The nanoBIO team at University of Illinois created a nanoBIO landing page with their tools.
Demonstration of 2D cell sorting with CompuCell3D
- Compucell3D Vascular Tumor
CompuCell3D Demo for Vascular Tumor Growth. Tumor secrets VEGF and attracts growth of vasculature towards it.
- Compucell3D Bacterium Macrophage
Macrophage hunting bacterium through a maze using CompuCell3D
An open-source simulation environment for multi-cell, single-cell-based modeling of tissues, organs and organisms.
- Functionalization Workbench
Using molecular dynamic simulation - explore the interactions between a molecular structure and substrate when they are linked together.
- Molecular Dynamics Showcase
View interesting features of a molecular dynamics trajectory file
- cadnano to PDB File Converter
Accepts CadNano files in the form of *.json and outputs a file in *.pdb which can be read by programs such as VMD.
- Finite Buffer Method for Direct Solution of Discrete Chemical Master Equation (fb-dCME)
Finite Buffer Method for Optimal State Space Enumeration and Direct Solution of Discrete Chemical Master Equation provides an efficient and optimal algorithm for enumerating state spaces and directly solving discrete chemical master equations, which is a fundamental method for modeling stochastic gene regulatory networks in systems biology.
Live Code via Jupyter
- Nanoparticle Assembly Lab
This code simulates the self-assembly of charged nanoparticles (NPs) into aggregates mediated by smaller, oppositely-charged linkers under different ionic physiological conditions.
- Polyvalent Nanoparticle Binding Simulator
This code simulates coarse-grained ligand-receptor binding of ligand-decorated virus particles interacting with a cell wall.
- Ions in Nanoconfinement
Empowers users to simulate ions confined between material surfaces that are nanometers apart, and extract the associated ionic structure.
- editor note - enter here