Related papers: Structure Space of Model Proteins --A Principle Co…
Protein one-dimensional (1D) structures such as secondary structure and contact number provide intuitive pictures to understand how the native three-dimensional (3D) structure of a protein is encoded in the amino acid sequence. However, it…
Recent decades have seen the discovery of numerous complex materials. At the root of the complexity underlying many of these materials lies a large number of possible contending atomic- and larger-scale configurations and the intricate…
An essential quantity to ensure evolvability of populations is the navigability of the genotype space. Navigability relies on the existence of sufficiently large genotype networks, that is ensembles of sequences with the same phenotype that…
We investigate the texture structures of lepton mass matrices with four (five) non-zero elements in the charged lepton mass matrix and three (four) vanishing cofactors in the neutrino mass matrix. Using weak basis transformations, all…
We propose a procedure to determine the dimension of the common factor space in a large, possibly non-stationary, dataset. Our procedure is designed to determine whether there are (and how many) common factors (i) with linear trends, (ii)…
We simulate a hard-sphere liquid in confined geometry where the separation of the two parallel, hard walls is smaller than two particle diameters. By systematically reducing the wall separation we analyze the behavior of structural and…
Proteins are biomolecules of life. They fold into a great variety of three-dimensional (3D) shapes. Underlying these folding patterns are many recurrent structural fragments or building blocks (analogous to `LEGO bricks'). This paper…
Protein structure prediction is a challenging and unsolved problem in computer science. Proteins are the sequence of amino acids connected together by single peptide bond. The combinations of the twenty primary amino acids are the…
One of the outstanding analytical problems in X-ray single particle imaging (SPI) is the classification of structural heterogeneity, which is especially difficult given the low signal-to-noise ratios of individual patterns and that even…
The geometric design of structures with optimized physical and chemical properties is one of the core topics in materials science. However, designing new functional materials is challenging due to the vast number of existing and the…
In this paper, we develop a finite mixture of convolutional distributions, a statistical model to analyze continuous data distributed approximately on a mixture of low-dimensional affine subspaces. The observations are assumed independent…
We present a simple physical model which demonstrates that the native state folds of proteins can emerge on the basis of considerations of geometry and symmetry. We show that the inherent anisotropy of a chain molecule, the geometrical and…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Quantitative structure-property relationships are crucial for the understanding and prediction of the physical properties of complex materials. For fluid flow in porous materials, characterizing the geometry of the pore microstructure…
Several materials, such as rocks, powders and molecules, are multi-component systems. However, compared to single-component systems, it is difficult to understand the physical component. In this study, as a coarse-grained model for powders…
We consider the problem of inferring the interactions between a set of N binary variables from the knowledge of their frequencies and pairwise correlations. The inference framework is based on the Hopfield model, a special case of the Ising…
Protein design is the inverse approach of the three-dimensional (3D) structure prediction for elucidating the relationship between the 3D structures and amino acid sequences. In general, the computation of the protein design involves a…
We simulate the bond and site percolation models on several three-dimensional lattices, including the diamond, body-centered cubic, and face-centered cubic lattices. As on the simple-cubic lattice [Phys. Rev. E, \textbf{87} 052107 (2013)],…
The paper investigates localized deformation patterns resulting from the onset of instabilities in lattice structures. The study is motivated by previous observations on discrete hexagonal lattices, where the onset of non-uniform,…
Following S\"odergren, we consider a collection of random variables on the space $X_n$ of unimodular lattices in dimension $n$: Normalizations of the angles between the $N = N(n)$ shortest vectors in a random unimodular lattice, and the…