Large Scale Tissue Morphogenesis Simulation on Heterogenous Systems Based on a Flexible Biomechanical Cell Model.

Area of Science:

• Computational Biology
• Biophysics
• Developmental Biology

Background:

• Multicellular tissue development (morphogenesis) is complex due to large cell numbers and intricate cell interactions.
• Understanding these mechanisms requires advanced in silico simulation tools.

Purpose of the Study:

• To develop novel computational tools for simulating complex biological tissue morphogenesis.
• To create a virtual cell model incorporating mechanical structures and cellular behaviors.
• To enable efficient parallel simulations using the OpenCL framework.

Main Methods:

• A virtual cell model was created, including mechanical components (membrane, cytoskeleton, cortex) and behaviors (mitosis, growth, differentiation, molecule dynamics, environmental constraints).
• An agent-based formalism was coupled with the virtual cell model.
• An OpenCL-based simulator was developed for efficient parallel processing on heterogeneous hardware (CPUs, GPUs).

Main Results:

• The virtual cell model and simulator were validated through two case studies: cell signaling-controlled proliferation and virtual limb growth.
• The simulation framework successfully replicated complex biological processes.

Conclusions:

• The proposed virtual cell model and OpenCL simulator provide a powerful platform for in silico investigation of tissue morphogenesis.
• This approach facilitates a deeper understanding of the mechanisms underlying multicellular tissue development.