Related papers: Random close packing in protein cores
The Fraunhofer diffraction of quantum particles from materials with sharp electron-density edges or symmetric bond structures is ubiquitous. In contrast, diffraction from atoms with characteristic asymptotically-diffused electron…
Protein representation and potential function are essential ingredients for studying proteins folding and protein prediction. We introduce a novel geometric representation of contact interactions using the edge simplices from alpha shape of…
Using computed x-ray tomography we determine the three dimensional (3d) structure of binary hard sphere mixtures as a function of composition and size ratio of the particles, q. Using a recently introduced four-point correlation function we…
Since the 1920s, packing arguments have been used to rationalize crystal structures in systems ranging from atomic mixtures to colloidal crystals. Packing arguments have recently been applied to complex nanoparticle structures, where they…
Determining the structure of a protein has been a decades-long open question. A protein's three-dimensional structure often poses nontrivial computation costs, when classical simulation algorithms are utilized. Advances in the transformer…
The paper presents a geometrical model for protein secondary structure analysis which uses only the positions of the $C_{\alpha}$-atoms. We construct a space curve connecting these positions by piecewise polynomial interpolation and…
Previous research has shown a strong correlation of protein folding rates to the native state geometry, yet a complete explanation for this dependence is still lacking. Here we study the rate-geometry relationship with a simple statistical…
Given the amino acid sequence of a protein, researchers often infer its structure and function by finding homologous, or evolutionarily-related, proteins of known structure and function. Since structure is typically more conserved than…
In this study, the distributions of protein structure classes (or folding types) of experimentally determined structures from a legacy dataset and a comprehensive database (SCOP) are modeled precisely with geometric constructs such as…
We point out that although a litany of studies have been published on atoms in hard-wall confinement, they have not been systematic or have not used robust numerical methods. We report a methodical study of atoms in hard-wall confinement…
Saturated random packing of particles built of two identical, relatively shifted spheres in two and three dimensional flat and homogeneous space was studied numerically using random sequential adsorption algorithm. The shift between centers…
We study the Hard Core Model on the graphs ${\rm {\bf \scriptstyle G}}$ obtained from Archimedean tilings i.e. configurations in $\scriptstyle \{0,1\}^{{\rm {\bf G}}}$ with the nearest neighbor 1's forbidden. Our particular aim in choosing…
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…
The available experimental information on the Range-Energy relation for protons stopped in hydrogen gas is summarized in the SRIM software package. The estimated precision of this data is several percents. Here we describe a possibility to…
Amphiphilic molecules spontaneously form self-assembly structures based on physical conditions such as molecular structure, concentration, and temperature. These structures exhibit various useful functions according to their morphology. The…
A protein is traditionally visualised as a piecewise linear discrete curve, and its geometry is conventionally characterised by the extrinsically determined Ramachandran angles. However, a protein backbone has also two independent intrinsic…
Superellipse sector particles (SeSPs) are segments of superelliptical curves that form a tunable set of hard-particle shapes for granular and colloidal systems. SeSPs allow for continuous parameterization of corner sharpness, aspect ratio,…
Alignment of molecules through electric fields minimizes the averaging over orientations, e. g., in single particle imaging experiments. The response of molecules to external ac electric fields is governed by their polarizability tensor,…
Advancements in the synthesis of faceted nanoparticles and colloids have spurred interest in the phase behavior of polyhedral shapes. Regular tetrahedra have attracted particular attention because they prefer local symmetries that are…
A statistical model of protein families, called profile conditional random fields (CRFs), is proposed. This model may be regarded as an integration of the profile hidden Markov model (HMM) and the Finkelstein-Reva (FR) theory of protein…