Related papers: Distribution of volume, microvoid percolation, and…
A matching algorithm for the identification of backbones in percolation problems is introduced. Using this procedure, percolation backbones are studied in two- to five-dimensional systems containing 1.7x10^7 sites, two orders of magnitude…
For biologically relevant macromolecules such as intrinsically disordered proteins, internal degrees of freedom that allow for shape changes have a large influence on both the motion and function of the compound. A detailed understanding of…
The formation of biomolecular condensates inside cells often involve intrinsically disordered proteins (IDPs), and several of these IDPs are also capable of forming droplet-like dense assemblies on their own, through liquid-liquid phase…
Proteins employ the information stored in the genetic code and translated into their sequences to carry out well-defined functions in the cellular environment. The possibility to encode for such functions is controlled by the balance…
We dynamically simulate fractionation (partitioning of particle species) during spinodal gas-liquid separation of a size-polydisperse colloid, using polydispersity up to ~40% and a skewed parent size distribution. We introduce a novel…
We present structural properties of two-dimensional polymers as far as they can be described by percolation theory. The percolation threshold, critical exponents and fractal dimensions of clusters are determined by computer simulation and…
Using the concepts of mixed volumes and quermassintegrals of convex geometry, we derive an exact formula for the exclusion volume for a general convex body that applies in any space dimension, including both the rotationally-averaged…
We suggest that the dynamics of stable viscous invasion fronts in porous media depends on the volume capacitance of the media. At high volume capacitance, our network simulations provide numerical evidence of a scaling relation between the…
We use confocal microscopy to study a random close packed sample of colloidal particles. We introduce an algorithm to estimate the size of each particle. Taking into account their sizes, we compute the compressibility of the sample as a…
Generating molecules that bind to specific proteins is an important but challenging task in drug discovery. Previous works usually generate atoms in an auto-regressive way, where element types and 3D coordinates of atoms are generated one…
We analyse the geometry of the Pipe Nebula, drawn by the distribution ($Q$-spatial parameter) and hierarchy ($\Lambda$ spatial segregation) of column density peaks previously detected and catalogued. By analysing the mass and volume density…
Several recent works have shown that protein structure can predict site-specific evolutionary sequence variation. In particular, sites that are buried and/or have many contacts with other sites in a structure have been shown to evolve more…
The close packing density of log-normal and bimodal distributed, surface-adsorbed particles or discs in 2D is studied by numerical simulation. For small spread in particle size, the system orders in a polycrystalline structure of hexagonal…
Semiconductor model is a system of parabolic partial differential equations with cross-diffusion phenomenon. Previous results showed that a weak solution exists and is not bounded in general. So semiconductor model was categorized as a…
Atomic diffusion affects the properties of various engineering materials, which predominantly occur in the polycrystalline state. A rigorous description of polycrystalline diffusion must therefore account for crystallographic defects,…
The interstellar medium (ISM) exhibits complex, multi-scale structures that are challenging to study due to their projection into two-dimensional (2D) column density maps. We present the Volume Density Mapper, a novel algorithm based on…
Scaling of folding properties of proteins is studied in a toy system -- the lattice Go model with various two- and three- dimensional geometries of the maximally compact native states. Characteristic folding times grow as power laws with…
Many of the existing stochastic models of gene expression contain the first-order decay reaction term that may describe active protein degradation or dilution. If the model variable is interpreted as the molecule number, and not…
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…
The structure and spatial statistical properties of amorphous ellipsoid assemblies have profound scientific and industrial significance in many systems, from cell assays to granular materials. This paper uses a fundamental theoretical…