Related papers: Information transfer through a signaling module wi…
Cells use temporal dynamical patterns to transmit information via signaling pathways. As optimality with respect to the environment plays a fundamental role in biological systems, organisms have evolved optimal ways to transmit information.…
Receptor-induced apoptosis is a complex signal transduction pathway involving numerous protein/protein interactions and post-transcriptional modifications. The response to death receptor stimulation varies significantly from one cell line…
Biochemical networks can respond to temporal characteristics of time-varying signals. To understand how reliably biochemical networks can transmit information we must consider how an input signal as a function of time--the input…
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 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…
This survey paper focuses on modulation aspects of molecular communication, an emerging field focused on building biologically-inspired systems that embed data within chemical signals. The primary challenges in designing these systems are…
Inter and intra-cellular signaling are essential for individual cells to execute various physiological tasks and accurately respond to changes in their environment. Signaling is carried out via diffusible molecules, the transport of which…
To thrive in dynamic environments, animals must be capable of rapidly and flexibly adapting behavioral responses to a changing context and internal state. Examples of behavioral flexibility include faster stimulus responses when attentive…
To maintain homeostasis, living cells process information with networks of interacting molecules. Traditional models for cellular information processing have focused on networks of chemical reactions between molecules. Here, we describe how…
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…
In recent years it is increasingly being recognized that biochemical signals are not necessarily constant in time and that the temporal dynamics of a signal can be the information carrier. Moreover, it is now well established that…
Cells are often considered input-output devices that maximize the transmission of information by converting extracellular stimuli (input) via signaling pathways (communication channel) to cell behavior (output). However, in biological…
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,…
Biological signaling is imagined as a combination of activation and transport. The former is triggered by local molecular interactions and the latter is the result of molecular diffusion. However, other fundamental physical principles of…
Signal transduction, the information processing mechanism in biological cells, is carried out by a network of biochemical reactions. The dynamics of driven biochemical reactions can be studied in terms of nonequilibrium statistical physics.…
Exchange of biochemical substances is essential way in establishing communication between bacterial cells. It is noticeable that all phases of the process are heavily influenced by perturbations of either internal or external parameters.…
Pulsatory activity patterns, driven by mechanochemical feedback, are prevalent in many biological systems. Here we present a theoretical framework to elucidate the mechanical origin and regulation of pulsatile activity patterns within…
Translation is a key step in the synthesis of proteins. Accordingly, cells have evolved an intricate array of control mechanisms to regulate this process. By constructing a multi-component mathematical framework for translation we uncover…
Sensory neurons are often described in terms of a receptive field, that is, a linear kernel through which stimuli are filtered before they are further processed. If information transmission is assumed to proceed in a feedforward cascade,…