Driven translocation dynamics of polynucleotides through a nanopore: off-lattice Monte-Carlo simulations

The driven translocation dynamics of a polynucleotide chain through a nanopore is studied using off-lattice Monte-Carlo simulations, which plays an important role in the nanopore sequencing of polynucleotides. We report a detailed study on the dependence of translocation dynamics on the chain length and the local geometry near the nanopore. In particular, we find that the length dependence of the infection time of the chain could exhibit very different behaviors for different geometries.     

Effect of Interaction upon Translocation of Confined Polymer Chain Through Nanopore

运用二维的键长涨落模型和蒙特卡洛方法研究高分子链从一个受限空间到自由空间穿孔过程中,链单体与纳米孔之间的相互作用.结果表明,在不同的链长和纳米孔交互作用下,高分子链成功穿越自由能能垒取决于链长和纳米孔长度,并且由于交互作用降低了自由能能垒,导致高分子链在纳米管的平均捕获时间缩短.     

Analytical solution to the problem of a temperature jump in a metal

An analytical solution to the problem of a temperature jump in a metal is obtained. The jump is caused by a heat flow to the surface. An exact expression for the heat-induced electric field is derived. Based on the exact expressions, the electric field profiles are plotted for different ratios of the electron free path to the Debye length. It is shown that the field profile near the surface may differ substantially from the Debye profile.     

Debye Length in a Neutral-beam-heated Plasma

The scale length for an effective shielding of a charged particle in a plasma is the Debye length, which is for Maxwellian velocity distributions determined by the ratio of the temperature to the density. However, fusion plasmas heated by neutral-beam injection (NBI) exhibit highly non-Maxwellian slowing-down velocity distributions. In this case, the evaluation of the characteristic shielding distance from these velocity distributions requires the solution of Fokker-Planck-Poisson equations. In this paper, the effect of NBI slowing-down velocity distributions on the shielding distance are discussed. Analytic expressions for the Debye length of a neutral-beam-heated plasma are given. The results are compared to the Maxwellian case.     

Sequence dependence of DNA translocation through a nanopore

We investigate the dynamics of DNA translocation through a nanopore using 2D Langevin dynamics simulations, focusing on the dependence of the translocation dynamics on the details of DNA sequences. The DNA molecules studied in this work are built from two types of bases A and C, which have been shown previously to have different interactions with the pore. We study DNA with repeating blocks A(n)C(n) for various values of n and find that the translocation time depends strongly on the block length 2n as well as on the orientation of which base enters the pore first. Thus, we demonstrate that the measurement of translocation dynamics of DNA through a nanopore can yield detailed information about its structure. We have also found that the periodicity of the block sequences is contained in the periodicity of the residence time of the individual nucleotides inside the pore.     

Thermal condensation mode in a dusty plasma

In the present work, the radiative condensation instability is investigated in the presence of dust charge fluctuations. We find that the charge variability of the grain reduces the growth rate of radiative mode only for fluctuation wavelength smaller or of the order of the Debye length and this reduction is not very large. Far from the Debye sphere, radiative mode can damp due to thermal conduction of electrons and ions     

Effect of surface properties on a temperature jump in a metal

The problem of temperature jump that is induced by a heat flux toward a metal surface is solved with regard to electron energy accommodation on the surface. The temperature profile is constructed for different ratios of the electron mean free path to the Debye length.     

Screened Forces between two Positive Ions in an Electron Bath

The force between two ions imbedded in a hot and dense electron gas is studied using classical Molecular Dynamics with a regularized Coulomb potential. It is found to be well represented by the Debye form but with a screening length that differs from the Debye length except at weak coupling.     

Probing nanotube-nanopore interactions

We demonstrate a new nanoscale system consisting of a nanotube threaded through a nanopore in aqueous solution. Its electrical and mechanical properties are sensitive to experimentally controllable conformational changes on sub-Angstrom length scales. Ionic current transport through a nanopore is significantly suppressed by the threading nanotube and the mechanical interactions between the nanotube and pore are accounted for by a folding geometry. The experiments provide first measurements of the longitudinal resolution and metrology of a solid-state nanopore "microscope." This new nanostructure provides a means to study molecule-nanotube interactions in conducting ionic solutions as well as geometrical and surface properties of nanopores and nanotubes.     

碱金属卤化物键长、德拜温度和热膨胀系数的温度效应

以碱金属卤化物为研究对象,根据局域键平均近似方法,从热膨胀系数的定义出发,建立热膨胀系数和键长的温度效应函数表达式。定量获取碱金属卤化物的键长、刚性因子、德拜温度和热膨胀系数。结果表明：①碱金属卤化物的热膨胀系数与结合能成反比;②同类碱金属卤化物中,从氟碱化物到碘碱化物德拜温度逐渐减小而热膨胀系数逐渐增大;③碱金属卤化物的键长在其德拜温度的三分之一处,由非线性转变为线性热伸长。     

Optical detection of DNA translocation through silicon nanopore by ultraviolet light

In this paper, we propose a new optical detection scheme for nanopore-based DNA sequencing with high resolution towards eventual base identification. We use ultraviolet light for excitation of a fluorescent probe attached to DNA and a nanopore in the silicon membrane that has a significantly large refractive index and an extinction coefficient at ultraviolet wavelengths. In this study, numerical electromagnetic simulation revealed that the z-polarization component (perpendicular to the membrane plane) of the electric field was dominant near the nanopore and generated a large electric field gradient at the nanopore exit, typically with a decay length of 2 nm for a nanopore with diameter of 7 nm. The large extinction coefficient contributed to reduction in background noise coming from fluorophore-labeled DNA strands that remain behind the membrane (the cis side of the membrane). We observed a high signal-to-noise ratio of single DNA translocation events under the application of an electric field.     

Screened electrostatics of charged particles on a water droplet

We study the electrostatic properties of charged particles trapped at an interface in a water-in-oil microemulsion. The electrostatic potential and the counterion distribution in the water droplet are given in terms of the ratio of the Debye screening length κ^-1 and the droplet radius R. In the limit R→∞ we recover the well-known results for a flat interface. Finite-size corrections are obtained in terms of the small parameter 1/κR. Part of the counterions spread along the interface and form a charged layer of one Debye length thickness. In particular, there is a uniform surface charge contribution. We derive explicit expressions for the electric field, the mobile charge density, and the charge-induced pressure on the interface.     

Screening of a charged dust particle within a nonlocal charging theory

We study the influence of the nonlocality of the electron energy distribution function on the dust particle charge screening in a two-component plasma of various inert gases and nitrogen at atmospheric pressure. For our analytical and numerical calculations, we have chosen the point sink model in the diffusion-drift approximation, which, in addition to the bulk production and loss of electrons and ions, also includes the heterogeneous processes of their absorption by a dust particle. We have established that the dust particle potential distribution in the problem under consideration is a superposition of three Debye exponentials with three different screening constants. The first constant practically coincides with the inverse Debye length. The second constant is determined by the inverse length travelled by the electrons and ions in the ambipolar diffusion process in the characteristic recombination time. The third constant coincides with the inverse characteristic distance of electron energy transfer through heat conduction in the characteristic time of electron energy establishment in the processes of heating by a beam of fast electrons and energy losses in elastic and inelastic collisions. We compare our numerical calculations of the screening constants with the analytical estimates obtained in the ambipolar diffusion approximation.     

The influence of the electron temperature gradient on the space-charge field in a d.c. discharge

The deviations of the space-charge field from its equilibrium value in the d.c. discharge plasma is investigated, taking into account the influence of changed electron temperature. Starting from the plasma-equations, the corresponding steady-state solution in a linear, one-dimensional approximation is found, on the assumption that the ion density disturbance is known and given as a function of the space coordinate, constant in time or only slowly varying with time. As the changed electron temperature influences the electron density, the space-charge field disturbance is no longer restricted (within the limit of the Debye screening length) by the dimension of the positive ion disturbance as is the case of the temperature uninfluenced field. The space charge field now extends widely out of the place of the ion disturbance, the extension being given by the dimension of the electron temperature relaxation length, which in order of magnitude equals the quantityl ₁=2U _e0 /E ₀. A solution in a closed analytical form (25) is found in the case of a quasineutral plasma. Even in this case of zero Debye length, temperature lengthening of the spacecharge field relaxation takes place. The appropriate numerical examples are given for the case of final (non-zero) Debye length.The authors wish to thank J. Václavík and V. Zárybnický for their stimulating remarks and helpful discussion.     

Contribution to the evaluation of transport coefficients in plasmas containing krypton and sodium

Electrical and thermal conductivities for low-temperature (2000 K to 20000 K) and high-pressure (0.1 MPa to 2.5 MPa) krypton plasma with some sodium (1% and 10%) as additive are presented. The plasma is treated as weakly non-ideal and having attained the local thermodynamical equilibrium states. The problem of the plasma non-ideality according to standard criteria is of the plasma Debye radius, with an improved cut-off length. Use is made of a previously derived modified Debye radius with the Landau length instead of the smallest ionic radii which allowed to regard the plasmas investigated as weakly non-ideal. This alteration in the evaluation of the Debye radius profoundly alters the equilibrium plasma compositions and their transport coefficients.     

The Single Langmuir Probe under Orbital-Limited Conditions in a Low-Density Collisional Plasma

The cylindrical Langmuir probe under orbital-limited conditions was used to determine the charge density in a low-density collisional plasma. The Langmuir's theory was applied to both electron and ion saturation currents in their respective accelerating regions. Present study indicates that the length of the probe significantly affects the probe characteristics. A probe of suitable length under orbital-limited conditions may be useful under the experimental conditions where the radius of the probe is much smaller than the Debye lengt.     

Nonuniform charge distribution effects on bremsstrahlung emission in drifting dusty plasmas

The effect of the nonuniform charge distribution due to the ion flow on the ion–dust grain bremsstrahlung process is investigated in dusty plasmas. The impact-parameter analysis is applied to the motion of the projectile ion in order to investigate the variation of the bremsstrahlung radiation cross section as a function of the impact parameter, Debye length, Mach number, radiation photon energy, and projectile energy. The result shows that the nonuniform charge distribution effect strongly enhances the bremsstrahlung cross section. It is also found that the bremsstrahlung radiation cross section decreases with increasing the Debye length.     

Influence of Debye Plasma on the KLL Dielectronic Recombination of H-Like Helium Ions

Using the Debye shielding model, the effects of plasma shielding on the dielectronic recombination processes of the H-like helium ions are investigated.It is found that plasma shielding causes a remarkable change in the Auger decay rate of the doubly excited 2p~2 ~3P_2 state.As a result,the dielectronic recombination cross sections from the doubly excited 2p~2 ~3p_2 state increases with the decreasing Debye shielding length.     

Free energy and scalings for polymer translocation through a nanopore: A molecular dynamics simulation study combined with milestoning

Coarse-grained molecular dynamics simulations combined with milestoning method are used to study the stochastic process of polymer chain translocation though a nanopore. We find that the scalings for polymer translocation process (the chain is initialized with the first monomer in the nanopore) and for polymer escape process (the chain is initialized with the middle monomer in the nanopore) are different. The translocation process is mainly controlled by the entropic barrier, while the polymer escape process is driven by the effective force due to free energy difference.