Related papers: Structure Space of Model Proteins --A Principle Co…
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…
Fundamental questions about the role of the quaternary structures are addressed using a statistical mechanics off-lattice model of a dimer protein. The model, in spite of its simplicity, captures key features of the monomer-monomer…
This paper investigates the structure-property relations of thin-walled lattices under dynamic longitudinal compression, characterized by their cross-sections and heights. These relations elucidate the interactions of different geometric…
This chapter deals with approaches for protein three-dimensional structure prediction, starting out from a single input sequence with unknown struc- ture, the 'query' or 'target' sequence. Both template based and template free modelling…
Principal component analysis is a useful dimension reduction and data visualization method. However, in high dimension, low sample size asymptotic contexts, where the sample size is fixed and the dimension goes to infinity,a paradox has…
The degree of static indeterminacy and its spatial distribution characterize load-bearing structures independent of a specific load case. The redundancy matrix stores the distribution of the static indeterminacy on its main diagonal, and…
Measuring the structure factor, S(q), of a dispersion of particles by Small-Angle X-ray Scattering provides a unique method to investigate the spatial arrangement of colloidal particles. However, it is impossible to find the exact location…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. In their classic paper Kyte and Doolittle (KD)…
We address protein structure prediction in the 3D Hydrophobic-Polar lattice model through two novel deep learning architectures. For proteins under 36 residues, our hybrid reservoir-based model combines fixed random projections with…
Hyperuniformity is the study of stationary point processes with a sub-Poisson variance in a large window. In other words, counting the points of a hyperuniform point process that fall in a given large region yields a small-variance Monte…
An exact analytical expression for the static structure factor $S(k)$ in disordered materials is derived from Fourier transformed neighbor distribution decompositions in real space, and permits to reconstruct the function $S(k)$ in an…
In this study, we present a novel approach along with the needed computational strategies for efficient and scalable feature engineering of the crystal structure in compounds of different chemical compositions. This approach utilizes a…
The coherent vortical structures in turbulent flow through a strong 16:1 3-D contraction, are studied using time-resolved volumetric measurements. Visualization using vorticity magnitude criterion shows the emergence of long, stretched…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learnt how to extract this information so as to predict the detailed, biological active, three-dimensional structure of…
We show that the hydrophobicity of sequences is the leading term in Miyazawa-Jernigan interactions. Being the source of additive (solvation) terms in pair-contact interactions, they were used to reduce the energy parameters while resulting…
Traditional member-based two-step design approaches included in current structural codes for steel structures, as well as more recent system-based direct-design alternatives, require building rigorous structural reliability frameworks for…
We investigate the local- and long-range structure of four different space-filling cellular patterns: bubbles in a quasi-2d foam plus Voronoi constructions made around points that are uncorrelated (Poisson patterns), low discrepancy (Halton…
We consider fixed-point equations for probability distributions on isometry classes of measured metric spaces. The construction is required to be recursive and tree-like, but we allow loops for the geodesics between points in the support of…
Structure-based protein design has attracted increasing interest, with numerous methods being introduced in recent years. However, a universally accepted method for evaluation has not been established, since the wet-lab validation can be…
We study in a fully selfconsistent approach the structure of a vortex in low density superfluid neutron matter. We determine that the matter density profile of a vortex shows a significant depletion in the region of the core, a feature…