Exploration of Extended Chemical Reaction Networks

Author

• Ramiro Santos, The University of Texas Rio Grande Valley

Date of Award

5-1-2026

Document Type

Thesis

Degree Name

Master of Science (MS)

Department

Computer Science

First Advisor

Austin Luchsinger

Second Advisor

Robert Schweller

Third Advisor

Tim Wylie

Abstract

Chemical Reaction Networks (CRNs) is a well-established model for analyzing distributed and concurrent systems. A central problem studied across CRNs is the reachability problem, which asks whether a target configuration can be obtained from a given initial configuration through a sequence of valid transitions. Classical CRNs are highly expressive but not Turing-universal; their reachability problem is Ackermann-complete, indicating extremely high computational complexity that nevertheless falls short of full universality.

In this thesis, we study Extended Models of Chemical Reaction Networks in which the dynamics of the system are modified. We analyze these models through two fundamental questions. First, simulation, we ask whether an extended CRN can simulate another model of computation. Second, reachability, we ask whether, given an initial configuration and a target configuration, there exists a sequence of reactions that transforms the former into the latter. We also study a refinement of reachability known as the Unique Sink problem, which asks whether all possible reaction sequences from a fixed initial configuration lead to the same target configuration.

We show that the increased computational power of these extended models arises from their ability to perform zero checking, that is, to detect the absence of a species. This capability fundamentally changes the reachability structure of the system. We construct simulations demonstrating that, once zero-checking is available, the model can simulate a deterministic Register Machine. As a consequence, these extended CRN models achieve Turing universality.

Our results characterize the precise role of zero-checking in extending CRNs beyond classical reachability limitations and clarify the relationship between simulation, reachability, and unique reachability in chemically inspired computational systems.

Comments

Copyright 2026 Ramiro Santos. All Rights Reserved. https://proquest.com/docview/3371410281

Recommended Citation

Santos, R. (2026). Exploration of Extended Chemical Reaction Networks [Master's thesis, The University of Texas Rio Grande Valley]. ScholarWorks @ UTRGV. https://scholarworks.utrgv.edu/etd/1962