Related papers: Discrete breathers in protein secondary structure
Metamaterials, i.e., artificially structured ("synthetic") media comprising weakly coupled discrete elements, exhibit extraordinary properties and they hold a great promise for novel applications including super-resolution imaging,…
Existence of breather (spatially localized, time periodic, oscillatory) solutions of the topological discrete sine-Gordon (TDSG) system, in the regime of weak coupling, is proved. The novelty of this result is that, unlike the systems…
In this paper we use a formal discrete-to-continuum procedure to derive a continuum variational model for two chains of atoms with slightly incommensurate lattices. The chains represent a cross-section of a three-dimensional system…
Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus…
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…
We have investigated interlayer interactions in the bilayer PtTe$_{2}$ system, which influence the electronic energy bands near the Fermi levels. Our diffusion Monte Carlo (DMC) calculations for the high-symmetry bilayer stackings (AA, AB,…
Strongly interacting one-dimensional (1D) Bose-Fermi mixtures form a tunable XXZ spin chain. Within the spin-chain model developed here, all properties of these systems can be calculated from states representing the ordering of the bosons…
Intrinsically disordered proteins (IDPs) are important for biological functions. In contrast to folded proteins, molecular recognition among certain IDPs is "fuzzy" in that their binding and/or phase separation are stochastically governed…
Conformation of a protein (CorA) is examined in a matrix with mobile solute constituents as a function of solute-residue interaction strength (f) by a coarse-grained model with a Monte Carlo simulation. Solute particles are found to reach…
Protein rigidity and flexibility can be analyzed accurately and efficiently using the program FIRST. Previous studies using FIRST were designed to analyze the rigidity and flexibility of proteins using a single static (snapshot) structure.…
We explore a recently proposed locally resonant granular system bearing harmonic internal resonators in a chain of beads interacting via Hertzian elastic contacts. In this system, we propose the existence of two types of configurations: (a)…
We propose a novel approach to detect the binding between proteins making use of the anomalous diffraction of natively present heavy elements inside the molecule 3D structure. In particular, we suggest considering sulfur atoms contained in…
Biological cells in soft materials can be modeled as anisotropic force contraction dipoles. The corresponding elastic interaction potentials are long-ranged ($\sim 1/r^3$ with distance $r$) and depend sensitively on elastic constants,…
We present initial results regarding the existence, stability and interaction of linear and nonlinear vibrational modes in a system of two coupled, one dimensional lattices with unequal numbers of masses. The effects on these nonlinear…
A simple one-dimensional lattice model is suggested to describe the experimentally observed plateau in force-stretching diagrams for some macromolecules. This chain model involves the nearest-neighbor interaction of a Morse-like potential…
We study spectral and transport properties of one-dimensional tight-binding $\mathcal{PT}$-symmetric chains with alternating couplings. Based on the transfer matrix method, we have analytically developed the expressions for the transmission…
We theoretically investigate the many-body dynamics of a tight-binding chain with dephasing noise on the infinite interval. We obtain the exact solution of an average particle-density profile for the domain wall and the alternating initial…
We investigate the formation process of nonlinear vibrational modes representing broad H-bridge multi--site breathers in a DNA--shaped double strand. Within a network model of the double helix we take individual motions of the bases within…
The formation of quasi-spherical cages from protein building blocks is a remarkable self-assembly process in many natural systems, where a small number of elementary building blocks are assembled to build a highly symmetric icosahedral…
We study the energy relaxation process in one-dimensional (1D) lattices with next-nearest-neighbor (NNN) couplings. This relaxation is produced by adding damping (absorbing conditions) to the boundary (free-end) of the lattice. Compared to…