ReaDDy

ReaDDy simulates interacting-particle reaction dynamics (iPRD) by combining molecular dynamics with reaction kinetics to model spatiotemporal behavior of particles in crowded and complex geometries.

Key Features:

• Interacting-Particle Reaction Dynamics (iPRD): Implements iPRD to simulate particle trajectories and interactions in continuous space.
• Combined molecular dynamics and reaction kinetics: Integrates molecular dynamics with reaction kinetics to represent both physical movement and chemical transformations.
• Predefined reaction rules: Allows particles to appear, disappear, or transform according to user-defined reaction rules.
• Crowded and complex geometries: Models reaction kinetics in crowded environments and complex molecular geometries such as polymers.
• Polymer reactions: Supports polymer-specific reaction mechanisms including polymer breaking and fusion.
• Spatiotemporal resolution: Captures detailed spatiotemporal reaction mechanisms relevant to signaling at cellular membranes and nano- to microscale chemistry.
• Hardware-specific simulation kernels: Provides simulation kernels with single- and multi-threaded CPU support.
• Extensible kernel architecture: Architecture is extensible to enable future GPU and multi-node kernels.
• Benchmark validation: Demonstrated efficiency and accuracy through benchmark examples.

Scientific Applications:

• Membrane signaling: Modeling signaling processes at cellular membranes with spatially resolved reaction dynamics.
• Polymer dynamics: Studying polymer behavior and reactions, including breaking and fusion, in crowded environments.
• Nano- to microscale chemistry: Simulating chemical reactions on the nano- to microscale within complex geometries.
• Crowded intracellular kinetics: Investigating reaction kinetics in dense and complex molecular environments.

Methodology:

Combines molecular dynamics with reaction kinetics under the interacting-particle reaction dynamics (iPRD) framework using predefined reaction rules for particle appearance, disappearance, and transformation; simulations execute on hardware-specific kernels with single- and multi-threaded CPU support and an extensible architecture for GPU and multi-node kernels.