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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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Agent Based Active Matter Simulations with Mechanica
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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Winter Interactive nanoBIO Workshop
04 Feb 2021 | | Contributor(s):: Ballard, Joshua Brendan (editor)
The Winter Interactive nanoBIO Workshop will walk students and researchers through how to understand a variety of biological problems using simulations based on cloud-based tools on nanoHUB or other easy to use platforms.
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Deep Learning for Time Series Illustrated by COVID-19 Infection Studies
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
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
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
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
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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Cycle Training App for PhysiCell
18 Dec 2020 | | Contributor(s):: Furkan Kurtoglu, Aneequa Sundus, Kali Nicole Konstantinopoulos, Drew Willis, Mary Chen, Randy Heiland, Paul Macklin
Training application for "Cycle" concept in PhysiCell.
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Winter Interactive nanoBIO Workshop
10 Dec 2020 |
The Winter Interactive nanoBIO Workshop will walk students and researchers through how to understand a variety of biological problems using simulations based on cloud-based tools on nanoHUB or other easy to use platforms. Each session will include some background material to understand the nature...
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Understanding COVID-19 Infection, Immune Response, and Drug Therapy through Multiscale, Multicellular Modeling and Simulation
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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PhysiCell model for tumor hypoxia
07 Aug 2020 | | Contributor(s):: Lima Da Rocha, Heber, Paul Macklin, Furkan Kurtoglu
Multicellular simulation in 2-D of tumor hypoxia.
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COVID-19 data analysis
07 Aug 2020 | | Contributor(s):: Randy Heiland, Paul Macklin
Perform data analysis in a Jupyter notebook using data from the pc4covid19 tool.
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Multicellular modeling of SARS-CoV-2 dynamics and virion mediated cell fusion with antiviral drug effects
27 Jul 2020 | | Contributor(s):: Yafei Wang, Michael Getz, Randy Heiland, Paul Macklin
Simulate SARS-CoV-2 dynamics and virion mediated cell fusion under pharmacodynamics effects with PhysiCell
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CompuCell3D v4 Main Tool
08 Jun 2020 | | Contributor(s):: Juliano Ferrari Gianlupi, T.J. Sego
Base tool for CompuCell3D version 4 and greater. Allows running any of the demos included with CC3D (/CompuCell3D_Demos/Demos)
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CompuCell3D - 2D wet foam coarsening
04 Jun 2020 |
Simulates foam coarsening in a 2D wet foam
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CompuCell3D - 2D wet foam coarsening with drainage
04 Jun 2020 |
Simulation of 2D wet foam with drainage (gravity)
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CompuCell3D - Cells random walking at different speeds
04 Jun 2020 | | Contributor(s):: Juliano Ferrari Gianlupi, T.J. Sego
Cells random walking at different speeds implemented through the motility plugin
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CompuCell3d cell sorting in a hexagonal lattice
04 Jun 2020 | | Contributor(s):: Juliano Ferrari Gianlupi, T.J. Sego
Showcases hexagonal lattice use in CompuCell3D by simulating cell sorting by difference in contact energies in a hexagonal lattice.
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CompuCell3D - Delta-Notch signaling in a group of cells
04 Jun 2020 | | Contributor(s):: Juliano Ferrari Gianlupi, T.J. Sego
CompuCell3D can solve individual cell's ODE and have the information of one cell affect another (implemented trough SBML)