TiFoSi

TiFoSi simulates the cellular dynamics of planar epithelia by modeling feedbacks between cellular mechanics and gene expression for mechanobiology research.

Key Features:

• Feedback Modeling: Simulates feedback loops between mechanical forces and genetic regulatory mechanisms in epithelial cells.
• Deterministic and Stochastic Modeling: Implements both deterministic and stochastic interactions between cellular mechanics and gene expression.
• Cell Population Interactions: Models interactions among distinct cell populations within epithelial tissues.
• Customizable Cell Cycle Design: Allows specification of custom cell cycle behaviors and cleavage properties.
• Protein Partitioning: Models protein number partitioning during cell division.
• Cell Communication Simulation: Simulates juxtacrine and paracrine signaling pathways for intercellular communication.
• XML Configuration: Defines in silico experiments via XML configuration files.
• Computational Performance: Supports computationally efficient simulation of complex epithelial dynamics.

Scientific Applications:

• Developmental Biology: Investigating interactions between gene expression and cell biomechanics during tissue development.
• Tissue Engineering: Exploring mechanisms relevant to engineered epithelial tissues where mechanics and signaling interact.
• Morphogenesis: Simulating epithelial morphogenesis driven by mechano-genetic feedbacks.
• Disease Progression: Studying how altered coupling between mechanics and gene expression affects disease-related epithelial dynamics.
• Hypothesis Testing: Formulating and testing hypotheses about emergent phenomena in epithelial dynamics.

Methodology:

In silico experiments are defined via XML configuration files and the software implements deterministic and stochastic models of feedback between cellular mechanics and gene expression, including customizable cell cycle and cleavage rules, protein partitioning during division, and juxtacrine/paracrine signaling among cell populations.