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Addressing Molecular Dynamics Time-scale Issues to Study Atomic-scale Friction
12 Oct 2010 | | Contributor(s):: Ashlie Martini
This presentation will include an introduction to several accelerated molecular dynamics methods. However, particular focus will be given to parallel replica (ParRep) dynamics in which atomistic simulations are run parallel in time to extend their total duration. The ParRep method is based on the...
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Atomic Picture of Plastic Deformation in Metals: Overview Lecture
24 Jan 2010 | | Contributor(s):: Alejandro Strachan
The lecture describes the objectives of the learning module and provides the necessary background for the activities. We briefly discuss the following topics:mechanical response of macroscopic polycrystalline metals during tensile testsmolecular dynamics simulations of materialsmechanical...
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Atomic Picture of Plastic Deformation in Metals: Prelab Lecture
24 Jan 2010 | | Contributor(s):: Alejandro Strachan
This lecture provides a detailed description of the activities the students will perform in the lab. We present a tutorial with step by step instructions on how to run MD simulations using the nano-Materials Simulation Toolkit. This lecture is part of the learning module Atomic Picture of Plastic...
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Atomistic Modeling of the Mechanical Properties of Nanostructured Materials
16 Apr 2007 | | 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 and twisting properties are considered in this study.
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Atomistic Modeling: Past, Present, and Future, MGI, ICME, etc.
03 Nov 2015 | | Contributor(s):: Paul Saxe
I will present a perspective on atomistic modeling — tools using quantum methods such as DFT, as well as molecular dynamics and Monte Carlo methods based on forcefields — over the past 30 years or so. While we are all caught up in the present, it is important to remember and realize...
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BNC Annual Research Review: An Introduction to PRISM and MEMS Simulation
04 Jun 2008 | | 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 year.
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Building a nanoHUB Graphical Interface for Exploring Protein Dynamics and Spectroscopy: the PigmentHunter App
18 Apr 2024 | | Contributor(s):: Safa Ahad
Running and analyzing protein molecular dynamics (MD) simulations can be time consuming and tedious. In this webinar, we introduce PigmentHunter , an online nanoHUB tool that enables “point-and-click” MD-based simulation of excitonic spectra of chlorophyll proteins based on PDB...
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Charge Transfer Across an Energy Transducing Integral Membrane Protein Complex
31 May 2007 | | 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 the energy transduction and transport activities across biological membranes. Such complexes...
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Computer Simulation of Nanoparticles, Viruses, and Electrical Power-Generating Bacteria
20 Mar 2007 | | 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. Multiscale techniques are used to obtain rigorous, coarse-grained equations for the migration and...
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Computing the Horribleness of Soft Condensed Matter
19 Oct 2007 | | 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 simulations of liquid argon and liquid water in the 1960's, there was no quantitatively rigorous molecular...
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Deciphering Energy Transfer in Photosynthesis with Multiscale Molecular Modeling
07 Dec 2023 | | Contributor(s):: Lyudmila V. Slipchenko
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Designing Machine Learning Surrogates for Molecular Dynamics Simulations
25 Nov 2021 | | Contributor(s):: JCS Kadupitiya
Molecular dynamics (MD) simulations accelerated by high-performance computing (HPC) methods are powerful tools for investigating and extracting the microscopic mechanisms characterizing the properties of soft materials such as self-assembled nanoparticles, virus capsids, confined electrolytes,...
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Development of the ReaxFF reactive force fields and applications to combustion, catalysis and material failure
12 Sep 2011 | | Contributor(s):: Adri van Duin
This lecture will describe how the traditional, non-reactive FF-concept can be extended for application including reactive events by introducing bond order/bond distance concepts. Furthermore, it will address how these reactive force fields can be trained against QM-data, thus greatly enhancing...
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Dynamics on the Nanoscale: Time-domain ab initio studies of quantum dots, carbon nanotubes and molecule-semiconductor interfaces
31 Jan 2008 | | 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 the excitation, charge, spin, and vibrational dynamics in a variety of novel materials, including...
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Energy and Nanoscience A More Perfect Union
27 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 few...
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Exploring the Nano World: Building Nanoscale Structures with Polymer Modeler
14 Jul 2023 | | Contributor(s):: Tongtong Shen
In this talk, I will showcase how atomic-level simulations can lead to a more fundamental understanding of PAN crystal structures and guide you through an interactive Polymer Modeler powered by nanoHUB.
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Fouling Mechanisms in Y-shaped Carbon Nanotubes
04 Apr 2007 | | 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 developed. One possible filter is a Y-shaped carbon nanotube (Y-tube). By changing the sizes of the...
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Hands-on Unsupervised Learning using Dimensionality Reduction via Matrix Decomposition (1st offering)
29 Apr 2020 | | Contributor(s):: Michael N Sakano, Alejandro Strachan
This tutorial introduces unsupervised machine learning algorithms through dimensionality reduction via matrix decomposition techniques in the context of chemical decomposition of reactive materials in a Jupyter notebook on nanoHUB.org. The tool used in this demonstration...
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Hands-on Unsupervised Learning using Dimensionality Reduction via Matrix Decomposition (2nd offering)
30 Apr 2020 | | Contributor(s):: Michael N Sakano, Alejandro Strachan
This tutorial introduces unsupervised machine learning algorithms through dimensionality reduction via matrix decomposition techniques in the context of chemical decomposition of reactive materials in a Jupyter notebook on nanoHUB.org. The tool used in this demonstration...
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Illinois Center for Cellular Mechanics: Discovery through the Computational Microscope
11 Feb 2009 | | Contributor(s):: Klaus Schulten
Computational MicroscopeAll-atom molecular dynamics simulations have become increasingly popular as a toolto investigate protein function and dynamics. However, researchers are usuallyconcerned about the short time scales covered by simulations, the apparentimpossibility to model large and...