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Designing Machine Learning Surrogates for Molecular Dynamics Simulations
Online Presentations | 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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Agent Based Active Matter Simulations with Mechanica
Online Presentations | 14 Nov 2021 | Contributor(s):: Somogyi, Andy T
Mechanica is an interactive mesh-free, chemistry and biology simulation environment, with an emphasis towards enabling users to model and simulate complex sub-cellular and cellular biological physics problems. Mechanica is designed first and foremost to enable users to work interactively...
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Deep Learning for Time Series Illustrated by COVID-19 Infection Studies
Online Presentations | 04 Feb 2021 | Contributor(s):: Geoffrey C. Fox
We show that one can study several sets of sequences or time-series in terms of an underlying evolution operator which can be learned with a deep learning network.
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How Simple Cell-Cell Interactions Lead to Complex Multicellular Dynamics
Online Presentations | 04 Feb 2021 | Contributor(s):: Paul Macklin
In this talk, we use agent-based simulation models to simulate (1) individual cell behaviors, (2) cell-cell interactions, and (3) cell-environment interactions to show how simple rules can give rise to complex multicellular phenomena. We showcase and explore free, interactive online tools to...
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Cancer Games: Interactive Simulation of the Effect of Resource Limitation on Cancer Somatic Evolution using nanoHUB CompuCell3D
Online Presentations | 04 Feb 2021 | Contributor(s):: James A Glazier
In this interactive mini-workshop we will use a very simple model of cancer somatic evolution and resource limitation based on one originally proposed by Heiko Enderling.
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Shape-changing Nanoparticles for Nanomedicine Applications
Online Presentations | 04 Feb 2021 | Contributor(s):: Vikram Jadhao
I will describe the nanoHUB tool “Nanoparticle Shape Lab” that enables simulations of the shape deformation of charged nanoparticles for a broad variety of nanoparticle material properties including nanoparticle surface charge, pattern, elasticity and solution conditions such...
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Biology of COVID-19 Attack on Epithelial Cells, understood from a Modeling and Simulation Perspective
Online Presentations | 04 Feb 2021 | Contributor(s):: Paul Macklin
n this session, we describe a community-driven effort to iteratively develop a multiscale, spatially-resolved open source model of SARS-CoV-2 dynamics and immune response in tissues.
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Understanding COVID-19 Infection, Immune Response, and Drug Therapy through Multiscale, Multicellular Modeling and Simulation
Online Presentations | 10 Dec 2020 | Contributor(s):: T.J. Sego
This workshop presents an open-source Python- and XML-scripted multiscale modeling and simulation framework of an epithelial tissue infected by a virus, a simplified cellular immune response and viral and immune-induced tissue damage and shows how to use it to model basic patterns of infection...
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Multiscale Multicellular Modeling of Tissue Function and Disease using CompuCell3D
Online Presentations | 03 Jun 2020 | Contributor(s):: James A Glazier, Juliano Ferrari Gianlupi
Multiscale multicellular models combine representations of subcellular biological networks, cell behaviors, tissue level effects and whole body effects to describe tissue outcomes during development, homeostasis and disease. I will briefly introduce these simulation methodologies, the CompuCell3D...
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Shape Changing Nanocontainers Tutorial
Online Presentations | 22 Apr 2020 | Contributor(s):: Vikram Jadhao
Course material companion materials for nanoparticle shape lab. Four files are associated with this course material: two video lectures, companion powerpoint slides, and a homework problem set.
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Overview of the nanoBIO Project Part A: General Features and Motivation of Project
Online Presentations | 28 Jan 2020 | Contributor(s):: Geoffrey C. Fox
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Overview of the nanoBIO Project Part B: Nano-Micro and Micro Units
Online Presentations | 28 Jan 2020 | Contributor(s):: Geoffrey C. Fox
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Overview of the nanoBIO Project Part C: Digital Twins and Engineered Health
Online Presentations | 28 Jan 2020 | Contributor(s):: Geoffrey C. Fox
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Overview of the nanoBIO Project Part D: Visualization and Experimental Validation
Online Presentations | 28 Jan 2020 | Contributor(s):: Geoffrey C. Fox
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Nanosphere Electrostatics Lab Tutorial
Online Presentations | 11 Nov 2019 | Contributor(s):: Jayanath Chamindu Sandanuwan Kadupitiya Kadupitige, Ballard, Joshua Brendan
Accurate knowledge of ionic structure & dynamics is critical to study nanoparticle dynamics. Nanoparticles are polarized in most solvents. Simulating the dynamics of ions near polarizable nanoparticles is challenging: Need to solve Poisson equation at every timestep....
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Perspectives on High-Performance Computing in a Big Data World: Part D - Learning Model Details and Agent-Based Simulations
Online Presentations | 17 Oct 2019 | Contributor(s):: Fox, Geoffrey C.
This lecture completes the discussion of MLforHPC. It covers Learning Model Details and Agents and Time-Series Case Studies.
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Perspectives on High-Performance Computing in a Big Data World: Part E - Challenges and Opportunities, Conclusions
Online Presentations | 17 Oct 2019 | Contributor(s):: Fox, Geoffrey C.
This lecture covers the computer science issues raised in this talk. The conclusions note that HPDC/HPC is essential; it is good to work closely with industry with student Internships and Collaborations; the Global AI and Modeling Supercomputer GAIMSC is a good framework with an HPC Cloud linked...
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Perspectives on High-Performance Computing in a Big Data World: Part C - MLaroundHPDC/HPC and MLAutotuning
Online Presentations | 10 Oct 2019 | Contributor(s):: Fox, Geoffrey C.
This is the first part of the discussion of MLforHPC. It includes MLAutotuning (Using ML to configure or autotune ML or HPC simulations and MLaroundHPC (Learning outputs from inputs).
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Perspectives on High-Performance Computing in a Big Data World: Part B - More on the Evolution of Interests and Communities
Online Presentations | 30 Sep 2019 | Contributor(s):: Fox, Geoffrey C.
This part contains several topics. It discusses the importance of industry in several facets of the field: SysML conference, clouds, MLPerf, the Global AI Supercomputer. The nature of data science and data engineering jobs. We emphasize the need for HPC. We finish by introducing MLforHPC (AI for...
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Perspectives on High-Performance Computing in a Big Data World: Part A - Data on the Evolution of Interests and Communities
Online Presentations | 13 Aug 2019 | Contributor(s):: Fox, Geoffrey C.
This lecture has an overall outline of the 5 part presentation. It covers trends seen from conferences and journals -- the number of papers, attendees and h5index. Then we look at relevant Google Trends. Cyberinfrastructure related activities are less buoyant than those for AI and ML.