Related papers: Enzyme localization can drastically affect signal …

The more we learn about the cytoplasm of cells, the more we realise that the cytoplasm is not uniform but instead is highly inhomogeneous. In any inhomogeneous solution, there are concentration gradients, and particles move either up or…

We consider hexagonal cellular automata with immediate cell neighbourhood and three cell-states. Every cell calculates its next state depending on the integral representation of states in its neighbourhood, i.e. how many neighbours are in…

We introduce a topology-based nonlinear network model of protein dynamics with the aim of investigating the interplay of spatial disorder and nonlinearity. We show that spontaneous localization of energy occurs generically and is a…

Molecular agitation more rapid than thermal Brownian motion is reported for cellular environments, motor proteins, synthetic molecular motors, enzymes, and common chemical reactions, yet that chemical activity couples to molecular motion…

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…

This paper studies the mitigation of intersymbol interference in a diffusive molecular communication system using enzymes that freely diffuse in the propagation environment. The enzymes form reaction intermediates with information molecules…

In this perspective, we discuss where and how accounting for electronic many-body polarization affects the accuracy of classical molecular dynamics simulations of biomolecules.While the effects of electronic polarization are highly…

We have performed a statistical analysis of the spatial distribution of operons in the transcriptional regulation network of Escherichia coli. The analysis reveals that operons that regulate each other and operons that are coregulated tend…

Diffusion of transported particles in the intracellular medium is described by means of a generalized diffusion equation containing forces due to the cytoskeleton network and to the protein motors. We find that the enhanced diffusion…

Chemotaxis of enzymes in response to gradients in the concentration of their substrate has been widely reported in recent experiments, but a basic understanding of the process is still lacking. Here, we develop a microscopic theory for…

Control over molecular scale electrical properties within nano junctions is demonstrated, utilizing site-directed C60 targeting into protein macromolecules as a doping means. The protein molecules, self-assembled in a miniaturized…

Inspired by recent experiments on chromosomal dynamics, we introduce an exactly solvable model for the interaction between a flexible polymer and a set of motor-like enzymes. The enzymes can bind and unbind to specific sites of the polymer…

For many networks, it is useful to think of their nodes as being embedded in a latent space, and such embeddings can affect the probabilities for nodes to be adjacent to each other. In this paper, we extend existing models of synthetic…

We study the effect of the crowded nature of the cellular cytoplasm on the translocation of a polymer through a pore in a membrane. By systematically treating the entropic penalty due to crowding, we show that the translocation dynamics are…

In this paper, we apply dimensional analysis to study a diffusive molecular communication system that uses diffusing enzymes in the propagation environment to mitigate intersymbol interference. The enzymes bind to information molecules and…

We used various analytical and numerical techniques to elucidate signal propagation in a small enzymatic cascade which is subjected to external and internal noise. The nonlinear character of catalytic reactions, which underlie protein…

We show that atoms or molecules subject to fields that couple their internal and translational (momentum) states may undergo a crossover from randomization (diffusion) to strong localization (sharpening) of their momentum distribution. The…

Internet, social media, neuronal or blood vessel are organized in complex networks. These networks are characterized by several quantities such as the underlying graph connectivity (topology), how they grow in time, scaling laws or by the…

Transport of molecules across membrane channels is investigated theoretically using exactly solvable discrete stochastic site-binding models. It is shown that the interaction potential between molecules and the channel has a strong effect…

Living cells respond to spatial signals. Signal transmission to the cell interior often involves the release of second messengers like $Ca^{2+}$ . They will eventually trigger a physiological response by activating kinases that in turn…