Related papers: Void distributions reveal structural link between …
We carry out a coarse-grained molecular dynamics simulation of phospholipid vesicles with transmembrane proteins. We measure the mean and Gaussian curvatures of our protein-embedded vesicles and quantitatively show how protein clusters…
What are the molecular mechanisms that dictate protein-protein binding stability and whether those are related to the ones behind protein fold stability are still largely open questions. Indeed, despite many past efforts, we still lack…
Numerous studies have investigated the differences and similarities between protein structures determined by solution NMR spectroscopy and those determined by x-ray crystallography. A fundamental question is whether any observed differences…
It is not merely the position of residues that are of utmost importance in protein function and stability, but the interactions between them. We illustrate, by using a network construction on a set of 595 non-homologous proteins, that…
Spatial organization of proteins in cells is important for many biological functions. In general, the nonlinear, spatially coupled models for protein-pattern formation are only accessible to numerical simulations, which has limited insight…
What are the structural determinants of protein sequence evolution? A number of site-specific structural characteristics have been proposed, most of which are broadly related to either the density of contacts or the solvent accessibility of…
The behavior of a system of two-dimensional elongated particles (discorectangles) packed into a slit between two parallel walls was analyzed using a simulation approach. The packings were produced using the random sequential adsorption…
CONTEXT: Cosmic voids are observed in the distribution of galaxies and, to some extent, in the dark matter distribution. If these distributions have fractal geometry, it must be reflected in the geometry of voids; in particular, we expect…
Lattice-model simulations and experiments of some small proteins suggest that folding is essentially controlled by a few conserved contacts. Residues of these conserved contacts form the minimum set of native contacts needed to ensure…
Topological properties of native folds are obtained from statistical analysis of 160 low homology proteins covering the four structural classes. This is done analysing one, two and three-vertex joint distribution of quantities related to…
The large-scale matter distribution represents a complex network of structure elements such as voids, clusters, filaments, and sheets. This network is spanned by a point distribution. The global properties of the point process can be…
Voids are a prominent feature of the galaxy distribution but their quantitative study is hindered by the lack of a precise definition of what constitutes a void. Here we propose a definition of voids in point distributions that uses methods…
The three dimensional structure of a protein is an outcome of the interactions of its constituent amino acids in 3D space. Considering the amino acids as nodes and the interactions among them as edges we have constructed and analyzed…
We numerically study the structure of the interactions occurring in three-dimensional systems of hard spheres at jamming, focusing on the large-scale behavior. Given the fundamental role they play in the configuration of jammed packings, we…
From the analysis of sizes of approximately 130 small icosahedral viruses we find that there is a typical structural capsid protein, having a mean diameter of 5 nm and a mean thickness of 3 nm, with more than two thirds of the analyzed…
We investigate the two-dimensional packing of extremely prolate (aspect ratio $\alpha=L/D>10$) granular materials, comparing experiments with Monte-Carlo simulations. The average packing fraction of particles with aspect ratio $\alpha=12$…
We study how well void-finding algorithms identify cosmic void regions and whether we can quantitatively and qualitatively compare the voids they find with dynamical information from the underlying matter distribution. Using the ORIGAMI…
Packing problems have been a source of fascination for millenia and their study has produced a rich literature that spans numerous disciplines. Investigations of hard-particle packing models have provided basic insights into the structure…
We numerically analyse the density field of three-dimensional randomly jammed packings of monodisperse soft frictionles spherical particles, paying special attention to fluctuations occurring at large lengthscales. We study in detail the…
Exploring and understanding the protein-folding problem has been a long-standing challenge in molecular biology. Here, using molecular dynamics simulation, we reveal how parallel distributed adjacent planar peptide groups of unfolded…