2026-07-21T14:16:18Z https://drops.dagstuhl.de/oai

oai:drops-oai.dagstuhl.de:23853 2025-11-12T13:29:44Z ddc:004 open_access

Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems Lee, Inhoo Buse, Salvador Winfree, Erik Differentiable Programming Chemical Reaction Networks Reaction-Diffusion Systems Many molecular systems are best understood in terms of prototypical species and reactions. The central dogma and related biochemistry are rife with examples: gene i is transcribed into RNA i, which is translated into protein i; kinase n phosphorylates substrate m; protein p dimerizes with protein q. Engineered nucleic acid systems also often have this form: oligonucleotide i hybridizes to complementary oligonucleotide j; signal strand n displaces the output of seesaw gate m; hairpin p triggers the opening of target q. When there are many variants of a small number of prototypes, it can be conceptually cleaner and computationally more efficient to represent the full system in terms of indexed species (e.g. for dimerization, M_p, D_pq) and indexed reactions (M_p + M_q → D_pq). Here, we formalize the Indexed Chemical Reaction Network (ICRN) model and describe a Python software package designed to simulate such systems in the well-mixed and reaction-diffusion settings, using a differentiable programming framework originally developed for large-scale neural network models, taking advantage of GPU acceleration when available. Notably, this framework makes it straightforward to train the models’ initial conditions and rate constants to optimize a target behavior, such as matching experimental data, performing a computation, or exhibiting spatial pattern formation. The natural map of indexed chemical reaction networks onto neural network formalisms provides a tangible yet general perspective for translating concepts and techniques from the theory and practice of neural computation into the design of biomolecular systems. Schloss Dagstuhl – Leibniz-Zentrum für Informatik Inhoo Lee and Salvador Buse and Erik Winfree 2025 Is Part Of LIPIcs, Volume 347, 31st International Conference on DNA Computing and Molecular Programming (DNA 31) (2025) InProceedings Text doc-type:ResearchArticle publishedVersion application/pdf doi:10.4230/LIPIcs.DNA.31.4 urn:nbn:de:0030-drops-238534 https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.4 eng https://creativecommons.org/licenses/by/4.0/legalcode