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Documents authored by Fazekas, Szilárd Zsolt

Document
DOI: 10.4230/LIPIcs.DNA.31.5
Programmable Co‑Transcriptional Splicing: Realizing Regular Languages via Hairpin Deletion

Authors: Da-Jung Cho, Szilárd Zsolt Fazekas, Shinnosuke Seki, and Max Wiedenhöft

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

Abstract
RNA co-transcriptionality, where RNA is spliced or folded during transcription from DNA templates, offers promising potential for molecular programming. It enables programmable folding of nanoscale RNA structures and has recently been shown to be Turing universal. While post-transcriptional splicing is well studied, co-transcriptional splicing is gaining attention for its efficiency, though its unpredictability still remains a challenge. In this paper, we focus on engineering co-transcriptional splicing, not only as a natural phenomenon but as a programmable mechanism for generating specific RNA target sequences from DNA templates. The problem we address is whether we can encode a set of RNA sequences for a given system onto a DNA template word, ensuring that all the sequences are generated through co-transcriptional splicing. Given that finding the optimal encoding has been shown to be NP-complete under the various energy models considered [Da-Jung Cho et al., 2025], we propose a practical alternative approach under the logarithmic energy model. More specifically, we provide a construction that encodes an arbitrary nondeterministic finite automaton (NFA) into a circular DNA template from which co-transcriptional splicing produces all sequences accepted by the NFA. As all finite languages can be efficiently encoded as NFA, this framework solves the problem of finding small DNA templates for arbitrary target sets of RNA sequences. The quest to obtain the smallest possible such templates naturally leads us to consider the problem of minimizing NFAs and certain practically motivated variants of it, but as we show, those minimization problems are computationally intractable.
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Da-Jung Cho, Szilárd Zsolt Fazekas, Shinnosuke Seki, and Max Wiedenhöft. Programmable Co‑Transcriptional Splicing: Realizing Regular Languages via Hairpin Deletion. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 5:1-5:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{cho_et_al:LIPIcs.DNA.31.5,
  author =	{Cho, Da-Jung and Fazekas, Szil\'{a}rd Zsolt and Seki, Shinnosuke and Wiedenh\"{o}ft, Max},
  title =	{{Programmable Co‑Transcriptional Splicing: Realizing Regular Languages via Hairpin Deletion}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{5:1--5:22},
  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.31.5},
  URN =		{urn:nbn:de:0030-drops-238548},
  doi =		{10.4230/LIPIcs.DNA.31.5},
  annote =	{Keywords: RNA Transcription, Co-Transcriptional Splicing, Finite Automata Simulation, NFA Minimization}
}
Document
DOI: 10.4230/LIPIcs.ISAAC.2024.28
Subsequence Matching and Analysis Problems for Formal Languages

Authors: Szilárd Zsolt Fazekas, Tore Koß, Florin Manea, Robert Mercaş, and Timo Specht

Published in: LIPIcs, Volume 322, 35th International Symposium on Algorithms and Computation (ISAAC 2024)

Abstract
In this paper, we study a series of algorithmic problems related to the subsequences occurring in the strings of a given language, under the assumption that this language is succinctly represented by a grammar generating it, or an automaton accepting it. In particular, we focus on the following problems: Given a string w and a language L, does there exist a word of L which has w as subsequence? Do all words of L have w as a subsequence? Given an integer k alongside L, does there exist a word of L which has all strings of length k, over the alphabet of L, as subsequences? Do all words of L have all strings of length k as subsequences? For the last two problems, efficient algorithms were already presented in [Adamson et al., ISAAC 2023] for the case when L is a regular language, and efficient solutions can be easily obtained for the first two problems. We extend that work as follows: we give sufficient conditions on the class of input-languages, under which these problems are decidable; we provide efficient algorithms for all these problems in the case when the input language is context-free; we show that all problems are undecidable for context-sensitive languages. Finally, we provide a series of initial results related to a class of languages that strictly includes the regular languages and is strictly included in the class of context-sensitive languages, but is incomparable to the of class context-free languages; these results deviate significantly from those reported for language-classes from the Chomsky hierarchy.
Cite as

Szilárd Zsolt Fazekas, Tore Koß, Florin Manea, Robert Mercaş, and Timo Specht. Subsequence Matching and Analysis Problems for Formal Languages. In 35th International Symposium on Algorithms and Computation (ISAAC 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 322, pp. 28:1-28:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{fazekas_et_al:LIPIcs.ISAAC.2024.28,
  author =	{Fazekas, Szil\'{a}rd Zsolt and Ko{\ss}, Tore and Manea, Florin and Merca\c{s}, Robert and Specht, Timo},
  title =	{{Subsequence Matching and Analysis Problems for Formal Languages}},
  booktitle =	{35th International Symposium on Algorithms and Computation (ISAAC 2024)},
  pages =	{28:1--28:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-354-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{322},
  editor =	{Mestre, Juli\'{a}n and Wirth, Anthony},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2024.28},
  URN =		{urn:nbn:de:0030-drops-221551},
  doi =		{10.4230/LIPIcs.ISAAC.2024.28},
  annote =	{Keywords: Stringology, String Combinatorics, Subsequence, Formal Languages, Context-Free Languages, Context-Sensitive Languages}
}
Document
DOI: 10.4230/LIPIcs.ISAAC.2022.37
On Algorithmic Self-Assembly of Squares by Co-Transcriptional Folding

Authors: Szilárd Zsolt Fazekas, Hwee Kim, Ryuichi Matsuoka, Shinnosuke Seki, and Hinano Takeuchi

Published in: LIPIcs, Volume 248, 33rd International Symposium on Algorithms and Computation (ISAAC 2022)

Abstract
Algorithms play a primary role in programming an orchestrated self-assembly of shapes into molecules. In this paper, we study the algorithmic self-assembly of squares by RNA co-transcriptional folding in its oritatami model. We formalize the square self-assembly problem in oritatami and propose a universal oritatami transcript made of 939 types of abstract molecules (beads) and of period 1294 that folds deterministically and co-transcriptionally at delay 3 and maximum arity into the n × n square modulo horizontal and vertical scaling factors for all sufficiently large n’s after building a Θ(log n) width "ruler" that measures n upon the seed of size Θ(log n) on which n is encoded in binary.
Cite as

Szilárd Zsolt Fazekas, Hwee Kim, Ryuichi Matsuoka, Shinnosuke Seki, and Hinano Takeuchi. On Algorithmic Self-Assembly of Squares by Co-Transcriptional Folding. In 33rd International Symposium on Algorithms and Computation (ISAAC 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 248, pp. 37:1-37:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{fazekas_et_al:LIPIcs.ISAAC.2022.37,
  author =	{Fazekas, Szil\'{a}rd Zsolt and Kim, Hwee and Matsuoka, Ryuichi and Seki, Shinnosuke and Takeuchi, Hinano},
  title =	{{On Algorithmic Self-Assembly of Squares by Co-Transcriptional Folding}},
  booktitle =	{33rd International Symposium on Algorithms and Computation (ISAAC 2022)},
  pages =	{37:1--37:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-258-7},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{248},
  editor =	{Bae, Sang Won and Park, Heejin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2022.37},
  URN =		{urn:nbn:de:0030-drops-173228},
  doi =		{10.4230/LIPIcs.ISAAC.2022.37},
  annote =	{Keywords: Algorithmic molecular self-assembly, Co-transcriptional folding, Oritatami system, Self-assembly of squares}
}
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