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Special Issue Editors

Dr. Ibuki Kawamata

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Guest Editor

1. Department of Robotics, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan
2. Natural Science Division, Faculty of Core Research, Ochanomizu University, Tokyo 112-8610, Japan
Interests: molecular robotics; DNA computing; DNA nanotechnology; DNA origami; molecular cybernetics

Dr. Yusuke Sato

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Guest Editor

Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai 980-8579, Japan
Interests: molecular robotics; molecular cybernetics; DNA computing; structural DNA nanotechnology; artificial cell biotechnology

Special Issue Information

Dear Colleagues,

Molecular robotics and molecular cybernetics are interdisciplinary research fields that aim to construct autonomous molecular systems by integrating devices built at a molecular level. In those fields, biomolecules such as DNA, RNA, peptides, and lipids are commonly used as building blocks owing to their programmability, functionality, and integrability. Various molecular devices have been designed and proposed using nucleic acid nanotechnology, molecular programming, artificial cell biotechnology, and protein engineering. Many microfluidic or lab-on-a-chip experiments have been conducted for integrating molecular devices to be observed under microscopy. As these techniques have progressed, a variety of systems have been demonstrated in the past few decades, such as DNA nanostructures, DNA computing logic gates, functional compartments, membrane-spanning peptides, and microfluidic devices for producing/observing a large number of vesicles. However, there are still open questions on how to develop autonomous molecular machinery in molecular robotics and realize chemical artificial intelligence in molecular cybernetics. In this Special Issue, contributions on molecular robotics and molecular cybernetics are welcome in forms such as original research articles, short communications, and review articles.

Dr. Yusuke Sato
Dr. Ibuki Kawamata
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Micromachines is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

Nano- and micro-fabrication
DNA and RNA nanotechnology
DNA and RNA computing
Liposomes and vesicles
Protein and peptide engineering
Artificial cell biotechnology
Microfluidic device
Molecular cybernetics
Molecular robotics

Published Papers (2 papers)

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Research

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20 pages, 1642 KiB

Open AccessArticle

Renewable DNA Proportional-Integral Controller with Photoresponsive Molecules

by Masaaki Tamba, Keiji Murayama, Hiroyuki Asanuma and Takashi Nakakuki

Micromachines 2022, 13(2), 193; https://doi.org/10.3390/mi13020193 - 26 Jan 2022

Cited by 5 | Viewed by 2421

Abstract

A molecular robot is an intelligent molecular system. A typical control problem of molecular robots is to maintain the concentration of a specific DNA strand at the desired level, which is typically attained by a molecular feedback control mechanism. A molecular feedback system can be constructed in a bottom-up method by transforming a nonlinear chemical reaction system into a pseudo-linear system. This method enables the implementation of a molecular proportional-integral (PI) controller on a DNA reaction system. However, a DNA reaction system is driven by fuel DNA strand consumption, and without a sufficient amount of fuel strands, the molecular PI controller cannot perform normal operations as a concentration regulator. In this study, we developed a design method for a molecular PI control system to regenerate fuel strands by introducing photoresponsive reaction control. To this end, we employed a photoresponsive molecule, azobenzene, to guide the reaction direction forward or backward using light irradiation. We validated our renewable design of the PI controller by numerical simulations based on the reaction kinetics. We also confirmed the proof-of-principle of our renewable design by conducting experiments using a basic DNA circuit. Full article

(This article belongs to the Special Issue Nano and Micro Scale Fabrication for Molecular Cybernetics and Molecular Robotics)

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Other

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7 pages, 863 KiB

Open AccessBrief Report

Controlling the Synchronization of Molecular Oscillators through Indirect Coupling

by Shiho Inagaki and Nathanael Aubert-Kato

Micromachines 2022, 13(2), 245; https://doi.org/10.3390/mi13020245 - 01 Feb 2022

Viewed by 1233

Abstract

In this article, we study the coupling of a collection of molecular oscillators, called repressilators, interacting indirectly through enzymatic saturation. We extended a measure of autocorrelation to identify the period of the whole system and to detect coupling behaviors. We explored the parameter space of concentrations of molecular species in each oscillator versus enzymatic saturation, and observed regions of uncoupled, partially, or fully coupled systems. In particular, we found a region that provided a sharp transition between no coupling, two coupled oscillators, and full coupling. In practical applications, signals from the environment can directly affect parameters such as local enzymatic saturation, and thus switch the system from a coupled to an uncoupled regime and vice-versa. Our parameter exploration can be used to guide the design of complex molecular systems, such as active materials or molecular robot controllers. Full article

(This article belongs to the Special Issue Nano and Micro Scale Fabrication for Molecular Cybernetics and Molecular Robotics)

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