Description

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).

All Categories (1-20 of 73)

1. (CC3D v3 - old) CompuCell3D Vascular Tumor

   Tools | 16 Apr 2019 | Contributor(s):: Juliano Ferrari Gianlupi, Somogyi, Andy T

   Simulate 3D vascular tumor with CompuCell3D

2. A virion endocytosis tissue simulator

   Tools | 13 Apr 2020 | Contributor(s):: Yafei Wang, Randy Heiland, Paul Macklin

   Simulate virus endocytosis (internalization), ACE2 receptor dynamics with PhysiCell

3. A virion infected-cell response tissue simulator

   Tools | 13 Apr 2020 | Contributor(s):: Yafei Wang, Randy Heiland, Paul Macklin

   Simulate infected cell response to virus with PhysiCell

4. A virion replication tissue simulator

   Tools | 13 Apr 2020 | Contributor(s):: Yafei Wang, Randy Heiland, Paul Macklin

   Simulate virus replication dynamics with PhysiCell

5. 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...

6. AMIGOS - Hypoxia

   Tools | 25 Apr 2019 | Contributor(s):: Furkan Kurtoglu, John Metzcar, Kali Nicole Konstantinopoulos, Timothy M Mahajan, Randy Heiland, Paul Macklin

   Modeling Tumor in Hypoxic Condition

7. 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.

8. 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.

9. Cloud-hosted Mathematical Models: Links between Education, Research, and Outreach

   Presentation Materials | 01 Aug 2019 | Contributor(s):: Paul Macklin

   To address the challenges facing undergraduate research, we tested lab structure that can scalably involve undergraduates in cutting-edge mathematical biology research. Teams of two-to-four undergraduates are jointly mentored by a graduate student (or senior personnel) and the lab’s...

10. CompuCell Cell Sorting Tool

    Tools | 09 Apr 2019 | Contributor(s):: Somogyi, Andy T

    simulate cell sorting with compucell 3d

11. CompuCell3D

    Tools | 16 May 2018 | Contributor(s):: Anwar Shaikh

    An open-source simulation environment for multi-cell, single-cell-based modeling of tissues, organs and organisms. Uses Cellular Potts Model to model cell behavior.

12. CompuCell3D - 2D wet foam coarsening

    Tools | 04 Jun 2020

    Simulates foam coarsening in a 2D wet foam

13. CompuCell3D - 2D wet foam coarsening with drainage

    Tools | 04 Jun 2020

    Simulation of 2D wet foam with drainage (gravity)

14. CompuCell3D - Bacterium Macrophage

    Tools | 17 Apr 2019 | Contributor(s):: Juliano Ferrari Gianlupi, Somogyi, Andy T

    Simulation of macrophage chasing bacterium

15. CompuCell3D - Cells random walking at different speeds

    Tools | 04 Jun 2020 | Contributor(s):: Juliano Ferrari Gianlupi, T.J. Sego

    Cells random walking at different speeds implemented through the motility plugin

16. CompuCell3D - Delta-Notch signaling in a group of cells

    Tools | 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)

17. CompuCell3D - Simulation of angiogenesis

    Tools | 04 Jun 2020 | Contributor(s):: Juliano Ferrari Gianlupi, T.J. Sego

    CompuCell3D simulates angiogenesis using chemical signals

18. CompuCell3D 3D Cell Sorting

    Tools | 09 Apr 2019 | Contributor(s):: Somogyi, Andy T

    CompuCell3D based application to simulate 3D cell sorting

19. CompuCell3d cell sorting in a hexagonal lattice

    Tools | 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.

20. CompuCell3D v4 - Bacterium Macrophage simulation

    Tools | 04 Jun 2020 | Contributor(s):: Juliano Ferrari Gianlupi, T.J. Sego

    Macrophage hunts bacterium in a maze