Constraints, Histones, and the 30 Nanometer Spiral

We investigate the mechanical stability of a segment of DNA wrapped around a histone in the nucleosome configuration. The assumption underlying this investigation is that the proper model for this packaging arrangement is that of an elastic rod that is free to twist and that writhes subject to mechanical constraints. We find that the number of constraints required to stabilize the nuclesome configuration is determined by the length of the segment, the number of times the DNA wraps around the histone spool, and the specific constraints utilized. While it can be shown that four constraints suffice, in principle, to insure stability of the nucleosome, a proper choice must be made to guarantee the effectiveness of this minimal number. The optimal choice of constraints appears to bear a relation to the existence of a spiral ridge on the surface of the histone octamer. The particular configuration that we investigate is related to the 30 nanometer spiral, a higher-order organization of DNA in chromatin.Comment: ReVTeX, 15 pages, 18 figure

Physical theory of the twentieth century and contemporary philosophy

It has been shown that the criticism of Pauli as well as of Susskind and Glogover may be avoided if the standard quantum-mechanical mathematical model has been suitably extended. There is not more any reason for Einstein's citicism, either, if in addition to some new results concerning Bell's inequalities and Belifante's argument are taken into account. The ensemble interpretation of quantum mechanics (or the hidden-variable theory) should be preferred, which is also supported by the already published results of experiments with three polarizers. Greater space in the text has been devoted also to the discussion of epistemological problems and some philosophical consequences.Comment: 12 page

Scattering of slow-light gap solitons with charges in a two-level medium

The Maxwell-Bloch system describes a quantum two-level medium interacting with a classical electromagnetic field by mediation of the the population density. This population density variation is a purely quantum effect which is actually at the very origin of nonlinearity. The resulting nonlinear coupling possesses particularly interesting consequences at the resonance (when the frequency of the excitation is close to the transition frequency of the two-level medium) as e.g. slow-light gap solitons that result from the nonlinear instability of the evanescent wave at the boundary. As nonlinearity couples the different polarizations of the electromagnetic field, the slow-light gap soliton is shown to experience effective scattering whith charges in the medium, allowing it for instance to be trapped or reflected. This scattering process is understood qualitatively as being governed by a nonlinear Schroedinger model in an external potential related to the charges (the electrostatic permanent background component of the field).Comment: RevTex, 14 pages with 5 figures, to appear in J. Phys. A: Math. Theo

Casimir-Polder forces: A non-perturbative approach

Within the frame of macroscopic QED in linear, causal media, we study the radiation force of Casimir-Polder type acting on an atom which is positioned near dispersing and absorbing magnetodielectric bodies and initially prepared in an arbitrary electronic state. It is shown that minimal and multipolar coupling lead to essentially the same lowest-order perturbative result for the force acting on an atom in an energy eigenstate. To go beyond perturbation theory, the calculations are based on the exact center-of-mass equation of motion. For a nondriven atom in the weak-coupling regime, the force as a function of time is a superposition of force components that are related to the electronic density-matrix elements at a chosen time. Even the force component associated with the ground state is not derivable from a potential in the ususal way, because of the position dependence of the atomic polarizability. Further, when the atom is initially prepared in a coherent superposition of energy eigenstates, then temporally oscillating force components are observed, which are due to the interaction of the atom with both electric and magnetic fields.Comment: 23 pages, 3 figures, additional misprints correcte

Coherent spin relaxation in molecular magnets

Numerical modelling of coherent spin relaxation in nanomagnets, formed by magnetic molecules of high spins, is accomplished. Such a coherent spin dynamics can be realized in the presence of a resonant electric circuit coupled to the magnet. Computer simulations for a system of a large number of interacting spins is an efficient tool for studying the microscopic properties of such systems. Coherent spin relaxation is an ultrafast process, with the relaxation time that can be an order shorter than the transverse spin dephasing time. The influence of different system parameters on the relaxation process is analysed. The role of the sample geometry on the spin relaxation is investigated.Comment: Latex file, 22 pages, 7 figure

Factors associated with diversity, quantity and zoonotic potential of ectoparasites on urban mice and voles

Wild rodents are important hosts for tick larvae but co-infestations with other mites and insects are largely neglected. Small rodents were trapped at four study sites in Berlin, Germany, to quantify their ectoparasite diversity. Host-specific, spatial and temporal occurrence of ectoparasites was determined to assess their influence on direct and indirect zoonotic risk due to mice and voles in an urban agglomeration. Rodent-associated arthropods were diverse, including 63 species observed on six host species with an overall prevalence of 99%. The tick Ixodes ricinus was the most prevalent species, found on 56% of the rodents. The trapping location clearly affected the presence of different rodent species and, therefore, the occurrence of particular host-specific parasites. In Berlin, fewer temporary and periodic parasite species as well as non-parasitic species (fleas, chiggers and nidicolous Gamasina) were detected than reported from rural areas. In addition, abundance of parasites with low host-specificity (ticks, fleas and chiggers) apparently decreased with increasing landscape fragmentation associated with a gradient of urbanisation. In contrast, stationary ectoparasites, closely adapted to the rodent host, such as the fur mites Myobiidae and Listrophoridae, were most abundant at the two urban sites. A direct zoonotic risk of infection for people may only be posed by Nosopsyllus fasciatus fleas, which were prevalent even in the city centre. More importantly, peridomestic rodents clearly supported the life cycle of ticks in the city as hosts for their subadult stages. In addition to trapping location, season, host species, body condition and host sex, infestation with fleas, gamasid Laelapidae mites and prostigmatic Myobiidae mites were associated with significantly altered abundance of I. ricinus larvae on mice and voles. Whether this is caused by predation, grooming behaviour or interaction with the host immune system is unclear. The present study constitutes a basis to identify interactions and vector function of rodent-associated arthropods and their potential impact on zoonotic diseases

Nonlinear spin relaxation in strongly nonequilibrium magnets

A general theory is developed for describing the nonlinear relaxation of spin systems from a strongly nonequilibrium initial state, when, in addition, the sample is coupled to a resonator. Such processes are characterized by nonlinear stochastic differential equations. This makes these strongly nonequilibrium processes principally different from the spin relaxation close to an equilibrium state, which is represented by linear differential equations. The consideration is based on a realistic microscopic Hamiltonian including the Zeeman terms, dipole interactions, exchange interactions, and a single-site anisotropy. The influence of cross correlations between several spin species is investigated. The critically important function of coupling between the spin system and a resonant electric circuit is emphasized. The role of all main relaxation rates is analyzed. The phenomenon of self-organization of transition coherence in spin motion, from the quantum chaotic stage of incoherent fluctuations, is thoroughly described. Local spin fluctuations are found to be the triggering cause for starting the spin relaxation from an incoherent nonequilibrium state. The basic regimes of collective coherent spin relaxation are studied.Comment: Latex file, 31 page

Origin of Pure Spin Superradiance

The question addressed in this paper is: What originates pure spin superradiance in a polarized spin system placed inside a resonator? The term "pure" means that no initial coherence is imposed on spins, and its appearance manifests a purely self-organized collective effect. The consideration is based on a microscopic model with dipole spin interactions. An accurate solution of evolution equations is given. The results show that the resonator Nyquist noise does not play, contrary to the common belief, any role in starting spin superradiance, but the emergence of the latter is initiated by local spin fluctuations. The decisive role of nonsecular dipole interactions is stressed.Comment: 1 file, 13 pages, RevTe

Thermoluminescence of zircon: a kinetic model

The mineral zircon, ZrSiO4, belongs to a class of promising materials for geochronometry by means of thermoluminescence (TL) dating. The development of a reliable and reproducible method for TL dating with zircon requires detailed knowledge of the processes taking place during exposure to ionizing radiation, long-term storage, annealing at moderate temperatures and heating at a constant rate (TL measurements). To understand these processes one needs a kinetic model of TL. This paper is devoted to the construction of such amodel. The goal is to study the qualitative behaviour of the system and to determine the parameters and processes controlling TL phenomena of zircon. The model considers the following processes: (i) Filling of electron and hole traps at the excitation stage as a function of the dose rate and the dose for both (low dose rate) natural and (high dose rate) laboratory irradiation. (ii) Time dependence of TL fading in samples irradiated under laboratory conditions. (iii) Short time annealing at a given temperature. (iv) Heating of the irradiated sample to simulate TL experiments both after laboratory and natural irradiation. The input parameters of the model, such as the types and concentrations of the TL centres and the energy distributions of the hole and electron traps, were obtained by analysing the experimental data on fading of the TL-emission spectra of samples from different geological locations. Electron paramagnetic resonance (EPR) data were used to establish the nature of the TL centres. Glow curves and 3D TL emission spectra are simulated and compared with the experimental data on time-dependent TL fading. The saturation and annealing behaviour of filled trap concentrations has been considered in the framework of the proposed kinetic model and comparedwith the EPR data associated with the rare-earth ions Tb3+ and Dy3+, which play a crucial role as hole traps and recombination centres. Inaddition, the behaviour of some of the SiOmn− centres has been compared with simulation results.

Electronic Coherence Dephasing in Excitonic Molecular Complexes: Role of Markov and Secular Approximations

We compare four different types of equations of motion for reduced density matrix of a system of molecular excitons interacting with thermodynamic bath. All four equations are of second order in the linear system-bath interaction Hamiltonian, with different approximations applied in their derivation. In particular we compare time-nonlocal equations obtained from so-called Nakajima-Zwanzig identity and the time-local equations resulting from the partial ordering prescription of the cummulant expansion. In each of these equations we alternatively apply secular approximation to decouple population and coherence dynamics from each other. We focus on the dynamics of intraband electronic coherences of the excitonic system which can be traced by coherent two-dimensional spectroscopy. We discuss the applicability of the four relaxation theories to simulations of population and coherence dynamics, and identify features of the two-dimensional coherent spectrum that allow us to distinguish time-nonlocal effects.Comment: 14 pages, 8 figure