SmartCell v4.3

SmartCell v4.3 simulates whole-cell diffusion-reaction networks using a mesoscopic stochastic reaction model to represent localisation and diffusion dynamics within cell geometries.

Key Features:

• General Framework: Supports modelling of diverse biological processes within arbitrary cell geometry.
• Mesoscopic Stochastic Reaction Model: Implements a mesoscopic stochastic reaction model to represent localisation and reaction events at mesoscopic scales.
• Localisation and Diffusion: Integrates localisation mechanisms and diffusion, employing stochastic algorithms to capture molecular movement and interaction randomness.
• Cellular Compartments and Growth: Models multiple cellular compartments and supports simulations involving cell growth dynamics.
• Biological Processes: Represents DNA transcription and translation, membrane diffusion, and multistep reactions.
• Constraints Application: Allows application of temporal and spatial constraints to models.

Scientific Applications:

• Spatial localisation studies: Investigates how spatial distribution of species affects network behavior compared with differential equation-based models.
• Signal transduction: Analyzes spatially resolved signal transduction dynamics.
• Metabolic pathways: Models metabolic pathway dynamics with explicit diffusion and localisation.
• Gene regulatory networks: Studies gene regulatory network dynamics including spatial effects on transcription and translation.
• Growth-dependent dynamics: Explores the influence of cell growth on intracellular diffusion-reaction networks.

Methodology:

Uses a mesoscopic stochastic reaction model with stochastic simulation algorithms that require multiple runs to obtain mean results and supports comparison of stochastic simulations with differential equation analyses.