Related papers: Multiplexing oscillatory biochemical signals
Even in the steady-state, the number of biomolecules in living cells fluctuates dynamically; and the frequency spectrum of this chemical fluctuation carries valuable information about the mechanism and the dynamics of the intracellular…
Fluctuations in the abundance of molecules in the living cell may affect its growth and well being. For regulatory molecules (e.g., signaling proteins or transcription factors), fluctuations in their expression can affect the levels of…
Chemical signaling is one of the ubiquitous mechanisms by which inter-cellular communication takes place at the microscopic level, particularly via chemotaxis. Such multi-cellular systems are popularly studied using continuum, mean-field…
Biological neural systems encode and transmit information as patterns of activity tracing complex trajectories in high-dimensional state-spaces, inspiring alternative paradigms of information processing. Heteroclinic networks, naturally…
We consider an anisotropically two-dimensional diffusion of a charged molecule (particle) through a large biological channel under an external voltage. The channel is modeled as a cylinder of three structure parameters: radius, length, and…
We study a stochastic epidemic model consisting of elements (organisms in a community or cells in tissue) with fixed positions, in which damage or disease is transmitted by diffusing agents ("signals") emitted by infected individuals. The…
Understanding relationship between noisy dynamics and biological network architecture is a fundamentally important question, particularly in order to elucidate how cells encode and process information. We analytically and numerically…
We study the dynamics of intracellular calcium oscillations in the presence of proteins that bind calcium on multiple sites and that are generally believed to act as passive calcium buffers in cells. We find that multisite calcium-binding…
This paper focuses on molecular communication (MC) systems using two types of signaling molecules which may participate in a reversible bimolecular reaction in the channel. The motivation for studying these MC systems is that they can…
There are three equivalent ways of representing two jointly observed real-valued signals: as a bivariate vector signal, as a single complex-valued signal, or as two analytic signals known as the rotary components. Each representation has…
Synthetic biology sets out to implement new functions in cells, and to develop a deeper understanding of biological design principles. In 2000, Elowitz and Leibler showed that by rational design of the reaction network, and using existing…
Many crucial biological processes operate with surprisingly small numbers of molecules, and there is renewed interest in analyzing the impact of noise associated with these small numbers. Twenty--five years ago, Berg and Purcell showed that…
Complex systems are often characterized by the interplay of multiple interconnected dynamical processes operating across a range of temporal scales. This phenomenon is widespread in both biological and artificial scenarios, making it…
Statistical properties of environments experienced by biological signaling systems in the real world change, which necessitate adaptive responses to achieve high fidelity information transmission. One form of such adaptive response is gain…
We theoretically describe how weak signals may be efficiently transmitted throughout more than one frequency range in noisy excitable media by kind of stochastic multiresonance. This serves us here to reinterpret recent experiments in…
The lifetime measurement of molecular excited state has been the subject of many papers and experiments. Very often the experimental data are fitted by single or bi exponential decays which in many case is the best fit that can be done…
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…
Living cells sense noisy biochemical signals crucial for survival, yet models incorporating intracellular signaling are limited. This study examines how cells sense chemotactic concentrations through phosphorylation readouts in Ca2+…
Quantitatively predictive models of biomolecular circuits are important tools for the design of synthetic biology and molecular communication circuits. The information content of typical time-lapse single-cell data for the inference of…
Recent observations of beating signals in the excitation energy transfer dynamics of photosynthetic complexes have been interpreted as evidence for sustained coherences that are sufficiently long-lived for energy transport and coherence to…