The Engineered nanoBIO node at Indiana University (IU) develops a powerful set of integrated computational nanotechnology products that address this complex, multiscale problem in both education and research and facilitate the discovery of customized, efficient, and safe nanoscale devices for biological applications. These apps, tools, and frameworks span the range from nanoscale particles (nano) to cellular scale structures (micro) to tissue scale morpohologies (macro).
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,...
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...
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.
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.
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...
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.
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...
Biology of COVID-19 Attack on Epithelial Cells, understood from a Modeling and Simulation Perspective
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.
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.
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...
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...
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.
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.
A virion pharmacodynamics response tissue simulator
27 Jul 2020 | | Contributor(s):: Yafei Wang, Randy Heiland, Paul Macklin
Simulate virus pharmacodynamics response with PhysiCell
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)
CompuCell3D - 2D wet foam coarsening
04 Jun 2020 |
Simulates foam coarsening in a 2D wet foam
CompuCell3D - 2D wet foam coarsening with drainage
Simulation of 2D wet foam with drainage (gravity)
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
CompuCell3d cell sorting in a hexagonal lattice
Showcases hexagonal lattice use in CompuCell3D by simulating cell sorting by difference in contact energies in a hexagonal lattice.
CompuCell3D - Delta-Notch signaling in a group of cells
CompuCell3D can solve individual cell's ODE and have the information of one cell affect another (implemented trough SBML)