arXiv subjects

Da-Jung Cho

Publications and source records attributed to Da-Jung Cho.

7 recordsLinked to original sources

arXiv2026

Deterministic Bandwidth of Finite Languages

Bandwidth restricts how far transitions can move under an ordering of the states in an automaton. While every finite language admits a bandwidth-2 NFA representation, the deterministic setting is substantially more restrictive. We investigate the bandwidth of partial DFAs accepting finite languages. We show that bounded bandwidth imposes strong structural restrictions on deterministic representations. We prove that there is an infinite hierarchy of classes of finite languages defined by deterministic bandwidth. As a special case of interest, we consider finite languages accepted by bandwidth-1 partial DFAs, and show that they admit a positional characterization, which yields a polynomial-time decision algorithm. We further study how the minimum DFA bandwidth can be estimated from the structure of the minimal DFA. We derive computable upper and lower bounds based on position-unfolding, and local growth of reachable residual states. These bounds can be computed efficiently and differ by at most a linear factor in the maximum word length. We also present a simple language family where the bounds match exactly.

cs.FL↗

arXiv2026

Bandwidth of Nondeterministic Finite Automata

Co-transcriptional splicing generates RNA sequences from a DNA template by deleting subsequences nondeterministically. Recent work showed how to encode an NFA into such a template, but the construction requires deleting subsequences whose length grows with the distance between states, which makes such deletions unlikely under the local nature of co-transcriptional splicing. We introduce $k$-bandwidth NFAs, in which transitions span at most $k$ states. These automata form a strict hierarchy of language classes. For finite languages, bandwidth $2$ suffices, and bandwidth $1$ can be decided in polynomial-time when the language is presented as a list of words. Minimizing the bandwidth is NP-hard even for fixed $k \geq 2$.

cs.FL↗

arXiv2025

Programmable Co-Transcriptional Splicing: Realizing Regular Languages via Hairpin Deletion

RNA co-transcriptionality, where RNA is spliced or folded during transcription from DNA templates, offers promising potential for molecular programming. It enables programmable folding of nano-scale RNA structures and has recently been shown to be Turing universal. While post-transcriptional splicing is well studied, co-transcriptional splicing is gaining attention for its efficiency, though its unpredictability still remains a challenge. In this paper, we focus on engineering co-transcriptional splicing, not only as a natural phenomenon but as a programmable mechanism for generating specific RNA target sequences from DNA templates. The problem we address is whether we can encode a set of RNA sequences for a given system onto a DNA template word, ensuring that all the sequences are generated through co-transcriptional splicing. Given that finding the optimal encoding has been shown to be NP-complete under the various energy models considered, we propose a practical alternative approach under the logarithmic energy model. More specifically, we provide a construction that encodes an arbitrary nondeterministic finite automaton (NFA) into a circular DNA template from which co-transcriptional splicing produces all sequences accepted by the NFA. As all finite languages can be efficiently encoded as NFA, this framework solves the problem of finding small DNA templates for arbitrary target sets of RNA sequences. The quest to obtain the smallest possible such templates naturally leads us to consider the problem of minimizing NFA and certain practically motivated variants of it, but as we show, those minimization problems are computationally intractable.

cs.FL↗

arXiv2025

A Formalization of Co-Transcriptional Splicing as an Operation on Formal Languages

RNA co-transcriptionality is the process where RNA sequences are spliced while being transcribed from DNA templates. This process holds potential as a key tool for molecular programming. Co-transcriptional folding has been shown to be programmable for assembling nano-scale RNA structures, and recent advances have proven its Turing universality. While post-transcriptional splicing has been extensively studied, co-transcriptional splicing is gaining attention for its potential to save resources and space in molecular systems. However, its unpredictability has limited its practical applications. In this paper, we focus on engineering co-transcriptional splicing, moving beyond natural occurrences to program RNA sequences that produce specific target sequences through DNA templates. We introduce contextual lariat deletion operations under three energy models - linear loop penalty, logarithmic loop penalty, and constantly bounded loop length - as well as bracketed contextual deletion, where deletion occurs solely based on context matching, without any structural constraints from hairpin loops. We examine the complexity of the template constructability problem associated with these operations and study the closure properties of the languages they generate, providing insights for RNA template design in molecular programming systems.

cs.FL↗

arXiv2020

Distributed Computation with Continual Population Growth

Computing with synthetically engineered bacteria is a vibrant and active field with numerous applications in bio-production, bio-sensing, and medicine. Motivated by the lack of robustness and by resource limitation inside single cells, distributed approaches with communication among bacteria have recently gained in interest. In this paper, we focus on the problem of population growth happening concurrently, and possibly interfering, with the desired bio-computation. Specifically, we present a fast protocol in systems with continuous population growth for the majority consensus problem and prove that it correctly identifies the initial majority among two inputs with high probability if the initial difference is $Ω(\sqrt{n\log n})$ where $n$ is the total initial population. We also present a fast protocol that correctly computes the NAND of two inputs with high probability. We demonstrate that combining the NAND gate protocol with the continuous-growth majority consensus protocol, using the latter as an amplifier, it is possible to implement circuits computing arbitrary Boolean functions.

math.PR↗

arXiv2018

Site-Directed Insertion: Decision Problems, Maximality and Minimality

Site-directed insertion is an overlapping insertion operation that can be viewed as analogous to the overlap assembly or chop operations that concatenate strings by overlapping a suffix and a prefix of the argument strings. We consider decision problems and language equations involving site-directed insertion. By relying on the tools provided by semantic shuffle on trajectories we show that one variable equations involving site-directed insertion and regular constants can be solved. We consider also maximal and minimal variants of the site-directed insertion operation.

cs.FL↗

arXiv2017

Outfix-guided insertion

Motivated by work on bio-operations on DNA strings, we consider an outfix-guided insertion operation that can be viewed as a generalization of the overlap assembly operation on strings studied previously. As the main result we construct a finite language $L$ such that the outfix-guided insertion closure of $L$ is non-regular. We consider also the closure properties of regular and (deterministic) context-free languages under the outfix-guided insertion operation and decision problems related to outfix-guided insertion. Deciding whether a language recognized by a deterministic finite automaton is closed under outfix-guided insertion can be done in polynomial time. The complexity of the corresponding question for nondeterministic finite automata remains open.

cs.FL↗