Structure and interactions of ultracold Yb ions and Rb atoms

In order to study ultracold charge-transfer processes in hybrid atom-ion traps, we have mapped out the potential-energy curves and molecular parameters for several low-lying states of the Rb, Yb+ system. We employ both a multireference configuration interaction and a full configuration interaction (FCI) approach. Turning points, crossing points, potential minima, and spectroscopic molecular constants are obtained for the lowest five molecular states. Long-range parameters, including the dispersion coefficients, are estimated from our ab initio data. The separated-atom ionization potentials and atomic polarizability of the ytterbium atom (ad=128.4 atomic units) are in good agreement with experiment and previous calculations. We present some dynamical calculations for (adiabatic) scattering lengths for the two lowest (Yb, Rb+) channels that were carried out in our work. However, we find that the pseudopotential approximation is rather limited in validity and only applies to nK temperatures. The adiabatic scattering lengths for both the triplet and singlet channels indicate that both are large and negative in the FCI approximation.

Magnetic short-range order in the new ternary phase Mn8Pd15Si7

A new compound, Mn8Pd15Si7, is reported to crystallize in a face centered cubic unit cell of dimension a = 12.0141(2) angstrom, space groupFm (3) over barm, and can thus be classified as a G-phase. The crystal structure was studied by single crystal X-ray diffraction, X-ray and neutron powder diffraction and electron diffraction. A filled Mg6Cu16Si7 type structure was found, corresponding to the Sc11Ir4 type structure. The magnetic properties were investigated by magnetization measurements and Reverse Monte Carlo modeling of low temperature magnetic short-range order (SRO). Dominating near neighbor antiferromagnetic correlations were found between the Mn atoms and geometric frustration in combination with random magnetic interactions via metal sites with partial Mn occupancy were suggested to hinder formation of long-range magnetic order. 

Shielding of ionic interactions by sulfur dioxide in an ionic liquid

The effect of adding SO(2) on the structure and dynamics of 1-butyl-3-methylimidazolium bromide (BMIBr) was investigated by low-frequency Raman spectroscopy and molecular dynamics (MD) simulations. The MD simulations indicate that the long-range structure of neat BMIBr is disrupted resulting in a liquid with relatively low viscosity and high conductivity, but strong correlation of ionic motion persists in the BMIBr-SO(2) mixture due to ionic pairing. Raman spectra within the 5 < omega < 200 cm(-1) range at low temperature reveal the short-time dynamics, which is consistent with the vibrational density of states calculated by MD simulations. Several time correlation functions calculated by MD simulations give further insights on the structural relaxation of BMIBr-SO(2).

Long- and medium-range components of the nuclear force in quark-model based calculations

Quark-model descriptions of the nucleon-nucleon interaction contain two main ingredients, a quark-exchange mechanism for the short-range repulsion and meson exchanges for the medium- and long-range parts of the interaction. We point out the special role played by higher partial waves, and in particular the (1)F(3), as a very sensitive probe for the meson-exchange pan employed in these interaction models. In particular, we show that the presently available models fail to provide a reasonable description of higher partial waves and indicate the reasons for this shortcoming.

TiO2-Cu photocatalysts: A study on the long- and short-range chemical environment of the dopant

In this study, the short- and long-range chemical environments of Cu dopant in TiO2 photocatalyst have been investigated. The Cu-doped and undoped TiO2 specimens were prepared by the sol-gel approach employing CuSO4·5H2O and Ti(O-iPr)4 precursors and subjecting the dried gels to thermal treatment at 400 and 500 C. The photocatalytic activity, investigated by methylene blue degradation under sunlight irradiation, showed a significantly higher efficiency of Cu-doped samples than that of pure TiO2. The X-ray diffraction results showed the presence of anatase phase for samples prepared at 400 and 500 C. No crystalline CuSO4 phase was detected below 500 C. It was also found that doping decreases the crystallite size in the (004) and (101) directions. Infrared spectroscopy results indicated that the chemical environment of sulfate changes as a function of thermal treatment, and UV-vis spectra showed that the band gap decreases with thermal treatment and Cu doping, showing the lowest value for the 400 C sample. X-ray absorption fine structure measurements and analysis refinements revealed that even after thermal treatment and photocatalytic assays, the Cu2+ local order is similar to that of CuSO4, containing, however, oxygen vacancies. X-ray photoelectron spectroscopy data, limited to the near surface region of the catalyst, evidenced, besides CuSO4, the presence of Cu1+ and CuO phases, indicating the active role of Cu in the TiO2 lattice. © 2013 Springer Science+Business Media New York.

Electrostatic potentials and polarization effects in proton-molecule interactions by means of multipoles from the quantum theory of atoms in molecules

Some atomic multipoles (charges, dipoles and quadrupoles) from the Quantum Theory of Atoms in Molecules (QTAIM) and CHELPG charges are used to investigate interactions between a proton and a molecule (F2, Cl2, BF, AlF, BeO, MgO, LiH, H2CO, NH3, PH3, BF3, and CO2). Calculations were done at the B3LYP/6-311G(3d,3p) level. The main aspect of this work is the investigation of polarization effects over electrostatic potentials and atomic multipoles along a medium to long range of interaction distances. Large electronic charge fluxes and polarization changes are induced by a proton mainly when this positive particle approaches the least electronegative atom of diatomic heteronuclear molecules. The search for simple equations to describe polarization on electrostatic potentials from QTAIM quantities resulted in linear relations with r-4 (r is the interaction distance) for many cases. Moreover, the contribution from atomic dipoles to these potentials is usually the most affected contribution by polarization what reinforces the need for these dipoles to a minimal description of purely electrostatic interactions. Finally, CHELPG charges provide a description of polarization effects on electrostatic potentials that is in disagreement with physical arguments for certain of these molecules. (c) 2012 Wiley Periodicals, Inc.

Multiple attractors, long chaotic transients, and failure in small-world networks of excitable neurons.

We study the dynamical states of a small-world network of recurrently coupled excitable neurons, through both numerical and analytical methods. The dynamics of this system depend mostly on both the number of long-range connections or ?shortcuts?, and the delay associated with neuronal interactions. We find that persistent activity emerges at low density of shortcuts, and that the system undergoes a transition to failure as their density reaches a critical value. The state of persistent activity below this transition consists of multiple stable periodic attractors, whose number increases at least as fast as the number of neurons in the network. At large shortcut density and for long enough delays the network dynamics exhibit exceedingly long chaotic transients, whose failure times follow a stretched exponential distribution. We show that this functional form arises for the ensemble-averaged activity if the failure time for each individual network realization is exponen- tially distributed

RNA tertiary interactions in the large ribosomal subunit: The A-minor motif

Analysis of the 2.4-Å resolution crystal structure of the large ribosomal subunit from Haloarcula marismortui reveals the existence of an abundant and ubiquitous structural motif that stabilizes RNA tertiary and quaternary structures. This motif is termed the A-minor motif, because it involves the insertion of the smooth, minor groove edges of adenines into the minor groove of neighboring helices, preferentially at C-G base pairs, where they form hydrogen bonds with one or both of the 2′ OHs of those pairs. A-minor motifs stabilize contacts between RNA helices, interactions between loops and helices, and the conformations of junctions and tight turns. The interactions between the 3′ terminal adenine of tRNAs bound in either the A site or the P site with 23S rRNA are examples of functionally significant A-minor interactions. The A-minor motif is by far the most abundant tertiary structure interaction in the large ribosomal subunit; 186 adenines in 23S and 5S rRNA participate, 68 of which are conserved. It may prove to be the universally most important long-range interaction in large RNA structures.

On the magnitude of the electrostatic contribution to ligand-DNA interactions.

A model based on the nonlinear Poisson-Boltzmann equation is used to study the electrostatic contribution to the binding free energy of a simple intercalating ligand, 3,8-diamino-6-phenylphenanthridine, to DNA. We find that the nonlinear Poisson-Boltzmann model accurately describes both the absolute magnitude of the pKa shift of 3,8-diamino-6-phenylphenanthridine observed upon intercalation and its variation with bulk salt concentration. Since the pKa shift is directly related to the total electrostatic binding free energy of the charged and neutral forms of the ligand, the accuracy of the calculations implies that the electrostatic contributions to binding are accurately predicted as well. Based on our results, we have developed a general physical description of the electrostatic contribution to ligand-DNA binding in which the electrostatic binding free energy is described as a balance between the coulombic attraction of a ligand to DNA and the disruption of solvent upon binding. Long-range coulombic forces associated with highly charged nucleic acids provide a strong driving force for the interaction of cationic ligands with DNA. These favorable electrostatic interactions are, however, largely compensated for by unfavorable changes in the solvation of both the ligand and the DNA upon binding. The formation of a ligand-DNA complex removes both charged and polar groups at the binding interface from pure solvent while it displaces salt from around the nucleic acid. As a result, the total electrostatic binding free energy is quite small. Consequently, nonpolar interactions, such as tight packing and hydrophobic forces, must play a significant role in ligand-DNA stability.

Van der Waals-corrected density functional theory: benchmarking for hydrogen-nanotube and nanotube-nanotube interactions

Density functional theory (DFT) is a powerful approach to electronic structure calculations in extended systems, but suffers currently from inadequate incorporation of long-range dispersion, or Van der Waals (VdW) interactions. VdW-corrected DFT is tested for interactions involving molecular hydrogen, graphite, single-walled carbon nanotubes (SWCNTs), and SWCNT bundles. The energy correction, based on an empirical London dispersion term with a damping function at short range, allows a reasonable physisorption energy and equilibrium distance to be obtained for H-2 on a model graphite surface. The VdW-corrected DFT calculation for an (8, 8) nanotube bundle reproduces accurately the experimental lattice constant. For H-2 inside or outside an (8, 8) SWCNT, we find the binding energies are respectively higher and lower than that on a graphite surface, correctly predicting the well known curvature effect. We conclude that the VdW correction is a very effective method for implementing DFT calculations, allowing a reliable description of both short-range chemical bonding and long-range dispersive interactions. The method will find powerful applications in areas of SWCNT research where empirical potential functions either have not been developed, or do not capture the necessary range of both dispersion and bonding interactions.

Identifying optimal lipid raft characteristics required to promote nanoscale protein-protein interactions on the plasma membrane

The dynamic lateral segregation of signaling proteins into microdomains is proposed to facilitate signal transduction, but the constraints on microdomain size, mobility, and diffusion that might realize this function are undefined. Here we interrogate a stochastic spatial model of the plasma membrane to determine how microdomains affect protein dynamics. Taking lipid rafts as representative microdomains, we show that reduced protein mobility in rafts segregates dynamically partitioning proteins, but the equilibrium concentration is largely independent of raft size and mobility. Rafts weakly impede small-scale protein diffusion but more strongly impede long-range protein mobility. The long-range mobility of raft-partitioning and raft-excluded proteins, however, is reduced to a similar extent. Dynamic partitioning into rafts increases specific interprotein collision rates, but to maximize this critical, biologically relevant function, rafts must be small (diameter, 6 to 14 nm) and mobile. Intermolecular collisions can also be favored by the selective capture and exclusion of proteins by rafts, although this mechanism is generally less efficient than simple dynamic partitioning. Generalizing these results, we conclude that microdomains can readily operate as protein concentrators or isolators but there appear to be significant constraints on size and mobility if microdomains are also required to function as reaction chambers that facilitate nanoscale protein-protein interactions. These results may have significant implications for the many signaling cascades that are scaffolded or assembled in plasma membrane microdomains.

Protein interactions studied by SAXS:effect of ionic strength and protein concentration for BSA in aqueous solutions

We have studied a series of samples of bovine serum albumin (BSA) solutions with protein concentration, c, ranging from 2 to 500 mg/mL and ionic strength, I, from 0 to 2 M by small-angle X-ray scattering (SAXS). The scattering intensity distribution was compared to simulations using an oblate ellipsoid form factor with radii of 17 x 42 x 42 A, combined with either a screened Coulomb, repulsive structure factor, S-SC(q), or an attractive square-well structure factor, S-SW(q). At pH = 7, BSA is negatively charged. At low ionic strength, I <0.3 M, the total interaction exhibits a decrease of the repulsive interaction when compared to the salt-free solution, as the net surface charge is screened, and the data can be fitted by assuming an ellipsoid form factor and screened Coulomb interaction. At moderate ionic strength (0.3-0.5 M), the interaction is rather weak, and a hard-sphere structure factor has been used to simulate the data with a higher volume fraction. Upon further increase of the ionic strength (I >= 1.0 M), the overall interaction potential was dominated by an additional attractive potential, and the data could be successfully fitted by an ellipsoid form factor and a square-well potential model. The fit parameters, well depth and well width, indicate that the attractive potential caused by a high salt concentration is weak and long-ranged. Although the long-range, attractive potential dominated the protein interaction, no gelation or precipitation was observed in any of the samples. This is explained by the increase of a short-range, repulsive interaction between protein molecules by forming a hydration layer with increasing salt concentration. The competition between long-range, attractive and short-range, repulsive interactions accounted for the stability of concentrated BSA solution at high ionic strength.

CTCF modulates Estrogen Receptor function through specific chromatin and nuclear matrix interactions

Enhancer regions and transcription start sites of estrogen-target regulated genes are connected by means of Estrogen Receptor long-range chromatin interactions. Yet, the complete molecular mechanisms controlling the transcriptional output of engaged enhancers and subsequent activation of coding genes remain elusive. Here, we report that CTCF binding to enhancer RNAs is enriched when breast cancer cells are stimulated with estrogen. CTCF binding to enhancer regions results in modulation of estrogen-induced gene transcription by preventing Estrogen Receptor chromatin binding and by hindering the formation of additional enhancer-promoter ER looping. Furthermore, the depletion of CTCF facilitates the expression of target genes associated with cell division and increases the rate of breast cancer cell proliferation. We have also uncovered a genomic network connecting loci enriched in cell cycle regulator genes to nuclear lamina that mediates the CTCF function. The nuclear lamina and chromatin interactions are regulated by estrogen-ER. We have observed that the chromatin loops formed when cells are treated with estrogen establish contacts with the nuclear lamina. Once there, the portion of CTCF associated with the nuclear lamina interacts with enhancer regions, limiting the formation of ER loops and the induction of genes present in the loop. Collectively, our results reveal an important, unanticipated interplay between CTCF and nuclear lamina to control the transcription of ER target genes, which has great implications in the rate of growth of breast cancer cells.

Long-term trends in fine particle number concentrations in the urban atmosphere of Brisbane : the relevance of traffic emissions and new particle formation

The measurement of submicrometre (< 1.0 m) and ultrafine particles (diameter < 0.1 m) number concentration have attracted attention since the last decade because the potential health impacts associated with exposure to these particles can be more significant than those due to exposure to larger particles. At present, ultrafine particles are not regularly monitored and they are yet to be incorporated into air quality monitoring programs. As a result, very few studies have analysed their long-term and spatial variations in ultrafine particle concentration, and none have been in Australia. To address this gap in scientific knowledge, the aim of this research was to investigate the long-term trends and seasonal variations in particle number concentrations in Brisbane, Australia. Data collected over a five-year period were analysed using weighted regression models. Monthly mean concentrations in the morning (6:00-10:00) and the afternoon (16:00-19:00) were plotted against time in months, using the monthly variance as the weights. During the five-year period, submicrometre and ultrafine particle concentrations increased in the morning by 105.7% and 81.5% respectively whereas in the afternoon there was no significant trend. The morning concentrations were associated with fresh traffic emissions and the afternoon concentrations with the background. The statistical tests applied to the seasonal models, on the other hand, indicated that there was no seasonal component. The spatial variation in size distribution in a large urban area was investigated using particle number size distribution data collected at nine different locations during different campaigns. The size distributions were represented by the modal structures and cumulative size distributions. Particle number peaked at around 30 nm, except at an isolated site dominated by diesel trucks, where the particle number peaked at around 60 nm. It was found that ultrafine particles contributed to 82%-90% of the total particle number. At the sites dominated by petrol vehicles, nanoparticles (< 50 nm) contributed 60%-70% of the total particle number, and at the site dominated by diesel trucks they contributed 50%. Although the sampling campaigns took place during different seasons and were of varying duration these variations did not have an effect on the particle size distributions. The results suggested that the distributions were rather affected by differences in traffic composition and distance to the road. To investigate the occurrence of nucleation events, that is, secondary particle formation from gaseous precursors, particle size distribution data collected over a 13 month period during 5 different campaigns were analysed. The study area was a complex urban environment influenced by anthropogenic and natural sources. The study introduced a new application of time series differencing for the identification of nucleation events. To evaluate the conditions favourable to nucleation, the meteorological conditions and gaseous concentrations prior to and during nucleation events were recorded. Gaseous concentrations did not exhibit a clear pattern of change in concentration. It was also found that nucleation was associated with sea breeze and long-range transport. The implications of this finding are that whilst vehicles are the most important source of ultrafine particles, sea breeze and aged gaseous emissions play a more important role in secondary particle formation in the study area.

Near real-time prediction of Zenith Tropospheric Delays for position estimation over long-baseline CORS network

This paper presents the preliminary results in establishing a strategy for predicting Zenith Tropospheric Delay (ZTD) and relative ZTD (rZTD) between Continuous Operating Reference Stations (CORS) in near real-time. It is anticipated that the predicted ZTD or rZTD can assist the network-based Real-Time Kinematic (RTK) performance over long inter-station distances, ultimately, enabling a cost effective method of delivering precise positioning services to sparsely populated regional areas, such as Queensland. This research firstly investigates two ZTD solutions: 1) the post-processed IGS ZTD solution and 2) the near Real-Time ZTD solution. The near Real-Time solution is obtained through the GNSS processing software package (Bernese) that has been deployed for this project. The predictability of the near Real-Time Bernese solution is analyzed and compared to the post-processed IGS solution where it acts as the benchmark solution. The predictability analyses were conducted with various prediction time of 15, 30, 45, and 60 minutes to determine the error with respect to timeliness. The predictability of ZTD and relative ZTD is determined (or characterized) by using the previously estimated ZTD as the predicted ZTD of current epoch. This research has shown that both the ZTD and relative ZTD predicted errors are random in nature; the STD grows from a few millimeters to sub-centimeters while the predicted delay interval ranges from 15 to 60 minutes. Additionally, the RZTD predictability shows very little dependency on the length of tested baselines of up to 1000 kilometers. Finally, the comparison of near Real-Time Bernese solution with IGS solution has shown a slight degradation in the prediction accuracy. The less accurate NRT solution has an STD error of 1cm within the delay of 50 minutes. However, some larger errors of up to 10cm are observed.