Related papers: Geometry Selects Highly Designable Structures
The thermodynamic behavior and structural properties of hydrophobic-polar (HP) lattice proteins interacting with attractive surfaces are studied by means of Wang-Landau sampling. Three benchmark HP sequences (48mer, 67mer, and 103mer) are…
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…
Mechanical metamaterials have continued to offer unprecedented tunability in mechanical properties, but most designs to date have prioritized attaining high stiffness and strength while sacrificing deformability. The emergence of woven…
We investigate the mechanisms underlying selective molecular recognition of single heteropolymers at chemically structured planar surfaces. To this end, we study systems with two-letter (HP) lattice heteropolymers by exact enumeration…
A typical protein structure is a compact packing of connected alpha-helices and/or beta-strands. We have developed a method for generating the ensemble of compact structures a given set of helices and strands can form. The method is tested…
Lattice protein models, as the Hydrophobic-Polar (HP) model, are a common abstraction to enable exhaustive studies on structure, function, or evolution of proteins. A main issue is the high number of optimal structures, resulting from the…
Linear polymers are represented as chains of hopping reptons and their motion is described as a stochastic process on a lattice. This admittedly crude approximation still catches essential physics of polymer motion, i.e. the universal…
In suitable environments, proteins, nucleic acids and certain synthetic polymers fold into unique conformations. This work shows that it is possible to construct lattice models of foldable heteropolymers by expressing the energy only in…
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…
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…
Despite the variety of protein sizes, shapes, and backbone configurations found in nature, the design of novel protein folds remains an open problem. Within simple lattice models it has been shown that all structures are not equally…
The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems -- the profound effects of evolution. I…
We produce a large class of hyperbolic homology 3-spheres admitting arbitrarily many distinct tight contact structures. We also produce a sub-class admitting arbitrarily many distinct tight contact structures within the same homotopy class…
Protein structures in nature often exhibit a high degree of regularity (secondary structures, tertiary symmetries, etc.) absent in random compact conformations. We demonstrate in a simple lattice model of protein folding that structural…
Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…
The microscopic structure of several amorphous substances often reveals complex patterns such as medium- or long-range order, spatial heterogeneity, and even local polycrystallinity. To capture all these features, models usually incorporate…
Protein structures are a very special class among all possible structures. It was suggested that a ``designability principle'' plays a crucial role in nature's selection of protein sequences and structures. Here we provide a theoretical…
Nonhamiltonian interaction of hamiltonian systems is considered. Dynamical equations are constructed by use of symmetric designs on Lie algebras. The results of analysis of these equations show that some class of symmetric designs on Lie…
The purpose of this work is two-fold. First, we introduce an efficient homogenization-based approach to perform topology optimization of coated structures with orthotropic infill material. By making use of the relaxed design space, we can…
A novel approach to heteropolymer design is proposed. It is based on the criterion by Kurosky and Deutsch, with which the probability of a target conformation in a conformation space is maximized at low but finite temperature. The key…