Formal Models of Biological Systems

Abstract

Recent biomedical research studies are focused in the mechanisms by which misfolded proteins lead to the generation of oxidative stress in the form of reactive oxygen species (ROS), often implicated in neurodegenerative diseases and aging. Moreover, biological experiments are designed to investigate how proteostasis depends on the balance between the folding capacity of chaperone networks and the continuous flux of potentially nonnative proteins. Nevertheless, biological experimental methods can examine the protein folding quality control mechanisms only in individual cells, but not in a multicellular level. Formal models offer a dynamic form of modelling, which allows to explore various parameter values in an integrated time-dependent system. This paper aims to present a formal approach of a mathematical descriptive model using as example a representation of a known molecular chaperone system and its relation to diseases associated to protein misfolding and neurodegeneration.

Using BTA Algorithm for Finding Nash Equilibrium Problem Aiming the Extraction of Rules in Rule Learning

“…Rule learning methods are popular techniques among data mining and machine learning methods with applications in expert systems, controller systems (especially fuzzy controller systems), describing economic processes and predicting related efficient strategies, distributed systems (especially cloud computing systems), informatics for prediction and detection of different biological structures. Generally speaking, rule learning methods are efficient in any given system dealing with rule-based strategies [40][17] [22] [3].…”

Modeling brain disorders using neuroinformatics in cellular physiology

“…Πιο συγκεκριμένα, οι εργασίες αυτές είνα οι , Theocharopoulou and Vlamos, 2015, Theocharopoulou et al, 2015a,b, Giannakis et al, 2016, Theocharopoulou and Bobori, 2016, Kapodistrias et al, 2017, Theocharopoulou et al, 2017b,a, Theocharopoulou and Vlamos, 2020, Theocharopoulou, 2020. Οι εργασίες που περιγράφονται στα (Theocharopoulou et al, 2017a, 2015a, Kapodistrias et al, 2017 είχαν σαν συ-συγγραφείς τους Παναγιώτη Βλάμο, Κατερίνα Μπόμπορη, Αντιγόνη Αβραμούλη, Νικόλαο Καποδίστρια.…”

“…In the next section we formally describe a mitochondria fusion model using a variant of membrane automata Theocharopoulou et al (2015b). Furthermore, a formal method of a mathematical descriptive approach is introduced, using as a case study the machinery of a known molecular chaperone system and its implication to diseases correlated to protein misfolding and neurodegeneration Theocharopoulou and Vlamos (2015), Theocharopoulou et al (2017b).…”

“…Most of the results reported in this dissertation have already been published in respectful peer-reviewed journals and have been presented in international conferences (followed up by v a paper publication in the conference proceedings) , Theocharopoulou and Vlamos, 2015, Theocharopoulou et al, 2015a,b, Giannakis et al, 2016, Theocharopoulou and Bobori, 2016, Kapodistrias et al, 2017, Theocharopoulou et al, 2017b,a, Theocharopoulou and Vlamos, 2020, Theocharopoulou, 2020. Publications in (Theocharopoulou et al, 2017a, 2015a, Kapodistrias et al, 2017 were co-authored with Bobori, Catherine, Avramouli, Antigoni and Kapodistrias, Nikolaos, respectively.…”