Theoretical study of the structural dependence of nuclear quadrupole frequencies in high-T_c superconductors

The remarkable difference between the nuclear quadrupole frequencies v_Q of Cu(1) and Cu(2) in YBa_2Cu_3O_6 and YBa_2Cu_3O_7 is analyzed. We calculate the ionic contribution to the electric field gradients and estimate, by using experimental results for Cu_2O and La_2CuO_4, the contribution of the d valence electrons. Thus, we determine v_Q1, v_Q2, and the asymmetry parameter η for YBa_2Cu_3O_6 and YBa_2Cu_3O_7. The number of holes in dthe Cu-O planes and chains is found to be important for the different behavior of v_Q1 and v_Q2.

Protein Folding Simulations: Confinement, External Fields and Sequence Design

The present Thesis looks at the problem of protein folding using Monte Carlo and Langevin simulations, three topics in protein folding have been studied: 1) the effect of confining potential barriers, 2) the effect of a static external field and 3) the design of amino acid sequences which fold in a short time and which have a stable native state (global minimum). Regarding the first topic, we studied the confinement of a small protein of 16 amino acids known as 1NJ0 (PDB code) which has a beta-sheet structure as a native state. The confinement of proteins occurs frequently in the cell environment. Some molecules called Chaperones, present in the cytoplasm, capture the unfolded proteins in their interior and avoid the formation of aggregates and misfolded proteins. This mechanism of confinement mediated by Chaperones is not yet well understood. In the present work we considered two kinds of potential barriers which try to mimic the confinement induced by a Chaperon molecule. The first kind of potential was a purely repulsive barrier whose only effect is to create a cavity where the protein folds up correctly. The second kind of potential was a barrier which includes both attractive and repulsive effects. We performed Wang-Landau simulations to calculate the thermodynamical properties of 1NJ0. From the free energy landscape plot we found that 1NJ0 has two intermediate states in the bulk (without confinement) which are clearly separated from the native and the unfolded states. For the case of the purely repulsive barrier we found that the intermediate states get closer to each other in the free energy landscape plot and eventually they collapse into a single intermediate state. The unfolded state is more compact, compared to that in the bulk, as the size of the barrier decreases. For an attractive barrier modifications of the states (native, unfolded and intermediates) are observed depending on the degree of attraction between the protein and the walls of the barrier. The strength of the attraction is measured by the parameter $\epsilon$. A purely repulsive barrier is obtained for $\epsilon=0$ and a purely attractive barrier for $\epsilon=1$. The states are changed slightly for magnitudes of the attraction up to $\epsilon=0.4$. The disappearance of the intermediate states of 1NJ0 is already observed for $\epsilon =0.6$. A very high attractive barrier ($\epsilon \sim 1.0$) produces a completely denatured state. In the second topic of this Thesis we dealt with the interaction of a protein with an external electric field. We demonstrated by means of computer simulations, specifically by using the Wang-Landau algorithm, that the folded, unfolded, and intermediate states can be modified by means of a field. We have found that an external field can induce several modifications in the thermodynamics of these states: for relatively low magnitudes of the field ($<2.06 \times 10^8$ V/m) no major changes in the states are observed. However, for higher magnitudes than ($6.19 \times 10^8$ V/m) one observes the appearance of a new native state which exhibits a helix-like structure. In contrast, the original native state is a $\beta$-sheet structure. In the new native state all the dipoles in the backbone structure are aligned parallel to the field. The design of amino acid sequences constitutes the third topic of the present work. We have tested the Rate of Convergence criterion proposed by D. Gridnev and M. Garcia ({\it work unpublished}). We applied it to the study of off-lattice models. The Rate of Convergence criterion is used to decide if a certain sequence will fold up correctly within a relatively short time. Before the present work, the common way to decide if a certain sequence was a good/bad folder was by performing the whole dynamics until the sequence got its native state (if it existed), or by studying the curvature of the potential energy surface. There are some difficulties in the last two approaches. In the first approach, performing the complete dynamics for hundreds of sequences is a rather challenging task because of the CPU time needed. In the second approach, calculating the curvature of the potential energy surface is possible only for very smooth surfaces. The Rate of Convergence criterion seems to avoid the previous difficulties. With this criterion one does not need to perform the complete dynamics to find the good and bad sequences. Also, the criterion does not depend on the kind of force field used and therefore it can be used even for very rugged energy surfaces.

Asymptotic model for shape resonance control of diatomics by intense non-resonant light: universality in the single-channel approximation

Non-resonant light interacting with diatomics via the polarizability anisotropy couples different rotational states and may lead to strong hybridization of the motion. The modification of shape resonances and low-energy scattering states due to this interaction can be fully captured by an asymptotic model, based on the long-range properties of the scattering (Crubellier et al 2015 New J. Phys. 17 045020). Remarkably, the properties of the field-dressed shape resonances in this asymptotic multi-channel description are found to be approximately linear in the field intensity up to fairly large intensity. This suggests a perturbative single-channel approach to be sufficient to study the control of such resonances by the non-resonant field. The multi-channel results furthermore indicate the dependence on field intensity to present, at least approximately, universal characteristics. Here we combine the nodal line technique to solve the asymptotic Schrödinger equation with perturbation theory. Comparing our single channel results to those obtained with the full interaction potential, we find nodal lines depending only on the field-free scattering length of the diatom to yield an approximate but universal description of the field-dressed molecule, confirming universal behavior.

Nutrient cycling and field-based partial nutrient balances in two mountain oases of Oman

Little is known about nutrient fluxes as a criterion to assess the sustainability of traditional irrigation agriculture in eastern Arabia. In this study GIS-based field research on terraced cropland and groves of date palm (Phoenix dactylifera L.) was conducted over 2 years in two mountain oases of northern Oman to determine their role as hypothesized sinks for nitrogen (N), phosphorus (P) and potassium (K). At Balad Seet 55% of the 385 fields received annual inputs of 100–500 kg N ha^-1 and 26% received 500–1400 kg N ha^-1. No N was applied to 19% of the fields which were under fallow. Phosphorus was applied annually at 1–90 kg ha^-1 on 46% of the fields, whereas 27% received 90–210 kg ha^-1. No K was applied to 27% of the fields, 32% received 1–300 kg K ha^-1, and the remaining fields received up to 1400 kg ha^-1. At Maqta N-inputs were 61–277 kg ha^-1 in palm groves and 112–225 kg ha^-1 in wheat (Triticum spp.) fields, respective P inputs were 9–40 and 14–29 kg ha^-1, and K inputs were 98–421 and 113–227 kg ha^-1. For cropland, partial oasis balances (comprising inputs of manure, mineral fertilizers, N2-fixation and irrigation water, and outputs of harvested products) were similar for both oases, with per hectare surpluses of 131 kg N, 37 kg P, and 84 kg K at Balad Seet and of 136 kg N, 16 kg P and 66 kg K at Maqta. This was despite the fact that N2-fixation by alfalfa (Medicago sativa L.), estimated at up to 480 kg ha^-1 yr^-1 with an average total dry matter of 22 t ha^-1, contributed to the cropland N-balance only at the former site. Respective palm grove surpluses, in contrast were with 303 kg N, 38 kg P, and 173 kg K ha^-1 much higher at Balad Seet than with 84 kg N, 14 kg P, and 91 kg K ha^-1 at Maqta. The data show that both oases presently are large sinks for nutrients. Potential gaseous and leaching losses could at least partly be controlled by a decrease in nutrient input intensity and careful incorporation of manure.

Intrinsic channel closing in strong-field single ionization of H2

Die Ionisation von H2 in intensiven Laserpulsen wird mit Hilfe der numerischen Integration der zeitabhängigen Schrödingergleichung für ein Einelektronenmodell untersucht, das die Vibrationsbewegung berücksichtigt. Die Spektren der kinetischen Elektronenenergie hängen stark von der Vibrationsquantenzahl des erzeugten H2+ Ions ab. Für bestimmte Vibrationszustände ist die Ausbeute der Elektronen in der Mitte des Plateaus stark erhöht. Der Effekt wird "channel closings" zugeschrieben, die in Atomen durch Variation der Laserintensität beobachtet wurden. The ionization of H2 in intense laser pulses is studied by numerical integration of the time-dependent Schrödinger equation for a single-active-electron model including the vibrational motion. The electron kinetic energy spectra in high-order above-threshold ionization are strongly dependent on the vibrational quantum number of the created H2+ ion. For certain vibrational states, the electron yield in the mid-plateau region is strongly enhanced. The effect is attributed to channel closings, which were previously observed in atoms by varying the laser intensity.

High laser field effects in multiphoton ionization of Na_2

Femtosecond pump/probe multiphoton ionization experiments on Na_2 molecules are performed. The dependence of the total Na^+_2 ion signal on the delay time and the intensity of the femtosecond laser pulses is studied in detail. It is observed that molecular vibrational wavepacket motion in different electronic states dominates the time dependence of the ion signal. For higher laser intensities the relative contributions from the A ^1 \summe^+_u and the 2 ^1 \produkt__g states change dramatically, indicating the increasing importance of a two-electron versus a one-electron process. For even stronger fields (10 ^12 W/ cm²) a vibrational wavepacket in the electronic ground state X ^1 \summe^+_g is formed and its dynamics is also observed in the transient Na^+_2 signal. Time-dependent quantum calculations are presented. The theoretical results agree well with the experiment.

Development of mechanical methods for cell-tray propagation and field transplanting of dwarf napiergrass (Pennisetum purpureum Schumach.)

Since dwarf napiergrass (Pennisetum purpureum Schumach.) must be propagated vegetatively due to lack of viable seeds, root splitting and stem cuttings are generally used to obtain true-to-type plant populations. These ordinary methods are laborious and costly, and are the greatest barriers for expanding the cultivation area of this crop. The objectives of this research were to develop nursery production of dwarf napiergrass in cell trays and to compare the efficiency of mechanical versus manual methods for cell-tray propagation and field transplanting. After defoliation of herbage either by a sickle (manually) or hand-mowing machine, every potential aerial tiller bud was cut to a single one for transplanting into cell trays as stem cuttings and placed in a glasshouse over winter. The following June, nursery plants were trimmed to a 25–cm length and transplanted in an experimental field (sandy soil) with 20,000 plants ha^(−1) either by shovel (manually) or Welsh onion planter. Labour time was recorded for each process. The manual defoliation of plants required 44% more labour time for preparing the stem cuttings (0.73 person-min. stemcutting^(−1)) compared to using hand-mowing machinery (0.51 person-min. stem-cutting^(−1)). In contrast, labour time for transplanting required an extra 0.30 person-min. m^(−2) (14%) using the machinery compared to manual transplanting, possibly due to the limited plot size for machinery operation. The transplanting method had no significant effect on plant establishment or plant growth, except for herbage yield 110 days after planting. Defoliation of herbage by machinery, production using a cell-tray nursery and mechanical transplanting reduced the labour intensity of dwarf napiergrass propagation.