Related papers: Sequential pattern formation governed by signaling…
Life presents fascinating examples of self-organization and emergent phenomena. In multi-cellular organisms, a multitude of cells interact to form and maintain highly complex body plans of well-defined size. In this thesis, we investigate…
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…
Visual segmentation is a key perceptual function that partitions visual space and allows for detection, recognition and discrimination of objects in complex environments. The processes underlying human segmentation of natural images are…
We propose a phenomenological model for pattern formation in a vertically vibrated layer of granular material. This model exhibits a variety of stable cellular patterns including standing rolls and squares as well as localized objects…
Under hard-agar and nutrient-rich conditions, a cell of $Bacillus$ $subtilis$ grows as a single filament owing to the failure of cell separation after each growth and division cycle. The self-elongating filament of cells shows sequential…
Gene networks exhibiting oscillatory dynamics are widespread in biology. The minimal regulatory designs giving rise to oscillations have been implemented synthetically and studied by mathematical modeling. However, most of the available…
Segments that span contiguous parts of inputs, such as phonemes in speech, named entities in sentences, actions in videos, occur frequently in sequence prediction problems. Segmental models, a class of models that explicitly hypothesizes…
Many patterning events in multi-cellular organisms rely on cell-to-cell contact signaling, such as the Notch pathway in metazoans. A particularly interesting phenomenon in this form of communication is lateral inhibition where a cell that…
Protein sequences serve as a natural record of the evolutionary constraints that shape their functional structures. We show that it is possible to use only sequence information to go beyond predicting native structures and global stability…
Sequential neuronal activity underlies a wide range of processes in the brain. Neuroscientific evidence for neuronal sequences has been reported in domains as diverse as perception, motor control, speech, spatial navigation and memory.…
We discovered a class of self-similar solutions in nonlinear models describing the formation of morphogen gradients, the concentration fields of molecules acting as spatial regulators of cell differention in developing tissues. These models…
From a coarse-grained perspective the motif of a self-activating species, activating a second species which acts as its own repressor, is widely found in biological systems, in particular in genetic systems with inherent oscillatory…
In the mammalian brain, many neuronal ensembles are involved in representing spatial structure of the environment. In particular, there exist cells that encode the animal's location and cells that encode head direction. A number of studies…
An autocatalytic pattern matching polymer system is studied as an abstract model for chemical ecosystem evolution. Highly ordered populations with particular sequence patterns appear spontaneously out of a vast number of possible states.…
Circadian clocks play a pivotal role in orchestrating numerous physiological and developmental events. Waveform shapes of the oscillations of protein abundances can be informative about the underlying biochemical processes of circadian…
Sensory perception (e.g. vision) relies on a hierarchy of cortical areas, in which neural activity propagates in both directions, to convey information not only about sensory inputs but also about cognitive states, expectations and…
Gene regulatory networks (GRNs) define the regulatory relationships among molecules such as transcription factors, chromatin remodelers, and target genes. GRNs play a critical role in diverse biological processes, including development,…
We propose a physical model for developmental process at cellular level to discuss the mechanism of epigenetic landscape. In our simplified model, a minimal model, the network of the interaction among cells generates the landscape…
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…
We study the effects of delayed coupling on timing and pattern formation in spatially extended systems of dynamic oscillators. Starting from a discrete lattice of coupled oscillators, we derive a generic continuum theory for collective…