CellModeller

CellModeller models large-scale multi-cellular systems, focusing on microbial biofilms, to simulate three-dimensional biophysical interactions, genetic regulation, and intercellular signaling for studying community organization and engineering synthetic biofilms.

Key Features:

• Multiscale Modeling: Combines three-dimensional biophysical models of individual cells with genetic regulation and intercellular signaling models to capture dynamics across biological scales.
• Three-Dimensional Biophysical Modeling: Simulates physical interactions and spatial arrangements of individual cells within biofilms to assess positional effects on community function.
• Genetic Regulation Models: Incorporates models of transcriptional regulation to simulate how gene expression influences cell behavior and biofilm development over time.
• Intercellular Signaling: Models signaling pathways that mediate communication between cells and coordinate collective behaviors within the biofilm.
• High-Performance GPU Scaling: Leverages parallel Graphics Processing Unit (GPU) architectures to scale simulations to >30,000 cells, enabling simulation of a ~100 μm diameter colony in approximately 30 minutes.

Scientific Applications:

• Synthetic Biofilm Design: Predicts spatial organization and functional outcomes of engineered bacterial communities to optimize yields in industrial biotechnology, including pharmaceutical ingredient production and biofuel generation.
• Medical Research on Biofilm Infections: Examines spatial organization and physiological cooperation in microbial biofilms to inform strategies for disrupting persistent, biofilm-associated infections.

Methodology:

Integrates three-dimensional biophysical modeling of individual cells, models of transcriptional regulation, intercellular signaling models, and parallel GPU-based computation.