Detection of DNA sequences using an alternating electric field in a nanopore capacitor

Molecular dynamics simulations revealed that back-and-forth motion of DNA strands through a 1 nm diameter pore exhibits sequence-specific hysteresis that arises from the reorientation of the DNA bases in the nanopore constriction. Such hysteresis of the DNA motion results in detectable changes of the electrostatic potential at the electrodes of the nanopore capacitor and in a sequence-specific drift of the DNA strand under an oscillating transmembrane bias. A strategy is suggested for sequencing DNA in a nanopore using the electric field that alternates periodically in time.     

The Brownian and Flow‐Driven Rotational Dynamics of a Multicomponent DNA Origami‐Based Rotor

Nanomechanical devices are becoming increasingly popular due to the very diverse field of potential applications, including nanocomputing, robotics, and drug delivery. DNA is one of the most promising building materials to realize complex 3D structures at the nanoscale level. Several mechanical DNA origami structures have already been designed capable of simple operations such as a DNA box with a controllable lid, bipedal walkers, and cargo sorting robots. However, the nanomechanical properties of mechanically interlinked DNA nanostructures that are in general highly deformable have yet to be extensively experimentally evaluated. In this work, a multicomponent DNA origami‐based rotor is created and fully characterized by electron microscopy under negative stain and cryo preparations. The nanodevice is further immobilized on a microfluidic chamber and its Brownian and flow‐driven rotational behaviors are analyzed in real time by single‐molecule fluorescence microscopy. The rotation in previous DNA rotors based either on strand displacement, electric field or Brownian motion. This study is the first to attempt to manipulate the dynamics of an artificial nanodevice with fluidic flow as a natural force.     

Stretching DNA using the electric field in a synthetic nanopore

The mechanical properties of DNA over segments comparable to the size of a protein-binding site (3-10 nm) are examined using an electric-field-induced translocation of single molecules through a nanometer diameter pore. DNA, immersed in an electrolyte, is forced through synthetic pores ranging from 0.5 to 1.5 nm in radius in a 10 nm thick Si(3)N(4) membrane using an electric field. To account for the stretching and bending, we use molecular dynamics to simulate the translocation. We have found a threshold for translocation that depends on both the dimensions of the pore and the applied transmembrane bias. The voltage threshold coincides with the stretching transition that occurs in double-stranded DNA near 60 pN.     

Determination of useful parameter space for a double-walled carbon nanotube based motor subjected to a sinusoidally varying electric field

A molecular dynamics analysis has been performed for a double-walled carbon-nanotube based motor driven by an externally applied sinusoidally varying electric field, in the presence of a ‘frozen’ sleeve. It is shown that to produce unidirectional (motor-like) rotation, it is necessary to operate over a ‘useful’ region in the parameter space defined by the amplitude and frequency of the applied electric field. For a given frequency, electric field amplitudes below a threshold are not able to overcome the potential energy barriers due to interaction of the rotating shaft with the frozen sleeve. This is followed by a range of amplitudes where unidirectional motion is observed. At still higher amplitudes, distortion of the shaft increases the potential energy barriers to levels higher than those that can be overcome by the electric field. For a given amplitude, as the frequency is varied, more complex behavior is obtained, which can be broken up into four regions. At low frequencies, large distortion of the shaft leads to an increase in potential energy barriers, hindering rotation. Over an intermediate range, unidirectional motion is observed. This is followed by an anomalous region, where resonant excitation of a characteristic mode of the shaft leads to very large distortions, which greatly enhances the barrier. The distortion falls off with further rise in frequency. A detailed physical explanation has also been provided for the anomalous behavior in terms of resonant excitation of characteristic modes.     

Direct observation of single native DNA molecules in a microchannel by differential interference contrast microscopy

Direct observation of single native DNA molecules in a microchannel was monitored without fluorescence-dye labeling. At a PDMS/glass microchip, the image of individual lambda-DNA molecules appear sharp and distinct in Nomarski differential interference contrast microscopy. Intercalator dyes affected the physical properties and dynamic behavior of individual DNA molecules. From the migration velocities in the microchannel it is evident that native DNA molecules migrated faster than DNA molecules labeled with the intercalator YOYO-1. This is because YOYO-1 increases the molecular weight and size of lambda-DNA and decreases the charge. The electric field strength and pH also affected the dynamics of single DNA molecules. We also observed that YOYO-labeled DNA was more stretched out compared to native DNA.     

The Dynamics of Oblate Drop Between Heterogeneous Plates Under Alternating Electric Field

The dynamics of the incompressible fluid drop under the non-uniform electric field are considered. The drop is bounded axially by two parallel solid planes and the case of heterogeneous plates is investigated. The external electric field acts as an external force that causes motion of the contact line. We assume that the electric current is alternative current and the AC filed amplitude is a spatially non-uniform function. In equilibrium, the drop has the form of a circular cylinder. The equilibrium contact angle is 0.5π. In order to describe this contact line motion the modified Hocking boundary condition is applied: the velocity of the contact line is proportional to the deviation of the contact angle and the speed of the fast relaxation processes, which frequency is proportional to twice the frequency of the electric field. The Hocking parameter depends on the polar angle, i.e. the coefficient of the interaction between the plate and the fluid (the contact line) is a function of the plane coordinates. This function is expanded in a series of the Laplace operator eigenfunctions.     

Nanopore translocation dynamics of a single DNA-bound protein

We study the translocation dynamics of a single protein molecule attached to a double-stranded DNA that is threaded through a solid-state nanopore by optical tweezers and an electric field (nanopore force spectroscopy). We find distinct asymmetric and retarded force signals that depend on the protein charge, the DNA elasticity and its counterionic screening in the buffer. A theoretical model where an isolated charge on an elastic, polyelectrolyte strand is experiencing an anharmonic nanopore potential was developed. Its results compare very well with the measured force curves and explain the experimental findings that the force depends linearly on the applied electric field and exhibits a small hysteresis during back and forth translocation cycles. Moreover, the translocation dynamics reflects the stochastic nature of the thermally activated hopping between two adjacent states in the nanopore that can be adequately described by Kramers rate theory.     

Nonlinear dynamics of interface between dielectric liquids in vertical electric and gravity fields

The development of instability on the interface between dielectric liquids in vertical electric and gravity fields has been studied. The possibility of a special regime of motion is established, in which the velocity potential is linearly related to the electric field potential. An integro-differential equation is derived for this regime, which describes a weakly nonlinear evolution of the interface. This equation admits the existence of broad classes of exact solutions that determine the dynamics of both periodic and localized perturbations of the interface.     

乳状液电磁场破乳法的研究

提出了一种利用电磁感应原理产生涡旋电场进行破乳的新方法。将螺线管、磁芯构成的电感器与电容器串联组成Ｌ－Ｃ谐振电路。在此电路中通过高频电流，使其在破乳器内产生高频磁场，从而感生出高频涡旋电场。在此电场的作用下，乳状液滴极化并加速其运动与碰撞，达到破乳的目的。该法在输入信号电压约３００Ｖ、电流几＋ｍＡ、频率２０ｋＨｚ的条件下，可感应出强度为几十＋ｋＶ／ｃｍ的涡旋电场，５ｍｉｎ内静态破乳率大于９８％。在     

Measuring the robson angle in vacuum arcs of various length

It is established that the Robson angle, which determines the direction of motion of a cathode spot of vacuum arc in a homogeneous electric field sloped relative to the cathode, depends mostly on the inter-electrode gap width. The dependence of the Robson angle on the field slope at various gap widths has been measured for molybdenum and tungsten cathodes. The knowledge of this angle is necessary for correct choice of the optimum magnetic field configuration controlling the cathode spot dynamics in setups for vacuum-arc deposition of various coatings and in vacuum commutation devices.     

PVA/PAA复合膜电响应特性的研究

通过研究PVA/PAA复合膜红外光谱特性,扫描电镜分析,及电场作用下膜通量的变化,阐明了PVA/PAA复合膜的电响应特性和规律。研究结果表明:制备的PVA/PAA复合膜中PVA与戊二醛已经发生交联反应形成酯键;-COOH基团的离子化是产生电响应的必要条件。随着PAA含量的增加,膜通量也明显的增加,表明体系中离子基团的数量(浓度)能够强烈影响PVA复合膜的直流电响应性;随着电场强度的增大,膜通量增加;在离子强度小于0.01mol/L时,膜通量随离子强度的增加而增加,但当离子强度大于0.01mol/L时,膜通量则呈现下降的趋势。在实验条件下,比较理想电响应条件为PVA∶PAA=1∶1,溶液离子强度为0.01mol/L。     

Dynamics of Charged Quantized Vortices

We study theoretically the dynamics of charged quantized vortices (CQVs). CQVs (ion-vortex complexes) have been used as an important probe in the field of quantum hydrodynamics. Recent experimental studies of quantum turbulence at very low temperatures utilize CQVs. In this work we propose the equation of motion of CQVs based on the vortex filament model. An analytical solution for a charged vortex ring shows how it expands under an electric field. Numerical simulation reveals the characteristic behavior of CQVs under an electric field.     

Measurement and Study of Electromagnetic Emission Generated by Tensile Fracture of Polymers and Carbon Fibres

Electromagnetic emission (EME) signals generated by tensile fracture of four different types of polymers and three different carbon fibre types are presented and discussed. A suitable set-up for the detection of the electric field component of EME generated by fracture of solids is proposed. Basic theoretical considerations are made about the coupling between these field components and the capacitive sensors used to directly measure the short ranged and low frequency (kHz–MHz) electric fields emitted by the generation of free surface charges and their spatial movement as dictated by the vibrational motion of the crack walls. Special focus is put on solids with low conductivity, where the influences of the material on the emitted fields is small and the detected electric signals almost solely depend on the source dynamics and the sensor characteristics. Analysis of the influence of the acquisition circuit is presented. The discussion of the electric signals emitted by tensile fracture of carbon fibres and polymer specimens comprises the influences of the material properties on the signals as well as correlations between the signals and the crack dynamics, including the crack propagation velocities.     

Sample stacking during membrane-mediated loading in automated DNA sequencing.

Microporous membrane-mediated loading is a novel and efficient sample injection technique for ultrathin slab gel electrophoresis-based automated DNA sequence analysis. The sequencing reaction mixture is spotted directly onto the tabs of the membrane loader, which is then inserted to close proximity of the straight edge of the separation gel. The use of a higher viscosity (> 60 cSt), low ionic strength (conductivity < 320 microS) well solution with a pH of more than one unit lower that of the separation and gel buffer system makes possible efficient stacking of the DNA sequencing fragments at the interface of the gel matrix. When the injection/separation process is initiated by the application of the electric field, a high local electric potential drop is formed across the low ionic strength well solution zone. This results in very fast migration of the DNA sequencing fragments toward the interface of the separation gel, where they stack up against the higher conductivity sieving matrix. During this stacking process, primarily the local pH mediates the actual mobility of the buffer co-ions (borate), forming the leading and terminating zones in the well solution and separation gel, respectively.     

Spin Dynamics and Spin Transport

Spin-orbit (SO) interaction critically influences electron spin dynamics and spin transport in bulk semiconductors and semiconductor microstructures. This interaction couples electron spin to dc and ac electric fields. Spin coupling to ac electric fields allows efficient spin manipulating by the electric component of electromagnetic field through the electric dipole spin resonance (EDSR) mechanism. Usually, it is much more efficient than the magnetic manipulation due to a larger coupling constant and the easier access to spins at a nanometer scale. The dependence of the EDSR intensity on the magnetic field direction allows measuring the relative strengths of the competing SO coupling mechanisms in quantum wells. Spin coupling to an in-plane electric field is much stronger than to a perpendicular field. Because electron bands in microstructures are spin split by SO interaction, electron spin is not conserved and spin transport in them is controlled by a number of competing parameters, hence, it is rather nontrivial. The relation between spin transport, spin currents, and spin populations is critically discussed. Importance of transients and sharp gradients for generating spin magnetization by electric fields and for ballistic spin transport is clarified.     

Modelling the effect of structure and base sequence on DNA molecular electronics

DNA is a material that has the potential to be used in nanoelectronic devices as an active component. However, the electronic properties of DNA responsible for its conducting behaviour remain controversial. Here we use a self-consistent quantum molecular dynamics method to study the effect of DNA structure and base sequence on the energy involved when electrons are added or removed from isolated molecules and the transfer of the injected charge along the molecular axis when an electric field is applied. Our results show that the addition or removal of an electron from DNA molecules is most exothermic for poly(dC)-poly(dG) in its B-form and poly(dA)-poly(dT) in its A-form, and least exothermic in its Z-form. Additionally, when an electric field is applied to a charged DNA molecule along its axis, there is electron transfer through the molecule, regardless of the number and sign of the injected charge, the molecular structure and the base sequence. Results from these simulations provide useful information that is hard to obtain from experiments and needs to be considered for further modelling aiming to improve charge transport efficiency in nanoelectronic devices based on DNA.     

Spin Dynamics and Spin Transport

Spin-orbit (SO) interaction critically influences electron spin dynamics and spin transport in bulk semiconductors and semiconductor microstructures. This interaction couples electron spin to dc and ac electric fields. Spin coupling to ac electric fields allows efficient spin manipulating by the electric component of electromagnetic field through the electric dipole spin resonance (EDSR) mechanism. Usually, it is much more efficient than the magnetic manipulation due to a larger coupling constant and the easier access to spins at a nanometer scale. The dependence of the EDSR intensity on the magnetic field direction allows measuring the relative strengths of the competing SO coupling mechanisms in quantum wells. Spin coupling to an in-plane electric field is much stronger than to a perpendicular field. Because electron bands in microstructures are spin split by SO interaction, electron spin is not conserved and spin transport in them is controlled by a number of competing parameters, hence, it is rather nontrivial. The relation between spin transport, spin currents, and spin populations is critically discussed. Importance of transients and sharp gradients for generating spin magnetization by electric fields and for ballistic spin transport is clarified.     

Biomolecule-recognition gating membrane using biomolecular cross-linking and polymer phase transition

We present for the first time a biomolecule-recognition gating system that responds to small signals of biomolecules by the cooperation of biorecognition cross-linking and polymer phase transition in nanosized pores. The biomolecule-recognition gating membrane immobilizes the stimuli-responsive polymer, including the biomolecule-recognition receptor, onto the pore surface of a porous membrane. The pore state (open/closed) of this gating membrane depends on the formation of specific biorecognition cross-linking in the pores: a specific biomolecule having multibinding sites can be recognized by several receptors and acts as the cross-linker of the grafted polymer, whereas a nonspecific molecule cannot. The pore state can be distinguished by a volume phase transition of the grafted polymer. In the present study, the principle of the proposed system is demonstrated using poly(N-isopropylacrylamide) as the stimuli-responsive polymer and avidin-biotin as a multibindable biomolecule-specific receptor. As a result of the selective response to the specific biomolecule, a clear permeability change of an order of magnitude was achieved. The principle is versatile and can be applied to many combinations of multibindable analyte-specific receptors, including antibody-antigen and lectin-sugar analogues. The new gating system can find wide application in the bioanalytical field and aid the design of novel biodevices.     

Translational motion of a polymer gel microrod via electrically induced wave propagation

The aim of the present study relies on the potential to control the motion of a polymer gel microrod by means of a suitable electric field. It is well known that a polyelectrolyte gel can change its conformation under the effects of an electric field. Inducing a local deformation in a gel rod, it is possible to propagate the deformation along the gel rod itself, shjfting it in the same direction as the electric field. This technique, which can be viewed as a sort of wave propagation method, can be used to perform a controlled translational motion of the whole gel body.A simple device has been designed to provide the desired application of the electric field and to study the gel microstructure response. Experimental measurements characterizing the main electro-kinetic properties of the polymer gel have been carried out, and the related results used in the simulation of the gel motion. Finally, real motion experiments have been performed.Both theoretical and experimental results show that this novel technique can induce and control the translational motion of a polymer gel microrod, but that a high degree of miniaturization of the system is still required to achieve reliability and performance necessary in technological and scientific applications.     

Ion Concentration Effect on Nanoscale Electrospray Modes

The phenomena and mechanism of electrospray modes in nanoscale are investigated from experiments and molecular dynamics simulations. It is found that the ionic concentration plays a crucial role in determining the dripping or the jetting modes in a nanoscale electrospray system. Molecular dynamics simulations uncover that the two modes are caused by the competition between the electric field stress and surface tension, which is similar to the mechanism in a macroscale electrospray system. However, in a nanoscale electrospray system, the two competing forces of the electric field stress and surface tension are more sensitive to the ion distributions than that in a macroscale electrospray system, in which the applied voltage and pressure dominate. With the decrease of the nozzle diameter to nanoscale, the ions not only affect the local electric field stress, but also destroy the hydrogen bonds among water molecules, which lead to that the ion concentration becomes a dominant factor in determining the electrospray modes in nanoscale. The discovery provides a novel method to control nanoscale electrospray modes, which may find potential applications for mass spectrometry, film deposition, and electrohydrodynamic printing.