Related papers: On the form of growing strings
Colloidal particles can self-assemble into various ordered structures in fluid flows that have potential applications in biomedicine, materials synthesis and encryption. These dynamic processes are also of fundamental interest for probing…
It has recently been discovered that many biological systems, when represented as graphs, exhibit a scale-free topology. One such system is the set of structural relationships among protein domains. The scale-free nature of this and other…
We solve several problems that involve imposing metrics on surfaces. The problem of a strip with a linear metric gradient is formulated in terms of a Lagrangean similar to those used for spin systems. We are able to show that the low energy…
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…
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…
The native conformation of structured proteins is stabilized by a complex network of interactions. We analyzed the elementary patterns that constitute such network and ranked them according to their importance in shaping protein sequence…
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…
Certain bacteria form filamentous colonies when the cells fail to separate after dividing. In Bacillus subtilis, Bacillus thermus, and cyanobacteria, the filaments can wrap into complex supercoiled structures as the cells grow. The…
Multicellular organisms comprise a diverse collection of stable tissues built from different cell types. It remains unclear how large numbers of interacting cells can precisely coordinate their gene expression during tissue…
In this paper we derive the general equilibrium equations of a polymer chain with a noncircular cross section by the variation of the free energy functional. From the equilibrium equation of the elastic ribbon we derive analytically the…
Self-assembly processes are widespread in nature, and lie at the heart of many biological and physical phenomena. The characteristics of self-assembly building blocks determine the structures that they form. Two crucial properties are the…
We develop a model of string dynamics with back-reaction from both scaling and non-scaling loops taken into account. The evolution of a string network is described by the distribution functions of coherence segments and kinks. We derive two…
Growth processes in many living organisms create thin, soft materials with an intrinsically hyperbolic geometry. These objects support novel types of mesoscopic defects - discontinuity lines for the second derivative and branch points -…
We review the recent fast progress in statistical physics of evolving networks. Interest has focused mainly on the structural properties of random complex networks in communications, biology, social sciences and economics. A number of giant…
The equilibrium structure of a Dinucleosome is studied using an elastic model that takes into account the force and torque balance conditions. Using the proper boundary conditions, it is found that the conformational energy of the problem…
Helical motifs are ubiquitious in macromolecular systems. The mechanism of spontaneous emergence of helicity is unknown, especially in cases where torsional interactions are absent. Emergence of helical order needs coordinated organization…
Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…
Phase separation has emerged as an essential concept for the spatial organization inside biological cells. However, despite the clear relevance to virtually all physiological functions, we understand surprisingly little about what phases…
The primary structure of proteins, that is their sequence, represents one of the most abundant set of experimental data concerning biomolecules. The study of correlations in families of co--evolving proteins by means of an inverse…
We argue that the stochastic dynamics of interacting agents which replicate, mutate and die constitutes a non-equilibrium physical process akin to aging in complex materials. Specifically, our study uses extensive computer simulations of…