Related papers: Void distributions reveal structural link between …
Proteins perform their biological functions through three-dimensional structures encoded by amino acid sequences, and ligand-binding protein co-design requires models that generate sequence-structure compatible proteins under explicit…
Connecting the collective behavior of disordered systems with local structure on the particle scale is an important challenge, for example in granular and glassy systems. Compounding complexity, in many scientific and industrial…
We aim at characterising dense cores in the clustered environments associated with massive star-forming regions. For this, we present an uniform analysis of VLA NH3(1,1) and (2,2) observations towards a sample of 15 massive star-forming…
The local structure of disordered jammed packings of monodisperse spheres without friction, generated by the Lubachevsky-Stillinger algorithm, is studied for packing fractions above and below 64%. The structural similarity of the particle…
Nuclear pores have an approximately uniform distribution in the nuclear envelope of most living cells. Hence, the morphology of the nuclear envelope is a spherical stomatocyte with a high genus. We have investigated the morphology of…
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…
Single domain proteins are thought to be tightly packed. The introduction of voids by mutations is often regarded as destabilizing. In this study we show that packing density for single domain proteins decreases with chain length. We find…
Understanding the interplay between ordered structures and substrate curvature is an interesting problem with versatile applications, including functionalization of charged supramolecular surfaces and modern microfluidic technologies. In…
We stress the importance of stochastic geometry as a branch of mathematical statistics particularly suited to model and investigate nontrivial spatial patterns. One of its key concepts, Voronoi tessellations, represents a versatile and…
This study investigates computationally the impact of particle size disparity and cohesion on force chain formation in granular media. The granular media considered in this study are bi-disperse systems under uniaxial compression,…
We study properties of jammed packings of frictionless spheres over a wide range of volume fractions. There exists a crossover volume fraction which separates deeply jammed solids from marginally jammed solids. In deeply jammed solids, all…
Although both RNA and proteins have densely packed native structures, chain organizations of these two biopolymers are fundamentally different. Motivated by the recent discoveries in chromatin folding that interphase chromosomes have…
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…
Understanding the biological function of knots in proteins and their folding process is an open and challenging question in biology. Recent studies classify the topology and geometry of knotted proteins by analysing the distribution of a…
Jamming in hard-particle packings has been the subject of considerable interest in recent years. In a paper by Torquato and Stillinger [J. Phys. Chem. B, 105 (2001)], a classification scheme of jammed packings into hierarchical categories…
The role of fixed degrees of freedom in soft/granular matter systems has broad applicability and theoretical interest. Here we address questions of the geometrical role that a scaffolding of fixed particles plays in tuning the threshold…
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…
Characterizing structural inhomogeneity is an essential step in understanding the mechanical response of amorphous materials. We introduce a threshold-free measure based on the field of vectors pointing from the center of each particle to…
The structure of lithium ion battery components, such as electrodes and separators, are commonly characterised in terms of their porosity and tortuosity. The ratio of these values gives the effective transport of lithium ions in the…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…