bluuebunny/crossref_metadata_2025 huggingface dataset:
Bottom-Up Influences on Working Memory: Behavioral and Electrophysiological Distraction Varies with Distractor Strength
Authors: Berti Stefan , Roeber Urte , Schröger Erich
Published: November 2004

Abstract. The present study investigates bottom-up effects serving the optimal balance between focusing attention on relevant information and distractibility by potentially significant events outside the focus of attention. We tested whether distraction, indicated by behavioral and event-related brain potential (ERP) measures, varies with the strength of task-irrelevant deviances. Twenty subjects performed a tone-duration discrimination task (200 or 400 ms sinusoidal tones presented equiprobably). The stimuli were presented with frequent standard (p = 0.84; 1000 Hz) or infrequent deviant (p = 0.16) pitch. These task-irrelevant pitch changes consisted in a frequency increase/decrease of 1%, 3%, 5%, or 10%. Each of them resulted in prolonged reaction times (RT) in the duration discrimination task and elicited the MMN, P3a, and RON components of the ERP. Importantly, these measures did increase as a function of pitch deviance. Separating the individual trials on the 1% deviation level into trials with and without RT prolongation, i.e., behavioral distraction effect, revealed that both subgroups had similar MMN, but P3a and RON were confined to the trials with RT prolongation. Results are interpreted within a model relating preattentive deviance detection, distraction, and working memory.
Motor Affordance and its Role for Visual Working Memory: Evidence from fMRI studies
Authors: Mecklinger Axel , Gruenewald Christin , Weiskopf Nikolaus , Doeller Christian F.
Published: November 2004

Abstract. We examined the role of motor affordances of objects for working memory retention processes. Three experiments are reported in which participants passively viewed pictures of real world objects or had to retain the objects in working memory for a comparison with an S2 stimulus. Brain activation was recorded by means of functional magnetic resonance imaging (fMRI). Retaining information about objects for which hand actions could easily be retrieved (manipulable objects) in working memory activated the hand region of the ventral premotor cortex (PMC) contralateral to the dominant hand. Conversely, nonmanipulable objects activated the left inferior frontal gyrus. This suggests that working memory for objects with motor affordance is based on motor programs associated with their use. An additional study revealed that motor program activation can be modulated by task demands: Holding manipulable objects in working memory for an upcoming motor comparison task was associated with left ventral PMC activation. However, retaining the same objects for a subsequent size comparison task led to activation in posterior brain regions. This suggests that the activation of hand motor programs are under top down control. By this they can flexibly be adapted to various task demands. It is argued that hand motor programs may serve a similar working memory function as speech motor programs for verbalizable working memory contents, and that the premotor system mediates the temporal integration of motor representations with other task-relevant representations in support of goal oriented behavior.
Anterior Prefrontal Cortex Contributions to Attention Control
Authors: Pollmann Stefan
Published: November 2004

Abstract. In a series of event-related functional magnetic resonance studies, we consistently found activation in anterior prefrontal cortex related to visual dimension changes in singleton search tasks. I review these data and discuss possible contributions of anterior prefrontal cortex to attention control in visual search. It is proposed that anterior prefrontal cortex may detect task-relevant stimulus changes when the target is ambiguously defined. This process may occur in the absence of awareness and may support visual dimension weighting by inhibition of the old relevant dimension in favor of the new dimension.
Determining Inhibition
Authors: Wagner Susanne , Gunter Thomas C.
Published: November 2004

Abstract. The current experiment assessed the relation between inhibitory mechanisms underlying language processing in working memory (WM) and the influence of a postulated internal cognitive trade-off between lexicon and context factors driving inhibition in sentence processing. Participants with high and low WM span ( Daneman & Carpenter, 1980 ) were presented with sentences that began with an ambiguous noun (being both homographic and homophonic). A cue towards the relevant meaning of the ambiguous word was presented three words later by another noun. Immediately after the cue, a verb was presented that finally disambiguated the ambiguous noun. In half of the cases, the final disambiguation was congruent with the disambiguation cue. In the other half, subjects had to realize that it was not the cued but the other meaning, which turned out to be relevant in the actual sentence. This experimental paradigm was identical to the one used in Gunter et al. (2003 ). In contrast to the original experiment, the filler items in the present study were unambiguous. Both groups showed a smaller N400 component for the cue related to the dominant as compared to the subordinate meaning, suggesting that the dominant meaning was more active in WM than the subordinate one. In the original experiment, only the high-span subjects manifested this effect. Thus, a change in the global experimental setting changed the use of WM-related inhibitory processes. Data also suggest that, as a default strategy, the lexicon-context trade-off of high-span subjects relies more on lexicon information than does that of low-span subjects.
Phase-Locking and Amplitude Modulations of EEG Alpha:
Authors: Herrmann Christoph S. , Senkowski Daniel , Röttger Stefan
Published: November 2004

Abstract. It has been demonstrated in numerous experiments that oscillatory EEG responses in the alpha frequency band (8-12 Hz) increase with memory load during the retention interval in working memory tasks. However, the findings diverge with respect to which measurement of alpha activity is influenced by memory processes. Here, we differentiate between evoked and total alpha activity in order to separate effects of phase-locking and amplitude modulation. We present data from a delayed-matching-to-sample task (S1-S2 paradigm) for which we compared EEG alpha responses between a perception and a memory condition. Increased total alpha activity was found in the retention interval for the memory as compared to the perception condition. Evoked alpha activity, however, did not differentiate between memory and perception conditions but, instead, was increased for the more complex condition of processing non-Kanizsa figures as compared to Kanizsa figures. Thus, our results demonstrate a functional differentiation between evoked and total alpha activity. While alpha phase locking seemed to be influenced mainly by task complexity, alpha amplitude clearly reflected memory demands in our paradigm.
Modeling of field‐aligned electron bursts by dispersive Alfvén waves in the dayside auroral region
Authors: Su Yi‐Jiun , Jones Samuel T. , Ergun Robert E. , Parker Scott E.
Published: November 2004

A linear, one‐dimensional gyrofluid code including electron inertia, electron pressure gradient, and finite ion gyroradius effects is applied to an inhomogeneous dayside auroral field line to determine the characteristics of propagating Alfvén waves with small perpendicular wavelengths. Test particles are then used to study the behavior of both magnetosheath (100 eV) and background ionospheric electrons (2 eV) under the influence of dispersive Alfvén waves. Although the test particle approach is not self‐consistent, the gyrofluid/test particle simulation is able to reproduce many of the features observed by low‐altitude satellites. The test particle simulations verify results from previous studies, such as reproducing electron energy and pitch‐angle dispersions, and in doing so, validate the approach. The test particle simulations also show how resonant particles can lead to low‐energy field‐aligned electron bursts that are commonly observed in the dayside auroral region. The new results in this study reveal the plasma conditions necessary for electron resonance. We show that an increased mass density (significant O+ density) in the acceleration region is an essential prerequisite to generate an electron burst. The primary effect of the O+ is to decrease the phase speed of the Alfvén wave. Furthermore, the full gyrokinetic effects of the O+ act to produce a region in which the Alfvén speed profile is gradually slowing, which allows electrons remaining within the wave to lower altitudes. In these electron bursts, the energy gain experienced by the majority of electrons ranges from tens to hundreds of eV. The trapping occurs if the parallel electric field is substantial enough (∼0.2 mV/m) in the acceleration region to accelerate the background electrons. An integrated energy flux of accelerated electrons is estimated to be 3 erg s−1 cm−2, about 20% of the Alfvén wave Poynting flux.
Sand flux in the northern Chihuahuan desert, New Mexico, USA, and the influence of mesquite‐dominated landscapes
Authors: Gillette Dale A. , Pitchford Ann M.
Published: November 2004

Measurements of sand flux over areas with different vegetation in the Chihuahuan desert show that mean, height‐integrated, horizontal flux values for mesquite‐dominated sites were higher than those for other kinds of vegetation. Sand transport over mesquite areas displayed seasonal variability for most years. This seasonal variability roughly followed the variability of strong winds. Sand transport rates for collectors within a short distance downwind of mesquite bushes were small compared to those for collectors at the end of streets (elongated patches of bare soil) aligned with wind direction. The increased rate of sand transport (wind erosion) associated with mesquite is important because mesquite‐dominated areas are increasing in the northern Chihuahuan desert and are therefore responsible for increasing land degradation (desertification).
Geochemical evidence of seismogenic‐induced anomalies in the dissolved gases of thermal waters: A case study of Umbria (Central Apennines, Italy) both during and after the 1997–1998 seismic swarm
Authors: Italiano F. , Martinelli G. , Rizzo A.
Published: November 2004

In this paper we present the first geochemical data set regarding long‐term monitoring of dissolved gases in thermal waters from a seismic area. Three sites in Umbria (Central Apennines, Italy) were studied both for the chemical and for the helium isotopic composition of the dissolved gases. Data were collected during and after the seismic crisis that struck the region in 1997–1998. The chemical composition of the dissolved gases revealed that a CO2‐rich gas phase was always mixed with an atmospheric‐derived component dominated by N2. A normal faulting marked the beginning of the seismic activity enhancing the release of CO2 on a regional scale. Variations in both the chemical and isotopic compositions of the dissolved gases were also observed as preseismic, synseismic, and postseismic phenomena related to the seismic shock of March 1998. Those geochemical modifications were interpreted as being the consequence of a drop in the CO2 degassing rate, in good agreement with the compressive focal mechanism of that seismic event. Furthermore, this interpretation was also consistent with the geologic and tectonic setting of the study area and induced us to postulate that changes in the local rock permeability, due to crustal deformations (i.e., coseismic deformation and postseismic release), were responsible for the geochemical modifications observed. On the basis of the foregoing, we have concluded that the geochemistry of dissolved gases in groundwaters represents a useful tool for the investigation of the relationships between circulating fluids and seismic activity.
Optimized stomatal conductance of vegetated land surfaces and its effects on simulated productivity and climate
Authors: Kleidon A.
Published: November 2004

The stomatal conductance of terrestrial vegetation affects the exchange fluxes of water and carbon at the land surface. Here, a dynamic vegetation model coupled to a climate model of intermediate complexity is used to demonstrate that an optimum stomatal conductance exists at which the rate of photosynthesis, and therefore vegetation productivity, is at a maximum. This maximum originates from two competing drivers that affect the rate of photosynthesis: (i) increased supply of atmospheric carbon dioxide with increased stomatal conductance and (ii) increased cloud cover, which reduces the supply of sunlight. The simulated climate with optimized stomatal conductance is close to the model's control simulation, but vegetation productivity is substantially enhanced. The existence of this optimum has potentially important implications for the adaptation of terrestrial productivity to different climates. If vegetation maintains this optimum not only in the present‐day, but also adapts to it during past (and future) climates, not considering this optimum and how it changes leads to a general underestimation of terrestrial productivity under different climates.
Regional comparison and assimilation of GOCART and MODIS aerosol optical depth across the eastern U.S.
Authors: Matsui Toshihisa , Kreidenweis Sonia M. , Pielke Roger A. , Schichtel Bret , Yu Hongbin , Chin Mian , Chu D. Allen , Niyogi Dev
Published: November 2004

This study compares aerosol optical depths (AOD) products from the Moderate Resolution Imaging Spectroradiometer (MODIS) and the Goddard Chemistry Aerosol Radiation and Transport (GOCART) model and their integrated products with ground measurements across the eastern U.S. from March 1, 2000 to December 31, 2001. The Terra MODIS Level‐3 (collection 4) AOD at 0.55 μm has better correlation, but consistently overestimates the values of the Aerosol Robotic Network (AERONET) measurements. GOCART has small biases for a 22‐month integration, and slight positive biases appeared for the cold season. These results are also supported by the comparison with the IMPROVE (Interagency Monitoring of Protected Visual Environments) light extinction index. The optimal interpolation improves the daily‐scale RMSE from either MODIS or GOCART alone. However, the regional biases in the aerosol products constitute a major constraint to the optimal estimate of AOD.
Geometric localization of STEREO CMEs
Authors: Pizzo V. J. , Biesecker D. A.
Published: November 2004

We describe a straightforward methodology for determining the location and other gross properties of CMEs within the coronagraph field of view in the upcoming STEREO mission observations. We use geometric triangulation upon a series of lines‐of‐sight taken from two spacecraft views that are locally tangent to the apparent edges of a CME. From the intersections of these lines‐of‐sight, we construct a set of stacked quadrilaterals that fully bound the structure and convey something of its location, shape, and size; a time sequence of such determinations can be used to determine the velocity. The technique is relatively robust and promises a substantial improvement in our capability to locate and characterize CMEs for research as well as forecasting purposes.
Shear‐wave splitting variations across an array in the southern North Island, New Zealand
Authors: Marson‐Pidgeon Katrina , Savage Martha K.
Published: November 2004

We observe significant spatial variations in shear wave splitting from deep teleseismic S and regional ScS recorded on an array in the fore‐arc region of the Hikurangi subduction zone, New Zealand. We also observe variations from different events recorded at the same station. The fast polarization directions range between 23° and 72° and the delay times range between 0.75 s and 1.80 s. These observations contrast with previous SKS studies in New Zealand where little spatial variation is seen, and highlights the importance of using a variety of phases with different periods. Our observations are consistent with a model in which a lateral anisotropic boundary runs ∼NE‐SW in a zone between Kapiti Island and ∼40 km east of the Tararua mountain range. The anisotropic boundary is possibly related to a prominent vertical velocity feature near Kapiti Island.
Lessons to be learned from the comparison of three satellite‐derived biomass burning products
Authors: Boschetti L. , Eva H. D. , Brivio P. A. , Grégoire J. M.
Published: November 2004

Thematic maps of active fires or burned areas derived from low resolution remotely sensed data are widely used as an input for the estimation of the atmospheric emissions due to biomass burning. The present work considers three of the global products available for year 2000: two burned area datasets (GBA2000 and GlobScar) and one active fires dataset (World Fire Atlas) and analyses the relative agreements and disagreements in terms of areal extents and geographic location of the fire activity. The intercomparison of the three datasets shows that, while there is generally a good spatial agreement, the disagreement in terms of areal estimates is major. Without a quantitative validation and calibration using high resolution data, the uncertainty of the areal estimates significantly increases the variance of the estimation of atmospheric emissions.
Compatibility analysis of precipitation and runoff trends over the large Siberian watersheds
Authors: Berezovskaya Svetlana , Yang Daqing , Kane Douglas L.
Published: November 2004

The consistency of long‐term yearly precipitation and runoff trends over the largest Arctic watersheds (Ob, Yenisei and Lena Rivers) is examined. Three gridded precipitation datasets (Climatic Research Unit, University of Delaware, NCEP) are used for comparative analyses with runoff data collected at basin outlets. The results generally demonstrate inconsistency in long‐term changes of basin precipitation and runoff. The Yenisei River runoff increases significantly, while precipitation data show mostly negative trends. The Ob River does not show any significant trend either in precipitation or runoff. Positive trend in the Lena River runoff is accompanied by a weak precipitation increase; however, the precipitation increase is not strong enough to support the observed runoff change. The inconsistency identified in basin precipitation and runoff trends suggests uncertainty in both the quality of basin precipitation and runoff datasets, as well as the perceived hydrologic factors impacting runoff change.
Interplanetary magnetic field at ∼9 AU during the declining phase of the solar cycle and its implications for Saturn's magnetospheric dynamics
Authors: Jackman C. M. , Achilleos N. , Bunce E. J. , Cowley S. W. H. , Dougherty M. K. , Jones G. H. , Milan S. E. , Smith E. J.
Published: November 2004

We study the interplanetary magnetic field (IMF) data obtained by the Cassini spacecraft during a ∼6.5‐month interval when the spacecraft was approaching Saturn at heliocentric distances between ∼8.5 and ∼8.9 AU. It is shown that the structure of the IMF is consistent with that expected to be formed by corotating interaction regions (CIRs) during the declining phase of the solar cycle, with two sectors during each solar rotation, and crossings of the heliospheric current sheet generally embedded within few‐day higher‐field compression regions, separated by several‐day lower‐field rarefaction regions. This pattern was disrupted in November 2003, however, by an interval of high activity on the Sun. These data have then been employed to estimate the voltage associated with open flux production at Saturn's magnetopause using an empirical formula adapted from Earth. The results show that the CIR‐related structuring of the IMF leads to corresponding structuring of the interplanetary interaction with Saturn's magnetosphere and hence also to intervals of very different dynamical behavior. During few‐day compression regions where the IMF strength is ∼0.5–2 nT, the average Dungey cycle voltage is estimated to be ∼100 kV, such that the open flux produced over such intervals is ∼30–40 GWb, similar to the typical total amount present in Saturn's magnetosphere. The magnetosphere is thus significantly driven by the solar wind interaction during such intervals. During some rarefaction intervals, on the other hand, the field strength remains ∼0.1 nT or less over several days, implying reconnection voltages of ∼10 kV or less, with negligible production of open flux. The magnetosphere is then expected to enter a quiescent state, dominated by internal processes. Overall, ∼100 GWb of open flux is estimated to be produced during each ∼25‐day solar rotation, about 3 times the typical flux contained in the tail, and sufficient to drive three to five substorms. We point out, however, that CIR‐related variations in solar wind dynamic pressure will also occur in synchronism with the field variations, which may also play a role in modulating the open flux in the system, thus reinforcing the synchronization of the pattern of growth and decay of open flux to the CIR pattern. Estimates of open flux production associated with the period of strong solar activity indicate that major magnetospheric dynamics were excited by reconnection‐mediated solar wind interaction during this interval.
Collisional shear instability in the equatorial F region ionosphere
Authors: Hysell D. L. , Kudeki E.
Published: November 2004

A collisional shear instability in a magnetized plasma is described and evaluated. The instability is related to electrostatic Kelvin Helmholtz but operates in inhomogeneous plasmas in the collisional regime. Boundary value analysis predicts that the linear growth rate for the instability could be comparable to that of the collisional interchange instability in the equatorial F region ionosphere under ideal conditions. An initial value simulation of a nonlinear model of the instability run under realistic conditions produces growing waves with a relatively long growth time (50 min) and with an initial wavelength of about 30 km. The simulation results are consistent with recent radar observations showing large‐scale plasma waves in the bottomside equatorial ionosphere at sunset prior to the onset of spread F conditions. The role of shear instability in preconditioning the F region for interchange instabilities to occur after sunset is discussed.
Structural and electronic evolution of the As(OH)3 molecule in high temperature aqueous solutions: An x-ray absorption investigation
Authors: Testemale Denis , Hazemann Jean-Louis , Pokrovski Gleb S. , Joly Yves , Roux Jacques , Argoud Roger , Geaymond Olivier
Published: November 2004

The geometrical and electronic structure of the arsenious acid molecule As(OH)3 in aqueous solutions has been investigated by x-ray absorption spectroscopy (XAS) within extended x-ray absorption spectroscopy (EXAFS) and x-ray absorption near edge structure (XANES), using realistic first-principle calculations in the latter case. This investigation was performed on aqueous solutions of arsenious acid from ambient to supercritical conditions (P=250 and 600 bars, T⩽500 °C) using a new optical cell. The analysis of the XAS spectra is consistent with (1) a constant As-O distance, (2) an opening of the O-As-O angles within the C3V pyramidal structure in the range 30–200 °C. This structural evolution comes along with a small decrease of the partial charges of the atoms in the As(OH)3 molecule. The explanation invoked for both structural and electronic modifications observed is the weakening of the interactions, through hydrogen bonds, between the As(OH)3 complex and water molecules. This is a fingerprint of the similar weakening of hydrogen bonding interactions in the solvent itself.
Ultrafast vibrational spectroscopy of water and aqueous N-methylacetamide: Comparison of different electronic structure/molecular dynamics approaches
Authors: Schmidt J. R. , Corcelli S. A. , Skinner J. L.
Published: November 2004

Kwac and Cho [J. Chem. Phys. 119, 2247 (2003)] have recently developed a combined electronic structure/molecular dynamics approach to vibrational spectroscopy in liquids. The method involves fitting ab initio vibrational frequencies for a solute in a cluster of solvent molecules to a linear combination of the electrostatic potentials on the solute atoms due to the charges on the solvent molecules. These authors applied their method to the N-methylacetamide-D/D2O system. We (S. A. Corcelli, C. P. Lawrence, and J. L. Skinner, [J. Chem. Phys. 120, 8107 (2004)]) have recently explored a closely related method, where instead of the electrostatic potential, the solute vibrational frequencies are fit to the components of the electric fields on the solute atoms due to the solvent molecules. We applied our method to the HOD/D2O and HOD/H2O systems. In order to make a direct comparison of these two approaches, in this paper we apply their method to the water system, and our method to the N-methylacetamide system. For the water system we find that the electric field method is superior to the potential approach, as judged by comparison with experiments for the absorption line shape. For the N-methylacetamide system the two methods are comparable.
An analysis of core effects on shape-consistent pseudopotentials
Authors: Fromager Emmanuel , Maron Laurent , Teichteil Christian , Heully Jean-Louis , Faegri Knut , Dyall Ken
Published: November 2004

Large core (seven-valence electrons) shape-consistent averaged relativistic pseudopotentials (AREP) including core effects have been derived for the halogen series (Cl,Br,I,At). The influence of core effects on the spin-orbit splitting of the halogen and alkali atoms is clearly demonstrated within an all-electron four-component atomic reference calculation by means of a perturbation analysis. In particular, it is shown that AREPs extracted at the Dirac–Coulomb–Fock level, which already include spin-orbit polarization effects, give excellent results for atomic spectroscopy and equilibrium distances of halogen dimers. We also show that in our approach the core effects, included by configuration interaction using the numerical GRASP code, are transferred to the averaged orbital one-electron energy, defined in a perturbational way. This leads to a modification of the extracted AREPs by core effects, which is illustrated by calculations of the first atomic excited states using these AREPs. These results support the validity of including core effects directly in the AREPs extracted in a shape-consistent scheme. The transferability to the atomic excited states as well as to the molecular case is also verified.
Characteristic of structures and π-hydrogen bond of dimers C2H4−nFn-HF (n=0,1,2)
Authors: Li Rui-Yan , Li Zhi-Ru , Wu Di , Li Ying , Chen Wei , Sun Chia-Chung
Published: November 2004

By the counterpoise-correlated potential energy surface method (interaction energy optimization), five structures of the C2H4−nFn-HF (n=0,1,2) dimers with all real frequencies have been obtained at MP2/aug-cc-pVDZ level. The influence of F substituent effect on the structure and π-hydrogen bond of dimer has been discussed. For C2H4−nFn-HF (n=1,2), the π-hydrogen bonds are elongated comparing with that for C2H4-HF. For C2H3F-HF, g-C2H2F2-HF, cis-C2H2F2-HF, the π-hydrogen bonds are further deformed. These changes (elongate, shift, and deformation) of π-hydrogen bond mainly come from deformation of π-electron cloud of C=C bond. The π-electron cloud is pushed towards the one C atom, the π H-bond shift also to the C direction. Since the two lobes of π-electron cloud have deviated slightly from the molecular vertical plane passing through C=C bond, the π-hydrogen bond is sloped. Intermolecular interaction energies of the dimers are calculated to be −3.9 for C2H4-HF, −2.8 for C2H3F-HF, −2.1 for g-C2H2F2-HF, −1.6 for cis-C2H2F2-HF, −1.3 kcal/mol for trans-C2H2F2-HF, at CCSD(T)/aug-cc-pVDZ level.
Calculation of flexoelectric coefficients for a nematic liquid crystal by atomistic simulation
Authors: Cheung David L. , Clark Stewart J. , Wilson Mark R.
Published: November 2004

Equilibrium molecular dynamics calculations have been performed for the liquid crystal molecule n-4-(trans-4-n-pentylcyclohexyl)benzonitrile (PCH5) using a fully atomistic model. Simulation data have been obtained for a series of temperatures in the nematic phase. The simulation data have been used to calculate the flexoelectric coefficients es and eb using the linear response formalism of Osipov and Nemtsov [M. A. Osipov and V. B. Nemtsov, Sov. Phys. Crstallogr. 31, 125 (1986)]. The temperature and order parameter dependence of es and eb are examined, as are separate contributions from different intermolecular interactions. Values of es and eb calculated from simulation are consistent with those found from experiment.
Local atomic structures of palladium nanowire
Authors: Hui Li , Wang B. L. , Wang J. L. , Wang G. H.
Published: November 2004

In this paper, investigation of the structure of palladium nanowire has been performed by using genetic algorithm simulation based on the molecular dynamics. Our calculation employs a well-fitted, tight-binding many-body potential for Pd atoms. Some local atomic structures and defects in nanowires have been reported. The melting behavior of palladium nanowire has also been investigated. An interesting result is that the diffusion of the central atoms results in the beginning of the melting. The moving central atoms build up a monostrand atomic chain during the melting process. The single atomic chain is very stable which can exist in a wide temperature region (800–950 K). The formation of the single atomic chain causes some new defects in the nanowire. And the new defects result in the decrease of the thermal stability of the nanowire. Interestingly, the liquid from the nanowire melting has a supercooled feature because the splitting of the second peak of pair correlation function is observed. The curves of the internal energy and the local cluster are used to monitor the phase transition. The melting of the nanowire is not only due to the single atomic diffusion, but also the diffusion of the local clusters.
Reducing a chemical master equation by invariant manifold methods
Authors: Roussel Marc R. , Zhu Rui
Published: November 2004

We study methods for reducing chemical master equations using the Michaelis-Menten mechanism as an example. The master equation consists of a set of linear ordinary differential equations whose variables are probabilities that the realizable states exist. For a master equation with s0 initial substrate molecules and e0 initial enzyme molecules, the manifold can be parametrized by s0 of the probability variables. Fraser’s functional iteration method is found to be difficult to use for master equations of high dimension. Building on the insights gained from Fraser’s method, techniques are developed to produce s0-dimensional manifolds of larger systems directly from the eigenvectors. We also develop a simple, but surprisingly effective way to generate initial conditions for the reduced models.
Polarization quantum beat spectroscopy of HCF(Ã1A″). II. Renner–Teller and spin–orbit mixing in the simplest singlet carbene
Authors: Ionescu Ionela , Fan Haiyan , Ionescu Eduard , Reid Scott A.
Published: November 2004

To further investigate the Renner–Teller (RT) effect and spin–orbit mixing in the Ã1A″←X̃1A′ system of the simplest singlet carbene, HCF, we report a detailed analysis of the Ka=1←0 subband of 204 using polarization quantum beat spectroscopy in combination with fluorescence excitation spectroscopy and lifetime measurements. This subband is perturbed both by RT and spin–orbit interactions, which are clearly differentiated due to the order-of-magnitude difference in matrix elements. We show that RT induced mixing with a high vibrational level of X̃1A′ leads to a splitting of this subband, and while the higher energy member is rotationally unperturbed, every line in the lower energy member is perturbed by spin–orbit mixing with background levels of ã3A″, as evidenced by large F19 and H1 hyperfine constants and Lande g factors. In contrast, the higher energy subband exhibits very small Lande g factors and hyperfine constants, which is explained within a model that incorporates only the Ã1A″-X̃1A′ interaction. We thus demonstrate that polarization quantum beat spectra provides efficient discrimination between RT and spin–orbit interactions. Analysis of the lower energy subband in concert with ab initio electronic structure calculations has yielded the first information on the F19 and H1 hyperfine structure of the ã3A″ state and the magnitude of the spin–orbit matrix elements.
Three-variable reversible Gray–Scott model
Authors: Mahara Hitoshi , Suematsu Nobuhiko J. , Yamaguchi Tomohiko , Ohgane Kunishige , Nishiura Yasumasa , Shimomura Masatsugu
Published: November 2004

Even though the field of nonequilibrium thermodynamics has been popular and its importance has been suggested by Demirel and Sandler [J. Phys. Chem. B 108, 31 (2004)], there are only a few investigations of reaction-diffusion systems from the aspect of thermodynamics. A possible reason is that model equations are complicated and difficult to analyze because the corresponding chemical reactions need to be reversible for thermodynamical calculations. Here, we introduce a simple model for calculation of entropy production rate: a three-variable reversible Gray–Scott model. The rate of entropy production in self-replicating pattern formation is calculated, and the results are compared with those reported based on the Brusselator model in the context of biological cell division.
Thermally induced sign change of Soret coefficient for dilute and semidilute solutions of poly(N-isopropylacrylamide) in ethanol
Authors: Kita Rio , Kircher Gunnar , Wiegand Simone
Published: November 2004

We studied the thermal diffusion behavior of poly(N-isopropylacrylamide) (PNiPAM) in ethanol in a temperature range from T=14.0 °C to T=40.0 °C by means of thermal diffusion forced Rayleigh scattering. The obtained Soret coefficient ST of PNiPAM was positive for lower temperatures (T<34 °C), while ST showed a negative value for higher temperatures (T>34 °C). This means PNiPAM molecules move to the cold side for temperatures T<34 °C, whereas they move to the warm side for T>34 °C. This is the first nonaqueous polymeric system for which a sign change with temperature has been observed. We performed static and dynamic light scattering experiments in the same temperature range. The second virial coefficient determined from dilute solutions by static light scattering (SLS) was positive in the comparable temperature range. The results of SLS for the semidilute solution showed a strong repulsion among PNiPAM chains which was enhanced by increasing temperature. These results imply that the observed thermally induced sign change of ST does not depend on the intermolecular interactions among PNiPAM chains.
Coarse-grained model for phospholipid/cholesterol bilayer
Authors: Murtola Teemu , Falck Emma , Patra Michael , Karttunen Mikko , Vattulainen Ilpo
Published: November 2004

We construct a coarse-grained (CG) model for dipalmitoylphosphatidylcholine (DPPC)/cholesterol bilayers and apply it to large-scale simulation studies of lipid membranes. Our CG model is a two-dimensional representation of the membrane, where the individual lipid and sterol molecules are described by pointlike particles. The effective intermolecular interactions used in the model are systematically derived from detailed atomic-scale molecular dynamics simulations using the Inverse Monte Carlo technique, which guarantees that the radial distribution properties of the CG model are consistent with those given by the corresponding atomistic system. We find that the coarse-grained model for the DPPC/cholesterol bilayer is substantially more efficient than atomistic models, providing a speedup of approximately eight orders of magnitude. The results are in favor of formation of cholesterol-rich and cholesterol-poor domains at intermediate cholesterol concentrations, in agreement with the experimental phase diagram of the system. We also explore the limits of the coarse-grained model, and discuss the general validity and applicability of the present approach.
Dynamics of surface water in ZrO2 studied by quasielastic neutron scattering
Authors: Mamontov E.
Published: November 2004

A quasielastic neutron scattering experiment has revealed the dynamics of surface water in a high surface area zirconium oxide in the temperature range of 300–360 K. The characteristic times of the rotational (picoseconds) and translational (tens of picoseconds) components of diffusion motion are well separated. The rotational correlation time shows an Arrhenius-type behavior with an activation energy of 4.48 kJ/mol, which is lower compared to bulk water. The rotational diffusion at room temperature is slower by about a factor of 2 compared to bulk water, whereas the translational diffusion slows down by a factor of 40. In contrast to bulk water, the translational correlation time exhibits an Arrhenius-type temperature dependence with an activation energy of 11.38 kJ/mol. Comparison of different models for jump diffusion processes suggests that water molecules perform two-dimensional jumps at a well-defined, almost temperature-independent distance of 4.21–4.32 Å. Such a large jump distance indicates a low molecular density of the layer of diffusing molecules. We argue that undissociated water molecules on an average form two hydrations layers on top of the surface layer of hydroxyl groups, and all the layers have similar molecular density. Quasielastic neutron scattering experiment assesses the dynamics of the outermost hydration layer, whereas slower motion of the water molecules in the inner hydration layer contributes to the elastic signal.
Torsion-induced phase transitions in fluids confined between chemically decorated substrates
Authors: Sacquin-Mora Sophie , Fuchs Alain H. , Schoen Martin
Published: November 2004

In this paper we investigate the phase behavior of a “simple” fluid confined to a chemically heterogeneous slit pore of nanoscopic width sz by means of Monte Carlo simulations in the grand canonical ensemble. The fluid-substrate interaction is purely repulsive except for elliptic regions of semiaxes A and B attracting fluid molecules. On account of the interplay between confinement (i.e., sz) and chemical decoration, three fluid phases are thermodynamically permissible, namely, gaslike and liquidlike phases and a “bridge phase” where the molecules are preferentially adsorbed by the attractive elliptic patterns and span the gap between the opposite substrate surfaces. Because of their lack of cylindrical symmetry, bridge phases can be exposed to a torsional strain 0⩽θ⩽π/2 by rotating the upper substrate while holding the lower one in position. Depending on the thermodynamic state of the confined fluid, torsion-induced first-order phase transitions are feasible during which a bridge phase may be transformed into either a gaslike (evaporation) or a liquidlike phase (condensation). Since the chemical patterns decorating the substrates are finite in size, system properties are not translationally invariant in any spatial direction. Therefore, in order to study these phase transitions, we resorted to the thermodynamic integration scheme developed earlier to calculate the grand potential Ω in a system of low symmetry.
Misfolded free energy surface of a peptide with αββ motif (1PSV) using the generalized Born solvation model
Authors: Pak Youngshang , Kim Eunae , Jang Soonmin
Published: November 2004

Using the replica exchange molecular dynamics method, we carried out ab initio folding study of 1PSV using AMBER param99MOD2 and the generalized Born (GB) solvation model. A total of 10 ns run for each replica resulted in a distorted free energy surface populated by two major misfolded conformers. The native structure of 1PSV was never located in the free energy surface. This distortion is mainly due to the defect of the current energy model including the GB solvation term. Therefore, the current energy model should be further improved for correct folding predictions of the proteins with a αββ motif.
Nitric acid oxidation of silicon at ∼120°C to form 3.5-nm SiO2∕Si structure with good electrical characteristics
Authors: Asuha  , Imai Shigeki , Takahashi Masao , Kobayashi Hikaru
Published: November 2004

3.5-nm-thick SiO2 layers can be formed at 120 °C by immersion of Si in 40 wt % nitric acid (HNO3) followed by immersion in an azeotropic mixture (i.e., 68 wt % HNO3). The former immersion produces a 1.1-nm SiO2 layer with a low atomic density of 2.19×1022∕cm2, where the layer acts as a catalyst for the decomposition of HNO3. The latter immersion results in a 3.5-nm SiO2 layer with a higher atomic density of 2.22×1022∕cm2. When the postmetalization annealing treatment at 250 °C in hydrogen is performed on the ⟨Al∕3.5-nmSiO2∕Si(100)⟩ metal-oxide semiconductor diodes, interface states are passivated and a low leakage current density (e.g., 8×10−4A∕cm2 at the forward gate bias of 1.5 V) is achieved.
Immobilization of molecular tubes on self-assembled monolayers of β-cyclodextrin and dodecanethiol inclusion complexes
Authors: Samitsu Sadaki , Shimomura Takeshi , Ito Kohzo , Hara Masahiko
Published: November 2004

A molecular tube (MT) is a tubular macromolecule formed by the one-dimensional linkage of α-cyclodextrins and exhibits molecular recognition for selecting the diameter of a polymer chain. In this letter, we immobilized MTs on a self-assembled monolayers (SAM) of inclusion complexes (DDT-CD) between dodecanethiol (DDT) and β-cyclodextrin (β-CD). The DDT-CD inclusion complexes formed uniform self-assembled monolayers on gold. We confirmed that the MTs were immobilized on the DDT-CD SAM using dynamic contact angle measurements, surface-plasmon resonance (SPR), and scanning probe microscopy (SPM).
Direct numerical simulation of transitional and turbulent buoyant planar jet flames
Authors: Mehravaran K. , Jaberi F. A.
Published: November 2004

The effects of gravity on the physical and compositional structures of transitional and turbulent diffusion flames are studied via analysis of the data generated by direct numerical simulation of a planar jet flame at various gravity conditions. A fully compressible, high-order compact, finite-difference computational scheme is used together with a global kinetics model for chemical reaction. The results of our nonreacting turbulent jet simulations are in good agreement with the available experimental data. The results of our reacting jet simulations are also consistent with previous findings and indicate that in the absence of gravity, combustion damps the flow instability, and hence reduces “turbulence production” and jet growth. However, in the “finite-gravity” conditions, combustion generated density variations may promote turbulence and enhance both the mixing and the combustion through buoyancy effects. Our results also indicate that the gravity effects on a transitional/turbulent jet flame is not limited to large-scale flame flickering, and there is a significant impact on small-scale turbulence and mixing as well. Furthermore, the analysis of compositional flame structures suggests that the finite-rate chemistry effects are more significant in finite-gravity conditions than in zero-gravity.
Pulsed supersonic expansion of nonvolatile solids
Authors: Christen Wolfgang , Geggier Stephanie , Grigorenko Svitlana , Rademann Klaus
Published: November 2004

A compact apparatus for transferring nonvolatile particles into the gas phase and depositing them on a solid surface has been built and tested successfully. As initial experiment, solid caffeine with a vanishingly low vapor pressure has been dissolved in supercritical carbon dioxide, expanded into vacuum using a pulsed, supersonic molecular beam, and detected using a simple residual gas analyzer.
Stochastic dynamics of adhesion clusters under shared constant force and with rebinding
Authors: Erdmann Thorsten , Schwarz Ulrich S.
Published: November 2004

Single receptor-ligand bonds have finite lifetimes, so that biological systems can dynamically react to changes in their environment. In cell adhesion, adhesion bonds usually act cooperatively in adhesion clusters. Outside the cellular context, adhesion clusters can be probed quantitatively by attaching receptors and ligands to opposing surfaces. Here we present a detailed theoretical analysis of the stochastic dynamics of a cluster of parallel bonds under shared constant loading and with rebinding. Analytical solutions for the appropriate one-step master equation are presented for special cases, while the general case is treated with exact stochastic simulations. If the completely dissociated state is modeled as an absorbing boundary, mean cluster lifetime is finite and can be calculated exactly. We also present a detailed analysis of fluctuation effects and discuss various approximations to the full stochastic description.
Nanosecond freezing of water under multiple shock wave compression: Optical transmission and imaging measurements
Authors: Dolan D. H. , Gupta Y. M.
Published: November 2004

Water samples were subjected to multiple shock wave compressions, generating peak pressures of 1–5 GPa on nanosecond time scales. This loading process approximates isentropic compression and leads to temperatures where the ice VII phase is more stable than the liquid phase above 2 GPa. Time resolved optical transmission and imaging measurements were performed to determine the solidification rate under such conditions. Freezing occurred faster at higher pressures as water was compressed further into the ice VII phase, in agreement with classical micleation theory. Water consistently froze when in contact with a silica window, whereas no solidification occurred in the presence of sapphire windows. The transition was determined to be a surface initiated process—freezing began via heterogeneous nucleation at the water/window interface and propagated over thicknesses greater than 0.01 mm. The first optical images of freezing on nanosecond time scales were obtained. These images demonstrate heterogeneous nucleation and irregular solid growth over 0.01–0.10 mm lateral length scales and are consistent with latent heat emission during the transformation. The combination of optical transmission and imaging measurements presented here provide the first consistent evidence for freezing on short time scales.