Related papers: Protein Pattern Formation
A novel mechanism for cell differentiation is proposed, based on the dynamic clustering in a globally coupled chaotic system. A simple model with metabolic reaction, active transport of chemicals from media, and cell division is found to…
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…
We present a systematic study of the influence of cell geometry on the orientational distribution of microtubules (MTs) nucleated from a single microtubule organizing center (MTOC). For simplicity we consider an elliptical cell geometry, a…
Polariton condensation can be regarded as a self-organization phenomenon, where phase ordering is established among particles in the system. In such condensed systems, further ordering can possibly occur in the particle density…
Recent experiments have exploited elastic instabilities in membranes to create complex patterns. However, the rational design of such structures poses many challenges, as they are products of nonlinear elastic behavior. We pose a simple…
The bipolar organization of the microtubule-based mitotic spindle is essential for the faithful segregation of chromosomes in cell division. Despite our extensive knowledge of genes and proteins, the physical mechanism of how the ensemble…
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…
In this work we approach cell migration under a large-scale assumption, so that the system reduces to a particle in motion. Unlike classical particle models, the cell displacement results from its internal activity: the cell velocity is a…
Protein dynamics is a fundamental element to comprehend their biological functions. However, a theoretical picture providing microscopic-detail explanation of its relevant features is still missing. One of the outmost relevant properties…
In this paper, we consider the problem of forming machine cell in cellular manufacturing (CM). The major problem in the design of a CM system is to identify the part families and machine groups and consequently to form manufacturing cells.…
Endothelial cells are responsible for the formation of the capillary blood vessel network. We describe a system of endothelial cells by means of two-dimensional molecular dynamics simulations of point-like particles. Cells' motion is…
Inverse protein folding, the process of designing sequences that fold into a specific 3D structure, is crucial in bio-engineering and drug discovery. Traditional methods rely on experimentally resolved structures, but these cover only a…
Understanding complex biological macromolecules, especially proteins, is vital for grasping their diverse chemical functions with direct impact in biology and pharmacology. While techniques like X-ray crystallography and cryo-electron…
Active stresses in biological cells and tissues drive many developmental processes. However, increasing experimental evidence suggests that additional mechanical interactions with surrounding material can play a crucial role in guiding…
Eukaryotic cells maintain their inner order by a hectic process of distillation of molecular factors taking place on the surface of their lipid membranes. To understand the properties of this molecular sorting process, a physical model of…
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,…
Notch signaling is an evolutionary conserved cell-cell communication pathway. Besides regulating cell-fate decisions at an individual cell level, Notch signaling coordinates the emergent spatiotemporal patterning in a tissue through…
Proteins, essential to biological systems, perform functions intricately linked to their three-dimensional structures. Understanding the relationship between protein structures and their amino acid sequences remains a core challenge in…
Elucidating the neurophysiological mechanisms underlying neural pattern formation remains an outstanding challenge in Computational Neuroscience. In this paper, we address the issue of understanding the emergence of neural patterns by…
Microtubules self-organize to form part of the cellular cytoskeleton. They give cells their shape and play a crucial role in cell division and intracellular transport. Strikingly, microtubules driven by motor proteins reorganize into stable…