Related papers: Physical Schemata Underlying Biological Pattern Fo…
We review the mathematical formalism underlying the modelling of stochasticity in biological systems. Beginning with a description of the system in terms of its basic constituents, we derive the mesoscopic equations governing the dynamics…
Proteins control many vital functions in living cells, such as cell growth and cell division. Reliable coordination of these functions requires the spatial and temporal organizaton of proteins inside cells, which encodes information about…
Essential life processes take place across multiple space and time scales in living organisms but understanding their mechanistic interactions remains an ongoing challenge. Advanced multiscale modeling techniques are providing new…
Biological systems, unlike physical or chemical systems, are characterized by the very inhomogeneous distribution of their components. The immune system, in particular, is notable for self-organizing its structure. Classically, the dynamics…
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…
Cellular bioelectricity describes the biological phenomenon in which cells in living tissue generate and maintain patterns of voltage gradients induced by differing concentrations of charged ions. A growing body of research suggests that…
Self-organization is ubiquitous in nature and mind. However, machine learning and theories of cognition still barely touch the subject. The hurdle is that general patterns are difficult to define in terms of dynamical equations and…
Spatial self-organization emerges in distributed systems exhibiting local interactions when nonlinearities and the appropriate propagation of signals are at work. These kinds of phenomena can be modeled with different frameworks, typically…
Biological sequences do not come at random. Instead, they appear with particular frequencies that reflect properties of the associated system or phenomenon. Knowing how biological sequences are distributed in sequence space is thus a…
In principle, all the natural systems such as biological, ecological and economical systems are structure-variable systems (in which some environment parameters are not fixed). In this Letter we show that data sequences from many…
From cytoskeletal networks to tissues, many biological systems behave as active materials. Their composition and stress-generation is affected by chemical reaction networks. In such systems, the coupling between mechanics and chemistry…
Control over the physical properties of materials is ubiquitously required in many fields. One means by which this can be achieved is controlling the internal structure of multi-component materials with an eye to enhancing mechanical…
How does growth encode form in developing organisms? Many different spatiotemporal growth profiles may sculpt tissues into the same target 3D shapes, but only specific growth patterns are observed in animal and plant development. In…
From the striped coats of zebras to the ripples in windblown sand, the natural world abounds with locally banded patterns. Such patterns have been of great interest throughout history, and, in the last twenty years, scientists in a wide…
We study non-equilibrium bacterial colony growth using a geometry-first, time-resolved analysis of morphology. From time-lapse microscopy data, we track the coupled evolution of area, perimeter, and boundary-sensitive shape descriptors…
Many developmental processes in biology utilize Notch-Delta signaling to construct an ordered pattern of cellular differentiation. This signaling modality is based on nearest-neighbor contact, as opposed to the more familiar mechanism…
In many tissues, cell type varies over single-cell length-scales, creating detailed spatial heterogeneities fundamental to physiological function. To gain understanding of this relationship between tissue function and detailed structure,…
Mathematical models of spatial population dynamics typically focus on the interplay between dispersal events and birth/death processes. However, for many animal communities, significant arrangement in space can occur on shorter timescales,…
We estimate density of defects frozen into a biological Turing pattern which was turned on at a finite rate. A self-locking of gene expression in individual cells, which makes the Turing transition discontinuous, stabilizes the pattern…
The structure and dynamics of tissue cultures depend strongly on the physical and chemical properties of the underlying substrate. Inspired by previous advances in the context of inorganic materials, the use of patterned culture surfaces…