Related papers: Information Transmission and Processing in G-Prote…
In order to respond to environmental signals, cells often use small molecular circuits to transmit information about their surroundings. Recently, motivated by concrete examples in signaling and gene regulation, a body of work has focused…
Living cells must control the reading out or "expression" of information encoded in their genomes, and this regulation often is mediated by transcription factors--proteins that bind to DNA and either enhance or repress the expression of…
Virtually all cells use energy and ion-specific membrane pumps to maintain large transmembrane gradients of Na$^+$, K$^+$, Cl$^-$, Mg$^{++}$, and Ca$^{++}$. Although they consume up to 1/3 of a cell's energy budget, the corresponding…
Biological Petri Nets (Bio-PNs) require extensions beyond classical formalism to capture biochemical reality: multiple reactions simultaneously affect shared metabolites through convergent production or regulatory coupling, while signal…
We study the phase transition of the Ising model in networks with core-periphery structures. By Monte Carlo simulations, we show that prior to the order-disorder phase transition the system organizes into an inhomogeneous intermediate phase…
Quantum information processing exploits all the features quantum mechanics offers. Among them there is the possibility to induce nonlinear maps on a quantum system by involving two or more identical copies of the given system in the same…
The first-order transition of the charge-transfer complex TTF-CA (tetrathiafulvalene-chloranil) is both a neutral-ionic and a Peierls transition. In related organic charge transfer complexes, cooling at ambient pressure increases the…
The thermodynamic entropy of coarse-grained (CG) models stands as one of the most important properties for quantifying the missing information during the CG process and for establishing transferable (or extendible) CG interactions. However,…
In this paper, we study the problem of formation keeping of a network of strictly passive systems when very coarse information is exchanged. We assume that neighboring agents only know whether their relative position is larger or smaller…
Computation in the brain involves multiple types of neurons, yet the organizing principles for how these neurons work together remain unclear. Information theory has offered explanations for how different types of neurons can optimize the…
An influence of nonlinear interference processes at quantum transitions under strong resonance electromagnetic fields on absorption, amplification and refractive indices as well as on four-wave mixing processes is investigated. Doppler…
We propose a new way of investigating phase transitions in the context of information theory. We use an information-entropic measure of spatial complexity known as configurational entropy (CE) to quantify both the storage and exchange of…
Given the stochastic nature of gene expression, genetically identical cells exposed to the same environmental inputs will produce different outputs. This heterogeneity has been hypothesized to have consequences for how cells are able to…
Physics perfectly describes neuronal operation, provided that we take into account that biology uses slow, positively charged ions rather than electrons as charge carriers and remove untested ad hoc hypotheses that contradict science's…
A toggle switch consists of two genes that mutually repress each other. This regulatory motif is active during cell differentiation and is thought to act as a memory device, being able to choose and maintain cell fate decisions. In this…
The so-called Mixed Feedback Loop (MFL) is a small two-gene network where protein A regulates the transcription of protein B and the two proteins form a heterodimer. It has been found to be statistically over-represented in statistical…
Living cells display a remarkable capacity to compartmentalize their functional biochemistry. A particularly fascinating example is the cell nucleus. Exchange of macromolecules between the nucleus and the surrounding cytoplasm does not…
The Unfolded Protein Response is the cell mechanism for maintaining the balance of properly folded proteins in the endoplasmic reticulum , the specialized cellular compartment. Although it is largely studied from a biological point of view,…
Fluctuations in biochemical networks, e.g., in a living cell, have a complex origin that precludes a description of such systems in terms of bipartite or multipartite processes, as is usually done in the framework of stochastic and/or…
This paper investigates voltage stability in inverter-based power systems concerning fold and saddle-node bifurcations. An analytical expression is derived for the sensitivity of the stability margin using the normal vector to the…