By Daniel A. Beard, Hong Qian, James B. Bassingthwaighte (auth.), Gabriel Ciobanu, Grzegorz Rozenberg (eds.)
This quantity includes papers excited by types and techniques utilized in fixing a few basic difficulties of biosciences. They characterize a large spectrum of various principles and traits. specifically, they mirror the surely interdisciplinary nature of study on modelling in molecular biology – the muse, rules and methods awarded during this quantity come from arithmetic, machine technological know-how, records, chemistry and biology.
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Additional resources for Modelling in Molecular Biology
Example text
However, at the same time the expected increase in average fitness is smaller, as we saw in the previous paragraph. Modelling Stochastic Clonal Interference 27 4 Numerical Simulation In order to measure fixation probabilities, we carried out 100, 000 replicates of the simulation for each set of parameters, and recorded the final outcome (all individuals unmarked, or marked as descendants of either advantageous mutant). 8. 2. We also studied a population of size N = 10, 000 for a subset of these parameters, in order to make sure that our results were robust against a change in population size.
The main function of the pump is to move sodium and potassium ions across a cell membrane, namely Na ions from inside to outside, and K ions from outside to inside. We use the π-calculus [10, 14] to describe the changing configurations and movements of the pump. We describe the molecular components as computational processes of the π-calculus, individual domains as communication channels, and molecular interaction as channel transmission according to the π-calculus rules. This abstraction helps us to reason about complex biological systems.
Regarding the relationship between the kinetic parameters of the transport process and the efficiency of the pump, we can mention that the rate constants of competing steps (that would decrease the efficiency) are small. This ensures that the binding and the release of substrate occur at the proper point in the cycle. For example, the reaction E1 + AT P E1 ∼ P + ADP of (2) is slower than the reaction described by (1). As a consequence, E1 has enough time to bind sodium ions before undergoing the transition to E2 .