Related papers: Using biochemical circuits to approximately comput…
We introduce the boundary reproduction number, adapted from the next generation matrix method, to assess whether an infusion of species will persist or become exhausted in a chemical reaction system. Our main contributions are as follows:…
We quantify the influence of the topology of a transcriptional regulatory network on its ability to process environmental signals. By posing the problem in terms of information theory, we may do this without specifying the function…
Transcriptional regulatory network inference methods have been studied for years. Most of them relie on complex mathematical and algorithmic concepts, making them hard to adapt, re-implement or integrate with other methods. To address this…
BACKGROUND: Transcriptional regulation is a key mechanism in the functioning of the cell, and is mostly effected through transcription factors binding to specific recognition motifs located upstream of the coding region of the regulated…
We use large deviation methods to calculate rates of noise-induced transitions between states in multistable genetic networks. We analyze a synthetic biochemical circuit, the toggle switch, and compare the results to those obtained from a…
We used various analytical and numerical techniques to elucidate signal propagation in a small enzymatic cascade which is subjected to external and internal noise. The nonlinear character of catalytic reactions, which underlie protein…
Chemical reaction networks describe interactions between biochemical species. Once an underlying reaction network is given for a biochemical system, the system dynamics can be modelled with various mathematical frameworks such as continuous…
Quantum repeater chains will form the backbone of future quantum networks that distribute entanglement between network nodes. Therefore, it is important to understand the entanglement distribution performance of quantum repeater chains,…
The detection of change-points in a spatially or time ordered data sequence is an important problem in many fields such as genetics and finance. We derive the asymptotic distribution of a statistic recently suggested for detecting…
We present an example of the practical implementation of a protocol for experimental bifurcation detection based on on-line identification and feedback control ideas. The idea is to couple the experiment with an on-line computer-assisted…
Analyzing time series in the frequency domain enables the development of powerful tools for investigating the second-order characteristics of multivariate processes. Parameters like the spectral density matrix and its inverse, the coherence…
We study the problem of computing outer bounds for the region of steady states of biochemical reaction networks modelled by ordinary differential equations, with respect to parameters that are allowed to vary within a predefined region.…
Molecular Communications (MC) is a bio-inspired communication technique that uses molecules to transfer information among bio-nano devices. In this paper, we focus on the detection problem for biological MC receivers employing ligand…
A fundamental challenge in probabilistic modeling is to balance expressivity and inference efficiency. Tractable probabilistic models (TPMs) aim to directly address this tradeoff by imposing constraints that guarantee efficient inference of…
Understanding the function of network motifs in an attempt to gain insight into how their combinations create larger reaction networks that drive cellular functions, has been a longstanding pursuit of systems biology. One specific objective…
A common method for analyzing the effects of molecular noise in chemical reaction networks is to approximate the underlying chemical master equation by a Fokker-Planck equation, and to study the statistics of the associated chemical…
Cells regulate themselves via dizzyingly complex biochemical processes called signaling pathways. These are usually depicted as a network, where nodes represent proteins and edges indicate their influence on each other. In order to…
This paper investigates two issues on identification of switched linear systems: persistence of excitation and numerical algorithms. The main contribution is a much weaker condition on the regressor to be persistently exciting that…
In a typical multi-standard military communication receiver, fast and reliable spectrum sensing unit is required to extract the information of multiple channels (frequency bands) present in a wideband input signal. In this paper, an energy…
Quantum communication enables a host of applications that cannot be achieved by classical communication means, with provably secure communication as one of the prime examples. The distance that quantum communication schemes can cover via…