Related papers: Void distributions reveal structural link between …
We have performed a novel experiment on granular packs composed of automatically swelling particles. By analyzing the Voronoi structure of packs going through the jamming transition, we show that the local configuration of a jamming pack is…
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,…
Voronoi Tessellations form an attractive and versatile geometrical asymptotic model for the foamlike cosmic distribution of matter and galaxies. In the Voronoi model the vertices are identified with clusters of galaxies. For a substantial…
A framework is presented for understanding the common character of proteins. Proteins are linear chain molecules. However, the simple model of a polymer viewed as spheres tethered together does not account for many of the observed…
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…
In the first paper of this series, we introduced Voronoi correlation functions to characterize the structure of maximally random jammed (MRJ) sphere packings across length scales. In the present paper, we determine a variety of correlation…
Three-dimensional discrete numerical simulation is used to investigate the properties of close-packed frictionless granular assemblies as a function of particle polydispersity and shape. Unlike some experimental results, simulations show…
A spatial distribution is hyperuniform if it has local density fluctuations that vanish in the limit of long length scales. Hyperuniformity is a well known property of both crystals and quasicrystals. Of recent interest, however, is…
A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G.…
Computer simulation was used to study the random sequential adsorption of identical discorectangles onto a continuous plane . The problem was analyzed for a wide range of discorectangle aspect ratios ($\varepsilon \in [1;100]$). We studied…
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…
We investigate membrane-mediated interactions between transmembrane proteins using coarse-grained models. We compare the effective potential of mean force (PMF) between two proteins, which are always aligned parallel to the z-axis of the…
We characterize the structure of maximally random jammed (MRJ) sphere packings by computing the Minkowski functionals (volume, surface area, and integrated mean curvature) of their associated Voronoi cells. The probability distribution…
We calculate the free volume distributions of nearly jammed packings of monodisperse and bidisperse hard sphere configurations. These distributions differ qualitatively from those of the fluid, displaying a power law tail at large free…
We determine the site and bond percolation thresholds for a system of disordered jammed sphere packings in the maximally random jammed state, generated by the Torquato-Jiao algorithm. For the site threshold, which gives the fraction of…
Proteins are linear chain molecules that play a central role in life and health. Protein native state folds are modular assemblies of space-filling building blocks of {\alpha}-helices, \{beta}-sheets and tight turns. Here we deduce the…
Recent studies classify the topology of proteins by analysing the distribution of their projections using knotoids. The approximation of this distribution depends on the number of projection directions that are sampled. Here we investigate…
Proteins, chain molecules of amino acids, behave in ways which are similar to each other yet quite distinct from standard compact polymers. We demonstrate that the Flory theorem, derived for polymer melts, holds for compact protein native…
Mapping between sequence and structure is currently an open problem in structural biology. Despite many experimental and computational efforts it is not clear yet how the structure is encoded in the sequence. Answering this question may…
The precise sequence of aminoacids plays a central role in the tertiary structure of proteins and their functional properties. The Hydrophobic-Polar lattice models have provided valuable insights regarding the energy landscape. We…