MEDYAN

MEDYAN simulates mechanochemical dynamics of active matter systems, integrating reactive coarse-grained mechanics and stochastic chemistry to model cytoskeletal actomyosin network structure and dynamics.

Key Features:

• Reactive Coarse-Grained Force Field: Employs a reactive coarse-grained force field to simulate active network evolution and mechanical deformations under stresses generated by molecular motors.
• Stochastic 3D Reaction–Diffusion: Treats chemical reaction and diffusion processes stochastically in three spatial dimensions.
• High-Resolution Mechanochemical Coupling: Deeply couples mechanical and chemical processes at high spatial resolution to capture non-linear, far-from-equilibrium behaviors.
• Structural Modeling with Cytoskeletal Chemistries: Implements a high-resolution structural modeling framework that integrates a minimally-complete set of cytoskeletal chemistries relevant to actomyosin systems.

Scientific Applications:

• Semi-Flexible Polymer Networks: Studies interacting semi-flexible polymers embedded in solutions with complex reaction–diffusion processes.
• Contractile Actomyosin Networks: Models networks composed of actin filaments, alpha-actinin cross-linking proteins, and non-muscle myosin IIA mini-filaments to investigate contractility and structural organization.
• Cross-Linker-Driven Structural Transitions: Captures switch-like transitions from random networks to ordered bundled structures when cross-linker concentration exceeds a threshold driven by myosin II contraction.
• Polarity and Alignment Dynamics: Reveals how myosin II mini-filaments and cross-linkers produce diverse actin filament polarity distributions and alignments influenced by actin turnover rates and super-diffusive behavior.
• Mechanosensation and Motor Accumulation: Demonstrates force-dependent accumulation of myosin II and the spontaneous generation of myosin II concentration gradients within the solution phase.
• Cellular Architecture Remodeling: Informs biological processes such as arc formation during lamellipodium-to-lamellum architectural remodeling.

Methodology:

Uses a reactive coarse-grained force field, stochastic treatment of reaction–diffusion in three spatial dimensions, and explicit mechanochemical coupling at high spatial resolution.