bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular evolution and intragenic recombination of the merozoite surface protein MSP-3α from the malaria parasitePlasmodium vivaxin Thailand
Authors: MASCORRO C. N. , ZHAO K. , KHUNTIRAT B. , SATTABONGKOT J. , YAN G. , ESCALANTE A. A. , CUI L.
Published: June 2005

The merozoite surface antigens of malaria parasites are prime anti-morbidity/mortality vaccine candidates. However, their highly polymorphic nature requires extensive surveys of parasite populations to validate vaccine designs. Previous studies have found 3 molecular types (A, B and C) of thePlasmodium vivaxmerozoite surface protein 3α (PvMSP-3α) among parasite field populations. Here we analysed completePvMSP-3α sequences from 17 clinicalP. vivaxisolates from Thailand and found that the nucleotide diversity was as high as that from samples widely separated by time and space. The polymorphic sites were not randomly distributed but concentrated in the N-terminal Ala-rich domain (block 2A), which is partially deleted in type B and C sequences. The size variations among type A sequences were due to small indels occurring in block 2A, whereas type B and C sequences were uniform in length with each type having a different large deletion. Analysis of synonymous and non-synonymous substitutions suggested that different selection forces were operating on different regions of the molecule. The numerous recombination sites detected within the Ala-rich domain suggested that intragenic recombination was at least partially responsible for the observed genetic diversity of thePvMSP-3α gene. Phylogenetic analysis failed to link any alleles to a specific geographical origin, even when different domains ofPvMSP-3α were used for analysis. The highly polymorphic nature and lack of geographical clustering of isolates suggest that more systematic investigations of thePvMSP-3α gene are needed to explore its evolution and vaccine potential.
Effect of phenotypic variation inXenorhabdus nematophilaon its mutualistic relationship with the entomopathogenic nematodeSteinernema carpocapsae
Authors: SICARD M. , TABART J. , BOEMARE N. E. , THALER O. , MOULIA C.
Published: June 2005

The entomopathogenic nematodeSteinernema carpocapsaeis mutualistically associated with the bacteriumXenorhabdus nematophila. Infective Juveniles (IJs) transportX. nematophilacells that provide them with good conditions to reproduce within the insect. In the laboratory, long term stationary-phase culture conditions sometimes leadX. nematophila's variant 1 cells, which were previously isolated from the worms, to spontaneously and irreversibly change into a new phenotypic variant (variant 2). In this paper, we tested the ability of each phenotypic variant to (i) be transmitted by IJs, (ii) to optimize the worm's fitness within the insect, and (iii) to counteract the effect of closely related antagonistic bacteria previously shown as being able to totally preventS. carpocapsae's reproduction within the insect. We found that IJs did associate with cells of both phenotypes but that the variant 2 cells were preferentially retained by the nematodes when both variants were present in the insect. Both phenotypic variants led to the same fitness ofS. carpocapsaein insects not infected by antagonistic bacteria. In insects infected by antagonistic bacteria, both variants were able to provide protection toS. carpocapsae. Nevertheless, this protection depended on the phenotypic variant and the antagonistic bacteria that were co-injected into the insect. Further analysis conducedin vitroshowed that this variability could be partly linked to the sensitivity of each antagonistic bacterium to xenorhabdicin, produced byX. nematophila.
Delayed transmission of a parasite is compensated by accelerated growth
Authors: HAKALAHTI T. , BANDILLA M. , VALTONEN E. T.
Published: June 2005

Compensatory or ‘catch-up’ growth following prolonged periods of food shortages is known to exist in many free-living animals. It is generally assumed that growth rates under normal circumstances are below maximum because elevated rates of growth are costly. The present paper gives experimental evidence that such compensatory growth mechanisms also exist in parasitic species. We explored the effect of periodic host unavailability on survival, infectivity and growth of the fish ectoparasiteArgulus coregoni. Survival and infectivity ofA. coregonimetanauplii deprived of a host for selected time periods were age dependent, which indicates that all metanauplii carry similar energy resources for host seeking. Following the periods off-host, metanauplii were allowed to settle on rainbow trout and were length measured until they reached gravidity. During early development on fish, body length of attachedA. coregoniwas negatively correlated with off-host period indicating a mechanism that creates size variance in an attached parasite cohort originally containing equal amounts of resources. However, over time the size differences between parasites became less pronounced and eventually parasites that were kept off-host for longest periods of time reached the length of those individuals that had been allowed to infect a host sooner.A. coregonithus appears to compensate for delayed growth resulting from an extended host searching period by elevated growth rates, although we show that such accelerated growth incurred a cost, through decreased life-expectancy.
Effect of hydrothermal ridge flank alteration on the in situ physical properties of uppermost oceanic crust
Authors: Bartetzko Anne
Published: June 2005

The circulation of cold water through the oceanic crust at mid‐ocean ridge flanks causes changes in the composition and physical properties of the crust. This study focuses on the effect of hydrothermal ridge flank alteration on in situ physical properties. P wave velocity, electrical resistivity, and natural radioactivity are compared. They are obtained from downhole logging operations in seven boreholes drilled by the Deep Sea Drilling Project and Ocean Drilling Program. Basement age ranges from 5.9 to 167 m.y. The comparison shows that the average values of P wave velocity and electrical resistivity increase with the logarithm of basement age for lava flows and pillow basalts. Natural radioactivity and potassium content do not show a statistically significant relation to the basement age. No direct influence of spreading rate or thickness of the sediment cover on the in situ physical properties can be observed. The increase in P wave velocity with age reflects the reduction in pore space due to the precipitation of secondary minerals. Electrical resistivity is low in young crust where conductive clays are important alteration minerals. It increases in old crust because electrically insulating minerals, such as carbonates, are formed as late stage alteration minerals. Natural radioactivity is influenced by the composition of the magma but also rises in altered rocks due to the formation of K‐rich clay minerals. The results of this study show that ridge flank hydrothermal alteration persists over longer‐term intervals than indicated by seismic experiments.
Fault branching and rupture directivity
Authors: Fliss Sonia , Bhat Harsha S. , Dmowska Renata , Rice James R.
Published: June 2005

Could the directivity of a complex earthquake be inferred from the ruptured fault branches it created? Typically, branches develop in forward orientation, making acute angles relative to the propagation direction. Direct backward branching of the same style as the main rupture (e.g., both right lateral) is disallowed by the stress field at the rupture front. Here we propose another mechanism of backward branching. In that mechanism, rupture stops along one fault strand, radiates stress to a neighboring strand, nucleates there, and develops bilaterally, generating a backward branch. Such makes diagnosing directivity of a past earthquake difficult without detailed knowledge of the branching process. As a field example, in the Landers 1992 earthquake, rupture stopped at the northern end of the Kickapoo fault, jumped onto the Homestead Valley fault, and developed bilaterally there, NNW to continue the main rupture but also SSE for 4 km forming a backward branch. We develop theoretical principles underlying such rupture transitions, partly from elastostatic stress analysis, and then simulate the Landers example numerically using a two‐dimensional elastodynamic boundary integral equation formulation incorporating slip‐weakening rupture. This reproduces the proposed backward branching mechanism based on realistic if simplified fault geometries, prestress orientation corresponding to the region, standard lab friction values for peak strength, and fracture energies characteristic of the Landers event. We also show that the seismic S ratio controls the jumpable distance and that curving of a fault toward its compressional side, like locally along the southeastern Homestead Valley fault, induces near‐tip increase of compressive normal stress that slows rupture propagation.
Lithospheric rheology in southern Italy inferred from postseismic viscoelastic relaxation following the 1980 Irpinia earthquake
Authors: Dalla Via G. , Sabadini R. , De Natale G. , Pingue F.
Published: June 2005

Postseismic relaxation is modeled for the Irpinia earthquake, which struck southern Italy in 1980. Our goal is to understand the mechanism of surface deformation due to stress relaxation in the deep portion of the crust‐lithosphere system for a shallow normal fault source and to infer the rheological properties of the lithosphere in the extensional environment of peninsular Italy. The modeling is carried out within the framework of our normal mode viscoelastic theory at high spatial resolution in order to accurately resolve the vertical surface displacements for a seismic source. The slip distribution over the faults is first inverted from coseismic leveling data, the misfit between observed and modeled vertical displacements being minimized by means of the L2 norm. Slip distribution is then used within the viscoelastic model to invert for the viscosities of the lower crust and generally of the lithosphere. Inversion is based on leveling data sampled along three lines crossing the epicentral area. Postseismic deformation in the Irpinia area is characterized by a broad region of crust upwarping in the footwall of the major fault and downwarping in the hanging wall that is responsible for the long‐wavelength features of the vertical displacement pattern. The χ2 analysis indicates that the Irpinia earthquake cannot constrain the rheology of the upper mantle but only of the crust; a full search in the viscosity spaces makes it possible to constrain the crustal viscosity to values of the order of 1019 Pa s, in agreement with previous studies carried out in different tectonic environments.
Impact of iceberg melting on Mediterranean thermohaline circulation during Heinrich events
Authors: Sierro F. J. , Hodell D. A. , Curtis J. H. , Flores J. A. , Reguera I. , Colmenero‐Hidalgo E. , Bárcena M. A. , Grimalt J. O. , Cacho I. , Frigola J. , Canals M.
Published: June 2005

Down‐core samples of planktonic and benthic foraminifera were analyzed for oxygen and carbon isotopes in International Marine Past Global Changes Study (IMAGES) core MD99‐2343 in order to study the interactions between climate change in the Northern Hemisphere and the western Mediterranean thermohaline circulation at times of Heinrich events (HE). Our results confirm the antiphase correlation between enhanced North Atlantic Deep Water formation and low ventilation in the Mediterranean. However, this study reveals that this antiphase relationship in deepwater formation between the North Atlantic and Mediterranean was interrupted during times of HE when the injection of large volumes of water from melting icebergs reached the entrance to the Mediterranean. These events, which lasted less than 1000 years, are represented by pronounced decreases in both planktonic δ18O and benthic δ13C signals. Lower salinities of Mediterranean surface water resulted in a slowdown of western Mediterranean deepwater overturn even though cold sea surface temperatures and drier climate should have resulted in enhanced deepwater formation.
A high‐resolution record of early Miocene Antarctic glacial history from ODP Site 1165, Prydz Bay
Authors: Williams Trevor , Handwerger David
Published: June 2005

ODP Site 1165, located 400 km northwest of Prydz Bay, contains a high‐resolution early Miocene record of pulses of ice‐rafted debris (IRD) originating from the ancestral Lambert Glacier system and the Antarctic coast to the east. The 520 m of early Miocene sediments consist of dark gray claystone with silt laminae (contourites) alternating with decimeter‐scale layers of greenish‐gray bioturbated claystone that commonly contain ice‐rafted debris. Downhole logs also record the alternations between the two facies: the IRD‐bearing greenish‐grey claystone corresponds to high resistivity and density values because of increased cementation by silica, and corresponds to lower natural gamma radiation values because of diluted clay content. The downhole logs thus allow a continuous and detailed stratigraphic record of the IRD‐bearing layers to be obtained. The IRD‐bearing layers represent deglaciations and interglacials, when a high flux of icebergs with incorporated material were melting out over the site; the contourite‐rich layers represent glacials, when the Polar Current over the site was relatively strong. The sequence is dated by magnetostratigraphy, and the timing of the major IRD pulses is paced by orbital eccentricity, indicating that the volume of the East Antarctic ice sheet also fluctuates on this timescale. After 19.7 Ma, minor precessional and subprecessional IRD layers appear in the record, indicating that the ice sheet becomes more prone to deglaciation through this interval, perhaps associated with the gradual warming trend through the early Miocene.
Probabilistic behavior of a regional envelope curve
Authors: Castellarin Attilio , Vogel Richard M. , Matalas Nicholas C.
Published: June 2005

A regional envelope curve (REC) summarizes the current bound on our experience of extreme floods in a region. Although RECs are available for many regions of the world, their traditional deterministic interpretation limits the use of the curves for design purposes, as magnitude, but not frequency of extreme flood events, can be quantified. A probabilistic interpretation of a REC is introduced via an estimate of its exceedance probability. The effect of intersite correlation on the exceedance probability is discussed. Monte Carlo experiments are performed to assess the performance of the estimate of the REC's exceedance probability. Generalized curves are presented for assessing the impact of regional intersite cross correlation on the likelihood of exceeding an observed REC. We also discuss how future developments in the theory of records may improve our ability to quantify the information content of a REC.
Application of temporal streamflow descriptors in hydrologic model parameter estimation
Authors: Shamir Eylon , Imam Bisher , Gupta Hoshin V. , Sorooshian Soroosh
Published: June 2005

This paper presents a parameter estimation approach based on hydrograph descriptors that capture dominant streamflow characteristics at three timescales (monthly, yearly, and record extent). The scheme, entitled hydrograph descriptors multitemporal sensitivity analyses (HYDMUS), yields an ensemble of model simulations generated from a reduced parameter space, based on a set of streamflow descriptors that emphasize the timescale dynamics of streamflow record. In this procedure the posterior distributions of model parameters derived at coarser timescales are used to sample model parameters for the next finer timescale. The procedure was used to estimate the parameters of the Sacramento soil moisture accounting model (SAC‐SMA) for the Leaf River, Mississippi. The results indicated that in addition to a significant reduction in the range of parameter uncertainty, HYDMUS improved parameter identifiability for all 13 of the model parameters. The performance of the procedure was compared to four previous calibration studies on the same watershed. Although our application of HYDMUS did not explicitly consider the error at each simulation time step during the calibration process, the model performance was, in some important respects, found to be better than in previous deterministic studies.
Mystery of the volcanic mass‐independent sulfur isotope fractionation signature in the Antarctic ice core
Authors: Pavlov A. A. , Mills M. J. , Toon O. B.
Published: June 2005

We simulate the record of sulfur mass‐independent fractionation (MIF) in sulfates found in the Antarctic ice cores from the 1991 eruption of Mt. Pinatubo. Discovery of MIF in sulfur isotopes in Archean/Early Proterozoic sediments and lack of MIF in sulfur in younger rocks placed a strict upper limit on the amount of oxidants and oxygen in the ancient Earth's atmosphere prior to 2.3 Gyr ago. However, recent measurements in ice cores suggest that some non‐zero MIF in sulfate can be delivered to Antarctica following large volcanic eruptions. Current photochemical experiments do not identify the specific reaction responsible for sulfur MIF production. Here we show that a time‐dependent non‐zero sulfur MIF can be delivered to the ground in the present atmosphere if the MIF–producing process is SO3photolysis. Fractionation from such photolysis has not been considered before, but is consistent with the available experimental data.
Indications for aggravation in summer heat conditions over the Mediterranean Basin
Authors: Ziv Baruch , Saaroni Hadas , Baharad Anat , Yekutieli Daniel , Alpert Pinhas
Published: June 2005

The summer temperature variations over the Mediterranean Basin were studied through the 850 hPa level for the months June–August along the period 1948–2003, based on the NCEP‐NCAR CDAS‐1 archive. The most prominent feature found is warming, larger than the global value, over the majority of the study region with a maximum of 0.04 Ky−1 over Sicily. At the same time, cooling was noted over Algeria and the Balkans. The trend for the 10% upper quantile of the days over the warming region was found larger than the seasonal, reaching 0.053 Ky−1, implying that heat waves lead the general long‐term trend. The shape of the long‐term curve was found to fit the global one over the warming region. No synoptic‐dynamic factor was found to account for the intensity and spatial distribution of the warming trend. This, together with the fit of the trend with the global one, suggests that the Mediterranean Basin manifests the increase in the greenhouse effect in the summer season.
Calculation of magnetic helicity of cylindrical flux rope
Authors: Hu Q. , Dasgupta B.
Published: June 2005

We examine a method of calculating the magnetic helicity of cylindrical magnetic flux rope of arbitrary cross section from in‐situ spacecraft data. First we examine the gauge invariance of the definition of relative helicity by Finn and Antonsen (1985). Two approaches based on Grad‐Shafranov equation are then described. A case study is presented to illustrate the method. The results show significant discrepancies from an earlier study utilizing axially symmetric models. We briefly discuss the potential applications for Sun‐Earth connection.
Shape and composition of PMC particles derived from satellite remote sensing measurements
Authors: Eremenko M. N. , Petelina S. V. , Zasetsky A. Y. , Karlsson B. , Rinsland C. P. , Llewellyn E. J. , Sloan J. J.
Published: June 2005

The Atmospheric Chemistry Experiment Fourier Transform Spectrometer (ACE‐FTS) on the SciSat satellite measured nearly 30 spectra of polar mesospheric clouds (PMCs) between 65° and 70°N from July 5 to 14, 2004. The ACE‐FTS measurements are augmented by UV observations made at the same latitude and time period by the Optical Spectrograph and Infrared Imager System (OSIRIS) on the Odin satellite. Our analysis of these measurements shows that PMC particles are composed of nonspherical ice crystals with mean (equivalent spherical) particle radii of 59 ± 5 nm.
Moments of Governance in is Outsourcing: Conceptualizing Effects of Contracts on Value Capture and Creation
Authors: Miranda Shaila M , Kavan C Bruce
Published: June 2005

Research on the governance of IS outsourcing has recognized two moments of governance: the formal outsourcing contract (promissory contract) and post-contractual relationship management (psychological contract). While this research has been prescriptive of contract terms that lead to successful outsourcing, there is need for clarity on what specific governance options are available at each moment of governance and how governance choices at one moment affect those at another, and consequently affect outsourcing outcomes. This paper draws on theoretical and empirical work in the areas of governance and contracts to develop a model of IS outsourcing governance, delineating specific moments of governance (MoG). It describes how the IS outsourcing context circumscribes market, hierarchy, and network governance options that are available at the promissory contract and psychological contract moments. Processes and structures that constitute governance choices at each moment of governance are identified. This analysis of outcomes recognizes an inherent tension in interorganizational relationships: firms’ desire for value capture or efficiency vs their desire for value creation or innovation. We explore how choices in formulating the promissory contract affect the psychological contract, and how psychological contract choices impact value capture and creation. The paper concludes by exploring the implications of the MoG model for practitioners and suggesting areas in which further conceptualization and empirical work may be beneficial.
Ultrafast proton transfer of 1-hydroxy-2-acetonaphthone: Reaction path from resonance Raman and transient absorption studies
Authors: Lochbrunner S. , Szeghalmi A. , Stock K. , Schmitt M.
Published: June 2005

The intramolecular degrees of freedom contributing to the ultrafast excited-state intramolecular proton transfer of 1-hydroxy-2-acetonaphthone are determined. Thereto, resonance Raman studies are combined with transient absorption measurements with 30-fs time resolution. Enhanced Raman intensity is found in coordinates that are dominantly associated with deformations and bond length changes in the naphthalene chromophore. This indicates that the primary changes after the optical excitation are a geometric relaxation of the chromophore. A ringing of the molecule after the ultrafast proton transfer is observed by the transient absorption measurements. It reveals the nuclear coordinates contributing to the reaction path beyond the Franck–Condon region. There, planar H-chelate ring deformations changing the donor-acceptor distance are found to dominate. The difference in the observed vibrational signatures indicates a significant turn in the reaction path.
Some rotational corrections to the acoustic energy equation in injection-driven enclosures
Authors: Majdalani J. , Flandro G. A. , Fischbach S. R.
Published: June 2005

This article presents rotational corrections to the energy stability equation in injection-driven porous enclosures used to simulate solid rocket motors. The evaluation of stability growth rate factors is carried out both numerically and asymptotically. Analytical expressions for the energy stability factors are obtained over a spectrum of physical parameters encompassing solid rocket motor operation. For all representative motors under investigation, the analytical estimates are shown to exhibit negligible errors compared to their numerical values. Both numerics and asymptotics converge in predicting less stable systems than projected by purely irrotational stability theory. The differences can be ascribed to the dismissal of time-dependent rotational coupling in some past formulations. The current study unravels the details of six additional growth rate corrections not accounted for previously. These include the rotational flow, inviscid vortical, viscous, pseudoacoustical, pseudorotational, and unsteady nozzle growth rate factors. The fourth and fifth terms are due to acoustical and vortical interactions with the often neglected pseudopressure. The sixth is due to the energy associated with the unsteady rotational flow exiting the porous enclosure. This study enables us to explain the influence of distinct flow variables on stability. Based on asymptotic approximations for individual growth rates, explicit criteria are presented in the form of critical Mach numbers, penetration numbers, or motor lengths that must not be exceeded in prevention of system instability. The net rotational corrections have been recently appended to the widely used Standard Stability Prediction code.
Direct determination of the free-carrier injection density, the free-carrier absorption, and the recombination factors in double heterostructure diodes by optical phase measurements. Part III
Authors: Reinhart F. K.
Published: June 2005

Accurate phase measurements over a temperature interval on double heterostructure laser (DH) diodes provide a means to directly measure the injected free-carrier density and the free-carrier absorption as a function of the injected current. This paper describes the underlying principles and demonstrates the validity of the simple concepts. The data permit to deduce the radiative and nonradiative recombination factors in nominally undoped active layers without taking resource to luminescence measurements. The results presented on GaAs and InGaAsP lattice matched to InP DH diodes show a good overall agreement with calculations based on a heuristic model. The radiative recombination factors at room temperature are near 5.3×10−11 and 2.0×10−11cm3s−1 for GaAs and for InGaAsP with a band gap of 1.122eV, respectively. The free-carrier absorption due to the injected carriers is strongly dispersive and proportional to the 2.3rd power of the wavelength. We show a strong temperature dependence of the free-carrier absorption that is more important in InGaAsP than in GaAs. The results are internally consistent without the need of any free parameter. The phase measurements can also be used to characterize the heat chirping of the active layers under pulsed current excitation.
High-resolution ultraviolet spectroscopy of p-fluorostyrene-water: Evidence for a σ-type hydrogen-bonded dimer
Authors: Chervenkov S. , Wang P. Q. , Braun J. E. , Georgiev S. , Neusser H. J. , Nandi Chayan K. , Chakraborty Tapas
Published: June 2005

Ab initio calculations predict four stable conformational structures of the singly hydrated cluster of p-fluorostyrene: two out of plane with π- and two in plane with σ-type intermolecular hydrogen bonding between p-fluorostyrene and water. We employed mass-selective resonance-enhanced two-photon ionization high-resolution (70-MHz FWHM laser bandwidth) spectroscopy to partially resolve the rotational structure of the 000 origin band of the S1←S0 electronic transition. A computer-aided fit based on genetic algorithms was used to analyze the experimental high-resolution spectrum and to determine the observed conformational structure. The good agreement between the experimental and the simulated spectra of the 000 band and the assignment of the other prominent bands as inter- and intramolecular vibrational progressions clearly demonstrates that the anti in-plane conformer is the most abundant one in the molecular beam. The existence of the σ-type hydrogen bond between p-fluorostyrene and water manifests that the electron attracting effect of fluorine dominates over the releasing mesomeric effect of the vinyl group and thus a π-type hydrogen bonding with the aromatic ring is not favored in this case.
Conformations and charge transport characteristics of biphenyldithiol self-assembled-monolayer molecular electronic devices: A multiscale computational study
Authors: Kim Yong-Hoon , Jang Seung Soon , Goddard William A.
Published: June 2005

We report a computational study of conformations and charge transport characteristics of biphenyldithiol (BPDT) monolayers in the (3×3)R30° packing ratio sandwiched between Au(111) electrodes. From force-field molecular-dynamics and annealing simulations of BPDT self-assembled monolayers (SAMs) with up to 100 molecules on a Au(111) substrate, we identify an energetically favorable herringbone-type SAM packing configuration and a less-stable parallel packing configuration. Both SAMs are described by the (23×3)R30° unit cell including two molecules. With subsequent density-functional theory calculations of one unit cell of the (i) herringbone SAM with the molecular tilt angle θ≈15°, (ii) herringbone SAM with θ≈30°, and (iii) parallel SAM with θ≈30°, we confirm that the herringbone packing configuration is more stable than the parallel one but find that the energy variation with respect to the molecule tilting within the herringbone packing is very small. Next, by capping these SAMs with the top Au(111) electrode, we prepare three molecular electronic device models and calculate their coherent charge transport properties within the matrix Green's function approach. Current–voltage (I–V) curves are then obtained via the Landauer–Büttiker formula. We find that at low-bias voltages (∣V∣≲0.2V) the I–V characteristics of models (ii) and (iii) are similar and the current in model (i) is smaller than that in (ii) and (iii). On the other hand, at higher-bias voltages (∣V∣≳0.5V), the I–V characteristics of the three models show noticeable differences due to different phenyl band structures. We thus conclude that the BPDT SAM I–V characteristics in the low-bias voltage region are mainly determined by the Si–Au interaction within the individual molecule-electrode contact, while both intramolecular conformation and intermolecular interaction can affect the BPDT SAM I–V characteristics in the high-bias voltage region.
Observation of resonant Interatomic Coulombic Decay in Ne clusters
Authors: Barth S. , Joshi S. , Marburger S. , Ulrich V. , Lindblad A. , Öhrwall G. , Björneholm O. , Hergenhahn U.
Published: June 2005

We have measured the electron spectra of Ne clusters after excitation with photon energies around the 2s inner valence threshold. At two photon energies below threshold, a resonantly enhanced surplus of low kinetic-energy electrons is observed. The kinetic energy of the peak does not vary with the photon energy and is slightly larger than the transition energy of Interatomic Coulombic Decay (ICD) above threshold. This leads us to assume that an ICD-like process is present. In analogy to the Auger and the resonant Auger decay this new phenomenon is termed resonant ICD.
THz instability by streaming carriers in high mobility solid-state plasmas
Authors: Riyopoulos S.
Published: June 2005

It is described how the interaction of streaming electron plasma waves with lattice waves may lead to a highly unstable coupled plasmon-phonon excitation in the THz range, in high mobility semiconductor materials. The underlying physical mechanism is related to the ubiquitous beam-plasma instability in electrostatically coupled fluids. Continuous amplification in transit, rather than localized amplification at the system boundary reflections, yields high growth rates and may lead to efficient THz generation.
Circular magnetization process of nanocrystalline wires as deduced from impedance measurements
Authors: Li Y.-F. , Vazquez M. , Chen D.-X.
Published: June 2005

The circular magnetization process of FeSiBCuNb amorphous and nanocrystalline wires has been followed by the impedance measurements as a function of the amplitude and the frequency of driving current. The domain structure and consequently, the magnetization process have been tailored by suitable thermal processing. The different circular coercivity mechanisms are deduced by analyzing the magnetic losses. We find that the coercivity is due to domain-wall pinning for wire with axial domain, while the coercivity is from domain nucleation for one with transverse domain structure. In addition, the influence of axially applied field H is different for wires with different domain structure. The application of tensile stress to a wire with positive magnetostriction can be taken as an axial induced anisotropy, which makes the circular permeability decrease and the coercivity increase. Finally, the influence of driving current frequency on the circular magnetization process has been also studied for the wire with transverse domain structure. The results indicate that the frequency effect is from the eddy-current damping.
Orbital specific chemistry: Controlling the pathway in single-molecule dissociation
Authors: Hahn J. R. , Ho W.
Published: June 2005

A scanning tunneling microscope (STM) was used to control the pathway of the dissociation of single O2 molecules chemisorbed on Ag(110) at 13K. Tunneling of electrons from the STM tip into the O2 caused dissociation of the molecule, giving rise to two adsorbed O atoms separated along the [11¯0] direction. In contrast, the ejection of electrons from the O2 molecule produced adsorbed O atoms separated along the [001] direction. These results illustrate that control of the dissociation pathway and product formation are associated with a specific molecular orbital located at the Fermi level.
Asynchronous multicanonical basin hopping method and its application to cobalt nanoclusters
Authors: Zhan Lixin , Chen Jeff Z. Y. , Liu Wing-Ki , Lai S. K.
Published: June 2005

The multicanonical basin hopping (MUBH) method, which uses a multicanonical weight in the basin hopping (BH) Monte Carlo method, was found to be very efficient for global optimization of large-scale systems such as Lennard-Jones clusters containing more than 150 atoms. We have implemented an asynchronous parallel version of the MUBH method using the message passing interface (MPI) to take advantage of the full usage of multiprocessors in either a homogeneous or heterogeneous computational environment. Based on the intrinsic properties of the Monte Carlo method, this MPI implementation used the task parallelism to minimize interthread data communication. For a Co nanocluster consisting of N atoms, we have applied the asynchronous multicanonical basin hopping (AMUBH) method (for 181<N⩽200), together with BH (for 2⩽N<150) and MUBH (for 150⩽N⩽180), to search for the molecular configuration of the global energy minimum. AMUBH becomes the only practical computational scheme for locating the energy minimum within realistic computational time for a relatively large cluster.
Brownian dynamics simulations of the self- and collective rotational diffusion coefficients of rigid long thin rods
Authors: Tao Yu-Guo , den Otter W. K. , Padding J. T. , Dhont J. K. G. , Briels W. J.
Published: June 2005

Recently a microscopic theory for the dynamics of suspensions of long thin rigid rods was presented, confirming and expanding the well-known theory by Doi and Edwards [The Theory of Polymer Dynamics (Clarendon, Oxford, 1986)] and Kuzuu [J. Phys. Soc. Jpn. 52, 3486 (1983)]. Here this theory is put to the test by comparing it against computer simulations. A Brownian dynamics simulation program was developed to follow the dynamics of the rods, with a length over a diameter ratio of 60, on the Smoluchowski time scale. The model accounts for excluded volume interactions between rods, but neglects hydrodynamic interactions. The self-rotational diffusion coefficients Dr(φ) of the rods were calculated by standard methods and by a new, more efficient method based on calculating average restoring torques. Collective decay of orientational order was calculated by means of equilibrium and nonequilibrium simulations. Our results show that, for the currently accessible volume fractions, the decay times in both cases are virtually identical. Moreover, the observed decay of diffusion coefficients with volume fraction is much quicker than predicted by the theory, which is attributed to an oversimplification of dynamic correlations in the theory.
Quantum-classical Liouville dynamics of nonadiabatic proton transfer
Authors: Hanna Gabriel , Kapral Raymond
Published: June 2005

A proton transfer reaction in a linear hydrogen-bonded complex dissolved in a polar solvent is studied using mixed quantum-classical Liouville dynamics. In this system, the proton is treated quantum mechanically and the remainder of the degrees of freedom is treated classically. The rates and mechanisms of the reaction are investigated using both adiabatic and nonadiabatic molecular dynamics. We use a nonadiabatic dynamics algorithm which allows the system to evolve on single adiabatic surfaces and on coherently coupled pairs of adiabatic surfaces. Reactive-flux correlation function expressions are used to compute the rate coefficients and the role of the dynamics on the coherently coupled surfaces is elucidated.
Stationary flow, first passage times, and macroscopic Fick’s first diffusion law: Application to flow enhancement by particle trapping
Authors: Bauer Wolfgang R. , Nadler Walter
Published: June 2005

A generalized macroscopic Fick’s first diffusion law is derived which describes steady-state particle flow between two baths explicitly as a function of the concentration gradient, acting as the thermodynamic driving force, times a functional of the first passage time. The latter is shown to be the ratio of the number of particles trapped between the baths and the first passage time. Particle trapping is shown to be a powerful mechanism by which flow can be enhanced. This is analyzed for two examples: a potential and an entropy trap.
Random walks in nanotube composites: Improved algorithms and the role of thermal boundary resistance
Authors: Duong Hai M. , Papavassiliou Dimitrios V. , Lee Lloyd L. , Mullen Kieran J.
Published: June 2005

Random walk simulations of thermal walkers are used to study the effect of interfacial resistance on heat flow in randomly dispersed carbon nanotube composites. The adopted algorithm effectively makes the thermal conductivity of the nanotubes themselves infinite. The probability that a walker colliding with a matrix-nanotube interface reflects back into the matrix phase or crosses into the carbon nanotube phase is determined by the thermal boundary (Kapitza) resistance. The use of “cold” and “hot” walkers produces a steady state temperature profile that allows accurate determination of the thermal conductivity. The effects of the carbon nanotube orientation, aspect ratio, volume fraction, and Kapitza resistance on the composite effective conductivity are quantified.
Secondary instability in forced wavelength Görtler vortices
Authors: Mitsudharmadi H. , Winoto S. H. , Shah D. A.
Published: June 2005

From an experimental study on the onset of secondary instability in forced wavelength Görtler vortices, it is found that the breakdown process of the Görtler vortices is due to the development of varicose and sinuous mode instabilities. The development of the varicose mode is characterized by the formation of horseshoe vortices that evolve downstream to form mushroom-like structures. This phenomenon is then followed by meandering of the vortices as an indication of the onset of sinuous mode instability, prior to turbulence. The spectrum analysis applied to the fluctuating velocity component shows the occurrence of peak frequency of about 150Hz, which is attributed to the fundamental secondary instability mode with its wavelength comparable to the spanwise wavelength of the primary Görtler vortices, at the location where the mushroom-like structures are clearly depicted in the mean velocity contours on the y-z plane. This confirms that the secondary instability is of the varicose type at the onset that is followed by the sinuous type downstream, prior to the breakdown of the vortices that will lead the boundary layer flow to turbulence. It is also found that the growth rate of the secondary instability observed is about 6.5 times higher than that of the Görtler instability, which leads to a breakdown of the streamwise structures and hence to turbulence.
Statistical mechanical theory for steady-state systems. III. Heat flow in a Lennard-Jones fluid
Authors: Attard Phil
Published: June 2005

A statistical mechanical theory for heat flow is developed based upon the second entropy for dynamical transitions between energy moment macrostates. The thermal conductivity, as obtained from a Green–Kubo integral of a time correlation function, is derived as an approximation from these more fundamental theories, and its short-time dependence is explored. A new expression for the thermal conductivity is derived and shown to converge to its asymptotic value faster than the traditional Green–Kubo expression. An ansatz for the steady-state probability distribution for heat flow down an imposed thermal gradient is tested with simulations of a Lennard-Jones fluid. It is found to be accurate in the high-density regime at not too short times, but not more generally. The probability distribution is implemented in Monte Carlo simulations, and a method for extracting the thermal conductivity is given.
Polypeptide foldings obtained with effective pair potentials
Authors: Pliego-Pastrana P. , Carbajal-Tinoco M. D.
Published: June 2005

We present a model of protein folding which is based on a potential function that describes the effective interaction between two amino acids (alanines, in this case). Our model is consistent with the formation of two important secondary structures, namely, an α-helix and a β-ladder. In each case, we estimate the density of states using a random walk in energy space. This function allows the direct calculation of certain thermodynamic properties. By means of the configurational temperature, we also verify that the obtained polypeptides are in their native state.
Low-frequency noise sources in as-prepared and aged GaN-based light-emitting diodes
Authors: Bychikhin S. , Pogany D. , Vandamme L. K. J. , Meneghesso G. , Zanoni E.
Published: June 2005

The low-frequency noise sources are investigated in as-prepared and aged GaN light-emitting diodes (LEDs). Accelerated aging is performed by thermal (300h at 240°C) and electrical forward-bias stressing (20 and 50mA for 2500h). At low currents I<IRTS, where IRTS is a critical current, the low-frequency noise is dominated by random telegraph signal (RTS) noise on top of the 1∕f noise. An explanation is given for the giant relative current jumps ΔI∕I≈50% and an expression for IRTS is derived. The RTS noise in our devices is a less-sensitive diagnostic tool for studying the results of accelerated aging. Two components of the 1∕f noise were observed: one is related to the quantum-well junction and the other is due to series resistance noise. The two 1∕f spectra have different current dependences. It was found that the junction 1∕f noise is not significantly affected by aging. However, a strong increase in series resistance noise, by a factor of 60–800 compared to unstressed devices, is observed after strong electrical and thermal aging. This high increase goes hand in hand with a relatively small increase in the value of the series resistance (13%–90%). This makes 1∕f noise a very sensitive reliability indicator for GaN LEDs after accelerated aging. We discuss the physical origin of LED degradation.
Stable, freestanding Ge nanocrystals
Authors: Sharp I. D. , Xu Q. , Liao C. Y. , Yi D. O. , Beeman J. W. , Liliental-Weber Z. , Yu K. M. , Zakharov D. N. , Ager J. W. , Chrzan D. C. , Haller E. E.
Published: June 2005

Freestanding Ge nanocrystals that are stable under ambient conditions have been synthesized in a two-step process. First, nanocrystals with a mean diameter of 5nm are grown in amorphous SiO2 by ion implantation followed by thermal annealing. The oxide matrix is then removed by selective etching in diluted HF to obtain freestanding nanocrystals on a Si wafer. After etching, nanocrystals are retained on the surface and the size distribution is not significantly altered. Freestanding nanocrystals are stable under ambient atmospheric conditions, suggesting formation of a self-limiting native oxide layer. For freestanding as opposed to embedded Ge nanocrystals, an additional amorphouslike contribution to the Raman spectrum is observed and is assigned to surface reconstruction-induced disordering of near-surface atoms.
Kinetics of two-step nucleation of crystals
Authors: Kashchiev Dimo , Vekilov Peter G. , Kolomeisky Anatoly B.
Published: June 2005

When the nucleation of a stable crystalline phase directly in a supersaturated old phase is greatly retarded, the crystal nuclei might nucleate within faster-forming particles of an intermediate phase. Here we present a theoretical investigation of the kinetics of this two-step nucleation of crystals and derive general expressions for the time dependence of the number of crystals nucleated within the particles of the intermediate phase. The results reveal that crystal nucleation can be strongly delayed by the slow growth of the particles and/or by the slow nucleation of the crystals in them. Furthermore, the linear part of the time dependence of the number of nucleated crystals is determined by the formation rate of the intermediate particles. This is in contrast with the one-step nucleation of crystals when this linear part is determined by the rate of crystal nucleation directly in the old phase. Criteria are proposed for distinction between the one- and two-step nucleation mechanisms, based on the supersaturation dependence of the delay time for nucleation. The application of the theoretical approach to the analysis of experimental data on the nucleation of crystals and other ordered aggregates of protein and other soluble materials is discussed.
Theoretical and experimental investigation of aqueous liquids contained in carbon nanotubes
Authors: Yarin Alexander L. , Yazicioglu Almila G. , Megaridis Constantine M. , Rossi Maria Pia , Gogotsi Yury
Published: June 2005

The dynamic response—as caused by different means of thermal stimulation or pressurization—of aqueous liquid attoliter volumes contained inside carbon nanotubes is investigated theoretically and experimentally. The experiments indicate an energetically driven mechanism responsible for the dynamic multiphase fluid behavior visualized in real time with high spatial resolution using electron microscopy. The theoretical model is formulated using a continuum approach, which combines temperature-dependent mass diffusion with intermolecular interactions in the fluid bulk, as well as in the vicinity of the carbon walls. Intermolecular forces are modeled by Lennard-Jones potentials. Several one-dimensional and axisymmetric cases are considered. These include situations which physically represent liquid volume pinchoff, jetting, or fluid relocation due to thermal stimulation by a steady or modulated electron beam, as well as liquid precipitation (condensation) from vapor due to overcooling or pressurization. Comparisons between theoretical predictions and experimental data demonstrate the ability of the model to describe the characteristic trends observed in the experiments.
Micro-Raman investigation of optical phonons in ZnO nanocrystals
Authors: Alim Khan A. , Fonoberov Vladimir A. , Shamsa Manu , Balandin Alexander A.
Published: June 2005

We have measured nonresonant and resonant Raman-scattering spectra from ZnO nanocrystals with an average diameter of 20nm. Based on our experimental data and comparison with the recently developed theory, we show that the observed shifts of the polar optical-phonon peaks in the resonant Raman spectra are not related to the spatial phonon confinement. The very weak dispersion of the polar optical phonons in ZnO nanocrystals does not lead to any noticeable redshift of the phonon peaks for 20-nm nanocrystals. The observed phonon shifts have been attributed to the local heating effects. We have demonstrated that even the low-power ultraviolet laser excitation, required for the resonant Raman spectroscopy, can lead to the strong local heating of ZnO nanocrystals. The latter causes significant (up to 14cm−1) redshift of the optical-phonon peaks compared to their position in bulk crystals. Nonresonant Raman excitation does not produce noticeable local heating. The obtained results can be used for identification of the phonons in the Raman spectra of ZnO nanostructures.