Search Results

Documents authored by Castellanos, Jose-Luis

Document
DOI: 10.4230/LIPIcs.ISAAC.2025.7
Polynomial Equivalence of Extended Chemical Reaction Models

Authors: Divya Bajaj, Jose-Luis Castellanos, Ryan Knobel, Austin Luchsinger, Aiden Massie, Adrian Salinas, Pablo Santos, Ramiro Santos, Robert Schweller, and Tim Wylie

Published in: LIPIcs, Volume 359, 36th International Symposium on Algorithms and Computation (ISAAC 2025)

Abstract
The ability to detect whether a species (or dimension) is zero in Chemical Reaction Networks (CRN), Vector Addition Systems, or Petri Nets is known to increase the power of these models - making them capable of universal computation. While this ability may appear in many forms, such as extending the models to allow transitions to be inhibited, prioritized, or synchronized, we present an extension that directly performs this zero checking. We introduce a new void genesis CRN variant with a simple design that merely increments the count of a specific species when any other species' count goes to zero. As with previous extensions, we show that the model is Turing Universal. We then analyze several other studied CRN variants and show that they are all equivalent through a polynomial simulation with the void genesis model, which does not merely follow from Turing-universality. Thus, inhibitor species, reactions that occur at different rates, being allowed to run reactions in parallel, or even being allowed to continually add more volume to the CRN, does not add additional simulation power beyond simply detecting if a species count becomes zero.
Cite as

Divya Bajaj, Jose-Luis Castellanos, Ryan Knobel, Austin Luchsinger, Aiden Massie, Adrian Salinas, Pablo Santos, Ramiro Santos, Robert Schweller, and Tim Wylie. Polynomial Equivalence of Extended Chemical Reaction Models. In 36th International Symposium on Algorithms and Computation (ISAAC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 359, pp. 7:1-7:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{bajaj_et_al:LIPIcs.ISAAC.2025.7,
  author =	{Bajaj, Divya and Castellanos, Jose-Luis and Knobel, Ryan and Luchsinger, Austin and Massie, Aiden and Salinas, Adrian and Santos, Pablo and Santos, Ramiro and Schweller, Robert and Wylie, Tim},
  title =	{{Polynomial Equivalence of Extended Chemical Reaction Models}},
  booktitle =	{36th International Symposium on Algorithms and Computation (ISAAC 2025)},
  pages =	{7:1--7:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-408-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{359},
  editor =	{Chen, Ho-Lin and Hon, Wing-Kai and Tsai, Meng-Tsung},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2025.7},
  URN =		{urn:nbn:de:0030-drops-249158},
  doi =		{10.4230/LIPIcs.ISAAC.2025.7},
  annote =	{Keywords: Chemical Reaction Networks, Simulations, Petri-nets, Vector Addition Systems, Bi-simulation, Turing-universality, Inhibitors}
}
Any Issues?
X

Feedback on the Current Page

CAPTCHA

Thanks for your feedback!

Feedback submitted to Dagstuhl Publishing

Could not send message

Please try again later or send an E-mail
© 2023-2025 Schloss Dagstuhl – LZI GmbH About DROPS Imprint Privacy Contact