Related papers: The close-packed triple helix as a possible new st…
The recently proposed close-packed motif for collagen is investigated using first principles semi-empirical wave function theory and Kohn-Sham density functional theory. Under these refinements the close-packed motif is shown to be stable.…
The primary building block of the body is collagen, which is found in the extracellular matrix and in many stress-bearing tissues such as tendon and cartilage. It provides elasticity and support to cells and tissues while influencing…
Collagen fibrils, cable-like assemblies of long biological molecules, are dominant components of connective tissues. Their determinant morphological and functional roles motivated a large number of studies concerning their formation and…
The predominant structural protein in vertebrates is collagen, which plays a key role in extracellular matrix and connective tissue mechanics. Despite its prevalence and physical importance in biology, the mechanical properties of molecular…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
Type I collagen fibrils have circular cross sections with radii mostly distributed in between 50 and 100 nm and are characterized by an axial banding pattern with a period of 67 nm. The constituent long molecules of those fibrils, the…
Optimal geometrical arrangements, such as the stacking of atoms, are of relevance in diverse disciplines. A classic problem is the determination of the optimal arrangement of spheres in three dimensions in order to achieve the highest…
Shortly after the determination of the first protein x-ray crystal structures, researchers analyzed their cores and reported packing fractions $\phi \approx 0.75$, a value that is similar to close packing equal-sized spheres. A limitation…
When a thin sheet is crushed into a small three-dimensional volume, it invariably forms a structure with a low volume fraction but high resistance to further compression. Being a far-from-equilibrium process, forced crumpling is not…
Protein structure is generally conceptualized as the global arrangement or of smaller, local motifs of helices, sheets, and loops. These regular, recurring secondary structural elements have well-understood and standardized definitions in…
This review presents recent progress in understanding constraints and consequences of close-packing geometry of filamentous or columnar materials possessing non-trivial textures, focusing in particular on the common motifs of twisted and…
We study the micromechanics of collagen-I gel with the goal of bridging the gap between theory and experiment in the study of biopolymer networks. Three-dimensional images of fluorescently labeled collagen are obtained by confocal…
We present a method for discovering dense packings of general convex hard particles and apply it to study the dense packing behavior of a one-parameter family of particles with tetrahedral symmetry representing a deformation of the ideal…
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…
Dense polyhedron packings are useful models of a variety of condensed matter and biological systems and have intrigued scientists mathematicians for centuries. Recently, organizing principles for the types of structures associated with the…
Predicting protein secondary structure using lattice model is one of the most studied computational problem in bioinformatics. Here secondary structure or three dimensional structure of protein is predicted from its amino acid sequence.…
In this paper, we introduce a three-dimensional mathematical model of collagen contraction with microbuckling based on the two-dimensional model previously developed by the authors. The model both qualitatively and quantitatively replicates…
The chain of algebraic geometry constructions permits to transfer from the minimal surface with zero instability index, and from the lattice over the ring of cyclotomic integers to the tetra-block helix. The tetra-block is the 7-vertex…
The design of photo-active collagen systems is presented as a basis for establishing biomimetic materials with varied network architecture and programmable macroscopic properties. Following in-house isolation of type I collagen, reaction…
The shape of the cross section of a dense fiber bundle is related to the symmetry of its molecular packing. However, this statement might be belied by type I collagen fibrils which have a rounded section of high symmetry while structural…