bluuebunny/crossref_metadata_2025 huggingface dataset:
Soil hydrological properties regulate grassland ecosystem responses to multifactor global change: A modeling analysis
Authors: Weng Ensheng , Luo Yiqi
Published: July 2008

We conducted a modeling study to evaluate how soil hydrological properties regulate water and carbon dynamics of grassland ecosystems in response to multifactor global change. We first calibrated a process‐based terrestrial ecosystem (TECO) model against data from two experiments with warming and clipping or doubled precipitation in Great Plains. The calibrated model was used to simulate responses of soil moisture, evaporation, transpiration, runoff, net primary production (NPP), ecosystem respiration (Rh), and net ecosystem production (NEP) to changes in precipitation amounts and intensity, increased temperature, and elevated atmospheric [CO2] along a soil texture gradient (sand, sandy loam, loam, silt loam, and clay loam). Soil available water capacity (AWC), which is the difference between field capacity and wilting point, was used as the index to represent soil hydrological properties of the five soil texture types. Simulation results showed that soil AWC altered partitioning of precipitation among runoff, evaporation, and transpiration, and consequently regulated ecosystem responses to global environmental changes. The fractions of precipitation that were used for evaporation and transpiration increased with soil AWC but decreased for runoff. High AWC could greatly buffer water stress during long drought periods, particularly after a large rainfall event. NPP, Rh, and NEP usually increased with AWC under ambient and 50% increased precipitation scenarios. With the halved precipitation amount, NPP, Rh, and NEP only increased from 7% to 7.5% of AWC followed by declines. Warming and CO2 effects on soil moisture, evapotranspiration, and runoff were magnified by soil AWC. Regulatory patterns of AWC on responses of NPP, Rh, and NEP to warming were complex. In general, CO2 effects on NPP, Rh, and NEP increased with soil AWC. Our results indicate that variations in soil texture may be one of the major causes underlying variable responses of ecosystems to global changes observed from different experiments.
Impact of the North Atlantic Oscillation on the trans‐Atlantic migrations of the European eel (Anguilla anguilla)
Authors: Kettle A. James , Bakker Dorothee C. E. , Haines Keith
Published: July 2008

Glass eel catches and FAO (Food and Agricultural Organization) landings of the European freshwater eel (Anguilla anguilla) show a decrease over the past 20 years. The long‐term trends in the time series mask an interannual fluctuation, which becomes apparent on the application of a high‐pass filter and autocorrelation analysis. Both the FAO landings and the glass eel catches show interannual fluctuations with a repeat period of 6–8 years, similar to the period of the North Atlantic Oscillation (NAO). Most glass eel catch monitoring stations are in phase. The glass eel catches show a significant negative correlation with the NAO lagged by 0–2 years, consistent with the hypothesis that the positive NAO phase has an adverse impact on the larval survival in and migration from the Sargasso Sea spawning location, one year prior to the arrival of the glass eels in Europe and North Africa. The FAO landings can be divided into two groups of different phase that have an approximate correspondence to the NAO dipole in winter rainfall in Europe and North Africa. One group (P) comprises Denmark, Ireland, Morocco, Netherlands, Norway, Sweden, Tunisia, and the United Kingdom, and the other group (N) comprises France, Germany, Italy, Poland, Portugal, Spain, and Turkey. At least for the interannual fluctuations, the success of the glass eel fishery (and eel recruitment) may be coupled with the number of migrating silver eels from the N group of countries and uncoupled with the P group of countries.
Computed tomography reconstruction of SO2 concentration distribution in the volcanic plume of Miyakejima, Japan, by airborne traverse technique using three UV spectrometers
Authors: Kazahaya Ryunosuke , Mori Toshiya , Kazahaya Kohei , Hirabayashi Jun‐ichi
Published: July 2008

We present here a new method for measuring the SO2 concentration distribution in a volcanic plume cross‐section, by using the airborne traverse technique with three UV spectrometers and calculating a computed tomography (CT) reconstruction. Our observation requires only one traverse, and is as easy as conventional measurements of SO2 flux. The plume is traverse scanned using three UV spectrometers aligned at three different zenith angles, and a CT technique initially designed for air pollutant monitoring was improved by using ‘Akaike's Bayesian Information Criterion' (ABIC). We applied this method to a volcanic plume at 10 km downwind from the caldera of Miyakejima volcano in Aug. 2004. The results of the application show that the profile of the plumes significantly changed in only a matter of a few minutes. Due to the flexibility and ease of the observation procedure, this method is widely applicable to various fields and shows promise in volcanic gas monitoring.
Stratospheric winter climate response to ENSO in three chemistry‐climate models
Authors: Fischer A. M. , Shindell D. T. , Winter B. , Bourqui M. S. , Faluvegi G. , Rozanov E. , Schraner M. , Brönnimann S.
Published: July 2008

Three different chemistry‐climate models are compared with respect to their simulation of the stratospheric response to extreme cases of ENSO. Ensemble simulations of an unusually warm ENSO event (1940–1941) compared to a very cold event (1975–1976) reveal a weaker and warmer polar vortex in the Northern Hemisphere winter. This follows from anomalously propagating waves decelerating the zonal flow and strengthening the residual mean circulation. Models are in good agreement in simulating the observed (statistically reconstructed for the case 1941) flow in the lower stratosphere over the Pacific North American region, but less so over the North Atlantic European sector with insufficient reproduction of the wave structure. Modeled column ozone is reduced in the Tropics and increased on average in the northern extra tropics in accord with the general pattern seen in observations and in line with an intensification of the Brewer‐Dobson circulation.
Aerosol impact and correction on temperature profile retrieval from MODIS
Authors: Zhang Jie , Zhang Qiang
Published: July 2008

Aerosols over desert areas can impact the temperature profile retrieval using infrared remote sensing techniques. Retrievals from Moderate Resolution Imaging Spectroradiometer (MODIS) Infrared (IR) radiances over the Gobi region in China show that atmospheric temperatures above the top of the boundary layer can be retrieved with a root mean square error (rmse) better than 2 K. In the boundary layer, the error in the temperature retrieval is largely due to limited spectral information and uncertainty of the radiative transfer model. The error in the retrieved atmospheric boundary layer temperature is positively correlated with aerosol optical depth (AOD) and estimated errors of skin temperature and surface IR emissivities. Taking into account the aerosol effect in the radiative transfer model, the temperature retrievals from MODIS are improved by approximately 0.38 K in the boundary layer depending on the aerosol optical depth (AOD).
Microbial contributions to climate change through carbon cycle feedbacks
Authors: Bardgett Richard D , Freeman Chris , Ostle Nicholas J
Published: July 2008

There is considerable interest in understanding the biological mechanisms that regulate carbon exchanges between the land and atmosphere, and how these exchanges respond to climate change. An understanding of soil microbial ecology is central to our ability to assess terrestrial carbon cycle–climate feedbacks, but the complexity of the soil microbial community and the many ways that it can be affected by climate and other global changes hampers our ability to draw firm conclusions on this topic. In this paper, we argue that to understand the potential negative and positive contributions of soil microbes to land–atmosphere carbon exchange and global warming requires explicit consideration of both direct and indirect impacts of climate change on microorganisms. Moreover, we argue that this requires consideration of complex interactions and feedbacks that occur between microbes, plants and their physical environment in the context of climate change, and the influence of other global changes which have the capacity to amplify climate-driven effects on soil microbes. Overall, we emphasize the urgent need for greater understanding of how soil microbial ecology contributes to land–atmosphere carbon exchange in the context of climate change, and identify some challenges for the future. In particular, we highlight the need for a multifactor experimental approach to understand how soil microbes and their activities respond to climate change and consequences for carbon cycle feedbacks.
Dipole-induced self-assembly of helical β-peptides
Authors: Miller Clark A. , Hernández-Ortiz Juan P. , Abbott Nicholas L. , Gellman Samuel H. , de Pablo Juan J.
Published: July 2008

In this work, the interactions between β-peptides are investigated for helix-forming peptides using molecular simulation. The role of electrostatic interactions in the self-assembly of these peptides is studied by calculating the dipole moment of various 14-helical β-peptides using molecular dynamics simulations. The stability of a β-peptide that is known to form a liquid crystalline phase is determined by calculating the potential of mean force using the expanded ensemble density of states method. This peptide is found to form a mechanically stable 14-helix in an implicit solvent model. The interaction between two of these peptides is examined by calculating the potential of mean force between the two peptides in implicit solvent. The peptides are shown to favorably associate in an end-to-end manner, driven largely by dipolar interactions. In order to understand the possible structures that form when many peptides interact in solution, a coarse-grained model is developed. Brownian dynamics simulations of the coarse-grained model at intermediate concentrations (1–50mM) are performed, and the aggregation behavior is understood by calculating the diffusivity and the radial distribution function. An analysis of the resultant structures reveals that the coarse-grained model of the peptide leads to the formation of spherical clusters.
A possible anthracene-based optical molecular switch driven by a reversible photodimerization reaction
Authors: Zhao P. , Fang C. F. , Xia C. J. , Wang Y. M. , Liu D. S. , Xie S. J.
Published: July 2008

By applying nonequilibrium Green’s function formalism combined with first-principles density functional theory, we investigate the electronic transport properties of an anthracene-based optical molecular switch. The molecules that comprise the switch can convert between the monomer and dimer forms upon photoexcitation, and two forms can keep stable over a wider temperature range. The transmission spectra of two forms are remarkably distinctive. Theoretical results show that the current through the monomer form is significantly larger than that through the dimer form, which suggests that this system has attractive potential application in future molecular switch technology.
Axially graded heteroepitaxy and Raman spectroscopic characterizations of Si1−xGex nanowires
Authors: Yang Jee-Eun , Park Won-Hwa , Kim Cheol-Joo , Kim Zee Hwan , Jo Moon-Ho
Published: July 2008

We report the axially graded heteroepitaxy of Si1−xGex nanowires, by the kinetic controls of the Au-catalytic decomposition of precursors during chemical vapor syntheses. Transmission electron microscope studies demonstrate that the relative composition of Si and Ge is continuously graded along the uniformly thick nanowires, sharing the same crystal structures with the continuously varying lattices. We also employed a confocal Raman scattering imaging technique, and showed that the local variations in Raman phonon bands, specific to Si and Ge alloying (νSi–Si, νSi–Ge, and νGe–Ge), can be spatially and spectrally resolved along the individual nanowires, within the spatial resolution of ∼500nm.
Selective polarization transfer using a single rf field
Authors: Rey Castellanos Eddy R. , Frueh Dominique P. , Wist Julien
Published: July 2008

NMR is a popular and mature technique used in fields as diverse as chemistry, biology, or material science. One reason for this versatility lies in its ability to correlate the nuclei that are present in one molecule to another. This provides the researcher with correlation maps allowing for studies of the molecules at an atomic level. Selective experiments allow isolation of one such correlation to focus on spins of interest. This leads to a savings in precious experimental time by reducing the dimension of the experiment, which in turn may enable one to record more elaborate experiments that would otherwise not be amenable within reasonable acquisition times. Here, we present an alternative method to selectively transfer magnetization using a single rf field. This technique, which we call single field polarization transfer, allows to obtain longitudinal two-spin order of two scalar-coupled spins when only one of them is irradiated. The method is easy to implement and does not depend on stringent conditions, such as Hartmann–Hahn matching for selective cross-polarization transfers or very long inversion pulses and identification of coupling satellites in selective population inversion experiments.
Metal clusters that freeze into high energy geometries
Authors: Jarrold Martin F. , Cao Baopeng , Starace Anne K. , Neal Colleen M. , Judd Oscar H.
Published: July 2008

Heat capacities measured for isolated aluminum clusters show peaks due to melting. For some clusters with around 60 and 80 atoms there is a dip in the heat capacities at a slightly lower temperature than the peak. The dips have been attributed to structural transitions. Here we report studies where the clusters are annealed before the heat capacity is measured. The dips disappear for some clusters, but in many cases they persist, even when the clusters are annealed to well above their melting temperature. This indicates that the dips do not result from badly formed clusters generated during cluster growth, as originally suggested. We develop a simple kinetic model of melting and freezing in a system consisting of one liquidlike and two solidlike states with different melting temperatures and latent heats. Using this model we are able to reproduce the experimental results including the dependence on the annealing conditions. The dips result from freezing into a high energy geometry and then annealing into the thermodynamically preferred solid. The thermodynamically preferred solid has the higher freezing temperature. However, the liquid can bypass freezing into the thermodynamically preferred solid (at high cooling rates) if the higher energy geometry has a larger freezing rate.
The thickness of a liquid layer on the free surface of ice as obtained from computer simulation
Authors: Conde M. M. , Vega C. , Patrykiejew A.
Published: July 2008

Molecular dynamic simulations were performed for ice Ih with a free surface by using four water models, SPC/E, TIP4P, TIP4P/Ice, and TIP4P/2005. The behavior of the basal plane, the primary prismatic plane, and of the secondary prismatic plane when exposed to vacuum was analyzed. We observe the formation of a thin liquid layer at the ice surface at temperatures below the melting point for all models and the three planes considered. For a given plane it was found that the thickness of a liquid layer was similar for different water models, when the comparison is made at the same undercooling with respect to the melting point of the model. The liquid layer thickness is found to increase with temperature. For a fixed temperature it was found that the thickness of the liquid layer decreases in the following order: the basal plane, the primary prismatic plane, and the secondary prismatic plane. For the TIP4P/Ice model, a model reproducing the experimental value of the melting temperature of ice, the first clear indication of the formation of a liquid layer, appears at about −100 °C for the basal plane, at about −80 °C for the primary prismatic plane, and at about −70 °C for the secondary prismatic plane.
An interpretative model for the anomalous behavior of some excess properties in mixed liquid systems: A relationship between excess molar volumes and excess compressibilities in strongly self-aggregated fluids
Authors: Raudino Antonio , Palombo Francesca , Cataliotti Rosario Sergio
Published: July 2008

A simple theoretical model based on the hole theory of the liquid state has been developed in order to find a relationship between the excess molar volume and the excess compressibility of a two-component fluid. The model has been extended to investigate strongly associating fluids dissolved in an apolar solvent. Such a model nicely explains our recent results obtained from a Brillouin scattering study of the nonideal mixture between tert-butyl alcohol and 2-2′ dimethyl butane. Its validity, however, seems to be rather general and it could be usefully applied to rationalize the excess properties of several nonideal binary fluid mixtures.
Rotationally invariant ab initio evaluation of Coulomb and exchange parameters for DFT+U calculations
Authors: Mosey Nicholas J. , Liao Peilin , Carter Emily A.
Published: July 2008

Conventional density functional theory (DFT) fails for strongly correlated electron systems due to large intra-atomic self-interaction errors. The DFT+U method provides a means of overcoming these errors through the use of a parametrized potential that employs an exact treatment of quantum mechanical exchange interactions. The parameters that enter into this potential correspond to the spherically averaged intra-atomic Coulomb (U) and exchange (J) interactions. Recently, we developed an ab initio approach for evaluating these parameters on the basis of unrestricted Hartree–Fock (UHF) theory, which has the advantage of being free of self-interaction errors and does not require experimental input [Mosey and Carter, Phys. Rev. B 76, 155123 (2007)]. In this work, we build on that method to develop a more robust and convenient ab initio approach for evaluating U and J. The new technique employs a relationship between U and J and the Coulomb and exchange integrals evaluated using the entire set of UHF molecular orbitals (MOs) for the system. Employing the entire set of UHF MOs renders the method rotationally invariant and eliminates the difficulty in selecting unambiguously the MOs that correspond to localized states. These aspects overcome two significant deficiencies of our earlier method. The new technique is used to evaluate U and J for Cr2O3, FeO, and Fe2O3. The resulting values of U-J are close to empirical estimates of this quantity for each of these materials and are also similar to results of constrained DFT calculations. DFT+U calculations using the ab initio parameters yield results that are in good agreement with experiment. As such, this method offers a means of performing accurate and fully predictive DFT+U calculations of strongly correlated electron materials.
Optical excitations of defects in realistic nanoscale silica clusters: Comparing the performance of density functional theory using hybrid functionals with correlated wavefunction methods
Authors: Zwijnenburg M. A. , Sousa C. , Sokol A. A. , Bromley S. T.
Published: July 2008

Optical excitations of low energy silica (SiO2)4 clusters obtained by global optimization, as opposed to constructed by hand, are studied using a range of theoretical methods. By focusing on the lowest energy silica clusters we hope to capture at least some of the characteristic ways by which the dry surfaces of silica nanosystems preferentially terminate. Employing the six lowest energy (SiO2)4 cluster isomers, we show that they exhibit a surprisingly wide range of geometries, defects, and associated optical excitations. Some of the clusters show excitations localized on isolated defects, which are known from previous studies using hydrogen-terminated versions of the defect in question. Other clusters, however, exhibit novel charge-transfer excitations in which an electron transfers between two spatially separated defects. In these cases, because of the inherent proximity of the constituent defects due to the small cluster dimensions, the excitation spectrum is found to be very different from that of the same defects in isolation. Excitation spectra of all clusters were calculated using time-dependent density functional theory (TD-DFT) and delta-SCF DFT (ΔDFT) methods employing two different hybrid density functionals (B3LYP and BB1K) differing essentially in the amount of incorporated Hartree–Fock-like exchange (HFLE). In all cases the results were compared with CASPT2 calculated values which are taken as a benchmark standard. In line with previous work, the spatially localized excitations are found to be well described by TD-DFT/B3LYP but which gives excitation energies that are significantly underestimated in the case of the charge-transfer excitations. The TD-DFT/BB1K combination in contrast is found to give generally good excitation energies for the lowest excited states of both localized and charge-transfer excitations. Finally, our calculations suggest that the increased quality of the predicted excitation spectra by adding larger amounts of HFLE is mainly due to an increased localization of the excited state associated with the elimination of spurious self-interaction inherent to (semi-)local DFT functionals.
Nucleation theory in Langevin’s approach and lifetime of a Brownian particle in potential wells
Authors: Alekseechkin N. V.
Published: July 2008

The multivariable theory of nucleation suggested by Alekseechkin [J. Chem. Phys. 124, 124512 (2006)] is further developed in the context of Langevin’s approach. The use of this approach essentially enhances the capability of the nucleation theory, because it makes possible to consider the cases of small friction which are not taken into account by the classical Zel’dovich–Frenkel theory and its multivariable extensions. The procedure for the phenomenological determination of the nucleation parameters is described. Using the similarity of the Kramers model with that of nucleation, the lifetime of a Brownian particle in potential wells in various dimensionalities is calculated with the help of the expression for the steady state nucleation rate.
Thermodynamic response functions of fluids: A microscopic approach based on NpT Monte Carlo
Authors: Piñeiro Manuel M. , Cerdeiriña Claudio A. , Medeiros Milton
Published: July 2008

On the basis of NpT Monte Carlo simulations, a detailed analysis on the microscopic origins of some specific features of thermodynamic response functions of fluids is performed. Specifically, the residual isobaric heat capacity Cpres, the isobaric thermal expansivity αp, and the isothermal compressibility κT for Lennard–Jones methane and optimized potential for liquid simulations (OPLS) methanol have been determined via standard techniques. For the former, data along the liquid, gas, and supercritical regions are presented, while a wide temperature range at a single supercritical pressure is covered for the latter. They have been obtained by computing the various pairwise fluctuations contributing to each property. Attention is mainly focused on isothermal and isobaric maxima found for both Cpres and αp, which have been rationalized at a molecular level using qualitative arguments. It is encountered that maxima emerge as a natural consequence of the destruction of fluid structure as temperature is increased or as pressure is decreased. The results for Lennard–Jones methane reveal the competition of energetic and volumetric effects, while those for OPLS methanol evidence that hydrogen-bonding is dominant as energetic effects are concerned. Further discussion on previous results and alternative approaches using equations of state as well as on closely related topics such as “maxima and critical phenomena” is included.
Midinfrared intersubband absorption in wide band gap II-VI ZnxCd1−xSe multiple quantum wells with metastable zincblende MgSe barriers
Authors: Li B. S. , Shen A. , Charles W. O. , Zhang Q. , Tamargo M. C.
Published: July 2008

The authors report the observation of midinfrared intersubband (ISB) absorption in MgSe∕ZnxCd1−xSe multiple quantum wells (MQWs) grown on (001) InP substrates by molecular beam epitaxy. The in situ reflection high energy electron diffraction shows that zincblende MgSe∕ZnxCd1−xSe MQWs can be grown with the introduction of ZnxCd1−xSe spacer layers. For quantum wells with the nominal well width of 11–15 ML (3.2–4.4nm) ISB absorption in the wavelength range of 3.3–4.9μm is observed. The conduction band offset (CBO) of the MgSe∕ZnxCd1−xSe heterostructure is estimated to be 1.2eV. Using the estimated CBO, the theoretically calculated interband and ISB transition energies agree well with photoluminescence and Fourier-transform infrared spectroscopy measurements. With such a large CBO, ISB transitions in this material system could be extended to the near infrared region.
Energy-dependent dynamics of large-ΔE collisions: Highly vibrationally excited azulene (E=20390 and 38580cm−1) with CO2
Authors: Yuan Liwei , Du Juan , Mullin Amy S.
Published: July 2008

We report the energy dependence of strong collisions of CO2 with highly vibrationally excited azulene for two initial energies, E=20390 and 38580cm−1. These studies show that both the distribution of transferred energy and the energy transfer rates are sensitive to the azulene energy. Highly excited azulene was prepared in separate studies by absorption of pulsed excitation at λ=532 or 266nm, followed by rapid radiationless decay from S1 or S4 to vibrationally excited levels of the ground electronic state. The appearance of scattered CO2 (0000) molecules with Erot>1000cm−1 was monitored by high-resolution transient IR absorption at λ=4.3μm. The average rotational and translational energies of the scattered CO2 molecules double when the azulene energy is increased by a factor of 2. The rate of energy transfer in strong collisions increases by nearly a factor of 4 when the azulene energy is doubled. The energy transfer probability distribution function for ΔE>3000cm−1 at each initial energy is an exponential decay with curvature that correlates with the energy dependence of the state density, in excellent agreement with predictions from GRETCHEN, a model based on Fermi’s golden rule to describe collisional quenching of highly excited molecules.
Integrated circuits based on nanoscale vacuum phototubes
Authors: Diamant Gilad , Halahmi Erez , Kronik Leeor , Levy Jeff , Naaman Ron , Roulston John
Published: July 2008

We present and experimentally verify a concept for electronic devices based on nanoscale vacuum phototubes. Such devices are expected to be both reliable and amenable to large-scale integration. We further suggest several generalizations of the concept and discuss possible applications and advantages.
Self-interaction correction and the optimized effective potential
Authors: Körzdörfer T. , Kümmel S. , Mundt M.
Published: July 2008

Self-interaction is one of the most substantial problems in present-day density functional theory. A widely used approach to overcome this problem is the self-interaction correction proposed by Perdew and Zunger. However, the thus given functional not only depends on the orbitals explicitly but is also variant under unitary transformation of the orbitals. In this manuscript, we present a generalized version of the optimized effective potential equation which is able to deal with both problems in one go. Calculations for molecules exemplify the approach.
Avalanching granular flows down curved and twisted channels: Theoretical and experimental results
Authors: Pudasaini Shiva P. , Wang Yongqi , Sheng Li-Tsung , Hsiau Shu-San , Hutter Kolumban , Katzenbach Rolf
Published: July 2008

Depth evolution and final deposits play a crucial role in the description of the dynamics of granular avalanches. This paper presents new and important results on the geometric deformation and measurements of avalanche depositions in laboratory granular flows and their comparisons with theoretical predictions through some benchmark problems for flows down curved and twisted channels merging into a horizontal plane. XY-table and analoglaser sensor are applied to measure geometries of deposited masses in the fanlike open transition and runout zones for different granular materials, different channel lengths, and different channel mouths in the runout zone. The model equations proposed by Pudasaini and Hutter [“Rapid shear flows of dry granular masses down curved and twisted channels,” J. Fluid Mech. 495, 193 (2003)] are used for theoretical prediction. We show that geometric parameters such as curvature, twist and local details of the channel play a crucial role in the description of avalanching debris and their deposits in the standstill. Asymmetric depositions and surface contours about the central line of the channel could not be produced and predicted by any other classical theories and available experiments in the literature as done in this paper. Such a role played by the geometrical parameters of the channel over physical parameters for the flow of granular materials down a general channel was not investigated before. It is demonstrated that the numerical simulations of the model equations and experimental observations are generally in good agreement.
Longitudinal coherence in thermal ghost imaging
Authors: Ferri F. , Magatti D. , Sala V. G. , Gatti A.
Published: July 2008

We show theoretically and experimentally that lensless ghost imaging with thermal light is fully interpretable in terms of classical statistical optics. The disappearance of the ghost image when the object and the reference planes are located at different distances from the source is due to the fading out of the intensity-intensity cross correlation between the two planes. Thus the visibility and the resolution of the ghost image are determined by the longitudinal coherence of the speckle beam, and no quantum explanation is necessary.
Second order coalescence conditions of molecular wave functions
Authors: Tew David P.
Published: July 2008

Kato’s cusp condition gives the exact first order dependence of molecular wave functions on interparticle separation near the coalescence of two charged particles. We derive conditions correct to second order in interparticle separation, which concern second order derivatives of the wave function at the coalescence point. For identical particle coalescence, we give equations correct to third order. In addition to a universal, particle dependent term, a system and state dependent term arises in the higher order conditions, which we interpret as an effect of Coulombic screening. We apply our analysis to the standard orbital-based methods of quantum chemistry and discuss the implications for Jastrow- and R12-type correlation factors.
Influence of asymmetry on vortex nucleation and annihilation in submicroscaled permalloy disk array
Authors: Wu Kuo-Ming , Horng Lance , Wang Jia-Feng , Wu Jong-Ching , Wu Yin-Hao , Lee Ching-Ming
Published: July 2008

Magnetic properties of vortex nucleation, annihilation, and switching field distribution (SFD) in NiFe disk arrays, where the elements are with 300nm diameter and different degrees of asymmetry, were investigated through measurements and simulations of hysteresis loop. The nucleation and annihilation of vortex state show strong dependences on the asymmetry. More interestingly, the width of SFD, the crucial factor for high-density storage application, oscillating with the degree of asymmetry is observed. The simulation results agree well with the experimental data.
Appearance of the bulk motif in Al clusters
Authors: Sun Jiao , Lu Wen-Cai , Li Ze-Sheng , Wang C. Z. , Ho K. M.
Published: July 2008

We have performed an unbiased search for the lowest-energy structures of medium-sized aluminum clusters Aln (n=19–26) using a genetic algorithm (GA) coupled with a tight-binding interatomic potential. Structural candidates obtained from our GA search were further optimized using density functional theory. It is found that the double icosahedron is not the most stable structure for Al19 but serves as the core for Al20 and Al21. The lowest-energy structures of Aln are found to undergo a transition to an aluminum bulk motif above Al23. In particular, the lowest-energy structure of Al26 is almost a fragment of the bulk face-centered-cubic crystal except for the stacking fault at the bottom layer. Anion clusters were also studied.
Noise-induced order in the chaos of the Belousov–Zhabotinsky reaction
Authors: Yoshimoto Minoru , Shirahama Hiroyuki , Kurosawa Shigeru
Published: July 2008

Noise can stabilize a metastable state in such a way that the system remains in this state for a longer time than in the absence of noise. When this phenomenon is observed in chaos, it is called “noise-induced order.” We have experimentally detected noise-induced order in the Belousov–Zhabotinsky reaction. That is, when noise is added to the chaos with the flow rate near the period-three oscillation, a decrease of the maximum Lyapunov exponent and a convergence of the Fourier spectrum are observed. Moreover, the analysis on the one-dimensional return map reveals that noise-induced order is caused by the convergence of the chaotic trajectory into the laminar region.
Quantum Trivelpiece–Gould waves in a magnetized dense plasma
Authors: Terças H. , Mendonça J. T. , Shukla P. K.
Published: July 2008

The dispersion relation for the electrostatic waves below the electron plasma frequency in a dense quantum plasma is derived by using the magnetohydrodynamic model. It is shown that in the classical case the dispersion relation reduces to the expression obtained for the well-known Trivelpiece–Gould (TG) modes. Attention is also devoted to the case of solitary waves associated with the nonlinear TG modes.
Two groups measure the quasiparticle charge of the 52 fractional quantum Hall state
Authors: Day Charles
Published: July 2008

After finding the expected value of e/4, experimenters hope next to uncover the state’s true nature and verify its suitability for quantum computation.
Collider data show evidence for a meson made of four quarks
Authors: Schwarzschild Bertram
Published: July 2008

It’s not obvious from quantum chromodynamics what sorts of unusual mesons and baryons experimenters should expect.
Revamped grants program offers R&D funds for ‘critical national needs’
Authors: Kramer David
Published: July 2008

The Technology Innovation Program replaces the controversial Advanced Technology Program for supporting high-risk R&D projects.
Comets and the early solar system
Authors: Brownlee Donald
Published: July 2008

The material in comets hasn’t changed much over the past few billion years. Spacecraft that were sent to image, probe, and sample passing comets offer a unique look back in time.
Probing physical properties at the nanoscale
Authors: Brukman Matthew J. , Bonnell Dawn A.
Published: July 2008

With the interaction between a sharp tip and a surface tailored using combinations of static and time-dependent external fields, scanning probe techniques can image far more than topographic structure.
Theory of the observed ultralow friction between sliding polyelectrolyte brushes
Authors: Sokoloff J. B.
Published: July 2008

It is shown using a method based on a modified version of the mean field theory of Miklavic and Marcelja [J. Phys. Chem. 92, 6718 (1988)] that it should be possible for osmotic pressure due to the counterions associated with the two polyelectrolyte polymer brush coated surfaces to support a reasonable load (i.e., about 106 Pa) with the brushes held sufficiently far apart to prevent entanglement of polymers belonging to the two brushes, thus avoiding what is believed to be the dominant mechanisms for static and dry friction.
Optical detection of deoxyribonucleic acid hybridization with InGaN∕GaN multiple quantum wells
Authors: Shih H. Y. , Chen T. T. , Wang C. H. , Chen K. Y. , Chen Y. F.
Published: July 2008

Based on the high surface sensitivity of piezoelectric polarization of strained nitride semiconductors, surface functionalized nitride light emitting devices (LEDs) provide an excellent opportunity for the development of biological sensors. To demonstrate our working principle, a probe chip based on In0.22Ga0.78N∕GaN multiple quantum wells has been constructed and exposed to target DNA solutions, matched and/or mismatched, with different concentrations. The pronounced changes of photoluminescence spectra as well as Raman scattering A1(LO) spectra in matched target DNA clearly illustrate the feasibility of our proposed mechanism. The results shown here open up a new possibility for the application of nitride LEDs in biosensor engineering.
Analysis of electrically biased paramagnetic defect centers in HfO2 and HfxSi1−xO2/(100)Si interfaces
Authors: Chen P. T. , Triplett B. B. , Chambers J. J. , Colombo L. , McIntyre P. C. , Nishi Y.
Published: July 2008

This study reports on the first experimental observations of electrically biased paramagnetic defects at 800 °C N2 annealed HfxSi1−xO2 (x=0.4, and 0.6)/(100)Si and HfO2/(100)Si interfaces in metal oxide silicon structures. These defects are examined by electrical-field controlled electron spin resonance (ESR) and correlated with capacitance-voltage (C-V) analysis. Distributions of ESR measured density of interface traps (ESR-Dit), Pb0 and Pb1, exhibit distinct charge humps and peaks in the Si bandgap with maximum defect density of 0.9–1.9×1012 cm−2 eV−1 in the Hf0.4Si0.6O2/Si interface. Three Pb0 and one Pb1 charged ESR-Dit peaks with density of 1.7–2.8×1012 cm−2 eV−1 are observed in the Hf0.6Si0.4O2/Si interface. Cross-sectional transmission electron microscopic images show decreasing interfacial layer (IL) thickness with increasing hafnium composition (x) at the HfxSi1−xO2/Si interface. The roughest IL observed at the HfO2/Si interface may have contributed to an ESR-Dit of Pb0 greater than 2×1013 cm−2 eV−1 and a pinned Fermi level near the midgap. It appears that the energy distributions of interface defects in HfxSi1−xO2/Si and HfO2/Si have different signatures compared to those at SiO2/Si interface, especially the charged peak near the midgap.
Sensitivity amplification in the phosphorylation-dephosphorylation cycle: Nonequilibrium steady states, chemical master equation, and temporal cooperativity
Authors: Ge Hao , Qian Min
Published: July 2008

A new type of cooperativity termed temporal cooperativity [Biophys. Chem. 105, 585 (2003); Annu. Rev. Phys. Chem. 58, 113 (2007)] emerges in the signal transduction module of phosphorylation-dephosphorylation cycle (PdPC). It utilizes multiple kinetic cycles in time, in contrast to allosteric cooperativity that utilizes multiple subunits in a protein. In the present paper, we thoroughly investigate both the deterministic (microscopic) and stochastic (mesoscopic) models and focus on the identification of the source of temporal cooperativity via comparing with allosteric cooperativity. A thermodynamic analysis confirms again the claim that the chemical equilibrium state exists if and only if the phosphorylation potential ΔG=0, in which case the amplification of sensitivity is completely abolished. Then we provide comprehensive theoretical and numerical analysis with the first-order and zero-order assumptions in PdPC, respectively. Furthermore, it is interestingly found that the underlying mathematics of temporal cooperativity and allosteric cooperativity are equivalent, and both of them can be expressed by “dissociation constants,” which also characterizes the essential differences between the simple and ultrasensitive PdPC switches. Nevertheless, the degree of allosteric cooperativity is restricted by the total number of sites in a single enzyme molecule that cannot be freely regulated, while temporal cooperativity is only restricted by the total number of molecules of the target protein that can be regulated in a wide range and gives rise to the ultrasensitivity phenomenon.
Stable long-time semiclassical description of zero-point energy in high-dimensional molecular systems
Authors: Garashchuk Sophya , Rassolov Vitaly A.
Published: July 2008

Semiclassical implementation of the quantum trajectory formalism [J. Chem. Phys. 120, 1181 (2004)] is further developed to give a stable long-time description of zero-point energy in anharmonic systems of high dimensionality. The method is based on a numerically cheap linearized quantum force approach; stabilizing terms compensating for the linearization errors are added into the time-evolution equations for the classical and nonclassical components of the momentum operator. The wave function normalization and energy are rigorously conserved. Numerical tests are performed for model systems of up to 40 degrees of freedom.
Diffractive-refractive optics: X-ray collimator
Authors: Hrdý Jaromír , Oberta Peter
Published: July 2008

Diffractive-refractive optics are x-ray focusing monochromators based on the diffraction on profiled crystal surface. Diffraction on longitudinal parabolic groove machined in crystal surface forms a sagittaly focused synchrotron radiation beam. Such kind of monochromator may be realized as a crystal with parabolic hole, where the beam is diffracted on the inner wall of the hole. Two such asymmetrically cut crystals set into antiparallel position, creating a dispersive (+,−,−,+) arrangement, form a sagittaly focusing x-ray monochromator which should be practically aberration-free. The focusing properties of such kind of monochromator are discussed in detail and it is shown for the first time that it can be used not only for focusing but also for creating highly parallel monochromatic beam in the broad region of the Bragg angles. This device with parabolic hole has not been tested experimentally yet.
Fluctuation-induced interactions between dielectrics in general geometries
Authors: Pasquali S. , Maggs A. C.
Published: July 2008

We study thermal Casimir and quantum nonretarded Lifshitz interactions between dielectrics in general geometries. We map the calculation of the classical partition function onto a determinant, which we discretize and evaluate with the help of Cholesky factorization. The quantum partition function is treated by path integral quantization of a set of interacting dipoles and reduces to a product of determinants. We compare the approximations of pairwise additivity and proximity force with our numerical methods. We propose a “factorization approximation” that gives rather good numerical results in the geometries that we study.
Daubechies wavelets as a basis set for density functional pseudopotential calculations
Authors: Genovese Luigi , Neelov Alexey , Goedecker Stefan , Deutsch Thierry , Ghasemi Seyed Alireza , Willand Alexander , Caliste Damien , Zilberberg Oded , Rayson Mark , Bergman Anders , Schneider Reinhold
Published: July 2008

Daubechies wavelets are a powerful systematic basis set for electronic structure calculations because they are orthogonal and localized both in real and Fourier space. We describe in detail how this basis set can be used to obtain a highly efficient and accurate method for density functional electronic structure calculations. An implementation of this method is available in the ABINIT free software package. This code shows high systematic convergence properties, very good performances, and an excellent efficiency for parallel calculations.
Essential energy space random walks to accelerate molecular dynamics simulations: Convergence improvements via an adaptive-length self-healing strategy
Authors: Zheng Lianqing , Yang Wei
Published: July 2008

Recently, accelerated molecular dynamics (AMD) technique was generalized to realize essential energy space random walks so that further sampling enhancement and effective localized enhanced sampling could be achieved. This method is especially meaningful when essential coordinates of the target events are not priori known; moreover, the energy space metadynamics method was also introduced so that biasing free energy functions can be robustly generated. Despite the promising features of this method, due to the nonequilibrium nature of the metadynamics recursion, it is challenging to rigorously use the data obtained at the recursion stage to perform equilibrium analysis, such as free energy surface mapping; therefore, a large amount of data ought to be wasted. To resolve such problem so as to further improve simulation convergence, as promised in our original paper, we are reporting an alternate approach: the adaptive-length self-healing (ALSH) strategy for AMD simulations; this development is based on a recent self-healing umbrella sampling method. Here, the unit simulation length for each self-healing recursion is increasingly updated based on the Wang–Landau flattening judgment. When the unit simulation length for each update is long enough, all the following unit simulations naturally run into the equilibrium regime. Thereafter, these unit simulations can serve for the dual purposes of recursion and equilibrium analysis. As demonstrated in our model studies, by applying ALSH, both fast recursion and short nonequilibrium data waste can be compromised. As a result, combining all the data obtained from all the unit simulations that are in the equilibrium regime via the weighted histogram analysis method, efficient convergence can be robustly ensured, especially for the purpose of free energy surface mapping.
Variable atomic radii for continuum-solvent electrostatics calculation
Authors: Zhou Baojing , Agarwal Manish , Wong Chung F.
Published: July 2008

We have developed a method to improve the description of solute cavity defined by the interlocking-sphere model for continuum-solvent electrostatics calculations. Many models choose atomic radii from a finite set of atom types or uses an even smaller set developed by Bondi [J. Phys. Chem. 68, 441 (1964)]. The new model presented here allowed each atom to adapt its radius according to its chemical environment. This was achieved by first approximating the electron density of a molecule by a superposition of atom-centered spherical Gaussian functions. The parameters of the Gaussian functions were then determined by optimizing a function that minimized the difference between the properties from the model and those from ab initio quantum calculations. These properties included the electrostatics potential on molecular surface and the electron density within the core of each atom. The size of each atom was then determined by finding the radius at which the electron density associated with the atom fell to a prechosen value. This value was different for different chemical elements and was chosen such that the averaged radius for each chemical element in a training set of molecules matched its Bondi radius. Thus, our model utilized only a few adjustable parameters—the above density cutoff values for different chemical elements—but had the flexibility of allowing every atom to adapt its radius according to its chemical environment. This variable-radii model gave better solvation energy for 31 small neutral molecules than the Bondi radii did, especially for a quantum mechanics/Poisson–Boltzmann approach we developed earlier. The improvement was most significant for molecules with large dipole moment. Future directions for further improvement are also discussed.