Related papers: Optimization of collective enzyme activity via spa…
We study analytically kinetics of an elementary bimolecular reaction scheme of the Langmuir-Hinshelwood type taking place on a d-dimensional catalytic substrate. We propose a general approach which takes into account explicitly the…
A hallmark of a plethora of intracellular signaling pathways is the spatial separation of activation and deactivation processes that potentially results in precipitous gradients of activated proteins. The classical Metabolic Control…
In this paper, we propose adding enzymes to the propagation environment of a diffusive molecular communication system as a strategy for mitigating intersymbol interference. The enzymes form reaction intermediates with information molecules…
A relationship between the preexponent of the rate constant and the distribution over activation barrier energies for enzymatic/protein reactions is revealed. We consider an enzyme solution as an ensemble of individual molecules with…
To understand the system-wide organization of metabolism, different lines of study have devised different categorizations of metabolites. The relationship and difference between categories can provide new insights for a more detailed…
Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into…
Localization phenomena permeate many branches of physics playing a fundamental role on dynamical processes evolving on heterogeneous networks. These localization analyses are frequently grounded, for example, on eigenvectors of adjacency or…
A comparison is made between conventional Michaelis-Menten kinetics and two models that take into account the duration of the conformational changes that take place at the molecular level during the catalytic cycle of a monomer. The models…
Biochemical covalent modification networks exhibit a remarkable suite of steady state and dynamical properties such as multistationarity, oscillations, ultrasensitivity and absolute concentration robustness. This paper focuses on conditions…
The presence of a phase transition in a finite system can be deduced, together with its order, from the shape of the distribution of the order parameter. This issue has been extensively studied in multifragmentation experiments, with…
The propagation of signalling molecules within cellular networks is affected by network topology, but also by the spatial arrangement of cells in the networks. Understanding the collective reaction--diffusion behaviour in space of signals…
Many functional units in biology, such as enzymes or molecular motors, are composed of several subunits that can reversibly assemble and disassemble. This includes oligomeric proteins composed of several smaller monomers, as well as protein…
Recently, we described a pathway analysis technique (paper 1) for analyzing generic schemes for single-molecule kinetics based upon the first-passage time distribution. Here, we employ this method to derive expressions for the Poisson…
The role of dimensionality (Euclidean versus fractal), spatial extent, boundary effects and system topology on the efficiency of diffusion-reaction processes involving two simultaneously-diffusing reactants is analyzed. We present…
Natural selection has shaped the evolution of cells and multi-cellular organisms such that social cooperation can often be preferred over an individualistic approach to metabolic regulation. This paper extends a framework for dynamic…
Cellular metabolism, the integrated interconversion of thousands of metabolic substrates through enzyme-catalyzed biochemical reactions, is the most investigated complex intercellular web of molecular interactions. While the topological…
When a system is in equilibrium, external perturbations yield a time series of non-equilibrium distributions, and recent experimental techniques give access to the non-equilibrium data that may contain critical information. Jinwoo and…
Elementary flux modes (EFMs) are pathways through a metabolic reaction network that connect external substrates to products. Using EFMs, a metabolic network can be transformed into its macroscopic counterpart, in which the internal…
Biochemical reactions typically occur at low copy numbers, but at once in crowded and diverse environments. Space and stochasticity therefore play an essential role in biochemical networks. Spatial-stochastic simulations have become a…
Single enzyme chemotaxis is a phenomenon by which a non-equilibrium spatial distribution of an enzyme is created and maintained by concentration gradients of the substrate and product of the catalyzed reaction. These gradients can arise…