Long-range donor-acceptor electron transport mediated by α helices.

We study the long-range electron and energy transfer mediated by a polaron on an α-helix polypeptide chain coupled to donor and acceptor molecules at opposite ends of the chain. We show that for specific parameters of the system, an electron initially located on the donor can tunnel onto the α helix, forming a polaron, which then travels to the other extremity of the polypeptide chain, where it is captured by the acceptor. We consider three families of couplings between the donor, the acceptor, and the chain and show that one of them can lead to a 90% efficiency of the electron transport from donor to acceptor. We also show that this process remains stable at physiological temperatures in the presence of thermal fluctuations in the system.

Directed polaron propagation in linear polypeptides induced by intramolecular vibrations and external electric pulses.

We study the propagation of α-helix polarons in a model describing the nonadiabatic interaction between an electron and a lattice of quantum mechanical oscillators at physiological temperature. We show that when excited by a subpicosecond electric pulse, as induced by experimentally observed subpicosecond charge separation, the polaron is displaced by up to hundreds of lattice sites before the electron becomes delocalised. We discuss biophysical implications of our results.

Donor-acceptor electron transport mediated by solitons.

We study the long-range electron and energy transfer mediated by solitons in a quasi-one-dimensional molecular chain (conjugated polymer, alpha-helical macromolecule, etc.) weakly bound to a donor and an acceptor. We show that for certain sets of parameter values in such systems an electron, initially located at the donor molecule, can tunnel to the molecular chain, where it becomes self-trapped in a soliton state, and propagates to the opposite end of the chain practically without energy dissipation. Upon reaching the end, the electron can either bounce back and move in the opposite direction or, for suitable parameter values of the system, tunnel to the acceptor. We estimate the energy efficiency of the donor-acceptor electron transport depending on the parameter values. Our calculations show that the soliton mechanism works for the parameter values of polypeptide macromolecules and conjugated polymers. We also investigate the donor-acceptor electron transport in thermalized molecular chains.

Thermal enhancement and stochastic resonance of polaron ratchets.

We study the ratchet drift of large polarons (solitons) in molecular diatomic chains induced by unbiased time periodic electric fields at nonzero temperature below its critical value. We show that, at a nonzero temperature, the critical value of the intensity of the electric field above which the ratchet phenomenon takes place is lower than at zero temperature for the same frequency of the field. We show that there is a range of temperatures for which the polaron drift is larger than that at zero temperature. We also show that temperature decreases the value of the lowest critical period of the field. And, finally, we demonstrate that there is a stochastic resonance in a polaron ratchet, namely that there is an optimal temperature at which the polaron drift is a maximum. The values of the stochastic resonance temperature, the lowest critical values of the field intensity, and its period depend on various parameters of the system and, in particular, on the anisotropy of the chain parameters. This temperature induced decrease of the critical value of the field intensity and its period, as well as the stochastic resonance itself, may be important for practical applications of the ratchet phenomenon in systems involving conducting polymers and other low-dimensional materials. They may also be important in some biological macromolecules where the ratchet phenomenon could take place in biomotors and energy and/or charge transport.

Biopolymer hairpin loops sustained by polarons.

We show that polarons can sustain looplike configurations in flexible biopolymers and that the size of the loops depend on both the flexural rigidity of the polymer and the electron-phonon coupling constant. In particular we show that for single stranded DNA (ssDNA) and polyacetylene such loops can have as few as seven monomers. We also show that these configurations are very stable under thermal fluctuations and so could facilitate the formation of hairpin loops of ssDNA.

Cryopreservation of apple in vitro axillary buds using droplet-vitrification.

In vitro axillary buds of two apple cultivars, Pinova and Jonagold, were successfully cryopreserved by droplet-vitrification. In vitro axillary buds of cv. Pinova were subjected to PVS2 for 15, 30, 45, 60, 80 or 100 min, while Jonagold buds were treated with PVS2 for 15, 30, 45 or 60 min. In addition, the effect of age of in vitro mother-plants on recovery after cryopreservation was evaluated. Recovery was performed on medium with various combinations of BA, IBA and GA3. Regrowth percentages for cv. Pinova increased in line with increasing PVS2 exposure durations, from 15 to 60 min. Cv. Jonagold showed a similar trend with an increase in regrowth from 30 to 60 min PVS2 exposure. Improved regrowth was observed when axillary buds were excised from aged mother-plants in comparison to those excised from plantlets that were regularly subcultured. The highest shoot regrowth was obtained when applying a 60 min PVS2 treatment to axillary buds excised from non-preconditioned 4-month old in vitro shoots and performing regrowth on recovery medium containing 4.50 microM BA and 0.50 microM IBA. This optimal protocol was also successfully applied to apple rootstocks M26 and Jork 9.

Ratchet dynamics of large polarons in asymmetric diatomic molecular chains.

We study the dynamics of large polarons in diatomic molecular chains, at zero temperature, under the influence of an external, periodic in time, electric field of zero mean value. We show that in asymmetric chains, i.e. chains with two different atoms per unit cell, a harmonic unbiased field causes a drift of such polarons. Such a drift current, known as the ratchet phenomenon, depends strongly on the parameters of the chain; in particular, on the extent of the anisotropy of the chain and on the size of the polaron. Moreover, the drift takes place only if the intensity and the period of the field exceed some critical values which also depend on the parameters of the chain. We show that this directed current of polarons is a complicated phenomenon. It takes place in dissipative systems with a broken spatial symmetry and is generated by the interplay between the Peierls-Nabarro barrier and the impact of the external field on the charged polarons. The dependence of the amplitude of the polaron oscillations, the size of the drift per period of the external field and the average velocity are determined as a function of the intensity of the field and of its frequency.

Scattering of sine-Gordon breathers on a potential well.

We analyze the scattering of the classical sine-Gordon breathers on a square potential well. We show that the scattering process depends not only on the vibration frequency of the breather and its incoming speed but also on its phase as well as the depth and width of the well. We show that the breather can pass through the well and exit with a speed different, sometimes larger, from the initial one. It can also be trapped and very slowly decay inside the well or bounce out of the well and go back to where it came from. We also show that the breather can split into a kink-antikink pair when it hits the well.

Solitons in alpha-helical proteins.

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, and dynamical properties of Davydov's solitons in an alpha helix. We show, analytically and numerically, that the corresponding system of nonlinear equations admits several types of stationary soliton solutions and that solitons which preserve helical symmetry are dynamically unstable: once formed, they decay rapidly when they propagate. On the other hand, the soliton which spontaneously breaks the local translational and helical symmetries possesses the lowest energy and is a robust localized entity. We also demonstrate that this soliton is the result of a hybridization of the quasiparticle states from the two lowest degenerate bands and has an inner structure which can be described as a modulated multihump amplitude distribution of excitations on individual spines. The complex and composite structure of the soliton manifests itself distinctly when the soliton is moving and some interspine oscillations take place. Such a soliton structure and the interspine oscillations have previously been observed numerically [A. C. Scott, Phys. Rev. A 26, 578 (1982)]. Here we argue that the solitons studied by Scott are hybrid solitons and that the oscillations arise due to the helical symmetry of the system and result from the motion of the soliton along the alpha helix. The frequency of the interspine oscillations is shown to be proportional to the soliton velocity.