Use of Büchi automata and randomness for the description of biological processes

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 Büchi 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 Büchi automata).

Infinite and standard computation with unconventional and quantum methods using automata

“…Finally, in this chapter we present a simple example with the novelty of combining Büchi automata with biological processes (Giannakis & Andronikos, 2015c) by associating them to specific functionalities, as explained through examples. Some of the definitions and the references in this chapter were taken from the published work in (Giannakis & Andronikos, 2015c) in the journal "International Journal of Scientific World" in 2015.…”

“…In particular, these are the works in ,b, 2016, Theocharopoulou & Giannakis, 2012, Giannakis & Andronikos, 2015c. The work in was co-authored by Christos Papalitsas and Theodore Andronikos, the by Christos Papalitsas, Kalliopi Kastampolidou, Alexandros Singh, and Theodore Andronikos, the journal paper described in (Giannakis et al, 2016) was co-authored by Georgia Theocharopoulou, Christos Papalitsas, Theodore Andronikos, and Panayiotis Vlamos, and the (Giannakis & Andronikos, 2015c by Theodore Andronikos.…”

“…Finally, in the end of this dissertation we provide the necessary abbreviations for the terminology we use throughout this thesis, as well as a useful index section of the most important terms within the main Chapters. Some of the definitions and the examples of Chapter 1 were taken from the published work in (Giannakis & Andronikos, 2015c) in the journal "International Journal of Scientific World" in 2015. Our results in Chapter 3 were published in (Giannakis & Andronikos, 2015a,b) in the journal of Natural Computing and the proceedings of Genedis 2014 in Corfu, respectfully.…”

“…Πιο συγκεκριμένα, οι εργασίες αυτές είναι οι ,b, 2016, Theocharopoulou & Giannakis, 2012, Giannakis & Andronikos, 2015c. Η εργασία που περιγρλαφεται στο είχε σαν συσυγγραφείς τους Χρήστο Παπαλίτσα και τον Θεόδωρο Ανδρόνικο, το άρθρο τους Χρήστο Παπαλίτσα, Καλλιόπη Κασταμπολίδου, Αλέξανδρο Σινγκ, και Θεόδωρο Ανδρόνικο, το άρθρο (Giannakis et al, 2016) από τους Γεωργία Θεοχαροπούλου, Χρήστο Παπαλίτσα, Θεόδωρο Ανδρόνικο, και Παναγιώτη Βλάμο, και, τέλος, οι εργασίες (Giannakis & Andronikos, 2015c τον Θεόδωρο Ανδρόνικο.…”

“…Ορισμένοι από τους ορισμούς και τα παραδείγματα του Κεφαλαίου 1 έχουν αντληθεί από τη δημοσιευμένη εργασία στο (Giannakis & Andronikos, 2015c) στο περιοδικό "International Journal of Scientific World" το 2015. Τα αποτελέσματά στο Κεφάλαιο 3 δημοσιεύτηκαν στα (Giannakis & Andronikos, 2015a,b) στο περιοδικόNatural Computing και στα πρακτικά του διεθνούς συνεδρίου Genedis 2014 στην Κέρκυρα, αντίστοιχα.…”