Related papers: Void distributions reveal structural link between …
The asymmetry in the shapes of folded and unfolded states are probed using two parameters, one being a measure of the sphericity and the other that describes the shape. For the folded states, whose interiors are densely packed, the radii of…
As a fundamental structural transition in complex networks, core percolation is related to a wide range of important problems. Yet, previous theoretical studies of core percolation have been focusing on the classical Erd\H{o}s-R\'enyi…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. Proteins are peptide chains decorated by amino…
We examine the spatial distribution and mass segregation of dense molecular cloud cores in a number of nearby star forming regions that span about four orders of magnitude in star formation activity. We use an approach based on the…
A jammed packing of frictionless spheres at zero temperature is perfectly specified by the network of contact forces from which mechanical properties can be derived. However, we can alternatively consider a packing as a geometric structure,…
The information regarding the structure of a single protein is encoded in the network of interacting amino acids. Considering each protein as a weighted and unweighted network of amino acids we have analyzed a total of forty nine protein…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
Proteins are constructed from a limited alphabet of ~20 amino acids, yet the origins and selection of this specific alphabet are unresolved. One largely overlooked aspect is whether elemental composition constrains the range of viable…
Cryo-electron microscopy (cryo-EM) has revolutionized experimental protein structure determination. Despite advances in high resolution reconstruction, a majority of cryo-EM experiments provide either a single state of the studied…
We utilize the extensive datasets available for the Perseus molecular cloud to analyze the relationship between the kinematics of small-scale dense cores and the larger structures in which they are embedded. The kinematic measures presented…
The coding space of protein sequences is shaped by evolutionary constraints set by requirements of function and stability. We show that the coding space of a given protein family--the total number of sequences in that family--can be…
We investigate theoretically the behavior of proteins as well as other large macromolecules which are incorporated into amphiphilic monolayers at the air-water interface. We assume the monolayer to be in the coexistence region of the…
In this work the linear elastic properties of materials containing spherical voids are calculated and compared using finite element simulations. The focus is on homogeneous solid materials with spherical, empty voids of equal size. The…
Connectedness percolation phenomena in the two-dimensional (2D) packing of binary mixtures of disks with different diameters were studied numerically. The packings were produced using random sequential adsorption (RSA) model with…
We analyze the large scale structure and fluctuations of jammed packings of size disperse spheres, produced in a granular experiment as well as numerically. While the structure factor of the packings reveals no unusual behavior for small…
Protein-stabilised emulsion gels can be studied in the theoretical framework of colloidal gels, because both protein assemblies and droplets may be considered as soft colloids. These particles differ in their nature, size and softness, and…
Proteins form a very important class of polymers. In spite of major advances in the understanding of polymer science, the protein problem has remained largely unsolved. Here, we show that a polymer chain viewed as a tube not only captures…
We introduce a model for particles that are extremely polydisperse in size compared to monodisperse and bidisperse systems. In two dimensions (2D), size polydispersity inhibits crystallization and increases packing fraction at jamming…
The massive exploitation of cosmic voids for precision cosmology in the upcoming dark energy experiments, requires a robust understanding of their internal structure, particularly of their density profile. We show that the void density…
Many biological tissues feature a heterogeneous network of fibers whose tensile and bending rigidity contribute substantially to these tissues' elastic properties. Rigidity percolation has emerged as a important paradigm for relating these…