Tags: NanoBio Node at Indiana

Description

Nanobio Node at Indiana

 

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 64)

  1. 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...

  2. 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...

  3. 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.

  4. 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.

  5. A virion pharmacodynamics response tissue simulator

    27 Jul 2020 | | Contributor(s):: Yafei Wang, Randy Heiland, Paul Macklin

    Simulate virus pharmacodynamics response with PhysiCell

  6. 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)

  7. CompuCell3D - 2D wet foam coarsening

    04 Jun 2020 |

    Simulates foam coarsening in a 2D wet foam

  8. CompuCell3D - 2D wet foam coarsening with drainage

    04 Jun 2020 |

    Simulation of 2D wet foam with drainage (gravity)

  9. 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

  10. 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.

  11. 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)

  12. CompuCell3D v4 - Bacterium Macrophage simulation

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

    Macrophage hunts bacterium in a maze

  13. CompuCell3D - Simulation of angiogenesis

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

    CompuCell3D simulates angiogenesis using chemical signals

  14. 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...

  15. 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

  16. 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.

  17. 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

  18. A virion replication tissue simulator

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

    Simulate virus replication dynamics with PhysiCell

  19. A virion endocytosis tissue simulator

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

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

  20. 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