mrdna

mrdna simulates the structure and dynamics of DNA nanostructures using a multi-resolution framework to generate atomistic-resolution conformations and analyze equilibrium behavior and environmental effects such as electric fields.

Key Features:

• Rapid Simulation: Produces atomistic-resolution structures of arbitrary DNA nanostructures in 30 minutes or less.
• High Fidelity and Accuracy: Demonstrates high fidelity through direct comparisons with cryo-electron microscopy (cryo-EM) reconstructions of multiple 3D DNA origami objects.
• Ensemble Characterization: Characterizes ensembles of conformations adopted by dynamic DNA nanostructures.
• Equilibrium Structure and Dynamics: Determines equilibrium structure and dynamics of DNA objects constructed by self-assembly, including wireframe DNA objects.
• Environmental Condition Analysis: Analyzes DNA object properties under various environmental conditions, including applied electric fields.
• Tool Integration: Integrates with existing DNA design and molecular graphics tools to enable interoperability with design workflows.

Scientific Applications:

• Design Optimization: Simulates the effects of design choices on the shape and function of self-assembled DNA objects to guide optimization.
• Dynamic Studies: Enables exploration of conformational flexibility and stability of dynamic DNA nanostructures.
• Environmental Impact Research: Simulates DNA structures under different environmental conditions to study how external factors influence nanoscale DNA behavior.

Methodology:

Multi-resolution simulation framework to generate atomistic-resolution structures, ensemble characterization for conformational sampling, equilibrium dynamics analysis, direct comparison with cryo-EM reconstructions, and simulation under applied electric fields.