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.     

Effect of channel-protein of a protein-like chain interaction on translocation through a finite channel

We study the translocation of a protein-like chain through a finite cylindrical channel using the pruned-enriched Rosenbluth method(PERM) and the modified orientation-dependent monomer-monomer interaction(ODI) model.Attractive channels(ε cp = 2.0,1.0,0.5),repulsive channels(ε cp = 0.5,1.0,2.0),and a neutral channel(ε cp = 0) are discussed.The results of the chain dimension and the energy show that Z0 = 1.0 is an important case to distinguish the types of the channels.For the strong attractive channel,more contacts form during the process of translocation.It is also found that an external force is needed to drive the chain outside of the channel with the strong attraction.While for the neutral,the repulsive,and the weak attractive channels,the translocation is spontaneous.     

Polymer translocation in a double-force arrangement

Using Langevin dynamics simulations, we investigate the translocation dynamics of an externally driven polymer chain through a nanopore, where a pulling force F is exerted on the first monomer whilst there is an opposing force F _E < F within the pore. Such a double-force arrangement has been proposed recently to allow better dynamical control of the translocation process in order to sequence biopolymers. We find that in the double-force arrangement translocation becomes slower as compared to the case under a single monomer pulling force of magnitude F - F _E , but scaling of the translocation time as a function of the chain length ∼ N ² does not change. The waiting time (m) for monomer m to exit the pore is found to be a monotonically increasing function of the bead number almost until m N , which indicates relatively well-defined slowing down and control of the chain velocity during translocation. We also study the waiting time distributions for the beads in the chain, and characterize in detail fluctuations in the bead positions and their transverse position coordinates during translocation. These data should be useful in estimating position-dependent sequencing errors in double-force experiments.     

Effect of channelben protein interaction on translocation of a protein-like chain through a finite channel

We study the translocation of a protein-like chain through a finite cylindrical channel using the pruned-enriched Rosenbluth method (PERM) and the modified orientation-dependent monomer-monomer interaction (ODI) model. Attractive channels (ε_cp=-2.0, -1.0, -0.5), repulsive channels (ε_cp=0.5, 1.0, 2.0), and a neutral channel (ε_cp =0) are discussed. The results of the chain dimension and the energy show that Z₀=1.0 is an important case to distinguish the types of the channels. For the strong attractive channel, more contacts form during the process of translocation. It is also found that an external force is needed to drive the chain outside of the channel with the strong attraction. While for the neutral, the repulsive, and the weak attractive channels, the translocation is spontaneous.     

打结高分子链穿孔行为的研究

以三叶草型结(即3₁结)为例,采用分子动力学(MD)方法,研究打结高分子链在外场力作用下穿越微孔的动力学过程.模拟发现,在拉动打结高分子链的过程中,结的大小呈涨落变化,直至最后散结.定性讨论了结的存在对高分子链穿孔速率的影响.在外场力作用下,打结高分子链平均穿孔时间(τ)与链长(N)满足标度关系τ～N ^α,其中标度系数α随外场力f增大而增大.对于短链,外场力越大,平均穿孔时间越短     

The stress tensor in entangled polymers

In entangled polymeric liquids, a subchain connecting two entanglements is an open system which can exchange particles (Kuhn segments) with its neighboring subchains along the polymer chain. We present a calculation of the subchain mechanical behavior as determined from the grand canonical formalism of statistical mechanics, with different subchains in the same chain sharing the same chemical potential. It is shown that the linear monomer density is a constant, as originally inferred by Doi and Edwards, but the tension is generally different from one subchain to another. Accounting for the latter effect leads to a new tensorial strain measure, somewhat different from that proposed by Doi and Edwards.     

Pulling an adsorbed polymer chain off a solid surface

The thermally assisted detachment of a self-avoiding polymer chain from an adhesive surface by an external force applied to one of the chain-ends is investigated. We perform our study in the “fixed height” statistical ensemble where one measures the fluctuating force, exerted by the chain on the last monomer when a chain-end is kept fixed at height h over the solid plane at different adsorption strength . The phase diagram in the h - plane is calculated both analytically and by Monte Carlo simulations. We demonstrate that in the vicinity of the polymer desorption transition a number of properties like fluctuations and probability distribution of various quantities behave differently, if h rather than f is used as an independent control parameter.     

Long-Time Asymptotics of Solutions to the Cauchy Problem for the Defocusing Nonlinear Schrödinger Equation with Finite-Density Initial Data. II. Dark Solitons on Continua

For Lax-pair isospectral deformations whose associated spectrum, for given initial data, consists of the disjoint union of a finitely denumerable discrete spectrum (solitons) and a continuous spectrum (continuum), the matrix Riemann–Hilbert problem approach is used to derive the leading-order asymptotics as of solutions to the Cauchy problem for the defocusing nonlinear Schrödinger equation ( NLSE), , with finite-density initial data

Exact effective force between star-polymers in a $\Theta$-solvent

We re-examine here the computation of the effective force between two star-polymers of respective numbers of branches f₁ and f₂, immersed in a common -solvent. Such a force originates essentially from the repulsive three-body interactions. To achieve this, we take advantage of some established results using renormalization theory for three-dimensional star-polymers, or conformal invariance for two-dimensional ones. We first show that, in dimension d = 3, the force, , decreases with the center-to-center distance r as , with the exact universal amplitude . Second, in dimension d = 2, we find that the force decays more slowly as , with the exact universal amplitude . For high distances compared to the gyration radius, , of a single polymer chain at the -point, an exponential decay of the force is expected.Received: 3 February 2004, Published online: 24 May 2004PACS: 61.25.Hq Macromolecular and polymer solutions; polymer melts; swelling - 05.20.-y Classical statistical mechanics     

Amplitude-squared squeezing in superposed coherent states

We study amplitude-squared squeezing of the Hermitian operator Z_θ=Z₁ cosθ+Z₂ sin θ, in the most general superposition state , of two coherent states and . Here operators Z_1,2 are defined by , a is annihilation operator, θ is angle, and complex numbers C_1,2 , α, β are arbitrary and only restriction on these is the normalization condition of the state . We define the condition for a state to be amplitude-squared squeezed for the operator Z_θ if squeezing parameter , where N=a⁺a and . We find maximum amplitude-squared squeezing of Z_θ in the superposed coherent state with minimum value 0.3268 of the parameter S for an infinite combinations with α- β= 2.16 exp [±i(π/4) + iθ/2], and with arbitrary values of (α+β) and θ. For this minimum value of squeezing parameter S, the expectation value of photon number can vary from the minimum value 1.0481 to infinity. Variations of the parameter S with different variables at maximum amplitude-squared squeezing are also discussed.     

Magnetization and magnetic phase diagrams of a spin-1/2 ferrimagnetic diamond chain at low temperature

We used the Jordan–Wigner transform and the invariant eigenoperator method to study the magnetic phase diagram and the magnetization curve of the spin-1/2 alternating ferrimagnetic diamond chain in an external magnetic field at finite temperature. The magnetization versus external magnetic field curve exhibits a 1/3 magnetization plateau at absolute zero and finite temperatures, and the width of the 1/3 magnetization plateau was modulated by tuning the temperature and the exchange interactions. Three critical magnetic field intensities H_(CB), H_(CE) and H_(CS) were obtained, in which the H_(CB) and H_(CE) correspond to the appearance and disappearance of the 1/3 magnetization plateau, respectively, and the higher H_(CS) correspond to the appearance of fully polarized magnetization plateau of the system. The energies of elementary excitation ωσ,k(σ = 1, 2, 3) present the extrema of zero at the three critical magnetic fields at 0 K, i.e., [hω_(3,k)(HCB)]_(min)= 0, [hω_(2,k)(H_(CE))]_(max)= 0 and [hω _(2,k)(H_(CS))]_(min)= 0, and the magnetic phase diagram of magnetic field versus different exchange interactions at 0 K was established by the above relationships. According to the relationships between the system's magnetization curve at finite temperatures and the critical magnetic field intensities, the magnetic field-temperature phase diagram was drawn. It was observed that if the magnetic phase diagram shows a three-phase critical point, which is intersected by the ferrimagnetic phase, the ferrimagnetic plateau phase, and the Luttinger liquid phase, the disappearance of the1/3 magnetization plateau would inevitably occur. However, the 1/3 magnetization plateau would not disappear without the three-phase critical point. The appearance of the 1/3 magnetization plateau in the low temperature region is the macroscopic manifestations of quantum effect.     

Roper resonances in chiral quark models

We derive a method to calculate the multi-channel K -matrix applicable to a broad class of models in which mesons linearly couple to the quark core. The method is used to calculate pion scattering amplitudes in the energy region of low-lying P11 and P33 resonances. A good agreement with experimental data is achieved if in addition to the elastic channel we include the and N ( channels where the -meson models the correlated two-pion decay. We solve the integral equation for the K -matrix in the approximation of separable kernels; it yields a sizable increase of the widths of the (1232) and the N(1440) resonances compared to the bare quark values.     

A Ruelle operator for a real Julia set

LetR be an expanding rational function with a real bounded Julia set, and let be a Ruelle operator acting in a space of functions analytic in a neighbourhood of the Julia set. We obtain explicit expressions for the resolvent function and, in particular, for the Fredholm determinantD()=det(I-L). It gives us an equation for calculating the escape rate. We relate our results to orthogonal polynomials with respect to the balanced measure ofR. Two examples are considered.The first named author was sponsored in part by the Landau Center for Research in Mathematical Analysis, supported by the Minerva Foundation (Germany)     

On the Modified Korteweg–De Vries Equation

We consider the large time asymptotic behavior of solutions to the Cauchy problem for the modified Korteweg–de Vries equation , with initial data . We assume that the coefficient is real, bounded and slowly varying function, such that , where . We suppose that the initial data are real-valued and small enough, belonging to the weighted Sobolev space . In comparison with the previous paper (Internat. Res. Notices 8 (1999), 395–418), here we exclude the condition that the integral of the initial data u ₀ is zero. We prove the time decay estimates and for all , where . We also find the asymptotics for large time of the solution in the neighborhood of the self-similar solution.     

Lifetime vibrational interference during the NO 1s-1π* resonant excitation studied by the NO+(A 1Π → X 1Σ+) fluorescence

Dispersed fluorescence from fragments formed after the de-excitation of the 1s^-1π^* resonances of N^*O and NO^* has been measured in the spectral range of 118–142 nm. This range is dominated by lines of atomic nitrogen and oxygen fragments and by the bands in the NO⁺ ion which result from the participator Auger decay of the 1s^-1π^* resonances. Ab-initio calculations of the transition probabilities between vibrational levels during the reaction NO N^*O ⇒ NO were used to explain the observed intensity dependence for the fluorescence bands on the exciting-photon energy across the resonances and on both v^′ and v^′′ vibrational quantum numbers. The multiplet structure of the 1s^-1π^* resonance and lifetime vibrational interference explain the observed exciting-photon energy dependence of the fluorescence intensity. A strong spin-orbit coupling between singlet and triplet states of NO⁺ is proposed to reduce additional cascade population of the state via radiative transitions from the and states and to explain remaining differences between measured and calculated integral fluorescence intensities.     

Retrodiction for coherent communication with homodyne or heterodyne detection

Previous work on the retrodictive theory of direct detection is extended to cover the homodyne detection of coherent optical signal states and . The retrodictive input state probabilities are obtained by the application of Bayes' theorem to the corresponding predictive distributions, based on the probability operator measure (POM) elements for the homodyne process. Results are derived for the retrodictive information on the complex amplitude of the signal field obtainable from the difference photocount statistics of both 4-port and 8-port balanced homodyne detection schemes. The local oscillator is usually assumed much stronger than the signal but the case of equal strengths in 4-port detection is also considered. The calculated probability distributions and error rates are illustrated numerically for values of signal and local oscillator strengths that extend from the classical to the quantum regimes.     

Examples of Twisted Cyclic Cocycles from Covariant Differential Calculi

For two covariant differential *-calculi, the twisted cyclic cocycle associated with the volume form is represented in terms of commutators for some self-adjoint operator and some *-representation of the underlying *-algebra.     

A constraint on physical quantum states in cosmological space-times

The problem of constructing the Hilbert space of physical states for a free scalar quantum field propagating on a cosmological background is considered. The concept of energy-momentum for such a field is discussed and it is noted that, according to current renormalization theory, for a state ¦M to have finite energy density its associated anticommutator function must be of a particular form first discussed by Hadamard. This restriction is shown to lead to a constraint on the construction of the Hilbert space of physical states. This constraint is used to reject a recently proposed scheme for the construction of this space which was based on a principle of energy minimization.This essay received an honourable mention from the Gravity Research Foundation for the year 1984.-Ed.     

Tunneling Across an Inhomogeneous Delta-Barrier

The authors deal with the tunneling of electrons across an inhomogeneous delta-barrier defined by the potential energy (where 0$$ " align="middle" border="0"> and 0$$ " align="middle" border="0"> are two constants). In particular, the perpendicular incidence of an electron with a given value of the wave vector is considered. The electron is forward-scattered into the region behind the barrier (region 2: 0$$ " align="middle" border="0"> ), i. e. the wave function is composed of plane waves with all wave vectors such that and \left. 0 \right)} $$ " align="middle" border="0"> ) (where ). Therefore, if 0$$ " align="middle" border="0"> , the wave function of the electron is represented as , where . An approximate formula is derived for the amplitude . The authors pay a special attention to the flow density and calculate this function in two cases: 1. for the plane and 2. for high values of is the diffraction angle). The authors discuss the relevance of their diffraction problem in a prospective quantum-mechanical theory of the tunneling of electrons across a randomly inhomogeneous Schottky barrier.     

Asymptotics for the Burgers Equation with Pumping

We consider the large time asymptotic behavior of solutions to the initial-boundary value problem We find large time asymptotic formulas of solutions for three different cases 1) a_±=±1, 2) a_±=1 and 3) a_±=0.