Related papers: Discrete breathers in protein secondary structure
The ubiquitous biomacromolecule DNA has an axial rigidity persistence length of ~50 nm, driven by its elegant double helical structure. While double and multiple helix structures appear widely in nature, only rarely are these found in…
The influence of structural constraints on the relaxation dynamics of three polyurea networks with varying degree of crosslinking, has been studied by means of a thorough analysis of broadband dielectric spectroscopy measurements. Two…
We prove the existence of discrete breathers (time-periodic, spatially localized solutions) in weakly coupled ferromagnetic spin chains with easy-axis anisotropy. Using numerical methods we then investigate the continuation of discrete…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
A minimal off-lattice model for alpha-helical proteins is presented. It is based on hydrophobicity forces and sequence independent local interactions. The latter are chosen so as to favor the formation of alpha-helical structure. They model…
Discrete breathers are time-periodic, spatially localized solutions of equations of motion for classical degrees of freedom interacting on a lattice. They come in one-parameter families. We report on studies of energy properties of breather…
Discrete breathers are time-periodic, spatially localized solutions of the equations of motion for a system of classical degrees of freedom interacting on a lattice. An important issue, not only from a theoretical point of view but also for…
Proteins are linear chain molecules that play a central role in life and health. Protein native state folds are modular assemblies of space-filling building blocks of {\alpha}-helices, \{beta}-sheets and tight turns. Here we deduce the…
Predicting protein secondary structure using lattice model is one of the most studied computational problem in bioinformatics. Here secondary structure or three dimensional structure of protein is predicted from its amino acid sequence.…
The existence and stability of dissipative breathers in rf SQUID (Superconducting Quantum Interference Device) arrays is investigated numerically. In such arrays, the nonlinearity which is intrinsic to each SQUID, along with the weak…
We describe and solve a discrete persistent chain model of protein binding on DNA, involving an extra sigma_i s at a site i of the DNA. This variable takes the value 1 or 0 depending on whether the site is occupied by a protein or not. In…
Specific protein-protein interactions are crucial in the cell, both to ensure the formation and stability of multi-protein complexes, and to enable signal transduction in various pathways. Functional interactions between proteins result in…
Many essential cellular processes, including cell division and the establishment of cell polarity during embryogenesis, are regulated by pattern-forming proteins. These proteins often need to bind to a substrate, such as the cell membrane,…
We study the structure and stability of discrete breathers (both pinned and mobile) in two-dimensional nonlinear anisotropic Schrodinger lattices. Starting from a set of identical one-dimensional systems we develop the continuation of the…
We present a family of discrete breathers, which exists in a nonlinear polarizability model of ferroelectric materials. The core-shell model is set up in its non-dimensionalized Hamiltonian form and its linear spectrum is examined.…
We have shown recently that the notion of poking pairwise interactions along a chain provides a unifying framework for understanding the formation of both secondary and the tertiary protein structure based on symmetry and geometry.…
We study the dynamics of moving discrete breathers in an interfaced piecewise DNA molecule. This is a DNA chain in which all the base pairs are identical and there exists an interface such that the base pairs dipole moments at each side are…
The proposal of this paper is to provide a simple angular random walk model to build up polypeptide structures, which encompass properties of dihedral angles of folded proteins. From this model, structures will be built with lengths ranging…
We propose a new mechanism of long-range coupling to excite low-frequency discrete breathers without the on-site potential. This mechanism is universal in long-range systems irrespective of the spatial boundary conditions, of topology of…
The native state structures of globular proteins are stable and well-packed indicating that self-interactions are favored over protein-solvent interactions under folding conditions. We use this as a guiding principle to derive the geometry…