Structure and function in rhodopsin: Topology of the C-terminal polypeptide chain in relation to the cytoplasmic loops*

Cysteine mutagenesis and site-directed spin labeling in the C-terminal region of rhodopsin have been used to probe the local structure and proximity of that region to the cytoplasmic loops. Each of the native amino acids in the sequence T335–T340 was replaced with Cys, one at a time. The sulfhydryl groups of all mutants reacted rapidly with the sulfhydryl reagent 4,4′-dithiodipyridine, which indicated a high degree of solvent accessibility. Furthermore, to probe the proximity relationships, a series of double Cys mutants was constructed. One Cys in all sets was at position 338 and the other was at a position in the sequence S240–V250 in the EF interhelical loop, at position 65 in the AB interhelical loop, or at position 140 in the CD interhelical loop. In the dark state, no significant disulfide formation was observed between C338 and C65 or C140 under the conditions used, whereas a relatively rapid disulfide formation was observed between C338 and C242 or C245. Spin labels in the double Cys mutants showed the strongest magnetic interactions between the nitroxides attached to C338 and C245 or C246. Light activation of the double mutant T242C/S338C resulted in slower disulfide formation, whereas interactions between nitroxides at C338 and C245 or C246 decreased. These results suggest the proximity of the C-terminal residue C338 to residues located on the outer face of a cytoplasmic helical extension of the F helix with an apparent increase of distance upon photoactivation.

Vacancy-induced magnetism in graphene and graphene ribbons

We address the electronic structure and magnetic properties of vacancies and voids both in graphene and graphene ribbons. By using a mean-field Hubbard model, we study the appearance of magnetic textures associated with removing a single atom (vacancy) and multiple adjacent atoms (voids) as well as the magnetic interactions between them. A simple set of rules, based on the Lieb theorem, link the atomic structure and the spatial arrangement of the defects to the emerging magnetic order. The total spin S of a given defect depends on its sublattice imbalance, but some defects with S=0 can still have local magnetic moments. The sublattice imbalance also determines whether the defects interact ferromagnetically or antiferromagnetically with one another and the range of these magnetic interactions is studied in some simple cases. We find that in semiconducting armchair ribbons and two-dimensional graphene without global sublattice imbalance, there is a maximum defect density above which local magnetization disappears. Interestingly, the electronic properties of semiconducting graphene ribbons with uncoupled local moments are very similar to those of diluted magnetic semiconductors, presenting giant Zeeman splitting.

Material Synthesis and Characterization on Low-Dimensional Cobaltates

In this thesis, results of the investigation of a new low-dimensional cobaltates Ba2-xSrxCoO 4 are presented. The synthesis of both polycrystalline and single crystalline compounds using the methods of conventional solid state chemical reaction and floating-zone optical furnace is first introduced. Besides making polycrystalline powders, we successfully, for the first time, synthesized large single crystals of Ba2CoO4. Single crystals were also obtained for Sr doped Ba2-xSrxCoO 4. Powder and single crystal x-ray diffraction results indicate that pure Ba2CoO4 has a monoclinic structure at room temperature. With Sr doping, the lattice structure changes to orthorhombic when x ≥ 0.5 and to tetragonal when x = 2.0. In addition, Ba2CoO4 and Sr2CoO4, have completely different basic building blocks in the structure. One is CoO4 tetrahedron and the later is CoO6 octahedron, respectively. Electronic and magnetic properties were characterized and discussed. The magnetic susceptibility, specific heat and thermal conductivity show that Ba2CoO4 has an antiferromagnetic (AF) ground state with an AF ordering temperature TN = 25 K. However, the magnitude of the Néel temperature TN is significantly lower than the Curie-Weiss temperature (:&thetas;: ∼ 110 K), suggesting either reduced-dimensional magnetic interactions and/or the existence of magnetic frustration. The AF interaction persists in all the samples with different doping concentrations. The Néel temperature doesn't vary much in the monoclinic structure regime but decreases when the system enters orthorhombic. Magnetically, Ba2CoO4 has an AF insulating ground state while Sr2CoO4 has a ferromagnetic (FM) metallic ground state. Neutron powder refinement results indicate a magnetic structure with the spin mostly aligned along the a-axis. The result from a μ-spin rotation/relaxation (μ+SR) experiment agrees with our refinement. It confirms the AF order in the ab -plane. We also studied the spin dynamics and its anisotropy in the AF phase. The results from inelastic neutron scattering show that spin waves have a clear dispersion along a-axis but not along c-axis, indicating spin anisotropy. This work finds the strong spin-lattice coupling in this novel complex material. The interplay between the two degrees of freedom results an interesting phase diagram. Further research is needed when large single crystal samples are available.

Interações magnéticas e elétricas em GaMnAs

In this paper, we will address together the magnetic and electrical properties of a particular semiconductor, the GaMnAs. The treatment will be done analytically in the first part of the work, according to the computational method for simulation of physical systems through the implementation of the expressions obtained in the first part. All study of magnetic contribution will be made using an interaction Kondo type, using an approach by Green functions. The electrical part, which consists of the Coulomb interactions between carriers and Mn ions, will be treated within the approach of multiple scattering. The implementation of the proposed method will calculate the Green functions converged as multiple scattering solution and use them as a starting point for the calculation of the effective magnetic interactions between Mn ions mediated charge carriers. The concentration parameters were varied for Mn ions and carriers as well. The combination of these two parameters can lead to insulating, metal samples with carriers in Fermi level to low or high mobility. As a result a correlation between the obtained carrier mobility and the strength of magnetic interaction. The greater mobility, the greater the intensity of the interaction.

Phase Transitions in Engineered Ultracold Quantum Systems

The study of quantum degenerate gases has many applications in topics such as condensed matter dynamics, precision measurements and quantum phase transitions. We built an apparatus to create 87Rb Bose-Einstein condensates (BECs) and generated, via optical and magnetic interactions, novel quantum systems in which we studied the contained phase transitions. For our first experiment we quenched multi-spin component BECs from a miscible to dynamically unstable immiscible state. The transition rapidly drives any spin fluctuations with a coherent growth process driving the formation of numerous spin polarized domains. At much longer times these domains coarsen as the system approaches equilibrium. For our second experiment we explored the magnetic phases present in a spin-1 spin-orbit coupled BEC and the contained quantum phase transitions. We observed ferromagnetic and unpolarized phases which are stabilized by the spin-orbit coupling’s explicit locking between spin and motion. These two phases are separated by a critical curve containing both first-order and second-order transitions joined at a critical point. The narrow first-order transition gives rise to long-lived metastable states. For our third experiment we prepared independent BECs in a double-well potential, with an artificial magnetic field between the BECs. We transitioned to a single BEC by lowering the barrier while expanding the region of artificial field to cover the resulting single BEC. We compared the vortex distribution nucleated via conventional dynamics to those produced by our procedure, showing our dynamical process populates vortices much more rapidly and in larger number than conventional nucleation.

Proton Magnetic-Resonance Study of Cycloheximide-Ribosome Interactions

Cycloheximide-ribosome interactions from sensitive and resistant organisms were studied by proton magnetic resonance spectroscopic techniques. The two methyl resonances of cycloheximide upon interaction with ribosomes from Saccharomyces cerevisiae showed preferential broadening. Comparison of cycloheximide line broadening as effected by ribosomes from S. cerevisiae (sensitive) and Microsporum canis (resistant) revealed that less cycloheximide is bound to the M. canis ribosomes. From the decrease in line broadening observed with increasing temperature it may be concluded that cycloheximide-ribosome interaction is a fast exchange reaction. Tetracycline did not compete with cycloheximide for binding site(s) on the ribosomes of S. cerevisiae.

Magnetic and dielectric interactions in nano zinc ferrite powder: Prepared by self-sustainable propellant chemistry technique

The structural, magnetic and dielectric properties of nano zinc ferrite prepared by the propellant chemistry technique are studied. The PXRD measurement at room temperature reveal that the compound is in cubic spinel phase, belong to the space group Fd (3) over barm. The unit cell parameters have been estimated from Rietveld refinement. The calculated force constants from FTIR spectrum corresponding to octahedral and tetrahedral sites at 375 and 542 cm(-1) are 6.61 x 10(2) and 3.77 x 10(2) N m(-1) respectively; these values are slightly higher compared to the other ferrite systems. Magnetic hysteresis and EPR spectra show superparamagnetic property nearly to room temperature due to comparison values between magnetic anisotropy energy and the thermal energy. The calculated values of saturation magnetization, remenant magnetization, coercive field and magnetic moment supports for the existence of multi domain particles in the sample. The temperature dependent magnetic field shows the spin freezing state at 30 K and the blocking temperature at above room temperature. The frequency dependent dielectric interactions show the variation of dielectric constant, dielectric loss and impedance as similar to other ferrite systems. The AC conductivity in the prepared sample is due to the presence of electrons, holes and polarons. The synthesized material is suitable for nano-electronics and biomedical applications. (C) 2014 Elsevier B.V. All rights reserved.

Generation of strong quasistatic magnetic fields in interactions of ultraintense and short laser pulses with overdense plasma targets

An analytical fluid model is proposed for the generation of strong quasistatic magnetic fields during normal incidence of a short ultraintense Gaussian laser pulse with a finite spot size on an overdense plasma. The steepening of the electron density profile in the originally homogeneous overdense plasma and the formation of electron cavitation as the electrons are pushed inward by the laser are included self-consistently. It is shown that the appearance of the cavitation plays an important role in the generation of quasistatic magnetic fields: the strong plasma inhomogeneities caused by the formation of the electron cavitation lead to the generation of a strong axial quasistatic magnetic field B-z. In the overdense regime, the generated quasistatic magnetic field increases with increasing laser intensity, while it decreases with increasing plasma density. It is also found that, in a moderately overdense plasma, highly intense laser pulses can generate magnetic fields similar to 100 MG and greater due to the transverse linear mode conversion process.

Studies of dinucleoside monophosphates and monomer-polynucleotide interactions by proton magnetic resonance

The nature of the intra- and intermolecular base-stacking interactions involving several dinucleoside monophosphates in aqueous solution have been investigated by proton magnetic resonance spectrosocopy, and this method has been applied to a study of the interaction of polyuridylic acid with purine and adenosine monomers.

The pmr spectra of adenylyl (3' → 5') cytidine (ApC) and cytidylyl (3' → 5') adenosine (CpA) have been studied as a function of concentration and temperature. The results of these studies indicate that the intramolecular base-stacking interactions between the adenine and cytosine bases of these dinucleoside monophosphates are rather strong, and that the stacking tendencies are comparable for the two sequence isomers. The chemical shifts of the cytosine H₅ and adenine H₂ protons, and their variations with temperature, were shown to be consistent with stacked conformations in which both bases of the dinucleoside monophosphates are preferentially oriented in the anti conformation as in similar dApdC, and dCpdA (dA = deoxyadenosine; dC = deoxycytidine) segments in double helical DNA. The intramolecular stacking interaction was found to have a pronounced effect on the conformations of the ribose moieties, and these conformational changes are discussed. The concentration studies indicate extensive self-association of these dinucleoside monophosphates, and analysis of the concentration data facilitated determination of the dimerization constant for the association process as well as the nature of the intermolecular complexes.

The dependence of the ribose conformation upon the extent of intramolecular base-stacking was used to demonstrate that the base-base interaction in cytidylyl (3' → 5') cytidine (CpC) is rather strong, while there appears to be little interaction between the two uracil bases of uridylyl (3' → 5') uridine (UpU).

Studies of the binding of purine to several ribose and deoxyribose dinucleoside monophosphates show that the mode of interaction is base-stacking, and evidence for the formation of a purine-dinucleoside monophosphate intercalated complex is presented. The purine proton resonances are markedly broadened in this complex, and estimates of the purine linewidths in the complex and the equilibrium constant for purine intercalation are obtained.

A study of the interaction of unsubstitued purine with polyuridylic acid at 29°C by pmr indicated that purine binds to the uracil bases of the polymer by base-stacking. The severe broadening of the purine proton resonances observed provides strong evidence for the intercalation of purine between adjacent uracil bases of poly U. This interaction does not result in a more rigid or ordered structure for the polymer.

Investigation of the interaction between adenosine and polyuridylic acid revealed two modes of interaction between the monomer and the polymer, depending on the temperature. At temperatures above 26°C or so, monomeric adenosine binds to poly U by noncooperative A-U base stacking. Below this temperature, a rigid triple-stranded 1A:2U complex is formed, presumably via cooperative hydrogen-bonding as has previously been reported.

These results clearly illustrate the importance of base-stacking in non-specific interactions between bases, nucleosides and nucleotides, and also reveal the important role of the base-stacking interactions in cooperatively for med structures involving specific base-pairing where both types of interaction are possible.

High- and low-latitude climate interactions: evidence for enhanced aridity of Asian monsoon dust source areas after 2.4 MYR from ODP Leg 117 magnetic susceptibility data

EXTRACT (SEE PDF FOR FULL ABSTRACT): Whole-core magnetic susceptibility can sometimes be used as a rapid and sensitive indicator of variations in the concentration of terrigenous material. We apply this approach to study the evolution of Plio-Pleistocene climatic cycles of terrigenous sedimentation at Ocean Drilling Program Site 721, on the Owen Ridge in the Arabian Sea.

Effects of electron-electron interactions on the electronic Raman scattering of graphite in high magnetic fields

We report the observation of strongly temperature (T)-dependent spectral lines in electronic Raman-scattering spectra of graphite in a high magnetic field up to 45 T applied along the c axis. The magnetic field quantizes the in-plane motion, while the out-of-plane motion remains free, effectively reducing the system dimension from 3 to 1. Optically created electron-hole pairs interact with, or shake up, the one-dimensional Fermi sea in the lowest Landau subbands. Based on the Tomonaga-Luttinger liquid theory, we show that interaction effects modify the spectral line shape from (ω-Δ)-1/2 to (ω-Δ)2α-1/2 at T = 0. At finite T, we predict a thermal broadening factor that increases linearly with T. Our model reproduces the observed T-dependent line shape, determining the electron-electron interaction parameter α to be ∼0.05 at 40 T. © 2014 American Physical Society.

Proton Probing Measurement of Electric and Magnetic Fields Generated by ns and ps Laser-Matter Interactions

The use of laser-accelerated protons as a particle probe for the detection of electric fields in plasmas has led in recent years to a wealth of novel information regarding the ultrafast plasma dynamics following high intensity laser-matter interactions. The high spatial quality and short duration of these beams have been essential to this purpose. We will discuss some of the most recent results obtained with this diagnostic at the Rutherford Appleton Laboratory (UK) and at LULI - Ecole Polytechnique (France), also applied to conditions of interest to conventional Inertial Confinement Fusion. In particular, the technique has been used to measure electric fields responsible for proton acceleration from solid targets irradiated with ps pulses, magnetic fields formed by ns pulse irradiation of solid targets, and electric fields associated with the ponderomotive channelling of ps laser pulses in under-dense plasmas.

Laboratory measurements of 0.7 GG magnetic fields generated during high-intensity laser interactions with dense plasmas

We report measurements of ultrahigh magnetic fields produced during intense (similar to10(20) Wcm(-2) mum(2)) laser interaction experiments with solids. We show that polarization measurements of high-order vuv laser harmonics generated during the interaction (up to the 15th order) suggest the existence of magnetic field strengths of 0.7+/-0.1 GG in the overdense plasma. Measurements using higher order harmonics indicate that denser regions of the plasma can be probed. This technique may be useful for measurements of multi-GG level magnetic fields which are predicted to occur at even higher intensities.