scholarly journals Field effect control of translocation dynamics in surround-gate nanopores

2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Makusu Tsutsui ◽  
Sou Ryuzaki ◽  
Kazumichi Yokota ◽  
Yuhui He ◽  
Takashi Washio ◽  
...  
Keyword(s):  
Solid State ◽  
Water Flow ◽  
Single Molecule ◽  
Ionic Current ◽  
Critical Issue ◽  
Hydrodynamic Drag ◽  
Single Particles ◽  
Drag Forces ◽  
Fine Control ◽  
Controllable Motion

AbstractControlling the fast electrophoresis of nano-objects in solid-state nanopores is a critical issue for achieving electrical analysis of single-particles by ionic current. In particular, it is crucial to slow-down the translocation dynamics of nanoparticles. We herein report that a focused electric field and associated water flow in a surround-gate nanopore can be used to trap and manipulate a nanoscale object. We fine-control the electroosmosis-induced water flow by modulating the wall surface potential via gate voltage. We find that a nanoparticle can be captured in the vicinity of the conduit by balancing the counteracting electrophoretic and hydrodynamic drag forces. By creating a subtle force imbalance, in addition, we also demonstrate a gate-controllable motion of single-particles moving at an extremely slow speed of several tens of nanometers per second. The present method may be useful in single-molecule detection by solid-state nanopores and nanochannels.

scholarly journals Comparing current noise in biological and solid-state nanopores

2019 ◽  
Author(s):  
A. Fragasso ◽  
S. Schmid ◽  
C. Dekker
Keyword(s):  
Solid State ◽  
Single Molecule ◽  
Signal To Noise Ratio ◽  
Low Cost ◽  
Ionic Current ◽  
Low Noise ◽  
Signal To Noise ◽  
Experimental Conditions ◽  
High Frequencies ◽  
Noise Ratio

AbstractNanopores bear great potential as single-molecule tools for bioanalytical sensing and sequencing, due to their exceptional sensing capabilities, high-throughput, and low cost. The detection principle relies on detecting small differences in the ionic current as biomolecules traverse the nanopore. A major bottleneck for the further progress of this technology is the noise that is present in the ionic current recordings, because it limits the signal-to-noise ratio and thereby the effective time resolution of the experiment. Here, we review the main types of noise at low and high frequencies and discuss the underlying physics. Moreover, we compare biological and solid-state nanopores in terms of the signal-to-noise ratio (SNR), the important figure of merit, by measuring free translocations of a short ssDNA through a selected set of nanopores under typical experimental conditions. We find that SiNx solid-state nanopores provide the highest SNR, due to the large currents at which they can be operated and the relatively low noise at high frequencies. However, the real game-changer for many applications is a controlled slowdown of the translocation speed, which for MspA was shown to increase the SNR >160-fold. Finally, we discuss practical approaches for lowering the noise for optimal experimental performance and further development of the nanopore technology.

The Dynamics of a Molecular Plug Docked onto a Solid-State Nanopore

2018 ◽  
Author(s):  
Xin Shi ◽  
Qiao Li ◽  
Rui Gao ◽  
Wei Si ◽  
Shao-Chuang Liu ◽  
...  
Keyword(s):  
Solid State ◽  
Single Molecule ◽  
Conformational Changes ◽  
Ionic Current ◽  
Observation Time ◽  
Random Coil ◽  
Dna Complexes ◽  
Dna Complex ◽  
Identification And Characterization

<a></a><a>Docking of a protein-DNA complex onto a nanopore can provide ample observation time for a detailed inspection of the complex, enabling collection of biophysical data for detection, identification, and characterization of the biomolecules. While docking of a protein-DNA complex onto a biological nanopore has enabled analytic applications of nanopores including DNA sequencing, the application of the same principle to solid-state nanopores is tempered by poor understanding of the docking process. Here, we elucidate the behaviour of individual protein-DNA complexes docked onto a solid-state nanopore by monitoring the nanopore ionic current. </a><a>Repeat docking of monovalent streptavidin-DNA complexes is found to produce ionic current blockades that fluctuate between discrete levels within the same current blockade. </a>We elucidate the roles of the protein plug and the DNA tether in the docking process, finding the docking configurations to determine the multitude of the current blockade levels whereas the frequency of the current level switching to be determined by the interactions between the molecules and the solid-state membrane. Finally, we prove the feasibility of using the nanopore docking principle for single molecule sensing using solid-state nanopores by detecting conformational changes of a tethered DNA molecule from a random coil to an i-motif states.

The Dynamics of a Molecular Plug Docked onto a Solid-State Nanopore

2018 ◽  
Author(s):  
Xin Shi ◽  
Qiao Li ◽  
Rui Gao ◽  
Wei Si ◽  
Shao-Chuang Liu ◽  
...  
Keyword(s):  
Solid State ◽  
Single Molecule ◽  
Conformational Changes ◽  
Ionic Current ◽  
Observation Time ◽  
Random Coil ◽  
Dna Complexes ◽  
Dna Complex ◽  
Identification And Characterization

<a></a><a>Docking of a protein-DNA complex onto a nanopore can provide ample observation time for a detailed inspection of the complex, enabling collection of biophysical data for detection, identification, and characterization of the biomolecules. While docking of a protein-DNA complex onto a biological nanopore has enabled analytic applications of nanopores including DNA sequencing, the application of the same principle to solid-state nanopores is tempered by poor understanding of the docking process. Here, we elucidate the behaviour of individual protein-DNA complexes docked onto a solid-state nanopore by monitoring the nanopore ionic current. </a><a>Repeat docking of monovalent streptavidin-DNA complexes is found to produce ionic current blockades that fluctuate between discrete levels within the same current blockade. </a>We elucidate the roles of the protein plug and the DNA tether in the docking process, finding the docking configurations to determine the multitude of the current blockade levels whereas the frequency of the current level switching to be determined by the interactions between the molecules and the solid-state membrane. Finally, we prove the feasibility of using the nanopore docking principle for single molecule sensing using solid-state nanopores by detecting conformational changes of a tethered DNA molecule from a random coil to an i-motif states.

scholarly journals Fast Fabrication of Solid-State Nanopores for DNA Molecule Analysis

Nanomaterials ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 2450
Author(s):  
Yin Zhang ◽  
Dexian Ma ◽  
Zengdao Gu ◽  
Lijian Zhan ◽  
Jingjie Sha
Keyword(s):  
Solid State ◽  
Single Molecule ◽  
Dna Analysis ◽  
Dielectric Breakdown ◽  
Ionic Current ◽  
Air Plasma ◽  
Dna Translocation ◽  
Accessible Method ◽  
Translocation Experiments ◽  
Single Molecule Analysis

Solid-state nanopores have been developed as a prominent tool for single molecule analysis in versatile applications. Although controlled dielectric breakdown (CDB) is the most accessible method for a single nanopore fabrication, it is still necessary to improve the fabrication efficiency and avoid the generation of multiple nanopores. In this work, we treated the SiNx membranes in the air–plasma before the CDB process, which shortened the time-to-pore-formation by orders of magnitude. λ-DNA translocation experiments validated the functionality of the pore and substantiated the presence of only a single pore on the membrane. Our fabricated pore could also be successfully used to detect short single-stranded DNA (ssDNA) fragments. Using to ionic current signals, ssDNA fragments with different lengths could be clearly distinguished. These results will provide a valuable reference for the nanopore fabrication and DNA analysis.

scholarly journals Single-Entity Detection With TEM-Fabricated Nanopores

2021 ◽  
Vol 9 ◽  
Author(s):  
Hongcheng Yang ◽  
Muhammad Saqib ◽  
Rui Hao
Keyword(s):  
Solid State ◽  
Single Molecule ◽  
Low Cost ◽  
Ionic Current ◽  
High Sensitivity ◽  
Protein Sequencing ◽  
Next Generation Sequencing Technology ◽  
Single Entity ◽  
Nanoparticle Detection ◽  
The Future

Nanopore-based single-entity detection shows immense potential in sensing and sequencing technologies. Solid-state nanopores permit unprecedented detail while preserving mechanical robustness, reusability, adjustable pore size, and stability in different physical and chemical environments. The transmission electron microscope (TEM) has evolved into a powerful tool for fabricating and characterizing nanometer-sized pores within a solid-state ultrathin membrane. By detecting differences in the ionic current signals due to single-entity translocation through the nanopore, solid-state nanopores can enable gene sequencing and single molecule/nanoparticle detection with high sensitivity, improved acquisition speed, and low cost. Here we briefly discuss the recent progress in the modification and characterization of TEM-fabricated nanopores. Moreover, we highlight some key applications of these nanopores in nucleic acids, protein, and nanoparticle detection. Additionally, we discuss the future of computer simulations in DNA and protein sequencing strategies. We also attempt to identify the challenges and discuss the future development of nanopore-detection technology aiming to promote the next-generation sequencing technology.

Single Molecule Solid State Light Emitting Electrochemical Cells with Lifetimes Superior to 3000 Hours

2008 ◽  
Author(s):  
Henk Bolink ◽  
Rubén D. Costa ◽  
Enrique Orti ◽  
Michele Sessolo ◽  
Stefan Graber ◽  
...  
Keyword(s):  
Solid State ◽  
Single Molecule ◽  
Electrochemical Cells ◽  
Light Emitting

scholarly journals Solid‐State Near‐Infrared Circularly Polarized Luminescence from Chiral YbIII‐Single‐Molecule Magnet

2021 ◽  
Author(s):  
Fabrice Pointillart ◽  
Bertrand Lefeuvre ◽  
Carlo Andrea Mattei ◽  
Jessica Flores Gonzalez ◽  
Frédéric Gendron ◽  
...  
Keyword(s):  
Solid State ◽  
Single Molecule ◽  
Near Infrared ◽  
Circularly Polarized ◽  
Single Molecule Magnet ◽  
Circularly Polarized Luminescence ◽  
Polarized Luminescence

Electric-Field Effects on Reactions Between Oxides

1997 ◽  
Vol 481 ◽  
Author(s):  
Matthew T. Johnson ◽  
Shelley R. Gilliss ◽  
C. Barry Carter
Keyword(s):  
Solid State ◽  
Electric Field ◽  
Elevated Temperatures ◽  
Ionic Current ◽  
Reaction Rates ◽  
Solid State Reactions ◽  
Interfacial Stability ◽  
Electric Field Effects ◽  
Thin Film Diffusion ◽  
Microscopy Techniques

ABSTRACTThin films of In2O3 and Fe2O3 have been deposited on (001) MgO using pulsed-laser deposition (PLD). These thin-film diffusion couples were then reacted in an applied electric field at elevated temperatures. In this type of solid-state reaction, both the reaction rate and the interfacial stability are affected by the transport properties of the reacting ions. The electric field provides a very large external driving force that influences the diffusion of the cations in the constitutive layers. This induced ionic current causes changes in the reaction rates, interfacial stability and distribution of the phases. Through the use of electron microscopy techniques the reaction kinetics and interface morphology have been investigated in these spinel-forming systems, to gain a better understanding of the influence of an electric field on solid-state reactions.

Slip Length Measurement of Water Flow on Graphite Surface Using Atomic Force Microscope

2014 ◽  
Vol 941-944 ◽  
pp. 1581-1584 ◽  
Author(s):  
Da Yong Li ◽  
Da Lei Jing ◽  
Yun Lu Pan ◽  
Khurshid Ahmad ◽  
Xue Zeng Zhao
Keyword(s):  
Atomic Force Microscope ◽  
Water Flow ◽  
Drag Force ◽  
Silicon Surface ◽  
Slip Length ◽  
Graphite Surface ◽  
Length Measurement ◽  
Hydrodynamic Drag ◽  
Experimental Measurements ◽  
Atomic Force

In this paper, we present experimental measurements of slip length of deionized (DI) water flow on a silicon surface and a graphite surface by using atomic force microscope. The results show that the measured hydrodynamic drag force is higher on silicon surface than that on graphite surface, and a measured slip length about 10 nm is obtained on the later surface.

Study of the Change of Performance of an Elastic Vertical Hydrofoil With Deformation

2014 ◽  
Author(s):  
Alexander Führing ◽  
Subha Kumpaty ◽  
Chris Stack
Keyword(s):  
Water Flow ◽  
Lift Coefficient ◽  
Flow Analysis ◽  
Turbulence Models ◽  
Flow Property ◽  
Performance Data ◽  
Cfd Analysis ◽  
Ansys Fluent ◽  
Drag Forces ◽  
Fluid Flow Analysis

In external and internal fluid flow analysis using numerical methods, most attention is paid to the properties of the flow assuming absolute rigidity of the solid bodies involved. However, this is often not the case for water flow or other fluids with high density. The pressure forces cause the geometry to deform which in turn changes the flow properties around it. Thus, a one-way and two-way Fluid-Structure Interaction (FSI) coupling is proposed and compared to a CFD analysis of a windsurfing fin in order to quantify the differences in performance data as well as the properties of the flow. This leads to information about the necessity of the use of FSI in comparison to regular CFD analysis and gives indication of the value of the enhanced results of the deformable analysis applied to water flow around an elastically deformable hydrofoil under different angles of attack. The performance data and flow property evaluation is done in ANSYS Fluent using the k-ω SST and k-ε model with a y+ of 1 and 35 respectively in order to be able to compare the behavior of both turbulence models. It is found that the overall lift coefficient in general is lower and that the flow is less turbulent because of softer transition due to the deformed geometry reducing drag forces. It is also found that the deformation of the tip of the hydrofoil leads to vertical lift forces. For the FSI analysis, one-way and two-way coupling were incorporated leading to the ability to compare results. It has been found that one-way coupling is sufficient as long as there is no stall present at any time.

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