Stretching simulation of an alpha-helical protein domain

10 Jan 2011 | Tools | Contributor(s): Markus Buehler, Justin Riley, Joo-Hyoung Lee, Jeffrey C Grossman

Uses steered molecular dynamics (SMD) to apply a tensile load to the ends of a molecule (such as an alpha-helical protein domain)

Crack Propagation Lab

06 Dec 2010 | Tools | Contributor(s): Markus Buehler, Justin Riley, Joo-Hyoung 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, Joo-Hyoung 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, Joo-Hyoung 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

a-Si:H Generator

Nano*High: Nature's Nasty Nanomachines: How Viruses Work, and How We Can Stop Them

27 Jan 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 nano-machines for millennia. Viruses are marvels of natural nano-engineering, but can pose a problem for human health. To combat these nano-machines, scientists are turning to recent developments …

Nano*High: X-rays, Lasers, and Molecular Movies

27 Jan 2010 | Online Presentations | Contributor(s): Roger W. Falcone

X-ray imaging is an excellent method to make visible what would normally be invisible - who hasn't had an X-ray at the doctor or dentist's office before? At the Lawrence Berkeley National Lab, the Advanced Light Source is a gigantic X-ray imaging machine. Dr. Roger Falcone discusses X-ray …

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 …

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 …

MIT Tools for Energy Conversion and Storage

13 Sep 2009 | Tools | Contributor(s): Jeffrey C Grossman, Joo-Hyoung Lee, Varadharajan Srinivasan, Alexander S McLeod, Lucas Wagner

Atomic-Scale Simulation Tools to Explore Energy Conversion and Storage Materials

Computational Nanoscience for Energy

10 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 cutting-edge simulation methods. This course …

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 Slater-Jastrow expansion of the wavefunction, and …

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 …

Computational Nanoscience, Pop-Quiz

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, Pop-Quiz Solutions

15 May 2008 | Teaching Materials | Contributor(s): Elif Ertekin, Jeffrey C Grossman

The solutions to the pop-quiz 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, particle-size distributions, the Lifshitz-Slyozov-Wagner model, thin film growth modes (Layer-by-Layer, Island growth, and Stranski-Krastanov), and …

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 …

Computational Nanoscience, Lecture 28: Wish-List, Reactions, and X-Rays.

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 chain-of-state methods such as the Nudged Elastic Band for determining energy barriers. The use of empirical, QM/MM methods are described. We …

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 In-Class 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 in-class simulations. Here we use the DFT for molecules and solids (Siesta) course toolkit. We cover a variety of solids, optimizing structures, testing k-point convergence, computing cohesive energies, and …

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, atomic-scale calculations of solids.

Computational Nanoscience, Lecture 16: More and Less than Hartree-Fock

30 Apr 2008 | Teaching Materials | Contributor(s): Jeffrey C Grossman, Elif Ertekin

In the lecture we discuss both techniques for going "beyond" Hartree-Fock in order to include correlation energy as well as techniques for capturing electronic structure effects while not having to solve the full Hartree-Fock equations (ie, semi-empirical methods). We also very briefly touch upon …