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Electron transfer (ET) between primary electron donors and acceptors is modeled in the photosystem II reaction center (RC). Our model includes (i) two discrete energy levels associated with donor and acceptor, interacting through a…
Information exchange is a critical process in all communication systems, including biological ones. The concept of retroactivity represents the loads that downstream modules apply to their upstream systems in biological circuits. This paper…
This paper considers a sequential estimation and sensor scheduling problem with one sensor and one estimator. The sensor makes sequential observations about the state of an underlying memoryless stochastic process, and makes a decision as…
Excitation transfer through interacting systems plays an important role in many areas of physics, chemistry, and biology. The uncontrollable interaction of the transmission network with a noisy environment is usually assumed to deteriorate…
Proteins are polymerized by cyclic machines called ribosome which use their messenger RNA (mRNA) track also as the corresponding template and the process is called translation. We explore, in depth and detail, the stochastic nature of the…
We develop numerical and analytical approaches to calculate mutual information between complete paths of two molecular components embedded into a larger reaction network. In particular, we focus on a continuous-time Markov chain formalism,…
Communication is compositional if complex signals can be represented as a combination of simpler subparts. In this paper, we theoretically show that inductive biases on both the training framework and the data are needed to develop a…
The method described in the first part for frequency-selectively measuring the transfer function and the noise power spectral density of the superimposed noise at the output of a disturbed, real system with nonlinearities using windowing…
We introduce a biologically detailed, stochastic model of gene expression describing the multiple rate-limiting steps of transcription, nuclear pre-mRNA processing, nuclear mRNA export, cytoplasmic mRNA degradation and translation of mRNA…
Microscopic biological systems operate far from equilibrium, are subject to strong fluctuations, and are composed of many coupled components with interactions varying in nature and strength. Researchers are actively investigating the…
We present a method for logical specification of the behavior of a system based on the specification of its components and for representing and specifying the effect of a class of communication "signaling pathways" among them. Variations in…
Cellular signaling networks have evolved to cope with intrinsic fluctuations, coming from the small numbers of constituents, and the environmental noise. Stochastic chemical kinetics equations govern the way biochemical networks process…
This study discusses acoustic dissipation, which contributes to inaccuracies in impedance tube measurements. To improve the accuracy of these measurements, this paper introduces a transfer function model that integrates diverse dissipation…
System dynamics is a popular approach in many fields of science and technology, but it has not been investigated for cell signaling pathways yet. It is a well formulated methodology used to analyze the components of a system considering the…
Synaptic integration is a prominent aspect of neuronal information processing. The detailed mechanisms that modulate synaptic inputs determine the computational properties of any given neuron. We study a simple model for the summation of…
The digital signal processing has greatly simplified the process of phase noise measurements, especially in oscillators, but its applications are largely confined to the frequencies below 400 MHz. We propose a novel transpose frequency…
Functional Principal Component Analysis is a reference method for dimension reduction of curve data. Its theoretical properties are now well understood in the simplified case where the sample curves are fully observed without noise.…
Stochasticity is both exploited and controlled by cells. Although the intrinsic stochasticity inherent in biochemistry is relatively well understood, cellular variation, or 'noise', is predominantly generated by interactions of the system…
Inferring functional relationships within complex networks from static snapshots of a subset of variables is a ubiquitous problem in science. For example, a key challenge of systems biology is to translate cellular heterogeneity data…
Sensors are the first element of the pathways that control the response of cells to their environment. After chemical, the next most important cue is mechanical, and protein complexes that produce or enable a chemical signal in response to…