Related papers: Information propagation in time through allosteric…
Life depends as much on the flow of information as on the flow of energy. Here we review the many efforts to make this intuition precise. Starting with the building blocks of information theory, we explore examples where it has been…
Appealing to several multivariate information measures---some familiar, some new here---we analyze the information embedded in discrete-valued stochastic time series. We dissect the uncertainty of a single observation to demonstrate how the…
We study how the dynamic equilibrium of the reversible protein-protein binding network in yeast Saccharomyces cerevisiae responds to large changes in abundances of individual proteins. The magnitude of shifts between free and bound…
Many biological, physical, and social interactions have a particular dependence on where they take place. In living cells, protein movement between the nucleus and cytoplasm affects cellular response (i.e., proteins must be present in the…
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…
Understanding design principles of molecular interaction networks is an important goal of molecular systems biology. Some insights have been gained into features of their network topology through the discovery of graph theoretic patterns…
Sensory neurons give highly variable responses to stimulation, which can limit the amount of stimulus information available to downstream circuits. Much work has investigated the factors that affect the amount of information encoded in…
Enzyme catalysis in reactors for industrial applications usually require an external intervention of the species involved in the chemical reactions. We analyze the most elementary open enzyme catalysis with competitive inhibition where a…
Many experiments in recent years have reported that, when exposed to their corresponding substrate, catalytic enzymes undergo enhanced diffusion as well as chemotaxis (biased motion in the direction of a substrate gradient). Among other…
In biochemical signaling, information is often encoded in oscillatory signals. However, the advantages of such a coding strategy over an amplitude encoding scheme of constant signals remain unclear. Here we study the dynamics of a simple…
The time taken for gene expression varies not least because proteins vary in length considerably. This paper uses an abstract, tuneable Boolean regulatory network model to explore gene expression time variation. In particular, it is shown…
We study a class of Stochastic Differential Equations (SDEs) with jumps modeling multistage Michaelis--Menten enzyme kinetics, in which a substrate is sequentially transformed into a product via a cascade of intermediate complexes. These…
The development of multicellular organisms relies on the precise coordination of molecular events across multiple spatial and temporal scales. Understanding how information flows from molecular interactions to cellular processes and tissue…
We study epidemic spreading processes in large networks, when the spread is assisted by a small number of external agents: infection sources with bounded spreading power, but whose movement is unrestricted vis-\`a-vis the underlying network…
There is currently growing interest in modeling the information diffusion on social networks across multi-disciplines. The majority of the corresponding research has focused on information diffusion independently, ignoring the network…
We introduce a novel method to analyse complete genomes and recognise some distinctive features by means of an adaptive compression algorithm, which is not DNA-oriented. We study the Information Content as a function of the number of…
[Background] Several studies have mentioned network modularity -- that a network can easily be decomposed into subgraphs that are densely connected within and weakly connected between each other -- as a factor affecting metabolic…
Engineered systems typically separate mechanical function from information processing, whereas biological systems can exploit physical structure as a medium for information processing and computation. Motivated by this contrast, recent work…
Living cells are continually exposed to environmental signals that vary in time. These signals are detected and processed by biochemical networks, which are often highly stochastic. To understand how cells cope with a fluctuating…
Regulatory networks consist of interacting molecules with a high degree of mutual chemical specificity. How can these molecules evolve when their function depends on maintenance of interactions with cognate partners and simultaneous…