Non-equilibrium effects in chaperone-assisted translocation of a stiff polymer

Chaperone-assisted biopolymer translocation is the main model proposed for translocation in vivo. A dynamical Monte Carlo method is used to simulate the translocation of a stiff homopolymer through a nanopore driven by chaperones. Chaperones are proteins that bind to the polymer near the wall and prevent its backsliding through Cis side. The important parameters include binding energy, size and the local concentration of the chaperones. The profile of these local concentrations, build up the chaperones distribution. Here we investigate the effects of binding energy, size and the exponential distribution of chaperones in their equilibration in each step of the polymer translocation needed for stable translocation time. The simulation results show that in case of chaperones with the size of a monomer ($\lambda =1$) and/or positive effective binding energy and/or uniform distribution, the chaperones binding equilibration rate/frequency is less than 5 times per monomer. However, in some special cases in the exponential distribution of chaperones with size $\lambda >1$ and negative effective binding energy the equilibration rate will diverge to more than 20 times per monomer. We show that this non-equilibrium effect results in supper diffusion, seen before. Moreover, we confirm the equilibration process theoretically.     

利用变压器研究两个互感线圈的串并联

利用变压器研究了两个互感线圈串并联的等效电感。     

Changes in the Effective Parameters of Averaged Motion in Nonlinear Systems Subject to Noise

We discuss how the effective parameters characterising averaged motion in nonlinear systems are affected by noise (random fluctuations). In this approach to stochastic dynamics, the stochastic system is replaced by its deterministic equivalent but with noise-dependent parameters. We show that it can help to resolve certain paradoxes and that it has a utility extending far beyond its usual application in passing from the microscopic equations of motion to the macroscopic ones. As illustrative examples, we consider the diode-capacitor circuit, a Brownian ratchet, and a generic stochastic resonance system. In the latter two cases we calculate for the first time their effective parameters of averaged motion as functions of noise intensity. We speculate that many other stochastic problems can be treated in a similar way. PACS: 05.10.Gg, 05.40.-a, 05.40.Jc     

Persistence of Eigenvalues and Multiplicity in the Dirichlet Problem for the Laplace Operator on Nonsmooth Domains

We consider the Dirichlet eigenvalue problem for the Laplace operator on a variable nonsmooth domain. We extend a result of Lupo and Micheletti concerning the structure of the set of domain perturbations which leave the multiplicity of an eigenvalue unchanged, and we study the set of perturbations which leave a certain eigenvalue unchanged.     

Optical filaments and optical bullets in dispersive nonlinear media

We have investigated the evolution of picosecond and femtosecond optical pulses governed by the amplitude vector equation in the optical and UV domains. We have written this equation in different coordinate frames, namely, in the laboratory frame, the Galilean frame, and the moving-in-time frame and have normalized it for the cases of different and equal transverse and longitudinal sizes of optical pulses or modulated optical waves. For optical pulses with a small transverse size and a large longitudinal size (optical filaments), we obtain the well-known paraxial approximation in all the coordinate frames, while for optical pulses with relatively equal transverse and longitudinal sizes (so-called light bullets), we obtain new non-paraxial nonlinear amplitude equations. In the case of optical fields with low intensity, we have reduced the nonlinear amplitude vector equations governing the light-bullet evolution to the linear amplitude equations. We have solved the linear equations using the method of Fourier transform. An unexpected new result is the relative stability of light bullets and the significant decrease in the diffraction enlargement of light bullets with respect to the case of long pulses in the linear propagation regime.     

Last Passage Time Statistics for Barrier-Crossing Processes

A concept of mean last passage time at the saddle point is proposed in order to compute both the lifetime and the escape rate of a particle in a metastable potential, where the backstreaming across the saddle point is taken into account. It is shown that the mean oscillating time around the saddle point is the longest one among all the time scales at high temperatures and the inverse of the mean last passage time at the saddle point is more close to the steady escape rate.     

Transmission time of a particle in the reflectionless Sech-squared potential: Quantum clock approach

We investigate the time for a particle to pass through the reflectionless Sech-squared potential. Using the Salecker-Wigner and Peres quantum clock an average transmission time of a Gaussian wave packet representing the particle is explicitly evaluated in terms of average momentum and travel distance. The average transmission time is shown to be shorter than the time of free-particle motion and very close to the classical time for wave packets with well-localized momentum states. Since the clock measures the duration of scattering process the average transmission time can be interpreted as the average dwell time.     

Integration of large chemical kinetic mechanisms via exponential methods with Krylov approximations to Jacobian matrix functions

Recent trends in hydrocarbon fuel research indicate that the number of species and reactions in chemical kinetic mechanisms is rapidly increasing in an effort to provide predictive capabilities for fuels of practical interest. In order to cope with the computational cost associated with the time integration of stiff, large chemical systems, a novel approach is proposed. The approach combines an exponential integrator and Krylov subspace approximations to the exponential function of the Jacobian matrix. The components of the approach are described in detail and applied to the ignition of stoichiometric methane–air and iso-octane–air mixtures, here described by two widely adopted chemical kinetic mechanisms. The approach is found to be robust even at relatively large time steps and the global error displays a nominal third-order convergence. The performance of the approach is improved by utilising an adaptive algorithm for the selection of the Krylov subspace size, which guarantees an approximation to the matrix exponential within user-defined error tolerance. The Krylov projection of the Jacobian matrix onto a low-dimensional space is interpreted as a local model reduction with a well-defined error control strategy. Finally, the performance of the approach is discussed with regard to the optimal selection of the parameters governing the accuracy of its individual components.     

Analytical and numerical solutions to the Davey–Stewartson equation with power-law nonlinearity

This paper studies the Davey–Stewartson equation. The traveling wave solution of this equation is obtained for the case of power-law nonlinearity. Subsequently, this equation is solved by the exponential function method. The mapping method is then used to retrieve more solutions to the equation. Finally, the equation is studied with the aid of the variational iteration method. The numerical simulations are also given to complete the analysis.     

A normalised residence time transport equation for the numerical simulation of combustion with high-temperature air

This study concerns the numerical simulation of turbulent non-premixed combustion in highly preheated air streams. One of the objectives is to settle an efficient computational procedure to proceed with the numerical simulation of large-scale industrial devices. It is also expected that the availability of such a computational framework may facilitate comprehensive sensitivity analyses as well as the development of mathematical models able to represent turbulence-chemistry interactions (TCI) in such conditions. Based on the salient physical ingredients that characterise scalar mixing, propagation, and self-ignition processes, a turbulent combustion modelling framework is thus introduced and applied to the numerical simulation of well-documented laboratory flames. In the corresponding geometries, the bulk flow velocities of the reactants streams can reach rather large values, which lead the flame to lift from the burner rim. Partially premixed flame edges thus stabilise the whole flame structure and the temperature of the oxidising stream can be increased by vitiation with burned gases so as to promote the corresponding flame-stabilisation processes. For sufficiently large values of the vitiated airstream temperature, self-ignition mechanisms may be triggered thus leading to a competition between mixing, propagation, and ignition processes. In this context, the ratio of the residence time to the self-ignition delay is thought to be a relevant variable to delineate the possible influence of ignition phenomena. Therefore, a modelled transport equation for this normalised residence time is considered. The performance of the corresponding modelling proposal is analysed with special emphasis placed on its ability to reproduce ‘memory’ or ‘lagrangian’ effects related to thermal aging processes. In this respect, it is noteworthy that the present set of computations makes use of tabulated quantities associated to (i) steady laminar one-dimensional diffusion flamelets, so as to describe the composition of combustion products, (ii) steady laminar one-dimensional premixed flamelets, to describe the flame brush propagation, and (iii) temporal evolution of zero-dimensional homogeneous mixtures to account for the possible occurrence of self-ignition phenomena. In particular, the tabulated self-ignition time value is used to evaluate the increase in the normalised residence time. Finally, two modelling parameters are put into evidence and studied through a detailed sensitivity analysis.