Related papers: Random close packing in protein cores
Point-proton density distributions are deduced for 130 stable nuclei from $^{7}\mathrm{Li}$ to $^{232}\mathrm{Th}$ from nuclear charge densities determined in elastic electron scattering. There are 171 cases are presented in model-dependent…
We study the distribution of hydrogen and various hydride configurations in realistic models of a-Si:H for two different concentration generated via experimentally constrained molecular relaxation approach (ECMR) [1]. The microstructure…
Sphere packings are essential to the development of physical models for powders, composite materials, and the atomic structure of the liquid state. There is a strong scientific need to be able to assess the fit of packing models to data,…
We link the thermodynamics of colloidal suspensions to the statistics of regular and random packings. Random close packing has defied a rigorous definition yet, in three dimensions, there is near universal agreement on the volume fraction…
Sequentially-built random sphere-packings have been numerically studied in the packing fraction interval $0.329 < \gamma < 0.586$. For that purpose fast running geometrical algorithms have been designed in order to build about 300…
This work reports a new methodology aimed at describing characteristics of protein structural shapes, and suggests a framework in which to resolve or classify automatically such structures into known families. This new approach to protein…
Protein folding and design are major biophysical problems, the solution of which would lead to important applications especially in medicine. Here a novel protein model capable of simultaneously provide quantitative protein design and…
We simulated the Coulomb explosion dynamics due to the fast ionization induced by high-intensity X-rays in six proteins that share similar atomic content and shape. We followed and projected the trajectory of the fragments onto a virtual…
Protein structure prediction is pivotal for understanding the structure-function relationship of proteins, advancing biological research, and facilitating pharmaceutical development and experimental design. While deep learning methods and…
We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use…
Folding of protein-like heteropolymers into unique 3D structures is investigated using Monte Carlo simulations on a cubic lattice. We found that folding time of chains of length $N$ scales as $N^\lambda$ at temperature of fastest folding.…
Protein structures in nature often exhibit a high degree of regularity (secondary structures, tertiary symmetries, etc.) absent in random compact conformations. We demonstrate in a simple lattice model of protein folding that structural…
We investigate the random close packing density, $\phi_\textrm{RCP}$, of polydisperse hard sphere systems using a theoretical framework based on the equilibrium model of crowding. We derive a closed-form solution for $\phi_\textrm{RCP}$ in…
Proteins tend to bury hydrophobic residues inside their core during the folding process to provide stability to the protein structure and to prevent aggregation. Nevertheless, proteins do expose some 'sticky' hydrophobic residues to the…
The densest amorphous packing of rigid particles is known as random close packing. It has long been appreciated that higher densities are achieved by using collections of particles with a variety of sizes. The variety of sizes is often…
We show that an analogy between crowding in fluid and jammed phases of hard spheres captures the density dependence of the kissing number for a family of numerically generated jammed states. We extend this analogy to jams of mixtures of…
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…
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…
Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. Due to their symmetry, these proteins constitute excellent model systems to investigate how evolution relates to structure,…
Protein structures are a very special class among all possible structures. It was suggested that a ``designability principle'' plays a crucial role in nature's selection of protein sequences and structures. Here we provide a theoretical…