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In this paper, we focus on activating only a few sensors, among many available, to estimate the state of a stochastic process of interest. This problem is important in applications such as target tracking and simultaneous localization and…

Predictive understanding of the myriads of signal transduction pathways in a cell is an outstanding challenge of systems biology. Such pathways are primarily mediated by specific but transient protein-protein interactions, which are…

We review the mathematical formalism underlying the modelling of stochasticity in biological systems. Beginning with a description of the system in terms of its basic constituents, we derive the mesoscopic equations governing the dynamics…

Biological systems are characterized by the ubiquitous roles of weak, that is, non-covalent molecular interactions, small, often very small, numbers of specific molecules per cell, and Brownian motion. These combine to produce stochastic…

Information theory provides powerful tools for understanding communication systems. This analysis can be applied to intercellular signal transduction, which is a means of chemical communication among cells and microbes. We discuss how to…

An algorithm that performs joint equalization and decoding for channels with nonlinear two-dimensional intersymbol interference is presented. The algorithm performs sum-product message-passing on a factor graph that represents the…

We look at the problem of signal transduction by extracellular agonist binding to a receptor protein at the membrane (sensor) via binding of G-proteins (effectors) to a highly integrative target molecule, such as the second messenger cAMP…

Bursting is a phenomenon found in a variety of physical and biological systems. For example, in neuroscience, bursting is believed to play a key role in the way information is transferred in the nervous system. In this work, we propose a…

Transmission spectroscopy, which consists of measuring the wavelength-dependent absorption of starlight by a planet's atmosphere during a transit, is a powerful probe of atmospheric composition. However, the expected signal is typically…

We investigate the problem of signal transduction via a descriptive analysis of the spatial organization of the complement of proteins exerting a certain function within a cellular compartment. We propose a scheme to assign a numerical…

System identification is of special interest in science and engineering. This article is concerned with a system identification problem arising in stochastic dynamic systems, where the aim is to estimate the parameters of a system along…

Force detectors rely on resonators to transduce forces into a readable signal. Usually these resonators operate in the linear regime and their signal appears amidst a competing background comprising thermal or quantum fluctuations as well…

Signal propagation in biochemical networks is characterized by the inherent randomness in gene expression and fluctuations of the environmental components, commonly known as intrinsic and extrinsic noise, respectively. We present a…

A general form of a many-body Hamiltonian is considered, which includes an interacting fermionic sub-system coupled to non-interacting extended fermionic and bosonic systems. We show that the exact dynamics of the extended bosonic system…

Transfer entropy is capable of capturing nonlinear source-destination relations between multi-variate time series. It is a measure of association between source data that are transformed into destination data via a set of linear…

Intrinsic transcriptional noise induced by operator fluctuations is investigated with a simple spin like stochastic model. The effects of transcriptional fluctuations in protein synthesis is probed by coupling transcription and translation…

We consider the stochastic patterns of a system of communicating, or coupled, self-propelled particles in the presence of noise and communication time delay. For sufficiently large environmental noise, there exists a transition between a…

Inductively coupled resonant circuits are affected by the so-called frequency splitting phenomenon at short distances. In the area of power electronics, tracking of one of the peak frequencies is state-of-the-art. In the data transmission…

We analyse the effect of intrinsic fluctuations on the properties of bistable stochastic systems with time scale separation operating under1 quasi-steady state conditions. We first formulate a stochastic generalisation of the quasi-steady…

In non-viral gene delivery, the variance of transgenic expression stems from the low number of plasmids successfully transferred. Here, we experimentally determine Lipofectamine- and PEI-mediated exogenous gene expression distributions from…