Article
Chemistry, Multidisciplinary
Wei Zhang, Zhibin Zhao, Min Tan, Adila Adijiang, Shurong Zhong, Xiaona Xu, Tianran Zhao, Emusani Ramya, Lu Sun, Xueyan Zhao, Zhiqiang Fan, Dong Xiang
Summary: The binding orientation of molecules with respect to the electrode is crucial for the performance of molecular devices. However, modulating the binding orientation of single molecules in situ remains challenging. In this study, we demonstrate that the conductance of pyridine-anchored molecular junctions can be controlled by the applied voltage using a STM-BJ technique. Flicker noise measurements and theoretical calculations support the notion that the orientation of nitrogen-gold bonds in the molecular junctions can be manipulated by the mechanical stretching force and electric fields.
Article
Chemistry, Analytical
Elnaz Aliyari, Lars Konermann
Summary: Native electrospray ionization (ESI)-mass spectrometry (MS) is commonly used for detecting and characterizing multi-protein complexes, however, nonspecific protein clustering in the ESI plume can distort results. This study combines experiments and molecular dynamics simulations to reveal insights into ESI clustering of proteins, demonstrating the formation of nonspecific protein clusters via solvent evaporation. Through MD simulations, the study confirms the viability of charged residue model (CRM) and ion evaporation model (IEM) pathways for protein clustering.
ANALYTICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Zhuang Yan, Xingxing Li, Yusen Li, Chuangcheng Jia, Na Xin, Peihui Li, Linan Meng, Miao Zhang, Long Chen, Jinlong Yang, Rongming Wang, Xuefeng Guo
Summary: In this study, we demonstrate two configurations of a graphene-porphyrin-graphene single-molecule junction (SMJ) driven by electric field and proton transfer. The transistor configuration shows exceptional field-effect performance with high on/off ratio and gate efficiency. The other configuration reveals controllable proton transfer and tautomerization switching. This work provides insights into constructing multifunctional molecular nanocircuits and understanding the intrinsic properties of matters at the molecular scale.
Article
Chemistry, Physical
Z. Balogh, G. Mezei, N. Tenk, A. Magyarkuti, A. Halbritter
Summary: We examine the benefits of neural network boosted, principal-component-projection-based, unsupervised data classification in single-molecule break junction measurements, demonstrating that this method can identify highly relevant trace classes based on the well-defined and well-visualized internal correlations of the dataset.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Nanoscience & Nanotechnology
F. J. Dominguez-Gutierrez, S. Papanikolaou, A. Esfandiarpour, P. Sobkowicz, M. Alava
Summary: The study investigates the effects of high temperature on the mechanical deformation properties of single crystalline Mo under nanoindentation, revealing that temperature increase changes dislocation densities, mechanisms, atomic displacements, and hardness. The characteristic formation of [001] dislocation junctions and high-temperature stability may be responsible for the persistent thermomechanical stability of Mo, contrasting with other BCC metals.
MATERIALS SCIENCE AND ENGINEERING A-STRUCTURAL MATERIALS PROPERTIES MICROSTRUCTURE AND PROCESSING
(2021)
Article
Chemistry, Physical
Xingzhou Yang, Songjun Hou, Meiling Su, Qian Zhan, Hanjun Zhang, Sergio M. Quintero, Xiaodong Liu, Junyang Liu, Wenjing Hong, Juan Casado, Qingqing Wu, Colin J. Lambert, Yonghao Zheng
Summary: It is found that the transport properties of a series of fluorene derivatives can be tuned by controlling the degree of localization of certain orbitals, leading to a significant enhancement in conductance. This new understanding of the role of radicals in single-molecule junctions opens up a novel design strategy for single-molecule-based spintronic devices.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Delin Sun, Stewart He, W. F. Drew Bennett, Camille L. Bilodeau, Olaf S. Andersen, Felice C. Lightstone, Helgi I. Ingolfsson
Summary: Research on gramicidin A (gA) subunit dimerization in lipid bilayers revealed a dimer structure with two subunits connected by six hydrogen bonds, as well as two additional dimer structures stabilized by four or two hydrogen bonds. The temporal evolution study found that the dimer can form directly with six hydrogen bonds, or through paths involving two or four hydrogen bonds.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
Jiake Wei, Bin Feng, Ryo Ishikawa, Tatsuya Yokoi, Katsuyuki Matsunaga, Naoya Shibata, Yuichi Ikuhara
Summary: Grain boundary migration in polycrystalline materials is crucial in modifying microstructures and properties, governed by the atomistic mechanism. Experimental findings show that the migration proceeds through cooperative shuffling of atoms along low-energy structures.
Article
Nanoscience & Nanotechnology
Shintaro Fujii, Enrique Montes, Haruna Cho, Yi Yue, Masaaki Koike, Tomoaki Nishino, Hector Vazquez, Manabu Kiguchi
Summary: In this paper, the tuning of the thermopower of single-molecule junctions of fullerene, 4,4'-bipyridine, and p-phenylenediamine using scanning tunneling microscopy-based break junction technique is demonstrated. The thermoelectric voltage of the junction is tuned by mechanically controlling the tip-electrode separation distance. The atomistic simulations illustrate the shifts in the conduction orbital energies induced by the mechanical compression of the junctions.
ADVANCED ELECTRONIC MATERIALS
(2022)
Article
Nanoscience & Nanotechnology
Yanni Jie, Dong Wang, Jianfeng Huang, Yongqiang Feng, Jun Yang, Jiawen Fang, Runfeng Chen
Summary: This paper presents a precise method for manufacturing molecular junctions, which involves microcontact printing and selective electroless deposition to create covalently bound metal thin film electrodes. The process results in high stability and reproducibility, paving the way for further research on MMM structures and electrical properties.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Review
Chemistry, Multidisciplinary
William Bro-Jorgensen, Joseph M. Hamill, Rasmus Bro, Gemma C. Solomon
Summary: This tutorial review describes the crucial aspects of applying machine learning to help users avoid common pitfalls. Examples based on single-molecule electron transport experiments demonstrate the application of machine learning and highlight the importance of careful application. The concepts explored are also applicable in other fields with similar data.
CHEMICAL SOCIETY REVIEWS
(2022)
Article
Physics, Multidisciplinary
Takayuki Ariga, Keito Tateishi, Michio Tomishige, Daisuke Mizuno
Summary: The study showed that noisy external forces can accelerate the movement of kinesin molecules, especially under large hindering loads. This behavior is consistent with a theoretical model of two-state reactions, suggesting a universal noise-induced acceleration mechanism in intracellular enzymes. This indicates that active fluctuations in cells are utilized to promote various physiological processes, rather than just being considered as noise.
PHYSICAL REVIEW LETTERS
(2021)
Article
Engineering, Chemical
Jing Sun, Qian Li, Ting Li, Keling Xu, Zhao Cui, Guangyue Li
Summary: The formation mechanism and uranium bioleaching model of bio-ore pellets in the one-step bioleaching process of uranium by Aspergillus niger were investigated. The results showed that the formation of bio-ore pellets could be divided into three phases, and the mechanical damage of hyphae and organic acid corrosion played important roles in uranium dissolution.
MINERALS ENGINEERING
(2022)
Article
Chemistry, Multidisciplinary
Enrique Montes, Hector Vazquez
Summary: Using density functional theory (DFT), the electronic and conducting properties of benzenediamine connected to gold electrodes via different tip structures were investigated. Different binding motifs and junction spectral properties were examined, with corrections to molecular resonances at the junction based on atomistic structure of the tip. DFT-based transmission spectra approximated by a Lorentzian model involving only the highest occupied molecular orbital (HOMO) can achieve conductance values in quantitative agreement with previous experiments.
APPLIED SCIENCES-BASEL
(2021)
Article
Mechanics
N. G. Hadjiconstantinou
Summary: The behavior of fluid at the solid boundary interface is affected by the potential landscape imposed by the solid, which is modeled as forced Brownian motion in a periodic potential landscape in this study. The model, using atomistic parameters, captures the slip process in both linear and nonlinear forcing regimes, with good agreement with molecular dynamics simulation and previous modeling results. An explicit expression for the Navier slip coefficient in terms of molecular-level system parameters is derived.
JOURNAL OF FLUID MECHANICS
(2021)
Review
Chemistry, Analytical
Akihide Arima, Makusu Tsutsui, Takashi Washio, Yoshinobu Baba, Tomoji Kawai
ANALYTICAL CHEMISTRY
(2021)
Article
Nanoscience & Nanotechnology
Tomoki Hayashida, Makusu Tsutsui, Sanae Murayama, Tomoko Nakada, Masateru Taniguchi
Summary: This study systematically characterized the effect of dielectric coatings on the capture-to-translocation dynamics of single particles in solid-state pores. By covering SiNx membranes with different coatings, the researchers were able to change the zeta-potential at the pore wall, leading to easier particle capture and slower translocation motion in the channel. These findings serve as a guide for engineering pore wall surfaces to optimize translocation dynamics for efficient sensing of particles and molecules.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Article
Nanoscience & Nanotechnology
Kexin Chen, Makusu Tsutsui, Fuwei Zhuge, Yue Zhou, Yaoyao Fu, Yuhui He, Xiangshui Miao
Summary: Nanochannel-based interfacial memristors in polydimethylsiloxane offer flexibility and low cost, with the ability to tune device conductance by modifying solution interface positions. The devices exhibit typical hysteresis loops under continuous sweep voltage, and the dynamic frequency characteristics are measured to explore the physical mechanism behind. A comprehensive model is proposed, incorporating continuous voltage changes and surface tension modifications to predict interface position changes and explain conductance switching and frequency property.
ADVANCED ELECTRONIC MATERIALS
(2021)
Article
Chemistry, Analytical
Sou Ryuzaki, Takao Yasui, Makusu Tsutsui, Kazumichi Yokota, Yuki Komoto, Piyawan Paisrisarn, Noritada Kaji, Daisuke Ito, Kaoru Tamada, Takahiro Ochiya, Masateru Taniguchi, Yoshinobu Baba, Tomoji Kawai
Summary: The study identified the shape distributions of EVs suspended in solution are dependent on cell types, serving as a potential discrimination index for cancer cells. It provides a basis and feasibility for a simple method of discriminating multiple types of cancer cells based on rapid analyses of EV shape distributions.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Physical
Makusu Tsutsui, Takayuki Takaai, Kazumichi Yokota, Tomoji Kawai, Takashi Washio
Summary: The study introduces a deep learning approach for denoising ionic current in resistive pulse sensing, enabling the detection of electrophoretically-driven translocation motions of single nanoparticles in a nano-corrugated nanopore. The noise reduction by convolutional auto-encoding neural network allows for the identification of corrugation-derived wavy signals in a high-dimensional feature space, facilitating the in-situ tracking of fast-moving single- and double-nanoparticles. This unlabeled learning method effectively removes noise without compromising temporal resolution, making it potentially useful in solid-state nanopore sensing applications for protein structure and polynucleotide sequence analysis.
Article
Chemistry, Analytical
Kazumichi Yokota, Muneaki Hashimoto, Kazuaki Kajimoto, Masato Tanaka, Sanae Murayama, Makusu Tsutsui, Yoshihiro Nakajima, Masateru Taniguchi, Masatoshi Kataoka
Summary: In this study, the resistive pulse method (RPM) was used to accurately discriminate cancer cells from leukocytes by measuring individual cell size, deformability, and surface charge in a solution with a low electrolyte concentration.
Article
Chemistry, Physical
Makusu Tsutsui, Kazumichi Yokota, Akihide Arima, Takashi Washio, Yoshinobu Baba, Tomoji Kawai
Summary: The authors introduce a method for in situ detection of single-molecule DNA in cells using an electrolysis technique, showcasing its application in single-cell lysis and analysis. They identify specific current signatures that reflect the folding status of DNA, indicating the potential for on-chip single-molecule sequencing and multi-omics analyses in the future.
Article
Chemistry, Analytical
Iat Wai Leong, Makusu Tsutsui, Kazumichi Yokota, Masateru Taniguchi
Summary: This study demonstrates the use of salt gradient for fine control of capture-to-translocation dynamics in solid-state nanopores, resulting in improved nanoparticle detection efficiency. The findings pave the way for enhancing nanopore sensing capability for detecting biomolecules.
ANALYTICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Makusu Tsutsui, Akihide Arima, Kazumichi Yokota, Yoshinobu Baba, Tomoji Kawai
Summary: This study evaluates the heating phenomenon caused by diffusive ion transport in nanoscale conduits using thermocouple-embedded SiNx pores. The research found steady-state ionic heat dissipation in confined nanospace. Additionally, smaller pores exhibited higher heating efficiency due to a decrease in through-water thermal conduction.
Article
Chemistry, Analytical
Shohei Kishimoto, Iat Wai Leong, Sanae Murayama, Tomoko Nakada, Yuki Komoto, Makusu Tsutsui, Masateru Taniguchi
Summary: A method was reported to fabricate well-defined fluidic channels for reliable resistive pulse sensing of individual objects in electrolyte solution. The technique involves direct sculpting of holes in polymer resist membrane using electron beam lithography, allowing creation of channels with controlled shapes and sizes. These lithographically-defined pores can be utilized in designing single-particle sensors for cell sorting and viral screening.
SENSORS AND ACTUATORS B-CHEMICAL
(2022)
Article
Chemistry, Physical
Takanori Morikawa, Makusu Tsutsui, Yuki Komoto, Kazumichi Yokota, Masateru Taniguchi
Summary: This study reported on the rectifying behavior mediated by heterogeneous contacts in single-molecule structures, revealing that aromatic molecules and different anchoring groups can enable stronger rectification and stabilize the properties of single-molecule diodes.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Makusu Tsutsui, Kazumichi Yokota, Yuhui He, Tomoji Kawai
Summary: A permittivity gradient approach is reported to amplify the ionic blockade characteristics of DNA in solid-state nanopore sensing. Positive gradients enhance ionic signals, while negative gradients cause adverse effects. This phenomenon provides a novel way to enhance the single-molecule sensitivity of nanopore sensing.
Article
Multidisciplinary Sciences
Iat Wai Leong, Shohei Kishimoto, Makusu Tsutsui, Masateru Taniguchi
Summary: This study reports on the interference of ion diffusion kinetics at liquid-electrode interfaces in nanopore sensing. The growing impedance at the liquid-metal interfaces was found to significantly affect the measurements of ionic current, leading to decreased stability and temporal resolution.
Article
Chemistry, Multidisciplinary
Makusu Tsutsui, Kazumichi Yokota, Iat Wai Leong, Yuhui He, Tomoji Kawai
Summary: This study evaluates the practical feasibility of the ultrathin nanopore membrane for energy conversion efficiency. The results show that single pores exhibit quasi-perfect cation selectivity, and integrating multiple pores in parallel can yield higher energy. However, excessive porosity leads to decreased energy conversion efficiency. These findings provide guidance for designing highly efficient nanopore membrane osmotic power generators.
CELL REPORTS PHYSICAL SCIENCE
(2022)
Article
Biochemical Research Methods
Shohei Kishimoto, Makusu Tsutsui, Kazumichi Yokota, Masateru Taniguchi
Summary: The study focused on the controlled movements of single nanoparticles passing through an octet nanochannel for accurate zeta-potential assessments, revealing an exponential decrease in translocation duration between channels. This finding allows for precise estimation of single-nanoparticle zeta potential and provides a useful tool for analyzing particles and molecules of variable sizes.
