Biomedical subjects

D M Basko

Publications and source records attributed to D M Basko.

8 recordsLinked to original sources

PubMed2006

Effect of water drag on diffusion of drifting polarons in DNA.

It has been shown, theoretically and experimentally, that a hole or an excess electron on a DNA molecule in solution forms a delocalized wave function, a polaron. For an all-adenine (A) sequence or a mixed sequence of guanines (G's) and A's, calculations taking into account the polarization of the solution give the wave function spread over approximately four bases, which appears to be in agreement with experiment. The polaron may move by hopping or by drift. Drift can take place in a region with all the same bases, for example, A's, by the polaron dropping an A on the trailing edge and picking up an A on the leading edge. For drift that is not too rapid, the necessity of the polarization changing as the polaron moves exerts a drag on the polaron. We calculate the drag by using a model introduced earlier to describe the polaron. We find the drag to be proportional to the velocity of the polaron and to the orientational relaxation time of the water molecules. The drag is also a function of the Coulomb interactions of the fractional charges on the bases constituting the polaron, as modified by the polarization charge induced in the solution. The diffusion rate and mobility for all A polarons, calculated taking into account the drag, are 8 x 10(-5) cm(2)/s and 3 x 10(-3) cm(2)/(V s), respectively. We believe that in the experimental studies that have been carried out on hole propagation in a series of A's it was drift being observed rather than the hopping of a localized hole between adjacent A's, as was assumed to be the case.

Adenine↗

PubMed2004

Dynamic localization and the Coulomb blockade in quantum dots under ac pumping.

We study conductance through a quantum dot under Coulomb blockade conditions in the presence of an external periodic perturbation. The stationary state is determined by the balance between the heating of the dot electrons by the perturbation and cooling by electron exchange with the cold contacts. We show that the Coulomb blockade peak can have a peculiar shape if heating is affected by dynamic localization, which can be an experimental signature of this effect.

Journal Article↗

PubMed2003

Hopping between localized Floquet states in periodically driven quantum dots.

The dynamic localization in energy space, suppression of the absorption of energy from an external microwave field due to quantum interference, was analyzed recently for a closed quantum dot in the absence of electron-electron interactions. Here a weak interaction is shown to lead to a finite absorption and heating, which may be viewed as hopping between localized Floquet states. The heating rate grows together with the electronic temperature, eventually destroying the localization.

Journal Article↗

PubMed2003

Dynamic localization in quantum dots: analytical theory.

We analyze the response of a complex quantum-mechanical system (e.g., a quantum dot) to a time-dependent perturbation phi(t). Assuming the dot to be described by random-matrix theory for the Gaussian orthogonal ensemble, we find the quantum correction to the energy absorption rate as a function of the dephasing time t(phi). If phi(t) is a sum of d harmonics with incommensurate frequencies, the correction behaves similarly to that for the conductivity deltasigma(d)(t(phi)) in the d-dimensional Anderson model of the orthogonal symmetry class. For a generic periodic perturbation, the leading quantum correction is absent as in the systems of the unitary symmetry class, unless phi(-t+tau)=phi(t+tau) for some tau, which falls into the quasi-1D orthogonal universality class.

Journal Article↗

PubMed2002

Self-trapping versus trapping: application to hole transport in DNA.

We address the problem of interplay between self-trapping effects and effects of an external potential, which may be relevant for many physical systems, such as polarons in solids or a Bose-Einstein condensate with attraction. If the potential consists of two different wells, the system initially localized in the shallower well may relax into the deeper well, or may not if stabilized by the self-trapping effect. We show how this picture can be applied to interpret results of recent experiments on electron transfer in the DNA molecule [Giese et al., Nature 412, 318 (2001)]. The results of our calculations agree well with the experimental findings, giving evidence that hole transport in DNA involves polaronic effects.

Chemical Phenomena↗

PubMed2002

Effect of solvation on hole motion in DNA.

An excess charge on a DNA chain in solution interacts with polar solvent molecules and mobile counterions. We give the first theoretical estimate of the resulting hole self-localization energy and calculate the corresponding contribution to hole mobility on a DNA stack consisting of a single base pair repeated.

DNA↗

PubMed2002

Stationary polaron motion in a polymer chain at high electric fields.

We study the stationary motion of a polaron in a conducting polymer in the presence of a high electric field. Using the Su-Schrieffer-Heeger model plus an electric field, we find that at polaron velocities not exceeding the sound velocity, the dissipation of the electronic energy into the lattice occurs via emission of phonons with single selected wave vector. For this case the corresponding contribution to the polaron mobility can be calculated analytically. We discuss the issue of the polaron stability with respect to dissociation in a very high field at supersonic velocities.

Journal Article↗

PubMed2001

Hole traps in DNA.

Sequences of guanines, GG and GGG, are known to be readily oxidized, forming radical cations, i.e., hole traps, on DNA. The trapping probability of GG is less than that of GGG. Lewis et al. (J. Am. Chem. Soc. 2000, 122, 12037) have used measurements on synthetic hairpins to determine the free energy liberated when a hole goes from the radical cation G(+) to GG or to GGG. They find these free energies to be of the order of thermal energy at room temperature, in contradiction to the expectation by many of much greater trap depths. We have calculated the wave function of a hole on G, on GG, and on GGG surrounded by adenines, as in the Lewis et al. experiments, using a simple tight-binding model. We find that to account for the shallow traps found by them it is necessary that the difference in ionization potentials of contiguous guanine and adenine be smaller by about 0.2 eV than the 0.4 eV found for isolated bases. Using this value and taking into account polaron formation, we find the wave functions of holes trapped on G, GG, or GGG to extend over approximately 6 sites (bases) and with energy level differences in good agreement with the values found by Lewis et al.

Cations↗