bluuebunny/crossref_metadata_2025 huggingface dataset:
CD4 expression on EL4 cells as an epiphenomenon of retroviral transduction and selection
Authors: Logan Grant J , Spinoulas Afroditi , Alexander Stephen I , Smythe Jason A , Alexander Ian E
Published: April 2004

The EL4 murine tumour cell line, isolated from a chemically induced lymphoma over 50 years ago, has been extensively exploited in immunological research. The conclusions drawn from many of these studies have been based on the presumption that EL4 cells maintain a stable phenotype during experimental manipulation. To the contrary, we have observed 100‐fold greater expression of cell surface CD4 (CD4high) on a subpopulation of EL4 cells following retroviral transduction and G418 selection when compared with unmodified populations. Although the mechanism responsible for this effect remains to be elucidated, the unexpected expression of CD4, a molecule that functions as both a coreceptor with the T‐cell receptor and ligand for the pro‐inflammatory cytokine IL‐16, has the potential to influence experimental outcomes. Upregulation of CD4 should be excluded when EL4 cells are utilized in experiments requiring a consistent immuno‐phenotype.
Type I interferon genes from the egg‐laying mammal, Tachyglossus aculeatus (short‐beaked echidna)
Authors: Harrison Gavan A , McNicol Kelly A , Deane Elizabeth M
Published: April 2004

The type I IFN are an important group of multifunctional cytokines that have, for whatever reason, evolved to a high level of complexity in eutherian mammals such as humans and mice. However, until recently, little was known about the type I IFN systems of the other two groups of extant mammals, the marsupials and the egg‐laying monotremes. Preliminary partial type I IFN sequences from the short‐beaked echidna were previously found to cluster only with the IFN‐β subtype in phylogenetic analyses, but a lack of sequence information made interpretation of these results tenuous. Here, we report cloning of the full‐length genes of representatives from the two previously defined groups of echidna type I IFN by genomic walking PCR. Along with analysis of conserved cysteine placement and promoter elements, phylogenetic analysis incorporating these sequences strongly suggest that the two groups of echidna type I IFN genes are in fact homologueous to IFN‐α and IFN‐β, confirming that the duplication leading to these two major classes of type I IFN occurred prior to the divergence of eutherians and monotremes some 180 million years ago. Thus, even though there are major differences in gene copy number and heterogeneity, separate IFN‐α and IFN‐β gene families are a feature of the cytokine networks of all three groups of living mammals.
Modification of mechanical properties of silicon nanocantilevers by self-ion implantation
Authors: Virwani Kumar R. , Malshe Ajay P. , Sood Dinesh K. , Elliman Robert G.
Published: April 2004

Nanoscale silicon beams (∼3 μm long, 250 nm wide, and 193 nm thick) were implanted with Si ions at energies of 100 and 35 keV and a dose of 1×1015 ions/cm2 and then tested using an atomic force microscope. The Young’s modulus of fully amorphous silicon nanostructures (thus formed at 100 keV) was measured to be 134.5 GPa, and the modulus of bimaterial silicon nanostructures (amorphous and single crystal formed at 35 keV energy) was measured to be 150.3 GPa. Thus, the fundamental mechanical properties of 3D silicon nanostructures can be controllably modified using ion implantation at nanometer scale. This has major implications for nanoelectromechanical systems and related devices.
A pulse sequence for directly measuring the anharmonicities of coupled vibrations: Two-quantum two-dimensional infrared spectroscopy
Authors: Fulmer Eric C. , Mukherjee Prabuddha , Krummel Amber T. , Zanni Martin T.
Published: April 2004

We have experimentally demonstrated a pulse sequence for the acquisition of heterodyned two-dimensional infrared (2D IR) spectra that correlates the overtone and combination bands to the fundamental frequencies. The spectra are generated by Fourier transforming the time domain signal that is allowed to evolve during one- and two-quantum coherence times. In this manner, the overtone and combination bands appear along the two-quantum axis, resulting in a direct determination of the diagonal and off-diagonal anharmonicities. To demonstrate this pulse sequence, we have collected two-quantum 2D IR spectra of a ruthenium dicarbonyl complex, extracted the diagonal and off-diagonal anharmonicities, and simulated the spectra using an exciton model. Several polarization conditions are presented that suppress the diagonal or cross peaks and we have used them to improve the accuracy of the measurement.
Dissociative photoionization of N2O in the region of the N2O+(B 2Π) state studied by ion–electron velocity vector correlation
Authors: Lebech M. , Houver J. C. , Dowek D. , Lucchese R. R.
Published: April 2004

Dissociative direct photoionization of the N2O(X 1Σ+) linear molecule via the N2O+(B 2Π) ionic state induced by linearly polarized synchrotron radiation P in the 18–22 eV photon energy range is investigated using the (VA+,Ve,P) vector correlation method, where VA+ is the nascent velocity vector of the NO+, N2+, or O+ ionic fragment and Ve that of the photoelectron. The DPI processes are identified by the ion–electron kinetic energy correlation, and the IχA+(θe,φe) molecular frame photoelectron angular distributions (MFPADs) are reported for the dominant reaction leading to NO+(X 1Σ+,v)+N(2D)+e. The measured MFPADs are found in satisfactory agreement with the reported multichannel Schwinger configuration interaction calculations, when bending of the N2O+(B 2Π) molecular ion prior to dissociation is taken into account. A significant evolution of the electron scattering anisotropies is observed, in particular in the azimuthal dependence of the MFPADs, characteristic of a photoionization transition between a neutral state of Σ symmetry and an ionic state of Π symmetry. This interpretation is supported by a simple model describing the photoionization transition by the coherent superposition of two sσ and dδ partial waves and the associated Coulomb phases.
Simplified crossover droplet model for adsorption of pure fluids in slit pores
Authors: Kiselev S. B. , Ely J. F.
Published: April 2004

We present a generalized crossover (GC) model for the excess adsorption of pure fluids at a flat solid–liquid interface, which reproduces scaling behavior of the excess adsorption in the critical region and is reduced to the classical, van der Waals-type analytical model far away from the bulk critical point. In developing this model, we used the density-functional theory (DFT) approach for the order parameter profile calculations with a generalized corresponding states model for the local free-energy density. The GC DFT model well represents the available experimental adsorption data for Kr/graphite, C2H4/graphite, C3H8/graphite, CO2/silica, and SF6/graphite systems in the entire density range 0<ρ⩽3ρc and temperatures up to 1.7Tc. In the critical region 0.5ρc<r⩽1.5ρc and T⩽1.15Tc, the GC DFT model is consistent with the predictions of the asymptotic renormalization-group crossover model for the critical adsorption in a semi-infinite system developed earlier. For the excess adsorption on the critical isochore, both theories predict a scaling-law behavior Γ∝τ−ν+β, but fail to reproduce a “critical depletion” of the excess adsorption along the critical isochore of the SF6/graphite system near Tc. We show that an anomalous decrease of adsorption observed in this system at τ=T/Tc−1<10−2 can be explained by finite-size effect and develop a simplified crossover droplet (SCD) model for the excess adsorption in a slit pore. With the effective size of the pore of L=50 nm, the SCD model reproduces all available experimental data for SF6/graphite, including the critical isochore data where τ→0, within experimental accuracy. At L≫ξb (where ξb is a bulk correlation length) the SCD model is transformed into the GC DFT model for semi-infinite systems. Application of the SCD model to the excess adsorption of carbon dioxide on the silica gel is also discussed.
Activated radiationless decay of rhodamine-3B: Nonequilibrium polarization effects in viscous solvents
Authors: Ferreira José A. B. , Costa Sı́lvia M. B.
Published: April 2004

Nonequilibrium polarization effects that arise in high viscous polar solvents are discussed as regards to the rhodamine-3B-activated radiationless process. Rate constants are interpreted using dipole isomerization theories which enable the recovery of a barrier top region wave number identical to that previously obtained in less viscous solvents [J. Phys Chem. A 104, 11909 (2000)]. The Onsager-frequency-dependent reaction field can model the friction effect on the rate constants that in glycerol were estimated also from an adiabatic charge-transfer model. The cusp barrier height is half the electronic coupling, as expected from the equality found for the frequencies of the reactant well and barrier top in this process. Coupling to solvent polarization modes can control the friction effect on the reactive mode. A two-dimensional reaction surface explains the photophysical features detected in the radiationless decay and a state energy diagram is proposed for rhodamine-3B.
Combined electronic structure/molecular dynamics approach for ultrafast infrared spectroscopy of dilute HOD in liquid H2O and D2O
Authors: Corcelli S. A. , Lawrence C. P. , Skinner J. L.
Published: April 2004

We present a new approach that combines electronic structure methods and molecular dynamics simulations to investigate the infrared spectroscopy of condensed phase systems. This approach is applied to the OH stretch band of dilute HOD in liquid D2O and the OD stretch band of dilute HOD in liquid H2O for two commonly employed models of water, TIP4P and SPC/E. Ab initio OH and OD anharmonic transition frequencies are calculated for 100 HOD⋅(D2O)n and HOD⋅(H2O)n (n=4–9) clusters randomly selected from liquid water simulations. A linear empirical relationship between the ab initio frequencies and the component of the electric field from the solvent along the bond of interest is developed. This relationship is used in a molecular dynamics simulation to compute frequency fluctuation time-correlation functions and infrared absorption line shapes. The normalized frequency fluctuation time-correlation functions are in good agreement with the results of previous theoretical approaches. Their long-time decay times are 0.5 ps for the TIP4P model and 0.9 ps for the SPC/E model, both of which appear to be somewhat too fast compared to recent experiments. The calculated line shapes are in good agreement with experiment, and improve upon the results of previous theoretical approaches. The methods presented are simple, and transferable to more complicated systems.
Mass transport following impulsive optical excitation
Authors: Wei Tai-Huei , Wang Chi-Chen , Wu Tzung-Tao , Chen Chen-Wei , Li Xin-Biao , Huang Tzer-Hsiang , Yang Sidney , Wei Tai-Ying
Published: April 2004

Transition from reverse-saturable absorption to saturable absorption of the chloroaluminum phthalocyanine solution excited by a giant laser pulse is ascribed not just to the saturation of excited state absorption, but also to the outward migration of the solute molecules at the laser beam center. While the saturation of excited state absorption occurs within a single picosecond laser pulse, the beam center population decrease is sustained much longer than the pulse duration. We distinguish these two mechanisms with the Z-scan technique, utilizing picosecond pulses with pulse-to-pulse separations ranging from 0.1 to 5.0 s.
Calculation of the transport properties of carbon dioxide. II. Thermal conductivity and thermomagnetic effects
Authors: Bock Steffen , Bich Eckard , Vogel Eckhard , Dickinson Alan S. , Vesovic Velisa
Published: April 2004

The transport properties of pure carbon dioxide have been calculated from the intermolecular potential using the classical trajectory method. Results are reported in the dilute-gas limit for thermal conductivity and thermomagnetic coefficients for temperatures ranging from 200 K to 1000 K. Three recent carbon dioxide potential energy hypersurfaces have been investigated. Since thermal conductivity is influenced by vibrational degrees of freedom, not included in the rigid-rotor classical trajectory calculation, a correction for vibration has also been employed. The calculations indicate that the second-order thermal conductivity corrections due to the angular momentum polarization (<2%) and velocity polarization (<1%) are both small. Thermal conductivity values calculated using the potential energy hypersurface by Bukowski et al. (1999) are in good agreement with the available experimental data. They underestimate the best experimental data at room temperature by 1% and in the range up to 470 K by 1%–3%, depending on the data source. Outside this range the calculated values, we believe, may be more reliable than the currently available experimental data. Our results are consistent with measurements of the thermomagnetic effect at 300 K only when the vibrational degrees of freedom are considered fully. This excellent agreement for these properties indicates that particularly the potential surface of Bukowski et al. provides a realistic description of the anisotropy of the surface.
Monomer basis-set truncation effects in calculations of interaction energies: A model study
Authors: Kaczmarek Anna , Sadlej Andrzej J. , Leszczynski Jerzy
Published: April 2004

Supermolecular interaction energies are analyzed in terms of the symmetry-adapted perturbation theory and operators defining the inaccuracy of the monomer wave functions. The basis set truncation effects are shown to be of first order in the monomer inaccuracy operators. On the contrary, the usual counterpoise correction schemes are of second order in these operators. Recognition of this difference is used to suggest an approach to corrections for basis-set truncation effects. Also earlier claims—that dimer-centered basis sets may lead to interaction energies free of basis-set superposition effects—are shown to be misleading. According to the present study the basis-set truncation contributions, evaluated by means of the symmetry-adapted perturbation theory with monomer-centered basis sets, provide physically and mathematically justified corrections to supermolecular results for interaction energies.
Body frames in the separation of collective angles in quantum N-body problems
Authors: Meremianin A. V.
Published: April 2004

The application of the concept of body-fixed reference frames, proposed by C. Eckart [Phys. Rev. 47, 552 (1935)], to the problem of the separation of three collective angles in quantum N-body problems is analyzed based on the technique recently developed by Meremianin and Briggs [Phys. Rep. 384, 121 (2003)]. Special attention is paid to the body frame defined by the “second Eckart condition” which minimizes vibro-rotational couplings near the equilibrium position. The important case of the Eckart frame for three-body systems is considered in detail. The connection of the basis vectors of the Eckart frame with Jacobi vectors is derived. All results of this work are valid for an arbitrary choice of internal (body-frame) coordinates.
Molecular dynamics simulations of transport and separation of carbon dioxide–alkane mixtures in carbon nanopores
Authors: Firouzi Mahnaz , Nezhad Kh. Molaai , Tsotsis Theodore T. , Sahimi Muhammad
Published: April 2004

The configurational-bias Monte Carlo method, which is used for efficient generation of molecular models of n–alkane chains, is combined for the first time with the dual control-volume grand-canonical molecular-dynamics simulation, which has been developed for studying transport of molecules in pores under an external potential gradient, to investigate transport and separation of binary mixtures of n–alkanes, as well as mixtures of CO2 and n–alkanes, in carbon nanopores. The effect of various factors, such as the temperature of the system, the composition of the mixture, and the pore size, on the separation of the mixtures is investigated. We also report the preliminary results of an experimental study of transport and separation of some of the same mixtures in a carbon molecular-sieve membrane with comparable pore sizes. The results indicate that, for the mixtures considered in this paper, even in very small carbon nanopores the energetic effects still play a dominant role in the transport and separation properties of the mixtures, whereas in a real membrane they are dominated by the membrane’s morphological characteristics. As a result, for the mixtures considered, a single pore may be a grossly inadequate model of a real membrane, and hence one must resort to three-dimensional molecular pore network models of the membrane.
Exploring the dynamics of hydrogen atom release from the radical–radical reaction of O(3P) with C3H5
Authors: Joo Sun-Kyu , Kwon Lee-Kyoung , Lee Hohjai , Choi Jong-Ho
Published: April 2004

The gas-phase radical–radical reaction dynamics of O(3P)+C3H5→H(2S)+C3H4O was studied at an average collision energy of 6.4 kcal/mol in a crossed beam configuration. The ground-state atomic oxygen [O(3P)] and allyl radicals (C3H5) were generated by the photolysis of NO2 and the supersonic flash pyrolysis of allyl iodide, respectively. Nascent hydrogen atom products were probed by the vacuum-ultraviolet–laser induced fluorescence spectroscopy in the Lyman-α region centered at 121.6 nm. With the aid of the CBS–QB3 level of ab initio theory, it has been found that the barrierless addition of O(3P) to C3H5 forms the energy-rich addition complexes on the lowest doublet potential energy surface, which are predicted to undergo a subsequent direct decomposition step leading to the reaction products H+C3H4O. The major counterpart C3H4O of the probed hydrogen atom is calculated to be acrolein after taking into account the factors of barrier height, reaction enthalpy, and the number of intermediates involved along the reaction pathway. The nascent H-atom Doppler profile analysis shows that the average center-of-mass translational energy of the H+C3H4O products and the fraction of the total available energy released as the translational energy were determined to be 3.83 kcal/mol and 0.054, respectively. On the basis of comparison with statistical calculations, the reaction proceeds through the formation of short-lived addition complexes rather than statistical, long-lived intermediates, and the polyatomic acrolein product is significantly internally excited at the moment of the decomposition.
Interelectronic angle densities of equivalent electrons in Hartree–Fock theory of atoms
Authors: Koga Toshikatsu , Matsuyama Hisashi
Published: April 2004

The interelectronic angle density A(θ12) is the probability density function that the angle θij (0⩽θij⩽π) subtended by the vectors ri and rj of any two electrons i and j becomes θ12. For equivalent electrons in atoms, it is shown that the density A(θ12) in the Hartree–Fock theory is given by a simple polynomial of cos θ12. Detailed expressions are reported for all LS terms arising from s2, pN (N=2–6), dN (N=2–10), and fN (N=2,12) electron configurations. With no modifications, the present results apply as well to the interelectronic angle density Ā(θ̄12) in momentum space, where θ̄12 is the angle between two electron momenta.
Quantum chemical density-functional theory calculations of the structures of defect C60 with four vacancies
Authors: Hang Hu Yun , Ruckenstein Eli
Published: April 2004

Quantum chemical density-functional theory (DFT) calculations have been carried out for the six isomers obtained by removing four adjacent atoms from C60. The most stable isomer consists of twelve 5-member and eighteen 6-member rings, indicating that the removal of some atoms from C60, which contains twelve 5-member rings and twenty 6-member rings, does not always generate larger holes. Each of the other five isomers contains at least one 4-member ring and one larger ring (7-, 8-, 9-, or 10-member ring) besides the 5- and 6-member rings. All isomers have similar structures for singlet and triplet spin multiplicities but with different stabilities. The ground states for two of the isomers are triplets, whereas the ground states for the other isomers are singlets. Furthermore, a comparison between the various isomers allowed one to examine the effect of the structure on the stability of fullerene cages.
Thermodynamics of β-amyloid fibril formation
Authors: Tiana G. , Simona F. , Broglia R. A. , Colombo G.
Published: April 2004

Amyloid fibers are aggregates of proteins. They are built out of a peptide called β-amyloid (Aβ) containing between 41 and 43 residues, produced by the action of an enzyme which cleaves a much larger protein known as the amyloid precursor protein (APP). X-ray diffraction experiments have shown that these fibrils are rich in β-structures, whereas the shape of the peptide displays an α-helix structure within the APP in its biologically active conformation. A realistic model of fibril formation is developed based on the 17 residues Aβ12-28 amyloid peptide, which has been shown to form fibrils structurally similar to those of the whole Aβ peptide. With the help of physical arguments and in keeping with experimental findings, the Aβ12-28 monomer is assumed to be in four possible states (i.e., native helix conformation, β-hairpin, globular low-energy state, and unfolded state). Making use of these monomeric states, oligomers (dimers, tertramers, and octamers) were constructed. With the help of short, detailed molecular dynamics calculations of the three monomers and of a variety of oligomers, energies for these structures were obtained. Making use of these results within the framework of a simple yet realistic model to describe the entropic terms associated with the variety of amyloid conformations, a phase diagram can be calculated of the whole many-body system, leading to a thermodynamical picture in overall agreement with the experimental findings. In particular, the existence of micellar metastable states seem to be a key issue to determine the thermodynamical properties of the system.
Jamming concepts in cold polymeric glasses
Authors: Koga Tsuyoshi , Edwards Sam F.
Published: April 2004

The purpose of the present paper is to propose an idea to construct the volume function W for polymer glasses and calculate the volume of polymer glasses as a function of the compactivity X utilizing a statistical-mechanical method developed for semiflexible polymers. We also discuss the analogue for glasses of “tapping” experiments which show the validity of statistical mechanics and the entropy concept in powders.
A finite-size scaling study of a model of globular proteins
Authors: Pagan D. L. , Gracheva M. E. , Gunton J. D.
Published: April 2004

Grand canonical Monte Carlo simulations are used to explore the metastable fluid–fluid coexistence curve of the modified Lennard-Jones model of globular proteins of ten Wolde and Frenkel [Science, 277, 1975 (1997)]. Using both mixed-field finite-size scaling and histogram-reweighting methods, the joint distribution of density and energy fluctuations is analyzed at coexistence to accurately determine the critical-point parameters. The subcritical coexistence region is explored using the recently developed hyper parallel tempering Monte Carlo simulation method along with histogram reweighting to obtain the density distributions. The phase diagram for the metastable fluid–fluid coexistence curve is calculated in close proximity to the critical point, a region previously unattained by simulations.
Atomic hydrogen interaction with Ru(101̄0)
Authors: Vesselli E. , Comelli G. , Rosei R.
Published: April 2004

The interaction of atomic hydrogen with clean and deuterium precovered Ru(101̄0) was studied by means of temperature-programmed desorption (TPD) spectroscopy. Compared to molecular hydrogen experiments, after exposure of the clean surface to gas-phase atomic hydrogen at 90 K, two additional peaks grow in the desorption spectra at 115 and 150 K. The surface saturation coverage, determined by equilibrium between abstraction and adsorption reactions, is 2.5 monolayers. Preadsorbed deuterium abstraction experiments with gas-phase atomic hydrogen show that a pure Eley–Rideal mechanism is not involved in the process, while a hot atom (HA) kinetics describes well the reaction. By least-squares fitting of the experimental data, a simplified HA kinetic model yields an abstraction cross section value of 0.5±0.2 Å2. The atomic hydrogen interaction with an oxygen precovered surface was also studied by means of both TPD and x-ray photoelectron spectroscopy: oxygen hydrogenation and water production take place already at very low temperature (90 K).
Characterization of the molecular parameters determining charge transport in anthradithiophene
Authors: Kwon O. , Coropceanu V. , Gruhn N. E. , Durivage J. C. , Laquindanum J. G. , Katz H. E. , Cornil J. , Brédas J. L.
Published: April 2004

The molecular parameters that govern charge transport in anthradithiophene (ADT) are studied by a joint experimental/theoretical approach involving high-resolution gas-phase photoelectron spectroscopy and quantum-mechanical methods. The hole reorganization energy of ADT has been determined by an analysis of the vibrational structure of the lowest ionization band in the gas-phase photoelectron spectrum as well as by density-functional theory calculations. In addition, various dimers and clusters of ADT molecules have been considered in order to understand the effect of molecular packing on the hole and electron intermolecular transfer integrals. The results indicate that the intrinsic electronic structure, the relevant intramolecular vibrational modes, and the intermolecular interactions in ADT are very similar to those in pentacene.
Signatures of β-sheet secondary structures in linear and two-dimensional infrared spectroscopy
Authors: Cheatum Christopher M. , Tokmakoff Andrei , Knoester Jasper
Published: April 2004

Using idealized models for parallel and antiparallel β sheets, we calculate the linear and two-dimensional infrared spectra of the amide I vibration as a function of size and secondary structure. The model assumes transition–dipole coupling between the amide I oscillators in the sheet and accounts for the anharmonic nature of these oscillators. Using analytical and numerical methods, we show that the nature of the one-quantum vibrational eigenstates, which govern the linear spectrum, is, to a large extent, determined by the symmetry of the system and the relative magnitude of interstrand interactions. We also find that the eigenstates, in particular their trends with system size, depend sensitively on the secondary structure of the sheet. While in practice these differences may be difficult to distinguish in congested linear spectra, we demonstrate that they give rise to promising markers for secondary structure in the two-dimensional spectra. In particular, distinct differences occur between the spectra of parallel and antiparallel β sheets and between β hairpins and extended β sheets.
Pattern formation in excitable media with concentration-dependent diffusivities
Authors: Roussel Marc R. , Wang Jichang
Published: April 2004

We study a model of pattern formation in an excitable medium with concentration-dependent diffusivities. The reaction terms correspond to a two-variable Gray–Scott model in which the system has only one stable steady state. The diffusion coefficients of the two species are assumed to have a functional relationship with the concentration of the autocatalyst. A transition from self-replicating behavior to stationary spots is observed as the influence of the local autocatalyst concentration on the diffusion process increases. Notably, the transition occurs even though there is no change in the relative diffusivities of the activator and inhibitor. The observed time-independent patterns exhibit an unusual dependence on the size and geometry of an initial perturbation. Initial perturbations with a large spatial size, for example, sometimes revert to the homogeneous equilibrium state, whereas perturbations of smaller spatial extent develop into stable spots at the same parameter values.
Collective dynamics in molten potassium: An inelastic x-ray scattering study
Authors: Monaco A. , Scopigno T. , Benassi P. , Giugni A. , Monaco G. , Nardone M. , Ruocco G. , Sampoli M.
Published: April 2004

The high-frequency collective dynamics of molten potassium has been investigated by inelastic x-ray scattering, disclosing an energy/momentum transfer region unreachable by previous inelastic neutron scattering (INS) experiments. We find that a two-step relaxation scenario, similar to that found in other liquid metals, applies to liquid potassium. In particular, we show how the sound velocity determined by INS experiments, exceeding the hydrodynamic value by ≈30%, is the higher limit of a speedup, located in the momentum region 1<Q<3 nm−1, which marks the departure from the isothermal value. We point out how this phenomenology is the consequence of a microscopic relaxation process that, in turn, can be traced back to the presence of “instantaneous” disorder, rather than to the crossover from a liquid to solidlike response.
Folding of small proteins using a single continuous potential
Authors: Kim Seung-Yeon , Lee Julian , Lee Jooyoung
Published: April 2004

Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single continuous potential (united-residue force field). In all cases, collapse occurs at a very early stage, and proteins fold into their nativelike conformations at appropriate temperatures. We also observe that glassy transitions occur at low temperatures. The simulation results demonstrate that the folding mechanism is controlled not only by thermodynamic factors but also by kinetic factors: The way a protein folds into its native structure is also determined by the convergence point of early folding trajectories, which cannot be obtained by the free energy surface.
Amplification of chirality in helical supramolecular polymers beyond the long-chain limit
Authors: Gestel Jeroen van , van der Schoot Paul , Michels M. A. J.
Published: April 2004

The optical activity of helical homopolymers devoid of chiral centers increases drastically when a small amount of homochiral monomers is incorporated into them. We study this so-called sergeants-and-soldiers effect of chirality amplification in solutions of helical supramolecular polymers with a theoretical model that bears a strong resemblance to a one-dimensional, two-component Ising model. In the limit of very long self-assembled helical polymers, the strength of the sergeants-and-soldiers effect depends strongly on the free energy of a helix reversal and less so on the concentration of aggregating material. Outside the long-chain limit, we find the reverse—that is, a strong concentration dependence and a weak dependence on the helix-reversal energy. Our treatment gives an excellent agreement with recently published circular-dichroism measurements on mixed aggregates of discotic molecules in the solvents water and n-butanol, at two different overall concentrations.
Ground and excited states of NH4: Electron propagator and quantum defect analysis
Authors: Ortiz J. V. , Martı́n I. , Velasco A. M. , Lavı́n C.
Published: April 2004

Vertical excitation energies of the Rydberg radical NH4 are inferred from ab initio electron propagator calculations on the electron affinities of NH4+. The adiabatic ionization energy of NH4 is evaluated with coupled-cluster calculations. These predictions provide optimal parameters for the molecular-adapted quantum defect orbital method, which is used to determine Einstein emission coefficients and radiative lifetimes. Comparisons with spectroscopic data and previous calculations are discussed.
Products of the addition of water molecules to Al3O3− clusters:  Structure, bonding, and electron binding energies in Al3O4H2−, Al3O5H4−, Al3O4H2, and Al3O5H4
Authors: Tenorio Francisco J. , Murray Ian , Martı́nez Ana , Klabunde Kenneth J. , Ortiz J. V.
Published: April 2004

Two stable products of reactions of water molecules with the Al3O3− cluster, Al3O4H2− and Al3O5H4−, are studied with electronic structure calculations. There are several minima with similar energies for both anions and the corresponding molecules. Dissociative absorption of a water molecule to produce an anionic cluster with hydroxide ions is thermodynamically favored over the formation of Al3O3−(H2O)n complexes. Vertical electron detachment energies of Al3O4H2− and Al3O5H4− calculated with ab initio electron propagator methods provide a quantitative interpretation of recent anion photoelectron spectra. Contrasts and similarities in these spectra may be explained in terms of the Dyson orbitals associated with each transition energy.
Fictive temperature, cooling rate, and viscosity of glasses
Authors: Yue Yuanzheng , von der Ohe Renate , Jensen Søren Lund
Published: April 2004

The physical correlation between the fictive temperature dependence of the cooling rate of the melts and the temperature dependence of the equilibrium viscosity has been found by doing differential scanning calorimetric and viscometric measurements on a silicate melt, and by performing finite element simulations of the fiber drawing from that melt. This correlation is governed by a correlation factor Kc (in Pa K) which is constant and universal for silicate glasses. The factor Kc is obtained in the cooling rate range from 10−2 to 106 K/s and is in good agreement with that theoretically predicted. The physical feature of the correlation is discussed in the paper. When the fictive temperature equals the actual temperature, a linear relation exists between the cooling rate and the Maxwell relaxation rate, the slope of which depends on the fragility of the glass melts. The Avramov equation is extended to describe the cooling rate dependence of the fictive temperature. The cooling rate equation contains only one adjusting parameter, i.e., the fragility parameter α.
Electron momentum spectroscopy of CF2Cl2: Experimental and theoretical momentum profiles for outer valence orbitals
Authors: Chen XiangJun , Zhou LiXia , Zhang XuHuai , Yin XiaoFeng , Xu ChunKai , Shan Xu , Wei Zheng , Xu KeZun
Published: April 2004

Electron momentum distributions for outer valence orbitals of CF2Cl2 have been obtained by (e,2e) electron momentum spectroscopy at an incident energy of 1200 eV+binding energy. The experimental electron momentum profiles are compared with Hartree–Fock and density functional theory (DFT) calculations using B3LYP hybrid functional with the 6-31G and 6-311+G* basis sets. Generally, the shapes of the experimental momentum profiles are well reproduced by DFT calculations using larger basis sets 6-311+G*. An attempt has been made to clarify the ordering of the outer valence orbitals, which have been in controversy, by comparing experimental results with B3LYP/6-311+G* calculations.
Complete basis set extrapolated potential energy, dipole, and polarizability surfaces of alkali halide ion-neutral weakly avoided crossings with and without applied electric fields
Authors: Giese Timothy J. , York Darrin M.
Published: April 2004

Complete basis set extrapolations of alkali halide (LiF, LiCl, NaF, NaCl) energy, dipole, and polarizability surfaces are performed with and without applied fields along the internuclear axis using state-averaged multireference configuration interaction. Comparison between properties (equilibrium separation, dissociation energy, crossing distance, diabatic coupling constant, dipole, and polarizability) derived from the extrapolated potential energy (or dipole) surfaces are made with those obtained from direct extrapolation from the basis set trends. The two extrapolation procedures are generally found to agree well for these systems. Crossing distances from this work are compared to those of previous work and values obtained from the Rittner potential. Complete basis set extrapolated crossing distances agree well with those derived from the Rittner potential for LiF, but were significantly larger for LiCl, NaF, and NaCl. The results presented here serve as an important set of benchmark data for the development of new-generation many-body force fields that are able to model charge transfer.
Formation of doubly positively charged diatomic ions of Mo22+ produced by Ar+ sputtering of an Mo metal surface
Authors: Franzreb Klaus , Sobers Richard C. , Lörinčı́k Jan , Williams Peter
Published: April 2004

Long-lived metastable doubly positively charged diatomic ions of Mo22+ have been produced by Ar+ bombardment of a molybdenum metal surface. These exotic molecular dications, such as for example O1(D1)+CO2Δ3M92,95o22+ at m/z 93.5, could be observed in positive ion mass spectra for ion flight times of ∼17 μs in a Cameca IMS-3f secondary ion mass spectrometer, when the ion extraction field was adjusted for detection of ions that are formed in the gas phase several micrometers in front of the sputtered surface. Mo22+ was observed at high primary current densities for projectile ions of Ar+, but could not be detected under very similar bombarding conditions for projectile ions of Xe+. Such a dependence of ion production by inert gas sputtering on the primary ion species [ionization energies: IP1(Ar)=15.76 eV and IP1(Xe)=12.13 eV] is unusual. It is shown that formation of Mo22+ dications takes place by resonant charge transfer in grazing gas-phase collisions between incoming projectile ions of Ar+ and sputtered molecular ions of Mo2+. The efficiency for such a resonant electron capture (Mo2++Ar+→Mo22++Ar) is of the order of 10−5 for the bombarding conditions in our mass spectrometer and corresponds to a cross section of a few 10−15 cm2.
Different adsorption structures of pyridine on Si(001) and Ge(001) surfaces
Authors: Kim Hyung-Jin , Cho Jun-Hyung
Published: April 2004

The adsorption and reaction of pyridine on the Si(001) and Ge(001) surfaces are investigated by first-principles density-functional calculations within the generalized gradient approximation. On both surfaces the N atom of pyridine initially reacts with the down atom of the dimer, forming a single bond between the N atom and the down atom. On Ge(001) such an adsorption configuration is most favorable, but on Si(001) a further reaction with a neighboring dimer occurs, resulting in formation of a bridge-type configuration. Especially we find that on Ge(001) the bridge-type configuration is less stable than the gas phase. Our results provide an explanation for a subtle difference in the adsorption structures of pyridine on Si(001) and Ge(001), which was observed from recent scanning tunneling microscopy experiments.
Dynamics of caged ions in glassy ionic conductors
Authors: Habasaki J. , Ngai K. L. , Hiwatari Y.
Published: April 2004

At sufficiently high frequency and low temperature, the dielectric responses of glassy, crystalline, and molten ionic conductors all invariably exhibit nearly constant loss. This ubiquitous characteristic occurs in the short-time regime when the ions are still caged, indicating that it could be a determining factor of the mobility of the ions in conduction at longer times. An improved understanding of its origin should benefit the research of ion conducting materials for portable energy source as well as the resolution of the fundamental problem of the dynamics of ions. We perform molecular dynamics simulations of glassy lithium metasilicate (Li2SiO3) and find that the length scales of the caged Li+ ions motions are distributed according to a Lévy distribution that has a long tail. These results suggest that the nearly constant loss originates from “dynamic anharmonicity” experienced by the moving but caged Li+ ions and provided by the surrounding matrix atoms executing correlated movements. The results pave the way for rigorous treatments of caged ion dynamics by nonlinear Hamiltonian dynamics.
Comparison of kinetic Monte Carlo and molecular dynamics simulations of diffusion in a model glass former
Authors: Middleton Thomas F. , Wales David J.
Published: April 2004

We present results from kinetic Monte Carlo (KMC) simulations of diffusion in a model glass former. We find that the diffusion constants obtained from KMC simulations have Arrhenius temperature dependence, while the correct behavior, obtained from molecular dynamics simulations, can be super-Arrhenius. We conclude that the discrepancy is due to undersampling of higher-lying local minima in the KMC runs. We suggest that the relevant connectivity of minima on the potential energy surface is proportional to the energy density of the local minima, which determines the “inherent structure entropy.” The changing connectivity with potential energy may produce a correlation between dynamics and thermodynamics.
Kinetics of Ca2+ complexation with some carbohydrates in aqueous solutions
Authors: Baucke E. , Behrends R. , Fuchs K. , Hagen R. , Kaatze U.
Published: April 2004

For solutions of four saccharides in water with alkaline-earth chlorides added ultrasonic attenuation spectra between 100 kHz and 2 GHz are reported and compared to those for carbohydrate solutions without salt. Calcium chloride does not alter the relaxation times in the spectra of D-glucose and D(+)-maltose solutions, reflecting the exocyclic hydroxymethyl group rotation, a saccharide–saccharide association, and, with the disaccharide, also motions of both rings of a molecule relative to one another. The spectra of D-xylose and D-fructose solutions are substantially changed by the salts. With both saccharides an additional term with relaxation time around some nanoseconds exists which is assigned to a rearrangement of a carbohydrate–cation complex. Other relaxation terms of these saccharide solutions are also subject to noticeable changes by the salt, indicating specific carbohydrate–cation interactions. The ultrasonic spectra show that such interactions may exist also with carbohydrates which do not display the particular hydroxyl group sequences that are considered to promote complexation with cations.
Mesoscopic model for diffusion-influenced reaction dynamics
Authors: Tucci Kay , Kapral Raymond
Published: April 2004

A hybrid mesoscopic multiparticle collision model is used to study diffusion-influenced reaction kinetics. The mesoscopic particle dynamics conserves mass, momentum, and energy so that hydrodynamic effects are fully taken into account. Reactive and nonreactive interactions with catalytic solute particles are described by full molecular dynamics. Results are presented for large-scale, three-dimensional simulations to study the influence of diffusion on the rate constants of the A+C⇌B+C reaction. In the limit of a dilute solution of catalytic C particles, the simulation results are compared with diffusion equation approaches for both the irreversible and reversible reaction cases. Simulation results for systems where the volume fraction φ of catalytic spheres is high are also presented, and collective interactions among reactions on catalytic spheres that introduce volume fraction dependence in the rate constants are studied.
Equation of state and structural changes in diaminodinitroethylene under compression
Authors: Peiris Suhithi M. , Wong Chak P. , Zerilli Frank J.
Published: April 2004

Structural changes in 1,1-diamino-2,2-dinitroethylene (DADNE, FOX-7) compressed to high pressure in diamond anvil cells were investigated using angle-dispersive x-ray diffraction analysis, Raman spectroscopy, and optical polarizing microscopy. The x-ray results show several changes above 1 GPa. When the x-ray data are indexed according to the ambient-pressure structure, DADNE shows anisotropic compression, with higher compression along the b axis than along the a or c axis. An ambient-temperature isothermal equation of state of DADNE was generated from these data. In addition, the experimentally obtained Raman spectra were matched with vibrational normal modes calculated using quantum chemistry calculations. The shifts in vibrational modes indicate changes in H-wagging vibrations with pressure.
A computational strategy for geometry optimization of ionic and covalent excited states, applied to butadiene and hexatriene
Authors: Boggio-Pasqua Martial , Bearpark Michael J. , Klene Michael , Robb Michael A.
Published: April 2004

We propose a computational strategy that enables ionic and covalent ππ* excited states to be described in a balanced way. This strategy depends upon (1) the restricted active space self-consistent field method, in which the dynamic correlation between core σ and valence π electrons can be described by adding single σ excitations to all π configurations and (2) the use of a new conventional one-electron basis set specifically designed for the description of valence ionic states. Together, these provide excitation energies comparable with more accurate and expensive ab initio methods—e.g., multiconfigurational second-order perturbation theory and multireference configuration interaction. Moreover, our strategy also allows full optimization of excited-state geometries—including conical intersections between ionic and covalent excited states—to be routinely carried out, thanks to the availability of analytical energy gradients. The prototype systems studied are the cis and trans isomers of butadiene and hexatriene, for which the ground 1A1/g, lower-lying dark (i.e., symmetry forbidden covalent) 2A1/g and spectroscopic 1B2/u (valence ionic) states were investigated.
Theoretical prediction of electronic structures of fully π-conjugated zinc oligoporphyrins with curved surface structures
Authors: Yamaguchi Yoichi
Published: April 2004

A theoretical prediction of the electronic structures of fully π-conjugated zinc oligoporphyrins with curved surface, ring, tube, and ball-shaped structures was conducted as the objective for the future development of triply meso–meso-, β–β-, and β–β-linked planar zinc oligoporphyrins. The excitation energies and oscillator strengths for the optimal ring and ball structures were calculated using the time-dependent density functional theory (DFT). Although there is an extremely small energy difference of <0.1 eV between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of the ring structure relative to the same-sized triply linked planar one, the Q and B bands of the former are smaller redshifted excitation energies and intensified oscillator strengths than those of the latter due to the structurally shortened effective π-conjugated lengths for the electron transition. It is expected that the ball structure becomes an excellent electron acceptor and shows the highly redshifted Q′ band in the near-IR region relative to the monomer. The minimum value of the HOMO–LUMO energy gaps of the infinite-length ring structures was estimated using periodic boundary conditions within the DFT, resulting in the metallic characters of both the tube structures with and without the spiral triply linked porphyrin array. The relation between the diameters and strain energies of the tube and ball structures was also examined. The present fused zinc porphyrins may become more colorful materials with new optelectronic properties including artificial photosynthesis than the carbon nanotubes and fullerenes when the axial coordinations of the central metal of porphyrins are functionally used.
Two- and three-body photodissociation of gas phase I3−
Authors: Hoops Alexandra A. , Gascooke Jason R. , Faulhaber Ann Elise , Kautzman Kathryn E. , Neumark Daniel M.
Published: April 2004

The photodissociation dynamics of I3− from 390 to 290 nm (3.18 to 4.28 eV) have been investigated using fast beam photofragment translational spectroscopy in which the products are detected and analyzed with coincidence imaging. At photon energies ⩽3.87 eV, two-body dissociation that generates I−+I2(A 3Π1u) and vibrationally excited I2−(X 2Σu+)+I(2P3/2) is observed, while at energies ⩾3.87 eV, I*(2P1/2)+I2−(X 2Σu+) is the primary two-body dissociation channel. In addition, three-body dissociation yielding I−+2I(2P3/2) photofragments is seen throughout the energy range probed; this is the dominant channel at all but the lowest photon energy. Analysis of the three-body dissociation events indicates that this channel results primarily from a synchronous concerted decay mechanism.