yalla

yalla simulates morphogenesis of mesenchymal and epithelial tissues using a GPU-accelerated parallel agent-based spheroid model to analyze cellular interactions, tissue polarity, protrusions, and migration.

Key Features:

• Agent-Based Modeling: yalla implements a parallel agent-based model to simulate individual cell behaviors and interactions within tissues.
• Spheroid Model Extension: Extends spheroid models with spin-like polarities to represent epithelial sheet polarity and directional properties.
• Pairwise Interactions: Uses pairwise interactions between agents to model cell adhesion, repulsion, and communication.
• GPU Implementation: Implemented in CUDA/C++ for GPU acceleration to enable large-scale, high-performance simulations.
• Protrusions and Migration Models: Includes models for cellular protrusions and migration to simulate dynamic cell movement and morphological change.

Scientific Applications:

• Tissue Polarity: Investigating establishment and maintenance of cell polarity in epithelial and mesenchymal contexts.
• Morphogenetic Movements: Modeling mechanisms of cell movement and organization during tissue morphogenesis.
• Cellular Interactions: Studying effects of cell adhesion, repulsion, and communication on tissue formation and function.

Methodology:

Parallel agent-based modeling with pairwise agent interactions; spheroid model augmented with spin-like polarities; CUDA/C++ GPU implementation; incorporation of protrusion and migration models.