Comment on "Influence of Noise on Force Measurements"

In a recent Letter [arXiv:1004.0874], Volpe et al. describe experiments on a colloidal particle near a wall in the presence of a gravitational field for which they study the influence of noise on the measurement of force. Their central result is a striking discrepancy between the forces derived from experimental drift measurements via their Eq. (1), and from the equilibrium distribution. From this discrepancy they infer the stochastic calculus realised in the system. We comment, however: (a) that Eq. (1) does not hold for space-dependent diffusion, and corrections should be introduced; and (b) that the "force" derived from the drift need not coincide with the "force" obtained from the equilibrium distribution.Comment: Comment submitted to a PRL letter; 1 page, 1 figur

Changes in the dynamical behavior of nonlinear systems induced by noise.

Weak noise acting upon a nonlinear dynamical system can have far-reaching consequences. The fundamental underlying problem - that of large deviations of a nonlinear system away from a stable or metastable state, sometimes resulting in a transition to a new stationary state, in response to weak additive or multiplicative noise - has long attracted the attention of physicists. This is partly because of its wide applicability, and partly because it bears on the origins of temporal irreversibility in physical processes. During the last few years it has become apparent that, in a system far from thermal equilibrium, even small noise can also result in qualitative change in the system's properties, e.g., the transformation of an unstable equilibrium state into a stable one, and vice versa, the occurrence of multistability and multimodality, the appearance of a mean field, the excitation of noise-induced oscillations, and noise-induced transport (stochastic ratchets). A representative selection of such phenomena is discussed and analyzed, and recent progress made towards their understanding is reviewed

Competition between noise and coupling in the induction of synchronisation.

We apply a Fokker-Planck analysis to investigate the relative influences of coupling strength and noise on the synchronisation of two phase oscillators. We go beyond earlier studies of noise-induced synchronisation (without couplings) and coupling-induced synchronisation (without common noise) to consider both effects together, and we obtain a result that is very different from a straightforward superposition of the effects of each agent acting alone: two regimes are possible depending on which agent is inducing the synchronisation. In each regime, one agent induces and the other hinders the synchronisation. In particular we show that, counterintuitively, coupling can sometimes inhibit synchronisation

Self-consistent analytic solution for the current and the access resistance in open ion channels.

A self-consistent analytic approach is introduced for the estimation of the access resistance and the current through an open ion channel for an arbitrary number of species. For an ion current flowing radially inward from infinity to the channel mouth, the Poisson-Boltzmann-Nernst-Planck equations are solved analytically in the bulk with spherical symmetry in three dimensions, by linearization. Within the channel, the Poisson-Nernst-Planck equation is solved analytically in a one-dimensional approximation. An iterative procedure is used to match the two solutions together at the channel mouth in a self-consistent way. It is shown that the currentvoltage characteristics obtained are in good quantitative agreement with experimental measurements

Recovering ‘lost’ information in the presence of noise: application to rodent–predator dynamics.

A Hamiltonian approach is introduced for the reconstruction of trajectories and models of complex stochastic dynamics from noisy measurements. The method converges even when entire trajectory components are unobservable and the parameters are unknown. It is applied to reconstruct nonlinear models of rodent–predator oscillations in Finnish Lapland and high-Arctic tundra. The projected character of noisy incomplete measurements is revealed and shown to result in a degeneracy of the likelihood function within certain null-spaces. The performance of the method is compared with that of the conventional Markov chain Monte Carlo (MCMC) technique

Applications of dynamical inference to the analysis of noisy biological time series with hidden dynamical variables.

We present a Bayesian framework for parameter inference in noisy, non-stationary, nonlinear, dynamical systems. The technique is implemented in two distinct ways: (i) Lightweight implementation: to be used for on-line analysis, allowing multiple parameter estimation, optimal compensation for dynamical noise, and reconstruction by integration of the hidden dynamical variables, but with some limitations on how the noise appears in the dynamics; (ii) Full scale implementation: of the technique with extensive numerical simulations (MCMC), allowing for more sophisticated reconstruction of hidden dynamical trajectories and dealing better with sources of noise external to the dynamics (measurements noise)

Stationary and Traveling Wave States of the Kuramoto Model with an Arbitrary Distribution of Frequencies and Coupling Strengths

We consider the Kuramoto model of an ensemble of interacting oscillators allowing for an arbitrary distribution of frequencies and coupling strengths. We define a family of traveling wave states as stationary in a rotating frame, and derive general equations for their parameters. We suggest empirical stability conditions which, for the case of incoherence, become exact. In addition to making new theoretical predictions, we show that many earlier results follow naturally from our general framework. The results are applicable in scientific contexts ranging from physics to biology.Comment: 5 pages, 1 figur

Enlargement of a low-dimensional stochastic web

We consider an archetypal example of a low-dimensional stochastic web, arising in a 1D oscillator driven by a plane wave of a frequency equal or close to a multiple of the oscillator’s natural frequency. We show that the web can be greatly enlarged by the introduction of a slow, very weak, modulation of the wave angle. Generalizations are discussed. An application to electron transport in a nanometre-scale semiconductor superlattice in electric and magnetic fields is suggested

Charge fluctuations and boundary conditions of biological ion channels:effect on the ionic transition rate

A self-consistent solution is derived for the Poisson-Nernst-Planck (PNP) equation, valid both inside a biological ion channel and in the adjacent bulk fluid. An iterative procedure is used to match the two solutions together at the channel mouth. Charge fluctuations at the mouth are modeled as shot noise flipping the height of the potential barrier at the selectivity site. The resultant estimates of the conductivity of the ion channel are in good agreement with Gramicidin experimental measurements and they reproduce the observed current saturation with increasing concentration