Related papers: Spatio-temporal patterns of active epigenetic turn…
The actomyosin cortex, a thin layer of a cross-linked polymer network near the cell surface, generates active forces that are responsible for cell shape changes. Many developmental processes that involve such cell shape changes, most…
The spatial structure of the cell is highly organized at all levels: from small complexes and assemblies, to local nano- and micro-clusters, to global, micrometer scales across and between cells. We suggest that this multiscale spatial cell…
Interactions between neighboring cells are essential for generating or refining patterns in a number of biological systems. We propose a discrete filtering approach to predict how networks of cells modulate spatially varying input signals…
The spatial positioning of chromosomes relative to functional nuclear bodies is intertwined with genome functions such as transcription. However, the sequence patterns and epigenomic features that collectively influence chromatin spatial…
Cell plasma membranes display a dramatically rich structural complexity characterized by functional sub-wavelength domains with specific lipid and protein composition. Under favorable experimental conditions, patterned morphologies can also…
We propose a modelling framework to analyse the stochastic behaviour of heterogeneous, multi-scale cellular populations. We illustrate our methodology with a particular example in which we study a population with an oxygen-regulated…
Machines are designed, assembled, and programmed to convert power into predetermined dynamics and functions. In contrast, living systems such as interacting cells and animal groups self-organize, synchronize, and perform complex tasks…
We numerically study stochastic resonance in the unzipping of a model double-stranded DNA by a periodic force. We observe multiple peaks in stochastic resonance in the output signal as the driving force frequency is varied for different…
Interrogating the evolution of biological changes at early stages of life requires longitudinal profiling of molecules, such as DNA methylation, which can be challenging with children. We introduce a probabilistic and longitudinal machine…
The onset of life is often framed around membrane bound compartments and encoded metabolism, leaving unresolved how spatial organization arose before stable boundaries. In this context, environmental gradients are usually treated as…
Biomolecular condensates constitute a newly recognized form of spatial organization in living cells. Although many condensates are believed to form as a result of phase separation, the physicochemical properties that determine the phase…
Fluorescence microscopy reveals that the contents of many (membrane-free) nuclear "bodies" exchange rapidly with the soluble pool whilst the underlying structure persists; such observations await a satisfactory biophysical explanation. To…
We study the phase diagram of the sine circle map lattice with random initial conditions and identify the various types of dynamical behaviour which appear here. We focus on the regions which show spatio-temporal intermittency and…
One of the hypothesized functions of biomolecular condensates is to act as chemical reactors, where chemical reactions can be modulated, i.e. accelerated or slowed down, while substrate molecules enter and products exit from the condensate.…
Three-dimensional interphase organization of metazoan genomes has been linked to cellular identity. However, the principles governing 3D interphase genome architecture and its faithful transmission through disruptive events of cell-cycle,…
Telomeres are repetitive sequences of nucleotides at the end of chromosomes, whose evolution over time is intrinsically related to biological ageing. In most cells, with each cell division, telomeres shorten due to the so-called end…
The phase diagram of a water solution of DNA and oppositely charged spherical macroions is studied. DNA winds around spheres to form beads-on-a-string complexes resembling the chromatin 10 nm fiber. At small enough concentration of spheres…
Living cells exhibit a complex organization comprising numerous compartments, among which are RNA- and protein-rich membraneless, liquid-like organelles known as biomolecular condensates. Energy-consuming processes regulate their formation…
The phase ordering dynamics of coupled chaotic bistable maps on lattices with defects is investigated. The statistical properties of the system are characterized by means of the average normalized size of spatial domains of equivalent spin…
The persistent dynamics in systems out of equilibrium, particularly those characterized by annihilation and creation of topological defects, is known to involve complicated spatiotemporal processes and is deemed difficult to control. Here…