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).
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...
Understanding COVID-19 Infection, Immune Response, and Drug Therapy through Multiscale, Multicellular Modeling and Simulation
10 Dec 2020 | | Contributor(s):: Sego, Timothy James
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)
CompuCell3D v4 - Bacterium Macrophage simulation
Macrophage hunts bacterium in a maze
CompuCell3D - Simulation of angiogenesis
CompuCell3D simulates angiogenesis using chemical signals
Multiscale Multicellular Modeling of Tissue Function and Dsease using CompuCell3D
03 Jun 2020 | | Contributor(s):: James A Glazier, Juliano Ferrari Gianlupi
I will briefly introduce these simulation methodologies, the CompuCell3D simulation environment and their applications, then focus on a multiscale simulation of an acute primary infection of an epithelial tissue infected by a virus like SARS-CoV-2, a simplified cellular immune response and...
COVID 19 Virtual Tissue Model - Tissue Infection and Immune Response Dynamics
26 May 2020 | | Contributor(s):: Josua Oscar Aponte-Serrano, T.J. Sego
Simulates tissue and immune system interactions during a viral lung infection
Shape Changing Nanocontainers Tutorial
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.
A virion infected-cell response tissue simulator
13 Apr 2020 | | Contributor(s):: Yafei Wang, Randy Heiland, Paul Macklin
Simulate infected cell response to virus with PhysiCell
A virion replication tissue simulator
Simulate virus replication dynamics with PhysiCell
A virion endocytosis tissue simulator
Simulate virus endocytosis (internalization), ACE2 receptor dynamics with PhysiCell
Souffle: Virus Capsid Assembly Lab
01 Apr 2020 | | Contributor(s):: Nilsson, Lauren, JCS Kadupitiya, Vikram Jadhao
Simulate assembly of flexible capsomeres into virus capsids and oligomers