Base pair opening and bubble transport in a DNA double helix induced by a protein molecule in a viscous medium

We study the nonlinear dynamics of a protein-DNA molecular system by treating DNA as a set of two coupled linear chains and protein in the form of a single linear chain sliding along the DNA at the physiological temperature in a viscous medium. The nonlinear dynamics of the above molecular system in general is governed by a perturbed nonlinear Schr\"{o}dinger equation. In the non-viscous limit, the equation reduces to the completely integrable nonlinear Schr\"{o}dinger (NLS) equation which admits N-soliton solutions. The soliton excitations of the DNA bases make localized base pair opening and travel along the DNA chain in the form of a bubble. This may represent the bubble generated during the transcription process when an RNA-polymerase binds to a promoter site in the DNA double helical chain. The perturbed NLS equation is solved using a perturbation theory by treating the viscous effect due to surrounding as a weak perturbation and the results show that the viscosity of the solvent in the surrounding damps out the amplitude of the soliton.Comment: 4. Submitted to Phys. Rev.

Benchmarking calculations of excitonic couplings between bacteriochlorophylls

Excitonic couplings between (bacterio)chlorophyll molecules are necessary for simulating energy transport in photosynthetic complexes. Many techniques for calculating the couplings are in use, from the simple (but inaccurate) point-dipole approximation to fully quantum-chemical methods. We compared several approximations to determine their range of applicability, noting that the propagation of experimental uncertainties poses a fundamental limit on the achievable accuracy. In particular, the uncertainty in crystallographic coordinates yields an uncertainty of about 20% in the calculated couplings. Because quantum-chemical corrections are smaller than 20% in most biologically relevant cases, their considerable computational cost is rarely justified. We therefore recommend the electrostatic TrEsp method across the entire range of molecular separations and orientations because its cost is minimal and it generally agrees with quantum-chemical calculations to better than the geometric uncertainty. We also caution against computationally optimizing a crystal structure before calculating couplings, as it can lead to large, uncontrollable errors. Understanding the unavoidable uncertainties can guard against striving for unrealistic precision; at the same time, detailed benchmarks can allow important qualitative questions--which do not depend on the precise values of the simulation parameters--to be addressed with greater confidence about the conclusions

Pecularities of Hall effect in GaAs/{\delta}<Mn>/GaAs/In\timesGa1-\timesAs/GaAs (\times {\approx} 0.2) heterostructures with high Mn content

Transport properties of GaAs/{\delta}/GaAs/In\timesGa1-\timesAs/GaAs structures containing InxGa1-xAs (\times {\approx} 0.2) quantum well (QW) and Mn delta layer (DL) with relatively high, about one Mn monolayer (ML) content, are studied. In these structures DL is separated from QW by GaAs spacer with the thickness ds = 2-5 nm. All structures possess a dielectric character of conductivity and demonstrate a maximum in the resistance temperature dependence Rxx(T) at the temperature {\approx} 46K which is usually associated with the Curie temperature Tc of ferromagnetic (FM) transition in DL. However, it is found that the Hall effect concentration of holes pH in QW does not decrease below TC as one ordinary expects in similar systems. On the contrary, the dependence pH(T) experiences a minimum at T = 80-100 K depending on the spacer thickness, then increases at low temperatures more strongly than ds is smaller and reaches a giant value pH = (1-2)\cdot10^13 cm^(-2). Obtained results are interpreted in the terms of magnetic proximity effect of DL on QW, leading to induce spin polarization of the holes in QW. Strong structural and magnetic disorder in DL and QW, leading to the phase segregation in them is taken into consideration. The high pH value is explained as a result of compensation of the positive sign normal Hall effect component by the negative sign anomalous Hall effect component.Comment: 19 pages, 6 figure

Far-infrared vibrational properties of linear C60 polymers: A comparison between neutral and charged materials

We report the far-infrared transmittance spectrum of a pure phase of the orthorhombic high-temperature and high-pressure C-60 polymer and compare the results with a previously published spectrum of the charged RbC60 orthorhombic polymer. Assignments for both spectra are made with the aid of first-principles quantum molecular dynamics simulations of the two materials. We find that the striking spectral differences between the neutral and charged linear fullerene polymers can be fully accounted for by charge effects on the C-60 ball

Far-infrared vibrational properties of high-pressure-high-temperature C60 polymers and the C60 dimer

We report high-resolution far-infrared transmission measurements of the 2 + 2 cycloaddition C-60 dimer and two-dimensional rhombohedral and one-dimensional orthorhombic high-pressure high-temperature C60 polymers. In the spectral region investigated(20-650 cm(-1)), we see no low-energy interball modes, but symmetry breaking of the linked C-60 balls is evident in the complex spectrum of intramolecular modes. Experimental features suggest large splittings or frequency shifts of some IhC60-derived modes that are activated by symmetry reduction, implying that the balls are strongly distorted in these structures. We have calculated the vibrations of all three systems by first-principles quantum molecular dynamics and use them to assign the predominant IhC60 symmetries of observed modes. Pur calculations show unprecedentedly large downshifts of T-1u(2)-derived modes and extremely large splittings of other modes, both of which are consistent with the experimental spectra. For the rhombohedral and orthorhombic polymers, the T-1u(2)-derived mode that is polarized along the bonding direction is calculated to downshift below any T-1u(1)-derived modes. We also identify a previously unassigned feature near 610 cm(-1) in all three systems as a widely split or shifted mode derived from various silent IhC60 vibrations, confirming a strong perturbation model for these linked fullerene structures

Localization effects in radiationally disordered high-temperature superconductors: Theoretical interpretation

Theoretical interpretation of recent experiments on radiationally disordered high-temperature superconductors is presented, based on the concepts of mutual interplay of Anderson localization and superconductivity. Microscopic derivation of Ginzburg-Landau coefficients for the quasi-two-dimensional system in the vicinity of localization transition is given in the framework of the self-consistent theory of localization. The 'minimal metallic conductivity' for the quasi-two-dimensional case is enhanced due to a small overlap of electronic states on the nearest neighbor conducting planes. This leads to a stronger influence of localization effects than in ordinary (three-dimensional) superconductors. From this point of view even the initial samples of high-temperature superconductors are already very close to Anderson transition. Anomalies of H(c2) are also analyzed, explaining the upward curvature of H(c2)(T) and apparent independence of dH(c2)/dT (T = T(sub c)) on the degree of disorder as due to localization effects. Researchers discuss the possible reasons of fast T(sub c) degradation due to the enhanced Coulomb effects caused by the disorder induced decrease of localization length. The appearance and growth of localized magnetic moments is also discussed. The disorder dependence of localization length calculated from the experimental data on conductivity correlates reasonably with the theoretical criterion for suppression of superconductivity in the system with localized electronic states