Abstract
The main topic of this study is the modelling and verification of biological systems using ω -automata. This work focuses on the protein folding problem and the infinite behaviour it features in many cases. Specifically, stochastic computational models with infinite input are used in this paper’s approach and indicative aspects of a biological problem are presented using both ω -automata and probabilistic Buchi automata (PBAs), making a novel attempt to establish their use in reasoning about biological processes. Necessary preliminary definitions and background towards this direction are provided. Finally, the pros and cons of each model are shown through examples. Overall, this work contributes by combining for the very first time PBAs with real biological mechanisms, with indicative examples, both with PBAs and NBAs (non-deterministic Buchi automata).
Highlights
It is a fact that many abstract mathematical models of computation are studied in the theory of computation
This work focuses on the protein folding problem and the infinite behaviour it features in many cases
Stochastic computational models with infinite input are used in this paper’s approach and indicative aspects of a biological problem are presented using both ω-automata and probabilistic Buchi automata (PBAs), making a novel attempt to establish their use in reasoning about biological processes
Summary
It is a fact that many abstract mathematical models of computation are studied in the theory of computation. Some of them include mechanisms, such as state machines (e.g. Turing machines, automata, etc.) Computer scientists study these abstract machines because of their simplicity in formulation and analysis, aiming to prove theories and results. Decision problems for certain logics use notions of this type of automata. Life sciences study them trying to shed more and more light on various aspects of these phenomena Such systems may be operating systems, biological processes etc. In the last section we try to stimulate future work towards this direction with thoughts and conclusions derived from our approach
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