arXiv subjects

V. D. Lakhno

Publications and source records attributed to V. D. Lakhno.

At least 19 recordsLinked to original sources

arXiv2026

On the effect of force on DNA in the Peyrard-Bishop-Dauxois model

This paper presents a numerical study of the dynamics of DNA double helix breakage under the influence of external forces using the Peyrard-Bishop-Dauxois (PBD) model. The PBD model represents DNA as a chain of nonlinearly coupled oscillators, which makes it possible to analyze the processes of melting and mechanical denaturation. The main focus is on cases where an external force is applied to the terminal or central site of a DNA molecule, simulating stretching at a constant rate. The critical force required to break hydrogen bonds, which depends on the point of application of the force, is calculated. It is found that the denaturation process occurs stepwise, with characteristic peaks in the force-time graphs. The phenomenon of hysteresis under periodic exposure to external forces is also studied, which is important for understanding energy losses and heating of the system.

physics.bio-ph↗

arXiv2023

Comparison of different thermostats in the Holstein model

When modeling charge dynamics in a chain of N sites at a temperature T, a Langevin thermostat and a Hamiltonian system, i.e., a chain heated to a given temperature before charge is injected, are compared. It is shown that the polaron disruption occurs in the same range of values of the thermal energy NT, however, T is not given by the initial data, but obtained after simulation from the average kinetic energy. For large T, the results averaged over a set of trajectories in a system with a Langevin thermostat and the results averaged over time for a Hamiltonian system are close, which does not contradict the Ergodic hypothesis.

cond-mat.stat-mech↗

arXiv2021

Charge Motion along Polynucleotide Chains in a Constant Electric Field Depends on the Charge Coupling Constant with Chain Displacements

Various regimes of a charge motion along a chain in a constant electric field are investigated. This motion is simulated on the basis of the Holstein model. Earlier studies demonstrate a possibility of a uniform motion of a charge in a constant electric field over very long distances. For small values of the electric field intensity a Holstein polaron can move at a constant velocity. As the electric field intensity increases, a charge motion acquires oscillatorily character, performing Bloch oscillations. Since the charge motion depends on the whole set of the system parameters the character of the motion depends not only on the value of the electric field intensity. Therefore, the electric field intensity for which the uniform motion takes place differs for chains with different parameters. The character of the charge motion and distribution is considered in chains with different values of the constant of coupling between the charge and the displacements of the chain. It is shown that the values of the electric field intensity for which the regime of a charge motion changes are different in chains with different values of the coupling constant. It is also demonstrated that for one and the same value of the electric field intensity, in chains with different values of the coupling constant either a uniform motion or an oscillatory motion, or a stationary polaron can be observed.

cond-mat.mes-hall↗

arXiv2021

Dependence of the nature of the Holstein polaron motion in a polynucleotide chain subjected to a constant electric field on the initial polaron state and the parameters of the chain

In this work, we consider the motion of a polaron in a polynucleotide Holstein molecular chain in a constant electric field. It is shown that the character of the polaron motion in the chain depends not only on the chosen parameters of the chain, but also on the initial distribution of the charge along the chain. It is shown that for a small set value of the electric field intensity and for fixed values of the chain parameters, changing only the initial distribution of the charge in the chain, it is possible to observe either a uniform movement of the charge along the chain, or an oscillatory mode of charge movement.

cond-mat.stat-mech↗

arXiv2020

Theoretical and Experimental Investigations of DNA Open States

Literature data on the properties of DNA open states are reviewed and analyzed. These states are formed as a result of strong DNA fluctuations and have a great impact on a number of biochemical processes; among them is charge transfer in DNA, for example. A comparative analysis of experimental data on the kinetics and thermodynamics of DNA open states for a wide temperature range was carried out. Discrepancies between the results of various experiments have been explained. Three types of DNA open states are recognized based on their differences in thermodynamic properties and other characteristics. Besides, an up-to-date definition of the term "open state" is given. A review is carried out for simple mathematical models of DNA in most of which the state of one pair is described by one or two variables. The main problems arising in theoretical investigations of heterogeneous DNA in the framework of models of this level are considered. The role of each group of models in interpretation of experimental data is discussed. Special consideration is given to the studies of the transfer and localization of the nucleotide pairs oscillations' energy by mechanical models. These processes are shown to play a key role in the dynamics of a heterogeneous duplex. Their theoretical interpretation is proven to be very important for the development of modern molecular biology and biophysics. The main features of the theoretical approaches are considered which enabled describing various experimental data. Prospects of the models' development are described, particular details of their optimization are suggested, and possible ways of modernization of some experimental techniques are discussed.

q-bio.BM↗

arXiv2018

Investigation of DNA denaturation in Peyrard-Bishop-Dauxois model by molecular dynamics method

The phase transition of $(PolyA/PolyT)_{100}$ duplex into the denaturated state is studied in the Peyrard-Bishop-Dauxois model by the method of direct molecular-dynamical modeling. The temperature dependencies of the total energy and heat capacity of the duplex are calculated. The approach applied can be used to calculate the statistical properties of the duplexes of any length and nucleotide composition.

cond-mat.soft↗

arXiv2015

Temperature dependence of electronic heat capacity in Holstein model

The dynamics of charge migration was modeled to calculate temperature dependencies of its thermodynamic equilibrium values such as energy and electronic heat capacity in homogeneous adenine fragments. The energy varies from nearly polaron one at T~0 to midpoint of the conductivity band at high temperatures. The peak on the graph of electronic heat capacity is observed at the polaron decay temperature.

physics.comp-ph↗

arXiv2015

Superconducting properties of 3D low-density TI-bipolaron gas

Consideration is given to thermodynamical properties of a three-dimensional Bose-condensate of translation-invariant bipolarons (TI-bipolarons). The critical temperature of transition, energy, heat capacity and the transition heat of TI-bipolaron gas are calculated. The results obtained are used to explain experiments on high-temperature superconductors.

cond-mat.supr-con↗

arXiv2015

Pekar's Ansatz and the Strong Coupling Problem in Polaron Theory

A detailed consideration is given to the translation-invariant theory of Tulub polaron constructed without the use of Pekar ansatz. A fundamental result of the theory is that the value of the polaron energy is lower than that obtained on the basis of Pekar ansatz which was considered as an asymptotically exact solution in the strong coupling limit. In the case of bipolarons the theory yields the best values of the coupling energy and critical parameters of their stability. Numerous physical consequences of the existence of translation-invariant polarons and bipolarons are discussed.

cond-mat.other↗

arXiv2015

Continuum Model of the One-Dimensional Holstein Bipolaron in DNA

The work is devoted to obtaining the 1D bipolaron functional by Holstein method for the continuum approximation. We analyzed the effect of electron correlations associated with the direct dependence of the wave function of the electron system from the electron-electron distance on the binding energy of the bipolaron. Numerical calculations of the bipolaron binding energy were performed according to the parameters of the system.

cond-mat.other↗

arXiv2015

Polaron Model of the Formation of Hydrated Electron States

A computer simulation of the formation of photoexcited electrons in water is performed within the framework of a dynamic model. The obtained results are discussed in comparison with experimental data and theoretical estimates.

cond-mat.other↗

arXiv2014

Large-radius Holstein polaron and the problem of spontaneous symmetry breaking

A translation-invariant solution is found for a large-radius Holstein polaron whose energy in the strong coupling limit is lower than that obtained by Holstein. The wave function corresponding to this solution is delocalized. A conclusion is made about the absence of a spontaneous symmetry breaking in the quantum system discussed.

cond-mat.other↗

arXiv2014

A new type of localized fast moving electronic excitations in molecular chains

It is shown that in a Holstein molecular chain placed in a strong longitudinal electric field some new types of excitations can arise. This excitations can transfer a charge over large distance (more than 1000 nucleotide pairs) along the chain retaining approximately their shapes. Excitations are formed only when a strong electric field either exists or quickly arises under especially preassigned conditions. These excitations transfer a charge even in the case when Holstein polarons are practically immobile. The results obtained are applied to synthetic homogeneous PolyG/PolyC DNA duplexes. They can be also provide the basis for explanation of famous H.W. Fink and C. Schönenberger experiment on long-range charge transfer in DNA.

cond-mat.mes-hall↗

arXiv2014

Scaling of Temperature Dependence of Charge Mobility in Molecular Holstein Chains

The temperature dependence of a charge mobility in a model DNA based on Holstein Hamiltonian is calculated for 4 types of homogeneous sequences It has turned out that upon rescaling all 4 types are quite similar. Two types of rescaling, i.e. those for low and intermediate temperatures, are found. The curves obtained are approximated on a logarithmic scale by cubic polynomials. We believe that for model homogeneous biopolymers with parameters close to the designed ones, one can assess the value of the charge mobility without carrying out resource-intensive direct simulation, just by using a suitable approximating function.

cond-mat.stat-mech↗

arXiv2014

Conditions for the Existence of Polaron States in Classical Molecular Chains at Finite Temperatures

Today in many articles the polaron states are calculated in classical molecular chains for zero temperature. At the same time it is assumed that polaron properties do not change significantly, if the temperature is nonzero, but much smaller than the characteristic energy equal to the depth of the polaron level. However, the results of computational experiments lead us to suggestion that in infinitely long chain the polaron is destroyed at any small different from zero temperature. The paper is devoted to the resolution of described "paradoxical" situation.

cond-mat.other↗

arXiv2014

Excitation of Bubbles and Breathers in DNA and Their Interaction with the Charge Carriers

The nonlinear excitations induced in DNA by external force are considered on the basis of Peyrard-Bishop-Dauxois model. It is shown that such impact can lead to creation of bubbles which can propogate through the molecule. The interaction of such bubbles with an excess electron or hole is considered. The numerical experiments demonstrate the possibility of charge transfer induced by bubbles. The possible applications of the obtained results in nanobioelectronics are discussed.

cond-mat.other↗

arXiv2013

Solvation Effects on Hole Mobility in the Poly G/Poly C Duplex

Theoretical calculations of solvation contribution to hole energy in a polynucleotide chain give very low hole mobility values at zero temperature, μ< 10^{-3} cm^2/(V s). We calculated hole mobility at physiological temperature for the Poly G/Poly C DNA duplex, which gave substantially larger mobility values. Mobility over the temperature range 20-400 K was calculated. Taking stacking interaction into account substantially increased hole mobility.

physics.bio-ph↗

arXiv2013

The Virial Theorem and the Ground State Problem in Polaron Theory

The virial theorem for the translation-invariant theory of a polaron [3] is discussed. It is shown that, in [3], Tulub made a nonoptimal choice of variational parameters in the strong-coupling limit, which led to the violation of the virial relations. The introduction of an additional variational parameter to the test function reduces the polaron energy and makes it possible to satisfy the relations of the virial theorem for a strong-coupling polaron (the Pekar 1 : 2 : 3 : 4 theorem).

cond-mat.other↗