bluuebunny/crossref_metadata_2025 huggingface dataset:
Chloride Accumulation in Mammalian Olfactory Sensory Neurons
Authors: Kaneko Hiroshi , Putzier Ilva , Frings Stephan , Kaupp U. Benjamin , Gensch Thomas
Published: September 2004

The generation of an excitatory receptor current in mammalian olfactory sensory neurons (OSNs) involves the sequential activation of two distinct types of ion channels: cAMP-gated Ca2+-permeable cation channels and Ca2+-gated Cl-channels, which conduct a depolarizing Cl-efflux. This unusual transduction mechanism requires an outward-directed driving force for Cl-, established by active accumulation of Cl-within the lumen of the sensory cilia. We used two-photon fluorescence lifetime imaging microscopy of the Cl--sensitive dye 6-methoxy-quinolyl acetoethyl ester to measure the intracellular Cl-concentration in dendritic knobs of OSNs from mice and rats. We found a uniform intracellular Cl-concentration in the range of 40-50 mm, which is indicative of active Cl-accumulation. Functional assays and PCR experiments revealed that NKCC1-mediated Cl-uptake through the apical membrane counteracts Cl-depletion in the sensory cilia, and thus maintains the responsiveness of OSNs to odor stimulation. To permit Cl-accumulation, OSNs avoid the “chloride switch”: they do not express KCC2, the main Cl-extrusion cotransporter operating in neurons of the adult CNS. Cl-accumulation provides OSNs with the driving force for the depolarizing Cl-current that is the basis of the low-noise receptor current in these neurons.
Comparison of IPSCs Evoked by Spiny and Fast-Spiking Neurons in the Neostriatum
Authors: Koos Tibor , Tepper James M. , Wilson Charles J.
Published: September 2004

Most neurons in the neostriatum are GABAergic spiny projection neurons with extensive local axon collaterals innervating principally other spiny projection neurons. The other source of GABAergic inputs to spiny neurons derives from a small number of interneurons, of which the best characterized are the parvalbumin-containing, fast-spiking interneurons. Spiny neuron collateral inhibition was not demonstrated until recently, because the IPSPs recorded at the soma are surprisingly small. In contrast, interneuronal inhibition was readily detected, comprising much larger IPSPs. Here, we report the application of quantal analysis and compartmental modeling to compare and contrast IPSCs in spiny neurons originating from axon collaterals and interneurons. The results indicate that individual release sites at spiny and interneuron synapses have similar quantal sizes and baseline release probabilities. Interneuronal unitary IPSCs are several times larger because of their proximal location on the neuron and because they have a larger number of transmitter release sites. Despite the small amount of current they can deliver to the soma, spiny cell collateral synapses had moderately high baseline release probabilities (0.5-0.9), suggesting that they are not weak because of some form of depression or modulation. The size of unitary collateral synaptic currents increased monotonically during development. These results argue against models of competitive inhibition in neostriatum, including those in which competitive inhibition is transiently effective during development and learning, and suggest a different role for the spiny cell axon collaterals.
The Neuropeptide Pigment-Dispersing Factor Coordinates Pacemaker Interactions in theDrosophilaCircadian System
Authors: Lin Yiing , Stormo Gary D. , Taghert Paul H.
Published: September 2004

InDrosophila, the neuropeptide pigment-dispersing factor (PDF) is required to maintain behavioral rhythms under constant conditions. To understand how PDF exerts its influence, we performed time-series immunostainings for the PERIOD protein in normal andpdfmutant flies over 9 d of constant conditions. Withoutpdf, pacemaker neurons that normally express PDF maintained two markers of rhythms: that of PERIOD nuclear translocation and its protein staining intensity. As a group, however, they displayed a gradual dispersion in their phasing of nuclear translocation. A separate group of non-PDF circadian pacemakers also maintained PERIOD nuclear translocation rhythms withoutpdfbut exhibited altered phase and amplitude of PERIOD staining intensity. Therefore,pdfis not required to maintain circadian protein oscillations under constant conditions; however, it is required to coordinate the phase and amplitude of such rhythms among the diverse pacemakers. These observations begin to outline the hierarchy of circadian pacemaker circuitry in theDrosophilabrain.
Intensity of mobile phone use and health compromising behaviours—how is information and communication technology connected to health‐related lifestyle in adolescence?
Authors: Leena Koivusilta , Tomi Lintonen , Arja Rimpelä
Published: September 2004

The association of mobile phone use with health compromising behaviours (smoking, snuffing, alcohol) was studied in a survey comprising a representative sample of 14–16‐year‐olds (N=3485) in 2001. Mobile phone was used by 89% of respondents and by 13% for at least 1 h daily. The intensity of use was positively associated with health compromising behaviours. The associations remained, although somewhat reduced, after including weekly spending money in the models. This study concludes that, at least in the present developmental level of communication technologies, intensive mobile phone use seems to be part of the same health‐related lifestyle as health compromising behaviours.
Lipid dependence and activity control of phosphatidylserine synthase from Escherichia coli
Authors: Linde Kajsa , Gröbner Gerhard , Rilfors Leif
Published: September 2004

The activity of phosphatidylserine synthase from Escherichia coli depends significantly on the nature and level of the lipids in the matrix, at which the enzyme is operating. To elucidate the role of anionic lipids in the regulation of PtdSer synthase, its activity was studied in mixed micelles containing phosphatidylglycerol (one charge) or diphosphatidylglycerol (two charges), the two main anionic membrane lipids in E. coli. Membrane association and activity of PtdSer synthase were increased by the two lipids, indicating their essential role in the positive regulation mechanism of the phosphatidylethanolamine level in the E. coli membrane.
Laccase from Melanocarpus albomyces binds effectively to cellulose
Authors: Kiiskinen Laura-Leena , Palonen Hetti , Linder Markus , Viikari Liisa , Kruus Kristiina
Published: September 2004

A laccase from the thermophilic fungus Melanocarpus albomyces was shown to bind to softwood and pure microcrystalline cellulose. The binding isotherm fitted well the Langmuir type one‐site binding model. The adsorption parameters indicated that M. albomyces laccase binds with high affinity to cellulose with a relatively low maximum binding capacity, as compared to the values for various cellulases. The binding was shown to be reversible and not influenced by non‐specific protein or 0.1–0.5 M Na2SO4. No binding was detected with laccases from Trametes hirsuta or Mauginiella sp., which suggests that binding to cellulose is typical for only some laccases.
Role of cytokines and chemokines in prion infections of the central nervous system
Authors: Burwinkel Michael , Riemer Constanze , Schwarz Anja , Schultz Julia , Neidhold Sabine , Bamme Theresa , Baier Michael
Published: September 2004

Prion infections of the central nervous system (CNS) are characterised by a reactive gliosis and the subsequent degeneration of neuronal tissue. The activation of glial cells, which precedes neuronal death, is likely to be initially caused by the deposition of misfolded, proteinase K‐resistant, isoforms (termed PrPres) of the prion protein (PrP) in the brain. Cytokines and chemokines released by PrPres‐activated glia cells may contribute directly or indirectly to the disease development by enhancement and generalisation of the gliosis and via cytotoxicity for neurons. However, the actual role of prion‐induced glia activation and subsequent cytokine/chemokine secretion in disease development is still far from clear. In the present work, we review our present knowledge concerning the functional biology of cytokines and chemokines in prion infections of the CNS.
Clinical, pathological and immunohistochemical study of feline mammary fibroepithelial hyperplasia following a single injection of depot medroxyprogesterone acetate
Authors: Loretti Alexandre Paulino , da Silva Ilha Marcia Regina , Ordás Javier , de las Mulas Juana Martín
Published: September 2004

Feline mammary fibroepithelial hyperplasia (FMFH) following a single injection of depot medroxyprogesterone acetate (MPA) was observed in eight intact young queens. The repository compound is marketed as a veterinary product by a local pharmaceutical company with an indication for contraception in cats. The drug was administered according to the recommended doses and injection frequencies. Serum hormone assays performed immediately before neutering and 3 weeks after neutering detected persistently high levels of progesterone suggesting that depot MPA was still exerting its influence. No corpora lutea were found in those cases ruling out ovaries as the main site of progesterone. Immunohistochemistry performed on the hyperplastic mammary glands detected progesterone receptors in the nuclei of ductal cells, and growth hormone (GH) and insulin-like growth factor-I (IGF-I) in the cytoplasm of ductal epithelium. Overdosing should be considered here as the animals received at least 10 mg/kg of depot MPA in a single injection. Progestin-induced local synthesis of GH and IGF-I in mammary epithelial cells is suggested as one of the pathogenic mechanisms involved in the development of FMFH.
Malfunctions of Central Control of Movement Studied with Slow Brain Potentials in Neurological Patients
Authors: Verleger Rolf
Published: September 2004

Abstract Studies are reviewed that used movement-related EEG potentials to investigate impairments of movement control in neurological patients. The EEG potentials reviewed are the Bereitschaftspotential (BP), Contingent Negative Variation (CNV), and components of the lateralized readiness potential (LRP). Patient groups included in this review are patients with infarction of the middle cerebral artery, Parkinson's disease, cerebellar disease, and amyotrophic lateral sclerosis. A rich body of evidence has been collected on Parkinson's disease, and somewhat less on cerebellar atrophy, contributing to an understanding of the impairments caused by these diseases. In contrast, not much research has been done in amyotrophic lateral sclerosis and in infarction patients. The latter is particularly striking since utility of this method for assessing residual capacities of affected motor areas seems rather obvious.
The Bilateral Origin of Movement-Related Potentials Preceding Unilateral Actions
Authors: Brunia C.H.M. , van Boxtel G.J.M. , Speelman J.D.
Published: September 2004

Abstract It is as yet unclear why a unilateral self-paced movement in human and nonhuman primates is preceded by a bilateral Bereitschaftspotential (BP) or readiness potential (RP). The RP consists of an early symmetrical part (termed BP1 or RP), presumably of supplementary motor area (SMA) origin, and a later contralaterally dominant part (termed BP2 or NS'), to which the primary motor cortex (M1) is thought to contribute. Apart from the SMA there are other motor areas in the mesial cortex, which might provide additional sources for these slow waves. Although bilateral intracortical sources of the RP are found in the premotor cortex ( Sasaki & Gemba, 1991 ), they play nearly any role in most discussions on the RP. Recently the very existence of the ipsilateral RP over MI has been doubted. RP recordings of two patients with an intracerebral electrode in the ventro-intermedius nucleus (Vim) of the thalamus are shown, suggesting that the ipsilateral RP is not the consequence of volume conduction or signal transmission via the corpus callosum. Rather they point to a subcortical source, from where the ipsilateral cortex is activated. Anatomical and recent RP recordings from Vim and subthalamic nucleus seem to support this interpretation.
Preparing for Action: Inferences from CNV and LRP
Authors: Leuthold Hartmut , Sommer Werner , Ulrich Rolf
Published: September 2004

Abstract The execution of efficient motor actions is often preceded by preparation in the central nervous system. Although this kind of preparation cannot be observed directly, it, nevertheless, shortens reaction time. In this review we focus on two types of action preparation, namely event and temporal preparation. In particular, we show how modern event-related brain potential techniques can be employed to determine both the covert processes underlying such preparatory effects as well as their locus within the processing chain between stimulus input and action output.
Event-Related Potentials as Indices of Time Processing: A Review
Authors: Macar Françoise , Vidal Franck
Published: September 2004

Abstract This review examines ERP data that document the mechanisms and neural bases of time processing in the millisecond-to-minute range. Several types of ERP attest to the existence of timing capacities. Among them, one component of the Contingent Negative Variation (CNV) provides an on-line index of timing. CNV data strengthen the temporal accumulator concept, designed to subtend duration encoding. This conclusion is based on four main results: The positive relationship between temporal estimates and CNV amplitude is an index of the accumulation mechanism; the CNV peak is an index of time-based decision making; the CNV relates to temporal encoding, whereas temporal long-term memory may be linked to shifts of positive polarity; learning effects on CNV amplitude depend on topographic features, thus revealing functional differences among brain regions with respect to timing.
Stress‐dependent permeability and fluid flow through parallel joints
Authors: Germanovich Leonid N. , Astakhov Dmitriy K.
Published: September 2004

It is well known that the permeability of a set of joints can significantly vary in response to in situ stress conditions and pressure of the flowing fluid. Frequently, joint sets are closely spaced, and although joint mechanical interaction could significantly affect their aperture, the interaction is usually ignored in the fluid flow models. It is rather obvious that this approach corresponds to the upper bound for flow rate and rock permeability. By taking into account the interaction between the joints, we show that modeling a joint set by an infinite array provides the lower bound. The difference between these bounds, however, can be rather large, so they may not always be used with the sufficient accuracy. From the conceptual standpoint, it is often tempting to model a set with a finite number of joints by an infinite array. The results obtained in this work clearly demonstrate that such a model may result in a significant underestimation (by orders of magnitude) of both the permeability and flow rate. Similarly, the assumption of noninteracting joints may significantly overestimate (also by orders of magnitude) the stress‐dependent permeability and flow rate compared to those computed more accurately when accounting for joint interaction. Because the internal pressure can, in fact, close the pressurized joints while two edge joints (end‐members) in the set remain widely open (since they are not suppressed from one side by the adjacent joints), unless the number of joints in the set is exceedingly large (typically, >103), the fluid flow through the joint set becomes highly heterogeneous, focusing in the edge joints. As a result, the permeability/flow rate dependence on the joint spacing is not monotonic but has a maximum and a minimum. The derived closed‐form expression for flow rate/permeability ratio is asymptotically accurate and allows computations for rather arbitrary joint sets.
Source waters and flow paths in an alpine catchment, Colorado Front Range, United States
Authors: Liu Fengjing , Williams Mark W. , Caine Nel
Published: September 2004

Source waters and flow paths of streamflow draining high‐elevation catchments of the Colorado Rocky Mountains were determined using isotopic and geochemical tracers during the 1996 snowmelt runoff season at two subcatchments of the Green Lakes Valley, Colorado Front Range. A two‐component hydrograph separation using δ18O indicates that new water dominated (82 ± 6%) streamflow at the 8‐ha Martinelli catchment and old water dominated (64 ± 2%) at the 225‐ha Green Lake 4 (GL4) catchment. Snowmelt became isotopically enriched as the melt season progressed, complicating the interpretation of source water models. Thus old water may be underestimated if the temporal variation in δ18O of snowmelt is ignored or extrapolated from point measurements to the catchment. Two‐component hydrograph separations for unreacted and reacted waters using a single geochemical tracer were not always meaningful. Three‐component hydrograph separations using end‐member mixing analysis indicated that subsurface flow contributed more than two thirds to the streamflow at both catchments. Talus fields contributed more than 40% of the total discharge during summer at the GL4 catchment. A conceptual model was established for flow generation based on these results. It is suggested that surface water and groundwater interactions are much more important to the quantity and quality of surface water in high‐elevation catchments than previously thought.
Analytical second-order geometrical derivatives of energy for the self-consistent-charge density-functional tight-binding method
Authors: Witek Henryk A. , Irle Stephan , Morokuma Keiji
Published: September 2004

Analytical formulation of the second-order geometrical derivatives of energy for the self-consistent-charge density-functional tight-binding (SCC-DFTB) method is presented. To test its quality and numerical performance, the derived formalism has been coded and applied for calculation of harmonic vibrational frequencies for a set of 17 small and medium size molecules. For this set, the average absolute deviation from experiment is 99 cm−1 for SCC-DFTB vs 62 cm−1 for the Møller-Plesset second-order perturbation theory with the cc-pVDZ basis set (MP2/cc-pVDZ) and 32 cm−1 for the B3LYP density functional method with the same basis set (B3LYP/cc-pVDZ), while the maximal deviation is 465 cm−1 vs 1741 cm−1 for MP2/cc-pVDZ and 112 cm−1 for B3LYP/cc-pVDZ. The SCC-DFTB results are in reasonable agreement with experiments as well as with ab initio and density-functional results, and are better than other semiempirical methods. The SCC-DFTB method allows for considerable computational time saving when compared to other methods while retaining similar overall accuracy. Data for a series of conjugated polyenes show that an analytical formulation of SCC-DFTB is noticeably faster than its numerical formulation.
Modeling vibrational spectra using the self-consistent charge density-functional tight-binding method. I. Raman spectra
Authors: Witek Henryk A. , Morokuma Keiji , Stradomska Anna
Published: September 2004

An extension of the self-consistent charge density-functional tight-binding (SCC-DFTB) method is presented that allows for calculating intensities of peaks in vibrational Raman spectra for very large molecules. The extension is based on a simple ansatz: an extra term, which describes interaction of an external electric field with induced atomic charges, is added to the SCC-DFTB energy expression. We apply the modified SCC-DFTB formalism for reproducing vibrational Raman spectra of 17 organic molecules. The calculated spectra are compared with experiment and with spectra obtained from density functional theory (DFT) calculations. We find that the SCC-DFTB method is capable of reproducing most of the features of experimental Raman spectra. Limitations and advantages of this approach are analyzed and suggestions for interpreting calculated SCC-DFTB Raman spectra are given.
Molecular elimination of Br2 in 248 nm photolysis of bromoform probed by using cavity ring-down absorption spectroscopy
Authors: Huang Hong-Yi , Chuang Wan-Ting , Sharma Ramesh C. , Hsu Ching-Yi , Lin King-Chuen , Hu Ching-Han
Published: September 2004

By using cavity ring-down spectroscopy technique, we have observed the channel leading to Br2 molecular elimination following photodissociation of bromoform at 248 nm. A tunable laser beam, which is crossed perpendicular to the photolysis laser beam in a ring-down cell, is used to probe the Br2 fragment in the B 3Πou+−X 1Σg+ transition using the range 515–524 nm. The ring-down time lasts 500 ns, so the rotational population of the Br2 fragment may not be nascent nature, but its vibrational population should be. The vibrational population ratio of Br2(v=1)/Br2(v=0)=0.8±0.2 implies that the fragmented Br2 is vibrationally hot. The quantum yield of the molecular elimination reaction is 0.23±0.05, consistent with the values of 0.26 and 0.16 reported in 234 and 267 nm photolysis of bromoform, respectively, using velocity ion imaging. A plausible photodissociation pathway is proposed, based upon this work and ab initio calculations. The Ã 1A2, B̃ 1E, and C̃ 1A1 singlet states of bromoform are probably excited at 248 nm. These excited states may couple to the high vibrational levels of the ground state X̃ 1A1 via internal conversion. This vibrationally excited bromoform readily surpasses a reaction barrier 389.6 kJ/mol prior to decomposition. The transition state structure tends to correlate with vibrationally hot Br2. Dissociation after internal conversion of the excited states to vibrationally excited ground state should result in a large fraction of the available energy to be partitioned in vibrational states of the fragments. The observed vibrationally hot Br2 fragment seems to favor the dissociation pathway from high vibrational levels of the ground state. Nevertheless, the other reaction channel leading to a direct impulsive dissociation from the excited states cannot be excluded.
Low-temperature susceptibility of concentrated magnetic fluids
Authors: Pshenichnikov Alexander F. , Lebedev Alexander V.
Published: September 2004

The initial susceptibility of concentrated magnetic fluids (ferrocolloids) has been experimentally investigated at low temperatures. The results obtained indicate that the interparticle dipole-dipole interactions can increase the susceptibility by several times as compared to the Langevin value. It is shown that good agreement between recent theoretical models and experimental observations can be achieved by introducing a correction for coefficients in the series expansion of susceptibility in powers of density and aggregation parameter. A modified equation for equilibrium susceptibility is offered to sum over corrections made by Kalikmanov (Statistical Physics of Fluids, Springer-Verlag, Berlin, 2001) and by B. Huke and M. Lücke (Phys. Rev. E 67, 051403, 2003). The equation gives good quantitative agreement with the experimental data in the wide range of temperature and magnetic particles concentration. It has been found that in some cases the magnetic fluid solidification occurs at temperature several tens of kelvins higher than the crystallization temperature of the carrier liquid. The solidification temperature of magnetic fluids is independent of particle concentration (i.e., magneto-dipole interparticle interactions) and dependent on the surfactant type and carrier liquid. This finding allows us to suggest that molecular interactions and generation of some large-scale structure from colloidal particles in magnetic fluids are responsible for magnetic fluid solidification. If the magnetic fluid contains the particles with the Brownian relaxation mechanism of the magnetic moment, the solidification manifests itself as the peak on the “susceptibility-temperature” curve. This fact proves the dynamic nature of the observed peak: it arises from blocking the Brownian mechanism of the magnetization relaxation.
Symmetries, vibrational instabilities, and routes to stable structures of clusters of Al, Sn, and As
Authors: Pushpa Raghani , Narasimhan Shobhana , Waghmare Umesh
Published: September 2004

We investigate the stability of small clusters using density functional theory to compute the total energy, forces, and vibrational frequencies using linear response. We exhibit an efficient and computationally low-cost route to finding stable structures, by starting with high-symmetry structures and distorting them according to their unstable modes. We illustrate this by application to 4-, 6-, and 13-atom clusters of Al, Sn, and As. This technique also naturally elucidates the origins of stability of the lower symmetry structures, which is variously due to the linear or pseudo Jahn-Teller effect, combined with a lowering of various contributions to the total energy. We show that the situation is more complex than has generally been appreciated.
Electronic g-tensors of solvated molecules using the polarizable continuum model
Authors: Rinkevicius Zilvinas , Telyatnyk Lyudmyla , Vahtras Olav , Ruud Kenneth
Published: September 2004

We present the implementation of density functional response theory combined with the polarizable continuum model (PCM), enabling first principles calculations of molecular g-tensors of solvated molecules. The calculated g-tensor shifts are compared with experimental g-tensor shifts obtained from electron paramagnetic resonance spectra for a few solvated species. The results indicate qualitative agreement between the calculations and the experimental data for aprotic solvents, whereas PCM fails to reproduce the electronic g-tensor behavior for protic solvents. This failure of PCM for protic solvents can be resolved by including into the model those solvent molecules which are involved in hydrogen bonding with the solute. The results for the protic solvents show that the explicit inclusion of the solvent molecules of the first solvation sphere is not sufficient in order to reproduce the behavior of the electronic g-tensor in protic solvents, and that better agreement with experimental data can be obtained by including the long-range electrostatic effects accounted for by the PCM approach on top of the explicit hydrogen-bonded complexes.
Monte Carlo simulations of segregation in Pt-Re catalyst nanoparticles
Authors: Wang Guofeng , Van Hove M. A. , Ross P. N. , Baskes M. I.
Published: September 2004

We have investigated the segregation of Pt atoms to the surfaces of Pt-Re nanoparticles using the Monte Carlo method and modified embedded-atom method potentials that we have developed for Pt-Re alloys. The Pt75Re25 nanoparticles (containing from 586 to 4033 atoms) are assumed to have disordered fcc configurations and cubo-octahedral shapes (terminated by {111} and {100} facets), while the Pt50Re50 and Pt25Re75 nanoparticles (containing from 587 to 4061 atoms) are assumed to have disordered hcp configurations and truncated hexagonal bipyramidal shapes (terminated by {0001} and {101̄1} facets). We predict that due to the segregation process the equilibrium Pt-Re nanoparticles would achieve a core-shell structure, with a Pt-enriched shell surrounding a Pt-deficient core. For fcc cubo-octahedral Pt75Re25 nanoparticles, the shells consist of almost 100 at. % of Pt atoms. Even in the shells of hcp truncated hexagonal bipyramidal Pt50Re50 nanoparticles, the concentrations of Pt atoms exceed 85 at. % (35 at. % higher than the overall concentration of Pt atoms in these nanoparticles). Most prominently, all Pt atoms will segregate to the surfaces in the hcp truncated hexagonal bipyramidal Pt25Re75 nanoparticles containing less than 1000 atoms. We also find that the Pt atoms segregate preferentially to the vertex sites, less to edge sites, and least to facet sites on the shell of Pt-Re nanoparticles.
Role of the F spin-orbit excited state in the F+HD reaction: Contributions to the dynamical resonance
Authors: Tzeng Yi-Ren , Alexander Millard H.
Published: September 2004

We report quantum mechanical calculations of excitation functions (relative reaction cross sections) for the F+HD reaction. We include three potential energy surfaces and an accurate treatment of all couplings (non-adiabatic, spin-orbit, and Coriolis). Comparison with experimental results [Dong, Lee, and Liu, J. Chem. Phys., 113, 3633 (2000)] show excellent agreement for the DF product channel and an improved but not perfect agreement for the HF product channel. In the former case, when weighted by the (16%) fractional population of the spin-orbit excited state (F*) in the beam, the overall reactivity of the F* is small (∼5%). For the HF product channel and with the same (16%) fractional weight, F* reactivity makes a contribution of ∼12% in the high-energy tail of the resonance peak. As a result, averaging over the population of F spin-orbit states in the beam changes the shape of the resonance. The greater the fraction of F* in the beam, the less pronounced will be the resonance modulation of the reaction excitation function.
Towards an assessment of the accuracy of density functional theory for first principles simulations of water. II
Authors: Schwegler Eric , Grossman Jeffrey C. , Gygi François , Galli Giulia
Published: September 2004

A series of 20 ps ab initio molecular dynamics simulations of water at ambient density and temperatures ranging from 300 to 450 K are presented. Car-Parrinello (CP) and Born-Oppenheimer (BO) molecular dynamics techniques are compared for systems containing 54 and 64 water molecules. At 300 K, an excellent agreement is found between radial distribution functions (RDFs) obtained with BO and CP dynamics, provided an appropriately small value of the fictitious mass parameter is used in the CP simulation. However, we find that the diffusion coefficients computed from CP dynamics are approximately two times larger than those obtained with BO simulations for T>400 K, where statistically meaningful comparisons can be made. Overall, both BO and CP dynamics at 300 K yield overstructured RDFs and slow diffusion as compared to experiment. In order to understand these discrepancies, the effect of proton quantum motion is investigated with the use of empirical interaction potentials. We find that proton quantum effects may have a larger impact than previously thought on structure and diffusion of the liquid.
Electron scattering from perfluorocyclobutane (c-C4F8)
Authors: Jelisavcic M. , Panajotovic R. , Kitajima M. , Hoshino M. , Tanaka H. , Buckman S. J.
Published: September 2004

We report experimental results for electron scattering from perfluorocyclobutane, c-C4F8, obtained from measurements in our two laboratories. A set of differential, integral, and momentum transfer cross sections is provided for elastic scattering for incident electron energies from 1.5 to 100 eV. Inelastic scattering (vibrational excitation) cross sections have been measured for incident electron energies of 1.5, 2, 5, 6, and 7 eV. In order to investigate the role of intermediate negative ions (resonances) in the scattering process we have also measured an excitation function for elastic scattering and vibrational excitation of the ground electronic state of C4F8 for incident energies between 0.6 and 20 eV. These results are compared with the limited amount of data available in the literature for scattering from this molecule.
Rotational excitations of N2O in small helium clusters and the role of Bose permutation symmetry
Authors: Paesani F. , Whaley K. B.
Published: September 2004

We present a detailed study of the energetics, structures, and Bose properties of small clusters of He4 containing a single nitrous oxide (N2O) molecule, from N=1 He4 up to sizes corresponding to completion of the first solvation shell around N2O (N=16 He4). Ground state properties are calculated using the importance-sampled rigid-body diffusion Monte Carlo method, rotational excited state calculations are made with the projection operator imaginary time spectral evolution method, and Bose permutation exchange and associated superfluid properties are calculated with the finite temperature path integral method. For N⩽5 the helium atoms are seen to form an equatorial ring around the molecular axis, at N=6 helium density starts to occupy the second (local) minimum of the N2O-He interaction at the oxygen side of the molecule, and N=9 is the critical size at which there is onset of helium solvation all along the molecular axis. For N⩾8 six He4 atoms are distributed in a symmetric, quasirigid ring around N2O. Path integral calculations show essentially complete superfluid response to rotation about the molecular axis for N⩾5, and a rise of the perpendicular superfluid response from zero to appreciable values for N⩾8. Rotational excited states are computed for three values of the total angular momentum, J=1–3, and the energy levels fitted to obtain effective spectroscopic constants that show excellent agreement with the experimentally observed N dependence of the effective rotational constant Beff. The non-monotonic behavior of the rotational constant is seen to be due to the onset of long He4 permutation exchanges and associated perpendicular superfluid response of the clusters for N⩾8. We provide a detailed analysis of the role of the helium solvation structure and superfluid properties in determining the effective rotational constants.
On the thermodynamic stability of clathrate hydrates IV: Double occupancy of cages
Authors: Tanaka Hideki , Nakatsuka Takeharu , Koga Kenichiro
Published: September 2004

We have extended the van der Waals and Platteeuw theory to treat multiple occupancy of a single cage of clathrate hydrates, which has not been taken into account in the original theory but has been experimentally confirmed as a real entity. We propose a simple way to calculate the free energy of multiple cage occupancy and apply it to argon clathrate structure II in which a larger cage can be occupied by two argon atoms. The chemical potential of argon is calculated treating it as an imperfect gas, which is crucial to predict accurate pressure dependence of double occupancy expected at high pressure. It is found that double occupancy dominates over single occupancy when the guest pressure in equilibrium with the clathrate hydrate exceeds 270 MPa.
Accurate vibrational-rotational partition functions and standard-state free energy values for H2O2 from Monte Carlo path-integral calculations
Authors: Lynch Vanessa Audette , Mielke Steven L. , Truhlar Donald G.
Published: September 2004

Accurate quantum mechanical partition functions and absolute free energies of H2O2 are determined using a realistic potential energy surface [J. Koput, S. Carter, and N. C. Handy, J. Phys. Chem. A 102, 6325 (1998)] for temperatures ranging from 300 to 2400 K by using Monte Carlo path integral calculations with new, efficient polyatomic importance sampling methods. The path centroids are sampled in Jacobi coordinates via a set of independent ziggurat schemes. The calculations employed enhanced-same-path extrapolation of trapezoidal Trotter Fourier path integrals, and the paths were constructed using fast Fourier sine transforms. Importance sampling was also used in Fourier coefficient space, and adaptively optimized stratified sampling was used in configuration space. The free energy values obtained from the path-integral calculations are compared to separable-mode approximations, to the Pitzer–Gwinn approximation, and to values in thermodynamic tables. Our calculations support the recently proposed revisions to the JANAF tables.
Gravity-induced liquid crystal phase transitions of colloidal platelets
Authors: van der Beek David , Schilling Tanja , Lekkerkerker Henk N. W.
Published: September 2004

The influence of gravity on a suspension of sterically stabilized colloidal gibbsite platelets is studied. An initially isotropic-nematic biphasic sample of such a suspension develops a columnar phase on the bottom on prolonged standing. This phenomenon is described using a simple osmotic compression model. We performed Monte Carlo simulations of cut spheres with aspect ratio L/D=1/15 and took data from the literature to supply the equations of state required for the model. We find that the model describes the observed three-phase equilibrium quite well.
Semiflexible polymers in a random environment
Authors: Dua Arti , Vilgis Thomas A.
Published: September 2004

We present using simple scaling arguments and one step replica symmetry breaking a theory for the localization of semiflexible polymers in a quenched random environment. In contrast to completely flexible polymers, localization of semiflexible polymers depends not only on the details of the disorder but also on the ease with which polymers can bend. The interplay of these two effects can lead to the delocalization of a localized polymer with an increase in either the disorder density or the stiffness. Our theory provides a general criterion for the delocalization of polymers with varying degrees of flexibility and allows us to propose a phase diagram for the highly folded (localized) states of semiflexible polymers as a function of the disorder strength and chain rigidity.
Can density functional methods be used for open-shell actinide molecules? Comparison with multiconfigurational spin-orbit studies
Authors: Clavaguéra-Sarrio Carine , Vallet Valérie , Maynau Daniel , Marsden Colin J.
Published: September 2004

The geometries, electronic structures, and vibrational frequencies of two isoelectronic compounds PuO22+ and PuN2 have been studied in detail at the density functional theory (DFT) and multiconfigurational ab initio levels of theory. Dynamic correlation was taken into account using second-order perturbation theory (CASPT2) and the variational difference-dedicated configuration interaction method for comparison with the results of the DFT study. Spin-orbit effects were included within the framework of an effective uncontracted spin-orbit configuration-interaction method which considers electron correlation effects and spin-orbit coupling on equal footing. The twelve lowest f-f electronic transitions are reported. The electronic ground state of both systems is found to be the Ω=4 component of Hg3. We thus disagree with an earlier assignment of the ground state of PuN2 [E. F. Archibong and A. K. Ray, J. Mol. Struct: THEOCHEM 530, 165 (2000)]. Spin-orbit effects are small on both the geometry and vibrational frequencies of the ground states of PuO22+ and PuN2, but they completely change the distribution of electronically excited states. A comparison of results obtained with the two classes of methods allows us to demonstrate that an unambiguous assignment of the electronic ground state and electronic spectra requires the use of multireference methods including spin-orbit coupling. Single-reference methods such as DFT provide a reasonable description of the electronic properties of ground states of these open-shell systems, and therefore also of their structural and vibrational properties. The experimental antisymmetric stretching frequency of matrix-isolated PuN2 is reproduced well by both CASPT2 and DFT calculations; generalized gradient approximation formulations of DFT are more successful than hybrid versions in this respect. Ground-state properties of UO22+, UN2, UO2, PuO22+, and PuN2 are compared and discussed.
Using nanoparticles to create self-healing composites
Authors: Lee Jae Youn , Buxton Gavin A. , Balazs Anna C.
Published: September 2004

The need for viable materials for optical communications, display technologies, and biomedical engineering is driving the creation of multilayer composites that combine brittle materials, such as glass, with moldable polymers. However, crack formation is a critical problem in composites where thin brittle films lie in contact with deformable polymer layers. Using computer simulations, we show that adding nanoparticles to the polymers yields materials in which the particles become localized at nanoscale cracks and effectively form “patches” to repair the damaged regions. Through micromechanics simulations, we evaluate the properties of these systems in the undamaged, damaged, and healed states and determine optimal conditions for harnessing nanoparticles to act as responsive, self-assembled “band aids” for composite materials. The results reveal situations where the mechanical properties of the repaired composites can potentially be restored to 75%–100% of the undamaged material.
The workings of a molecular thermometer: The vibrational excitation of carbon tetrachloride by a solvent
Authors: Graham Polly B. , Matus Kira JM , Stratt Richard M.
Published: September 2004

An intriguing energy-transfer experiment was recently carried out in methanol/carbon tetrachloride solutions. It turned out to be possible to watch vibrational energy accumulating in three of carbon tetrachloride’s modes following initial excitation of O-H and C-H stretches in methanol, in effect making those CCl4 modes “molecular thermometers” reporting on methanol’s relaxation. In this paper, we use the example of a CCl4 molecule dissolved in liquid argon to examine, on a microscopic level, just how this kind of thermal activation occurs in liquid solutions. The fact that even the lowest CCl4 mode has a relatively high frequency compared to the intermolecular vibrational band of the solvent means that the only solute-solvent dynamics relevant to the vibrational energy transfer will be extraordinarily local, so much so that it is only the force between the instantaneously most prominent Cl and solvent atoms that will significantly contribute to the vibrational friction. We use this observation, within the context of a classical instantaneous-pair Landau-Teller calculation, to show that energy flows into CCl4 primarily via one component of the nominally degenerate, lowest frequency, E mode and does so fast enough to make CCl4 an excellent choice for monitoring methanol relaxation. Remarkably, within this theory, the different symmetries and appearances of the different CCl4 modes have little bearing on how well they take up energy from their surroundings—it is only how high their vibrational frequencies are relative to the solvent intermolecular vibrational band edge that substantially favors one mode over another.
Strong enhancement of vibrational relaxation by Watson-Crick base pairing
Authors: Woutersen Sander , Cristalli Gloria
Published: September 2004

We have studied the ultrafast dynamics of NH-stretch vibrational excitations in Watson-Crick base pairs consisting of adenine and uracil derivatives. To estimate the influence of the A:U hydrogen bonding on the vibrational dynamics, we have also studied the uracil derivative in monomeric form. The vibrational relaxation of the NH-stretching mode is found to occur much faster in the Watson-Crick base pair than in monomeric uracil. From the delay dependence of the transient vibrational spectra, it can be concluded that both in base-paired and monomeric uracil, the energy relaxation takes place in two steps, the first step being a rapid transfer of energy from the NH-stretching mode to an accepting mode, the second step the relaxation of this accepting mode. The transient spectra show evidence that in the base pair the hydrogen bond between the nucleobases acts as the accepting mode, and that the hydrogen bonding between the bases is responsible for the extremely fast vibrational relaxation in this system.
Chiral Heterocyclic Ligands. X. Synthesis and Metal Complexes of Hindered and Chiral 2,2′-Bipyrimidines
Authors: Downard Alison J. , Phillips Ian G. , Steel Peter J.
Published: September 2004

The first examples of 2,2′-bipyrimidine ligands incorporating bulky or chiral substituents have been prepared by nickel(0)-mediated homo-coupling reactions of chloropyrimidines. The 4,4′-di-(tert-butyl) derivative 2 and the chiral derivative 5, with 4,5-fused bornane groups, have been shown to form mononuclear metal complexes in which they coordinate through the less hindered nitrogen donors.
From Penicillin to the Ribosome: Revolutions in the Determination and Use of Molecular Structure in Chemistry and Biology
Authors: Baker Edward N.
Published: September 2004

A revolution in structural analysis is in progress in the biological sciences that parallels a similar revolution that took place in chemistry 40–50 years ago. This has major implications for chemistry, offering exciting opportunities at the interface between chemistry and biology. The advances are driven by the value of structural information in biology, for understanding biological function, and for applications in structure-based drug design and structural genomics. Two directions are apparent: towards technically challenging biological structures and assemblies, typified by the potassium channel and the ribosome; and towards high-throughput structure determination of many, smaller, proteins, as in structural genomics. In this review, the advances in molecular biology and in structure determination by X-ray crystallography that make these developments possible are discussed, together with appropriate examples.
Revision of the Paramunna complex (Isopoda : Asellota : Paramunnidae)
Authors: Just Jean , Wilson George D. F.
Published: September 2004

This paper presents a global review of the current unwieldy concept of the genus Paramunna Sars, 1866. The study is based mainly on large new collections of material from Australia and subantarctic islands south of Tasmania and New Zealand. Of the four genera previously synonymised with Paramunna, Austrimunna Richardson, 1906 is revived (type species A. antarctica), Leptaspidia Bate & Westwood, 1867 and Metamunna Tattersall, 1905 are considered indeterminable, while Austronanus Hodgson, 1910 is not considered part of the Paramunna complex. Forty-three species, 27 new, are treated, mostly from Australia and adjacent subantarctic islands. Fifteen species currently in Paramunna do not belong in this complex. The type genus Paramunna Sars, 1866 comprises four known species, P. bilobata Sars, 1866, P. capensis Vanh�ffen, 1914, P. integra Nordenstam, 1933 and P. koreana Malyutina & Ushakova, 2001, and four new species. Nine new genera are created based on a cladistic analysis (type species, original combination): Ascionana (A. darwinia, sp. nov.), Epipedonana (E. profunda, sp. nov.), Harrietonana (Austrimunna subtriangulata Richardson, 1908), Kiklonana (Paramunna arnaudi Amar & Roman, 1974), Omonana (O. brachycephala, sp. nov.), Pagonana (Paramunna rostrata Hodgson, 1910), Palanana (Austrimunna serrata Richardson, 1908), Spiculonana (S. platysoma, sp. nov) and Sporonana (S. robusta, sp. nov.). Six species of Paramunna are transferred to other genera in the complex: P. simplex Menzies, 1962 and P.�parasimplex Winkler, 1994 to Omonana, gen. nov.; P. dilatata Vanh�ffen, 1914 to Pagonana, gen. nov.; P. gaini (Richardson, 1913) to Palanana gen. nov.; P. laevifrons Stebbing, 1910 and P. rhipis Shimomura & Mawatari, 1999 to Ascionana, gen. nov. Paramunna shornikovi Malyutina & Ushakova, 2001, is synonymised with P. rhipis. Keys to genera and species (if more than two in a genus) are given. Terminal males (males with elongated cephalon and massively enlarged pereonite 1) are documented in several genera. The distribution of the complex confirms that this part of the Paramunnidae is a Southern Hemisphere, shallow water group. Species previously thought to be circumpolar prove to be species complexes, with each species having a small distribution.
Partitioned Bremer support localises significant conflict in bee flies (Diptera : Bombyliidae : Anthracinae)
Authors: Lambkin Christine L.
Published: September 2004

Partitioned Bremer support examination of combined cladistic analyses indicates nodes at which the support from the partitions differs, and also identifies the location of character disagreement generated by the combination of data matrices. Significant character incongruence was found between mtDNA sequence data and adult morphological characters from three tribes of bee flies (Diptera : Bombyliidae : Anthracinae : Villini, Anthracini, Exoprosopini). Partitioned Bremer support quantitatively reveals the location of significant conflict between characters from the different partitions. Examination of several partitioned support measures show which characters contributed to the disagreement at that node. A very high value of increased support at another node occurred upon combination of the data partitions and was also examined using these support measures.