Wavefront depinning transition in discrete one-dimensional reaction-diffusion systems

Pinning and depinning of wavefronts are ubiquitous features of spatially discrete systems describing a host of phenomena in physics, biology, etc. A large class of discrete systems is described by overdamped chains of nonlinear oscillators with nearest-neighbor coupling and controlled by constant external forces. A theory of the depinning transition for these systems, including scaling laws and asymptotics of wavefronts, is presented and confirmed by numerical calculations.Comment: 4 pages, 4 figure

Depinning transitions in discrete reaction-diffusion equations

We consider spatially discrete bistable reaction-diffusion equations that admit wave front solutions. Depending on the parameters involved, such wave fronts appear to be pinned or to glide at a certain speed. We study the transition of traveling waves to steady solutions near threshold and give conditions for front pinning (propagation failure). The critical parameter values are characterized at the depinning transition and an approximation for the front speed just beyond threshold is given.Comment: 27 pages, 12 figures, to appear in SIAM J. Appl. Mat

Theory of defect dynamics in graphene: defect groupings and their stability

We use our theory of periodized discrete elasticity to characterize defects in graphene as the cores of dislocations or groups of dislocations. Earlier numerical implementations of the theory predicted some of the simpler defect groupings observed in subsequent Transmission Electron Microscope experiments. Here we derive the more complicated defect groupings of three or four defect pairs from our theory, show that they correspond to the cores of two pairs of dislocation dipoles and ascertain their stability.Comment: 11 pages, 7 figures; replaced figure

Nonequilibrium dynamics of a fast oscillator coupled to Glauber spins

A fast harmonic oscillator is linearly coupled with a system of Ising spins that are in contact with a thermal bath, and evolve under a slow Glauber dynamics at dimensionless temperature $\theta$. The spins have a coupling constant proportional to the oscillator position. The oscillator-spin interaction produces a second order phase transition at $\theta=1$ with the oscillator position as its order parameter: the equilibrium position is zero for $\theta>1$ and non-zero for $\theta< 1$. For $\theta<1$, the dynamics of this system is quite different from relaxation to equilibrium. For most initial conditions, the oscillator position performs modulated oscillations about one of the stable equilibrium positions with a long relaxation time. For random initial conditions and a sufficiently large spin system, the unstable zero position of the oscillator is stabilized after a relaxation time proportional to $\theta$. If the spin system is smaller, the situation is the same until the oscillator position is close to zero, then it crosses over to a neighborhood of a stable equilibrium position about which keeps oscillating for an exponentially long relaxation time. These results of stochastic simulations are predicted by modulation equations obtained from a multiple scale analysis of macroscopic equations.Comment: 30 pages, 9 figure

Spin-oscillator model for DNA/RNA unzipping by mechanical force

We model unzipping of DNA/RNA molecules subject to an external force by a spin-oscillator system. The system comprises a macroscopic degree of freedom, represented by a one-dimensional oscillator, and internal degrees of freedom, represented by Glauber spins with nearest-neighbor interaction and a coupling constant proportional to the oscillator position. At a critical value $F_c$ of an applied external force $F$, the oscillator rest position (order parameter) changes abruptly and the system undergoes a first-order phase transition. When the external force is cycled at different rates, the extension given by the oscillator position exhibits a hysteresis cycle at high loading rates whereas it moves reversibly over the equilibrium force-extension curve at very low loading rates. Under constant force, the logarithm of the residence time at the stable and metastable oscillator rest position is proportional to $(F-F_c)$ as in an Arrhenius law.Comment: 9 pages, 6 figures, submitted to PR

Statics and dynamics of a harmonic oscillator coupled to a one-dimensional Ising system

We investigate an oscillator linearly coupled with a one-dimensional Ising system. The coupling gives rise to drastic changes both in the oscillator statics and dynamics. Firstly, there appears a second order phase transition, with the oscillator stable rest position as its order parameter. Secondly, for fast spins, the oscillator dynamics is described by an effective equation with a nonlinear friction term that drives the oscillator towards the stable equilibrium state.Comment: Proceedings of the 2010 Granada Semina

Self-sustained current oscillations in the kinetic theory of semiconductor superlattices

We present the first numerical solutions of a kinetic theory description of self-sustained current oscillations in n-doped semiconductor superlattices. The governing equation is a single-miniband Boltzmann-Poisson transport equation with a BGK (Bhatnagar-Gross-Krook) collision term. Appropriate boundary conditions for the distribution function describe electron injection in the contact regions. These conditions seamlessly become Ohm's law at the injecting contact and the zero charge boundary condition at the receiving contact when integrated over the wave vector. The time-dependent model is numerically solved for the distribution function by using the deterministic Weighted Particle Method. Numerical simulations are used to ascertain the convergence of the method. The numerical results confirm the validity of the Chapman-Enskog perturbation method used previously to derive generalized drift-diffusion equations for high electric fields because they agree very well with numerical solutions thereof.Comment: 26 pages, 16 figures, to appear in J. Comput. Phy

Protein unfolding and refolding as transitions through virtual states

Single-molecule atomic force spectroscopy probes elastic properties of titin, ubiquitin and other relevant proteins. We explain bioprotein folding dynamics under both length- and force-clamp by modeling polyprotein modules as particles in a bistable potential, weakly connected by harmonic spring linkers. Multistability of equilibrium extensions provides the characteristic sawtooth force-extension curve. We show that abrupt or stepwise unfolding and refolding under force-clamp conditions involve transitions through virtual states (which are quasi-stationary domain configurations) modified by thermal noise. These predictions agree with experimental observations.Comment: 6 pages, accepted for publication in EPL http://iopscience.iop.org/ep