Johan L. A. Dubbeldam

Driven polymer translocation through a nanopore: A manifestation of anomalous diffusion

We study the translocation dynamics of a polymer chain threaded through a nanopore by an external force. By means of diverse methods (scaling arguments, fractional calculus and Monte Carlo simulation) we show that the relevant dynamic variable, the translocated number of segments s(t), displays an anomalous diffusive behavior even in the presence of an external force. The anomalous dynamics of the translocation process is governed by the same universal exponent α=2/(2ν+2−γ1), where ν is the Flory exponent and γ1 the surface exponent, which was established recently for the case of non-driven polymer chain threading through a nanopore. A closed analytic expression for the probability distribution function W(s, t), which follows from the relevant fractional Fokker-Planck equation, is derived in terms of the polymer chain length N and the applied drag force f. It is found that the average translocation time scales as . Also the corresponding time-dependent statistical moments, and reveal unambiguously the anomalous nature of the translocation dynamics and permit direct measurement of α in experiments. These findings are tested and found to be in perfect agreement with extensive Monte Carlo (MC) simulations.

Polymer translocation through a nanopore: A showcase of anomalous diffusion

The translocation dynamics of a polymer chain through a nanopore in the absence of an external driving force is analyzed by means of scaling arguments, fractional calculus, and computer simulations. The problem at hand is mapped on a one-dimensional anomalous diffusion process in terms of the reaction coordinate s (i.e., the translocated number of segments at time t ) and shown to be governed by a universal exponent alpha=2(2nu+2-gamma(1), where nu is the Flory exponent and gamma(1) is the surface exponent. Remarkably, it turns out that the value of alpha is nearly the same in two and three dimensions. The process is described by a fractional diffusion equation which is solved exactly in the interval 0<s<N with appropriate boundary and initial conditions. The solution gives the probability distribution of translocation times as well as the variation with time of the statistical moments <s(t) and <s2(t)-<s(t)>2, which provide a full description of the diffusion process. The comparison of the analytic results with data derived from extensive Monte Carlo simulations reveals very good agreement and proves that the diffusion dynamics of unbiased translocation through a nanopore is anomalous in its nature.

Self-pulsations of lasers with saturable absorber: dynamics and bifurcations.

Abstract We consider the Yamada model, a set of three differential equations constituting a simple model for self-pulsations in (semiconductor) lasers with saturable absorber. A complete picture of all possible dynamics is presented in terms of two-dimensional bifurcation diagrams, in which we find a Bogdanov–Takens bifurcation as an organizing center. This shows that pulses are indeed created in a homoclinic bifurcation (or saddle connection). For suitable values of (relative) absorption we also find regions of multistability, yielding the possibility of hysteresis. The influence of noise on the dynamics is discussed.

Forced translocation of a polymer: Dynamical scaling versus molecular dynamics simulation

We suggest a theoretical description of the force-induced translocation dynamics of a polymer chain through a nanopore. Our consideration is based on the tensile (Pincus) blob picture of a pulled chain and the notion of a propagating front of tensile force along the chain backbone, suggested by Sakaue [Phys. Rev. E 76, 021803 (2007); Phys. Rev. E 81, 041808 (2010); Eur. Phys. J. E 34, 135 (2011)]. The driving force is associated with a chemical potential gradient that acts on each chain segment inside the pore. Depending on its strength, different regimes of polymer motion (named after the typical chain conformation: trumpet, stem-trumpet, etc.) occur. Assuming that the local driving and drag forces are equal (i.e., in a quasistatic approximation), we derive an equation of motion for the tensile front position X(t). We show that the scaling law for the average translocation time 〈τ〉 changes from ∼ N2ν/f1/ν to ∼ N^1+ν/f (for the free-draining case) as the dimensionless force f[over ̃]R=aNνf/T (where a, N, ν, f, and T are the Kuhn segment length, the chain length, the Flory exponent, the driving force, and the temperature, respectively) increases. These and other predictions are tested by molecular-dynamics simulation. Data from our computer experiment indicate indeed that the translocation scaling exponent α grows with the pulling force f[over ̃]R, albeit the observed exponent α stays systematically smaller than the theoretically predicted value. This might be associated with fluctuations that are neglected in the quasistatic approximation.

Fractional Brownian motion approach to polymer translocation: The governing equation of motion

We suggest a governing equation that describes the process of polymer-chain translocation through a narrow pore and reconciles the seemingly contradictory features of such dynamics: (i) a Gaussian probability distribution of the translocated number of polymer segments at time t after the process has begun, and (ii) a subdiffusive increase of the distribution variance Δ(t) with elapsed time Δ(t)∝t(α). The latter quantity measures the mean-squared number s of polymer segments that have passed through the pore Δ(t)=([s(t)-s(t=0)](2)), and is known to grow with an anomalous diffusion exponent α<1. Our main assumption [i.e., a Gaussian distribution of the translocation velocity v(t)] and some important theoretical results, derived recently, are shown to be supported by extensive Brownian dynamics simulation, which we performed in 3D. We also numerically confirm the predictions made recently that the exponent α changes from 0.91 to 0.55 to 0.91 for short-, intermediate-, and long-time regimes, respectively.

Long time evolution of atherosclerotic plaques

The evolution of atherosclerosis in general, and the influence of wall shear stress on the growth of atherosclerotic plaques in particular, is an intricate phenomenon which is still only partly understood. We therefore propose a qualitative mathematical model which consists of a number of ordinary differential equations for the concentrations of the most relevant constituents of the atherosclerotic plaque. These equations were studied both for the case that the wall shear stress is a parameter (model A), and for the case in which the plaque evolution is coupled to the blood flow (model B) which results in a time dependent wall shear stress. We find that both models exhibit a class of marginally stable equilibria, all reflecting states in which the plaque only grows for a short period of time after a perturbation. The uncoupled model A, however, shows bi-stability between this class of equilibria and another equilibrium state in which the plaque experiences unlimited growth in time, if the LDL cholesterol intake exceeds a threshold value. In model B the bi-stability vanishes, but we find that there is still a critical value of the LDL cholesterol intake beyond which the lumen radius drastically decreases. We show that this decrease is quite sensitive to the value of the wall shear stress.

Theory of mode-locked semiconductor lasers with finite absorber relaxation times.

We investigate the influence of a finite absorber relaxation time on passively mode-locked semiconductor lasers. We find that the mode-locking mechanism of Haus is surprisingly susceptible to small perturbations and small changes in the parameters. Even when the absorber relaxation time is much larger than the pulse duration, it typically is still short enough to be a crucial part of the physics of mode-locking. Allowing for a finite absorber relaxation time, we find that stable operation of a mode-locked semiconductor is possible over a wide range of parameters. We argue that the pulse duration is inversely proportional to the square root of the pulse energy.

Force spectroscopy of polymer desorption: theory and molecular dynamics simulations

Forced detachment of a single polymer chain, strongly adsorbed on a solid substrate, is investigated by two complementary methods: a coarse-grained analytical dynamical model, based on the Onsager stochastic equation, and Molecular Dynamics (MD) simulations with a Langevin thermostat. The suggested approach makes it possible to go beyond the limitations of the conventional Bell-Evans model. We observe a series of characteristic force spikes when the pulling force is measured against the cantilever displacement during detachment at constant velocity vc (displacement control mode) and find that the average magnitude of this force increases as vc increases. The probability distributions of the pulling force and the end-monomer distance from the surface at the moment of the final detachment are investigated for different adsorption energies ε and pulling velocities vc. Our extensive MD simulations validate and support the main theoretical findings. Moreover, the simulations reveal a novel behavior: for a strong-friction and massive cantilever the force spike pattern is smeared out at large vc. As a challenging task for experimental bio-polymer sequencing in future we suggest the fabrication of a stiff, super-light, nanometer-sized AFM probe.

Space-Time Fractional Schrödinger Equation With Composite Time Fractional Derivative

Abstract The fractional Schrödinger equation has recently received substantial attention. We generalize the fractional Schrödinger equation to the Hilfer time derivative and the Caputo space derivative, and solve this equation for an infinite potential by using the Adomian decomposition method. The infinite domain solution of the space-time fractional Schrödinger equation in the case of Riesz space fractional derivative is obtained in terms of the Fox H-functions. We interpret our results for the fractional Schrödinger equation by introducing a complex effective potential in the standard Schrödinger equation, which can be used to describe quantum transport in quantum dots.

Power-Imbalance Allocation Control of Power Systems-Secondary Frequency Control

The traditional secondary frequency control of power systems restores nominal frequency by steering Area Control Errors (ACEs) to zero. Existing methods are a form of integral control with the characteristic that large control gain coefficients introduce an overshoot and small ones result in a slow convergence to a steady state. In order to deal with the large frequency deviation problem, which is the main concern of the power system integrated with a large number of renewable energy, a faster convergence is critical. In this paper, we propose a secondary frequency control method named Power-Imbalance Allocation Control (PIAC) to restore the nominal frequency with a minimized control cost, in which a coordinator estimates the power imbalance and dispatches the control inputs to the controllers after solving an economic power dispatch problem. The power imbalance estimation converges exponentially in PIAC, both overshoots and large frequency deviations are avoided. In addition, when PIAC is implemented in a multi-area controlled network, the controllers of an area are independent of the disturbance of the neighbor areas, which allows an asynchronous control in the multi-area network. A Lyapunov stability analysis shows that PIAC is locally asymptotically stable and simulation results illustrate that it effectively eliminates the drawback of the traditional integral control based methods.