相关论文: A Reversibility Parameter for a Markovian Stepper

We use fitness graphs, or directed cube graphs, for analyzing evolutionary reversibility. The main application is antimicrobial drug resistance. Reversible drug resistance has been observed both clinically and experimentally. If drug…

Identifying and characterizing mutational paths is an important issue in evolutionary biology and in bioengineering. We here introduce a generic description of mutational paths in terms of the goodness of sequences and of the mutational…

Observability is a modelling property that describes the possibility of inferring the internal state of a system from observations of its output. A related property, structural identifiability, refers to the theoretical possibility of…

A continuous-time random walk in the quarter plane with homogeneous transition rates is considered. Given a non-negative reward function on the state space, we are interested in the expected stationary performance. Since a direct derivation…

1. Complex systems of moving and interacting objects are ubiquitous in the natural and social sciences. Predicting their behavior often requires models that mimic these systems with sufficient accuracy, while accounting for their inherent…

In this paper, we propose the reduced model for the full dynamics of a bicycle and analyze its nonlinear behavior under a proportional control law for steering. Based on the Gibbs-Appell equations for the Whipple bicycle, we obtain a…

We characterize a class of Markovian dynamics using the concept of divisible dynamical map. Moreover we provide a family of criteria which can distinguish Markovian and non-Markovian dynamics. These Markovianity criteria are based on a…

We have developed a novel method to evaluate the potential profile of a molecular motor at each chemical state from only the probe's trajectory and applied it to a rotary molecular motor F$_1$-ATPase. By using this method, we could also…

Learning-rate steps are usually treated as hyperparameters. This paper isolates a local beliefspace calculation: when an update is modeled as a projected forward step on the probability simplex, admissibility means contractivity in the…

The effect of interactions on dynamics of coupled motor proteins is investigated theoretically. A simple stochastic discrete model, that allows to calculate explicitly the dynamic properties of the system, is developed. It is shown that…

Over the last three decades, there has been a considerable effort within the applied probability community to develop techniques for bounding the convergence rates of general state space Markov chains. Most of these results assume the…

Movement primitives are an important policy class for real-world robotics. However, the high dimensionality of their parametrization makes the policy optimization expensive both in terms of samples and computation. Enabling an efficient…

In this work we study, at the single molecular level, the thermodynamic and dynamic characteristics of an enzymatic reaction comprising a rate limiting step. We investigate how the stability of the enzyme-state stationary probability…

The reduction of high-dimensional systems to effective models on a smaller set of variables is an essential task in many areas of science. For stochastic dynamics governed by diffusion processes, a general procedure to find effective…

Identifiability of parameters is an essential property for a statistical model to be useful in most settings. However, establishing parameter identifiability for Bayesian networks with hidden variables remains challenging. In the context of…

We study the ensemble velocity of non-processive motor proteins, described with multiple chemical states. In particular, we discuss the velocity as a function of ATP concentration. Even a simple model which neglects the strain-dependence of…

Molecular simulations can provide microscopic insight into the physical and chemical driving forces of complex molecular processes. Despite continued advancement of simulation methodology, model errors may lead to inconsistencies between…

We rigorously show that the probability to have a specific trajectory of an externally perturbed classical open system satisfies a universal symmetry for Liouvillian reversible dynamics. It connects the ratio between the probabilities of…

We theoretically study the transport properties of self-propelled particles on complex structures, such as motor proteins on filament networks. A general master equation formalism is developed to investigate the persistent motion of…

A particle moves randomly over the integer points of the real line. Jumps of the particle outside the membrane (a fixed "locally perturbating set") are i.i.d., have zero mean and finite variance, whereas jumps of the particle from the…