PubMed Health⌕ Search

Biomedical subjects

Yu B Gaididei

Publications and source records attributed to Yu B Gaididei.

6 recordsLinked to original sources
PubMed2006

Conformational transformations induced by the charge-curvature interaction: Mean-field approach.

A simple phenomenological model for describing the conformational dynamics of biological macromolecules via the nonlinearity-induced instabilities is proposed. It is shown that the interaction between charges and bending degrees of freedom of closed molecular aggregates may act as drivers giving impetus to conformational dynamics of biopolymers. It is demonstrated that initially circular aggregates may undergo transformation to polygonal shapes and possible application to aggregates of bacteriochlorophyl a molecules is considered.

Bacteriochlorophyll A↗
PubMed2004

Bubble generation in a twisted and bent DNA-like model.

The DNA molecule is modeled by a parabola embedded chain with long-range interactions between twisted base pair dipoles. A mechanism for bubble generation is presented and investigated in two different configurations. Using random normally distributed initial conditions to simulate thermal fluctuations, a relationship between bubble generation, twist and curvature is established. An analytical approach supports the numerical results.

Journal Article↗
PubMed2004

Multipeaked polarons in soft potentials.

We consider a minimal coupled charge / excitation-lattice model capturing a competition between linear polaronic self-trapping and the self-focusing effects of a soft nonlinear on-site potential. The standard single-humped polaron ceases to exist above a critical value of the coupling strength, closely related to the inflection point in the nonlinear potential. For couplings beyond this critical value, we find that successive multihumped polaronic solutions correspond to the lowest-energy stationary states of the system, which may admit interesting quantum resonance behavior.

Journal Article↗
PubMed2002

Solitons in triangular and honeycomb dynamical lattices with the cubic nonlinearity.

We study the existence and stability of localized states in the discrete nonlinear Schrödinger equation on two-dimensional nonsquare lattices. The model includes both the nearest-neighbor and long-range interactions. For the fundamental strongly localized soliton, the results depend on the coordination number, i.e., on the particular type of lattice. The long-range interactions additionally destabilize the discrete soliton, or make it more stable, if the sign of the interaction is, respectively, the same as or opposite to the sign of the short-range interaction. We also explore more complicated solutions, such as twisted localized modes and solutions carrying multiple topological charge (vortices) that are specific to the triangular and honeycomb lattices. In the cases when such vortices are unstable, direct simulations demonstrate that they typically turn into zero-vorticity fundamental solitons.

Journal Article↗
PubMed2001

Interplay of nonlinearity and geometry in a DNA-related, Klein-Gordon model with long-range dipole-dipole interaction.

Most of the studies on mathematical models of DNA are limited to next neighbor interaction. However, the coupling between base pairs is thought to be caused by dipole interaction, and, when the DNA strand is bent, the distances between base pairs become shorter, therefore the interactions with distant base pairs have to be taken into account. In this paper we analyze the existence and stability of breathers, i.e., localized oscillations in a simple model of bent DNA with long-range dipole interaction. Breathers have been suggested as precursors of the denaturation bubble.

Journal Article↗