Active dynamics of filaments in motility assays

We study the active dynamics of single and interacting cytoskeletal filaments in motility assays, in which immobilized motor proteins bind the filaments to a surface and actively pull them along this surface. We present a model which couples the overdamped dynamics of filaments, the active dynamics of motor heads, and the elasticity of motor stalks and which can be used for Langevin dynamics simulations. Single filaments perform a persistent random walk, which we characterize by several simulation results. For interacting filaments with a repulsive interaction of filaments, the motor-driven dynamics of filaments leads to a non-equilibrium phase transition which generalizes the isotropic-nematic phase transition of the corresponding equilibrium system, the hard-rod fluid. Langevin dynamics simulations and analytical theory show that the motor activity enhances the tendency for nematic ordering.     

Complex dynamics in the Oregonator model with linear delayed feedback

The Belousov-Zhabotinsky (BZ) reaction can display a rich dynamics when a delayed feedback is applied. We used the Oregonator model of the oscillating BZ reaction to explore the dynamics brought about by a linear delayed feedback. The time-delayed feedback can generate a succession of complex dynamics: period-doubling bifurcation route to chaos; amplitude death; fat, wrinkled, fractal, and broken tori; and mixed-mode oscillations. We observed that this dynamics arises due to a delay-driven transition, or toggling of the system between large and small amplitude oscillations, through a canard bifurcation. We used a combination of numerical bifurcation continuation techniques and other numerical methods to explore the dynamics in the strength of feedback-delay space. We observed that the period-doubling and quasiperiodic route to chaos span a low-dimensional subspace, perhaps due to the trapping of the trajectories in the small amplitude regime near the canard; and the trapped chaotic trajectories get ejected from the small amplitude regime due to a crowding effect to generate chaotic-excitable spikes. We also qualitatively explained the observed dynamics by projecting a three-dimensional phase portrait of the delayed dynamics on the two-dimensional nullclines. This is the first instance in which it is shown that the interaction of delay and canard can bring about complex dynamics.     

Scale and space localization in the Kuramoto-Sivashinsky equation

We describe a wavelet-based approach to the investigation of spatiotemporally complex dynamics, and show through extensive numerical studies that the dynamics of the Kuramoto-Sivashinsky equation in the spatiotemporally chaotic regime may be understood in terms of localized dynamics in both space and scale (wave number). A projection onto a spline wavelet basis enables good separation of scales, each with characteristic dynamics. At the large scales, one observes essentially slow Gaussian dynamics; at the active scales, structured "events" reminiscent of traveling waves and heteroclinic cycles appear to dominate; while the strongly damped small scales display intermittent behavior. The separation of scales and their dynamics is invariant as the length of the system increases, providing additional support for the extensivity of the spatiotemporally complex dynamics claimed in earlier works. We show also that the dynamics are spatially localized, discuss various correlation lengths, and demonstrate the existence of a characteristic interaction length for instantaneous influences. Our results motivate and advance the search for localized, low-dimensional models that capture the full behavior of spatially extended chaotic partial differential equations. (c) 1999 American Institute of Physics.     

Chaotic Dynamics in an Electronic Model of a Genetic Network

We consider dynamics in a class of piecewise-linear ordinary differential equations and in an electronic circuit that model genetic networks. In these models, gene activity varies continuously in time. However, as in Boolean or discrete-time switching networks, gene activity is driven high or low based only on whether the activities of the regulating genes are high or low (i.e., above or below certain thresholds). Depending on the “regulatory logic”, these models can exhibit simple dynamics, like stable fixed points or oscillation, or chaotic dynamics. The observed qualitative and quantitative differences between the dynamics in the idealized equations and the dynamics in the electronic circuit lead us to focus attention on the analysis of the dynamics as a function of parameter values. We propose new techniques for solving the inverse problem – the problem of inferring the regulatory logic and parameters from time series data. We also give new symbolic and statistical methods for characterizing dynamics in these networks.     

Boundary-equilibrium bifurcations in piecewise-smooth slow-fast systems

In this paper we study the qualitative dynamics of piecewise-smooth slow-fast systems (singularly perturbed systems) which are everywhere continuous. We consider phase space topology of systems with one-dimensional slow dynamics and one-dimensional fast dynamics. The slow manifold of the reduced system is formed by a piecewise-continuous curve, and the differentiability is lost across the switching surface. In the full system the slow manifold is no longer continuous, and there is an O(?) discontinuity across the switching manifold, but the discontinuity cannot qualitatively alter system dynamics. Revealed phase space topology is used to unfold qualitative dynamics of planar slow-fast systems with an equilibrium point on the switching surface. In this case the local dynamics corresponds to so-called boundary-equilibrium bifurcations, and four qualitative phase portraits are uncovered. Our results are then used to investigate the dynamics of a box model of a thermohaline circulation, and the presence of a boundary-equilibrium bifurcation of a fold type is shown.     

Modelling of creep hysteresis in ferroelectrics

In the current paper, a macroscopic model is proposed to simulate the hysteretic dynamics of ferroelectric ceramics with creep phenomenon incorporated. The creep phenomenon in the hysteretic dynamics is attributed to the rate-dependent characteristic of the polarisation switching processes induced in the materials. A non-convex Helmholtz free energy based on Landau theory is proposed to model the switching dynamics. The governing equation of single-crystal model is formulated by applying the Euler–Lagrange equation. The polycrystalline model is obtained by combining the single crystal dynamics with a density function which is constructed to model the weighted contributions of different grains with different principle axis orientations. In addition, numerical simulations of hysteretic dynamics with creep phenomenon are presented. Comparison of the numerical results and their experimental counterparts is also presented. It is shown that the creep phenomenon is captured precisely, validating the capability of the proposed model in a range of its potential applications.     

Avalanches in a nonlinear oscillator chain in a periodic potential

We consider the dynamics of a chain of coupled units evolving in a periodic substrate potential. The chain is initially in a flat state and situated in a potential well. A bias force, acting as a weak driving mechanism, is applied at a single unit of the chain. We study the instigation of directed transport in two types of system: (i) a microcanonical situation associated with deterministic and conservative dynamics and (ii) the Langevin dynamics when the system is in contact with a heat bath. Interestingly, for the deterministic and conservative dynamics the directed transport is drastically enhanced compared with its Langevin counterpart. In particular, in the deterministic and conservative regime a self-organised redistribution of energy triggers huge-sized avalanches yielding ultimately accelerated transport of the chain. In contrast, in the thermally-assisted process between avalanches the chain settles always into a pinned metastable state impeding continual accelerated chain motion.     

Dynamics of a tethered polymer in shear flow

The dynamics of a single polymer tethered to a solid surface in a shear flow was observed using fluorescently labeled DNA chains. Dramatic shear enhanced temporal fluctuations in the chain extension were observed. The rate of these fluctuations initially decreased for increasing shear rate gamma; and increased above a critical gamma;. Simulations revealed that these anomalous dynamics arise from a continual recirculating motion of the chain or cyclic dynamics. These dynamics arise from a coupling of the chain velocity in the flow direction to thermally driven fluctuations of the chain in the shear gradient direction.     

Ultrafast carrier dynamics in single-wall carbon nanotubes

Time-resolved carrier dynamics in single-wall carbon nanotubes is investigated by means of two-color pump-probe experiments. The recombination dynamics is monitored by probing the transient photobleaching observed on the interband transitions of the semiconducting tubes. This dynamics takes place on a 1 ps time scale which is 1 order of magnitude slower than in graphite. Transient photoinduced absorption is observed for nonresonant probing and is interpreted as a global redshift of the pi-plasmon resonance. We show that the opening of the band gap in semiconducting carbon nanotubes determines the nonlinear response dynamics over the whole visible and near-infrared spectrum.     

固态高分子体系多尺度分子运动的核磁共振研究

固体核磁共振技术是研究固态高分子材料中结构和分子动力学的一种非常重要和有效的手段. 该技术的一个重要特点是可以通过合理的实验方法,实现对研究体系中从低频(Hz)到中频(kHz)乃至高频(MHz)范围内分子运动的观测. 因此,固体核磁共振技术非常适合研究高分子体系中各类不同尺度分子运动. 该文首先简要介绍核磁共振研究分子运动的基本原理和方法,以及固态高分子体系的结构和分子动力学特点,然后结合固态高分子体系中的一些例子对核磁共振在固态高分子多尺度分子运动方面的一些研究成果展开讨论.     

Aging in the random energy model

The random energy model (REM) has become a key reference model for glassy systems. In particular, it is expected to provide a prime example of a system whose dynamics shows aging, a universal phenomenon characterizing the dynamics of complex systems. The analysis of its activated dynamics is based on so-called trap models, introduced by Bouchaud, that are also used to mimic the dynamics of more complex disordered systems. In this Letter we report the first results that justify rigorously the trap model predictions in the REM.     

Scaling laws and memory effects in the dynamics of liquids and proteins

Recent progress in the numerical calculation of memory functions from molecular dynamics simulations allowed the gaining of deeper insight into the relaxation dynamics of liquids and proteins. The concept of memory functions goes back to the work of R. Zwanzig on the generalized Langevin equation, and it was the basis for the development of various dynamical models for liquids. In this article we present briefly a method for the numerical calculation of memory functions, which is then applied to study their scaling behavior in normal and fractional Brownian dynamics. It has been shown recently that the model of fractional Brownian dynamics constitutes effectively a link between protein dynamics on the nanosecond time scale, which is accessible to molecular dynamics simulations and thermal neutron scattering, and the much longer time scale of functional protein dynamics, which can be studied by fluorescence correlation spectroscopy. The text was submitted by the authors in English. Affiliated with the University of Orléans.     

Experimental measurement of chaotic attractors in solid mechanics(a))

In this paper a review is given of experimental techniques in chaotic dynamics of solid mechanical systems based on modern ideas of nonlinear dynamics. These methods include Poincare maps, double Poincare sections, symbol dynamics, and fractal dimension. The physical problems discussed include nonlinear elastic beams, forced motion of a string, flow-induced vibration of a rod, forced motions of a magnetic pendulum, and rigid body dynamics of a magnet and high-temperature superconductor.     

Active nonlinear microrheology in a glass-forming Yukawa fluid

A molecular dynamics computer simulation of a glass-forming Yukawa mixture is used to study the anisotropic dynamics of a single particle pulled by a constant force. Beyond linear response, a scaling regime is found where a force-temperature superposition principle of a Peclet number holds. In the latter regime, the diffusion dynamics perpendicular to the force can be mapped on the equilibrium dynamics in terms of an effective temperature, whereas parallel to the force a superdiffusive behavior is seen in the long-time limit. This behavior is associated with a hopping motion from cage to cage and can be qualitatively understood by a simple trap model.     

Dispersion and mixing in quasigeostrophic turbulence

The dynamics of passive Lagrangian tracers in three-dimensional quasigeostrophic turbulence is studied numerically and compared with the behavior of two-dimensional barotropic turbulence. Despite the different Eulerian properties of the two flows, the Lagrangian dynamics of passively advected tracers in three-dimensional quasigeostrophic turbulence is very similar to that of barotropic turbulence. In both systems, coherent vortices play a major role in determining the mixing and dispersion properties. This work indicates that recent results on particle dynamics in barotropic, two-dimensional turbulence carry over to more realistic baroclinic flows, such as those encountered in the large-scale dynamics of the atmosphere and ocean.     

Lattice-scale domain wall dynamics in ferroelectrics

Ferroelectric domain walls are atomically thin, and consequently their dynamics are sensitive to the periodic potential of the underlying lattice. Despite their central role in domain dynamics, lattice-scale effects have never been directly observed. We investigate local domain dynamics in thin film ferroelectrics using atomic-force microscopy. Upon combined dc and ac electric driving, fluctuations in the local piezoresponse are observed. Fourier analysis of the fluctuations reveals the presence of narrow band and broad band noise, and Barkhausen jumps. The narrow band noise is attributed to dynamics associated with lattice-scale pinning and is reproduced by a simple physical model.     

Ultrafast spin dynamics including spin-orbit interaction in semiconductors

This Letter presents a theoretical investigation of ultrafast spin-dependent carrier dynamics in semiconductors due to strong spin-orbit coupling using holes in bulk GaAs as a model system. By computing the microscopic carrier dynamics in the anisotropic hole-band structure including spin-orbit coupling, we obtain spin-relaxation times in quantitative agreement with measured hole-spin relaxation times [Phys. Rev. Lett. 89, 146601 (2002)10.1103/PhysRevLett.89.146601]. We show that different optical techniques for the measurement of hole-spin dynamics yield different results, in contrast to the case of electron-spin dynamics.