Related papers: Pattern localization to a domain edge
Protein structure prediction remains to be an open problem in bioinformatics. There are two main categories of methods for protein structure prediction: Free Modeling (FM) and Template Based Modeling (TBM). Protein threading, belonging to…
Proteins, by virtue of their central role in most biological processes, represent one of the key subjects of the study of molecular evolution. Inherent to the indispensability of proteins for living cells is the fact that a given protein…
Understanding how proteins structurally interact is crucial to modern biology, with applications in drug discovery and protein design. Recent machine learning methods have formulated protein-small molecule docking as a generative problem…
Since its foundations, more than one hundred years ago, the field of structural biology has strived to understand and analyze the properties of molecules and their interactions by studying the structure that they take in 3D space. However,…
The goal of structure-based drug discovery is to find small molecules that bind to a given target protein. Deep learning has been used to generate drug-like molecules with certain cheminformatic properties, but has not yet been applied to…
Proteins perform critical processes in all living systems: converting solar energy into chemical energy, replicating DNA, as the basis of highly performant materials, sensing and much more. While an incredible range of functionality has…
This paper investigates steady state solutions of a vasculogenesis model governed by coupled partial differential equations in a bounded two dimensional domain. Explicit steady state solutions are analytically constructed, and their…
The reaction-diffusion models have been extensively applied to explain the mechanism of pattern formations in early embryogenesis based on geometrically confined microtissues consisting of human pluripotent stem cells. Recently, mechanical…
Spatiotemporal patterns are common in biological systems. For electrically-coupled cells previous studies of pattern formation have mainly used external forcing as the main bifurcation parameter. The purpose of this paper is to show that…
We propose a model for cell polarization as a response to an external signal which results in a system of PDEs for different variants of a protein on the cell surface and interior respectively. We study stationary states of this model in…
Pattern formation, arising from systems of autonomous reaction-diffusion equations, on networks has become a common topic of study in the scientific literature. In this work we focus primarily on directed networks. Although some work prior…
Theories of localised pattern formation are important to understand a broad range of natural patterns, but are less well-understood than more established mechanisms of domain-filling pattern formation. Here, we extend recent work on pattern…
We performed an extensive numerical study of a two-dimensional reaction-diffusion system of the activator-inhibitor type in which domain patterns can form. We showed that both multidomain and labyrinthine patterns may form spontaneously as…
In this work, the influence of geometry and domain size on spatiotemporal pattern formation is investigated to establish parameter spaces for a cross-diffusive reaction-diffusion model on an annulus. By applying linear stability theory, we…
The response of proteins to chemical reactions or impulsive excitation that occurs within the molecule has fascinated chemists for decades. In recent years ultrafast X-ray studies have provided ever more detailed information about the…
This review is a tutorial for scientists interested in the problem of protein structure prediction, particularly those interested in using coarse-grained molecular dynamics models that are optimized using lessons learned from the energy…
Construction of a scaffold structure that supports a desired motif, conferring protein function, shows promise for the design of vaccines and enzymes. But a general solution to this motif-scaffolding problem remains open. Current…
Diffusion-driven instability is a fundamental mechanism underlying pattern formation in spatially extended systems. In almost all existing works, diffusion across the links of the underlying network is modeled through scalar weights,…
Protein structure prediction is one of the most important problems in computational biology. The most successful computational approach, also called template-based modeling, identifies templates with solved crystal structures for the query…
Recently described stochastic models of protein evolution have demonstrated that the inclusion of structural information in addition to amino acid sequences leads to a more reliable estimation of evolutionary parameters. We present a…