 Oct 2009  Tools  Contributor(s): Ian Michael Rousseau, Jeffrey C Grossman, Vladimir Bulovic, Polina Anikeeva
Examine charge and exciton transport in nanostructured optoelectonic devices

Nano*High: Nanoscience for High School Students
02 Feb 2010  Series  Contributor(s): Alexander S McLeod, Jeffrey B. Neaton, Jeffrey C Grossman
The Materials Sciences Division at the University of California's Lawrence Berkeley National Laboratory invites you and your students to Nano*High, a series of free Saturday morning lectures by UC Berkeley professors and LBNL senior scientists conducting research from nanoscience to molecular medicine, and climate change to astrophysics. 20092010 will be our seventh year of Nano*High. Last year over 900 students and their teachers attended at least one talk. Nano*High talks are aimed at all ...

nanoHUB PhotoVoltaics Reference Zone
27 Jan 2010  Teaching Materials  Contributor(s): Alexander S McLeod, Jeffrey B. Neaton, Jeffrey C Grossman
Need information on the science of photovoltaics and solar cell technology? Find it here!
The nanoHUB PhotoVoltaics Reference Zone is the right destination for finding general information about photovoltaic solar cell science and technology, as well as for viewing news articles and getting access to some great PV resource links. Sponsored by the nanoHUB and the Center of Integrated Nanomechanical Systems (COINS)  a joint collaboration for nanoscience education and outreach among UC Berkeley, …

MIT Tools for Energy Conversion and Storage
13 Sep 2009  Tools  Contributor(s): Jeffrey C Grossman, JooHyoung Lee, Varadharajan Srinivasan, Alexander S McLeod, Lucas Wagner
AtomicScale Simulation Tools to Explore Energy Conversion and Storage Materials

Computational Nanoscience for Energy
15 Sep 2009  Teaching Materials  Contributor(s): Jeffrey C Grossman, Alexander S McLeod
Materials for energy conversion and storage can be greatly improved by taking advantage of unique effects that occur at the nanoscale. In many cases, these improvements are due to fundamental microscopic mechanisms that can be understood and predicted by cuttingedge simulation methods. This course will provide students with the fundamentals of computational problemsolving techniques that are used to elucidate the atomicscale behavior of energy conversion and storage nanomaterials.
Jeffrey ...

SIESTA
05 Mar 2008  Tools  Contributor(s): Lucas Wagner, Jeffrey C Grossman, Joe Ringgenberg, daniel richards, Alexander S McLeod, Eric Isaacs, Jeffrey B. Neaton
Use SIESTA to perform electronic structure calculations

CNT Heterojunction Modeler
20 Mar 2008  Tools  Contributor(s): Joe Ringgenberg, Joydeep Bhattacharjee, Jeffrey B. Neaton, Jeffrey C Grossman
Study the structure and electronic properties of carbon nanotubes with linear heterojunctions.

Computational Nanoscience, Lecture 20: Quantum Monte Carlo, part I
15 May 2008  Teaching Materials  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, and show how we can recover the some of the correlation energy using a variational approach to optimizing this form of the wavefunction.Lucas K. Wagner
University of California, Berkeley

Computational Nanoscience, Lecture 21: Quantum Monte Carlo, part II
15 May 2008  Teaching Materials  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 approximation is described as well. We conclude with a few examples demonstrating the application of VMC and DMC to methane and ethane.Lucas K. Wagner
University of California, Berkeley

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

Computational Nanoscience, Lecture 23: Modeling Morphological Evolution
15 May 2008  Teaching Materials  Contributor(s): Elif Ertekin, Jeffrey C Grossman
In this lecture, we present an introduction to modeling the morphological evolution of materials systems. We introduce concepts of coarsening, particlesize distributions, the LifshitzSlyozovWagner model, thin film growth modes (LayerbyLayer, Island growth, and StranskiKrastanov), and morphological instabilities. An introduction to phase field modeling, diffuse interface models, and CahnHilliard and CahnAllen analysis is presented. We conclude with some examples of phase field methods ...

Computational Nanoscience, Lecture 27: Simulating Water and Examples in Computational Biology
16 May 2008  Teaching Materials  Contributor(s): Elif Ertekin, Jeffrey C Grossman
In this lecture, we describe the challenges in simulating water and introduce both explicit and implicit approaches. We also briefly describe protein structure, the Levinthal paradox, and simulations of proteins and protein structure using First Principles approaches and Monte Carlo sampling.University of California, Berkeley

Computational Nanoscience, Lecture 28: WishList, Reactions, and XRays.
16 May 2008  Teaching Materials  Contributor(s): Jeffrey C Grossman, Elif Ertekin
After a brief interlude for class feedback on the course content and suggestions for next semester, we turn to modeling chemical reactions. We describe chainofstate methods such as the Nudged Elastic Band for determining energy barriers. The use of empirical, QM/MM methods are described. We give some examples of Hartree Fock and DFT methods applied to determining dissociation energies, and show where these methods can fail.University of California, Berkeley

Computational Nanoscience, Lecture 29: Verification, Validation, and Some Examples
16 May 2008  Teaching Materials  Contributor(s): Jeffrey C Grossman, Elif Ertekin
We conclude our course with a lecture of verification, and validation. We describe what each of these terms means, and provide a few recent examples of nanoscale simulation in terms of these concepts.University of California, Berkeley

Computational Nanoscience, Lecture 19: Band Structure and Some InClass Simulation: DFT for Solids
30 Apr 2008  Teaching Materials  Contributor(s): Jeffrey C Grossman, Elif Ertekin
In this class we briefly review band structures and then spend most of our class on inclass simulations. Here we use the DFT for molecules and solids (Siesta) course toolkit. We cover a variety of solids, optimizing structures, testing kpoint convergence, computing cohesive energies, and computing band structures and density of states.

Computational Nanoscience, Lecture 18.5: A Little More, and Lots of Repetition, on Solids
30 Apr 2008  Teaching Materials  Contributor(s): Jeffrey C Grossman, Elif Ertekin
Here we go over again some of the basics that one needs to know and understand in order to carry out electronic structure, atomicscale calculations of solids.

Computational Nanoscience, Lecture 16: More and Less than HartreeFock
30 Apr 2008  Teaching Materials  Contributor(s): Jeffrey C Grossman, Elif Ertekin
In the lecture we discuss both techniques for going "beyond" HartreeFock in order to include correlation energy as well as techniques for capturing electronic structure effects while not having to solve the full HartreeFock equations (ie, semiempirical methods). We also very briefly touch upon the pseudopotential approximation.