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Apps

nanoBIO Developed Apps

Ions in Nanoconfinement (nano)

This app empowers users to simulate ions confined between material surfaces that are nanometers apart, and extract the associated ionic structure. The app facilitates investigations for a wide array of ionic and environmental parameters using standard molecular dynamics (MD) method for unpolarizable surfaces.

Nanosphere Electrostatics Lab (nano)

This app allows users to simulate the self-assembly of ions near a spherically shaped nanoparticle, and extract the effective electrostatic properties..

Nanoparticle Assembly Lab (nano)

Simulate assembly of nanoparticles into aggregates in physiological conditions.

 

Polyvalent Nanoparticle Binding Simulator (nano)

Simulates the binding of ligand-decorated nanoparticles to cell membrane driven by ligand-cell-receptor attraction

 

Souffle: Virus Capsid Assembly Lab (nano)

Simulate assembly of flexible capsomeres into virus capsids and oligomers.

 

Nanoparticle Shape Lab  (nano)

The shape of nanocontainers determines their ability to act as targeted drug delivery carriers by modulating their biodistribution and bioavailability.  This app simulates the shape deformation of soft-matter-based deformable, charged nanocontainers for a broad variety of nanocontainer material properties and solution conditions. Molecular dynamics based simulated annealing is used to minimize the energy of the nanocontainer for a given set of material and solution parameters.

CompuCellSort (micro)

simulate cell sorting with compucell 3d

 

Compucell3D Vascular Tumor (micro)

Simulate 3D vascular tumor with CompuCell3D

 

Compucell3D Bacterium Macrophage (micro)

Simulation of macrophage chasing bacterium

 

COVID 19 Virtual Tissue Model - Tissue Infection and Immune Response Dynamics (micro)

Simulates tissue and immune system interactions during a viral lung infection

 

PhysiCell for COVID-19 (macro)

  This model simulates replication dynamics of SARS-CoV-2 (coronavirus / COVID19) in a layer of epithelium. It is being rapidly prototyped and refined with community support. See related: PC4COVID19: Rapid Community Prototyping of a Coronavirus (COVID-19) Replication Simulator

 

PhysiCell: cancer nanotherapy simulator (macro)

This app allows users to design and explore new and novel nanotherapies, where engineered nanoparticles are conjugated to novel cancer therapeutics. Users can simulate the growth and migration of cancer cells in the tissue environment, as well as pharamcodynamic response to user-designed therapeutics. Adapted from the PhysiCell Framework

PhysiCell: cancer-immune model (macro)

  PhysiCell model of immune cells attacking a heterogeneous tumor

 

PhysiCell: biased random migration generator (macro)

  PhysiCell demonstration of biased random cell migration

 

PhysiCell: tumor heterogeneity (macro)

  2D simulation of tumor heterogeneity

 

PhysiCell: invader-scout-attacker system (macro)

  PhysiCell model of an invader-scout-attacker multicellular system

 

  PhysiCell: cancer biorobots simulation (macro)

  2D simulation of biorobots delivering a drug to cancer cells

 

PhysiCell: Extracellular Matrix Modeling (macro)

  An extracellular matrix model developed in PhysiCell

 

PhysiCell: Thanos vs. Avengers multicellular demonstrator (macro)

This app demonstrates chemotactic migration, cell-cell contact interactions, and iterating across cells to apply a random event. It also explores the impact of varying the number and strength of different cells in a complex, stochastic adversarial system.

 

PhysiCell workshop training (macro)

This tool is intended to be used at PhysiCell training workshops. It is general purpose in the sense that it provides a GUI that includes 1) a Terminal tab to compile and run a PhysiCell model, and 2) a Plotting tab to visualize results.

PhysiCell: Motility Training App (macro)

To account for cell movement, PhysiCell includes a set of parameters that govern speed and direction of cell motility. The biased, random motility of cells is determined by the following equation:where b is the level of bias in movement (migration bias), ξ is a random unit vector of length 1, and dbias is the direction.

PhysiCell: Replication Competent Oncolytic Virus in Epithelial cell layer (macro)

This app demonstrates the interaction between a replication competent oncolytic viruse and a layer of epithelial cells. In this model, epithelial cells (pink) divide while consuming oxygen, with greater availability of oxygen driving faster proliferation. 

PhysiCell: AMIGOS - Hypoxia (macro)

Hypoxic conditions occur in the center of tumor after tumor cells use and deplete oxygen. Hypoxic cells secrete signaling chemicals to induce vascularization, such as vascular epithelial growth factor (VEGF).

 

PhysiCell: liver tissue mechanobiology (macro)

Simulates the liver tissue mechanobiology on cancer metastatic seeding.

 

 

Externally Developed Apps

PhysiCell: Death Training App

Cells do not keep growing and dividing forever. Eventually, they undergo cell death, in which cells lyse (burst)and decay. PhysiCell supports two models of cell death: apoptosis and necrosis. Apoptosis is programmed cell death, which contributes to regular growth and function. 

 

PhysiCell: Wound Healing

  In silico demonstration of in vitro scratch wound healing using PhysiCell

 

PhysiBoSS Simulation with ECM

  Agent based multicellular simulation with extracellular matrix interaction.

 

PhysiCell: infected system and off-site immune system

  In this app, we developed a dynamic interaction model which contains two systems: an infected system of cells and a off-site immune system that responds to the infection. 

Replication Competent Oncolytic Virus expressing secretable trimeric TRAIL: hypothesis testing

  This app demonstrates the interaction between a replication competent oncolytic viruse and a layer of epithelial cells. It uses the PhysiCell software published PhysiCell in Ghaffarizadeh et al. (2018). In this model, epithelial cells (pink) divide while consuming oxygen, with greater availability of oxygen driving faster proliferation. 

PhysiBoSS: cell fate decision in TNF Boolean model

  This app demonstrates the population dynamics in a multicellular system where cells run a Boolean network model representing the TNF signalling pathway and when exposed to TNF.

Spatial Pattern Formation in Cell Based Models

Multi-species Biofilm on Wound Surface

This tool aims to model two bacterial species which form a biofilm on the surface of a chronic wound.