Related papers: Protein Pattern Formation
Pattern formation in biological tissues plays an important role in the development of living organisms. Since the classical work of Alan Turing, a pre-eminent way of modelling has been through reaction-diffusion mechanisms. More recently,…
Proteins are macromolecules that perform essential functions in all living organisms. Designing novel proteins with specific structures and desired functions has been a long-standing challenge in the field of bioengineering. Existing…
Different models such as diffusion-collision and nucleation-condensation have been used to unravel how secondary and tertiary structures form during protein folding. However, a simple mechanism based on physical principles that provide an…
Filament formation by non-cytoskeletal enzymes has been known for decades, yet only relatively recently has its wide-spread role in enzyme regulation and biology come to be appreciated. This comprehensive review summarizes what is known for…
Nonequilibrium membrane pattern formation is studied using meshless membrane simulation. We consider that molecules bind to either surface of a bilayer membrane and move to the opposite leaflet by flip--flop. When binding does not modify…
Protein structure prediction has reached revolutionary levels of accuracy on single structures, yet distributional modeling paradigms are needed to capture the conformational ensembles and flexibility that underlie biological function.…
Protein structures in nature often exhibit a high degree of regularity (secondary structures, tertiary symmetries, etc.) absent in random compact conformations. We demonstrate in a simple lattice model of protein folding that structural…
In this article we highlight chemotaxis (cellular movement) as a rich source of potential engineering applications and computational models, highlighting current research and possible future work. We first give a brief description of the…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
One of the many ways cells transmit information within their volume is through steady spatial gradients of different proteins. However, the mechanism through which proteins without any sources or sinks form such single-cell gradients is not…
Proteins are the common constituents of all living cells. They are molecular machines that interact with each other as well as with other cell products and carry out a dizzying array of functions with distinction. These interactions follow…
Cellular functions are established through biological evolution, but are constrained by the laws of physics. For instance, the physics of protein folding limits the lengths of cellular polypeptide chains. Consequently, many cellular…
Bone-mass formation in human is looked at to understand the underlying dynamics with an eye on healing of bone-fracture and non-unions in non-invasive pathways. Three biological cells osteoblasts, osteoclasts and osteocytes are important…
We propose a continuum model for pattern formation, based on the multiphase model framework, to explore in vitro cell patterning within an extracellular matrix. We demonstrate that, within this framework, chemotaxis-driven cell migration…
In vivo and in vitro systems of cells and extra-cellular matrix (ECM) systems are well known to form ordered patterns of orientationally aligned fibers. Here, we interpret them as active analogs of the (disordered) isotropic to the…
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,…
The rheological properties of biological tissues are core to processes such as cancer metastasis, wound healing and embryo development. The emergence of tissue and organ structures during morphogenesis requires the precise formation of…
A key feature of many developmental systems is their ability to self-organize spatial patterns of functionally distinct cell fates. To ensure proper biological function, such patterns must be established reproducibly, by controlling and…
In this review, we discuss modularity and hierarchy in biological systems. We review examples from protein structure, genetics, and biological networks of modular partitioning of the geometry of biological space. We review theories to…
The emergence of spatial patterns and organized growth is a hallmark of developing tissues. While symmetry-breaking and scaling laws govern these processes, how cells coordinate spatial patterning with size regulation remains unclear. Here,…