Molecular modelling studies of binding of DACD derivatives into G-Quadruplex DNA: comparison of force field and quantum polarized ligand docking methods

The DNA G-qadruplexes are one of the targets being actively explored for anti-cancer therapy by inhibiting them through small molecules. This computational study was conducted to predict the binding strengths and orientations of a set of novel dimethyl-amino-ethyl-acridine (DACA) analogues that are designed and synthesized in our laboratory, but did not diffract in Synchrotron light.Thecrystal structure of DNA G-Quadruplex(TGGGGT)4(PDB: 1O0K) was used as target for their binding properties in our studies.We used both the force field (FF) and QM/MM derived atomic charge schemes simultaneously for comparing the predictions of drug binding modes and their energetics. This study evaluates the comparative performance of fixed point charge based Glide XP docking and the quantum polarized ligand docking schemes. These results will provide insights on the effects of including or ignoring the drug-receptor interfacial polarization events in molecular docking simulations, which in turn, will aid the rational selection of computational methods at different levels of theory in future drug design programs. Plenty of molecular modelling tools and methods currently exist for modelling drug-receptor or protein-protein, or DNA-protein interactionssat different levels of complexities.Yet, the capasity of such tools to describevarious physico-chemical propertiesmore accuratelyis the next step ahead in currentresearch.Especially, the usage of most accurate methods in quantum mechanics(QM) is severely restricted by theirtedious nature. Though the usage of massively parallel super computing environments resulted in a tremendous improvement in molecular mechanics (MM) calculations like molecular dynamics,they are still capable of dealing with only a couple of tens to hundreds of atoms for QM methods. One such efficient strategy that utilizes thepowers of both MM and QM are the QM/MM hybrid methods. Lately, attempts have been directed towards the goal of deploying several different QM methods for betterment of force field based simulations, but with practical restrictions in place. One of such methods utilizes the inclusion of charge polarization events at the drug-receptor interface, that is not explicitly present in the MM FF.

Measuring variation in potato roots in both field and glasshouse: the search for useful yield predictors and a simple screen for root traits

Aims Potatoes have an inadequate rooting system for efficient acquisition of water and minerals and use disproportionate amounts of irrigation and fertilizer. This research determines whether significant variation in rooting characteristics of potato exists, which characters correlate with final yield and whether a simple screen for rooting traits could be developed. Methods Twenty-eight genotypes of Solanum tuberosum groups Tuberosum and Phureja were grown in the field; eight replicate blocks to final harvest, while entire root systems were excavated from four blocks. Root classes were categorised and measured. The same measurements were made on these genotypes in the glasshouse, 2 weeks post emergence. Results In the field, total root length varied from 40 m to 112 m per plant. Final yield was correlated negatively with basal root specific root length and weakly but positively with total root weight. Solanum tuberosum group Phureja genotypes had more numerous roots and proportionally more basal than stolon roots compared with Solanum tuberosum, group Tuberosum genotypes. There were significant correlations between glasshouse and field measurements. Conclusions Our data demonstrate that variability in rooting traits amongst commercially available potato genotypes exists and a robust glasshouse screen has been developed. By measuring potato roots as described in this study, it is now possible to assess rooting traits of large populations of potato genotypes.

A new South American network to study the atmospheric electric field and its variations related to geophysical phenomena

In this paper we present the capability of a new network of field mill sensors to monitor the atmospheric electric field at various locations in South America; we also show some early results. The main objective of the new network is to obtain the characteristic Universal Time diurnal curve of the atmospheric electric field in fair weather, known as the Carnegie curve. The Carnegie curve is closely related to the current sources flowing in the Global Atmospheric Electric Circuit so that another goal is the study of this relationship on various time scales (transient/monthly/seasonal/annual). Also, by operating this new network, we may also study departures of the Carnegie curve from its long term average value related to various solar, geophysical and atmospheric phenomena such as the solar cycle, solar flares and energetic charged particles, galactic cosmic rays, seismic activity and specific meteorological events. We then expect to have a better understanding of the influence of these phenomena on the Global Atmospheric Electric Circuit and its time-varying behavior.

Relationship between the near-Earth interplanetary field and the coronal source flux: dependence on timescale

The Ulysses spacecraft has shown that the radial component of the heliospheric magnetic field is approximately independent of latitude. This has allowed quantification of the total open solar flux from near-Earth observations of the interplanetary magnetic field. The open flux can also be estimated from photospheric magnetograms by mapping the fields up to the ‘‘coronal source surface’’ where the field is assumed to be radial and which is usually assumed to be at a heliocentric distance r = 2.5R_{S} (a mean solar radius, 1R_{S} = 6.96x10^{8} m). These two classes of open flux estimate will differ by the open flux that threads the heliospheric current sheet(s) inside Earth’s orbit at 2.5R_{S} < r < 1R{1} (where the mean Earth-Sun distance, 1R_{1} = 1 AU = 1.5 x 10^{11} m). We here use near-Earth measurements to estimate this flux and show that at sunspot minimum it causes only a very small (approximately 0.5%) systematic difference between the two types of open flux estimate, with an uncertainty that is of order ±24% in hourly values, ±16% in monthly averages, and between -6% and +2% in annual values. These fractions may be somewhat larger for sunspot maximum because of flux emerging at higher heliographic latitudes.

DIFFUSION OF MAGNETIC FIELD AND REMOVAL OF MAGNETIC FLUX FROM CLOUDS VIA TURBULENT RECONNECTION

The diffusion of astrophysical magnetic fields in conducting fluids in the presence of turbulence depends on whether magnetic fields can change their topology via reconnection in highly conducting media. Recent progress in understanding fast magnetic reconnection in the presence of turbulence reassures that the magnetic field behavior in computer simulations and turbulent astrophysical environments is similar, as far as magnetic reconnection is concerned. This makes it meaningful to perform MHD simulations of turbulent flows in order to understand the diffusion of magnetic field in astrophysical environments. Our studies of magnetic field diffusion in turbulent medium reveal interesting new phenomena. First of all, our three-dimensional MHD simulations initiated with anti-correlating magnetic field and gaseous density exhibit at later times a de-correlation of the magnetic field and density, which corresponds well to the observations of the interstellar media. While earlier studies stressed the role of either ambipolar diffusion or time-dependent turbulent fluctuations for de-correlating magnetic field and density, we get the effect of permanent de-correlation with one fluid code, i.e., without invoking ambipolar diffusion. In addition, in the presence of gravity and turbulence, our three-dimensional simulations show the decrease of the magnetic flux-to-mass ratio as the gaseous density at the center of the gravitational potential increases. We observe this effect both in the situations when we start with equilibrium distributions of gas and magnetic field and when we follow the evolution of collapsing dynamically unstable configurations. Thus, the process of turbulent magnetic field removal should be applicable both to quasi-static subcritical molecular clouds and cores and violently collapsing supercritical entities. The increase of the gravitational potential as well as the magnetization of the gas increases the segregation of the mass and magnetic flux in the saturated final state of the simulations, supporting the notion that the reconnection-enabled diffusivity relaxes the magnetic field + gas system in the gravitational field to its minimal energy state. This effect is expected to play an important role in star formation, from its initial stages of concentrating interstellar gas to the final stages of the accretion to the forming protostar. In addition, we benchmark our codes by studying the heat transfer in magnetized compressible fluids and confirm the high rates of turbulent advection of heat obtained in an earlier study.

On the Casimir energy for a massive quantum scalar field and the cosmological constant

We present a rigorous, regularization-independent local quantum field theoretic treatment of the Casimir effect for a quantum scalar field of mass mu not equal 0 which yields closed form expressions for the energy density and pressure. As an application we show that there exist special states of the quantum field in which the expectation value of the renormalized energy-momentum tensor is, for any fixed time, independent of the space coordinate and of the perfect fluid form g(mu,nu)rho with rho > 0, thus providing a concrete quantum field theoretic model of the cosmological constant. This rho represents the energy density associated to a state consisting of the vacuum and a certain number of excitations of zero momentum, i.e., the constituents correspond to lowest energy and pressure p <= 0. (C) 2009 Elsevier Inc. All rights reserved.

Coherent states of a particle in a magnetic field and the Stieltjes moment problem

A solution to a version of the Stieltjes moment. problem is presented. Using this solution, we construct a family of coherent states of a charged particle in a uniform magnetic field. We prove that these states form an overcomplete set that is normalized and resolves the unity. By the help of these coherent states we construct the Fock-Bergmann representation related to the particle quantization. This quantization procedure takes into account a circle topology of the classical motion. (C) 2009 Elsevier B.V. All rights reserved.

Electronic states in quantum rings: electric field and eccentricity effects

The polarization effects of in-plane electric fields and eccentricity on electronic and optical properties of semiconductor quantum rings (QRs) are discussed within the effective-mass approximation. As eccentric rings may appropriately describe real (grown or fabricated) QRs, their energy spectrum is studied. The interplay between applied electric fields and eccentricity is analysed, and their polarization effects are found to compensate for appropriate values of eccentricity and field intensity. The importance of applied fields in tailoring the properties of different nanoscale materials and structures is stressed.

Evolution of magnetic field and spin period in accreting neutron stars

Based on the accretion-induced magnetic field decay model, in which a frozen field and an incompressible fluid are assumed, we obtain the following results: (1) an analytic relation between the magnetic field and spin period, if the fastness parameter of the accretion disk is neglected (The evolutionary tracks of accreting neutron stars in the P-B diagram in our model are different from the equilibrium period lines when the influence of the fastness parameter is taken into account.); (2) the theoretical minimum spin period of an accreting neutron star is max(1.1ms (DeltaM/M(circle dot))(-1)R(6)(-5/14) I(45)(M/M(circle dot))(-1/2),1.1ms (M/M(circle dot))(-1/2) R(6)(17/14)), independent of the accretion rate (X-ray luminosity) but dependent on the total accretion mass, DeltaM; however, the minimum magnetic field depends on the accretion rate; (3) the magnetic field strength decreases faster with time than does the period.

Spinorial field and Lyra geometry

The Dirac field is studied in a Lyra space-time background by means of the classical Schwinger Variational Principle. We obtain the equations of motion, establish the conservation laws, and get a scale relation relating the energy-momentum and spin tensors. Such scale relation is an intrinsic property for matter fields in Lyra background.

Self-bound droplet of Bose and Fermi atoms in one dimension: Collective properties in mean-field and Tonks-Girardeau regimes

We investigate a dilute mixture of bosons and spin-polarized fermions in one dimension. With an attractive Bose-Fermi scattering length the ground state is a self-bound droplet, i.e., a Bose-Fermi bright soliton where the Bose and Fermi clouds are superimposed. We find that the quantum fluctuations stabilize the Bose-Fermi soliton such that the one-dimensional bright soliton exists for any finite attractive Bose-Fermi scattering length. We study density profile and collective excitations of the atomic bright soliton showing that they depend on the bosonic regime involved: mean-field or Tonks-Girardeau.

Magnetic-field and confinement effects on the effective Land, g factor in AlxGa1-xAs parabolic quantum wells

The magnetic-field and confinement effects on the Land, factor in AlxGa1-xAs parabolic quantum wells under magnetic fields applied parallel or perpendicular to the growth direction are theoretically studied. Calculations are performed in the limit of low temperatures and low electron density in the heterostructure. The g factor is obtained by taking into account the effects of non-parabolicity and anisotropy of the conduction band through the 2 x 2 Ogg-McCombe Hamiltonian, and by including the cubic Dresselhaus spin-orbit term. A simple formula describing the magnetic-field dependence of the effective Land, factor is analytically derived by using the Rayleigh-Schrodinger perturbation theory, and it is found in good agreement with previous experimental studies devoted to understand the behavior of the g factor, as a function of an applied magnetic field, in semiconductor heterostructures. Present numerical results for the effective Land, factor are shown as functions of the quantum-well parameters and magnetic-field strength, and compared with available experimental measurements.

Kinetics of the polarization reversal process in a non-constant applied electric field and the generalized superposition principle

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Action of dwarf mucuna, pigeon pea and stylos anthes on weed under field and laboratory conditions

The quality and allelopathy properties of dwarf mucuna, dwarf pigeon pea and stylosanthes as cover crops on corn and weed species were evaluated. Seeds were sown in October 2007, with a control treatment, in 20 plots of 4×5m, with five replicates. Weed population was determined 30 and 60 days after sowing. At 90 days, plants were mowed and the residues left to remain on the plot. Fresh and dry mass of the cover crops were determined and the allelopathic potential of aqueous extract of their aerial part was tested. The extract was chemically characterized and applied on seeds of weeds and corn. The experimental design was completely randomized and averages compared by the Scott-Knott test at 5% significance. The cover crops showed to be effective in the control of weeds. The highest values in fresh and dry mass were obtained for dwarf pigeon pea, followed by dwarf mucuna; fresh mass increased 72 and 34%, respectively, compared to the control. The extract with dwarf mucuna affected arrowleaf sida germination. The use of green manure in the summer or between harvests ensures that crop rotation is carried out properly and warrants its benefits.