Related papers: What Is the Trait d'Union between Retroactivity an…
Retroactivity arises when the coupling of a molecular network $\mathcal{U}$ to a downstream network $\mathcal{D}$ results in signal propagation back from $\mathcal{D}$ to $\mathcal{U}$. The phenomenon represents a breakdown in modularity of…
The molecular network in an organism consists of transcription/translation regulation, protein-protein interactions/modifications and a metabolic network, together forming a system that allows the cell to respond sensibly to the multiple…
Central to the functioning of a living cell is its ability to control the readout or expression of information encoded in the genome. In many cases, a single transcription factor protein activates or represses the expression of many genes.…
Biomolecular communication demands that interactions between parts of a molecular system act as scaffolds for message transmission. It also requires an evolving and organized system of signs - a communicative agency - for creating and…
In order to transmit biochemical signals, biological regulatory systems dissipate energy with concomitant entropy production. Additionally, signaling often takes place in challenging environmental conditions. In a simple model regulatory…
Signal transduction in biological cells is effected by signaling pathways that typically include multiple feedback loops. Here we analyze information transfer through a prototypical signaling module with biochemical feedback. The module…
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…
Signal transduction, or signal-processing capability, is a fundamental property of nature that manifests universally across systems of different scales -- from quantum behaviour to the biological. This includes the detection of…
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…
Feedback in sensory biochemical networks can give rise to bifurcations in cells' behavioral response. These bifurcations share many properties with thermodynamic critical points. Evidence suggests that biological systems may operate near…
Intracellular biochemical networks fluctuate dynamically due to various internal and external sources of fluctuation. Dissecting the fluctuation into biologically relevant components is important for understanding how a cell controls and…
A model for autonomous feedback control of particle transport through a large number of channels is introduced. Interactions among the particles can lead to a strong suppression of fluctuations in the particle number statistics. Within a…
Cellular decision making is based on regulatory circuits that associate signal thresholds to specific physiological actions. This transmission of information is subjected to molecular noise what can decrease its fidelity. Here, we show…
Gene regulatory circuits show significant stochastic fluctuations in their circuit signals due to the low copy number of transcription factors. When a gene circuit component is connected to an existing circuit, the dynamic properties of the…
Many biological regulatory systems process signals out of steady state and respond with a physiological delay. A simple model of regulation which respects these features shows how the ability of a delayed output to transmit information is…
Ambient backscatter is an intriguing wireless communication paradigm that allows small devices to compute and communicate by using only the power they harvest from radio-frequency (RF) signals in the air. Ambient backscattering devices…
Biological information processing manifests a huge variety in its complexity and capability among different organisms, which presumably stems from the evolutionary optimization under limited computational resources. Starting from the…
Information transmission in biological signaling circuits has often been described using the metaphor of a noise filter. Cellular systems need accurate, real-time data about their environmental conditions, but the biochemical reaction…
Cooperative interactions among the binding of multiple signaling molecules is a common mechanism for enhancing the sensitivity of biological signaling systems. It is widely assumed that this increase in sensitivity of the mean response…
Many of the chemical reactions that take place within a living cell are irreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks…