Related papers: Distribution of volume, microvoid percolation, and…
Three-dimensional single-component ideal gas systems composed of model homogeneous rigid molecules in various molecular shapes and sizes are simulated by a molecular Monte Carlo simulation technique. We reveal that percolation thresholds of…
We consider the cluster and backbone mass distributions between two lines of arbitrary orientations and lengths in porous media in three dimensions, and model the porous media by bond percolation at the percolation threshold $p_c$. We…
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…
One of the basic problems in discrete geometry is to determine the most efficient packing of congruent replicas of a given convex set $K$ in the plane or in space. The most commonly used measure of efficiency is density. Several types of…
In this study, we present a method of pattern mining based on network theory that enables the identification of protein structures or complexes from synthetic volume densities, without the knowledge of predefined templates or human biases…
Size segregation in bedload transport is studied numerically with a coupled fluid-discrete element model. Starting from an initial deposit of small spherical particles on top of a large particle bed, the segregation dynamics of the bed is…
Several acquisitions of X-ray microtomography have been performed on a beads packing while it compacts under vertical vibrations. An image analysis allows to study the evolution of the packing structure during its progressive densification.…
A vertically shaken granular medium hosts a blade rotating around a fixed vertical axis, which acts as a mesorheological probe. At high densities, independently from the shaking intensity, the blade's dynamics show strong caging effects,…
The problem of diffusion in a porous medium with a spatially varying porosity is considered. The particular microstructure analyzed comprises a collection of impenetrable spheres, though the methods developed are general. Two different…
The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the…
The diffusion of particles trapped in long narrow channels occurs predominantly in one dimension. Here, molecular dynamics simulation is used to study the inertial dynamics of two-dimensional hard disks, confined to long, narrow,…
Proteins are composed of chains of amino acids that fold into complex three-dimensional structures. Several key features, such as the radius of gyration, fraction of core amino acids $f_{\rm core}$, packing fraction $\langle \phi\rangle$ of…
In this work we examine how volume exclusion caused by regions of high chromatin density might influence the time required for proteins to find specific DNA binding sites. The spatial variation of chromatin density within mouse olfactory…
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…
An analysis of the general concept of volume variation partition of a porous body is presented, introducing the breathing coefficient, defined as the ratio of two volume variations. Considering a total volume of a porous body, composed of…
In nature the three-dimensional structure of a protein is encoded in the corresponding gene. In this paper we describe a new method for encoding the three-dimensional structure of a protein into a binary sequence. The feature of the method…
We present a geometry-independent method for determining the shapes of radial volume density profiles of astronomical objects whose geometries are unknown, based on a single column density map. Such profiles are often critical to understand…
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,…
A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains…
We use coarse grained molecular dynamics simulations to investigate diffusion properties of sheared lipid membranes with embedded transmembrane proteins. In membranes without proteins, we find normal in-plane diffusion of lipids in all flow…