Related papers: Distribution of volume, microvoid percolation, and…
Dense packing of hydrophobic residues in the cores of globular proteins determines their stability. Recently, we have shown that protein cores possess packing fraction $\phi \approx 0.56$, which is the same as dense, random packing of amino…
Intracellular protein patterns regulate many vital cellular functions, such as the processing of spatiotemporal information or the control of shape deformations. To do so, pattern-forming systems can be sensitive to the cell geometry by…
Atomic packing is an important metric for characterizing protein structures, as it significantly influences various features including the stability, the rate of evolution and the functional roles of proteins. Packing in protein structures…
We present in this paper a quantitative method for defining void size in large-scale structure based on percolation threshold density. Beginning with two-dimensional gravitational clustering simulations smoothed to the threshold of…
The evolution of occupied volume under progressive fragmentation of granular matter is studied using a purely geometric model. Rather than modelling disorder directly, properties are investigated by analysing highly ordered reference…
It is shown that the density of modes of the vibrational spectrum of globular proteins is universal, i.e., regardless of the protein in question it closely follows one universal curve. The present study, including 135 proteins analyzed with…
The effect of molecule size (excluded volume) and the range of interaction on the surface tension, phase diagram and nucleation properties of a model globular protein is investigated using a combinations of Monte Carlo simulations and…
In this letter, the possible dynamic scaling properties of protein molecules in folding are investigated theoretically by assuming that the protein molecules are percolated networks. It is shown that the fractal character and the fractal…
Voids exist in proteins as packing defects and are often associated with protein functions. We study the statistical geometry of voids in two-dimensional lattice chain polymers. We define voids as topological features and develop a simple…
Introduced more than fifty years ago, dynamic light scattering is routinely used to determine the size distribution of colloidal suspensions, as well as of macromolecules in solution, such as proteins, nucleic acids, and their complexes.…
The percolation threshold for flow or conduction through voids surrounding randomly placed spheres is rigorously calculated. With large scale Monte Carlo simulations, we give a rigorous continuum treatment to the geometry of the…
The evolution, regulation and sustenance of biological complexity is determined by protein-protein interaction network that is filled with dynamic events. Recent experimental evidences point out that clustering of proteins has a vital role…
We study the problem of continuum percolation in infinite volume Gibbs measures for particles with an attractive pair potential, with a focus on low temperatures (large $\beta$). The main results are bounds on percolation thresholds…
Wolumes is a fast and stand-alone computer program written in standard C that allows the measure of atom volumes in proteins. Its algorithm is a simple discretization of the space by means of a grid of points at 0.75 Angstroms from each…
In cell membranes, proteins and lipids diffuse in a highly crowded and heterogeneous landscape, where aggregates and dense domains of proteins or lipids obstruct the path of diffusing molecules. In general, hindered motion gives rise to…
Interstellar medium widely exists in the universe at multi-scales. In this study, we introduce the {\it Multi-scale Decomposition Reconstruction} method, an equation-based model designed to derive width maps of interstellar medium…
Aims. We develop an extended percolation method to allow the comparison of geometrical properties of the real cosmic web with the simulated dark matter web for an ensemble of over- and under-density systems. Methods. We scan density fields…
Using analytical calculations and computer simulations we consider both the lateral diffusion of a membrane protein and the fluctuation spectrum of the membrane in which the protein is embedded. The membrane protein interacts with the…
The copy number of any protein fluctuates among cells in a population; characterizing and understanding these fluctuations is a fundamental problem in biophysics. We show here that protein distributions measured under a broad range of…
A method is proposed for the characterisation of the entropy of cellular structures, based on the compactivity concept for granular packings. Hamiltonian-like volume functions are constructed both in two and in three dimensions, enabling…