Related papers: On the form of growing strings
The theory of elastic rods can be used to describe certain geometric and topological properties of the DNA molecules. A similar effective field theory approach was previously suggested to describe the conformations and dynamics of proteins.…
Aligned finger structures, with a characteristic width, emerges during the slow drainage of a liquid/granular mixture in a tilted Hele-Shaw cell. A transition from vertical to horizontal alignment of the finger structures is observed as the…
We examine the dynamical evolution of the state of a neurone, with particular care to the non-equilibrium nature of the forces influencing its movement in state space. We combine non-equilibrium statistical mechanics and dynamical systems…
During animal development and homeostasis, the structure of tissues, including muscles, blood vessels and connective tissues adapts to mechanical strains in the extracellular matrix (ECM). These strains originate from the differential…
The concept of evolutionary development of structures constituted a \emph{real} revolution in biology: it was possible to understand how the very complex structures of life can arise in an out-of-equilibrium system. The investigation of…
Statistical analysis of alignments of large numbers of protein sequences has revealed "sectors" of collectively coevolving amino acids in several protein families. Here, we show that selection acting on any functional property of a protein,…
In this work we employ various methods of analysis (unfolding simulations and comparative analysis of structures and sequences of proteomes of thermophilic organisms) to show that organisms can follow two major strategies of thermophilic…
We use numerical simulations to show how noninteracting hard particles binding to a deformable elastic shell may self-assemble into a variety of linear patterns. This is a result of the nontrivial elastic response to deformations of shells.…
Novel numerical techniques, validated by an analysis of barnase and chymotrypsin inhibitor, are used to elucidate the paramount role played by the geometry of the protein backbone in steering the folding to the correct native state. It is…
Branched structures that evolve over time critically determine the function of various natural and engineered systems, including growing vasculature, neural arborization, pulmonary networks such as lungs, river basins, power distribution…
The functioning of machines typically requires a concerted action of their parts. This requirement also holds for molecular motors that drive vital cellular processes and imposes constraints on their conformational changes as well as the…
Cellular phenotype is characterized by different components such as cell size, protein content and cell cycle time. These are global variables that are the outcome of multiple internal microscopic processes. Accordingly, they display some…
When a polymer solution is uniaxially stretched and held fixed at both ends, the solution quickly separates into droplets connected by strings and takes the beads-on-string structure. The string then becomes thinner by capillary forces.…
Disordered networks of semiflexible filaments are common support structures in biology. Familiar examples include fibrous matrices in blood clots, bacterial biofilms, and essential components of cells and tissues of plants, animals, and…
Many growing networks possess accelerating statistics where the number of links added with each new node is an increasing function of network size so the total number of links increases faster than linearly with network size. In particular,…
Prion and prion-like molecules are a type of self replicating aggregate protein that have been implicated in a variety of neurodegenerative diseases. Over recent decades the molecular dynamics of prions have been characterized both…
We study a large data set of protein structure ensembles of very diverse sizes determined by nuclear magnetic resonance. By examining the distance-dependent correlations in the displacement of residues pairs and conducting finite size…
Recently, unusual and strikingly beautiful seahorse-like growth patterns have been observed under conditions of quasi-two-dimensional growth. These `S'-shaped patterns strongly break two-dimensional inversion symmetry; however such broken…
The growth of multicomponent structures in simulations and experiments often results in kinetically trapped, nonequilibrium objects. In such cases we have no general theoretical framework for predicting the outcome of the growth process.…
We present a simple three-dimensional model to describe the autonomous expansion of a substrate which grows driven by the local mean curvature of its surface. The model aims to reproduce the nest construction process in arboreal…