2 Search Results for "Ovchinnikov, Alexey"

Document
DOI: 10.4230/LIPIcs.DNA.31.4
Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems

Authors: Inhoo Lee, Salvador Buse, and Erik Winfree

Published in: LIPIcs, Volume 347, 31st International Conference on DNA Computing and Molecular Programming (DNA 31) (2025)

Abstract
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.
Cite as

Inhoo Lee, Salvador Buse, and Erik Winfree. Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 4:1-4:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{lee_et_al:LIPIcs.DNA.31.4,
  author =	{Lee, Inhoo and Buse, Salvador and Winfree, Erik},
  title =	{{Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{4:1--4:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-399-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{347},
  editor =	{Schaeffer, Josie and Zhang, Fei},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.4},
  URN =		{urn:nbn:de:0030-drops-238534},
  doi =		{10.4230/LIPIcs.DNA.31.4},
  annote =	{Keywords: Differentiable Programming, Chemical Reaction Networks, Reaction-Diffusion Systems}
}
Document
DOI: 10.4230/DagSemProc.06271.4
Bounds and algebraic algorithms in differential algebra: the ordinary case

Authors: Marc Moreno Maza, Oleg Golubitsky, Marina V. Kondratieva, and Alexey Ovchinnikov

Published in: Dagstuhl Seminar Proceedings, Volume 6271, Challenges in Symbolic Computation Software (2006)

Abstract
Consider the Rosenfeld-Groebner algorithm for computing a regular decomposition of a radical differential ideal generated by a set of ordinary differential polynomials. This algorithm inputs a system of differential polynomials and a ranking on derivatives and constructs finitely many regular systems equivalent to the original one. The property of regularity allows to check consistency of the systems and membership to the corresponding differential ideals. We propose a bound on the orders of derivatives occurring in all intermediate and final systems computed by the Rosenfeld-Groebner algorithm and outline its proof. We also reduce the problem of conversion of a regular decomposition of a radical differential ideal from one ranking to another to a purely algebraic problem.
Cite as

Marc Moreno Maza, Oleg Golubitsky, Marina V. Kondratieva, and Alexey Ovchinnikov. Bounds and algebraic algorithms in differential algebra: the ordinary case. In Challenges in Symbolic Computation Software. Dagstuhl Seminar Proceedings, Volume 6271, pp. 1-9, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2007)

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@InProceedings{morenomaza_et_al:DagSemProc.06271.4,
  author =	{Moreno Maza, Marc and Golubitsky, Oleg and Kondratieva, Marina V. and Ovchinnikov, Alexey},
  title =	{{Bounds and algebraic algorithms in differential algebra: the ordinary case}},
  booktitle =	{Challenges in Symbolic Computation Software},
  pages =	{1--9},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2007},
  volume =	{6271},
  editor =	{Wolfram Decker and Mike Dewar and Erich Kaltofen and Stephen Watt},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.06271.4},
  URN =		{urn:nbn:de:0030-drops-10219},
  doi =		{10.4230/DagSemProc.06271.4},
  annote =	{Keywords: Differential algebra, Rosenfeld Groebner Algorithm}
}
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