bluuebunny/crossref_metadata_2025 huggingface dataset:
Application of the VH‐TDMA technique to coastal ambient aerosols
Authors: Johnson G. , Ristovski Z. , Morawska L.
Published: August 2004

A newly developed VH‐TDMA has been used for the first time to measure the volatile fractions and post volatilization hygroscopic growth factors of ambient aerosols in the coastal marine and urban environments. The results are compared with comparable data for laboratory generated aerosols of known composition. Measurements conducted on coastal Aitken mode particles showed volatilization behavior similar to laboratory generated aerosols composed of methane sulfonic acid and ammonium sulfate. Measurements conducted on 60 nm particles during nucleation events contained a greater fraction of material with similar volatility to ammonium sulfate than was found at other times. These particles were hygroscopic but less so than pure ammonium sulfate. Measurements conducted in the Brisbane central business district during sea breeze conditions show similar behavior to the coastal aerosol, but with additional low volatility species. This aerosol may originate from urban sources or from marine particles acquiring additional secondary aerosol species during transport.
Simulating oceanic CaCO3 export production in the greenhouse
Authors: Heinze C.
Published: August 2004

A model scenario for the change in global marine biogenic CaCO3 export production (CaCO3 = calcium carbonate) due to increasing atmospheric carbon dioxide partial pressure is carried out. Findings from laboratory experiments, which suggest a decrease of biocalcification at higher pCO2, are extrapolated to the world ocean by use of the biogeochemical ocean general circulation model HAMOCC. For an A1B IPCC emission scenario and constant emission rates after year 2100, the simulation predicts a global decrease of biological CaCO3 export production by about 50% in year 2250. The negative feedback due to this drop in CaCO3 export on the atmospheric CO2 concentration is small as compared to the anthropogenic CO2 emissions. This negative feedback will potentially be compensated by a shallower remineralization of organic carbon.
Interaction potentials and rovibrational spectroscopy of HeN-OCS complexes
Authors: Paesani F. , Whaley K. B.
Published: August 2004

We present a new vibrationally averaged He-OCS potential energy surface that is obtained from a combination of Møller-Plesset perturbation theory for the helium-molecule interaction and coupled cluster theory for the intramolecular vibrational potential. Employing this potential in quantum Monte Carlo calculations for HeN-OCS complexes shows a blueshift of the OCS vibration for small N that is followed by a transition to a redshift for larger N. The size dependence of the vibrational shift is in good agreement with recent experimental measurements. We then make a comparative study of the effective rotational spectroscopic constants Beff and Deff calculated for small N values with this vibrationally averaged potential, with the corresponding values obtained from three previous He-OCS potentials. We find that the vibrationally averaged potential provides the most accurate description of the spectroscopic constants over the size range N=1–8 for which experimental data are available. We rationalize this improved description in terms of the detailed differences in the secondary minimum and saddle point regions of the underlying He-OCS interaction potential, in addition to the behavior at the lowest potential minimum. This analysis indicates that the spectroscopy of complexes with N>1 provides valuable information on the shape of the potential energy surface in regions that are not accessed by the N=1 He-OCS complex, but that are important for understanding the molecular spectroscopy in larger complexes and in droplets.
Solvent-driven dewetting and rim instability
Authors: Lee Sarng H. , Yoo Pil J. , Kwon S. Joon , Lee Hong H.
Published: August 2004

An experimental method suitable for reproducible results has been used to investigate dewetting behavior of thin films of solvent-laden polymer. This solvent-driven dewetting enables one to change spreading coefficient by an order of magnitude that is not readily realizable in thermal dewetting and to study polar interactions that have not been fully exploited experimentally. While the film instability is similar to that found in thermal dewetting, the rim instability is quite different. Two different types of the rim instability have been found. With a polar solvent, the rim instability changes from one type to another with increasing film thickness whereas the unstable rim becomes stable for an apolar solvent.
The extended Perdew-Burke-Ernzerhof functional with improved accuracy for thermodynamic and electronic properties of molecular systems
Authors: Xu Xin , Goddard William A.
Published: August 2004

Density functional theory (DFT) has become the method of choice for many applications of quantum mechanics to the study of the electronic properties of molecules and solids. Despite the enormous progress in improving the functionals, the current generation is inadequate for many important applications. As part of the quest of finding better functionals, we consider in this paper the Perdew-Burke-Ernzerhof (PBE) functional, which we believe to have the best theoretical foundation, but which leads to unacceptable errors in predicting thermochemical data (heats of formation) of molecular systems [mean absolute deviation (MAD)=16.9 kcal/mol against the extended G2 data set of 148 molecules]. Much improved thermochemistry is obtained with hybrid DFT methods that include part of the Hartree-Fock exchange [thus B3LYP (Becke’s three parameter scheme combining Hartree-Fock exchange, Becke gradient corrected exchange functional and Lee-Yang-Parr correlational functional) with MAD=3.1 kcal/mol and PBE0 (Perdew’s hybrid scheme using PBE exchange and correlation functionals) with MAD=4.8 kcal/mol]. However we wish to continue the quest for a pure density-based DFT. Thus we optimized the four free parameters (μ, κ, α, and β) in PBE theory against experimental atomic data and the van der Waals interaction properties of Ne2, leading to the xPBE extended functional, which significantly outperforms PBE for thermochemical properties MAD reduced to 8.0 kcal/mol while being competitive or better than PBE for predictions of geometric parameters, ionization potentials, electron affinities, and proton affinities and for the description of van der Waals and hydrogen bond interactions. Thus xPBE significantly enlarges the field of applications available for pure DFT. The functional forms thus obtained for the exchange and correlational functionals may be useful for discovering new improved functionals or formalisms.
Simple minimum principle to derive a quantum-mechanical/ molecular-mechanical method
Authors: Yasuda Koji , Yamaki Daisuke
Published: August 2004

We propose a minimum principle to derive a QM/MM (quantum-mechanical/molecular-mechanical) method from the first principle. We approximate the Hamiltonian of a spectator substituent as the structure-dependent effective Hamiltonian in a least-squares sense. This effective Hamiltonian is expanded with the orthogonal operator set called the normal-ordered product. We determine the structure-dependent energy that corresponds to the classical MM energy and the extra one-electron potential that takes account of the interface effects. This QM/MM method is free from the double-counting problem and the artificial truncation of the localized molecular orbitals. As a numerical example we determine the one-electron effective Hamiltonian of the methyl group. This effective Hamiltonian is applied to the ethane and CH3CH2X molecules (X=CH3, NH2, OH, F, COOH, NH3+, OH2+, and COO−). It reproduced the relative energies, potential energy curves, and the Mulliken populations of the all-electron calculations fairly well.
Theoretical studies on the electronic structure of Ti8C12 isomers
Authors: Deng Ke , Duan Wenhui , Gu Binglin
Published: August 2004

Density functional calculation are performed to study Ti8C12 isomers (Td, C3v, and D2d) in the neutral, cationic, and anionic charge states. C3v symmetry is found to be the most stable geometry for the neutral and anion, and the C3v and D2d isomers to be quasi-iso-energetic lowest for the cation. The electronic structure analysis show that d electron tends to be localized in the ground state. The theoretical assignment for the features in the experimental photoelectron spectra is given. All results obtained are in good agreement with the available experimental data and indicate that the C3v and D2d isomers may coexist in the photoelectron spectroscopy experiment.
Multiconfigurational second-order perturbation study of the decomposition of the radical anion of nitromethane
Authors: Arenas Juan F. , Otero Juan C. , Peláez Daniel , Soto Juan , Serrano-Andrés Luis
Published: August 2004

The doublet potential energy surfaces involved in the decomposition of the nitromethane radical anion (CH3NO2−) have been studied by using the multistate extension of the multiconfigurational second-order perturbation method (MS-CASPT2) in conjunction with large atomic natural orbital-type basis sets. A very low energy barrier is found for the decomposition reaction: CH3NO2−→[CH3NO2]−→CH3+NO2−. No evidence has been obtained on the existence of an isomerization channel leading to the initial formation of the methylnitrite anion (CH3ONO−) which, in a subsequent reaction, would yield nitric oxide (NO). In contrast, it is suggested that NO is formed through the bimolecular reaction: CH3+NO2−→[CH3O-N-O]−→CH3O−+NO. In particular, the CASSCF/MS-CASPT2 results indicate that the methylnitrite radical anion CH3ONO− does not represent a minimum energy structure, as concluded by using density functional theory (DFT) methodologies. The inverse symmetry breaking effect present in DFT is demonstrated to be responsible for such erroneous prediction.
Low-temperature nucleation in a kinetic Ising model under different stochastic dynamics with local energy barriers
Authors: Buendı́a Gloria M. , Rikvold Per Arne , Park Kyungwha , Novotny M. A.
Published: August 2004

Using both analytical and simulational methods, we study low-temperature nucleation rates in kinetic Ising lattice-gas models that evolve under two different Arrhenius dynamics that interpose between the Ising states a transition state representing a local energy barrier. The two dynamics are the transition-state approximation [T. Ala-Nissila, J. Kjoll, and S. C. Ying, Phys. Rev. B 46, 846 (1992)] and the one-step dynamic [H. C. Kang and W. H. Weinberg, J. Chem. Phys. 90, 2824 (1989)]. Even though they both obey detailed balance and are here applied to a situation that does not conserve the order parameter, we find significant differences between the nucleation rates observed with the two dynamics, and between them and the standard Glauber dynamic [R. J. Glauber, J. Math. Phys. 4, 294 (1963)], which does not contain transition states. Our results show that great care must be exercised when devising kinetic Monte Carlo transition rates for specific physical or chemical systems.
Electron propagator theory calculations of molecular photoionization cross sections: The first-row hydrides
Authors: Seabra G. M. , Kaplan I. G. , Zakrzewski V. G. , Ortiz J. V.
Published: August 2004

Together with ionization potentials, cross sections provide valuable information for the interpretation of photoelectron spectra. We have developed a program to perform ab initio calculations of photoionization cross sections within the electric dipole approximation using electron propagator theory. Applications to the first-row hydrides CH4, NH3, H2O, and HF, using several approximations for the propagator self-energy and the plane-wave and orthogonalized-plane-wave approximations to represent the photoelectron, as well as comparison to experimental data, are presented. This program is implemented within the quantum chemistry package GAUSSIAN.
Calculation of current densities using gauge-including atomic orbitals
Authors: Jusélius Jonas , Sundholm Dage , Gauss Jürgen
Published: August 2004

A method for calculating the various components of the magnetically induced current-density tensor using gauge-including atomic orbitals is described. The method is formulated in the framework of analytical derivative theory, thus enabling implementation at the Hartree–Fock self-consistent-field (HF-SCF) as well as at electron-correlated levels. First-order induced current densities have been computed up to the coupled-cluster singles and doubles level (CCSD) augmented by a perturbative treatment of triple excitations [CCSD(T)] for carbon dioxide and benzene and up to the full coupled-cluster singles, doubles, and triples (CCSDT) level in the case of ozone. The applicability of the gauge including magnetically induced current method to larger molecules is demonstrated by computing first-order current densities for porphin and hexabenzocoronene at the HF-SCF and density-functional theory level. Furthermore, a scheme for obtaining quantitative values for the induced currents in a molecule via numerical integration over the current flow is presented. For benzene, a perpendicular magnetic field induces a (field dependent) ring current of 12.8 nA T−1 at the HF-SCF level using a triple-zeta basis set augmented with polarization functions (TZP). At the CCSD(T)/TZP level the induced current was found to be 11.4 nA T−1. Gauge invariance and its relation to charge-current conservation is discussed.
Local-field effects on the spontaneous emission rate of CdTe and CdSe quantum dots in dielectric media
Authors: Wuister Sander F. , de Mello Donegá Celso , Meijerink Andries
Published: August 2004

The refractive index dependence of the spontaneous emission rate is determined using organically capped CdSe and CdTe quantum dots as probes. The radiative lifetime of the exciton emission is measured in a variety of apolar solvents with refractive indices n between 1.37 and 1.50. It is demonstrated that quantum dots provide a model system for testing theories on the influence of local-field effects on the spontaneous emission rate. The experimentally observed influence of n on the radiative lifetime is smaller than predicted by well-known models for local-field corrections but is in good agreement with a recently developed fully microscopic model for the local-field enhancement of the spontaneous emission rate.
Density functional theory for semiflexible and cyclic polyatomic fluids
Authors: Cao Dapeng , Wu Jianzhong
Published: August 2004

The effects of bond angle and chain stiffness on the structures of semiflexible polyatomic fluids are investigated by incorporating the bending potential into a density functional theory [Y. X. Yu and J. Z. Wu, J. Chem. Phys. 117, 2368 (2002)] that combines a modified fundamental measure theory for the excluded-volume effects and the first-order thermodynamics perturbation theory for the chain connectivity. The refined density functional theory faithfully reproduces the density profiles and conformational properties of a variety of triatomic fluids near a hard wall in which extensive Monte Carlo simulation data are available. In particular, the theory is able to capture the structures of rigid cyclic trimers where all segments are identical. The variation of local density profiles with respect to the chain length of confined polyatomic fluids is also explored. For quadratomic fluids confined in slit pores, the density profile of the middle segments exhibits novel double peaks that are absent in a fully flexible chain model. In addition, the density functional theory is applied to predicting the conformational properties and adsorption behavior of heterogeneous triatomic fluids of type “ABB” mimicking surfactant molecules. The competition between surface adsorption and self-association of trimers consisting of surface active and self-binding “A” segments and neutral “B” segment is explored.
Geometry, dipole moment, polarizability and first hyperpolarizability of polymethineimine: An assessment of electron correlation contributions
Authors: Jacquemin Denis , André Jean-Marie , Perpète Eric A.
Published: August 2004

We have investigated the geometries as well as the longitudinal dipole moment (μ), polarizability (α), and first hyperpolarizability (β) of polymethineimine oligomers using different approaches [Hartree–Fock (HF), second-order Møller–Plesset (MP2), and hybrid density functional theory (DFT) methods (B3LYP and PBE0)] for evaluating the geometries and the nonlinear optical properties. It turns out that (i) HF and the selected DFT methods provide the incorrect sign for β of short and medium size oligomers. (ii) The B3LYP and PBE0 electron correlation correction are too small for μ, too large for α, and for some oligomer lengths, they are in the wrong direction for β. (iii) On the contrary to polyacetylene, the hybrid-DFT geometries are in poor agreement with MP2 geometries; the former showing much smaller bond length alternations.
Quantum and classical studies of vibrational motion of CH5+ on a global potential energy surface obtained from a novel ab initio direct dynamics approach
Authors: Brown Alex , McCoy Anne B. , Braams Bastiaan J. , Jin Zhong , Bowman Joel M.
Published: August 2004

We report a full dimensional, ab initio based potential energy surface for CH5+. The ab initio electronic energies and gradients are obtained in direct-dynamics calculations using second-order Møller-Plesset perturbation theory with the correlation consistent polarized valence triple zeta basis. The potential energy and the dipole moment surfaces are fit using novel procedures that ensure the full permutational symmetry of the system. The fitted potential energy surface is tested by comparing it against additional electronic energy calculations and by comparing normal mode frequencies at the three lowest-lying stationary points obtained from the fit against ab initio ones. Well-converged diffusion Monte Carlo zero-point energies, rotational constants, and projections along the CH and HH bond lengths and the tunneling coordinates are presented and compared with the corresponding harmonic oscillator and standard classical molecular dynamics ones. The delocalization of the wave function is analyzed through comparison of the CH5+ distributions with those obtained when all of the hydrogen atoms are replaced by H2 and H3. The classical dipole correlation function is examined as a function of the total energy. This provides a further probe of the delocalization of CH5+.
Intense-field modulation of NO2 multiphoton dissociation dynamics
Authors: Schmidt T. W. , López-Martens R. B. , Roberts G.
Published: August 2004

We report on the dynamics of multiphoton excitation and dissociation of NO2 at wavelengths between 395 and 420 nm and intensities between 4 and 10 TW cm−2. The breakup of the molecule is monitored by NO A 2Σ+n′=1,0→X 2Πrn″=0 fluorescence as a function of time delay between the driving field and a probe field which depletes the emission. It is found that generation of n′=0 and 1 NO A 2Σ+ results in different fluorescence modulation patterns due to the intense probe field. The dissociation dynamics are interpreted in terms of nuclear motions over light-induced potentials formed by coupling of NO2 valence and Rydberg states to the applied field. Based on this model, it is argued that the time and intensity dependences of A 2Σ+n′=0→X 2Πrn″=0 fluorescence are consistent with delayed generation of NO A 2Σ+n′=0 via a light-induced bond-hardening brought about by the transient coupling of the dressed Ã 2B2 and Rydberg 3sσ Σg+2 states of the parent molecule. The increasingly prompt decay of A 2Σ+n′=1→X 2Πrn″=0 fluorescence with increasing intensity, on the other hand, is consistent with a direct surface crossing between the X̃ 2A1 and 3sσ Σg+2 dressed states to generate vibrationally excited products.
Disjoining pressure measurements using a microfabricated groove for a molecularly thin polymer liquid film on a solid surface
Authors: Fukuzawa Kenji , Kawamura Jun , Deguchi Takanori , Zhang Hedong , Mitsuya Yasunaga
Published: August 2004

A method for measuring disjoining pressure of a molecularly thin liquid film on a solid surface by using a microfabricated groove has been developed. The shape of the meniscus of a thin film in the microgroove was measured with an atomic force microscope, and the disjoining pressure was obtained from the capillary pressure obtained from the measured curvature of the meniscus. Our method is applicable to a film with a thickness greater than the diameter of gyration in the polymer molecule. Moreover, the method can detect the changes in the disjoining pressure caused by ultraviolet light irradiation, and it is effective in investigating the intermolecular interaction between a thin film and a solid surface.
Large-scale molecular dynamics simulations of alkanethiol self-assembled monolayers
Authors: Vemparala Satyavani , Karki Bijaya B. , Kalia Rajiv K. , Nakano Aiichiro , Vashishta Priya
Published: August 2004

Large-scale molecular dynamics simulations of self-assembled alkanethiol monolayer systems have been carried out using an all-atom model involving a million atoms to investigate their structural properties as a function of temperature, lattice spacing, and molecular chain length. Our simulations show that the alkanethiol chains of 13-carbons tilt from the surface normal by a collective angle of 25° along next-nearest-neighbor direction at 300 K. The tilt structure of 13-carbon alkanethiol system is found to depend strongly on temperature and exhibits hysteresis. At 350 K the 13-carbon alkanethiol system transforms to a disordered phase characterized by small collective tilt angle, flexible tilt direction, and random distribution of backbone planes. The tilt structure also depends on lattice spacing: With increasing lattice spacing a the tilt angle increases rapidly from a nearly zero value at a=4.7 Å to as high as 34° at a=5.3 Å at 300 K for 13-carbon alkanethiol system. Finally, the effects of the molecular chain length on the tilt structure are significant at high temperatures.
Ammonia adsorption on and diffusion into thin ice films grown on Pt(111)
Authors: Takaoka T. , Inamura M. , Yanagimachi S. , Kusunoki I. , Komeda T.
Published: August 2004

Ammonia adsorption on and diffusion into thin ice films grown on a Pt(111) surface were studied using Fourier transform infrared spectroscopy (FTIR) and thermal desorption spectroscopy. After exposing the crystalline ice film to ammonia molecules at 45 K (ammonia/ice film), we have detected an intriguing feature at 1470 cm−1 in the FTIR spectra, which is derived from the adsorption of ammonia on the ice with a characteristic structure which appears in thin film range. The peak intensity of this feature decreases gradually as the thickness of the substrate ice increases. In addition, we have detected a feature at 1260 cm−1 which appears after annealing the ammonia/ice film. The feature corresponds to the ammonia molecules which reach the ice/Pt(111) interface through the ice film. Intriguingly, the intensity of this feature decreases with the ice thickness and there is a linear relation of the peak intensity of the features at 1470 and 1260 cm−1. We propose a model in which the solubility of the ammonia molecules is much higher for the thin ice film than that for the ideal ice.
Phase-stabilized two-dimensional electronic spectroscopy
Authors: Brixner Tobias , Mančal Tomáš , Stiopkin Igor V. , Fleming Graham R.
Published: August 2004

Two-dimensional (2D) spectroscopy is a powerful technique to study nuclear and electronic correlations between different transitions or initial and final states. Here we describe in detail our development of inherently phase-stabilized 2D Fourier-transform spectroscopy for electronic transitions. A diffractive-optic setup is used to realize heterodyne-detected femtosecond four-wave mixing in a phase-matched box geometry. Wavelength tunability in the visible range is accomplished by means of a 3 kHz repetition-rate laser system and optical parametric amplification. Nonlinear signals are fully characterized by spectral interferometry. Starting from fundamental principles, we discuss the origin of phase stability and the precise calibration of excitation-pulse time delays using movable glass wedges. Automated subtraction of undesired scattering terms removes experimental artifacts. On the theoretical side, the response-function formalism is extended to describe molecules with three electronic levels, and the shape of 2D spectral features is discussed. As an example for this technique, experimental 2D spectra are shown for the dye molecule Nile Blue in acetonitrile at 595 nm, recorded for a series of population times. Simulations explore the influence of different model parameters and qualitatively reproduce the experimental results. We show that correlations between different electronically excited states can be determined from the spectra. The technique described here can be used to measure the third-order response function of complex systems covering several electronic transitions.
Path integral approach to Brownian motion driven with an ac force
Authors: Chen L. Y. , Nash P. L.
Published: August 2004

Brownian motion in a periodic potential driven by an ac (oscillatory) force is investigated for the full range of damping constant from the overdamped limit to the underdamped limit. The path (functional) integral approach is advanced to produce formulas for the probability distribution function and for the current of the Brownian particle in response to an ac driving force. The negative friction Langevin dynamics technique is employed to evaluate the dc current for various parameters without invoking the overdamped or the underdamped approximation. The dc current is found to have nonlinear dependence upon the damping constant, the potential parameter, and the ac force magnitude and frequency.
Field-induced alignment of a smectic-A phase: A time-resolved x-ray diffraction investigation
Authors: Bras W. , Emsley J. W. , Levine Y. K. , Luckhurst G. R. , Seddon J. M. , Timimi B. A.
Published: August 2004

The field-induced alignment of a smectic-A phase is, in principle, a complicated process involving the director rotation via the interaction with the field and the layer rotation via the molecular interactions. Time-resolved nuclear magnetic resonance spectroscopy has revealed this complexity in the case of the director alignment, but provides no direct information on the motion of the layers. Here we describe a time-resolved x-ray diffraction experiment using synchrotron radiation to solve the challenging problem of capturing the diffraction pattern on a time scale which is fast in comparison with that for the alignment of the smectic layers. We have investigated the alignment of the smectic-A phase of 4-octyl-4′-cyanobiphenyl by a magnetic field. The experiment consists of creating a monodomain sample of the smectic-A phase by slow cooling from the nematic phase in a magnetic field with a flux density of 7 T. The sample is then turned quickly through an angle φ0 about an axis parallel to the x-ray beam direction but orthogonal to the field. A sequence of two-dimensional small angle x-ray diffraction patterns are then collected at short time intervals. Experiments were carried out for different values of φ0, and at different temperatures. The results show that the alignment behavior changes fundamentally when φ0 exceeds 45°, and that there is a sharp change in the alignment process when the temperature is less than 3 °C below the smectic-A—nematic transition. The results of the x-ray experiments are in broad agreement with the NMR results, but reveal major phenomena concerning the maintenance of the integrity of the smectic-A layer structure during the alignment process.
Potential energy constrained molecular dynamics simulations
Authors: Rapallo Arnaldo
Published: August 2004

A method for carrying out molecular dynamics simulations in which the potential energy U of the molecular system is constrained at its initial value is developed and thoroughly tested. The constraint is not introduced within the framework of the Lagrange multipliers technique, rather it is fulfilled in a natural way by carrying out the simulations in terms of suitable sets of delocalized coordinates. Such coordinates are defined by an appropriate tuning of the Baker, Kessi, and Delley internal delocalized nonredundant coordinates technique [J. Chem. Phys. 105, 192 (1996)]. The proposed method requires multiple evaluations of energy and gradients in each step of the molecular dynamics simulation, so that constant U simulations suffer some overhead compared to ordinary simulations. But the particular formulation of the delocalized coordinates and of the equations of motion greatly simplifies all the various steps required by the Baker’s technique, thus allowing for the efficient implementation of the method itself. The technique is reliable and allows for very high accuracy in the potential energy conservation during the whole simulation. Moreover, it proved to be free of drift troubles which can occur when standard constraint methods are straightforwardly implemented without the application of appropriate correcting techniques.
On the mechanism of reorientational and structural relaxation in supercooled liquids: The role of border dynamics and cooperativity
Authors: Kim Joohyun , Keyes T.
Published: August 2004

Molecular dynamics simulation and analysis based upon the many-body potential energy landscape (PEL) are employed to characterize single molecule reorientation and structural relaxation, and their interrelation, in deeply supercooled liquid CS2. The rotational mechanism changes from small-step Debye diffusion to sudden large angle reorientation (SLAR) as the temperature falls below the mode-coupling temperature Tc. The onset of SLAR is explained in terms of the PEL; it is an essential feature of low-T rotational dynamics, along with the related phenomena of dynamic heterogeneity and the bifurcation of slow and fast relaxation processes. A long trajectory in which the system is initially trapped in a low energy local minimum, and eventually escapes, is followed in detail, both on the PEL and in real space. During the trapped period, “return” dynamics occurs, always leading back to the trap. Structural relaxation is identified with irreversible escape to a new trap. These processes lead to weak and strong SLAR, respectively; strong SLAR is a clear signal of structural relaxation. Return dynamics involves small groups of two to four molecules, while a string-like structure composed of all the active groups participates in the escape. It is proposed that, rather than simple, nearly instantaneous, one-dimensional barrier crossings, relaxation involves activation of the system to the complex, multidimensional region on the borders of the basins of attraction of the minima for an extended period.
Counterion associative behavior with flexible polyelectrolytes
Authors: Prabhu Vivek M. , Amis Eric J. , Bossev Dobrin P. , Rosov Nicholas
Published: August 2004

At low ionic strength, organic counterions dress a flexible charged polymer as measured directly by small-angle neutron scattering and neutron spin-echo spectroscopy. This dressed state, quantified by the concentration dependence of the static correlation length, illustrates the polymer-counterion coupled nature on the nanometer length scale. The counterions, made visible by selective hydrogen and deuterium labeling, undress from the polymeric template by addition of sodium chloride. The addition of this electrolyte leads to two effects: increased Debye electrostatic screening and decoupled organic counterion-polymer correlations. Neutron spin-echo spectroscopy measures a slowing down of the effective diffusion coefficient of the labeled counterions at the length scale of 8 nm, the static correlation length, indicating the nanosecond counterion dynamics mimics the polymer. These experiments, performed with semidilute solutions of tetramethylammonium poly(styrene sulfonate) [(h-TMA+) d-PSS], apply to relevant biopolymers including single and double stranded DNA and unfolded proteins, which undergo orchestrated dynamics of counterions and chain segments to fold, unfold, and assemble.
Ionic effect on combing of single DNA molecules and observation of their force-induced melting by fluorescence microscopy
Authors: Liu Yu-Ying , Wang Peng-Ye , Dou Shuo-Xing , Wang Wei-Chi , Xie Ping , Yin Hua-Wei , Zhang Xing-Dong , Xi Xu Guang
Published: August 2004

Molecular combing is a powerful and simple method for aligning DNA molecules onto a surface. Using this technique combined with fluorescence microscopy, we observed that the length of λ-DNA molecules was extended to about 1.6 times their contour length (unextended length, 16.2 μm) by the combing method on hydrophobic polymethylmetacrylate coated surfaces. The effects of sodium and magnesium ions and pH of the DNA solution were investigated. Interestingly, we observed force-induced melting of single DNA molecules.
Quadrupole and octupole polarizabilities for the ground states of lithiumlike systems from Z=3 to 20
Authors: Chen Chao , Wang Zhi-Wen
Published: August 2004

The quadrupole and octupole polarizabilities for the ground states of lithiumlike systems from Z=3 to 20 are calculated with the full-core plus correlation method. For the neutral lithium atom, the typical patterns of convergence of the quadrupole and octupole polarizabilities are analyzed. The calculated quadrupole and octupole polarizabilities of the ground state for lithium atom are compared with the previous theoretical results obtained by other methods; our predictions agree with the most accurate reports in the literature very well. For lithiumlike ions, our prediction may provide valuable reference data for other accurate theoretical calculations in future.
Shape and motility of a model cell: A computational study
Authors: Satyanarayana S. V. M. , Baumgaertner A.
Published: August 2004

We have investigated the shape, size, and motility of a minimal model of an adherent biological cell using the Monte Carlo method. The cell is modeled as a two dimensional ring polymer on the square lattice enclosing continuously polymerizing and depolymerizing actin networks. Our lattice model is an approximate representation of a real cell at a resolution of one actin molecule, 5 nm. The polymerization kinetics for the actin network are controlled by appropriate reaction probabilities which correspond to the correct experimental reaction rates. Using the simulation data we establish various scaling laws relating the size of the model cell to the concentration of polymerized and unpolymerized actin molecules and the length of the enclosing membrane. The computed drift velocities, which characterize the motility of the cell, exhibit a maximum at a certain fraction of polymerized actin which agrees with physiological fractions observed in experiments. The appearance of the maximum is related to the competition between the polymerization-induced protrusion of the membrane and the concomitant suppression of membrane fluctuations.
Cranklike conformational transitions in polyethylene
Authors: Nigro B. , Di Stefano D. , Rassu A. , Moro G. J.
Published: August 2004

Molecular dynamics simulations of a variety of polymeric systems provide the evidence for two different kinds of conformational transitions: independent single bond transitions and cranklike transitions (or correlated bond transitions). While single bond transitions can be rationalized according to standard theories of activated processes controlled by the saddle point crossing, a more complex description is required for the other type of transitions. In a recent work devoted to the analysis of the simplified chain model with three rotors [B. Nigro and G. J. Moro, J. Phys. Chem. B 106, 7365 (2002)], a theory has been proposed for cranklike transitions represented as a kinetic process between equilibrium states differing by two torsional angles (i.e., two bond transitions). Moreover their rate coefficients were estimated on the basis of a local expansion about the bifurcation of the separatrices departing from the potential function maximum. In the present work the same theory is applied to a model for long alkyl chains in solution, in order to rationalize the behavior of cranklike transitions in polyethylene and to recognize the molecular features controlling them. We obtain probabilities of occurrence of cranklike transitions in substantial agreement with simulation results. Furthermore, the theory is capable of explaining the dependence of the rate on the separation between the two reactive bonds, as well as the dependence on the conformational state of the starting configuration. In particular, selection rules for next-to-nearest neighbor transitions are recovered from the shape of the separatrices and the location of the corresponding bifurcations.
Nematic-amorphous polymer interfaces in the presence of a compatibilizer
Authors: Hamm M. , Goldbeck-Wood G. , Fraaije J. G. E. M. , Zvelindovsky A. V.
Published: August 2004

We introduce and apply a variant of a dynamic self-consistent field simulation in two dimensions to predict the structure of interfaces between a nematic and an amorphous polymer compatibilized by a diblock copolymer. First, we investigate the effect of the nematic order on the polymer polymer interface without compatibilizer. Then we include the compatibilizer and consider two interfacial setups previously used in experiments, i.e., the bilayer setup and the trilayer setup. In the bilayer setup the diblock copolymer is mixed into the amorphous homopolymer and migrates to the interface in the course of the simulation forming a layered structure. We compare the amount of copolymer at the interface for initial concentrations of the copolymer below and above the critical micelle concentration. In the trilayer setup the initial thickness of the diblock copolymer is varied. The resulting interfacial morphology evolves in the competition between the lamellar structure induced by the interface and a micellar structure, which is intrinsic to the copolymer.
Hydrogen loss from nucleobase nitrogens upon electron attachment to isolated DNA and RNA nucleotide anions
Authors: Liu Bo , Hvelplund Preben , Brøndsted Nielsen Steen , Tomita Shigeo
Published: August 2004

Electron transfer to isolated nucleotide monoanions in collisions with Na vapor induces hydrogen loss from nitrogen of the transient nucleobase anion. The cross section for this process is linearly correlated with the number of N-H hydrogens and is highest for guanine. The process is much faster than microseconds since only dehydrogenated dianions survived for mass spectrometric detection. The lifetime of the adenosine 5′-monophospate dianions was measured to be 0.2 ms in an electrostatic ion storage ring but also a longer-lived component with a lifetime of at least 10 ms was identified. Implications of dissociation along the N-H coordinate for a nucleotide in DNA are briefly discussed in terms of Watson-Crick base pairs.
Dynamical density functional theory and its application to spinodal decomposition
Authors: Archer A. J. , Evans R.
Published: August 2004

We present an alternative derivation of the dynamical density functional theory for the one-body density profile of a classical fluid developed by Marconi and Tarazona [J. Chem. Phys. 110, 8032 (1999)]. Our derivation elucidates further some of the physical assumptions inherent in the theory and shows that it is not restricted to fluids composed of particles interacting solely via pair potentials; rather it applies to general, multibody interactions. The starting point for our derivation is the Smoluchowski equation and the theory is therefore one for Brownian particles and as such is applicable to colloidal fluids. In the second part of this paper we use the dynamical density functional theory to derive a theory for spinodal decomposition that is applicable at both early and intermediate times. For early stages of spinodal decomposition our nonlinear theory is equivalent to the (generalized) linear Cahn–Hilliard theory, but for later times it incorporates coupling between different Fourier components of the density fluctuations (modes) and therefore goes beyond Cahn–Hilliard theory. We describe the results of calculations for a model (Yukawa) fluid which show that the coupling leads to the growth of a second maximum in the density fluctuations, at a wave number larger than that of the main peak.
Efficient formulation of the stochastic simulation algorithm for chemically reacting systems
Authors: Cao Yang , Li Hong , Petzold Linda
Published: August 2004

In this paper we examine the different formulations of Gillespie’s stochastic simulation algorithm (SSA) [D. Gillespie, J. Phys. Chem. 81, 2340 (1977)] with respect to computational efficiency, and propose an optimization to improve the efficiency of the direct method. Based on careful timing studies and an analysis of the time-consuming operations, we conclude that for most practical problems the optimized direct method is the most efficient formulation of SSA. This is in contrast to the widely held belief that Gibson and Bruck’s next reaction method [M. Gibson and J. Bruck, J. Phys. Chem. A 104, 1876 (2000)] is the best way to implement the SSA for large systems. Our analysis explains the source of the discrepancy.
A field theoretical approach to calculate electronic Born-Oppenheimer coupling terms
Authors: Vértesi T. , Vibók Á. , Halász G. J. , Baer M.
Published: August 2004

In this paper we suggest to consider the spatial distribution of the Born-Oppenheimer nonadiabatic coupling terms as fields which are created by sources, located at degeneracy points, and which can be derived using the ordinary mathematical tools of field theory. It is shown that the curl-divergence equations as formed within a given Hilbert space [M. Baer, Chem. Phys. Lett. 35, 112 (1975)] can be converted into a set of inhomogeneous coupled Poisson equations which are solved for a given set of boundary conditions. The method is applied to the three-state Hilbert subspace of the H3 system. The numerical results are compared with ab initio calculations for which a very encouraging fit is found.
A quasidegenerate formulation of the second order n-electron valence state perturbation theory approach
Authors: Angeli Celestino , Borini Stefano , Cestari Mirko , Cimiraglia Renzo
Published: August 2004

The n-electron valence state perturbation theory (NEVPT) is reformulated in a quasidegenerate (QD) approach. The new theory allows the treatment of cases where the proximity of the energies causes artifacts in the zero order description. Problems of quasidegeneration are relevant in the dynamics involving regions at avoided crossings (or conical intersections) and in spectroscopy where the energies and oscillator strengths can be strongly influenced by the mixing of states of different nature. Two test cases are analyzed concerning (a) the ionic-neutral avoided crossing in LiF and (b) the valence/Rydberg mixing in the excited states of ethene. The QD-NEVPT2 is shown to be a useful tool for such systems.
The behavior of fluids near solutes: A density functional theory and computer simulation study
Authors: Reddy Govardhan , Yethiraj Arun
Published: August 2004

The density distribution of solvent near a solute particle is studied using density functional theory and Monte Carlo simulation. The fluid atoms interact with each other via a hard sphere plus Yukawa potential, and interact with the solute via a hard sphere potential. For small solute sizes, the solvent displays liquidlike ordering near the particle. When the solute become larger, a drying transition is observed at state points near the coexistence conditions of the solvent. These predictions are similar to those of a recent theory for the hydrophobic effect by Lum, Chandler, and Weeks [J. Phys. Chem. 103, 4570 (1999)], although a comparison with simulations shows that the theory of this work is quantitatively more accurate. The connection between density functional methods and the LCW approach is also established.
Molecular dynamics simulation of optically trapped colloidal particles at an oil-water interface
Authors: Sun Jizhong , Stirner T.
Published: August 2004

Using molecular dynamics simulations, we calculate the net force on a colloidal particle trapped by an optical tweezer and confined within a particle monolayer which is in motion relative to the trapped particle. The calculations are compared with recent experimental data on polystyrene particles located at an oil-water interface. Good agreement between theory and experiment is obtained over the investigated range of lattice constants for an interaction mechanism between the polystyrene particles which is dominated by an effective dipole-dipole potential. The assumed interaction mechanism is consistent with the formation of surface charge dipoles at the particle-oil interface due to the dissociaton of the hydrophilic sulfate headgroups at the surface of the polystyrene particles. A possible physical mechanism for the formation of the surface charge dipoles, involving a diffuse cloud of fully hydrated counterions, is described, and the fraction of surface groups contributing to the formation of surface charge dipoles is estimated to be of the order of 10−1 for the present system.
Low-energy electron scattering cross section for the production of CO within solid films of carbon dioxide
Authors: Deschamps M. C. , Michaud M. , Sanche L.
Published: August 2004

We report absolute electron scattering cross sections σp for the production of CO within thin solid film of carbon dioxide (CO2) condensed on a solid Ar substrate. The CO fragments, which remain trapped within the bulk of the carbon dioxide film, are detected in situ by recording energy losses to their lowest triplet electronic state a 3Π using high-resolution electron-energy-loss spectroscopy. The production of CO is studied as a function of the electron exposure, film thickness, and incident electron energy between 2 and 30 eV, a range within which most of the secondary electrons are created in systems irradiated by high-energy particles. The energy dependence is characterized by a feature around 4 eV with σp=(7.0±4.0)×10−18 cm2, a minimum around 7 eV, a strong rise up to a large and broad maximum around 15 eV with σp=(5.4±2.5)×10−17 cm2, a decrease to a minimum around 18.5 eV, and finally a monotonous increase up to 30 eV. The CO production is discussed in terms of the formation of electron resonances or transient anion states, which may lead directly to the fragmentation of the molecule via dissociative electron attachment or indirectly by decaying into an entirely repulsive part of the corresponding excited neutral and positive ion states.
New electronic spectra of the HCCl and DCCl Ã-X̃ vibronic bands
Authors: Lin Chia-Shih , Chen Ying-En , Chang Bor-Chen
Published: August 2004

The dispersed fluorescence spectra following the excitation of several Ã←X̃ vibronic bands of HCCl and DCCl at visible wavelengths were successfully acquired in a discharge supersonic free jet expansion using an intensified charge-coupled device detector. The dispersed fluorescence spectra reveal more details of the X̃1 A′ state vibrational structure in these molecules than previous reports. Dispersed fluorescence spectra of all four isotopomers (HC35Cl, HC37Cl, DC35Cl, and DC37Cl) were obtained. These dispersed fluorescence spectra exhibit the vibrational structures up to ≈6000 cm−1 above the zero-point level and determine the vibrational structures of HC37Cl and DC37Cl. Complete vibrational parameters including fundamental frequencies, anharmonicities, and coupling constants were determined for the HCCl/DCCl X̃1 A′ state. Furthermore, perturbations from the background triplet state ã3 A″ and emission to triplet state levels were observed in the spectra. The singlet-triplet energy gap from the zero-point level could be determined to be 2167 cm−1 (6.20±0.05 kcal/mol) in HCCl and to be 2187 cm−1 (6.25±0.05 kcal/mol) in DCCl. Additionally, some of the Ã←X̃ excitation spectrum are reported for HCCl and DCCl.