### Shinnosuke SEKI

Department of Computer and Network Engineering | Associate Professor |

Cluster I (Informatics and Computer Engineering) | Associate Professor |

Researcher Information

### Field Of Study

### Career

- Sep. 2018 - Present

Ecole Normale Superieure de Lyon, Invited Professor, France - Sep. 2013 - Mar. 2015

Academy of Finland, Postdoctoral Researcher, Principal Investigator, Finland - Feb. 2012 - Aug. 2013

Aalto University, Department of Information and Computer Science, Postdoctoral Researcher, Finland - 01 May 2011 - 15 Feb. 2012

Kyoto University, 薬学研究科, 博士研究員 - Sep. 2010 - Apr. 2011

University of Western Ontario, Department of Computer Science, Postdoctoral Researcher, Canada

### Educational Background

### Member History

- Feb. 2024 - Present

Member, Program Committee of the IEEE 3rd Conference on Information Technology and Data Science (CITDS 2024) - Nov. 2023 - Present

Member, Program Committee of the 26th International Conference on Descriptional Complexity of Formal Systems (DCFS 2024), Society - Sep. 2023 - Present

Co-chair, Program Committee of the 30th International Conference on DNA Computing and Molecular Programming (DNA30), Society - Aug. 2023 - Present

Member, Organizing Committee of the 28th International Conference on Implementation and Application of Automata (CIAA 2024), Society - Jul. 2023 - Present

Member, Organizing Committee of the 21st International Conference on Unconventional Computation and Natural Computation (UCNC 2024), Society - Sep. 2022 - Present

Member, Steering Committee of the International Conference on Machines, Computations, and Universality (MCU), Society - Oct. 2021 - Present

Co-chair, Steering Committee of the International Conference on Unconventional Computation and Natural Computation (UCNC), Co-chair - Sep. 2019 - Present

Area Editor, New Generation Computing, Editorial Board, Society - Apr. 2018 - Present

Advisory Board, Springer Natural Computing Book-Series, Society - Aug. 2017 - Present

Member, Steering Committee of International Conference on Developments in Language Theory (DLT), Society - Sep. 2022 - Sep. 2023

Member, Program Committee of the 29th International Conference on DNA Computing and Molecular Programming (DNA29), Society - Sep. 2022 - Sep. 2023

Member, Program Committee of the 27th International Conference on Implementation and Application of Automata (CIAA2023), Society - Jul. 2022 - Jul. 2023

Member, Program Committee of the 25th International Conference on Descriptional Complexity of Formal Systems (DCFS 2023), Society - Apr. 2022 - Jul. 2023

Member, Program Committee of the 19th Conference on Computability in Europe (CiE2023), Society - 01 Apr. 2018

専門委員, 情報処理学会アルゴリズム研究会 - 01 Apr. 2018

関 新之助, 情報処理学会アルゴリズム研究会 - 01 Oct. 2014

関 新之助, 情報処理学会論文誌「数理モデル化と応用」編集委員会, Society

Research Activity Information

### Award

### Paper

- Towards composable computations by RNA co-transcriptional folding: A proof-of-concept demonstration of nested loops in oritatami

Szilárd Zsolt Fazekas; Naoya Iwano; Yu Kihara; Ryuichi Matsuoka; Shinnosuke Seki; Hinano Takeuchi

Corresponding, Theoretical Computer Science, Elsevier BV, 999, 114550-114550, Jun. 2024, Peer-reviwed, Invited

Scientific journal, English - Freezing 1-tag systems with states

Szilard Zsolt Fazekas; Shinnosuke Seki

Corresponding, Electronic Proceedings in Theoretical Computer Science (EPTCS), Proceedings of the 16th International Conference on Automata and Formal Languages (AFL 2023), 386, 82-95, Sep. 2023, Peer-reviwed

International conference proceedings, English - Ok: A kinetic model for locally reconfigurable molecular systems

Pierre Marcus; Nicolas Schabanel; Shinnosuke Seki

Corresponding, Visions of DNA Nanotechnology at 40 for the Next 40, 229-240, May 2023, Peer-reviwed, Invited

Scientific journal, English - Oritatami systems assemble shapes no less complex than tile assembly model (aTAM)

Daria Pchelina; Nicolas Schabanel; Shinnosuke Seki; Guillaume Theyssier

Proceedings of the 39th International Symposium on Theoretical Aspects of Computer Science (STACS 2022), LIPIcs 219, 51:1-51:23, 09 Mar. 2022, Peer-reviwed

International conference proceedings, English - Square network on a word

Szilard Zsolt Fazekas; Shinnosuke Seki

Theoretical Computer Science, Elsevier, 894, 26, 121-134, Nov. 2021, Peer-reviwed, Left-aligned last occurrences of squares (double-square) have provided profound insights into the question of how many distinct squares can be packed on a word ω of length n and brought the best known upper bound 11n/6. Other types of alignments such as being center-aligned as well as long distance relations such as being the occurrences of the same square incorporate the squares on ω into a bipartite graph of the squares and positions {1,2,…,n}, which we call the square network. Packing more and more squares in a limited space certainly induces specific kinds of subgraphs once the square density exceeds a threshold, and if one of the subgraphs is known to be forbidden, the threshold provides an upper bound on the number of distinct squares. In this paper, we designate a specific position of double-squares as P1 and obtain certain induced subgraphs as well as forbidden ones guaranteed by the presence of P1-aligned double squares; an induced subgraph of particular interest expresses the global uniqueness of squares involved.

Scientific journal, English - Simple intrinsic simulation of cellular automata in oritatami molecular folding model

Daria Pchelina; Nicolas Schabanel; Shinnosuke Seki; Yuki Ubukata

Proceedings of the 14th Latin American Theoretical Informatics Symposium (LATIN 2020), Springer, LNCS 12118, 425-436, 05 Jan. 2021, Peer-reviwed

International conference proceedings, English - Linear bounds on the size of the conformations in greedy deterministic oritatami

Szilard Zsolt Fazekas; Hwee Kim; Ryuichi Matsuoka; Reoto Morita; Shinnosuke Seki

International Journal of Foundations of Computer Science, World Scientific Publishing Company, 32, 5, 575-596, 2021, Peer-reviwed

Scientific journal, English - A general architecture of oritatami systems for simulating arbitrary finite automata

Yo-Sub Han; Hwee Kim; Yusei Masuda; Shinnosuke Seki

Theoretical Computer Science, Springer, 870, 16, 29-52, 2021, Peer-reviwed

Scientific journal, English - Counting infinitely by oritatami co-transcriptional folding

Kohei Maruyama; Shinnosuke Seki

Natural Computing, Springer, 20, 2, 329-340, 2021, Peer-reviwed

Scientific journal, English - Transcript design problem of oritatami systems

Yo-Sub Han; Hwee Kim; Shinnosuke Seki

Natural Computing, Springer, 19, 2, 323-335, 2020, Peer-reviwed

Scientific journal, English - Self-attraction removal from oritatami systems

Yo-Sub Han; Hwee Kim; Trent A. Rogers; Shinnosuke Seki

International Journal of Foundations of Computer Science, 30, 6-7, 1047-1067, 2019, Peer-reviwed

Scientific journal, English - On the Power of Oritatami Cotranscriptional Folding with Unary Bead Sequence.

Szilárd Zsolt Fazekas; Kohei Maruyama; Reoto Morita; Shinnosuke Seki

Proceedings of the 15th International Conference on Theory and Applications of Models of Computation (TAMC 2019), Springer, LNCS 11436, 188-207, 2019, Peer-reviwed

International conference proceedings, English - Oritatami: a computational model for molecular co-transcriptional folding

Cody Geary; Pierre-Etienne Meunier; Nicolas Schabanel; Shinnosuke Seki

International Journal of Molecular Sciences, MDPI, 20, 9, 2259, 2019, Peer-reviwed

Scientific journal, English - Single-stranded architectures for computing

Shinnosuke Seki

Proceedings of the 23rd International Conference on Developments in Language Theory (DLT 2019), Springer, LNCS 11647, 41-56, 2019, Peer-reviwed, Invited

International conference proceedings, English - Nondeterministic seedless oritatami systems and hardness of testing their equivalence

Yo-Sub Han; Hwee Kim; Makoto Ota; Shinnosuke Seki

Natural Computing, Springer, 17, 1, 67-79, 2018, Peer-reviwed

Scientific journal, English - Towards the algorithmic molecular self-assembly of fractals by cotranscriptional folding

Yusei Masuda; Shinnosuke Seki; Yuki Ubukata

Proceedings of the 23rd International Conference on Implementation and Applications of Automata (CIAA2018), Springer, LNCS, 10977, 261-273, 2018, Peer-reviwed

International conference proceedings, English - Know when to fold 'em: Self-assembly of shapes by folding in oritatami

Erik Demaine; Jacob Hendricks; Meagan Olsen; Matthew J. Patitz; Trent A. Rogers; Nicolas Schabanel; Shinnosuke Seki; Hadley Thoams

Proceedings of the 24th International Conference on DNA Computing and Molecular Programming (DNA 24), Springer, LNCS, 11145, 19-36, 2018, Peer-reviwed

International conference proceedings, English - Transcript design problem of oritatami systems

Yo-Sub Han; Hwee Kim; Shinnosuke Seki

Proceedings of the 24th International Conference on DNA Computing and Molecular Programming (DNA 24), Springer, LNCS, 11145, 139-154, 2018, Peer-reviwed

International conference proceedings, English - Proving the Turing universality of oritatami co-transcriptional folding

Cody Geary; Pierre-Etienne Meunier; Nicolas Schabanel; Shinnosuke Seki

Proceedings of the 29th International Symposium on Algorithms and Computation (ISAAC2018), Schloss Dagstuhl, LIPIcs 123, 23:1-23:13, 2018, Peer-reviwed

International conference proceedings, English - The Complexity of Fixed-Height Patterned Tile Self-Assembly

Shinnosuke Seki; Andrew Winslow

INTERNATIONAL JOURNAL OF FOUNDATIONS OF COMPUTER SCIENCE, WORLD SCIENTIFIC PUBL CO PTE LTD, 28, 5, 465-482, Aug. 2017, Peer-reviwed, We characterize the complexity of the PATS problem for patterns of fixed height and color count in variants of the model where seed glues are either chosen or fixed and identical (so-called non-uniform and uniform variants). We prove that both variants are NP-complete for patterns of height 2 or more and admit O(n)-time algorithms for patterns of height 1. We also prove that if the height and number of colors in the pattern is fixed, the non-uniform variant admits a O(n)-time algorithm while the uniform variant remains NP-complete. The NP-completeness results use a new reduction from a constrained version of a problem on finite state transducers.

Scientific journal, English - Self-attraction removal from oritatami systems

Yo-Sub Han; Hwee Kim; Trent A. Rogers; Shinnosuke Seki

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer Verlag, 10316, 164-176, 2017, Peer-reviwed, RNA cotranscriptional folding refers to the phenomenon in which an RNA transcript folds upon itself while being synthesized (transcribed). Oritatami is a computational model of this phenomenon, which lets its transcript, a sequence of beads (abstract molecules) fold cotranscriptionally via interactions between beads according to its ruleset. In this paper, we study the problem of removing self-attractions, which lets a bead interact with another bead of the same kind, from a given oritatami system without changing its behavior. We provide an algorithm for that with overhead linear in the delay parameter, which should be considerably smaller than the length of its transcript. We also show that this overhead is tight.

International conference proceedings, English - Oritatami System; a Survey and the Impossibility of Simple Simulation at Small Delays

Trent A. Rogers; Shinnosuke Seki

FUNDAMENTA INFORMATICAE, IOS PRESS, 154, 1-4, 359-372, 2017, Peer-reviwed, RNA sequences start folding immediately as they are synthesized by RNA polymerase (cotranscriptional folding). The oritatami system (OS) is a novel mathematical model to study computational aspects of cotranscriptional folding. In this paper, we first provide a survey throughout existing research topics and results on oritatami systems and offer research directions of significance. Simulation of an oritatami system in a different ratio (delay) of transcription speed to the speed of folding is one of them. We will introduce a simple notion of simulation, and prove that there is an OS of delay delta that cannot be simulated by any oritatami system at larger delay.

Scientific journal, English - Self-attraction removal from oritatami systems

Yo-Sub Han; Hwee Kim; Trent A. Rogers; Shinnosuke Seki

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer Verlag, 10316, 164-176, 2017, Peer-reviwed, RNA cotranscriptional folding refers to the phenomenon in which an RNA transcript folds upon itself while being synthesized (transcribed). Oritatami is a computational model of this phenomenon, which lets its transcript, a sequence of beads (abstract molecules) fold cotranscriptionally via interactions between beads according to its ruleset. In this paper, we study the problem of removing self-attractions, which lets a bead interact with another bead of the same kind, from a given oritatami system without changing its behavior. We provide an algorithm for that with overhead linear in the delay parameter, which should be considerably smaller than the length of its transcript. We also show that this overhead is tight.

International conference proceedings, English - The extended equation of Lyndon and Schutzenberger

Florin Manea; Mike Muller; Dirk Nowotka; Shinnosuke Seki

Journal of Computer and System Sciences, Elsevier, 85, 132-167, 26 Nov. 2016, Peer-reviwed

Scientific journal, English - Rule set design problems for oritatami system

Makoto Ota; Shinnosuke Seki

Theoretical Computer Science, Elsevier, 671, 26-35, 22 Sep. 2016, Peer-reviwed

Scientific journal, English - Programming biomolecules that fold greedily during transcription

Cody Geary; Pierre-Etienne Meunier; Nicolas Schabanel; Shinnosuke Seki

MFCS 2016: 41st International Symposium on Mathematical Foundations of Computer Science, LIPIcs 58, 43:1-43:14, 22 Aug. 2016, Peer-reviwed

International conference proceedings, English - Binary pattern tile set synthesis is NP-hard

Lila Kari; Steffen Kopecki; Pierre-Etienne Meunier; Matthew J. Patitz; Shinnosuke Seki

Algorithmica, Springer, 78, 1, 1-46, 26 Apr. 2016, Peer-reviwed

Scientific journal, English - The Complexity of Fixed-Height Patterned Tile Self-assembly

Shinnosuke Seki; Andrew Winslow

Implementation and Application of Automata, SPRINGER INT PUBLISHING AG, 9705, LNCS 9705, 248-259, 2016, Peer-reviwed, We characterize the complexity of the PATSproblem for patterns of fixed height and color count in variants of the model where seed glues are either chosen or fixed and identical (so-called non-uniform and uniform variants). We prove that both variants are NP-complete for patterns of height 2 or more and admit O(n)-time algorithms for patterns of height 1. We also prove that if the height and number of colors in the pattern is fixed, the non-uniform variant admits a O(n)-time algorithm while the uniform variant remains NP-complete. The NP-completeness results use a new reduction from a constrained version of a problem on finite state transducers.

International conference proceedings, English - Nondeterministic seedless oritatami systems and hardness of testing their equivalence

Yo-Sub Han; Hwee Kim; Makoto Ota; Shinnosuke Seki

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer Verlag, 9818, 19-34, 2016, Peer-reviwed, The oritatami system (OS) is a model of computation by cotranscriptional folding, being inspired by the recent experimental succeess of RNA origami to self-assemble an RNA tile cotranscriptionally.The OSs implemented so far, including binary counter and Turing machine simulator, are deterministic, that is, uniquely fold into one conformation, while nondeterminism is intrinsic in biomolecular folding.We introduce nondeterminism to OS (NOS) and propose an NOS that chooses an assignment of Boolean values nondeterministically and evaluates a logical formula on the assignment.This NOS is seedless in the sense that it does not require any initial conformation to begin with like the RNA origami.The NOS allows to prove the co-NP hardness of deciding, given two NOSs, if there exists no conformation that one of them folds into but the other does not.

International conference proceedings, English - A manually-checkable proof for the NP-hardness of 11-color pattern self-assembly tileset synthesis

Aleck Johnsen; Ming-Yang Kao; Shinnosuke Seki

Journal of Combinatorial Optimization, Springer, 33, 2, 496-529, 24 Nov. 2015, Peer-reviwed

Scientific journal, English - Program Size and Temperature in Self-Assembly

Ho-Lin Chen; David Doty; Shinnosuke Seki

ALGORITHMICA, SPRINGER, 72, 3, 884-899, Jul. 2015, Peer-reviwed, Winfree's abstract Tile Assembly Model is a model of molecular self-assembly of DNA complexes known as tiles, which float freely in solution and attach one at a time to a growing "seed" assembly based on specific binding sites on their four sides. We show that there is a polynomial-time algorithm that, given an square, finds the minimal tile system (i.e., the system with the smallest number of distinct tile types) that uniquely self-assembles the square, answering an open question of Adleman et al. (Combinatorial optimization problems in self-assembly, STOC 2002). Our investigation leading to this algorithm reveals other positive and negative results about the relationship between the size of a tile system and its "temperature" (the binding strength threshold required for a tile to attach).

Scientific journal, English - Dynamic Simulation of 1D Cellular Automata in the Active aTAM

Natasa Jonoska; Daria Karpenko; Shinnosuke Seki

NEW GENERATION COMPUTING, SPRINGER, 33, 3, 271-295, Jul. 2015, Peer-reviwed, The Active aTAM is a tile based model for self-assembly where tiles are able to transfer signals and change identities according to the signals received. We extend Active aTAM to include deactivation signals and thereby allow detachment of tiles. We show that the model allows a dynamic simulation of cellular automata with assemblies that do not record the entire computational history but only the current updates of the states, and thus provide a way for (a) algorithmic dynamical structural changes in the assembly and (b) reusable space in self-assembly. The simulation is such that at a given location the sequence of tiles that attach and detach corresponds precisely to the sequence of states the synchronous cellular automaton generates at that location.

Scientific journal, English - 3-color bounded patterned self-assembly

Lila Kari; Steffen Kopecki; Shinnosuke Seki

NATURAL COMPUTING, SPRINGER, 14, 2, 279-292, Jun. 2015, Peer-reviwed, The problem of patterned self-assembly tile set synthesis (PATS) is to find a minimal tile set which uniquely self-assembles into a given pattern. Czeizler and Popa proved the NP-completeness of PATS and Seki showed that the PATS problem is already NP-complete for patterns with 60 colors. In search for the minimal number of colors such that PATS remains NP-complete, we introduce multiple bound PATS (MBPATS) where we allow bounds for the numbers of tile types of each color. We show that MBPATS is NP-complete for patterns with just three colors and, as a byproduct of this result, we also obtain a novel proof for the NP-completeness of PATS which is more concise than the previous proofs.

Scientific journal, English - Square-Density Increasing Mappings

Florin Manea; Shinnosuke Seki

COMBINATORICS ON WORDS, WORDS 2015, SPRINGER-VERLAG BERLIN, 9304, 160-169, 2015, Peer-reviwed, The square conjecture claims that the number of distinct squares, factors of the form xx, in a word is at most the length of the word. Being associated with it, it is also conjectured that binary words have the largest square density. That is, it is sufficient to solve the square conjecture for words over binary alphabet. We solve this subsidiary conjecture affirmatively, or more strongly, we prove the irrelevance of the alphabet size in solving the square conjecture, as long as the alphabet is not unary. The tools we employ are homomorphisms with which one can convert an arbitrary word into a word with strictly larger square density over an intended alphabet.

International conference proceedings, English - Semilinear Sets and Counter Machines: a Brief Survey

Oscar H. Ibarra; Shinnosuke Seki

FUNDAMENTA INFORMATICAE, IOS PRESS, 138, 1-2, 61-76, 2015, Peer-reviwed, Semilinear sets are one of the most important concepts in theoretical computer science, as illustrated by the fact that the set of nonnegative integer solutions to any system of Diophantine equations is semilinear. Parikh's theorem enables us to represent any semilinear set as a push-down automaton (PDA). We summarize recent results on the descriptional complexity of conversions among different representations of a semilinear set: as a vector set (conventional), a finite automaton (FA), a PDA, etc.. We also discuss semilinearity-preserving operations like union, intersection, and complement. We use Parikh's theorem to enlarge the class of finite-state machines that can represent semilinear sets. In particular, we give a simpler proof of a known result that characterizes semilinear sets in terms of machines with reversal-bounded counters. We then investigate the power of such a machine with only one counter in the context of a long-standing conjecture about repetition on words.

Scientific journal, English - Binary Pattern Tile Set Synthesis Is NP-hard

Lila Kari; Steffen Kopecki; Pierre-Etienne Meunier; Matthew J. Patitz; Shinnosuke Seki

Automata, Languages, and Programming, Pt I, SPRINGER-VERLAG BERLIN, 9134, 1022-1034, 2015, Peer-reviwed, We solve an open problem, stated in 2008, about the feasibility of designing efficient algorithmic self-assembling systems which produce 2-dimensional colored patterns. More precisely, we show that the problem of finding the smallest tile assembly system which will self-assemble an input pattern with 2 colors (i.e., 2-Pats) is NP-hard. One crucial lemma makes use of a computer-assisted proof, which is a relatively novel but increasingly utilized paradigm for deriving proofs for complex mathematical problems. This tool is especially powerful for attacking combinatorial problems, as exemplified by the proof for the four color theorem and the recent important advance on the Erdos discrepancy problem using computer programs. In this paper, these techniques will be brought to a new order of magnitude, computational tasks corresponding to one CPU-year. We massively parallelize our program, and provide a full proof of its correctness. Its source code is freely available online.

International conference proceedings, English - Transfer matrix analysis of one-dimensional majority cellular automata with thermal noise

Remi Lemoy; Alexander Mozeika; Shinnosuke Seki

JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL, IOP PUBLISHING LTD, 47, 10, 105001-105001, Mar. 2014, Peer-reviwed, Thermal noise in a cellular automaton (CA) refers to a random perturbation in its function which eventually leads the automaton to an equilibrium state controlled by a temperature parameter. We study the one-dimensional majority-3 CA under this model of noise. Without noise, each cell in the automaton decides its next state by majority voting among itself and its left and right neighbour cells. Transfer matrix analysis shows that the automaton always reaches a state in which every cell is in one of its two states with probability 1/2 and thus cannot remember even one bit of information. Numerical experiments, however, support the possibility of reliable computation for a long but finite time.

Scientific journal, English - A Stronger Square Conjecture on Binary Words

Natasa Jonoska; Florin Manea; Shinnosuke Seki

SOFSEM 2014: THEORY AND PRACTICE OF COMPUTER SCIENCE, SPRINGER-VERLAG BERLIN, 8327, 339-350, 2014, Peer-reviwed, We propose a stronger conjecture regarding the number of distinct squares in a binary word. Fraenkel and Simpson conjectured in 1998 that the number of distinct squares in a word is upper bounded by the length of the word. Here, we conjecture that in the case of a word of length n over the alphabet {a, b}, the number of distinct squares is upper bounded by 2k-1/2k+2n, where k is the least of the number of a's and the number of b's. We support the conjecture by showing its validity for several classes of binary words. We also prove that the bound is tight.

International conference proceedings, English - Operational State Complexity under Parikh Equivalence

Giovanna J. Lavado; Giovanni Pighizzini; Shinnosuke Seki

DESCRIPTIONAL COMPLEXITY OF FORMAL SYSTEMS, DCFS 2014, SPRINGER-VERLAG BERLIN, 8614, 294-305, 2014, Peer-reviwed, We investigate, under Parikh equivalence, the state complexity of some language operations which preserve regularity. For union, concatenation, Kleene star, complement, intersection, shuffle, and reversal, we obtain a polynomial state complexity over any fixed alphabet, in contrast to the intrinsic exponential state complexity of some of these operations in the classical version. For projection we prove a superpolynomial state complexity, which is lower than the exponential one of the corresponding classical operation. We also prove that for each two deterministic automata A and B it is possible to obtain a deterministic automaton with a polynomial number of states whose accepted language has as Parikh image the intersection of the Parikh images of the languages accepted by A and B. Finally, we prove that for each finite set there exists a small context-free grammar defining a language with the same Parikh image.

International conference proceedings, English - Generalised Lyndon-Schutzenberger Equations

Florin Manea; Mike Mueller; Dirk Nowotka; Shinnosuke Seki

MATHEMATICAL FOUNDATIONS OF COMPUTER SCIENCE 2014, PT I, SPRINGER-VERLAG BERLIN, 8634, 402-+, 2014, Peer-reviwed, We fully characterise the solutions of the generalised Lyndon-Schutzenberger word equations u(1) ... u(l) = v(1) ... v(m)w(1) ... w(n), where u(i) is an element of {u, theta(u)} for all 1 <= i <= l, v(j) is an element of {v, theta(v)} for all 1 < j <= m, w(k) is an element of {w, theta(w)} for all 1 <= k <= n, and theta is an antimorphic involution. More precisely, we show for which f, m, and n such an equation has only theta-periodic solutions, i.e., u, v, w is an element of {t, theta(t)}* for some word t, closing an open problem by Czeizler et al. (2009).

International conference proceedings, English - On computational complexity of graph inference from counting

Szilárd Zsolt Fazekas; Hiro Ito; Yasushi Okuno; Shinnosuke Seki; Kei Taneishi

Natural Computing, Springer, 12, 4, 589-603, Dec. 2013, Peer-reviwed, In de novo drug design, chemical compounds are quantitized as real-valued vectors called chemical descriptors, and an optimization algorithm runs on known drug-like chemical compounds in a database and outputs an optimal chemical descriptor. Since structural information is needed for chemical synthesis, we must infer chemical graphs from the obtained descriptor. This is formalized as a graph inference problem from a real-value vector. By generalizing subword history, which was originally introduced in formal language theory to extract numerical information of words and languages based on counting, we propose a comprehensive framework to investigate the computational complexity of chemical graph inference. We also propose a (pseudo-)polynomial-time algorithm for inferring graphs in a class of practical importance from spectrums. © 2012 Springer Science+Business Media Dordrecht.

Scientific journal, English - On the open problem of Ginsburg concerning semilinear sets and related problems

Oscar H. Ibarra; Shinnosuke Seki

THEORETICAL COMPUTER SCIENCE, ELSEVIER SCIENCE BV, 501, 11-19, Aug. 2013, Peer-reviwed, In his 1966 book, "The Mathematical Theory of Context-Free Languages", S. Ginsburg posed the following open problem: Find a decision procedure for determining if an arbitrary semilinear set is a finite union of stratified linear sets. It turns out that this problem (which remains open) is equivalent to the problem of synchronizability of multitape machines. Given an n-tape automaton M of a given type (e.g., nondeterministic pushdown automaton (NPDA), nondeterministic finite automaton (NFA), etc.) with a one-way read-only head per tape and a right end marker on each tape, we say that M is 0-synchronized (or aligned) if for every n-tuple x = (x(1), . . . , x(n)) that is accepted, there is an accepting computation on x such that at any time during the computation, all heads except those that have reached the end marker are on the same position (i.e., aligned). One of our main contributions is to show that Ginsburg's problem is equivalent to deciding for an arbitrary n-tape NFA M accepting L(M) subset of a(1)* x . . . x a(n)* (where n >= 1 and a(1) , . . . , a(n) an are distinct symbols) whether there exists an equivalent 0-synchronized n-tape NPDA M'. Ginsburg's problem is decidable if M' is required to be an NFA, and we will generalize this decidability over bounded inputs. It is known that if the inputs are unrestricted, the problem is undecidable. We also show several other related decidability and undecidability results.

It may appear, as one of the referees suggested in an earlier version of this paper, that our main result can be written in first order logic. We explain why this is not the case in the Introduction. (C) 2013 Elsevier B.V. All rights reserved.

Scientific journal, English - The power of nondeterminism in self-assembly

Nathan Bryans; Ehsan Chiniforooshan; David Doty; Lila Kari; Shinnosuke Seki

Theory of Computing, 9, 1-29, 2013, Peer-reviwed

Scientific journal, English - On the behavior of tile assembly system at high temperatures

Shinnosuke Seki; Yasushi Okuno

Computability, IOS Press, 2, 2, 107-124, 2013, Peer-reviwed, Behavior of Winfree's tile assembly system (TAS) at high temperatures is investigated in combination with integer programming of a specific form called threshold programming. First, we propose a way to build bridges from the Boolean satisfiability problem (SAT) to threshold programming, and further to TAS's behavior, in order to prove the NP-hardness of optimizing temperatures of TASs that behave in a way given as input. These bridges will take us further to two important results on the behavior of TASs at high temperatures. The first says that arbitrarily high temperatures are required to assemble some shape by a TAS of 'reasonable' size. The second is that for any temperature τ ≥ 4 given as a parameter, it is NP-hard to find the minimum size TAS that self-assembles a given shape at a temperature at most τ.

Scientific journal, English - Convering nondeterministic automata and context-free grammars into Parikh equivalent one-way and two-way deterministic automata

Giovanna J. Lavado; Giovanni Pighizzini; Shinnosuke Seki

Information and Computation, Elsevier, 228-229, 1-15, 2013, Peer-reviwed

Scientific journal, English - On the boundedness property of semilinear sets

Oscar H. Ibarra; Shinnosuke Seki

TAMC 2013: Proceedings of the 10th Annual Conference on Theory and Applications of Models of Computation, Springer, LNCS 7876, 156-168, 2013, Peer-reviwed

International conference proceedings, English - Combinatorial optimization in pattern assembly (extended abstract)

Shinnosuke Seki

UCNC 2013: Proceedings of the Unconventional Computation and Natural Computation - 12th International Conference, Springer, LNCS 7956, 220-231, 2013, Peer-reviwed

International conference proceedings, English - 3-Color Bounded Patterned Self-assemblyY

Lila Kari; Steffen Kopecki; Shinnosuke Seki

DNA COMPUTING AND MOLECULAR PROGRAMMING, DNA 2013, SPRINGER-VERLAG BERLIN, 8141, 105-117, 2013, Peer-reviwed, Patterned self-assembly tile set synthesis (Pats) is the problem of finding a minimal tile set which uniquely self-assembles into a given pattern. Czeizler and Popa proved the NP-completeness of Pats and Seki showed that the Pats problem is already NP-complete for patterns with 60 colors. In search for the minimal number of colors such that Pats remains NP-complete, we introduce multiple bound Pats (mbPats) where we allow bounds for the numbers of tile types of each color. We show that mbPats is NP-complete for patterns with just three colors and, as a byproduct of this result, we also obtain a novel proof for the NP-completeness of Pats which is more concise than the previous proofs.

International conference proceedings, English - Computing Minimum Tile Sets to Self-Assemble Color Patterns

Aleck C. Johnsen; Ming-Yang Kao; Shinnosuke Seki

ALGORITHMS AND COMPUTATION, SPRINGER-VERLAG BERLIN, 8283, 699-710, 2013, Peer-reviwed, Patterned self-assembly tile set synthesis (PATS) aims at finding a minimum tile set to uniquely self-assemble a given rectangular pattern. For k >= 1, k-PATS is a variant of PATS that restricts input patterns to those with at most k colors. We prove the NP-hardness of 29-PATS, where the best known is that of 60-PATS.

International conference proceedings, English - One-reversal counter machines and multihead automata: Revisited

Ehsan Chiniforooshan; Mark Daley; Oscar H. Ibarra; Lila Kari; Shinnosuke Seki

THEORETICAL COMPUTER SCIENCE, ELSEVIER SCIENCE BV, 454, 81-87, Oct. 2012, Peer-reviwed, We investigate the power of (1-reversal) counter machines (finite automata with multiple counters, where each counter can "reverse" only once, i.e., once a counter decrements, it can no longer increment) and one-way multihead finite automata (finite automata with multiple one-way input heads) as a language acceptor. They can be non-deterministic as well as augmented with a pushdown stack. First, we prove that adding a pushdown stack properly strengthens the deterministic counter machines. Non-deterministic counter machines with a pushdown stack are then compared with multihead finite automata. The proof of their incomparability involves an interesting technique: an assumption that a language be accepted by a non-deterministic counter machine would bring a contradictory algorithm to decide an undecidable language. Furthermore, we will show that over bounded languages, these two kinds of machines have the same power, and neither non-determinism nor a pushdown stack makes them stronger. (C) 2012 Elsevier B.V. All rights reserved.

Scientific journal, English - CHARACTERIZATIONS OF BOUNDED SEMILINEAR LANGUAGES BY ONE-WAY AND TWO-WAY DETERMINISTIC MACHINES

Oscar H. Ibarra; Shinnosuke Seki

INTERNATIONAL JOURNAL OF FOUNDATIONS OF COMPUTER SCIENCE, WORLD SCIENTIFIC PUBL CO PTE LTD, 23, 6, 1291-1305, Sep. 2012, Peer-reviwed, A hounded language L subset of x(1)* ... x(k)* (for some k >= 1 and not-necessarily distinct nonempty words x(1), ... , x(k)) is bounded semilinear if the set Q(L) - {(i(1), ..., i(k)) vertical bar x(1)(i1) ... x(k)(ik) is an element of L} is semilinear, We give characterizations of bounded semilinear languages in terms of one-way and two-way deterministic counter machines.

Scientific journal, English - Absoluteness of subword inequality is undecidable

Shinnosuke Seki

THEORETICAL COMPUTER SCIENCE, ELSEVIER SCIENCE BV, 418, 116-120, Feb. 2012, Peer-reviwed, In a given word, one can count the number of occurrences of other words as a scattered subword. These counts can be "added" and/or "multiplied." A subword history gives an instruction of what words to be counted and how these counts to be added and multiplied with other counts or integer constants, and hence, determines its unique value in a given word. Mateescu, Salomaa, and Yu asked: "is it decidable whether the value of a given subword history is non-negative in all words over a given alphabet?" (absoluteness problem). Another important problem is of whether there exists a word in which the value of a given subword history becomes 0 (equality problem). In this paper, we prove the undecidability of the equality problem and show that the equality problem is polynomial-time Karp reducible to the absoluteness problem: thus, the absoluteness problem is also undecidable. This approach solves the open problem actually under stronger conditions than supposed originally. (C) 2011 Elsevier B.V. All rights reserved.

Scientific journal, English - Iterated Hairpin Completions of Non-crossing Words

Lila Kari; Steffen Kopecki; Shinnosuke Seki

SOFSEM 2012: THEORY AND PRACTICE OF COMPUTER SCIENCE, SPRINGER-VERLAG BERLIN, 7147, 337-+, 2012, Peer-reviwed, Iterated hairpin completion is an operation on formal languages that is inspired by the hairpin formation in DNA biochemistry. Iterated hairpin completion of a word (or more precisely a singleton language) is always a context-sensitive language and for some words it is known to be non-context-free. However, it is unknown whether regularity of iterated hairpin completion of a given word is decidable. Also the question whether iterated hairpin completion of a word can be context-free but not regular was asked in literature. In this paper we investigate iterated hairpin completions of non-crossing words and, within this setting, we are able to answer both questions. For non-crossing words we prove that the regularity of iterated hairpin completions is decidable and that if iterated hairpin completion of a non-crossing word is not regular, then it is not context-free either.

International conference proceedings, English - Triangular and hexagonal tile self-assembly systems

Lila Kari; Shinnosuke Seki; Zhi Xu

WTCS 2012: Proceedings of the International Workshop on Theoretical Computer Science, Springer, LNCS 7160, 357-375, 2012, Peer-reviwed

International conference proceedings, English - Converting nondeterministic automata and context-free grammars into Parikh equivalent deterministic automata

Giovanna J. Lavado; Giovanni Pighizzini; Shinnosuke Seki

DLT 2012: Proceedings of the 16th International Conference on Developments in Language Theory, Springer, LNCS 7410, 284-295, 2012, Peer-reviwed

International conference proceedings, English - SCHEMA FOR PARALLEL INSERTION AND DELETION: REVISITED

Lila Kari; Shinnosuke Seki

INTERNATIONAL JOURNAL OF FOUNDATIONS OF COMPUTER SCIENCE, WORLD SCIENTIFIC PUBL CO PTE LTD, 22, 7, 1655-1668, Nov. 2011, Peer-reviwed, A general framework of parallel insertion and deletion based on p-schemata is proposed. A p-schema is a set of tuples of words. When being used for parallel insertion of a language into a word, an element of p-schema specifies how to split the word into factors between which the language to be inserted. As its inverse operation, parallel deletion based on the p-schema is defined. Several algebraic properties of these operations such as closure properties of language classes under them are proved. The main contribution of this paper is to propose algorithms to solve language equations involving p-schema-based insertions or deletions based on syntactic congruence. These algorithms not only decide whether a given equation has a solution but construct the set of all of its maximal or minimal solutions. The algorithms are extensible so as to solve some multiple-variables equations and inequalities. Related undecidability results are also presented.

Scientific journal, English - An extension of the Lyndon-Schutzenberger result to pseudoperiodic words

Elena Czeizler; Eugen Czeizler; Lila Kari; Shinnosuke Seki

INFORMATION AND COMPUTATION, ACADEMIC PRESS INC ELSEVIER SCIENCE, 209, 4, 717-730, Apr. 2011, Peer-reviwed, One of the particularities of information encoded as DNA strands is that a string u contains basically the same information as its Watson Crick complement, denoted here as theta(u). Thus, any expression consisting of repetitions of u and theta(u) can be considered in some sense periodic. In this paper, we give a generalization of Lyndon and Schutzenberger's classical result about equations of the form u(l) = V(n)W(m) to cases where both sides involve repetitions of words as well as their complements. Our main results show that, for such extended equations, if l >= 5, n, m >= 3, then all three words involved can be expressed in terms of a common word t and its complement theta(t). Moreover, if l >= 5, then n = m = 3 is an optimal bound. These results are established based on a complete characterization of all possible overlaps between two expressions that involve only some word u and its complement theta(u), which is also obtained in this paper. Crown Copyright (C) 2011 Published by Elsevier Inc. All rights reserved.

Scientific journal, English - Block insertion and deletion on trajectories

Bo Cui; Lila Kari; Shinnosuke Seki

THEORETICAL COMPUTER SCIENCE, ELSEVIER SCIENCE BV, 412, 8-10, 714-728, Mar. 2011, Peer-reviwed, In this paper, we introduce block insertion and deletion on trajectories, which provide us with a new framework to study properties of language operations. With the parallel syntactical constraint provided by trajectories, these operations properly generalize several sequential as well as parallel binary language operations such as catenation, sequential insertion, k-insertion, parallel insertion, quotient, sequential deletion, k-deletion, etc.

We establish some relationships between the new operations and shuffle and deletion on trajectories, and obtain several closure properties of the families of regular and context-free languages under the new operations. Moreover, we obtain several decidability results of three types of language equation problems which involve the new operations. The first one is to answer, given languages L-1, L-2, L-3 and a trajectory set T. whether the result of an operation between L-1 and L-2 on the trajectory set T is equal to L-3. The second one is to answer, for three given languages L-1, L-2, L-3, whether there exists a set of trajectories such that the block insertion or deletion between L-1 and L-2 on this trajectory set is equal to L-3. The third problem is similar to the second one, but the language L-1 is unknown while languages L-2, L-3 as well as a trajectory set T are given. Crown Copyright (C) 2010 Published by Elsevier B.V. All rights reserved.

Scientific journal, English - PROPERTIES OF PSEUDO-PRIMITIVE WORDS AND THEIR APPLICATIONS

Lila Kari; Benoit Masson; Shinnosuke Seki

INTERNATIONAL JOURNAL OF FOUNDATIONS OF COMPUTER SCIENCE, WORLD SCIENTIFIC PUBL CO PTE LTD, 22, 2, 447-471, Feb. 2011, Peer-reviwed, A pseudo-primitive word with respect to an antimorphic involution theta is a word which cannot be written as a catenation of occurrences of a strictly shorter word t and theta(t). Properties of pseudo-primitive words are investigated in this paper. These properties link pseudo-primitive words with essential notions in combinatorics on words such as primitive words, (pseudo)-palindromes, and (pseudo)-commutativity. Their applications include an improved solution to the extended Lyndon-Schutzenberger equation u(1) u(2) ... u(l) = v(1) ... v(n) w(1) ... w(m), where u(1),..., u(l) is an element of {u, theta(u)}, v(1),..., v(n) is an element of (v, theta(v)}, and w(1),..., w(m) is an element of {w, theta(w)} for some words u, v, w, integers l,n,m >= 2, and an antimorphic involution theta. We prove that for l >= 4, n, m >= 3, this equation implies that u, v, w can be expressed in terms of a common word t and its image theta(t). Moreover, several cases of this equation where l = 3 are examined.

Scientific journal, English - Triangular Tile Self-assembly Systems

Lila Kari; Shinnosuke Seki; Zhi Xu

DNA COMPUTING AND MOLECULAR PROGRAMMING, SPRINGER-VERLAG BERLIN, 6518, 89-99, 2011, Peer-reviwed, We discuss theoretical aspects of the self-assembly of triangular tiles; in particular, right triangular tiles and equilateral triangular tiles. Contrary to intuition, we show that triangular tile assembly systems and square tile assembly systems are not comparable in general. More precisely, there exists a square tile assembly system S such that no triangular tile assembly system that is a division of S produces the same final supertile. There also exists a deterministic triangular tile assembly system T such that no square tile assembly system produces the same final supertiles while preserving border glues. We discuss the assembly of triangles by triangular tiles and show triangular systems with Theta(log N/log log N) tiles that can self-assemble into a triangular supertile of size Theta(N(2)). Lastly, we show that triangular tile assembly systems, either right-triangular or equilateral, are Turing universal.

International conference proceedings, English - Scalable, Time-Responsive, Digital, Energy-Efficient Molecular Circuits Using DNA Strand Displacement

Ehsan Chiniforooshan; David Doty; Lila Kari; Shinnosuke Seki

DNA COMPUTING AND MOLECULAR PROGRAMMING, SPRINGER-VERLAG BERLIN, 6518, 25-36, 2011, Peer-reviwed, We propose a novel theoretical biomolecular design to implement any Boolean circuit using the mechanism of DNA strand displacement. The design is scalable: all species of DNA strands can in principle be mixed and prepared in a single test tube, rather than requiring separate purification of each species, which is a barrier to large-scale synthesis. The design is time-responsive: the concentration of output species changes in response to the concentration of input species, so that time-varying inputs may be continuously processed. The design is digital: Boolean values of wires in the circuit are represented as high or low concentrations of certain species, and we show how to construct a single-input, single-output signal restoration gate that amplifies the difference between high and low, which can be distributed to each wire in the circuit to overcome signal degradation. This means we can achieve a digital abstraction of the analog values of concentrations. Finally, the design is energy-efficient: if input species are specified ideally (meaning absolutely 0 concentration of unwanted species), then output species converge to their ideal concentrations at steady-state, and the system at steady-state is in (dynamic) equilibrium, meaning that no energy is consumed by irreversible reactions until the input again changes.

International conference proceedings, English - ORTHOGONAL SHUFFLE ON TRAJECTORIES

Mark Daley; Lila Kari; Shinnosuke Seki; Petr Sosik

INTERNATIONAL JOURNAL OF FOUNDATIONS OF COMPUTER SCIENCE, WORLD SCIENTIFIC PUBL CO PTE LTD, 22, 1, 213-222, Jan. 2011, Peer-reviwed, A language L is called the orthogonal shuffle of the language L(1) with the language L(2), along the trajectory set T if every word in L is uniquely obtained as the shuffle between a word in L(1), a word in L(2) along a trajectory word in T. In this paper we investigate properties of the orthogonal shuffle on trajectories, as well as several types of language equations using this language operation. As a corollary, we obtain several properties of orthogonal catenation, orthogonal literal shuffle and orthogonal insertion.

Scientific journal, English - K-Comma Codes and Their Generalizations

Bo Cui; Lila Kari; Shinnosuke Seki

FUNDAMENTA INFORMATICAE, IOS PRESS, 107, 1, 1-18, 2011, Peer-reviwed, In this paper, we introduce the notion of k-comma codes-a proper generalization of the notion of comma-free codes. For a given positive integer k, a k-comma code is a set L over an alphabet Sigma with the property that L Sigma(k) L boolean AND Sigma(+) L Sigma(+) = empty set. Informally, in a k-comma code, no codeword can be a subword of the catenation of two other codewords separated by a "comma" of length k. A k-comma code is indeed a code, that is, any sequence of codewords is uniquely decipherable. We extend this notion to that of k-spacer codes, with commas of length less than or equal to a given k. We obtain several basic properties of k-comma codes and their generalizations, k-comma intercodes, and some relationships between the families of k-comma intercodes and other classical families of codes, such as infix codes and bifix codes. Moreover, we introduce the notion of n-k-comma intercodes, and obtain, for each k >= 0, several hierarchical relationships among the families of n-k-comma intercodes, as well as a characterization of the family of 1-k-comma intercodes.

Scientific journal, English - On the Regularity of Iterated Hairpin Completion of a Single Word

Lila Kari; Shinnosuke Seki; Steffen Kopecki

FUNDAMENTA INFORMATICAE, IOS PRESS, 110, 1-4, 201-215, 2011, Peer-reviwed, Hairpin completion is an abstract operation modeling a DNA bio-operation which receives as input a DNA strand w = x alpha y (alpha) over bar, and outputs w ' = x alpha y (alpha) over bar(x) over bar, where (x) over bar denotes the Watson-Crick complement of x. In this paper, we focus on the problem of finding conditions under which the iterated hairpin completion of a given word is regular. According to the numbers of words alpha and (alpha) over bar that initiate hairpin completion and how they are scattered, we classify the set of all words w. For some basic classes of words w containing small numbers of occurrences of alpha and (alpha) over bar, we prove that the iterated hairpin completion of w is regular. For other classes with higher numbers of occurrences of alpha and (alpha) over bar, we prove a necessary and sufficient condition for the iterated hairpin completion of a word in these classes to be regular.

Scientific journal, English - The Power of Nondeterminism in Self-Assembly

Nathaniel Bryans; Ehsan Chiniforooshan; David Doty; Lila Kari; Shinnosuke Seki

PROCEEDINGS OF THE TWENTY-SECOND ANNUAL ACM-SIAM SYMPOSIUM ON DISCRETE ALGORITHMS, SIAM, 590-602, 2011, Peer-reviwed, We investigate the role of nondeterminism in Winfree's abstract tile assembly model, which was conceived to model artificial molecular self-assembling systems constructed from DNA. By nondeterminism we do not mean a magical ability such as that possessed by a nondeterministic algorithm to search an exponential-size space in polynomial time. Rather, we study realistically implementable systems that retain a different sense of determinism in that they are guaranteed to produce a unique shape but are nondeterministic in that they do not guarantee which tile types will be placed where within the shape.

We show a "molecular computability" result: there is an infinite shape S that is uniquely assembled by a tile system but not by any deterministic tile system. We show a "molecular complexity" result: there is a finite shape S that is uniquely assembled by a tile system with c tile types, but every deterministic tile system that uniquely assembles S has more than c tile types. In fact we extend the technique to derive a stronger (classical complexity theoretic) result, showing that the problem of finding the minimum number of tile types that uniquely assemble a given finite shape is Sigma(P)(2)- complete. In contrast, the problem of finding the minimum number of deterministic tile types that uniquely assemble a shape is NP-complete [5].

International conference proceedings, English - One-Reversal Counter Machines and Multihead Automata: Revisited

Ehsan Chiniforooshan; Mark Daley; Oscar H. Ibarra; Lila Kari; Shinnosuke Seki

SOFSEM 2011: THEORY AND PRACTICE OF COMPUTER SCIENCE, SPRINGER-VERLAG BERLIN, 6543, 166-177, 2011, Peer-reviwed, Among the many models of language acceptors that have been studied in the literature are multihead finite automata (finite automata with multiple one-way input heads) and 1-reversal counter machines (finite automata with multiple counters, where each counter can only "reverse" once, i.e., once a counter decrements, it can no longer increment). The devices can be deterministic or nondeterministic and can be augmented with a pushdown stack. We investigate the relative computational power of these machines. Our results (where C-1 and C-2 are classes of machines) are of the following types:

1. Machines in C-1 and C-2 are incomparable.

2. Machines in C-1 are strictly weaker than machines in C-2.

In obtaining results of these types, we use counting and "cut-and-paste" arguments as well as an interesting technique that shows that if a language were accepted by a device in a given class, then all recursively enumerable languages would be decidable.

International conference proceedings, English - Characterizations of bounded semilinear languages by one-way and two-way deterministic machines

Oscar H. Ibarra; Shinnosuke Seki

AFL 2011: Proceedings of the 13th International Conference on Automata and Formal Languages, 211-224, 2011, Peer-reviwed

International conference proceedings, English - Program Size and Temperature in Self-assembly

Ho-Lin Chen; David Doty; Shinnosuke Seki

ALGORITHMS AND COMPUTATION, SPRINGER-VERLAG BERLIN, 7074, 445-+, 2011, Peer-reviwed, Winfree's abstract Tile Assembly Model (aTAM) is a model of molecular self-assembly of DNA complexes known as tiles, which float freely in solution and attach one at a time to a growing "seed" assembly based on specific binding sites on their four sides. We show that there is a polynomial-time algorithm that, given an n x n square, finds the minimal tile system (i.e., the system with the smallest number of distinct tile types) that uniquely self-assembles the square, answering an open question of Adleman, Cheng, God, Huang, Kempe, Moisset de Espanes, and Rothemund (Combinatorial Optimization Problems in Self-Assembly, STOC 2002). Our investigation leading to this algorithm reveals other positive and negative results about the relationship between the size of a tile system and its "temperature" (the binding strength threshold required for a tile to attach).

International conference proceedings, English - On a special class of primitive words

Elena Czeizler; Lila Kari; Shinnosuke Seki

THEORETICAL COMPUTER SCIENCE, ELSEVIER SCIENCE BV, 411, 3, 617-630, Jan. 2010, Peer-reviwed, When representing DNA molecules as words, it is necessary to take into account the fact that a word u encodes basically the same information as its Watson-Crick complement theta(u), where theta denotes the Watson-Crick complementarity function. Thus, an expression which involves only a word u and its complement can be still considered as a repeating sequence. In this context, we define and investigate the properties of a special class of primitive words, called pseudo-primitive words relative to theta or simply theta-primitive words, which cannot be expressed as such repeating sequences. For instance, we prove the existence of a unique theta-primitive root of a given word, and we give some constraints forcing two distinct words to share their theta-primitive root. Also, we present an extension of the well-known Fine and Wilf theorem, for which we give an optimal bound. (C) 2009 Elsevier B.V. All rights reserved.

Scientific journal, English - An Improved Bound for an Extension of Fine and Wilf's Theorem and Its Optimality

Lila Kari; Shinnosuke Seki

FUNDAMENTA INFORMATICAE, IOS PRESS, 101, 3, 215-236, 2010, Peer-reviwed, Considering two DNA molecules which are Watson-Crick (WK) complementary to each other "equivalent" with respect to the information they encode enables us to extend the classical notions of repetition, period, and power. WK-complementarity has been modelled mathematically by an antimorphic involution theta, i.e., a function theta such that theta( xy) = theta(y)theta(x) for any x, y is an element of Sigma*, and theta(2) is the identity. The WK-complementarity being thus modelled, any word which is a repetition of u and theta(u) such as u u, u theta(u)u, and u theta(u)theta(u)theta(u) can be regarded repetitive in this sense, and hence, called a theta-power of u. Taking the notion of theta-power into account, the Fine and Wilf's theorem was extended as "given an antimorphic involution theta and words u, v, if a theta-power of u and a theta-power of v have a common prefix of length at least b (vertical bar u vertical bar, vertical bar v vertical bar) = 2 vertical bar u vertical bar + vertical bar v vertical bar - gcd (vertical bar u vertical bar, vertical bar v vertical bar), then u and v are theta-powers of a same word." In this paper, we obtain an improved bound b' (vertical bar u vertical bar, vertical bar v vertical bar) = b (vertical bar u vertical bar, vertical bar v vertical bar) -[gcd (vertical bar u vertical bar, vertical bar v vertical bar)/2.. Then we show all the cases when this bound is optimal by providing all the pairs of words (u,v) such that they are not theta-powers of a same word, but one can construct a theta-power of u and a theta-power of v whose maximal common prefix is of length equal to b'(vertical bar u vertical bar, vertical bar v vertical bar) - 1. Furthermore, we characterize such words in terms of Sturmian words.

Scientific journal, English - Schema for Parallel Insertion and Deletion

Lila Kari; Shinnosuke Seki

DEVELOPMENTS IN LANGUAGE THEORY, SPRINGER-VERLAG BERLIN, 6224, 267-278, 2010, Peer-reviwed, We propose a general framework for parallel insertion/deletion operations based on p-schemata. A p-schema is a set of tuples of words. When being used for parallel insertion of a language into a word, an element of a p-schema specifies how to split the given word into factors between which the insertion of the language will take place. Parallel deletion based on a p-schema is defined as an "inverse" operation of parallel insertion based on the p-schema. Several well-known language operations are particular cases of p-schema-based insertions or deletions: catenation, Kleene star, reverse catenation, sequential insertion, parallel insertion, insertion next to a given letter, contextual insertion, right and left quotient, sequential deletion, parallel deletion. Additional operations that can be defined using p-schemata include contextual parallel insertion, as well as parallel insertion (deletion) of exactly n words, at most n words, an arbitrary number of words. We also consider the decidability and undecidability of existence of solutions of language equations involving p-schema-based parallel insertion/deletion.

International conference proceedings, English - Twin-roots of words and their properties

Lila Kari; Kalpana Mahalingam; Shinnosuke Seki

THEORETICAL COMPUTER SCIENCE, ELSEVIER SCIENCE BV, 410, 24-25, 2393-2400, May 2009, Peer-reviwed, In this paper we generalize the notion of an iota-symmetric word, from an antimorphic involution, to an arbitrary involution iota as follows: a nonempty word w is said to be iota-symmetric if w = alpha beta = iota(beta alpha) for some words alpha, beta. We propose the notion of iota-twin-roots (x, y) of an iota-symmetric word w. We prove the existence and uniqueness of the iota-twin-roots of ail iota-symmetric word, and show that the left factor alpha and right factor beta of any factorization of w as w = alpha beta = iota(beta alpha), can be expressed in terms of the iota-twin-roots of w. In addition, we show that for any involution iota, the catenation of the iota-twin-roots of w equals the primitive root of w. We also provide several characterizations of the iota-twin-rots of a word, for iota being a morphic or antimorphic involution. Crown Copyright (C) 2009 Published by Elsevier B.V. All rights reserved.

Scientific journal, English - On pseudoknot-bordered words and their properties

Lila Kari; Shinnosuke Seki

JOURNAL OF COMPUTER AND SYSTEM SCIENCES, ACADEMIC PRESS INC ELSEVIER SCIENCE, 75, 2, 113-121, Feb. 2009, Peer-reviwed, We Study a generalization of the classical notions of [)ordered and unbordered words, motivated by biomolecular Computing. DNA strands can be viewed as finite strings over the alphabet [A, G, C, T), and are used in biomolecular computing to encode information. Due to the fact that A is Witson-Crick complementary to T and G to C, DNA single strands that are Watson-Crick complementary can bind to each other or to themselves forming so-called secondary structures, Most of these secondary structures are undesirable for biomolecular computational purposes since the strands they involve cannot further interact with other strands. This paper studies pseudoknot-bordered words, a mathematical formalization of pseudoknot-like inter- and intra-molecular structures. In this context, pseudoknot-unbordered words model DNA or RNA strands that will be free of such secondary structures. We obtain several properties of pseudoknot-bordered and -unbordered words. We also address Following problem: Given a pseudoknot-unbordered word u, does {u}(+) consist of pseudoknot-unbordered words only? We show that this is not generally true. We find that a sufficient condition for {u}(+) to consist of pseudoknot-unbordered words only is that it be not primitive. All of our results hold for arbitrary antimorphic involutions, of which the DNA Watson-Crick complementarity function is a particular case. Crown Copyright (c) 2008 Published by Elsevier Inc. All rights reserved.

Scientific journal, English - An Efficient Multiple Alignment Method for RNA Secondary Structures Including Pseudoknots

Shinnosuke Seki; Satoshi Kobayashi

NATURAL COMPUTING, PROCEEDINGS, SPRINGER, 1, 179-+, 2009, Peer-reviwed, Pseudoknots, one of the key components of RNA secondary structures, have been almost systematically intractable because of the difficulty in modeling them. Tree adjoining grammars have proved to be promising for this problem but the question of how to make TAG-based applications practical enough to analyze RNAs of thousands nucleotides remains open. This paper addresses this problem. It makes use of biological properties of pseudoknots, the scarcity and short-bp property. Experiments showed that our algorithm can align RNAs of the length tip to about 2400 nucleotides with biologically meaningful outputs extremely fast on the standard workstation environment. An executable version of our implementation is available at http://www.csd.uwo.ca/(similar to)sseki/

International conference proceedings, English - Towards the Sequence Design Preventing Pseudoknot Formation

Lila Kari; Shinnosuke Seki

NATURAL COMPUTING, PROCEEDINGS, SPRINGER, 1, 101-110, 2009, Peer-reviwed, This paper addresses a pseudoknot-freeness problem of DNA and RNA sequences, motivated by biomolecular computing. Watson-Crick (WK) complementarity forces DNA strands to fold into themselves and form so-called secondary structures, which are usually undesirable for biomolecular computational purposes. This paper studies pseudoknot-bordered words, a mathematical formalization of a common secondary structure, the pseudoknot. We obtain several properties of WK-pseudoknot-bordered and -unbordered words. One of the main results of the paper is that a sufficient condition for a WK-pseudoknot-unbordered word u to result in all words in u(+) being WK-pseudoknot-unbordered is for u not to be a primitive word.

International conference proceedings, English - Duplication in DNA Sequences

Masami Ito; Lila Kari; Zachary Kincaid; Shinnosuke Seki

ALGORITHMIC BIOPROCESSES, SPRINGER-VERLAG BERLIN, LNCS 5257, 43-+, 2009, Peer-reviwed, The duplication and repeat-deletion operations are the basis of a formal language theoretic model of errors that can occur during DNA replication. During DNA replication, subsequences of a strand of DNA may be copied several times (resulting in duplications) or skipped (resulting in repeat-deletions). As formal language operations, iterated duplication and repeat-deletion of words and languages have been well studied in the literature. However, little is known about single-step duplications and repeat-deletions. In this paper, we investigate several properties of these operations, including closure properties of language families in the Chomsky hierarchy and equations involving these operations. We also make progress toward a characterization of regular languages that are generated by duplicating a regular language.

International conference proceedings, English - On the Reversibility of Parallel Insertion, and Its Relation to Comma Codes

Bo Cui; Lila Kari; Shinnosuke Seki

ALGEBRAIC INFORMATICS, SPRINGER-VERLAG BERLIN, 5725, 204-219, 2009, Peer-reviwed, This paper studies Conditions under which the operation of parallel insertion can be reversed by parallel deletion. i.e.. when does the equality (L(1) double left arrow L(2)) double right arrow L(2) = L(1) hold for languages L(1) and L(2). We obtain a complete characterization of the solutions in the special M. se when both languages involved are singleton words. We also define comma codes, a family of codes with the property that, if L(2) is a comma code, then the above equation holds for any language L(1) subset of Sigma*. Lastly, we generalize the notion of comma codes to that of comma intercodes of index m. Besides several properties, we prove that the families of comma intercedes of index m form an infinite proper inclusion hierarchy, the first element which is a subset of the family of infix codes, and the last element of which is a subset of the family of bifix codes.

International conference proceedings, English - An Extension of the Lyndon Schutzenberger Result to Pseudoperiodic Words

Elena Czeizler; Eugen Czeizler; Lila Kari; Shinnosuke Seki

DEVELOPMENTS IN LANGUAGE THEORY, PROCEEDINGS, SPRINGER-VERLAG BERLIN, 5583, 183-+, 2009, Peer-reviwed, One of the particularities of information encoded as DNA strands is that a string u contains basically the same information as its Watson-Crick complement, denoted here as theta(u). Thus, any expression consisting of repetitions of u and theta(u) can be considered in some sense periodic. In this paper we give a generalization of Lyndon and Schutzenberger's classical result about equations of the form u(l) = upsilon(n)omega(m), to cases where both sides involve repetitions of words as well as their complements. Our main results show that, for such extended equations, if l >= 5, n, m >= 3, then all three words involved can be expressed in terms of a common word t and its complement theta(t). Moreover. if l >= 5, then n = m = 3 is an optimal bound. We also obtain a complete characterization of all possible overlaps between two expressions that involve only some word u and its complement theta(u).

International conference proceedings, English - On a special class of primitive words

Elena Czeizler; Lila Kari; Shinnosuke Seki

MATHEMATICAL FOUNDATIONS OF COMPUTER SCIENCE 2008, PROCEEDINGS, SPRINGER-VERLAG BERLIN, 5162, 265-277, 2008, Peer-reviwed, When representing DNA molecules as words, it is necessary to take into account the fact that a word u encodes basically the same information as its Watson-Crick complement theta(u), where theta denotes the Watson-Crick complementarity function. Thus, an expression which involves only a word u and its complement can be still considered as a, repeating sequence. In this context, we define and investigate the properties of a special class of primitive words, called theta-primitive, which cannot be expressed as such repeating sequences. For instance, we prove the existence of a unique theta-primitive root of a given word, and we give some constraints forcing two distinct words to share their theta-primitive root. Also, we present an extension of the well-known Fine and Wilf Theorem, for which we give an optimal bound.

International conference proceedings, English - A grammatical approach to the alignment of structure-annotated strings

S Seki; S Kobayashi

IEICE TRANSACTIONS ON INFORMATION AND SYSTEMS, IEICE-INST ELECTRONICS INFORMATION COMMUNICATIONS ENG, E88D, 12, 2727-2737, Dec. 2005, Peer-reviwed, In this paper, we are concerned with a structural ambiguity problem of tree adjoining grammars (TAGS), which is an essential problem when we try to model consensus structures of given set of ribonucleic acid (RNA) secondary structures by TAGS. RNA secondary structures can be represented as strings with structural information, and TAGS have a descriptive capability of this kind of strings, what we call structure-annotated strings. Thus, we can model RNA secondary structures by TAGs. It is sufficient to use existing alignment methods for just computing the optimal alignment between RNA secondary structures. However, when we also want to model the resulting alignment by grammars, if we adopt these existing methods, then we may fail in modeling the alignment result by grammars. Therefore, it is important to introduce a new alignment method whose alignment results can be appropriately modeled by grammars. In this paper, we will propose an alignment method based on TAG'S derivations each corresponding to a given RNA secondary structure. For an RNA secondary structure, there exist a number of derivations of TAGS which correspond to the structure. From the grammatical point of view, the property of TAGS drives us to the question how we should choose a derivation from these candidates in order to obtain an optimal alignment. This is the structural ambiguity problem of TAGS, which will be mainly discussed in this paper. For dealing with this problem appropriately, we will propose an edit distance between two structure-annotated strings, and then present an algorithm which computes an optimal alignment based on the edit distance.

Scientific journal, English - Efficient learning of k-reversible context-free grammars from positive structural examples

S Seki; S Kobayashi

GRAMMATICAL INFERENCE: ALGORITHMS AND APPLICATIONS, PROCEEDINGS, SPRINGER-VERLAG BERLIN, 3264, 285-287, 2004, Peer-reviwed, This paper discusses on the learnability of context free grammars(CFGs) within the framework of identification in the limit from positive structural examples. We will introduce a new subclass of CFGs, called a class of k-reversible context-free grammars and propose an O(kdn(3)) algorithm for learning this new subclass of CFGs, where d is the maximum of the ranks of given skeletal trees, and n is the total size of the given examples.

Scientific journal, English - Hierarchical Alignment of RNA secondary structures including pseudoknots

Shinnosuke Seki; Atsushi Kijima; Satoshi Kobayashi; Genichi Sanpei

GIW 2004: Proceedings of the 15th International Conference on Genome Informatics, 117-1-117-2, 2004, Peer-reviwed

International conference proceedings, English

### MISC

- RNA折り紙

関 新之助

Lead, 2019, 電子情報通信学会誌, 102, 4, 330-334, Japanese, Peer-reviwed, Invited - Cotranscriptional folding: A frontier in molecular engineering a challenge for computer scientists

Shinnosuke Seki

SIAM (Society for Industrial and Applied Mathematics), 01 May 2017, SIAM News, Not assigned yet, English, Peer-reviwed, Introduction scientific journal

### Books and other publications

- Special issue of New Generation Computing devoted to Hagiya-sensei's 64th birthday.

English, Joint editor, Springer, Aug. 2022 - Special issue of Natural Computing devoted to the International Conference on Unconventional Computation and Natural Computation (UCNC 2019)

Ian McQuillan; Shinnosuke Seki

English, Joint editor, Springer, 2021 - Special issue of International Journal of Foundations of Computer Science (IJFCS) devoted to Developments in Language Theory 2018

Shinnosuke Seki

English, Editor, World Scientific, Sep. 2020 - Proceedings of the 18th International Conference on Unconventional Computation and Natural Computation (UCNC2019, Tokyo, Japan, June 3-7, 2019)

English, Joint editor, Springer, 2019 - Proceedings of the 18th International Conference on Unconventional Computation and Natural Computation

English, Joint editor, Springer, 2019 - Proceedings of the 22nd International Conference on Developments in Language Theory (DLT2018, Tokyo, Japan, September 10-14, 2018)

Scholarly book, English, Joint editor, Springer, 06 Aug. 2018 - Encyclopedia of Algorithms

Shinnosuke Seki

Dictionary or encycropedia, English, Single work, Patterned Self-Assembly Tile Set Synthesis, Springer, 2016 - Handbook of Natural Computing

Lila Kari; Shinnosuke Seki; Petr Sosik

Scholarly book, English, Contributor, Springer, 2012 - Proc. 14th International Conference on Developments in Language Theory

Yuan Gao; Hanlin Lu; Shinnosuke Seki; Sheng Yu

Scholarly book, English, Editor, Springer, 2010

### Lectures, oral presentations, etc.

- How complex shapes can RNA fold into?

Shinnosuke Seki

Invited oral presentation, English, 17th International Conference on Reachability Problems (RP 2023), Invited, Peer-reviewed

13 Oct. 2023

11 Oct. 2023- 13 Oct. 2023 - Freezing 1-Tag systems with states

Szilard Zsolf Fazekas

Oral presentation, English, 16th International Conference on Automata and Formal Languages (AFL 2023), Peer-reviewed

06 Sep. 2023

05 Sep. 2023- 07 Sep. 2023 - On algorithmic self-assembly of squares by co-transcriptional folding

Ryuichi Matsuoka

Oral presentation, English, The 33rd International Symposium on Algorithms and Computation (ISAAC 2022), Hanyang University, Seoul, Republic of Korea, Peer-reviewed

20 Dec. 2022

19 Dec. 2022- 21 Dec. 2022 - Single-stranded architectures for computing by RNA co-transcriptional folding

Shinnosuke Seki

Public discourse, English, Invited, Ajou University, Suwon, Republic of Korea

15 Dec. 2022 - Single-stranded architectures for RNA co-transcriptional folding

Shinnosuke Seki

Invited oral presentation, English, Moving and Computing 2022 (MaC2022), Invited, University of Pisa, Pisa, Italy, International conference

19 Sep. 2022 - Single-stranded architectures for RNA co-transcriptional folding

Shinnosuke Seki

Invited oral presentation, English, Dagstuhl seminar 22381: Rational Design of Ribonucleic Acids, Invited, Schloss Dagstuhl, Dagstuhl, Germany, International conference

19 Sep. 2022 - Turedo a new computational model for molecular nanobots?

Nicolas Schabanel

Invited oral presentation, English, Computability in Europe (CiE 2022), Invited, Swansea University, International conference

14 Jul. 2022 - Oritatami systems assemble shapes no less complex than tile assembly model

Nicolas Schabanel

Oral presentation, English, 39th International Symposium on Theoretical Aspects of Computer Science (STACS 2022), International conference

15 Mar. 2022 - Algorithmic self-assembly of squares in oritatami

松岡 龍一

Oral presentation, English, 2021年度 冬のLAシンポジウム, 京都大学数理解析研究所, Domestic conference

01 Feb. 2021 - Simple intrinsic simulation of cellular automata in oritatami molecular folding model

Daria Pchelina

Oral presentation, English, 14th Latin American Symposium on Theoretical Informatics (LATIN 2020), Invited, International conference

05 Jan. 2021 - Les oritatamis tracent des dessins indécidables

Nicolas Schabanel

Oral presentation, French, Journées SDA2 2020: Systèmes Dynamiques, Automates et Algorithmes, Caen, France, International conference

04 Dec. 2020 - Single-stranded architectures for computing

Shinnosuke Seki

Oral presentation, English, 1st International Conference on Information Technology and Data Science, Invited, University of Debrecen, Debrecen, Hungary, International conference

06 Nov. 2020 - A single-stranded architecture for infinite counting

Shinnosuke Seki

Public discourse, English, Invited, Politecnico di Torino (Torino, Italy)

27 Jan. 2020 - Counting infinitely by oritatami co-transcriptional folding

Kohei Maruyama

Oral presentation, English, SOFSEM2020: 46th International Conference on Current Trends in Theory and Practice of Informatics, Limassol, Cyprus, International conference

20 Jan. 2020 - Single-stranded architectures for computing

Shinnosuke Seki

Invited oral presentation, English, 23rd International Conference on Developments in Language Theory (DLT 2019), Invited, University of Warsaw, Warsaw, Poland, International conference

05 Aug. 2019 - A general architecture of oritatami systems for simulating arbitrary finite automata

Shinnosuke Seki

Oral presentation, English, CIAA2019: 24th International Conference on Implementation and Application of Automata, Slovak Academy of Science, Kosice, Slovakia, International conference

22 Jul. 2019 - On the power of oritatami cotranscriptional folding with unary bead sequence

Kohei Maruyama; Reoto Morita

Oral presentation, English, TAMC2019: 15th Annual Conference on Theory and Applications of Models of Computation, International conference

13 Apr. 2019 - Proving the Turing universality of oritatami cotranscriptional folding

Nicolas Schabanel

Oral presentation, English, 29th International Symposium on Algorithms and Computation (ISAAC2018), International conference

16 Dec. 2018 - Know when to fold 'em: Self-assembly of shapes by folding in oritatami

Nicolas Schabanel

Oral presentation, English, DNA24: 24th International Conference on DNA Computing and Molecular Programming, International conference

08 Oct. 2018 - Transcript desing problem of oritatami systems

Hwee Kim

Oral presentation, English, DNA24: 24th International Conference on DNA Computing and Molecular Programming, International conference

08 Oct. 2018 - Towards the algorithmic molecular self-assembly of fractals by cotranscriptional folding

Yusei Masuda; Yuki Ubukata

Oral presentation, English, 23rd International Conference on Implementation and Application of Automata (CIAA 2018), International conference

30 Jul. 2018 - Proving Turing universality of cotranscriptional folding

Shinnosuke Seki

Oral presentation, English, 2018 Zassenhaus Groups and Friends Conference, Invited, University of South Florida, Tampa, FL, USA, International conference

06 Apr. 2018 - Self-Assembly of shapes by cotranscriptional folding

Shinnosuke Seki

Oral presentation, English, Invited, Department of Mathematics and Statistics, University of South Florida

02 Apr. 2018 - Cotranscriptional Folding: A Frontier in Molecular Engineering

Shinnosuke Seki

Oral presentation, English, 京都大学数理解析研究所RIMS共同研究（公開型）「代数系、論理、言語とその周辺領域」, Domestic conference

20 Feb. 2018 - Proving Turing universality of cotranscriptional folding

Shinnosuke Seki

Oral presentation, Japanese, 京都大学数理解析研究所RIMS共同研究（公開型）「アルゴリズムと計算理論の基礎と応用」, Domestic conference

05 Feb. 2018 - Turing completeness of RNA cotarnsccriptional folding

Shinnosuke Seki

Invited oral presentation, English, SICE Molecular Robotics Seminar, 4th JST Seminar on Ethical Issues for Molecular Robots, Invited, Hakata, Japan, Domestic conference

19 Jan. 2018 - Self-attraction removal from oritatami systems

Hwee Kim

Oral presentation, English, 19th International Conference on Descriptional Complexity of Formal Systems, Milan, Italy, International conference

03 Jul. 2017 - Bit string bifurcation by cotranscriptional folding

Yusei Masuda; Yuki Ubukata

Oral presentation, English, 1st International Workshop on Oritatami, Shinnosuke Seki, University of Arkansas, International conference

06 Jun. 2017 - Bit string bifurcation by cotranscriptional folding

Yusei Masuda; Yuki Ubukata

Oral presentation, English, 11th International Workshop on Natural Computing, Akita International University, International conference

13 May 2017 - Self-assembly at nano scale by molecular Xerox

Shinnosuke Seki

Invited oral presentation, English, 11th International Workshop on Natural Computing, Invited, Akita International University, Akita, Japan, International conference

13 May 2017 - Nano-scale self-assembly using molecular Xerox

Shinnosuke Seki

Oral presentation, Japanese, 第2回 若手研究者のための熱利用・環境技術ワークショップ, Invited, 化学工学会エネルギー部会熱利用分科会, 東京都八王子市, Domestic conference

02 Dec. 2016 - Oritatami, a novel frontier in molecular self-assembly

Shinnosuke Seki

Invited oral presentation, English, Invited, Yonsei University

21 Nov. 2016 - Oritatami, a novel mathematical model of RNA cotranscriptional folding

Shinnosuke Seki

Public discourse, English, Invited, Akita University, Akita, Japan

20 Oct. 2016 - Nondeterministic seedless oritatami systems and hardness of testing their equivalence

Hwee Kim

Oral presentation, English, The 22nd International Conference on DNA Computing and Molecular Programming (DNA 22), Munich, Germany, International conference

04 Sep. 2016 - Programming biomolecules that fold greedily during transcription

Pierre-Etienne Meunier

Oral presentation, English, 41st International Symposium on Mathematical Foundations of Computer Science (MFCS 2016), International conference

22 Aug. 2016 - The complexity of fixed-height patterned tile self-assembly

Shinnosuke Seki

Oral presentation, English, 21st International Conference on Implementation and Application of Automata (CIAA 2016), Seoul, Republic of Korea, International conference

19 Jul. 2016 - Folding Turing is hard but feasible

Nicolas Schabanel

Oral presentation, English, Highlights of Algorithms (HALG 2016), Paris, France, International conference

06 Jun. 2016 - Molecular cotranscriptional folding: A novel challenge in theory and applications of self-assembly

Shinnosuke Seki

Public discourse, English, Invited, University of South Florida, Tampa, Florida, USA

25 Jan. 2016 - Molecular cotranscriptional folding: A novel topic in theory and applications of self-assembly

Shinnosuke Seki

Invited oral presentation, English, 5th Interdisciplinary Research and Global Outlook (IRAGO2015)

22 Oct. 2015 - Square-density increasing mappings

Shinnosuke Seki

Oral presentation, English, 10th International Conference on Combinatorics on Words (WORDS2015), International conference

14 Sep. 2015 - Computational complexity of inverse word search problem

Hiro Ito

Oral presentation, English, 12th International Symposium on Operations Research and Its Applications (ISORA2015), International conference

21 Aug. 2015 - Efficient universal computation by molecular cotranscriptional folding

Shinnosuke Seki

Oral presentation, English, 21st International Conference on DNA Computing and Molecular Programming (DNA21), Wyss Institute for Biologically inspired Engineering at Harvard University, International conference

17 Aug. 2015 - Binary pattern tile set synthesis is NP-hard

Shinnosuke Seki

Oral presentation, English, 42nd International Colloquium on Automata, Languages, and Programming (ICALP2015), International conference

04 Jul. 2015 - Oritatami, a model of cotranscriptional folding

Shinnosuke Seki

Public discourse, English, Invited, Turku, Finland, International conference

04 Mar. 2015 - Generalized Lyndon-Schutzenberger equations

Florin Manea

Oral presentation, English, MFCS2014: 39th International Symposium on Mathematical Foundations of Computer Science, Budapest, Hungary, International conference

25 Aug. 2014 - Operational state complexity under Parikh equivalence

Shinnosuke Seki

Public symposium, English, DCFS2014: 16th International Workshop on Descriptional Complexity of Formal Systems, Turku, Finland, International conference

05 Aug. 2014 - DNA pattern self-assembly: Introduction and recent breakthroughs

Nicolas Schabanel

Invited oral presentation, English, Complexite et Algorithmes: Algorithmes naturels, Invited, Universite Paris Diderot, LIAFA, Paris, France, International conference

09 Jun. 2014 - Stronger square conjecture on binary words

Shinnosuke Seki

Oral presentation, English, SOFSEM2014: 40th International Conference on Current Trends in Theory and Practice of Computer Science, International conference

25 Jan. 2014 - A stronger square conjecture on binary words

Shinnosuke Seki

Invited oral presentation, English, Invited, Slovak Academy of Science, Kosice, Slovakia

24 Jan. 2014 - Computing minimum tile sets to self-assembly color patterns

Aleck Johnson

Oral presentation, English, ISAAC2013: 24th International Symposium on Algorithms and Computation, Hong Kong, International conference

16 Dec. 2013 - How many repetitions can you put on a sequence?

Shinnosuke Seki

Invited oral presentation, English, Invited, University of North Florida, Jacksonville, FL, USA

07 Nov. 2013 - Combinatorial optimization in pattern-assembly

Shinnosuke Seki

Invited oral presentation, English, Invited, University of North Florida, Jacksonville, FL, USA

06 Nov. 2013 - Combinatorial optimization in pattern-assembly

Shinnosuke Seki

Invited oral presentation, English, Invited, Northwestern University, Evanston, IL, USA

13 Oct. 2013 - 3-color bounded patterned self-assembly

Steffen Kopecki

Oral presentation, English, DNA 19: 19th International Conference on DNA Computing and Molecular Programming, Tempe, Arizona, USA, International conference

22 Sep. 2013 - Combinatorial optimization in pattern assembly (extended abstract)

Shinnosuke Seki

Oral presentation, English, UCNC2013: 12th International Conference on Unconventional Computation and Natural Computation, Milan, Italy, International conference

01 Jul. 2013 - On the boundedness property of semilinear sets

Shinnosuke Seki

Oral presentation, English, TAMC2013: 10th Annual Conference on Theory and Applications of Models of Computation, Hong Kong, International conference

20 May 2013 - DNA pattern self-assembly

Shinnosuke Seki

Invited oral presentation, English, Invited, Yonsei University, Seoul, Republic of Korea

15 May 2013 - DNA pattern self-assembly

Shinnosuke Seki

Invited oral presentation, English, Helsinki Institute for Information Technology (HIIT), Helsinki, Finland

24 Apr. 2013 - Roles that temperature plays in self-assembly

Shinnosuke Seki

Invited oral presentation, English, Invited, University of South Florida, Tampa, FL, USA

30 Nov. 2012 - Combinatorial optimization in pattern assembly

Shinnosuke Seki

Invited oral presentation, English, Invited, California Institute of Technology, Pasadena, California, USA

02 Nov. 2012 - Descriptional complexity in Parikh equivalence

Shinnosuke Seki

Invited oral presentation, English, Invited, University of Western Ontario, London, ON, Canada

18 Oct. 2012 - Conveting nondeterministic automata and context-free grammars into Parikh equivalent deterministic automata

Giovanni Pighizzini

Oral presentation, English, DLT2012: 16th International Conference on Developments in Language Theory, Taipei, Taiwan, International conference

14 Aug. 2012 - On the behavior of tile assembly system at high temperatures

Shinnosuke Seki

Oral presentation, English, CiE2012: Turing Centenary Conference - How the World Computes, Cambridge, UK, International conference

18 Jun. 2012 - Triangular and hexagonal tile self-assembly systems

Zhi Xu

Oral presentation, English, WTCS2012: International Workshop on Theoretical Computer Science, Auckland, New Zealand, International conference

21 Feb. 2012 - On the behavior of tile assembly system at high temperatures

Shinnosuke Seki

Invited oral presentation, English, Slovak Academy of Science, Kosice, Slovakia

30 Jan. 2012 - Iterated hairpin completions of non-crossing words

Shinnosuke Seki

Oral presentation, English, SOFSEM2012: 38th International Conference on Current Trends in Theory and Practice of Computer Science, Spindleruv Mlyn, Czech Republic, International conference

21 Jan. 2012 - In the century of communication

Shinnosuke Seki

Invited oral presentation, English, Invited, 島根大学, 松江、日本

13 Dec. 2011 - Program size and temperature in self-assembly

David Doty

Oral presentation, English, ISAAC2011: 22nd International Symposium on Algorithms and Computation, Yokohama, Japan, International conference

05 Dec. 2011 - Roles that temperature play in self-assembly

Shinnosuke Seki

Invited oral presentation, English, Invited, University of Western Ontario, London, ON, Canada

10 Nov. 2011 - Number theory and computational efficiency in chemoinformatics

Shinnosuke Seki

Invited oral presentation, English, Invited, University of Western Ontario, London, ON, Canada

03 Nov. 2011 - Number theory and computational efficiency in chemoinformatics

Shinnosuke Seki

Invited oral presentation, English, Invited, University of Pavol Jozef Safarik, Kosice, Slovakia

25 Aug. 2011 - An introduction to the world of self-assembly

Shinnosuke Seki

Invited oral presentation, English, Invited, Slovak Academy of Science, Kosice, Slovakia

24 Aug. 2011 - Characterizations of bounded semilinear languages by one-way and two-way deterministic machines

Shinnosuke Seki

Oral presentation, English, AFL2011: 13th International Conference on Automata and Formal Languages, Debrecen, Hungary, International conference

20 Aug. 2011 - Scalable, time-responsive, digital, energy-efficient, moleculer circuits using DNA strand displacement

David Doty

Poster presentation, English, DNA16: 16th International Conference on DNA Computing and Molecular Programming, Hong Kong, International conference

14 Jun. 2011 - One-reversal counter machines and multihead automata: revisited

Shinnosuke Seki

Oral presentation, English, SOFSEM2011: 37th International Conference on Current Trends in Theory and Practice of Computer Science, High Tatras, Slovakia, International conference

22 Jan. 2011 - Power of nondeterminism in self-assembly

David Doty

Oral presentation, English, SODA2011: ACM-SIAM Symposium on Discrete Algorithms, San Fransisco, California, USA, International conference

22 Jan. 2011 - Schema for parallel insertion and deletion

Shinnosuke Seki

Oral presentation, English, DLT2010: 14th International Conference on Developments in Language Theory, London, ON, Canada, International conference

17 Aug. 2010 - Triangular tile self-assembly systems

Shinnosuke Seki

Poster presentation, English, DNA16: 16th International Conference on DNA Computing and Molecular Programming, Hong Kong, International conference

14 Jun. 2010 - Schema for parallel insertion and deletion

Shinnosuke Seki

Invited oral presentation, English, Workshop on Formal Languages and Automata III, Invited, Kyoto Sangyo University, Kyoto, Japan, International conference

12 Dec. 2009 - An extension of fundamental notions in combinatorics on words inspired by DNA information encoding

Shinnosuke Seki

Invited oral presentation, English, Invited, Universitate Potsdam, Potsdam, Germany

06 Jul. 2009 - An extension of the Lyndon-Schutzenberger result to pseudoperiodic words

Shinnosuke Seki

Oral presentation, English, DLT2009: 13th International Conference on Developments in Language Theory, Stuttgard, Germany, International conference

30 Jun. 2009 - On the reversibility of parallel insertion, and its relation to comma codes

Bo Cui

Oral presentation, English, CAI2009: 3rd International Conference on Algebraic Informatics, Thessaloniki, Greece, International conference

19 May 2009 - Duplication in DNA sequences

Zachary Kincaid

Oral presentation, English, DLT2008: 12th International Conference on Developments in Language Theory, Kyoto, Japan, International conference

16 Sep. 2008 - On a special class of primitive words

Elena Czeizler

Oral presentation, English, MFCS2008: 33rd International Symposium on Mathematical Foundations of Computer Science, Torun, Poland, International conference

27 Aug. 2008 - Towards the sequence design preventing pseudoknot formation

Shinnosuke Seki

Oral presentation, English, IWNC2007: 2nd International Workshop on Natural Computing, Nagoya, Japan, International conference

10 Dec. 2007 - An efficient multiple alignment method for DNA secondary structures including pseudoknots

Shinnosuke Seki

Oral presentation, English, IWNC2007: 2nd International Workshop on Natural Computing, Nagoya, Japan, International conference

10 Dec. 2007 - Hierarchical alignment of RNA secondary structures including pseudoknots

Shinnosuke Seki

Poster presentation, English, GIW2004: 15th International Workshop on Genome Informatics, Yokohama, Japan, International conference

13 Dec. 2004 - Efficient learning of k-reversible context-free grammars from positive structural examples

Shinnosuke Seki

Poster presentation, English, ICGI: 7th International Colloquium on Grammatical Inferences, Athens, Greece, International conference

11 Oct. 2004

### Courses

- Formal Language Theory

Oct. 2021 - Present

The University of Electro-Communications - MICS実験第2

Oct. 2020 - Present

The University of Electro-Communications - 情報領域演習第2

Apr. 2020 - Present

The University of Electro-Communications - 大学院技術英語

Apr. 2020 - Present

The University of Electro-Communications - Exercise in Informatics 1

Oct. 2017 - Mar. 2023

The University of Electro-Communications - MICS実験第一

The University of Electro-Communications - K過程輪講

The University of Electro-Communications - 総合コミュニケーション科学

The University of Electro-Communications - Combinatorics

Aalto University

### Research Themes

- 文字列の辞書式順序の組合せ論とその応用

坂内 英夫

01 Apr. 2020 - 31 Mar. 2024 - 共転写性フォールディングの本質的計算完全性

01 Apr. 2020 - 31 Mar. 2023 - 万能折り畳みシステムの小型化とその限界

29 Jun. 2018 - 31 Mar. 2020 - 国際会議UCNC2019への助成

Shinnosuke Seki

Tateishi Science and Technology Foundation

25 Sep. 2018 - 07 Jun. 2019 - 国際会議DLT2018への助成

Shinnosuke Seki

National Institute of Information and Communications Technology (NICT), Support for the 22nd International Conference on Developments in Language Theory (DLT 2018), Principal investigator

01 Apr. 2018 - 共転写性フォールディングによる自己組織化システムの実際的設計と最適化

01 Apr. 2016 - 31 Mar. 2018 - 国際会議DLT2018への助成

Shinnosuke Seki

The Telecommunications Advancement Foundation, シンポジウム・セミナー 振興普及援助

01 Sep. 2017 - 機関選抜のため、研究テーマはなし

Shinnosuke Seki

Japan Science and Technology Agency, Principal investigator

06 Aug. 2015 - 31 Mar. 2017 - 国際会議DLT2018への助成

（株）久保田情報技研, 国際会議DLT2018開催支援寄付金

2017 - 共転写性フォールディングの数理モデル化とチューリング完全性

Shinnosuke Seki

Principal investigator

01 Apr. 2015 - 31 Mar. 2016 - Practical designs of molecular self-assembly systems and their optimization

Shinnosuke Seki

Academy of Finland, Principal investigator

01 Sep. 2013 - 31 Mar. 2015