Related papers: Cell-to-cell information at a feedback-induced bif…
Cells use biochemical networks to translate environmental information into intracellular responses. These responses can be highly dynamic, but how the information is encoded in these dynamics remains poorly understood. Here we investigate…
Inferring the directionality of interactions between cellular processes is a major challenge in systems biology. Time-lagged correlations allow to discriminate between alternative models, but they still rely on assumed underlying…
Living cells deploy many resources to sense their environments, including receptors, downstream signaling molecules, time and fuel. However, it is not known which resources fundamentally limit the precision of sensing, like weak links in a…
This paper considers an electro-chemical based communication model for intercellular communication in plants. Many plants, such as Mimosa pudica (the "sensitive plant"), employ electrochemical signals known as action potentials (APs) for…
We map a class of well-mixed stochastic models of biochemical feedback in steady state to the mean-field Ising model near the critical point. The mapping provides an effective temperature, magnetic field, order parameter, and heat capacity…
We present the results of detailed numerical study of a model for the sharing and sorting of informations in a community consisting of a large number of agents. The information gathering takes place in a sequence of mutual bipartite…
This Thesis explores how tools from Statistical Physics and Information Theory can help us describe and understand complex systems. In the first part, we study the interplay between internal interactions, environmental changes, and…
The interplay between two basic quantities -- quantum communication and information -- is investigated. Quantum communication is an important resource for quantum states shared by two parties and is directly related to entanglement.…
Biological information processing as implemented by regulatory and signaling networks in living cells requires sufficient specificity of molecular interaction to distinguish signals from one another, but much of regulation and signaling…
We extend the concept that life is an informational phenomenon, at every level of organisation, from molecules to the global ecological system. According to this thesis: (a) living is information processing, in which memory is maintained by…
In statistical physics entropy is usually introduced as a global quantity which expresses the amount of information that would be needed to specify the microscopic configuration of a system. However, for lattice models with infinitely many…
We show that when cells communicate by contact-mediated interactions, heterogeneity in cell shapes and sizes leads to qualitatively distinct collective behavior in the tissue. For inter-cellular coupling that implements lateral inhibition,…
The combination of protrusions and retractions in the movement of polarized cells leads to understand the effect of possible synchronisation between the two ends of the cells. This synchronisation, in turn, could lead to different dynamics…
Biological organisms are open, adaptve systems that can respond to changes in environment in specific ways. Adaptation and response can be posed as an optimization problem, with a tradeoff between the benefit obtained from a response and…
Biomolecules stochastically occupy different possible configurations with probabilities given by non-equilibrium steady-state distributions. These distributions are determined by the transition rate constants between different…
Inspired by biological communication systems, molecular communication has been proposed as a viable scheme to communicate between nano-sized devices separated by a very short distance. Here, molecules are released by the transmitter into…
The growth rate of organisms depends both on external conditions and on internal states, such as the expression levels of various genes. We show that to achieve a criterion mean growth rate over an ensemble of conditions, the internal…
Information thermodynamics relates the rate of change of mutual information between two interacting subsystems to their thermodynamics when the joined system is described by a bipartite stochastic dynamics satisfying local detailed balance.…
The rate of electron transfer between a molecular species and a metal, each at a different local temperature, is examined theoretically through implementation of a bithermal (characterized by two temperatures) Marcus formalism. Expressions…
Genetic regulatory networks enable cells to respond to the changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits…