Stretching-induced conductance variations as fingerprints of contact configurations in single-molecule junctions

Molecule-electrode contact atomic structures are a critical factor that characterizes molecular devices, but their precise understanding and control still remain elusive. Based on combined first-principles calculations and single-molecule break junction experiments, we herein establish that the conductance of alkanedithiolate junctions can both increase and decrease with mechanical stretching and the specific trend is determined by the S-Au linkage coordination number (CN) or the molecule-electrode contact atomic structure. Specifically, we find that the mechanical pulling results in the conductance increase for the junctions based on S-Au CN two and CN three contacts, while the conductance is minimally affected by stretching for junctions with the CN one contact and decreases upon the formation of Au monoatomic chains. Detailed analysis unravels the mechanisms involving the competition between the stretching-induced upshift of the highest occupied molecular orbital-related states toward the Fermi level of electrodes and the deterioration of molecule-electrode electronic couplings in different contact CN cases. Moreover, we experimentally find a higher chance to observe the conductance enhancement mode under a faster elongation speed, which is explained by ab initio molecular dynamics simulations that reveal an important role of thermal fluctuations in aiding deformations of contacts into low-coordination configurations that include monoatomic Au chains. Pointing out the insufficiency in previous notions of associating peak values in conductance histograms with specific contact atomic structures, this work resolves the controversy on the origins of ubiquitous multiple conductance peaks in S-Au-based single-molecule junctions.Comment: 11 pages, 4 figures; to be published in J. Am. Chem. So

Ionic Signal Amplification of DNA in a Nanopore

Ionic signal amplification is a key challenge for single-molecule analyses by solid-state nanopore sensing. Here, a permittivity gradient approach for amplifying ionic blockade characteristics of DNA in a nanofluidic channel is reported. The transmembrane ionic current response is found to change substantially through modifying the liquid permittivity at one side of a pore with an organic solvent. Imposing positive liquid permittivity gradients with respect to the direction of DNA electrophoresis, this study observes the resistive ionic signals to become larger due to the varying contributions of molecular counterions. On the contrary, negative gradients render adverse effects causing conductive ionic current pulses upon polynucleotide translocations. Most importantly, both the positive and negative gradients are demonstrated to be capable of amplifying the ionic signals by an order of magnitude with a 1.3-fold difference in the transmembrane liquid dielectric constants. This phenomenon allows a novel way to enhance the single-molecule sensitivity of nanopore sensing that may be useful in analyzing secondary structures and genome sequence of DNA by ionic current measurements.This is the pre-peer reviewed version of the following article: Tsutsui, M., Yokota, K., He, Y., Kawai, T., Ionic Signal Amplification of DNA in a Nanopore. Small Methods 2022, 6, 2200761, which has been published in final form at https://doi.org/10.1002/smtd.202200761. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving

Electrochemical response of biased nanoelectrodes in solution

Novel approaches to DNA sequencing and detection require the measurement of electrical currents between metal probes immersed in ionic solution. Here, we experimentally demonstrate that these systems maintain large background currents with a transient response that decays very slowly in time and noise that increases with ionic concentration. Using a non-equilibrium stochastic model, we obtain an analytical expression for the ionic current that shows these results are due to a fast electrochemical reaction at the electrode surface followed by the slow formation of a diffusion layer. During the latter, ions translocate in the weak electric field generated after the initial rapid screening of the strong fields near the electrode surfaces. Our theoretical results are in very good agreement with experimental findings

A noise-driven attractor switching device

Problems with artificial neural networks originate from their deterministic nature and inevitable prior learnings, resulting in inadequate adaptability against unpredictable, abrupt environmental change. Here we show that a stochastically excitable threshold unit can be utilized by these systems to partially overcome the environmental change. Using an excitable threshold system, attractors were created that represent quasi-equilibrium states into which a system settles until disrupted by environmental change. Furthermore, noise-driven attractor stabilization and switching were embodied by inhibitory connections. Noise works as a power source to stabilize and switch attractors, and endows the system with hysteresis behavior that resembles that of stereopsis and binocular rivalry in the human visual cortex. A canonical model of the ring network with inhibitory connections composed of class 1 neurons also shows properties that are similar to the simple threshold system.Comment: 9 pages, 2 tables, and 6 figures. will appear in Phy.Rev.E, vol.79, issue

Metal Ion-dependent Effects of Clioquinol on the Fibril Growth of an Amyloid β Peptide

This research was originally published in the Journal of Biological Chemistry. Bakthisaran Raman, Tadato Ban, Kei-ichi Yamaguchi, Miyo Sakai, Tomoji Kawai, Hironobu Naiki and Yuji Goto. Metal Ion-dependent Effects of Clioquinol on the Fibril Growth of an Amyloid β Peptide. J. Biol. Chem. 2005; 280, 16157-16162. © the American Society for Biochemistry and Molecular Biolog

Cooperative Dynamics of an Artificial Stochastic Resonant System

We have investigated cooperative dynamics of an artificial stochastic resonant system, which is a recurrent ring connection of neuron-like signal transducers (NST) based on stochastic resonance (SR), using electronic circuit experiments. The ring showed quasi-periodic, tunable oscillation driven by only noise. An oscillation coherently amplified by noise demonstrated that SR may lead to unusual oscillation features. Furthermore, we found that the ring showed synchronized oscillation in a chain network composed of multiple rings. Our results suggest that basic functions (oscillation and synchronization) that may be used in the central pattern generator of biological system are induced by collective integration of the NST element.Comment: 13 pages, 4 figure

Nanoarrays of tethered lipid bilayer rafts on poly(vinyl alcohol) hydrogels

Lipid rafts are cholesterol-and sphingolipid-rich domains that function as platforms for signal transduction and other cellular processes. Tethered lipid bilayers have been proposed as a promising model to describe the structure and function of cell membranes. We report a nano(submicro) array of tethered lipid bilayer raft membranes (tLBRMs) comprising a biosensing platform. Poly(vinyl alcohol) (PVA) hydrogel was directly patterned onto a solid substrate, using ultraviolet-nanoimprint lithography (UV-NIL), as an inert barrier to prevent biofouling. The robust structures of the nanopatterned PVA hydrogel were stable for up to three weeks in phosphate-buffered saline solution despite significant swelling (100% in height) by hydration. The PVA hydrogel strongly restricted the adhesion of vesicles, resulting in an array of highly selective hydrogel nanowells. tLBRMs were not formed by direct vesicle fusion, although raft vesicles containing poly(ethylene glycol) lipopolymer were selectively immobilized on gold substrates patterned with PVA hydrogel. The deposition of tLBRM nano(submicro) arrays was accomplished by a mixed, self-assembled monolayer-assisted vesicle fusion method. The monolayer was composed of a mixture of 2-mercaptoethanol and poly(ethylene glycol) lipopolymer, which promoted vesicle rupture. These results suggest that the fabrication of inert nanostructures and the site-selective modification of solid surfaces to induce vesicle rupture may be essential in the construction of tLBRM nano(submicro) arrays using stepwise self-assembly.This work was supported by Core Research for Evolutional Science and Technology (CREST) of Japan Science and Technology Agency (JST), and New Energy and Indstrial Technology Development Organization (NEDO)