158 Works

Melting point simulation using OpenKIM

Martin Hunt & Alejandro Strachan
Computes melting point using a coexistence technique using interatomic potentials from OpenKIM

Peking University Resistive-Switching Random Access Memory (RRAM) Verilog-A Model

Weijie Xu & Jinfeng Kang
The Peking University RRAM Model is a SPICE-compatible compact model which is designed for simulation of metal-oxide based RRAM devices. It captures typical DC and AC electrical behaviors of the RRAM devices with physics-based model descriptions.

FunUQ for MD

Sam Reeve & Alejandro Strachan
Functional uncertainty quantification for molecular dynamics

Polyvalent Nanoparticle Binding Simulator

, JCS Kadupitiya & Vikram Jadhao
Simulates the binding of ligand-decorated nanoparticles to cell membrane driven by ligand-cell-receptor attraction

Jupyter Notebook (hub version 6.0)

Martin Hunt
Jupyter notebook running in anaconda-6 environment

PhysiCell: infected system and off-site immune system

Parichit Sharma & Yafei Wang
Studying the interaction between an ODE driven offsite system and a system under invasion through Agent Based Modelling in PhysiCell.

Replication Competent Oncolytic Virus expressing secretable trimeric TRAIL: hypothesis testing

Adrianne Jenner & Paul Macklin
Using PhysiCell to simulate a replication competent oncolytic virus expressing secretable trimeric TRAIL which induces apoptosis in nearby cells

Nanosphere Electrostatics Lab

JCS Kadupitiya, Nicholas Brunk, Sohile Ali, & Vikram Jadhao
The Nanosphere Electrostatics Lab empowers users to simulate the self-assembly of ions near a spherically shaped nanoparticle, and extract the effective electrostatic properties.

AMIGOS - Hypoxia

Furkan Kurtoglu, John Metzcar, Paul Macklin & Randy Heiland
Modeling Tumor in Hypoxic Condition

Multi-species Biofilm on Wound Surface

Furkan Kurtoglu & Aneequa Sundus
This is a class project that aims modeling two-species biofilm that grows on a wound

Zooley's Notebook

Shawn Rice
An example Jupyter Notebook

Nanoparticle Assembly Lab

JCS Kadupitiya, Nicholas Brunk, Masaki Uchida, & Vikram Jadhao
Simulate assembly of nanoparticles into aggregates in physiological conditions

Ions in Nanoconfinement

JCS Kadupitiya, Nasim Anousheh, Suresh Marru, & Vikram Jadhao
The Ions in Nanoconfinement app empowers users to simulate ions confined between material surfaces that are nanometers apart, and extract the associated ionic structure.

PhysiCell for tumor heterogeneity

Randy Heiland & Paul Macklin
2D simulation of tumor heterogeneity

PhysiCell cancer-immune model

Paul Macklin & Randy Heiland
PhysiCell model of immune cells attacking a heterogeneous tumor

LAMMPS driver tool for potential calibration

Saaketh Desai & Alejandro Strachan
Calculates basic properties of interest with a given interatomic potential and is used to drive the calibration of the potential.

PhysiCell: biased random migration demonstrator

Paul Macklin & Randy Heiland
PhysiCell demonstration of biased random cell migration

Jupyter Examples

Martin Hunt
Users Manual and Examples for Jupyter

Calibration using DAKOTA

Saaketh Desai & Alejandro Strachan
Uses DAKOTA to perform deterministic and Bayesian calibration

Motility Training App

Furkan Kurtoglu, Aneequa Sundus, Kali Konstantinopoulos & Mary Chen
Training application for "Motility" concept in PhysiCell.

Motility Training App for PhysiCell

Furkan Kurtoglu, Aneequa Sundus, Kali Konstantinopoulos, Drew Willis, Mary Chen, Randy Heiland & Paul Macklin
Training application for "Motility" concept in PhysiCell.

PhysiCell cancer biorobots simulation

Randy Heiland & Paul Macklin
2D simulation of biorobots delivering a drug to cancer cells

Hierarchical material optimization

Miguel Cuaycong
Assembles all possible configurations of a structural level in a Hierarchical Material.

Process Lab: Concentration-Dependent Diffusion

Shuqing Cao, Yang Liu & Peter Griffin
This modules simulates both the standard diffusion and concentration-dependent diffusion.

PhysiCell biorobots simulation

Randy Heiland
2D sim of director, worker, and cargo cells.

Registration Year

  • 2019

Resource Types

  • Software