Related papers: Multiplexing oscillatory biochemical signals
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,…
Single-cell studies often show significant phenotypic variability due to the stochastic nature of intra-cellular biochemical reactions. When the numbers of molecules, e.g., transcription factors and regulatory enzymes, are in low abundance,…
Cellular transformations which involve a significant phenotypical change of the cell's state use bistable biochemical switches as underlying decision systems. In this work, we aim at linking cellular decisions taking place on a time scale…
Living cells sense their environment through the binding of extra-cellular molecular ligands to cell surface receptors. Puzzlingly, vast numbers of signaling pathways exhibit a high degree of cross talk between different signals whereby…
Transport of neural signals in the brain is challenging, owing to neural interference and neural noise. There is experimental evidence of multiplexing of sensory information across population of neurons, particularly in the vertebrate…
We present DiSH-Sim, a simulator for large discrete models of biological signal transduction pathways, capable of simulating networks with multi-valued elements in both deterministic and stochastic manner. We focus on order of update and…
Communication systems for multicasting information and energy simultaneously to more than one user are investigated. In the system under study, a transmitter sends the same message and signal to multiple receivers over distinct and…
Feedback loops are major components of biochemical systems. Many systems show multiple such (positive or negative) feedback loops. Nevertheless, very few quantitative analyses address the question how such multiple feedback loops evolved.…
Mutual information is a theoretically grounded metric for quantifying cellular signaling pathways. However, its measurement demands characterization of both input and output distributions, limiting practical applications. Here, we present…
For information transmission a binary symmetric channel is used. There is also another noisy binary symmetric channel (feedback channel), and the transmitter observes without delay all the outputs of the forward channel via that feedback…
In many biological systems localized mechanical information is transmitted by mechanically neutral chemical signals. Typical examples include contraction waves in acto-myosin cortex at cellular scale and peristaltic waves at tissue level.…
The structure of a genetic network is uncovered by studying its response to external stimuli (input signals). We present a theory of propagation of an input signal through a linear stochastic genetic network. It is found that there are…
Electrical signals play the primary role in rapid communication among organs, tissues and cells in biosystems. We have analyzed and discussed three phenomena of electrical communication in biosystems, including direction-changing movement…
Cellular signaling is essential in information processing and decision making. Therefore, a variety of experimental approaches have been developed to study signaling on bulk and single-cell level. Single-cell measurements of signaling…
Molecular communication between biological entities is a new paradigm in communications. Recently, we studied molecular communication between two nodes formed from synthetic bacteria. Due to high randomness in behavior of bacteria, we used…
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…
We present a class of systems for which the signal-to-noise ratio as a function of the noise level may display a multiplicity of maxima. This phenomenon, referred to as stochastic multiresonance, indicates the possibility that periodic…
This work proposes a two-dimensional electrophysiological model for describing neuronal responses to external electric stimuli under patch-clamped conditions. Our proposed model successfully captures the key features of the Hodgkin-Huxley…
Collective cell migration in response to a chemical cue occurs in many biological processes such as morphogenesis and cancer metastasis. Clusters of migratory cells in these systems are capable of responding to gradients of less than 1%…
Biochemical signaling cascades transmit intracellular information while dissipating energy under nonequilibrium conditions. We model a cascade as a code string and apply information-entropy ideas to quantify an optimal transmission rate. A…