bluuebunny/crossref_metadata_2025 huggingface dataset:
Geometry optimization in quantum Monte Carlo with solution mapping: Application to formaldehyde
Authors: Schuetz C. A. , Frenklach M. , Kollias A. C. , Lester W. A.
Published: October 2003

The solution mapping methodology is presented as a method of geometry optimization of molecules in the quantum Monte Carlo method. Applied to formaldehyde as a test system, this approach is found to yield optimized bond lengths and bond angle in the diffusion Monte Carlo method that lie within experimental error. The variational Monte Carlo optimized geometry also lies within experimental error, with the exception of the CH bond length, which is slightly underestimated. Additionally, the resulting quadratic representation of the potential energy surface in the region of the minimum is used to calculate three of the force constants and harmonic frequencies.
Homogeneous nucleation in inhomogeneous media. I. Nucleation in a temperature gradient
Authors: Reguera David , Rubı́ J. M.
Published: October 2003

We introduce a general formalism to analyze nucleation phenomena in inhomogeneous media which considers the influence of the metastable phase, which is treated as a heat bath in which clusters are embedded, in the dynamics of the nucleation process. A kinetic equation for the evolution of the probability density of the clusters, taking into account possible inhomogeneities in the bath, is derived using mesoscopic nonequilibrium thermodynamics. From it, we obtain the nucleation rate and analyze the role played by the metastable phase in the process. We discuss in particular condensation and polymer crystallization in a temperature gradient.
Mercury vapor detection with a self-sensing, resonating piezoelectric cantilever
Authors: Rogers B. , Manning L. , Jones M. , Sulchek T. , Murray K. , Beneschott B. , Adams J. D. , Hu Z. , Thundat T. , Cavazos H. , Minne S. C.
Published: October 2003

A microcantilever with an integrated piezoelectric film is demonstrated as a mercury vapor detector. The cantilever is self-sensing and self-actuating, and therefore does not need alignment of an external, optical detection system. This gives the new sensor system an advantage in array applications. Mercury vapor, when adsorbed onto gold on the cantilever, causes the stiffness, and therefore the natural frequency, of the cantilever to increase as a result of mercury gold amalgamation. This shift is detected using the piezoelectric portion of the cantilever in conjunction with a bridge circuit and amplifier. A mercury concentration of 93 ppb in nitrogen is detected.
Stable kilohertz rate molecular beam laser ablation sources
Authors: Smits Marc , de Lange C. A. , Ullrich Susanne , Schultz T. , Schmitt M. , Underwood Jonathan G. , Shaffer James P. , Rayner D. M. , Stolow Albert
Published: October 2003

We describe a stable kHz rate laser ablation/desorption supersonic molecular beam source for use in kHz rate laser experiments. With the development of modern lasers that typically operate at kHz rates, a need has arisen for stable molecular beam laser ablation/desorption sources for the study of involatile species. Many biomolecules of interest cannot be brought into the gas phase without thermal decomposition by simply heating the substrate and most (especially refractory) metals have melting and boiling points that are impossible to reach with conventional ovens. The source is based upon strong nonresonant interaction of a dithering laser focus with a rotating and translating solid rod, hydrodynamic transport of the ablated/desorbed material in helium or argon, and subsequent supersonic expansion. Further design details include flexible and easy adjustment of the source for rapid prototyping and optimization for kHz rate performance. Due to the high rate of sample removal, a major concern is clogging of the nozzle and laser input channel due to both material condensation and debris formation. In order to illustrate the range of applications, we demonstrate (1) the kHz laser ablation of a high temperature refractory metal (niobium) for use in studies of metal clusters; and (2) the kHz laser desorption and jet cooling of an involatile biomolecule (the DNA base guanine) for use in spectroscopic and dynamical studies. This kHz source design has been shown to be stable for over 12 continuous hours of operation (>4×107 laser shots) and can be readily scaled to even higher repetition rates (>10 kHz).
Theoretical study of the structure of lithium clusters
Authors: Fournier René , Bo Yi Cheng Joey , Wong Anna
Published: October 2003

Lithium clusters Lin (n=5 to 20) were studied by Kohn–Sham theory with local spin density and gradient-corrected energy functionals. We used a Tabu Search algorithm for structure optimization. The lowest energy Lin isomers that we found fall in two categories: (i) the pentagonal bipyramid, icosahedron, and related structures which are typical of most pair potentials, and (ii) structures containing centered square antiprisms which are reminiscent of the bulk bcc structure and have two characteristic peaks in the pair distribution function, one near 2.60 Å and the other near 3.05 Å. Calculated isomer energies and vibrational frequencies suggest that, at room temperature, many cluster sizes should show liquidlike behavior or coexistence of multiple isomers. The number of unpaired electrons “M” as a function of cluster size “n” generally alternates between 0 (singlet) and 1 (doublet), but some cluster sizes display anomalous spin magnetic moments M(n); they are M(13)=5, M(16)=2, M(17)=3, and M(18)=2. The Li7, Li8, Li19, and Li20 clusters are particularly stable: they each have a very compact structure and a shape consistent with the ellipsoidal jellium model.
Influence of the aliphatic chain on the (hydrogen-bonded) p-aminobenzonitrile complexes with methanol and ethanol
Authors: Alejandro Estela , Landajo Carlos , Longarte Asier , Fernández José A. , Castaño Fernando
Published: October 2003

The 4-aminobenzonitrile (ABN) molecule has two active sites amenable to hydrogen bonding to methanol (MeOH) and ethanol (EtOH): the amino, –NH2, and the cyano, –CN, groups. Two-color resonance enhanced multiphoton ionization time-of-flight mass spectroscopy and hole burning spectroscopy in addition to the ionization energies provides sound evidence of the occurrence of two isomers in the ABN(MeOH)1 complex and one single isomer for the ABN(EtOH)1 complex. Combining the outcomes from the ABN/methanol and ABN/ethanol experiments with ab initio computations at reliable theory levels one identifies the preferred solvation sites and the optimized geometries. A discussion of the role of the aliphatic chains on the geometry of the isomers and other properties is presented.
CO 2 desorption dynamics on specified sites and surface phase transitions of Pt(110) in steady-state CO oxidation
Authors: Rzeźnicka Izabela , Goula Moula Md. , Morales de la Garza Leonard , Ohno Yuichi , Matsushima Tatsuo
Published: October 2003

The spatial and velocity distributions of desorbing product CO2 were studied in the steady-state CO oxidation on Pt(110) by cross-correlation time-of-flight techniques. The surface structure transformation was monitored by LEED in the course of the catalyzed reaction. In the active region, where the surface was highly reconstructed into the missing-row form, CO2 desorption split into two directional lobes collimated along 25° from the surface normal in the plane including the [001] direction, indicating the CO2 formation on inclined (111) terraces. The translational temperature was maximized at the collimation angle, reaching about 1900 K. On the other hand, CO2 desorption sharply collimated along the surface normal at CO pressures where (1×2) domains disappeared. The distribution change from an inclined desorption to a normally directed one was abrupt at the CO pressure where the half-order LEED spot already disappeared. This switching point was more sensitive than LEED towards the complete transformation from (1×2) to (1×1) and was then used to construct a surface phase diagram for working reaction sites in the pressure range from 1×10−7 Torr to 1×10−4 Torr of oxygen. The turnover frequency of CO2 formation was enhanced on (1×2) domains with increasing CO pressure.
Ordered binary monolayer composed of two organic molecules: Copper-phthalocyanine and 3,4,9,10-perylene-tetra-carboxylic-dianhydride on Cu(111)
Authors: Bobisch C. , Wagner Th. , Bannani A. , Möller R.
Published: October 2003

The two planar organic molecules copper-phthalocyanine (CuPc) and 3,4,9,10-perylene-tetracarboxylic-dianhydride (PTCDA) are found to form an ordered mixed monolayer on Cu(111). The layers have been prepared by exposing the surface to an equivalent of a little bit more than half of a monolayer of CuPc and the same amount of PTCDA followed by thermal annealing. The investigations by scanning tunneling microscopy reveal regular patterns with a commensurate unit cell which contains one CuPc and two PTCDA molecules.
Molecular-dynamics simulation of forces between nanoparticles in a Lennard-Jones liquid
Authors: Qin Yong , Fichthorn Kristen A.
Published: October 2003

Molecular-dynamics simulations are utilized to simulate solvation and van der Waals forces between two nanoparticles immersed in a Lennard-Jones liquid. Three different sizes and shapes of nanoparticles with solvophilic and solvophobic properties are investigated. We compare different methods for calculating van der Waals forces. For solvophilic nanoparticles, the solvation forces oscillate between attraction and repulsion as the particle separation is increased. Solvophilic solvation forces are comparable to or stronger than van der Waals forces. In the solvophobic case, solvation forces are attractive. We find that surface roughness can significantly affect the solvation-force profile for solvophilic nanoparticles. Our results indicate that surface roughness can alter the balance between solvation and van der Waals forces in a solvophilic colloidal suspension and that a desirable force balance can be achieved by choosing nanoparticles with certain textures and/or shapes.
Criteria for formation of metallic glasses: The role of atomic size ratio
Authors: Lee Hyon-Jee , Cagin Tahir , Johnson William L. , Goddard William A.
Published: October 2003

We consider metallic alloys of Cu*, Cu, and Cu** in which the atoms differ only in their atomic radii and examine how the size ratio affects the local orders in the alloy systems. These studies use molecular dynamics simulations in which the atomic interactions are modeled with a Sutton–Chen many-body potential. Considering rapid cooling of these binary and ternary alloys from the melt, we find three regimes defined by the magnitude of atomic size ratio λ (λ⩽1.0): with (i) large size ratios of 0.95<λ⩽1.0, crystallization occurs; (ii) with moderate size ratios of 0.60⩽λ⩽0.95, a glass phase forms; and (iii) with small size ratios of λ<0.60, the alloy phase separates into pure phases and crystallize. From analyzing the structures of these binary and ternary alloys, we find that the liquid phase is characterized by local structures in which bonded atoms have local fivefold symmetry, which becomes more prominent as the glass phase forms. For phases that crystallize this local fivefold symmetry disappears as the long-range order of the crystalline phase dominates. The fivefold symmetry in the glass phase is mainly due to the icosahedral cluster formation. Energetically, the formation of icosahedral cluster is favored at the atomic size ratio of λ∼0.85, which is close to the λ at which our analyses shows the maximum in the fivefold symmetry and the number of icosahedral clusters. As λ decreases further, the phase separation is observed. The fivefold symmetry character and the number of icosahedral cluster shows the local minimum at this onset of the phase separation.
A closed reduced description of the kinetics of phase transformation in a lattice system based on Glauber’s master equation
Authors: Berim Gersh O. , Ruckenstein Eli
Published: October 2003

A generalized kinetic Ising model is applied to the description of phase transformations in lattice systems. A procedure, based on the conjecture that the probability distribution function of the states of the system is similar to the equilibrium one, is used for closing the infinite chain of kinetic equations. The method is illustrated by treating as an example the one-dimensional Ising model. The predicted rate of phase transformation (RPT) demonstrates various time behaviors dependent upon the details of the interactions between spins and a heat bath. If the parameters W0 and W the reciprocals of which characterize, respectively, the time scales of growth (decay) and splitting (coagulation) of clusters have the same order of magnitude, then the RPT is constant during almost the entire transformation process. For the case W=0, which corresponds to the absence of splitting and coagulation of clusters, the phase transformation follows an exponential law in the final stage and is linear with respect to time during the initial one. It has a similar behavior for W0≫W≠0; however, the RPT in the final stage is much smaller in the last case than for W=0. In the absence of supersaturation, RPT decreases to zero as T→Tc, where Tc(=0 K) is the phase transition temperature for a one-dimensional model. The time-dependent size distribution of clusters is for all times exponential with respect to the cluster size. The average size of the cluster far from both equilibrium and initial state grows linearly in time. Both the above quantities behave in a manner similar to those obtained by Monte Carlo simulations for systems of higher dimension.
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Br−–C6H6, and I−–C6H6 anion complexes: Infrared spectra and ab initio calculations
Authors: Loh Z. M. , Wilson R. L. , Wild D. A. , Bieske E. J. , Zehnacker A.
Published: October 2003

Vibrational predissociation spectroscopy is used to obtain infrared spectra of the Cl−–C6H6, Br−–C6H6, and I−–C6H6 complexes in the region of the benzene CH stretch vibrations (2800–3200 cm−1). The infrared spectra of the three dimers are similar, each exhibiting several narrow bands (full width at half maximum <10 cm−1) that are only slightly redshifted from the absorptions of the free benzene molecule. Ab initio calculations predict that the most stable form of the three complexes is a planar C2v structure in which the halide is hydrogen bonded to two adjacent CH groups. The planar C2v structure in which the halide is linearly H bonded to a single CH group is predicted to be slightly less stable than the bifurcated form. Comparisons between experimental and theoretically predicted infrared spectra confirm that the bifurcated structure is indeed the most stable conformer for all three complexes. Ab initio calculations show that the electron density transfer from the halide to the benzene is not limited to the σ*(CH) orbitals adjacent to the halide, but extends to the σ domain of the benzene ring, consistent with the moderate shift of the CH stretch frequencies. The presence of weak satellite bands is explained in terms of Fermi resonances reminiscent of the benzene Fermi tetrad or hot bands involving the in-plane intermolecular bend vibration.
Infrared laser spectroscopy of CCO radical in the region of the C–C stretching fundamental
Authors: Abusara Z. , Sorensen T. S. , Moazzen-Ahmadi N.
Published: October 2003

The C–C stretching fundamental ν3 and the difference band 2ν3−ν3 of the CCO radical have been measured in the gas phase using a tunable infrared diode laser spectrometer. The CCO radical was produced using a flowing mixture of carbon suboxide and helium subjected to a hollow-cathode discharge. The spectral region between 1035–1085 cm−1 was probed. Fifty-five and fifty-three rovibrational transitions were measured in the ν3 and 2ν3−ν3 bands, respectively. The analyses of these bands yielded spectroscopic constants for (001) and (002) vibrational states. The band origins for ν3 and 2ν3−ν3 were determined to be 1066.82407(54) and 1061.91084(63) cm−1, respectively. To check the consistency of the data in this work and those in the C–O stretching region, several lines from the ν1+ν3−ν1 band were also recorded. These lines were observed at their predicted frequency.
The pure rotational spectrum of TiF (X 4Φr): 3d transition metal fluorides revisited
Authors: Sheridan P. M. , McLamarrah S. K. , Ziurys L. M.
Published: October 2003

The pure rotational spectrum of TiF in its X 4Φr (v=0) ground state has been measured using millimeter/sub-millimeter wave direct absorption techniques in the range 140–530 GHz. In ten out of the twelve rotational transitions recorded, all four spin–orbit components were observed, confirming the Φr4 ground state assignment. Additional small splittings were resolved in several of the spin components in lower J transitions, which appear to arise from magnetic hyperfine interactions of the F19 nucleus. In contrast, no evidence for Λ-doubling was seen in the data. The rotational transitions of TiF were analyzed using a case (a) Hamiltonian, resulting in the determination of rotational and fine structure constants, as well as hyperfine parameters for the fluorine nucleus. The data were readily fit in a case (a) basis, indicating strong first order spin–orbit coupling and minimal second-order effects, as also evidenced by the small value of λ, the spin–spin parameter. Moreover, only one higher order term, η, the spin–orbit/spin–spin interaction term, was needed in the analysis, again suggesting limited perturbations in the ground state. The relative values of the a, b, and c hyperfine constants indicate that the three unpaired electrons in this radical lie in orbitals primarily located on the titanium atom and support the molecular orbital picture of TiF with a σ1δ1π1 single electron configuration. The bond length of TiF (1.8342 Å) is significantly longer than that of TiO, suggesting that there are differences in the bonding between 3d transition metal fluorides and oxides.
Relations among several nuclear and electronic density functional reactivity indexes
Authors: Torrent-Sucarrat Miquel , Luis Josep M. , Duran Miquel , Toro-Labbé Alejandro , Solà Miquel
Published: October 2003

An expansion of the energy functional in terms of the total number of electrons and the normal coordinates within the canonical ensemble is presented. A comparison of this expansion with the expansion of the energy in terms of the total number of electrons and the external potential leads to new relations among common density functional reactivity descriptors. The formulas obtained provide explicit links between important quantities related to the chemical reactivity of a system. In particular, the relation between the nuclear and the electronic Fukui functions is recovered. The connection between the derivatives of the electronic energy and the nuclear repulsion energy with respect to the external potential offers a proof for the “Quantum Chemical le Chatelier Principle.” Finally, the nuclear linear response function is defined and the relation of this function with the electronic linear response function is given.
On the halide hydration study: Development of first-principles halide ion-water interaction potential based on a polarizable model
Authors: Ayala Regla , Martı́nez José M. , Pappalardo Rafael R. , Sánchez Marcos Enrique
Published: October 2003

The development of first-principles halide-water interaction potentials for fluoride and iodide anions is presented. The model adopted is the mobile charge densities in harmonic oscillator that allows for a flexible and polarizable character of the interacting particles. The set of points of the quantum mechanical potential energy surfaces are calculated up to the MP2 level. The nonadditive many-body contributions were included explicitly at the three-body terms. Structural and energetic properties of the [X(H2O)n]− clusters (n=1–6) are studied with the new interaction potentials developed. Halide aqueous solutions are also studied by means of Monte Carlo simulations. The agreement between experimental and our predicted estimations shows the good behavior of the proposed potentials. The developed potentials are able to properly describe both the microsolvation of clusters in gas phase and their hydration in aqueous solutions. The different nature of the interactions among F−, Br−, I− and water appears in the set of studied properties, thus giving a gradual change in the behavior along the group.
High resolution ion imaging study of BrCl photolysis in the wavelength range 330–570 nm
Authors: Beckert Marco , Wouters Eloy R. , Ashfold Michael N. R. , Wrede Eckart
Published: October 2003

The photodissociation of jet-cooled BrCl molecules has been investigated at many different excitation wavelengths in the range 330–570 nm by velocity map imaging of the ground state Br and ground and spin–orbit excited Cl atom products. Image analysis confirms literature values for the energies of the ground, Br(2P3/2)+Cl(2P3/2), and first excited [Br(2P3/2)+Cl(2P1/2)] dissociation asymptotes, and provides measures of the electronic branching into these two active product channels, and the recoil anisotropy of each set of products, as a function of parent vibrational level (v″⩽2) and excitation wavelength. The availability of such experimental data allows mapping of the partial cross-sections for parallel (i.e., ΔΩ=0) and perpendicular (i.e., ΔΩ=±1) absorption as a function of excitation energy, and thus deconvolution of the room temperature parent absorption spectrum into contributions associated with excitation to the A 3Π(1), B 3Π(0+), and C 1Π(1) excited states of BrCl. This analysis of the continuous absorption spectrum of BrCl, when considered in conjuction with existing spectroscopic data for the ground electronic state and for the bound levels supported by the B state potential, allows determination of key regions of the potential energy curves for, and transition moments to, each of these three excited states. Further wave packet calculations, which reproduce the experimentally measured wavelength dependent product channel branching ratios and product recoil anisotropies very well, serve to validate the excited state potential energy functions so derived and allow estimation of the strength (∼80 cm−1) of the coupling between the bound (B) and dissociative (Y) diabatic states of 0+ symmetry.
Bonding in the homologous series CsAu, CsAg, and CsCu studied at the 4-component density functional theory and coupled cluster levels
Authors: Fossgaard O. , Gropen O. , Eliav E. , Saue T.
Published: October 2003

We have studied the effect of relativity, electron correlation and the lanthanide contraction on the spectroscopic constants, dissociation energies and dipole moments of the homologous series CsAu, CsAg, and CsCu. We observe a relativistic strengthening of the bond in all cases, particularly for CsAu, but all three compounds are predicted to exist on both the relativistic and nonrelativistic levels of theory with bond strengths more than 1 eV. The effect of the lanthanide contraction on the bonding in CsAu has been studied using a pseudoatom model of the Au atom and is shown to contribute to the strength and polarity of the bond, albeit to a lesser degree than relativity. We present a new estimate of the experimentally derived value of the CsAu dissociation energy using spectroscopic constants calculated at the coupled cluster CCSD(T) level. The new value (2.53 eV) is slightly lower than the previous estimate by Busse and Weil (2.58 eV) and is in excellent agreement with the corresponding CCSD(T) value. We have employed 4-component density functional theory at the B3LYP level, and the spectroscopic constants calculated with this method are in good agreement with coupled cluster results. For dipole moments the B3LYP values appear on the other hand to be too low and this requires further investigation.
Particle packing in soft- and hard-potential liquids
Authors: Vieira Pablo A. , Lacks Daniel J.
Published: October 2003

Molecular simulations are carried out to test whether the disordered packing configurations that are stable in soft potential systems are also stable in hard potential systems, and vice versa. To carry out this test, the properties of packing configurations corresponding to energy minima are examined as the steepness of the interparticle potential changes. A normal mode analysis shows that as the steepness of the potential changes, energy minima flatten out and disappear. Thus packing configurations that are stable for a soft potential system are not stable for hard potential systems, and vice versa. This result for disordered particle packing configurations contrasts with the result for the ordered packing configurations that underlie crystals, in which the same packing configurations are stable in both soft and hard potential systems.
Matrix-induced nanoparticle interactions in a polymer melt: A molecular dynamics simulation study
Authors: Bedrov Dmitry , Smith Grant D. , Smith James S.
Published: October 2003

A molecular dynamics simulation study of the influence of a polymer melt matrix consisting of bead-necklace polymers on the effective interaction between two spherical nanoparticles was performed. The potential of mean force (POMF) between the two nanoparticles as well as entropy and energy contributions to the POMF was determined as a function of nanoparticle separation. The role of energy on the POMF was investigated by varying the strength of the polymer–nanoparticle interaction and comparing structure and POMF with those obtained for an athermal model. All features of the POMF as a function of nanoparticle separation were found to be strongly correlated with the polymer matrix density, the structure of the polymer at the nanoparticle interface, and the structure of the polymer in the interparticle region. The POMF was not found to correlate with polymer chain dimensions (e.g., radius of gyration) in contrast to colloidal suspensions in dilute and semidilute solutions. Both energy and entropy effects were found to make important contributions to the POMF. For the athermal system, where all matrix-induced interactions are entropic in nature, the nanoparticle POMF was found to exhibit qualitatively different behavior from that of the energetic systems.
An improved Monte Carlo method for direct calculation of the density of states
Authors: Shell M. Scott , Debenedetti Pablo G. , Panagiotopoulos Athanassios Z.
Published: October 2003

We present an efficient Monte Carlo algorithm for determining the density of states which is based on the statistics of transition probabilities between states. By measuring the infinite temperature transition probabilities—that is, the probabilities associated with move proposal only—we are able to extract excellent estimates of the density of states. When this estimator is used in conjunction with a Wang–Landau sampling scheme [F. Wang and D. P. Landau, Phys. Rev. Lett. 86, 2050 (2001)], we quickly achieve uniform sampling of macrostates (e.g., energies) and systematically refine the calculated density of states. This approach requires only potential energy evaluations, continues to improve the statistical quality of its results as the simulation time is extended, and is applicable to both lattice and continuum systems. We test the algorithm on the Lennard-Jones liquid and demonstrate good statistical convergence properties.
Conformational behavior of a single polymer chain confined by a two-dimensional harmonic potential in good solvents
Authors: Shew Chwen-Yang
Published: October 2003

Monte Carlo simulations have been conducted to investigate the conformational behavior of a flexible chain polymer confined to a two-dimensional harmonic potential. The polymer molecule is modeled as a tangent hard sphere chain, and the two-dimensional harmonic potential is chosen to mimic nonrigid cylindrical pores. The simulations show that as field strength is increased, the mean chain dimension decreases first and then increases again after passing a minimum due to anisotropic deformation. A modified Flory-type theory is utilized to derive the power laws for the chain deformation against the strength of the applied field in different directions. These power laws agree with the simulations at strong fields when the confined polymer molecule exhibits a rodlike conformation. Meanwhile, a simple model, consisting of a dimer in a two-dimensional harmonic potential, is solved to elucidate the alignment of chain segments in very strong applied potentials. From this model, the crossover regime of a tangent hard sphere chain from the rodlike chain to a totally stretched chain at limiting strong fields is identified. Furthermore, a first-order perturbation theory is employed to interpolate the mean chain size for different field strengths. The field strength corresponding to the minimum mean chain size decreases as chain length is increased, consistent with the prediction of the modified Flory-type theory. These studies provide physical insights into the conformational behavior of a flexible polymer chain in nonspherical two-dimensional harmonic potentials.
Coarse-grained stochastic processes and kinetic Monte Carlo simulators for the diffusion of interacting particles
Authors: Katsoulakis Markos A. , Vlachos Dionisios G.
Published: October 2003

We derive a hierarchy of successively coarse-grained stochastic processes and associated coarse-grained Monte Carlo (CGMC) algorithms directly from the microscopic processes as approximations in larger length scales for the case of diffusion of interacting particles on a lattice. This hierarchy of models spans length scales between microscopic and mesoscopic, satisfies a detailed balance, and gives self-consistent fluctuation mechanisms whose noise is asymptotically identical to the microscopic MC. Rigorous, detailed asymptotics justify and clarify these connections. Gradient continuous time microscopic MC and CGMC simulations are compared under far from equilibrium conditions to illustrate the validity of our theory and delineate the errors obtained by rigorous asymptotics. Information theory estimates are employed for the first time to provide rigorous error estimates between the solutions of microscopic MC and CGMC, describing the loss of information during the coarse-graining process. Simulations under periodic boundary conditions are used to verify the information theory error estimates. It is shown that coarse-graining in space leads also to coarse-graining in time by q2, where q is the level of coarse-graining, and overcomes in part the hydrodynamic slowdown. Operation counting and CGMC simulations demonstrate significant CPU savings in continuous time MC simulations that vary from q3 for short potentials to q4 for long potentials. Finally, connections of the new coarse-grained stochastic processes to stochastic mesoscopic and Cahn–Hilliard–Cook models are made.
Transport properties of liquid para-hydrogen: The path integral centroid molecular dynamics approach
Authors: Yonetani Yoshiteru , Kinugawa Kenichi
Published: October 2003

Several fundamental transport properties of a quantum liquid para-hydrogen (p-H2) at 17 K have been numerically evaluated by means of the quantum dynamics simulation called the path integral centroid molecular dynamics (CMD). For comparison, classical molecular dynamics (MD) simulations have also been performed under the same condition. In accordance with the previous path integral simulations, the calculated static properties of the liquid agree well with the experimental results. For the diffusion coefficient, thermal conductivity, and shear viscosity, the CMD predicts the values closer to the experimental ones though the classical MD results are far from the reality. The agreement of the CMD result with the experimental one is especially good for the shear viscosity with the difference less than 5%. The calculated diffusion coefficient and the thermal conductivity agree with the experimental values at least in the same order. We predict that the ratio of bulk viscosity to shear viscosity for liquid p-H2 is much larger than classical van der Waals simple liquids such as rare gas liquids.
A Monte Carlo study of the chiral columnar organizations of dissymmetric discotic mesogens
Authors: Berardi R. , Cecchini M. , Zannoni C.
Published: October 2003

We study the relation between the chirality of a discotic mesogen and that of the chiral columnar aggregates that they can spontaneously form by self-assembly. We discuss first the different types of chiral columns that can be in principle obtained. We introduce then a simple two-site Gay–Berne dissymmetric molecular model where chirality can be easily varied and perform extensive NPT Monte Carlo simulations of samples of these particles for different chiralities. At low temperatures we find nematic discotic and columnar mesophases formed by overall chiral columns and we analyze the results in terms of suitably defined observables and chiral correlation functions. We find that, at least for our model system, the columnar chirality is not originating from a regular helical or spiral arrangement of particles but it is mainly due to one-particle high-chirality defects separated by low-chirality domains.
A state-selected study of the H2+(X,v+=0–17,N+=1)+Ne proton transfer reaction using the pulsed-field ionization–photoelectron–secondary ion coincidence scheme
Authors: Zhang T. , Qian X.-M. , Tang X. N. , Ng C. Y. , Chiu Y. , Levandier D. J. , Miller J. S. , Dressler R. A.
Published: October 2003

The endothermic proton transfer reaction, H2+(v+,N+=1)+Ne→NeH++H(ΔH=0.54 eV), is investigated over a broad range of reactant vibrational energies using the pulsed-field ionization–photoelectron–secondary ion coincidence (PFI–PESICO) scheme. For the lowest vibrational levels, v+=0 and 1, a detailed translational energy dependence is also presented using a continuous approach for preparing reactant ions with monochromatic VUV. Sharp threshold onsets are observed, suggesting the importance of long-lived intermediates or resonances. At a translational energy, ET=0.7 eV, absolute state-selected reaction cross sections are measured for all reactant vibrational levels v+=0–17. For levels v+=0–6, the cross sections grow rapidly with vibrational quantum, above which the cross sections saturate at a value of ∼13±4 Å2. At levels v+>13, the cross sections decline, probably due to competition with the dissociation channel. At a translational energy, ET=1.7 eV, absolute state-selected reaction cross sections are measured for reactant vibrational levels spanning the range between v+=0 and 14. Cross section growth is observed from v+=0–7, above which the cross sections no longer exhibit a steady trend. At ET=4.5 eV, cross sections are reported for vibrational levels covering the range between v+=0 and 12. The cross sections are substantially lower at this high translational energy, however, they still exhibit a substantial vibrational enhancement below v+=8. The present measurements are compared with quasiclassical trajectory (QCT) calculations. The comparison can be categorized by three distinct total energy (Etot=ET+Evib) regimes. For Etot<1 eV, the experimental cross sections exceed the QCT results, consistent with important quantum effects at low energies. For 1<Etot<3 eV, excellent agreement is observed between the PFI–PESICO cross sections and the QCT calculations. At total energies exceeding 3 eV, the experimental results are generally higher, probably because QCT overpredicts competition from the dissociation channel.
Conformational space annealing and an off-lattice frustrated model protein
Authors: Kim Seung-Yeon , Lee Sung Jong , Lee Jooyoung
Published: October 2003

A global optimization method, conformational space annealing (CSA), is applied to study a 46-residue protein with the sequence B9N3(LB)4N3B9N3(LB)5L, where B, L, and N designate hydrophobic, hydrophilic, and neutral residues, respectively. The 46-residue BLN protein is folded into the native state of a four-stranded β barrel. It has been a challenging problem to locate the global minimum of the 46-residue BLN protein since the system is highly frustrated and consequently its energy landscape is quite rugged. The CSA successfully located the global minimum of the 46-mer for all 100 independent runs. The CPU time for CSA is about seventy times less than that for simulated annealing (SA), and its success rate (100%) to find the global minimum is about eleven times higher. The amount of computational effort used for CSA is also about ten times less than that of the best global optimization method yet applied to the 46-residue BLN protein, the quantum thermal annealing with renormalization. The 100 separate CSA runs produce the global minimum 100 times as well as the other 5950 final conformations corresponding to a total of 2361 distinct local minima of the protein. Most of the final conformations have relatively small root-mean-square deviation values from the global minimum, independent of their diverse energy values. Very close to the global minimum, there exist quasi-global-minima which are frequently obtained as one of the final answers from SA runs. We find that there exist two largest energy gaps between the quasi-global-minima and the other local minima. Once a SA run is trapped in one of these quasi-global-minima, it cannot be folded into the global minimum before crossing over the two large energy barriers, clearly demonstrating the reason for the poor success rate of SA.
Large anharmonic effects in the infrared spectra of the symmetrical CH3NO2−⋅(H2O) and CH3CO2−⋅(H2O) complexes
Authors: Myshakin Evgeniy M. , Jordan Kenneth D. , Sibert Edwin L. , Johnson Mark A.
Published: October 2003

The observed IR spectra of the CH3NO2−⋅(H2O) and CH3CO2−⋅(H2O) complexes display sequences of up to seven transitions in the region of the OH stretch fundamentals. This is indicative of strong anharmonic coupling between the OH stretch modes and one or more low-frequency modes. Cubic force fields have been calculated for these two complexes using the MP2 method, and these have been used to calculate the vibrational spectra and to identify the key couplings responsible for the “extra” lines in the observed spectra. In addition, a simple adiabatic model involving the OH stretch and intermolecular rock vibrations is introduced and shown to account in an near quantitative manner for the structure in the OH stretch region of the spectra.
Ab initio quantum chemical calculations for fullerene cages with large holes
Authors: Hu Yun Hang , Ruckenstein Eli
Published: October 2003

One of the important issues in endohedral fullerene chemistry is the generation of a suitable window for atoms or small molecules to enter into the fullerene cages. In this paper, the structure and stability of fullerenes possessing holes, formed by removing one or more adjacent atoms from the C60 clusters, are examined via ab initio Hartree–Fock and density functional theory calculations. When vacancies are created in the C60 cluster, some of the original 5- and 6-member rings are destroyed, resulting in defect structures, containing larger rings (7-, 8-, and 9-member rings) and abutting 5-member rings. It was also found that the ground state is a singlet for the defect C60 structure with two vacancies and a triplet for the defect structures with one or three vacancies. The vacancies decrease the cluster stability. However, among these defect structures, the two-vacancy defect C60 with a 7-member ring is the most stable and has a hole with a sufficiently large diameter (3.22 Å) for atoms or small molecules to pass through. Therefore, this fullerene cage could provide an excellent cage for fullerene endohedral complexes and as a storage place for fuels (such as H2).
Multiconfigurational self-consistent field study of the silicon carbide (001) surface
Authors: Tamura Hiroyuki , Gordon Mark S.
Published: October 2003

Multiconfigurational self-consistent field calculations have been performed to investigate structural and electronic properties of cubic silicon carbide (001) (SiC (001)) surfaces. The dimer on silicon-terminated SiC (001) (Si–SiC (001)) is found to be diradical in nature, due to destabilization of the π bond by bending the dimer. Since the SiC lattice constant is larger than that of diamond, the >C=C< dimer on the carbon-terminated SiC (001) (C–SiC (001)) surface is flatter and its π bond is stronger than those on diamond (001). The bridging dimer on the C–SiC (001) exhibits relatively small multiconfigurational character despite its bent geometry. H2 adsorption onto the Si–SiC (001) diradical dimer is more favorable than that onto the partial π bonded Si (001) dimer. As the dimer geometry becomes flatter, the π bond becomes stronger and the H2 adsorption on the dimer becomes less favorable.
Bent silicon crystal in the Laue geometry to resolve x-ray fluorescence for x-ray absorption spectroscopy
Authors: Kropf A. J. , Finch R. J. , Fortner J. A. , Aase S. , Karanfil C. , Segre C. U. , Terry J. , Bunker G. , Chapman L. D.
Published: October 2003

A highly strained, curved silicon crystal in the Laue geometry has been used as a large-area x-ray fluorescence analyzer for x-ray absorption spectroscopy. The analyzer is able to resolve the Lα fluorescence lines for neighboring actinide elements. A large gain in the signal to background ratio has been demonstrated for small quantities of Np in the presence of U, with the U fluorescence peak approaching 1000 times the magnitude of the off-peak background.
Detection and volume estimation of semiconductor quantum dots from atomic force microscope images
Authors: Oh Sangwook , Hyon Chankyeong , Sull Sanghoon , Hwang Sungwoo , Park Yongju
Published: October 2003

An automated quantum dot detection and volume estimation method of atomic force microscope images are proposed and implemented. Quantum dot detection is based on the image-segmentation method widely used in image processing. We used a modified local watershed algorithm, which produces stable and effective segmentation results in order to detect the peak position of the quantum dot of the atomic force microscopy image. An effective volume estimation of the quantum dot is performed by intelligently determining the boundary of the quantum dot at each height step and by simply adding small volume fractions lying inside of the quantum dot boundary. Our volume estimation results are quantitatively analyzed by comparison with the quantum dot volume obtained by assuming conical and pyramidal shapes. The detection results of our method are quantitatively compared with the results of two other methods for general grain detection, and with a transmission electron micrograph of the quantum dot. Finally, information such as the number of quantum dots, the density, the size and the height distribution are also provided as a result of implementing our method. This method can be applied to detect and estimate volume of a similar shape with a different size.
Time-resolved study of the symmetric SN2-reaction I−+CH3I
Authors: Wester Roland , Bragg Arthur E. , Davis Alison V. , Neumark Daniel M.
Published: October 2003

Time-resolved photoelectron spectroscopy of negative ions has been applied to study the title reaction as a model system for gas phase SN2 reactions. Starting from the precursor cluster I2−⋅CH3I, the interaction of the reactants I− and CH3I is initiated by a pump pulse and the subsequent dynamics are observed with a delayed probe pulse used to detach the excess electron and measure their photoelectron spectra. Using two different pump photon energies, which lead to different amounts of internal energy available to the reaction complex, a number of dynamical features have been observed. For small internal excitation, the reactants only form stable, albeit vibrationally excited, I−⋅CH3I complexes. However, with increased internal excitation, complexes are formed that exhibit biexponential decay back to I− and CH3I reactants with time scales of 0.8 and 10 ps. Similar dynamics are expected for entrance channel complex formed in the first step of a gas phase SN2 reaction.
Generalized equation of state and exclusion factor for multicomponent systems
Authors: Rusanov Anatoly I.
Published: October 2003

The recent theory of an equation of state of a fluid mixture is improved by generalizing the master equation form and analyzing the dependence of the exclusion factor on the mixture composition and cluster size. The formulas for computing the limiting value of the exclusion factor for a rarefied gaseous state and other parameters of an equation of state are derived for a multicomponent system. The previous variant of the theory is shown to be applicable to mixtures with the particle size ratios not exceeding 2. The theory presented in this paper has no restriction concerning the particle size ratios in a multicomponent system. The equation of state obtained is also reformulated in terms of reduced density.
Structural and thermochemical properties of the hydroxymethyl (CH2OH) radical: A high precision ab initio study
Authors: Marenich Aleksandr V. , Boggs James E.
Published: October 2003

The variational solution of the CH2OH nuclear problem was performed by treatment of CH2OH as a planar molecule with highly anharmonic vibrations. A sophisticated dynamic model to describe the structural flexibility of CH2OH was applied. The detailed analysis of the rovibrational Hamiltonian is shown. The electron problem solution was obtained by use of the coupled cluster electron correlation technique and the augmented correlation-consistent polarized basis sets of triple- and quadruple-ζ qualities. The geometry and energy parameters were extrapolated to the complete basis set limit. The partition functions of CH2OH were calculated by the explicit summation of vibrational and rotational levels. The heat of formation of CH2OH, ΔfH∘(298.15 K)=−17.0±0.7 kJ/mol, was calculated by a study of the CH2OH→CH2O+H reaction using the augmented basis set of quintuple-ζ quality and the relativistic and core-valence corrections of the total energies. Some structural and thermodynamic properties of CH2O are reported.
High speed tapping mode atomic force microscopy in liquid using an insulated piezoelectric cantilever
Authors: Rogers B. , Sulchek T. , Murray K. , York D. , Jones M. , Manning L. , Malekos S. , Beneschott B. , Adams J. D. , Cavazos H. , Minne S. C.
Published: October 2003

Quicker imaging times for tapping mode atomic force microscopy in liquid could provide a real-time imaging tool for studying dynamic phenomena in physiological conditions. We demonstrate faster imaging speed using microcantilevers with integrated piezoelectric actuators. The exposed electric components of the cantilever necessitate an insulation scheme for use in liquid; three coating schemes have been tested. Preliminary tapping mode images have been taken using the insulated microactuator to simultaneously vibrate and actuate the cantilever over topographical features in liquid, including a high speed image of steps on a mica surface in water and an image of two e coli bacteria taken in saline solution at 75.5 μm/s, a threefold improvement in bandwidth versus conventional piezotube actuators.
Bragg grating performance in Er–Sn-doped germanosilicate fiber for simultaneous measurement of wide range temperature (to 500 °C) and strain
Authors: Pal Suchandan , Sun Tong , Grattan Kenneth T. V. , Wade Scott A. , Collins Stephen F. , Baxter Gregory W. , Dussardier Bernard , Monnom Gérard
Published: October 2003

A fiber-optic sensing scheme for the simultaneous measurement of strain and a wide range of temperatures has been investigated by combining the properties of the fiber Bragg grating (FBG) and the fluorescence from a rare-earth-doped photosensitive fiber. The temperature-dependent fluorescence peak power ratio of the two peaks occurring around 1535 nm and 1552 nm from the amplified spontaneous emission due to the I13/24↔4I15/2 transitions in Er3+-doped tin–germanosilicate fiber, with 980 nm pumping, and the dual functionality of the FBG were exploited in this scheme. The sensor is based on a single FBG written in a small length (∼10 cm) of the above fiber, which can be used for the simultaneous measurement of strain and temperature over ranges of 0–1150 με and 22–500 °C, with root-mean-square errors of 36 με and 6 °C, respectively.