PhD Oral Exam - Mohiul Islam, Electrical and Computer Engineering

When studying for a doctoral degree (PhD), candidates submit a thesis that provides a critical review of the current state of knowledge of the thesis subject as well as the student’s own contributions to the subject. The distinguishing criterion of doctoral graduate research is a significant and original contribution to knowledge.

Once accepted, the candidate presents the thesis orally. This oral exam is open to the public.

Abstract

String is a new computer language designed specifically for the implementation of ‘ribozymes’, the active entities within a new (highly simplified) model of proto-cellular life. The purpose of the model is the study of the abstract nature of simple cellular life and its relationship to computation. This model contains passive and active entities; passive entities are data and active ones are executable data (or programs). All programs in our model are written or evolved in String. In this thesis, we describe String and provide examples of both hand-written and evolved String programs belonging to different functional categories needed for cellular operation (e.g., mass transporter, information transporter, transformer, replicator and translator). Results from the evolutionary runs are presented and discussed, where almost all ribozymes reached their optimum fitness. The latest measures of robustness and evolvability are presented, and are applied to String programs. Next we have example String programs show-casing it as a homoiconic programming language, where programs are capable of manipulating itself. A 2-state 3-symbol universal Turing machine is also written in String, to prove its Turing-completeness. Finally, we present a complete ProtoCell model with an artificial metabolic cycle at its core. This cycle is simulated using a Gillespie algorithm, where String-encoded ribozymes act the ‘enzymes’ catalysing the different chemical reactions of the metabolic cycle. This cycle will provide the essential material building blocks (or their precursors) and energy currency of the ProtoCell. The genomic subsystem is integrated with ProtoCell with a changing concentration of each ribozyme using self regulating differential equations, while membrane subsystem consists of a permeable membrane diffusing atoms and energy while transporting molecules between the cytoplasm and the environment. After independent stable simulation of the individual subsystems, we combined all three subsystems to have a continuously running stable ProtoCell simulation.