Related papers: On the kinks and dynamical phase transitions of al…
We investigate some aspects of the soliton dynamics in an alpha-helical protein macromolecule within the steric Davydov-Scott model. Our main objective is to elucidate the important role of the helical symmetry in the formation, stability…
We consider the Davydov model of {\alpha}-helix protein chain with both exciton-exciton and excitonphonon couplings and investigate on the evolution of elliptic solitons. In the discrete regime of the adiabatic limit, we analytically and…
We use the torsional angles of the protein chain as generalized coordinates in the canonical formalism, derive canonical equations of motion, and investigate the coordinate dependence of the kinetic energy expressed in terms of the…
The transport of energy inside protein $\alpha$-helices is studied by deriving a system of quantum equations of motion from the Davydov Hamiltonian with the use of the Schr\"odinger equation and the generalized Ehrenfest theorem.…
I discuss the digital disorder introduced by Rosu and Canessa [Phys. Rev. E 47, R3818 (1993)] in the Davydov model of energy diffusion along \alpha-helix protein chains. The digitally disordered Davydov beta kinks display self-organized…
We suggest that Davidov's solitons, propagating through the backbone of a protein, can mediate conformational transition and folding of a protein to its native state. A simple toy model is presented in which a Non Linear Schrodinger (NLS)…
The essential biological processes that sustain life are catalyzed by protein nano-engines, which maintain living systems in far-from-equilibrium ordered states. To investigate energetic processes in proteins, we have analyzed the system of…
Davydov's model of solitons in alpha-helix protein chains is shown to display features of self-organized criticality (SOC), i.e., power law behaviour of correlations in space and 1/f-noise, as a consequence of considering random peptide…
Davydov's model of solitons in alpha-helix protein chains is shown to display features of self-organized criticality (SOC), i.e., power law behaviour of correlations in space and 1/f-noise, as a consequence of considering random peptide…
Different aspects of protein folding are illustrated by simplified polymer models. Stressing the diversity of side chains (residues) leads one to view folding as the freezing transition of an heteropolymer. Technically, the most common…
The authors study the short-time dynamics of helix-forming polypeptide chains using an all-atom representation of the molecules and an implicit solvation model to approximate the interaction with the surrounding solvent. The results confirm…
The Hamiltonian dynamics of chains of nonlinearly coupled particles is numerically investigated in two and three dimensions. Simple, off-lattice homopolymer models are used to represent the interparticle potentials. Time averages of…
We propose a protein model based on a hierarchy of constraints that force the protein to follow certain pathways when changing conformation. The model exhibits a first order phase transition, cooperativity and is exactly solvable. It also…
We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding…
Protein clamps provide the cell with effective mechanisms for sensing of environmental changes and triggering adaptations that maintain homeostasis. The general physical mechanism behind protein clamping action, however, is poorly…
I propose a variation of the standard worm--like chain model to account for internal order parameter (helix/coil) fields on the polymer chain. This internal order parameter field influences polymer conformational statistics by locally…
We analyze a model statistical description of the polypeptide chain helix-coil transition, where we take into account the specificity of its primary sequence, as quantified by the phase space volume ratio of the number of all accessible…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
In this paper we suggest a theoretical method based on the statistical mechanics for treating the alpha-helix-random coil transition in alanine polypeptides. We consider this process as a first-order phase transition and develop a theory…
The similarity in the thermodynamic properties of two completely different theoretical models for the helix-coil transition is examined critically. The first model is an all-atomic representation for a poly-alanine chain, while the second…