Contributions of topological polar-polar contacts to achieve better folding stability of 2D/3D HP lattice proteins: An in silico approach

<abstract> <p>Many of the simplistic hydrophobic-polar lattice models, such as Dill's model (called <bold>Model 1</bold> herein), are aimed to fold structures through hydrophobic-hydrophobic interactions mimicking the well-known hydrophobic collapse present in protein structures. In this work, we studied 11 designed hydrophobic-polar sequences, S₁-S₈ folded in 2D-square lattice, and S₉-S₁₁ folded in 3D-cubic lattice. And to better fold these structures we have developed <bold>Model 2</bold> as an approximation to convex function aimed to weight hydrophobic-hydrophobic but also polar-polar contacts as an augmented version of <bold>Model 1</bold>. In this partitioned approach hydrophobic-hydrophobic ponderation was tuned as <italic>α</italic>-1 and polar-polar ponderation as <italic>α</italic>. This model is centered in preserving required hydrophobic substructure, and at the same time including polar-polar interactions, otherwise absent, to reach a better folding score now also acquiring the polar-polar substructure. In all tested cases the folding trials were better achieved with <bold>Model 2</bold>, using <italic>α</italic> values of 0.05, 0.1, 0.2 and 0.3 depending of sequence size, even finding optimal scores not reached with <bold>Model 1</bold>. An important result is that the better folding score, required the lower <italic>α</italic> weighting. And when <italic>α</italic> values above 0.3 are employed, no matter the nature of the hydrophobic-polar sequence, banning of hydrophobic-hydrophobic contacts started, thus yielding misfolding of sequences. Therefore, the value of <italic>α</italic> to correctly fold structures is the result of a careful weighting among hydrophobic-hydrophobic and polar-polar contacts.</p> </abstract>

History of the reciprocal lattice

History of the development of the reciprocal lattice is reviewed. The reciprocal lattice as an essential tool for the study of diffraction experiments by ordered structures and characterization of their structural properties is widely taught in any text of solid state or chemistry, but usually without discussion of its history. This article aims to give a coherent historical perspective on the reciprocal lattice. First, a basic introduction to the reciprocal lattice concept, its mathematical foundation and physical origin, and its relationship with the direct lattice is provided. Then a detailed chronicle of ideas leading to the concept of the reciprocal lattice is presented, including a review of the contributions of Gibbs, Ewald, and others. The polar lattice concept, the great ancestor of the reciprocal lattice, is presented.

A degenerate polar lattice for cloaking in full two-dimensional elastodynamics and statics

A lattice design of a cloak for full two-dimensional elasticity is suggested when the background continuum is isotropic with Lamé parameters (λ, μ ) satisfying μ ≤ λ. The lattice is polar in the sense that it elastically resists rotations; and is degenerate meaning it admits a stressless collapse mechanism. These characteristics are attained through the use of appropriately distributed restoring torques in conjunction with hinge-like spring-mass contacts. Thus, the lattice is proven to exhibit a rank-3 elasticity tensor lacking the minor symmetries. Accordingly, it rigorously adheres to the form-invariance requirements of the transformation method under the Brun–Guenneau–Movchan gauge. The cloak is numerically tested in statics and in dynamics under pressure and shear incident waves and shows satisfactory performance. Finally, a theoretical generalization extends the design to three dimensions and to arbitrarily anisotropic backgrounds so as to enable cloaking as well as other transformation-based static and dynamic field manipulation techniques in these cases.

Kikuchi pattern analysis of noncentrosymmetric crystals

Different models of Kikuchi pattern formation are compared with respect to their applicability to noncentrosymmetric crystals, and the breakdown of Friedel's rule in experimental electron backscatter diffraction (EBSD) patterns is discussed. DifferentAIIIBVsemiconductor materials are used to evaluate the resulting asymmetry of Kikuchi band profiles for polar lattice planes. By comparison with the characteristic etch pit morphology on a single-crystal surface, the polar character of the measured lattice planes can be assigned absolutely. The presented approach enables point-group-resolved orientation mapping, which goes beyond the commonly applied Laue group analysis in EBSD.