Related papers: Distribution of volume, microvoid percolation, and…
The choice of structural resolution is a fundamental aspect of protein modelling, determining the balance between descriptive power and interpretability. Although atomistic simulations provide maximal detail, much of this information is…
We study the nature of voids defined as single-stream regions that have not undergone shell-crossing. We use ORIGAMI to determine the cosmic web morphology of each dark matter particle in a suite of cosmological $N$-body simulations, which…
Diffusive transport is a universal phenomenon, throughout both biological and physical sciences, and models of diffusion are routinely used to interrogate diffusion-driven processes. However, most models neglect to take into account the…
Cryo-EM reconstruction algorithms seek to determine a molecule's 3D density map from a series of noisy, unlabeled 2D projection images captured with an electron microscope. Although reconstruction algorithms typically model the 3D volume as…
The newly developed "void expansion method" allows for an efficient generation of porous packings of spherical particles over a wide range of volume fractions using the discrete element method. Particles are randomly placed under addition…
The interaction of a protein with its environment can be understood and controlled via its 3D structure. Experimental methods for protein structure determination, such as X-ray crystallography or cryogenic electron microscopy, shed light on…
Every realistic instance of a percolation problem is faced with some degree of polydispersity, e.g., the pore-size distribution of an inhomogeneous medium, the size distribution of filler particles in composite materials, or the vertex…
In the first paper of this series [S. Torquato, J. Chem. Phys. {\bf 136}, 054106 (2012)], analytical results concerning the continuum percolation of overlapping hyperparticles in $d$-dimensional Euclidean space $\mathbb{R}^d$ were obtained,…
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…
Studies of disordered heterogeneous media and galaxy cosmology share a common goal: analyzing the distribution of particles at `microscales' to predict physical properties at `macroscales', whether for a liquid, composite material, or…
Natural protein sequences that self-assemble to form globular structures are compact with high packing densities in the folded states. It is known that proteins unfold upon addition of denaturants, adopting random coil structures. The…
An accurate estimation of the Protein Space size, in light of the factors that govern it, is a long-standing problem and of paramount importance in evolutionary biology, since it determines the nature of protein evolvability. A simple…
In this paper, we apply dimensional analysis to study a diffusive molecular communication system that uses diffusing enzymes in the propagation environment to mitigate intersymbol interference. The enzymes bind to information molecules and…
The diffusion of finite-size hard-core interacting particles in two- or three-dimensional confined domains is considered in the limit that the confinement dimensions become comparable to the particle's dimensions. The result is a nonlinear…
After the recent ground-breaking advances in protein structure prediction, one of the remaining challenges in protein machine learning is to reliably predict distributions of structural states. Parametric models of fluctuations are…
Employing the discrete element method, we study the rheology of dense granular media mixtures, varying in size, density, and frictional properties of particles, across a spectrum from quasi-static to inertial regimes. By accounting for the…
Studies of random close packing of spheres have advanced our knowledge about the structure of systems such as liquids, glasses, emulsions, granular media, and amorphous solids. When these systems are confined their structural properties…
The statistical analysis of cosmic large-scale structure is most often based on simple two-point summary statistics, like the power spectrum or the two-point correlation function of a sample of galaxies or other types of tracers. In…
Describing the diffusion of particles through crowded, confined environments with which they can interact is of considerable biological and technological interest. Under conditions where the confinement dimensions become comparable to the…
Comments: 6 pages RevTeX, 6 Postscript figures. We review a statistical mechanics treatment of the stability of globular proteins based on a simple model Hamiltonian taking into account protein self interactions and protein-water…