Related papers: Michaelis-Menten Relations for Complex Enzymatic N…
The major biochemical networks of the living cell, the network of interacting genes and the network of biochemical reactions, are highly interdependent, however, they have been studied mostly as separate systems so far. In the last years an…
Autocatalytic chemical networks play a predominant role in a large number of natural systems such as in metabolic pathways and in ecological networks. Despite recent efforts, the precise impact of thermodynamic constraints on these networks…
We consider Markov processes, which describe e.g. queueing network processes, in a random environment which influences the network by determining random breakdown of nodes, and the necessity of repair thereafter. Starting from an explicit…
We provide a detailed multiscale analysis of a system of particles interacting through a dynamical network of links. Starting from a microscopic model, via the mean field limit, we formally derive coupled kinetic equations for the particle…
We perform experiments and phase model simulations with a ring network of oscillatory electrochemical reactions to explore the effect of random connections and non-isochronocity of the interactions on the pattern formation. A few additional…
One of the main tasks of post-genomic informatics is to systematically investigate all molecules and their interactions within a living cell so as to understand how these molecules and the interactions between them relate to the function of…
Electric circuits manipulate electric charge and magnetic flux via a small set of discrete components to implement useful functionality over continuous time-varying signals represented by currents and voltages. Much of the same…
A simple model for the formation of the polymer-enzyme conjugates has been proposed and described using corresponding extension of the Wertheim's first-order thermodynamic perturbation theory (TPT1) for the system of associating chain…
Over the last two decades, network science has greatly advanced our understanding of how the collective behaviors of a complex system emerge from the interactions among its basic units. Multiplex networks, i.e. networks with many layers,…
Starting from the detailed catalytic mechanism of a biocatalyst we provide a coarse-graining procedure which, by construction, is thermodynamically consistent. This procedure provides stoichiometries, reaction fluxes (rate laws), and…
Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…
The control of chemical reactions is a recurring theme in physics and chemistry. Traditionally, chemical reactions have been investigated by tuning thermodynamic parameters, such as temperature or pressure. More recently, physical methods…
Complex networks describe a wide range of systems in nature and society. Frequently cited examples include Internet, WWW, a network of chemicals linked by chemical reactions, social relationship networks, citation networks, etc. The…
In nonequilibrium chemical reaction systems, a fundamental relationship between unbalanced kinetic one-way fluxes and thermodynamic chemical driving forces is believed to exists. However this relation has been rigorously demonstrated only…
This paper deals with temporal enzyme distribution in the activation of biochemical pathways. Pathway activation arises when production of a certain biomolecule is required due to changing environmental conditions. Under the premise that…
We present a simple mathematical framework for the description of the dynamics of glassy systems in terms of a random walk in a complex energy landscape pictured as a network of minima. We show how to use the tools developed for the study…
A model multilevel molecule described by two sets of rotational internal energy levels of different parity and degenerate ground states, coupled by a constant interaction, is considered, by assuming that the random collisions in a gas of…
There are many processes in biology in which mechanical forces are generated. Force-bearing networks can transduce locally developed mechanical signals very extensively over different parts of the cell or tissues. In this article we conduct…
The driving force for active physical and biological systems is determined by both the underlying landscape and the non-equilibrium curl flux. While landscape can be quantified in the experiments by the histograms of the collecting…
We demonstrate and characterize a first-principles approach to modeling the mass action dynamics of metabolism. Starting from a basic definition of entropy expressed as a multinomial probability density using Boltzmann probabilities with…