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Lecture 7: Molecular Dynamics Simulation: Calculating Non-bounded Interactions in Real Space
Online Presentations | 25 Jul 2024 | Contributor(s):: Ming Chen
This lecture discusses details about how to calculate non-bounded interactions in real space.
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Lecture 6: Molecular Dynamics Simulation: Common Force Field Forms
Online Presentations | 25 Jul 2024 | Contributor(s):: Ming Chen
This lecture introduce a type of approximated potential energy function: force fields. A set of common function forms used for simulating molecular systems are discussed.
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SMMDS Lectue 5: Potential Energy Function
Online Presentations | 19 Jul 2024 | Contributor(s):: Ming Chen
This lecture introduce the potential energy function used in Lagrangian mechanics and Hamiltonian machanics. Specifically, the lecture introduce how to use quantum mechanics to generate a potential energy function for molecules and materials.
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SMMDS Lecture 4: Hamiltonian Mechanics
Online Presentations | 19 Jul 2024 | Contributor(s):: Ming Chen
This lecture introduce a third formulism of classical mechanics: Hamiltonian Mechanics. Hamiltonian Mechanics provides a fundamental theory for molecular dynamics simulation.
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SMMDS Lecture 8: Molecular Dynamics Simulation - Coulomb Interaction and Ewald Summation
Online Presentations | 10 Jul 2024 | Contributor(s):: Ming Chen
This lecture introduce the detailed methods of calculating Coulomb interactions and the Ewald summation method.
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Introduction to Python Programming
Online Presentations | 10 Jul 2024 | Contributor(s):: Ashley Ringer McDonald, Jessica Nash, The Micro Nano Technology - Education Center
In this tutorial, students will be introduced to basic python programming skills which are useful in data analysis and machine learning applications.
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Theories in Statistical Mechanics and Molecular Dynamics Simulations
Courses | 20 Jun 2024 | Contributor(s):: Ming Chen
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SMMDS Lecture 9: Molecular Dynamics Simulation - Ewald Summation
Online Presentations | 20 Jun 2024 | Contributor(s):: Ming Chen
This lecture introduce the detailed theoretical background and implementation of Ewald Summation/Particle Mesh Ewald Summation.
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Building a nanoHUB Graphical Interface for Exploring Protein Dynamics and Spectroscopy: the PigmentHunter App
Online Presentations | 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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Integrating Programming and Cheminformatics into the Molecular Science Curriculum: Resources from the Molecular Sciences Software Institute using nanoHUB
Online Presentations | 31 Jan 2024 | Contributor(s):: Ashley Ringer McDonald
This presentation will describe open-source curriculum from the Molecular Sciences Software Institute (the MolSSI) to teach programming and cheminformatics using nanoHUB. The MolSSI is an NSF-funded institute that aims to improve software, education, and training in the computational molecular...
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Qiskit
Presentation Materials | 11 Dec 2023 | Contributor(s):: Manas Sajjan
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Olusegun Odunayo Felix
https://nanohub.org/members/410227
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NanoHUB Jupyter Notebooks for Research and Education
Online Presentations | 15 Jun 2023 | Contributor(s):: Michael Earl Reppert
Prof. Reppert presents and over view of using nanoHUB Jupyter Notebooks to create applications for teaching chemistry. Also presented is a summary of the notebooks developed by his group.
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A Summary of Chemistry Teaching Tools on nanoHUB Developed at Northwestern University
Online Presentations | 15 Jun 2023 | Contributor(s):: George C. Schatz
Prof. George Schatz presents a summary of tools used in teaching chemistry.
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Exploring Chemistry Resources in nanoHUB
Online Presentations | 15 Jun 2023 | Contributor(s):: Amy Joo
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Jeevan Patra
https://nanohub.org/members/392378
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Teaching and Learning with the MIT Atomic Scale Modeling Toolkit's Classical and Quantum Atomic Modeling Applications
Online Presentations | 23 Dec 2022 | Contributor(s):: Enrique Guerrero
We will perform molecular dynamics computations using LAMMPS, simple Monte Carlo simulations including the Ising model, and run quantum chemistry and density functional theory computations.
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Interactive Modeling of Materials with Density Functional Theory Using the Quantum ESPRESSO Interface within the MIT Atomic Scale Modeling Toolkit
Online Presentations | 22 Nov 2022 | Contributor(s):: Enrique Guerrero
We will explore the Quantum ESPRESSO interface within the MIT Atomic-Scale Modeling Toolkit with interactive examples. We will review the basics of density functional theory and then focus on the tool’s capabilities.
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A Guide to the MIT Atomic Scale Modeling Toolkit for nanoHUB.org
Teaching Materials | 22 Nov 2022 | Contributor(s):: Enrique Guerrero
This document is a guide to the Quantum ESPRESSO application within the >MIT Atomic Scale Modeling Toolkit The guide was designed to be presented as part II of the nanoHUB seminar “A condensed matter physics class and a Course-based Undergraduate Research Experience (CURE) with the MIT...
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Chemical and Physical Properties of Endohedrally Doped Nanodiamonds
Teaching Materials | 09 Nov 2022 | Contributor(s):: Tomekia Simeon
The semiempirical electronic structure Parametric Method 3 (PM3) at the nanoHUB.org website is introduced to the student in this assignment. In particular, this semiempirical method is applied to study dopant semiconductor materials intercalated in two types of nanodiamond (ND) complexes:...