T7

T7 simulates intracellular infection kinetics of bacteriophage T7 to model how genetic variation and environmental resource availability affect growth rates, fitness, and robustness.

Key Features:

• In Silico Mutant Generation: Generates over 150,000 in silico mutants of bacteriophage T7 to explore genetic variation effects on intracellular growth kinetics.
• Environmental Simulation: Evaluates growth rates and growth efficiencies across two host resource regimes: a realistic finite-resource environment and a hypothetical infinite-resource environment.
• Robustness Analysis: Assesses robustness to parameter perturbations and to changes in genetic element ordering, finding general robustness to parameter changes and fragility when genetic element order is altered.
• Fitness Evaluation: Identifies that wild-type T7 exhibits near-optimal fitness in finite-resource environments, consistent with minimizing resource wastage.
• Correlation Analysis: Quantifies a strong correlation between fitness and growth efficiency in finite-resource environments.

Scientific Applications:

• Evolutionary Biology Research: Simulation of evolutionary pressures on phage T7 to study robustness and adaptive strategies under resource constraints.
• Genetic Engineering and Synthetic Biology: Analysis of the impact of genetic element ordering on phage growth to inform engineering of viral vectors or synthetic organisms.
• Pharmaceutical Development: Informing phage therapy design by optimizing phage growth and fitness under resource-limited conditions.

Methodology:

Computational modeling to simulate and analyze growth kinetics of T7 mutants and compare simulations across finite and infinite resource environments.