Related papers: Physics and modelling of intracellular diffusion
We calculate the diffusion coefficient of an active tracer in a schematic crowded environment, represented as a lattice gas of passive particles with hardcore interactions. Starting from the master equation of the problem, we put forward a…
Reaction-diffusion processes are the foundational model for a diverse range of complex systems, ranging from biochemical reactions to social agent-based phenomena. The underlying dynamics of these systems occur at the individual…
The spatio-temporal dynamics of a population present one of the most fascinating aspects and challenges for ecological modelling. In this article we review some simple mathematical models, based on one dimensional…
We introduce and analyze a model for the transport of particles or energy in extended lattice systems. The dynamics of the model acts on a discrete phase space at discrete times but has nonetheless some of the characteristic properties of…
The response of cells during spreading and motility is dictated by several multi-physics events, which are triggered by extracellular cues and occur at different time-scales. For this sake, it is not completely appropriate to provide a cell…
Different families of models first developed for fluid mechanics have been extended to road, pedestrian, or intracellular transport. These models allow to describe the systems at different scales and to account for different aspects of…
The hydrodynamic effects of macromolecular crowding inside cells is often studied in vitro by using polymers as crowding reagents. Confinement of polymers inside cell-sized droplets has been shown to affect the diffusion of small molecules.…
Intracellular protein patterns govern essential cellular functions by dynamically redistributing proteins between membrane-bound and cytosolic states, conserving their total numbers. This review presents a theoretical framework for…
To maintain homeostasis, living cells process information with networks of interacting molecules. Traditional models for cellular information processing have focused on networks of chemical reactions between molecules. Here, we describe how…
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…
Numerical investigation of the interaction of electromagnetic fields with eukaryotic cells requires specifically adapted computer models. Virtual microdosimetry, used to investigate exposure, requires volumetric cell models, which are…
Probing the transport of fluids within confined domains is important in many areas including material science, catalysis, food science, and cell biology. The diffusion propagator fully characterizes the diffusion process, which is highly…
Over the past decade, advances in super-resolution microscopy and particle-based modeling have driven an intense interest in investigating spatial heterogeneity at the level of single molecules in cells. Remarkably, it is becoming clear…
Models of particle propagation in causal set theory are investigated through simulations. For the swerves model the simulations are shown to agree with the expected continuum diffusion behaviour. Given the limitations on the simulated…
Chemical reactions inside cells are generally considered to happen within fixed-size compartments. Needless to say, cells and their compartments are highly dynamic. Thus, such stringent assumptions may not reflect biochemical reality, and…
The physical and chemical environment inside cells is of fundamental importance to all life but has traditionally been difficult to determine on a subcellular basis. Here we combine cutting-edge genomically integrated FRET biosensing to…
The combination of protrusions and retractions in the movement of polarized cells leads to understand the effect of possible synchronisation between the two ends of the cells. This synchronisation, in turn, could lead to different dynamics…
Cellular signaling is essential in information processing and decision making. Therefore, a variety of experimental approaches have been developed to study signaling on bulk and single-cell level. Single-cell measurements of signaling…
We study diffusion in systems of classical particles whose dynamics conserves the total center of mass. This conservation law leads to several interesting consequences. In finite systems, it allows for equilibrium distributions that are…
We perform molecular dynamic simulations of liquid nanoparticles deposited on a disordered substrate. The motion of the nanoparticle is characterised by a 'stick and roll' diffusive process. Long simulation times ($\simeq \mu s$), analysis…