NERDSS

NERDSS simulates structure-resolved reaction-diffusion self-assembly to model cell-scale, minutes-long dynamic assembly and disassembly processes.

Key Features:

• Structure-Resolved Reaction-Diffusion Algorithm: Implements a structure-resolved reaction-diffusion algorithm that simulates large, reversible assemblies where individual sites are governed by specific reaction rules.
• Rule-Based Model Construction: Enables rule-based definitions for molecular interactions and assembly pathways.
• Rigid, Multi-Site Molecule Representation: Represents proteins as rigid, multi-site molecules with orientation-specific binding upon interaction.

Scientific Applications:

• Multi-Component Assembly Modeling and Optimization: Simulates and optimizes models of multi-component assembly against experimental data over time.
• Clathrin-Mediated Endocytosis: Captures clathrin cage formation dynamics by modulating interaction strengths, introducing cooperativity, or localizing clathrin to membranes.
• Enzyme-Driven Disassembly: Predicts how enzymes drive disassembly by altering lipid populations on cell membranes.
• Viral Lattice Assembly: Models assembly of viral lattices to simulate complex biological structure formation.
• Circadian Clock Models: Replicates oscillations in protein expression levels in circadian clock models.

Methodology:

Integrates a structure-resolved reaction-diffusion algorithm with rule-based model construction; represents proteins as rigid, multi-site molecules with orientation-specific binding; simulates large, reversible assemblies and couples detailed structural information with dynamic reaction-diffusion processes.