Related papers: Effect of macromolecular crowding on the rate of d…
Chaotic internal degrees of freedom of a molecule can act as noise and affect the diffusion of the molecule on a substrate. A separation of time scales between the fast internal dynamics and the slow motion of the centre of mass on the…
The reversible reactions like A+B <-> C in the many-component diffusive system affect the diffusive properties of the constituents. The effective conjugation of irreversible processes of different dimensionality takes place due to the…
Cell reproduction involves replication of diverse molecule species, in contrast to simple replication system with fewer components. Here, we address why such diversity is sustained despite the efficiency of simple replication systems, using…
A molecule traveling in a realistic propagation environment can experience stochastic interactions with other molecules and the environment boundary. The statistical behavior of some isolated phenomena, such as dilute unbounded molecular…
We discuss effects of the stepping kinetics of molecular motors on their traffic behavior on crowded filaments using a simple two-state chemomechanical cycle. While the general traffic behavior is quite robust with respect to the detailed…
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…
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…
Aggregation and fragmentation of single molecules in the cell environment lead to a spectrum of diffusivities and to statistical laws of movement very different from typical Brownian motion. Current models of intracellular transport do not…
Bacteria and plankton populations living in oceans and lakes reproduce and die under the in- fluence of turbulent currents. Turbulent transport interacts in a complex way with the dynamics of populations because the typical reproduction…
Molecular dynamics simulations are used to show that strong magnetization significantly increases the space and time scales associated with interparticle correlations. The physical mechanism responsible is a channeling effect whereby…
One of the important challenges facing high resolution molecular dynamics calculations is to reproduce biological functions that occur in the macroscopic world and involve macroscopic variables. Some of these functions can be well described…
30% of the DNA in E. coli bacteria is covered by proteins. Such high degree of crowding affect the dynamics of generic biological processes (e.g. gene regulation, DNA repair, protein diffusion etc.) in ways that are not yet fully…
We study a two-species bidirectional exclusion process, and a single species variant, which is motivated by the motion of organelles and vesicles along microtubules. Specifically, we are interested in the clustering of the particles and…
Dynamical reaction-diffusion processes and meta-population models are standard modeling approaches for a wide variety of phenomena in which local quantities - such as density, potential and particles - diffuse and interact according to the…
We study the ability to maintain information in a population of reacting polymers under the influence of decay, i.e., spontaneous breakdown of large polymers. At a certain decay rate, it becomes impossible to maintain a significant…
The glassy cytoplasm, crowded with bio-macromolecules, is fluidized in living cells by mechanical energy derived from metabolism. Characterizing the living cytoplasm as a non-equilibrium system is crucial in elucidating the intricate…
In this paper, influence of crowding by inert particles on the geminate reaction kinetics is theoretically investigated. Time evolution equations for the survival probability of a geminate pair are derived from the master equation taking…
An ensemble of directed macromolecules on a lattice is considered, where the constituting molecules are chosen as a random sequence of N different types. The same type of molecules experiences a hard-core (exclusion) interaction. We study…
Periodic reversals of the direction of motion in systems of self-propelled rod shaped bacteria enable them to effectively resolve traffic jams formed during swarming and maximize their swarming rate. In this paper, a connection is found…
Complex biological and physical transport processes are often described through systems of interacting particles. Excluded-volume effects on these transport processes are well studied, however the interplay between volume exclusion and…