Related papers: Structure Space of Model Proteins --A Principle Co…
Despite the remarkable success of large large-scale neural networks, we still lack unified notation for thinking about and describing their representational spaces. We lack methods to reliably describe how their representations are…
Proteins are large biomolecules that regulate all living organisms and consist of one or several chains. The primary structure of a protein chain is a sequence of amino acid residues whose three main atoms (alpha-carbon, nitrogen, and…
The statistical analysis of tree structured data is a new topic in statistics with wide application areas. Some Principal Component Analysis (PCA) ideas were previously developed for binary tree spaces. In this study, we extend these ideas…
Proteins are an example of heteropolymers able to self-assemble in specific target structures. The self-assembly of designed artificial heteropolymers is still, to the best of our knowledge, not possible with control over the single chain…
Quantifying the relationship between geometric descriptors of microstructure and effective properties like permeability is essential for understanding and improving the behavior of porous materials. In this paper, we employ a previously…
The present work provides a profound analytical and numerical analysis of the material properties of SFRC on the mesoscale as well as the resulting correlation structure taking into account the probabilistic characteristics of the fiber…
Analysis of the geometric properties of a mean-field HP model on a square lattice for protein structure shows that structures with large number of switch backs between surface and core sites are chosen favorably by peptides as unique ground…
In real world applications dealing with compositional datasets, it is easy to face the presence of structural zeros. The latter arise when, due to physical limitations, one or more variables are intrinsically zero for a subset of the…
For multivariate regularly random vectors of dimension $d$, the dependence structure of the extremes is modeled by the so-called angular measure. When the dimension $d$ is high, estimating the angular measure is challenging because of its…
The structures of proteins exhibit secondary elements composed of helices and loops. Comparison of several water-only hydrophobicity scales with the functionalities of two repeat proteins shows that these secondary elements possess…
Isotopic fluctuations in fragment formation are investigated in a quasi-analytical description of the spinodal decomposition scenario. By exploiting the fluctuation-dissipation relations the covariance matrix of density fluctuations is…
We consider a two-letter self-avoiding (square) lattice heteropolymer model of N_H (out ofN) attracting sites. At zero temperature, permanent links are formed leading to collapse structures for any fraction rho_H=N_H/N. The average chain…
The spatial organization of complex biochemical reactions is essential for the regulation of cellular processes. Membrane-less structures called foci containing high concentrations of specific proteins have been reported in a variety of…
Several aspects of the internal structure of pseudoscalar mesons, accessible through generalized parton distributions in their zero-skewness limit, are examined. These include electromagnetic and gravitational form factors related to charge…
Proteins constitute a large group of macromolecules with a multitude of functions for all living organisms. Proteins achieve this by adopting distinct three-dimensional structures encoded by the sequence of their constituent amino acids in…
Two types of average structures of a single knotted ring polymer are studied by Brownian dynamics simulations. For a ring polymer with N segments, its structure is represented by a 3N -dimensional conformation vector consisting of the…
Changes in lattice structure across sub-regions of protein crystals are challenging to assess when relying on whole crystal measurements. Because of this difficulty, macromolecular structure determination from protein micro and nano…
The structural properties of dense random packings of identical hard spheres (HS) are investigated. The bond order parameter method is used to obtain detailed information on the local structural properties of the system for different…
In this notice we would like to study the fractal structure of the set of high points for the membrane model in the critical dimension d=4. We are able to compute the Hausdorff dimension of the set of points which are atypically high, and…
A two amino acid (hydrophobic and polar) scheme is used to perform the design on target conformations corresponding to the native states of twenty single chain proteins. Strikingly, the percentage of successful identification of the nature…