Miljko V. Satarić

Modified extended tanh-function method and nonlinear dynamics of microtubules

Abstract We here present a model of nonlinear dynamics of microtubules (MT) in the context of modified extended tanh-function (METHF) method. We rely on the ferroelectric model of MTs published earlier by Sataric et al. [1] where the motion of MT subunits is reduced to a single longitudinal degree of freedom per dimer. It is shown that such nonlinear model can lead to existence of kink solitons moving along the MTs. An analytical solution of the basic equation, describing MT dynamics, was compared with the numerical one and a perfect agreement was demonstrated. It is now clearer how the values of the basic parameters of the model, proportional to viscosity and internal electric field, impact MT dynamics. Finally, we offer a possible scenario of how living cells utilize these kinks as signaling tools for regulation of cellular traffic as well as MT depolymerisation.

Nonlinear dynamics of microtubules —A longitudinal model

In the present letter we describe a model of nonlinear dynamics of microtubules (MTs) assuming a single longitudinal degree of freedom per tubulin dimer. This is a longitudinal displacement of a dimer at a certain position with respect to the neighbouring one. A nonlinear partial differential equation, describing dimers dynamics within MT, is solved both analytically and numerically. It is shown that such a nonlinear model can lead to the existence of kink solitons moving along the MTs. The internal electrical field strength is calculated using two procedures and a perfect agreement between the results is demonstrated. This enabled the estimation of the total energy, kink velocity and kink width. To simplify the calculation of the total energy we stated and proved a useful auxiliary theorem.

Localized modulated waves and longitudinal model of microtubules

We here study nonlinear dynamics of microtubule (MT). A so-called u - model is explained in detail. A single longitudinal degree of freedom per MT subunits is assumed. It is known that a continuum approximation of a basic discrete dynamical equation of motion enables existence of kink and antikink solitons along MT. In this paper we use semi-discrete approximation for this equation and show that modulated solitonic waves could propagate as well. We suggest possible biological implications of these waves. Also, a detailed parameter analysis is performed.

Transverse interaction in DNA molecule

Interaction between nucleotides at a same site belonging to different strands is studied. This interaction is modelled by a Morse potential which depends on two parameters. We study a relationship between the parameters characterizing AT and CG pairs. We show that certain circumstances, i.e. certain values of these parameters, bring about a negligible influence of inhomogeneity on the solitonic dynamics.

DNA-RNA transcription as an impact of viscosity

The impact of viscosity on DNA dynamics is studied both analytically and numerically. It is assumed that the viscosity exists at the segments where DNA molecule is surrounded by RNA polymerase. We demonstrate that the frictional forces destroy the modulation of the incoming solitonic wave. We show that viscosity, crucial for demodulation, is essential for DNA-RNA transcription.

Morse potential in DNA molecule – An experiment proposal

We rely on the helicoidal Peyrard-Bishop model for DNA dynamics. Interaction between nucleotides at a same site belonging to different strands is modelled by a Morse potential energy. This potential depends on two parameters that are different for AT and CG pairs, which is a possible source for inhomogeneity. It was shown recently (Zdravković and Satarić 2011) that certain values of these parameters bring about a negligible influence of inhomogeneity on the solitonic dynamics. We propose an experiment that should be carried out in order to determine the values of both of these parameters.

Gravitational symmetry breaking leads to a polar liquid crystal phase of microtubules in vitro.

Recent space-flight experiments performed by Tabonys team provided further evidence that a microgravity environment strongly affects the spatio-temporal organization of microtubule assemblies. Characteristic time and length scales were found that govern the organization of oriented bundles under Earths gravitational field (GF). No such organization has been observed in a microgravity environment. This paper discusses physical mechanisms resulting in pattern formation under gravity and its disappearance in microgravity. The subtle interplay between chemical kinetics, diffusion, gravitational drift, thermal fluctuations, electrostatic interactions and liquid crystalline characteristics provides a plausible scenario.

KINK SOLITONS IN DNA

We study DNA dynamics relying on the plane-base rotator model for DNA. It is shown that this dynamics can be represented by kink and antikink solitons. We demonstrate that two velocities are relevant and these are the velocities of both a double and a single stranded DNA. A key question is which one is bigger as this is related to a value of the ratio of two parameters describing the hydrogen and the covalent interactions in DNA. If the velocity of double stranded DNA is larger than one of the single stranded chain then the two ferromagnetic strands are coupled antiferromagnetically. Otherwise, the two DNA strands are coupled ferromagnetically. We discuss possible experiments based on micromanipulation techniques that should be carried out to determine these velocities and the solitonic width.

Nonlinear DNA dynamics: Nonlinearity versus dispersion

In the present paper we study the impact of dispersion and nonlinearity on DNA dynamics. We rely on the helicoidal Peyrard-Bishop model and use the fact that nonlinear DNA dynamics represents an interplay between nonlinearity and dispersion. We state that a dispersion coefficient P and a coefficient of nonlinearity Q, existing in nonlinear Schrodinger equation, are mutually dependent and show how function Q(P) and P(Q) can be obtained. Also, we show how all this can be used to find a possible interval for the parameter describing helicoidal structure of DNA.

Modeling of relay helix functional dynamics and feasibility of experimental verification by neutron scattering.

Cellular long-range transport involves motor proteins (MPs) (especially, kinesin and myosin) which contain a so-called relay helix. Its motion is of crucial importance to the conversion of chemical energy released in ATP hydrolysis into the coordinated mechanical movement of the entire motor protein. In this paper, we propose two combined nonlinear mechanisms for this particular functional activity and suggest the application of neutron scattering assays to experimentally determine the incoherent dynamic structure factor S(q,ω). We argue that this type of experiment is not only feasible but it could offer significant insights into the mechanism of MP function at a molecular level.