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Combustion in Nanobubbles (generated from water electrolysis)
Presentation Materials | 27 Aug 2018 | Contributor(s):: Shourya Jain, Li Qiao
A long-pursued goal, which is also a grand challenge, in nanoscience and nanotechnology is to create nanoscale devices, machines and motors that can do useful work. However, loyal to the scaling law, combustion would be impossible at nanoscale be- cause the heat loss would profoundly dominate...
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LAMMPS Structure Analysis Toolkit
Tools | 01 Aug 2018 | Contributor(s):: Nicholas J Finan, Saaketh Desai, Sam Reeve, Alejandro Strachan
Perform structural analysis on trajectories in LAMMPS dump format
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Nanosphere Electrostatics Lab
Tools | 22 May 2018 | Contributor(s):: JCS Kadupitiya, Nicholas Brunk, Sohile Ali, Fox, Geoffrey C., Vikram Jadhao
The Nanosphere Electrostatics Lab empowers users to simulate the self-assembly of ions near a spherically shaped nanoparticle, and extract the effective electrostatic properties.
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Focused Ion Beam Molecular Dynamics
Tools | 24 Apr 2018 | Contributor(s):: Joshua Michael Stout, Sixian Jia
3-D Molecular Dynamics Simulation of a Gallium FIB on Silicon
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Ions in Nanoconfinement
Tools | 22 Dec 2017 | Contributor(s):: Kadupitige Kadupitiya, Nasim Anousheh, Suresh Marru, Fox, Geoffrey C., Vikram Jadhao
The Ions in Nanoconfinement app empowers users to simulate ions confined between material surfaces that are nanometers apart, and extract the associated ionic structure.
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LAMMPS Data-File Generator
Tools | 01 Aug 2017 | Contributor(s):: Carlos Miguel Patiño, Lorena Alzate-Vargas, Chunyu Li, Benjamin P Haley, Alejandro Strachan
The LAMMPS Data-File Generator generates LAMMPS data files to perform molecular dynamics simulations in LAMMPS using Dreiding or PCFF force field energy terms
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Atomistic Polymer Workflow Notebook
Tools | 19 Oct 2017 | Contributor(s):: Benjamin P Haley
Run PolymerModeler and nuSIMM tools to create atomistic polymer systems
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THERMAL CNT
Tools | 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
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Applying Machine Learning to Computational Chemistry: Can We Predict Molecular Properties Faster without Compromising Accuracy?
Presentation Materials | 26 Jul 2017 | Contributor(s):: Hanjing Xu, Pradeep Kumar Gurunathan
Non-covalent interactions are crucial in analyzing protein folding and structure, function of DNA and RNA, structures of molecular crystals and aggregates, and many other processes in the fields of biology and chemistry. However, it is time and resource consuming to calculate such interactions...
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Structure-Force Field Generator for Molecular Dynamics Simulations
Online Presentations | 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...
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Multiscale Modelling of Nanoparticle Suspensions
Online Presentations | 09 Jun 2017 | Contributor(s):: Pietro Asinari
In the present work a multiscale modelling approach is implemented to relate the nanoscale phenomena to the macroscopic bulk properties of nano-suspensions. Specifically, Molecular Dynamics (MD) simulations and Brownian Dynamics (BD) are synergistically integrated to understand the mechanisms...
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Glass transition temperature notebook
Tools | 22 May 2017 | Contributor(s):: Benjamin P Haley, Lorena Alzate-Vargas
Calculate the glass transition temperature of an atomistic, amorphous system by running MD simulations in a notebook
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Vacancy Formation Energy with MD
Tools | 03 May 2017 | Contributor(s):: Sam Reeve, Alejandro Strachan
Calculate vacancy formation energy with molecular dynamics and various atomic interaction models
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PREPRINT: Molecular Modeling of the Microstructure Evolution during the Carbonization of PAN-Based Carbon Fibers
Papers | 23 Mar 2017 | Contributor(s):: Alejandro Strachan, Saaketh Desai
PREPRINTDevelopment of high strength carbon fibers (CFs) requires an understanding of the relationship between the processing conditions, microstructure and resulting properties. We developed a molecular model that combines kinetic Monte Carlo (KMC) and molecular dynamics (MD) techniques to...
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Introduction to Molecular Dynamics Showcase
Downloads | 10 Feb 2017 | Contributor(s):: Chen-Yu Li, Karl Steven Decker (editor), Aleksei Aksimentiev
In this tutorial, we will demonstrate how to use the MD showcase builder tool to create a showcase. We will start from the simplest example – creating a showcase from a PDB file – and move on to more complicated examples. We will also cover how to add a description, change...
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Molecular Dynamics (Mark Asta)
Presentation Materials | 13 Jan 2017
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Fundamentals of Phonon Transport Modeling L1: Introduction
Presentation Materials | 03 Jan 2017 | Contributor(s):: Alan McGaughey, Xiulin Ruan
Part of the 2016 IMECE Tutorial: Fundamentals of Phonon Transport Modeling: Formulation, Implementation, and Applications.
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Fundamentals of Phonon Transport Modeling L2: MD Simulation, Green Kubo, Direct Method
Presentation Materials | 03 Jan 2017 | Contributor(s):: Xiulin Ruan, Alan McGaughey
Part of the 2016 IMECE Tutorial: Fundamentals of Phonon Transport Modeling: Formulation, Implementation, and Applications.
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LAMMPS structure generator
Tools | 01 Nov 2016 | Contributor(s):: Benjamin P Haley
Convert a molecular structure file to a LAMMPS data file with force field parameters
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OpenKIM Explorer
Tools | 09 Jun 2015 | Contributor(s):: Dan Karls, Benjamin P Haley, Alejandro Strachan, Ryan S Elliott, Ellad B Tadmor
Run interatomic potentials from the OpenKIM Repository in LAMMPS