Related papers: Distribution of volume, microvoid percolation, and…
This note presents a simulation method for investigating the relationship between porosity and particle size distribution in porous media characterization. The method simulates particle packing based on particle size distributions,…
We analyzed folding routes predicted by a variational model in terms of a generalized formalism of the capillarity scaling theory for 28 two-state proteins. The scaling exponent ranged from 0.2 to 0.45 with an average of 0.33. This average…
The density of a protein molecule is a key property within a variety of experimental techniques. We present a computational method for determining protein mass density that explicitly incorporates hydration effects. Our approach uses…
The biological activity and functional specificity of proteins depend on their native three-dimensional structures determined by inter- and intra-molecular interactions. In this paper, we investigate the geometrical factor of protein…
Proteins are biological polymers that underlie all cellular functions. The first high-resolution protein structures were determined by x-ray crystallography in the 1960s. Since then, there has been continued interest in understanding and…
We propose a simple analytical method for estimating the central volume density of prestellar molecular cloud cores from their column density profiles. Prestellar cores feature a flat central part of the column density and volume density…
We measure the two-point density correlations and Voronoi cell distributions of cyclically sheared granular spheres obtained with a fluorescence technique and compare them with random packing of frictionless spheres. We find that the radial…
This chapter discusses geometric models of biomolecules and geometric constructs, including the union of ball model, the weigthed Voronoi diagram, the weighted Delaunay triangulation, and the alpha shapes. These geometric constructs enable…
We study a reaction-diffusion model posed on two distinct spatial scales that accounts for diffusion, aggregation, fragmentation, and deposition of populations of colloidal particles within a porous material. In this model, the macroscopic…
We give a geometrically exact treatment of percolation through voids around assemblies of randomly placed impermeable barrier particles, introducing a computationally inexpensive approach to finding critical barrier density thresholds…
A coarse-grained variational model is used to investigate the polymer dynamics of barrier crossing for a diverse set of two-state folding proteins. The model gives reliable folding rate predictions provided excluded volume terms that induce…
In this study, the distributions of protein structure classes (or folding types) of experimentally determined structures from a legacy dataset and a comprehensive database (SCOP) are modeled precisely with geometric constructs such as…
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…
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…
We develop a model to describe the properties of random assemblies of polydisperse hard spheres. We show that the key features to describe the system are (i) the dependence between the free volume of a sphere and the various coordination…
Uniform powder spreading is a requisite for creating consistent, high-quality components via powder bed additive manufacturing (AM), wherein layer density and uniformity are complex functions of powder characteristics, spreading kinematics,…
Molecular dynamics simulations of myoglobin and aspartate aminotransferase, with explicit solvent, are shown to accurately reproduce the experimentally measured molar volumes. Single amino-acid substitution at VAL39 of aspartate…
Using a coarse-grained model, self-organized assembly of proteins (e.g. CorA and its inner segment iCorA) is studied by examining quantities such as contact profile, radius of gyration, and structure factor as a function of protein…
A probabilistic discrete model for 2D protein crystal growth is presented. This model takes into account the available space and can describe growing processes of different nature due to the versatility of its parameters which gives the…
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 $\alpha=12$…