Micromachines

Editorial

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2 pages, 163 KiB

Open AccessEditorial

Editorial on the Special Issue on Recent Advances of Molecular Machines and Molecular Robots

by Masahiro Takinoue and Ryuji Kawano

Micromachines 2020, 11(12), 1031; https://doi.org/10.3390/mi11121031 - 24 Nov 2020

Cited by 1 | Viewed by 1787

Abstract

Molecular machines and molecular robots are a highly interdisciplinary research field including material science, chemistry, biotechnology, biophysics, soft matter physics, micro-electromechanical systems (MEMS), and computer science [...] Full article

(This article belongs to the Special Issue Recent Advances of Molecular Machines and Molecular Robots)

Research

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8 pages, 2928 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

DNA Ring Motif with Flexible Joints

by Shiyun Liu, Satoshi Murata and Ibuki Kawamata

Micromachines 2020, 11(11), 987; https://doi.org/10.3390/mi11110987 - 31 Oct 2020

Cited by 5 | Viewed by 4167

Abstract

The invention of DNA origami has expanded the geometric complexity and functionality of DNA nanostructures. Using DNA origami technology, we develop a flexible multi-joint ring motif as a novel self-assembling module. The motif can connect with each other through self-complementary sequences on its [...] Read more.

The invention of DNA origami has expanded the geometric complexity and functionality of DNA nanostructures. Using DNA origami technology, we develop a flexible multi-joint ring motif as a novel self-assembling module. The motif can connect with each other through self-complementary sequences on its segments. The flexible joints can be fixed in a straightened position as desired, thereby allowing the motif to take various shapes. We can adjust the number of flexible joints and the number of connectable segments, thereby enabling programmable self-assembly of the motif. We successfully produced the motif and evaluated several self-assembly patterns. The proposed multi-joint ring motif can provide a novel method for creating functional molecular devices. Full article

(This article belongs to the Special Issue Recent Advances of Molecular Machines and Molecular Robots)

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15 pages, 2709 KiB

Open AccessArticle

8-(Pyridin-2-yl)quinolin-7-ol as a Platform for Conjugated Proton Cranes: A DFT Structural Design

by Anton Georgiev and Liudmil Antonov

Micromachines 2020, 11(10), 901; https://doi.org/10.3390/mi11100901 - 29 Sep 2020

Cited by 14 | Viewed by 2490

Abstract

Theoretical design of conjugated proton cranes, based on 7-hydroxyquinoline as a tautomeric sub-unit, has been attempted by using ground and excited state density functional theory (DFT) calculations in various environments. The proton crane action request existence of a single enol tautomer in ground [...] Read more.

Theoretical design of conjugated proton cranes, based on 7-hydroxyquinoline as a tautomeric sub-unit, has been attempted by using ground and excited state density functional theory (DFT) calculations in various environments. The proton crane action request existence of a single enol tautomer in ground state, which under excitation goes to the excited keto tautomer through a series of consecutive excited-state intramolecular proton transfer (ESIPT) steps with the participation of the crane sub-unit. A series of substituted pyridines was used as crane sub-units and the corresponding donor-acceptor interactions were evaluated. The results suggest that the introduction of strong electron donor substituents in the pyridine ring creates optimal conditions for 8-(pyridin-2-yl)quinolin-7-ols to act as proton cranes. Full article

(This article belongs to the Special Issue Recent Advances of Molecular Machines and Molecular Robots)

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15 pages, 4989 KiB

Open AccessArticle

Accelerating the Finite-Element Method for Reaction-Diffusion Simulations on GPUs with CUDA

by Hedi Sellami, Leo Cazenille, Teruo Fujii, Masami Hagiya, Nathanael Aubert-Kato and Anthony J. Genot

Micromachines 2020, 11(9), 881; https://doi.org/10.3390/mi11090881 - 22 Sep 2020

Cited by 3 | Viewed by 3353

Abstract

DNA nanotechnology offers a fine control over biochemistry by programming chemical reactions in DNA templates. Coupled to microfluidics, it has enabled DNA-based reaction-diffusion microsystems with advanced spatio-temporal dynamics such as traveling waves. The Finite Element Method (FEM) is a standard tool to simulate [...] Read more.

DNA nanotechnology offers a fine control over biochemistry by programming chemical reactions in DNA templates. Coupled to microfluidics, it has enabled DNA-based reaction-diffusion microsystems with advanced spatio-temporal dynamics such as traveling waves. The Finite Element Method (FEM) is a standard tool to simulate the physics of such systems where boundary conditions play a crucial role. However, a fine discretization in time and space is required for complex geometries (like sharp corners) and highly nonlinear chemistry. Graphical Processing Units (GPUs) are increasingly used to speed up scientific computing, but their application to accelerate simulations of reaction-diffusion in DNA nanotechnology has been little investigated. Here we study reaction-diffusion equations (a DNA-based predator-prey system) in a tortuous geometry (a maze), which was shown experimentally to generate subtle geometric effects. We solve the partial differential equations on a GPU, demonstrating a speedup of ∼100 over the same resolution on a 20 cores CPU. Full article

(This article belongs to the Special Issue Recent Advances of Molecular Machines and Molecular Robots)

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10 pages, 1930 KiB

Open AccessCommunication

Modeling a Microtubule Filaments Mesh Structure from Confocal Microscopy Imaging

by Yutaka Ueno, Kento Matsuda, Kaoru Katoh, Akinori Kuzuya, Akira Kakugo and Akihiko Konagaya

Micromachines 2020, 11(9), 844; https://doi.org/10.3390/mi11090844 - 10 Sep 2020

Cited by 4 | Viewed by 3135

Abstract

This study introduces a modeling method for a supermolecular structure of microtubules for the development of a force generation material using motor proteins. 3D imaging by confocal laser scanning microscopy (CLSM) was used to obtain 3D volume density data. The density data were [...] Read more.

This study introduces a modeling method for a supermolecular structure of microtubules for the development of a force generation material using motor proteins. 3D imaging by confocal laser scanning microscopy (CLSM) was used to obtain 3D volume density data. The density data were then interpreted by a set of cylinders with the general-purpose 3D modeling software Blender, and a 3D network structure of microtubules was constructed. Although motor proteins were not visualized experimentally, they were introduced into the model to simulate pulling of the microtubules toward each other to yield shrinking of the network, resulting in contraction of the artificial muscle. From the successful force generation simulation of the obtained model structure of artificial muscle, the modeling method introduced here could be useful in various studies for potential improvements of this contractile molecular system. Full article

(This article belongs to the Special Issue Recent Advances of Molecular Machines and Molecular Robots)

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11 pages, 1821 KiB

Open AccessArticle

Microfluidic Formation of Honeycomb-Patterned Droplets Bounded by Interface Bilayers via Bimodal Molecular Adsorption

by Shougo Fujiwara, Kan Shoji, Chiho Watanabe, Ryuji Kawano and Miho Yanagisawa

Micromachines 2020, 11(7), 701; https://doi.org/10.3390/mi11070701 - 20 Jul 2020

Cited by 14 | Viewed by 5440

Abstract

Assembled water-in-oil droplets bounded by lipid bilayers are used in synthetic biology as minimal models of cell tissue. Microfluidic devices successfully generate monodispersed droplets and assemble them via droplet interface bilayesr (DIB) formation. However, a honeycomb pattern of DIB-bounded droplets, similar to epithelial [...] Read more.

Assembled water-in-oil droplets bounded by lipid bilayers are used in synthetic biology as minimal models of cell tissue. Microfluidic devices successfully generate monodispersed droplets and assemble them via droplet interface bilayesr (DIB) formation. However, a honeycomb pattern of DIB-bounded droplets, similar to epithelial tissues, remains unrealized because the rapid DIB formation between the droplets hinders their ability to form the honeycomb pattern. In this paper, we demonstrate the microfluidic formation of a honeycomb pattern of DIB-bounded droplets using two surfactants with different adsorption rates on the droplet surface. A non-DIB forming surfactant (sorbitan monooleate, Span 80) was mixed with a lipid (1,2-dioleoyl-sn-glycero-3-phosphocholine, PC), whose adsorption rate on the droplet surface and saturated interfacial tension were lower than those of Span 80. By changing the surfactant composition, we established the conditions under which the droplets initially form a honeycomb pattern and subsequently adhere to each other via DIB formation to minimize the interfacial energy. In addition, the reconstituted membrane protein nanopores at the DIBs were able to transport molecules. This new method, using the difference in the adsorption rates of two surfactants, allows the formation of a honeycomb pattern of DIB-bounded droplets in a single step, and thus facilitates research using DIB-bounded droplet assemblies. Full article

(This article belongs to the Special Issue Recent Advances of Molecular Machines and Molecular Robots)

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18 pages, 2895 KiB

Open AccessArticle

Environment-Sensitive Intelligent Self-Reproducing Artificial Cell with a Modification-Active Lipo-Deoxyribozyme

by Muneyuki Matsuo, Yuiko Hirata, Kensuke Kurihara, Taro Toyota, Toru Miura, Kentaro Suzuki and Tadashi Sugawara

Micromachines 2020, 11(6), 606; https://doi.org/10.3390/mi11060606 - 22 Jun 2020

Cited by 13 | Viewed by 3545

Abstract

As a supramolecular micromachine with information flow, a giant vesicle (GV)-based artificial cell that exhibits a linked proliferation between GV reproduction and internal DNA amplification has been explored in this study. The linked proliferation is controlled by a complex consisting of GV membrane-intruded [...] Read more.

As a supramolecular micromachine with information flow, a giant vesicle (GV)-based artificial cell that exhibits a linked proliferation between GV reproduction and internal DNA amplification has been explored in this study. The linked proliferation is controlled by a complex consisting of GV membrane-intruded DNA with acidic amphiphilic catalysts, working overall as a lipo-deoxyribozyme. Here, we investigated how a GV-based artificial cell containing this lipo-deoxyribozyme responds to diverse external and internal environments, changing its proliferative dynamics. We observed morphological changes (phenotypic expression) in GVs induced by the addition of membrane precursors with different intervals of addition (starvation periods). First, we focused on a new phenotype, the “multiple tubulated” form, which emerged after a long starvation period. Compared to other forms, the multiple tubulated form is characterized by a larger membrane surface with a heavily cationic charge. A second consideration is the effect of the chain length of encapsulated DNA on competitive proliferation. The competitive proliferation among three different species of artificial cells containing different lengths of DNA was investigated. The results clearly showed a distinct intervention in the proliferation dynamics of the artificial cells with each other. In this sense, our GV-based artificial cell can be regarded as an intelligent supramolecular machine responding to external and internal environments, providing a new concept for developing molecular machines and robotics. Full article

(This article belongs to the Special Issue Recent Advances of Molecular Machines and Molecular Robots)

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Review

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20 pages, 9251 KiB

Open AccessReview

Recent Advances in Liposome-Based Molecular Robots

by Kan Shoji and Ryuji Kawano

Micromachines 2020, 11(9), 788; https://doi.org/10.3390/mi11090788 - 20 Aug 2020

Cited by 18 | Viewed by 5969

Abstract

A molecular robot is a microorganism-imitating micro robot that is designed from the molecular level and constructed by bottom-up approaches. As with conventional robots, molecular robots consist of three essential robotics elements: control of intelligent systems, sensors, and actuators, all integrated into a [...] Read more.

A molecular robot is a microorganism-imitating micro robot that is designed from the molecular level and constructed by bottom-up approaches. As with conventional robots, molecular robots consist of three essential robotics elements: control of intelligent systems, sensors, and actuators, all integrated into a single micro compartment. Due to recent developments in microfluidic technologies, DNA nanotechnologies, synthetic biology, and molecular engineering, these individual parts have been developed, with the final picture beginning to come together. In this review, we describe recent developments of these sensors, actuators, and intelligence systems that can be applied to liposome-based molecular robots. First, we explain liposome generation for the compartments of molecular robots. Next, we discuss the emergence of robotics functions by using and functionalizing liposomal membranes. Then, we discuss actuators and intelligence via the encapsulation of chemicals into liposomes. Finally, the future vision and the challenges of molecular robots are described. Full article

(This article belongs to the Special Issue Recent Advances of Molecular Machines and Molecular Robots)

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21 pages, 5655 KiB

Open AccessReview

Development of Artificial Cell Models Using Microfluidic Technology and Synthetic Biology

by Koki Kamiya

Micromachines 2020, 11(6), 559; https://doi.org/10.3390/mi11060559 - 30 May 2020

Cited by 29 | Viewed by 7866

Abstract

Giant lipid vesicles or liposomes are primarily composed of phospholipids and form a lipid bilayer structurally similar to that of the cell membrane. These vesicles, like living cells, are 5–100 μm in diameter and can be easily observed using an optical microscope. As [...] Read more.

Giant lipid vesicles or liposomes are primarily composed of phospholipids and form a lipid bilayer structurally similar to that of the cell membrane. These vesicles, like living cells, are 5–100 μm in diameter and can be easily observed using an optical microscope. As their biophysical and biochemical properties are similar to those of the cell membrane, they serve as model cell membranes for the investigation of the biophysical or biochemical properties of the lipid bilayer, as well as its dynamics and structure. Investigation of membrane protein functions and enzyme reactions has revealed the presence of soluble or membrane proteins integrated in the giant lipid vesicles. Recent developments in microfluidic technologies and synthetic biology have enabled the development of well-defined artificial cell models with complex reactions based on the giant lipid vesicles. In this review, using microfluidics, the formations of giant lipid vesicles with asymmetric lipid membranes or complex structures have been described. Subsequently, the roles of these biomaterials in the creation of artificial cell models including nanopores, ion channels, and other membrane and soluble proteins have been discussed. Finally, the complex biological functions of giant lipid vesicles reconstituted with various types of biomolecules has been communicated. These complex artificial cell models contribute to the production of minimal cells or protocells for generating valuable or rare biomolecules and communicating between living cells and artificial cell models. Full article

(This article belongs to the Special Issue Recent Advances of Molecular Machines and Molecular Robots)

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