IMPETUS – Interactive MultiPhysics EnvironmenT for Unified Simulations

an object oriented, easy-to-use, high performance, C++ program for three-dimensional simulations of complex physical systems that can benefit a large variety of research areas, especially in cell mechanics. The program implements cross-communication between locally interacting particles and continuum models residing in the same physical space while a network facilitates long-range particle interactions. Message Passing Interface is used for inter-processor communication for all simulations.

IMPETUS VR – Immersive Virtual Reality Environment for IMPETUS Simulations

Simulations - Long & Short Format

IMPETUS VR is an interactive virtual reality environment for particle dynamics simulations using IMPETUS. This is a tool using immersive interactive virtual reality technology to assist users to develop molecular dynamics simulations by placing the user in the live simulation world to interact with and reconfigure the particles.

MD-R - Molecular Dynamics library for Repast

The MD-R toolkit provides a three-dimensional continuous space projection and a large set of short-range molecular dynamics (MD) tools for the Agent-based modeling toolkit Repast HPC.

The 3D projection gives Repast HPC the ability to simulate agents in three dimensional Cartesian space and it manages all MPI operations for parallel computing. The MD-R toolkit utilizes the provided 3D space projection to run short-range Molecular Dynamics simulations. It includes integration algorithms, thermostats, and potential functions for interacting agents. MD-R was designed to be intuitive and user friendly. Users are not required to have advanced knowledge of MD to create a simulation with MD-R. The toolkit automatically handles all major MD operations such as initiation, recording of MD parameters, creation of cell lists and neighbor lists containing the agents. It also determines when the agents need to be synchronized and applies thermodynamic constrains.

Three-dimensional continuous space projection for Repast

MD-R - 3D Projection - The Three-dimensional continuous space projection for Repast HPC is available to download here (link not available)

A demo to run the 3D space is available to download here (link not available)

• Instruction for the demo is located in the 'readme' folder in the demo and can be viewed here: txt , pdf (link not available)
• This 3D demo model uses AtomEye for molecular visualization. Please download AtomEye to view the motion of agents. (link not available)

Molecular Dynamics library for Repast

The Molecular Dynamics library for Repast is available to download here (link not available)

A demo to run a molecular dynamics library for repast is available to download here (link not available)

• Instruction for the demo is located in the 'readme' folder in the demo and can be viewed here: txt , pdf (link not available)
• The template files are located in the folder mdr-templates in the demo folder or it can be downloaded from here (link not available)
• This demo model uses AtomEye for molecular visualization. Please download AtomEye to view the motion of agents (link not available)

Additional Software

This is an in-house developped set of MATLAB functions useful for counting and quantifying the morphology of red blood cells from light microscopy videos.

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