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

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

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

Bifurcation analysis and phase diagram of a spin-string model with buckled states

We analyze a one-dimensional spin-string model, in which string oscillators are linearly coupled to their two nearest neighbors and to Ising spins representing internal degrees of freedom. String-spin coupling induces a long-range ferromagnetic interaction among spins that competes with a spin-spin antiferromagnetic coupling. As a consequence, the complex phase diagram of the system exhibits different flat rippled and buckled states, with first or second order transition lines between states. The two-dimensional version of the model has a similar phase diagram, which has been recently used to explain the rippled to buckled transition observed in scanning tunnelling microscopy experiments with suspended graphene sheets. Here we describe in detail the phase diagram of the simpler one-dimensional model and phase stability using bifurcation theory. This gives additional insight into the physical mechanisms underlying the different phases and the behavior observed in experiments.Comment: 15 pages, 7 figure

Ripples in a string coupled to Glauber spins

Each oscillator in a linear chain (a string) interacts with a local Ising spin in contact with a thermal bath. These spins evolve according to Glauber dynamics. Below a critical temperature, a rippled state in the string is accompanied by a nonzero spin polarization. The system is shown to form ripples in the string which, for slow spin relaxation, vibrates rapidly about quasi-stationary states described as snapshots of a coarse-grained stroboscopic map. For moderate observation times, ripples are observed irrespective of the final thermodynamically stable state (rippled or not).Comment: 5 pages, 2 figure

Theory of force-extension curves for modular proteins and DNA hairpins

We study a model describing the force-extension curves of modular proteins, nucleic acids, and other biomolecules made out of several single units or modules. At a mesoscopic level of description, the configuration of the system is given by the elongations of each of the units. The system free energy includes a double-well potential for each unit and an elastic nearest-neighbor interaction between them. Minimizing the free energy yields the system equilibrium properties whereas its dynamics is given by (overdamped) Langevin equations for the elongations, in which friction and noise amplitude are related by the fluctuation-dissipation theorem. Our results, both for the equilibrium and the dynamical situations, include analytical and numerical descriptions of the system force-extension curves under force or length control and agree very well with actual experiments in biomolecules. Our conclusions also apply to other physical systems comprising a number of metastable units, such as storage systems or semiconductor superlattices