Dwell time symmetry in random walks and molecular motors

The statistics of steps and dwell times in reversible molecular motors differ from those of cycle completion in enzyme kinetics. The reason is that a step is only one of several transitions in the mechanochemical cycle. As a result, theoretical results for cycle completion in enzyme kinetics do not apply to stepping data. To allow correct parameter estimation, and to guide data analysis and experiment design, a theoretical treatment is needed that takes this observation into account. In this paper, we model the distribution of dwell times and number of forward and backward steps using first passage processes, based on the assumption that forward and backward steps correspond to different directions of the same transition. We extend recent results for systems with a single cycle and consider the full dwell time distributions as well as models with multiple pathways, detectable substeps, and detachments. Our main results are a symmetry relation for the dwell time distributions in reversible motors, and a relation between certain relative step frequencies and the free energy per cycle. We demonstrate our results by analyzing recent stepping data for a bacterial flagellar motor, and discuss the implications for the efficiency and reversibility of the force-generating subunits. Key words: motor proteins; single molecule kinetics; enzyme kinetics; flagellar motor; Markov process; non-equilibrium fluctuations.Comment: revtex, 15 pages, 8 figures, 2 tables. v2: Minor revision, corrected typos, added references, and moved mathematical parts to new appendice

Sequential Detection with Mutual Information Stopping Cost

This paper formulates and solves a sequential detection problem that involves the mutual information (stochastic observability) of a Gaussian process observed in noise with missing measurements. The main result is that the optimal decision is characterized by a monotone policy on the partially ordered set of positive definite covariance matrices. This monotone structure implies that numerically efficient algorithms can be designed to estimate and implement monotone parametrized decision policies.The sequential detection problem is motivated by applications in radar scheduling where the aim is to maintain the mutual information of all targets within a specified bound. We illustrate the problem formulation and performance of monotone parametrized policies via numerical examples in fly-by and persistent-surveillance applications involving a GMTI (Ground Moving Target Indicator) radar

Optimal Bayesian Quickest Detection for Hidden Markov Models and Structured Generalisations

In this paper we consider the problem of quickly detecting changes in hidden Markov models (HMMs) in a Bayesian setting, as well as several structured generalisations including changes in statistically periodic processes, quickest detection of a Markov process across a sensor array, quickest detection of a moving target in a sensor network and quickest change detection (QCD) in multistream data. Our main result establishes an optimal Bayesian HMM QCD rule with a threshold structure. This framework and proof techniques allow us to to elegantly establish optimal rules for several structured generalisations by showing that these problems are special cases of the Bayesian HMM QCD problem. We develop bounds to characterise the performance of our optimal rule and provide an efficient method for computing the test statistic. Finally, we examine the performance of our rule in several simulation examples and propose a technique for calculating the optimal threshold

Probability flux as a method for detecting scaling

We introduce a new method for detecting scaling in time series. The method uses the properties of the probability flux for stochastic self-affine processes and is called the probability flux analysis (PFA). The advantages of this method are: 1) it is independent of the finiteness of the moments of the self-affine process; 2) it does not require a binning procedure for numerical evaluation of the the probability density function. These properties make the method particularly efficient for heavy tailed distributions in which the variance is not finite, for example, in Levy alpha-stable processes. This utility is established using a comparison with the diffusion entropy (DE) method