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Diverse processes--e.g. bioremediation, biofertilization, and microbial drug delivery--rely on bacterial migration in disordered, three-dimensional (3D) porous media. However, how pore-scale confinement alters bacterial motility is unknown…
Stochastic dynamics govern many important processes in cellular biology, and an underlying theoretical approach describing these dynamics is desirable to address a wealth of questions in biology and medicine. Mathematical tools exist for…
We study a generic model for the polarisation and motility of self-propelled soft objects, biological cells or biomimetic systems, interacting with a viscous substrate. The active forces generated by the cell on the substrate are modelled…
We study the stochastic hydrodynamics of colonies of flagellated swimming cells, typified by multicellular choanoflagellates, which can form both rosette and chainlike shapes. The objective is to link cell-scale dynamics to colony-scale…
A cell is polarised when it has developed a main axis of organisation through the reorganisation of its cytosqueleton and its intracellular organelles. Polarisation can occur spontaneously or be triggered by external signals, like gradients…
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…
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 activity of growing living bacteria was investigated using real-time and in situ rheology -- in stationary and oscillatory shear. Two different strains of the human pathogen Staphylococcus aureus -- strain COL and its isogenic cell wall…
In bacteria such as $\textit{Escherichia coli}$, DNA is compacted into a nucleoid near the cell center, while ribosomes$-$molecular complexes that translate messenger RNAs (mRNAs) into proteins$-$are mainly localized at the poles. We study…
Cell-to-cell variability is inherent to numerous biological processes, including cell migration. Quantifying and characterizing the variability of migrating cells is challenging, as it requires monitoring many cells for long time windows…
Experimental studies of cell motility in culture have shown that under adequate conditions these living organisms possess the ability to organize themselves into complex structures. Such structures may exhibit a synergy that greatly…
In this paper, we proposed a stochastic model which describes two species of particles moving in counterflow. The model generalizes the theoretical framework describing the transport in random systems since particles can work as mobile…
A toggle switch consists of two genes that mutually repress each other. This regulatory motif is active during cell differentiation and is thought to act as a memory device, being able to choose and maintain cell fate decisions. In this…
We study the dynamics of a Brownian motion with a diffusion coefficient which evolves stochastically. We first study this process in arbitrary dimensions and find the scaling form and the corresponding scaling function of the position…
Hard sphere suspensions are well recognized model systems of statistical physics and soft condensed matter. We here investigate the temporal evolution of the immediate environment of nucleating and growing crystals and/or their global scale…
We investigate a model for spatial epidemics explicitly taking into account bi-directional movements between base and destination locations on individual mobility networks. We provide a systematic analysis of generic dynamical features of…
Animal movement exhibits complex behavior which can be influenced by unobserved environmental conditions. We propose a model which allows for a spatially-varying movement rate and spatially-varying drift through a semiparametric potential…
Cytotoxic T lymphocytes (T cells) and natural killer cells form a tight contact, the immunological synapse (IS), with target cells, where they release their lytic granules containing perforin/granzyme and cytokine containing vesicles.…
We address the problem of proteasomal protein translocation and introduce a new stochastic model of the proteasomal digestion (cleavage) of proteins. In this model we account for the protein translocation and the positioning of cleavage…
We discuss the problem of proteasomal degradation of proteins. Though proteasomes are important for all aspects of the cellular metabolism, some details of the physical mechanism of the process remain unknown. We introduce a stochastic…