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In this paper, we introduce new integrators of Newton-Cotes type and investigate the connection between these new methods, differential methods, and symplectic integrators. From the literature, we can see that several one step symplectic integrators have been obtained based on symplectic geometry. However, the investigation of multistep symplectic integrators is very poor. In this paper, we introduce a new numerical method of closed Newton-Cotes type and we write it as a symplectic multilayer structure. We apply the symplectic schemes in order to solve Hamilton's equations of motion which are linear in position and momentum. We observe that the Hamiltonian energy of the system remains almost constant as integration proceeds. [ABSTRACT FROM AUTHOR]

In this paper, we present a new approach to study the probability distribution of the radius of gyration of freely jointed chains. In this approach, we study the joint distribution PN(Rg2,Rvector G), where Rg is the radius of gyration and Rvector G is the vector from the first bead to the center of the chain. We derive an iteration relation between the probability distributions of chains with lengths N and N+1. When the chain length is large, the iteration relation can be approximated by an evolution equation with integral determining condition. The equation is solved to obtain the probability distribution function, which yields the known result obtained by Fixman [J. Chem. Phys. 36, 306 (1962)] using the integral method. We hope the iteration method in this paper could be used to study the probability distribution of the structure factor of polymer molecules. [ABSTRACT FROM AUTHOR]

The addition of zinc complexes to the syntheses of indium phosphide nanocrystals (InP NCs) has become commonplace, due to their ability to alter and significantly improve observed optical properties. In this paper, the role of zinc complexes on the synthesis and observed properties of InP is carefully examined. Produced InP and InP:Zn2+ NCs are thoroughly characterized from both structural (core and surface) and optical perspectives over a wide range of Zn2+ compositions (0%–43% atomic content). We find no differences in the physical (NC size and polydispersity) and structural properties (crystallographic phase) of InP and InP:Zn2+ NCs. Optically, significant changes are observed when zinc is added to InP syntheses, including blueshifted absorption edges and maxima, increased quantum yields, and the near elimination of surface state emission. These improved optical properties result from surface passivation by zinc carboxylate moieties. Changes to the optical properties begin at zinc concentrations as low as 5%, demonstrating the high sensitivity of InP optical properties to exogenous species. [ABSTRACT FROM AUTHOR]

Potential energy surface (PES) holds the key in understanding a number of atomic clusters or molecular phenomena. However, due to the high dimension and incredible complexity of PES, only indirect methods can be used to characterize a PES of a given system in general. In this paper, a branched dynamic lattice searching method was developed to travel the PES, which was described in detail by a single-root network (SRN). The advantage of SRN is that it reflects the topological relation between different conformations and highlights the size of each structure energy trap. On the basis of SRN, to demonstrate how to transform one conformation to another, the transition path that connects two local minima in the PES was constructed. Herein, we take Lennard-Jones (LJ) clusters at the sizes of 38, 55, and 75 as examples. It is found that the PES of these three clusters have many local funnels and each local funnel represents one morphology. If a morphology is located more frequently, it will lie in a larger local funnel. Besides, certain steps of the transition path were generated successfully, such as changing from icosahedral to truncated octahedral of the LJ38-cluster. Though we do not exhibit all the parts of the PES or all transition paths, this method indeed works well in the local area and can be used more widely. [ABSTRACT FROM AUTHOR]

Local coupled-cluster theory provides an algorithm for measuring electronic correlation quickly, using only the spatial locality of localized electronic orbitals. Previously, we showed [J. Subotnik et al., J. Chem. Phys. 125, 074116 (2006)] that one may construct a local coupled-cluster singles-doubles theory which (i) yields smooth potential energy surfaces and (ii) achieves near linear scaling. That theory selected which orbitals to correlate based only on the distances between the centers of different, localized orbitals, and the approximate potential energy surfaces were characterized as smooth using only visual identification. This paper now extends our previous algorithm in three important ways. First, locality is now based on both the distances between the centers of orbitals as well as the spatial extent of the orbitals. We find that, by accounting for the spatial extent of a delocalized orbital, one can account for electronic correlation in systems with some electronic delocalization using fast correlation methods designed around orbital locality. Second, we now enforce locality on not just the amplitudes (which measure the exact electron-electron correlation), but also on the two-electron integrals themselves (which measure the bare electron-electron interaction). Our conclusion is that we can bump integrals as well as amplitudes, thereby gaining a tremendous increase in speed and paradoxically increasing the accuracy of our LCCSD approach. Third and finally, we now make a rigorous definition of chemical smoothness as requiring that potential energy surfaces not support artificial maxima, minima, or inflection points. By looking at first and second derivatives from finite difference techniques, we demonstrate complete chemical smoothness of our potential energy surfaces (bumping both amplitudes and integrals). These results are significant both from a theoretical and from a computationally practical point of view. [ABSTRACT FROM AUTHOR]

After many unsuccessful efforts, the structure of solid CD4 III finally has been solved. In this paper, we examine if the known tunneling spectra are consistent with the orientational potentials at the two sites with different symmetries. To this end, we study the rotational kinetic energy of the molecules, construct appropriate pocket states for the tunneling problem, and set up a model potential. Approximate energy levels are obtained from the Ritz variational principle. The agreement between the experimentally determined tunneling frequencies and the calculations is rather good, corroborating the findings of the structural analysis. A continuation of this paper will deal with the partly deuterated methanes. [ABSTRACT FROM AUTHOR]

The first part of this paper deals with the enumeration of all possible stereoisomers (or polytypes) of a binary (two-colored) icosahedron (either noncentered or centered) via Polya’s theorem. The numbers of achiral and chiral structures for each combination of the two types of atoms (or colors) A and B are determined. In cluster chemistry, A and B may represent two different kinds of atoms (e.g., main-group elements vs transition metals) in a heteronuclear cluster, two different ligand environments in a homonuclear cluster, or atoms and holes (vacant sites) in an icosahedral cluster with missing vertices. The second part deals with the electronic requirements of binary icosahedral clusters where A and B may represent main-group elements and transition metals, or, atoms and holes. Significantly different electron counts are observed for centered vs noncentered icosahedral clusters, depending upon the nature of the interstitial atom. Thus, icosahedral clusters can be classified into four broad categories according to their electron counts: Type I: the majority are those with 13 electron pairs as represented by noncentered icosahedral clusters, or those centered with main-group elements or early transition metals as the interstitial atom; Type II: those with more than 13 electron pairs as exemplified by centered icosahedral clusters with late transition metals as the interstitial atom; and Types III and IV: those with less than 13 electron pairs as observed for centered Au icosahedral clusters. The atom and electron counting rules developed are rationalized in terms of molecular orbital theory. The utilities of the atom and electron counting rules in systematizing structural and spectroscopic data of icosahedral clusters (in both solid-state and gas-phase) as well as in rationalizing the variations of the electron counts in different icosahedral cluster systems are discussed. [ABSTRACT FROM AUTHOR]

In this paper we investigate the dynamic properties of the minimal Bell-Lavis (BL) water model and their relation to the thermodynamic anomalies. The BL model is defined on a triangular lattice in which water molecules are represented by particles with three symmetric bonding arms interacting through van der Waals and hydrogen bonds. We have studied the model diffusivity in different regions of the phase diagram through Monte Carlo simulations. Our results show that the model displays a region of anomalous diffusion which lies inside the region of anomalous density, englobed by the line of temperatures of maximum density. Further, we have found that the diffusivity undergoes a dynamic transition which may be classified as fragile-to-strong transition at the critical line only at low pressures. At higher densities, no dynamic transition is seen on crossing the critical line. Thus evidence from this study is that relation of dynamic transitions to criticality may be discarded. [ABSTRACT FROM AUTHOR]

Gillespie’s direct method (DM) [D. Gillespie, J. Chem. Phys. 81, 2340 (1977)] for exact stochastic simulation of chemical reaction systems has been widely adopted. It is easy to implement but requires large computation for relatively large systems. Recently, two more efficient methods, next reaction method (NRM) [M. A. Gibson and J. Bruck, J. Phys. Chem. A 105, 1876 (2000)] and optimized DM (ODM) [Y. Cao et al., J. Chem. Phys. 121, 4059 (2004)], have been developed to improve simulation speed. It has been demonstrated that the ODM is the state-of-the-art most efficient method for exact stochastic simulation of most practical reaction systems. In this paper, we first develop an exact stochastic simulation algorithm named ODMK that is more efficient than the ODM. We then develop an approximate method named K-skip method to further accelerate simulation. Using two chemical reaction systems, we demonstrate that our ODMK and K-skip method can save 20%–30% and 70%–80% simulation time, respectively, comparing to the ODM. We also show that our ODMK and K-skip method provide almost the same simulation accuracy as the ODM. [ABSTRACT FROM AUTHOR]

Nonequilibrium molecular dynamics simulations are performed on a dense simple dipolar fluid under a planar Couette shear flow. Shear generates heat, which is removed by thermostatting terms added to the equations of motion of the fluid particles. The spatial structure of simple fluids at high shear rates is known to depend strongly on the thermostatting mechanism chosen. Kinetic thermostats are either biased or unbiased: biased thermostats neglect the existence of secondary flows that appear at high shear rates superimposed upon the linear velocity profile of the fluid. Simulations that employ a biased thermostat produce a string phase where particles align in strings with hexagonal symmetry along the direction of the flow. This phase is known to be a simulation artifact of biased thermostatting, and has not been observed by experiments on colloidal suspensions under shear flow. In this paper, we investigate the possibility of using a suitably directed electric field, which is coupled to the dipole moments of the fluid particles, to stabilize the string phase. We explore several thermostatting mechanisms where either the kinetic or configurational fluid degrees of freedom are thermostated. Some of these mechanisms do not yield a string phase, but rather a shear-thickening phase; in this case, we find the influence of the dipolar interactions and external field on the packing structure, and in turn their influence on the shear viscosity at the onset of this shear-thickening regime. [ABSTRACT FROM AUTHOR]

In this paper, ice nanotubes confined in carbon nanotubes are investigated by molecular dynamics. The trigonal, square, pentagonal, and hexagonal water tubes are obtained, respectively. The current-voltage (I-V) curves of water nanotubes are found to be nonlinear, and fluctuations of conductance spectra of these ice nanotubes show that the transport properties of ice nanotubes are quite different from those of bulk materials. Our studies indicate that the conductance gap of ice nanotube is related to the difference value from the Fermi energy EF to the nearest molecular energy level E0. Increasing the diameter of a water molecular nanostructure results in the increase of the conductance. [ABSTRACT FROM AUTHOR]

The satellite transitions acquired in real time by magic angle spinning (STARTMAS) NMR experiment combines a train of pulses with sample rotation at the magic angle to refocus the first- and second-order quadrupolar broadening of spin I=3/2 nuclei in a series of echoes, while allowing the isotropic chemical and quadrupolar shifts to evolve. The result is real-time isotropic NMR spectra at high spinning rates using conventional MAS equipment. In this paper we describe in detail how STARTMAS data can be acquired and processed with ease on commercial equipment. We also discuss the advantages and limitations of the approach and illustrate the discussion with numerical simulations and experimental data from four different powdered solids. [ABSTRACT FROM AUTHOR]

In this paper we establish the temperature dependence of the kinetic coefficient associated with crystal growth into the supercooled liquid for a wide range of organic and inorganic materials. We show that the kinetic coefficient for crystal growth scales with the shear viscosity η as η-ξ and that the exponent depends systematically on the fragility of the liquid. The greater the fragility (i.e., deviation away from an Arrhenius temperature dependence for η), the larger the difference 1-ξ. We argue that this breakdown in scaling between the crystal growth kinetics and the viscosity is a manifestation of heterogeneous dynamics in supercooled liquids. In addition, we show that the absolute growth rate at intermediate viscosities is correlated with the entropy difference between the liquid and the crystal. [ABSTRACT FROM AUTHOR]

Adsorption/desorption isotherms in porous materials are commonly used for characterization. In order to analyze the data, accurate calculations of fluid adsorption in various complex pore models are required. The reversible, low adsorption portion of the isotherm is generally well described by molecular simulation, since the relevant fluid/substrate interactions are described at molecular level. This molecular approach is, however, ineffective in the hysteresis region because the large scale spatial distribution of heterogeneities in the pore network is beyond the computer capabilities. On the other hand, coarse grained approaches are more suited to take into account this porous network complexity at large scale and discuss the hysteresis nature, but the molecular description is lost. In this paper, a multiscale approach is introduced which allows both a molecular description of fluid/substrate interactions, and taking into account the connectivity between the various domains in a porous material. The case of argon confined in heterogeneous tubular silica mesopores (MCM-41 or oxidized porous silicon) is considered. Comparison with the simple independent domain theory shows the strong influence of quenched disorder. It is also shown that the independent pore model significantly overestimates the hysteresis width. The effect of pore ends open at only one or at both ends is addressed. [ABSTRACT FROM AUTHOR]

Angle-resolved photoelectron spectra from rotationally selected à 1Au state acetylene have been recorded using velocity-map imaging. Several Renner-Teller split vibrational bands have been observed and assigned, showing good agreement with previous zero kinetic energy photoelectron (ZEKE) work [S. T. Pratt, P. M. Dehmer, and J. L. Dehmer, J. Chem. Phys. 99, 6233 (1993); S.-J. Tang, Y.-C. Chou, J. J.-M. Lin, and Y.-C. Hsu, ibid. 125, 133201 (2006).] The extracted photoelectron angular distributions (PADs) corresponding to these bands show a strong dependence on the vibronic angular momentum projection quantum number K+. Subbands with odd K+ show PADs with maximum intensity along the polarization vector of the ionizing laser beam, while those with even K+ show PADs with maximum intensity perpendicular to this direction. Velocity-map images recorded at low photoelectron energies approach rotational resolution of the ion, and the evolution of the PADs with increasing rotational level prepared in the à 1Au state indicates the potential of a “complete” determination of the photoionization dynamics of the à 1Au state. This is further investigated in the following paper. [ABSTRACT FROM AUTHOR]

This paper presents an optimized effective potential (OEP) approach based on density functional theory (DFT) for individual excited states that implements a simple method of taking the necessary orthogonality constraints into account. The amended Kohn-Sham (KS) equations for orbitals of excited states having the same symmetry as the ground one are proposed. Using a variational principle with some orthogonality constraints, the OEP equations determining a local exchange potential for excited states are derived. Specifically, local potentials are derived whose KS determinants minimize the total energies and are simultaneously orthogonal to the determinants for states of lower energies. The parametrized form of an effective DFT potential expressed as a direct mapping of the external potential is used to simplify the OEP integral equations. A performance of the presented method is examined by exchange-only calculations of excited state energies for simple atoms and molecules. [ABSTRACT FROM AUTHOR]

Cis, cis-peroxynitrous acid is known to be an intermediate in atmospheric reactions between OH and NO2 as well as HOO and NO. The infrared absorption spectra of matrix-isolated cc-HOONO and cc-DOONO in argon have been observed in the range of 500–8000 cm-1. Besides the seven fundamental vibrational modes that have been assigned earlier for this molecule [Zhang et al., J. Chem. Phys. 124, 084305 (2006)], more than 50 of the overtone and combination bands have been observed for cc-HOONO and cc-DOONO. Ab initio CCSD(T)/atomic natural orbital anharmonic force field calculations were used to help guide the assignments. Based on this study of the vibrational overtone transitions of cis, cis-HOONO that go as high as 8000 cm-1 and the earlier paper on the vibrational fundamentals, we conclude that the CCSD(T)/ANO anharmonic frequencies seem to correct to ±35 cm-1. The success of the theoretically predicted anharmonic frequencies {υ} in assigning overtone spectra of HOONO up to 8000 cm-1 suggests that the CCSD(T)/ANO method is producing a reliable potential energy surface for this reactive molecule. [ABSTRACT FROM AUTHOR]

In this paper we present a new form of the nucleation theorems applicable to heterogeneous nucleation. These heterogeneous nucleation theorems allow, for the first time, direct determination of properties of nanoclusters formed on pre-existing particles from measured heterogeneous nucleation probabilities. The theorems can be used to analyze the size (first theorem) and the energetics (second theorem) of heterogeneous clusters independent of any specific nucleation model. We apply the first theorem to the study of small water and n-propanol clusters formed at the surface of 8 nm silver particles. According to the experiments the size of the two-component critical clusters is found to be below 90 molecules, and only less than 20 molecules for pure water, less than 300 molecules for pure n-propanol. These values are drastically smaller than the ones predicted by the classical nucleation theory, which clearly indicates that the nucleating clusters are too small to be quantitatively described using a macroscopic theory. [ABSTRACT FROM AUTHOR]

The conjugation of an uncharged polymer to DNA fragments makes it possible to separate DNA by free-solution electrophoresis. This end-labeled free-solution electrophoresis method has been shown to successfully separate ssDNA with single monomer resolution up to about 110 bases. It is the aim of this paper to investigate in more detail the coupled hydrodynamic and electrophoretic deformation of the ssDNA-label conjugate at fields below 400 V/cm. Our model is an extension of the theoretical approach originally developed by Stigter and Bustamante [Biophys. J. 75, 1197 (1998)] to investigate the problems of a tethered chain stretching in a hydrodynamic flow and of the electrophoretic stretch of a tethered polyelectrolyte. These two separate models are now used together since the charged DNA is “tethered” to the uncharged polymer (and vice versa), and the resulting self-consistent model is used to predict the deformation and the electrophoretic velocity for the hybrid molecule. Our theoretical and experimental results are in good qualitative agreement. [ABSTRACT FROM AUTHOR]

We study the time series produced by blinking quantum dots, by means of an aging experiment, and we examine the results of this experiment in the light of two distinct approaches to complexity, renewal and slow modulation. We find that the renewal approach fits the result of the aging experiment, while the slow modulation perspective does not. We make also an attempt at establishing the existence of an intermediate condition. [ABSTRACT FROM AUTHOR]

We expand upon the results for the force-extension behavior of single-collapsed polymer chains to consider the mechanical response of networks of cross-linked globular polymers in poor solvent. Force-strain curves are obtained under the affine deformation approximation for networked globules with both disordered and ordered globule conformations. Due to their large stored lengths, these networks would be capable of reaching extremely large strains. They also show anomalous nonmonotonic force-strain response, as a consequence of the nonmonotonic force-extension curves of their constituent globules. Finally, we consider the stability of ordered and disordered globules in these networks and propose means taken from biological and colloid science to stabilize networked globules. [ABSTRACT FROM AUTHOR]

The new symplectic molecular dynamics (MD) integrators presented in the first paper of this series were applied to perform MD simulations of water. The physical properties of a system of flexible TIP3P water molecules computed by the new integrators, such as diffusion coefficients, orientation correlation times, and infrared (IR) spectra, are in good agreement with results obtained by the standard method. The comparison between the new integrators’ and the standard method’s integration time step sizes indicates that the resulting algorithm allows a 3.0 fs long integration time step as opposed to the standard leap-frog Verlet method, a sixfold simulation speed-up. The accuracy of the method was confirmed, in particular, by computing the IR spectrum of water in which no blueshifting of the stretching normal mode frequencies is observed as occurs with the standard method. [ABSTRACT FROM AUTHOR]

Despite the importance of the C3H radical in both combustion and interstellar space, the reactions of C3H toward stable molecules have never been studied. In this paper, we report our detailed mechanistic study on the radical-molecule reaction C3H+H2O at the Becke's three parameter Lee–Yang–Parr–B3LYP/6-311G(d,p) and coupled cluster with single, double, and triple excitations-CCSD(T)/6-311G(2d,p) (single-point) levels. It is shown that the C3H+H2O reaction initially favors formation of the carbene-insertion intermediates HCCCHOH (1a,1b) rather than the direct H- or OH-abstraction process. Subsequently, the isomers (1a,1b) can undergo a direct H- extrusion to form the well-known product propynal HCCCHO (P5). Highly competitively, (1a,1b) can take the successive 1,4- and 1,2-H-shift interconversion to isomer H2CCCHO(2a,2b) and then to isomer H2CCHCO(3a,3b), which can finally take a direct C–C bond cleavage to give product C2H3 and CO (P1). The other products are kinetically much less feasible. With the overall entrance barrier 10.6 kcal/mol, the title reaction can be important in postburning processes. Particularly, our calculations suggest that the title reaction may play a role in the formation of the intriguing interstellar molecule, propynal HCCCHO. The calculated results will also be useful for the analogous C3H reactions such as with ammonia and alkanes. [ABSTRACT FROM AUTHOR]

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. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Recently, experimental and theoretical studies on the water system are very active and noticeable. A transferable intermolecular potential seven points approach including fluctuation charges and flexible body (ABEEM-7P) based on a combination of the atom-bond electronegativity equalization and molecular mechanics (ABEEM/MM), and its application to small water clusters are explored and tested in this paper. The consistent combination of ABEEM and molecular mechanics (MM) is to take the ABEEM charges of atoms, bonds, and lone-pair electrons into the intermolecular electrostatic interaction term in molecular mechanics. To examine the charge transfer we have used two models coming from the charge constraint types: one is a charge neutrality constraint on whole water system and the other is on each water molecule. Compared with previous water force fields, the ABEEM-7P model has two characters: (1) the ABEEM-7P model not only presents the electrostatic interaction of atoms, bonds and lone-pair electrons and their changing in respond to different ambient environment but also introduces “the hydrogen bond interaction region” in which a new parameter k[sub lp,H](R[sub lp,H]) is used to describe the electrostatic interaction of the lone-pair electron and the hydrogen atom which can form the hydrogen bond; (2) nonrigid but flexible water body permitting the vibration of the bond length and angle is allowed due to the combination of ABEEM and molecular mechanics, and for van der Waals interaction the ABEEM-7P model takes an all atom–atom interaction, i.e., oxygen–oxygen, hydrogen–hydrogen, oxygen–hydrogen interaction into account. The ABEEM-7P model based on ABEEM/MM gives quite accurate predictions for gas-phase state properties of the small water clusters (H[sub 2]O)[sub n] (n=2–6), such as optimized geometries, monomer dipole moments, vibrational frequencies, and cluster interaction energies. Due to its explicit description of charges and the hydrogen bond, the ABEEM-7P model will be applied to discuss properties of liquid water, ice, aqueous solutions, and biological systems. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

In this paper we investigate the influence of self-affine roughness on the friction coefficient μ[sub f] of a rubber body under incomplete contact onto a solid surface. The roughness is characterized by the rms amplitude w, the correlation length ξ, and the roughness exponent H. It is shown that with increasing surface roughening at short and/or long length scales (decreasing H and/or increasing ratio w/ξ, respectively), the maximum of the friction coefficient μ[sub f] shifts to lower sliding velocities. The latter occurs only for conditions of incomplete contact for small contact length scales λ (<ξ). In all cases, the friction coefficient μ[sub f] increases monotonically with decreasing roughness exponent H and/or increasing roughness ratio w/ξ and attains its maximum value for sufficiently large contact length scales (>ξ). © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The method, introduced in the preceding paper, for recasting molecular self-consistent field (SCF) or density functional theory (DFT) orbitals in terms of intrinsic minimal bases of quasiatomic orbitals, which differ only little from the optimal free-atom minimal-basis orbitals, is used to elucidate the bonding in several silicon clusters. The applications show that the quasiatomic orbitals deviate from the minimal-basis SCF orbitals of the free atoms by only very small deformations and that the latter arise mainly from bonded neighbor atoms. The Mulliken population analysis in terms of the quasiatomic minimal-basis orbitals leads to a quantum mechanical interpretation of small-ring strain in terms of antibonding encroachments of localized molecular-orbitals and identifies the origin of the bond-stretch isomerization in Si[sub 4]H[sub 6]. In the virtual SCF/DFT orbital space, the method places the qualitative notion of virtual valence orbitals on a firm basis and provides an unambiguous ab initio identification of the frontier orbitals. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The stress–strain relations and the yield behavior of a model glass (a 80:20 binary Lennard-Jones mixture) [W. Kob and H. C. Andersen, Phys. Rev. E 52, 4134 (1995)] is studied by means of molecular dynamics simulations. In a previous paper [F. Varnik, L. Bocquet, J.-L. Barrat, and L. Berthier, Phys. Rev. Lett. 90, 095702 (2003)] it was shown that, at temperatures below the glass transition temperature, T[sub g], the model exhibits shear banding under imposed shear. It was also suggested that this behavior is closely related to the existence of a (static) yield stress (under applied stress, the system does not flow until the stress σ exceeds a threshold value σ[sub y]). A thorough analysis of the static yield stress is presented via simulations under imposed stress. Furthermore, using steady shear simulations, the effect of physical aging, shear rate and temperature on the stress–strain relation is investigated. In particular, we find that the stress at the yield point (the “peak”-value of the stress–strain curve) exhibits a logarithmic dependence both on the imposed shear rate and on the “age” of the system in qualitative agreement with experiments on amorphous polymers [C. Ho Huu and T. Vu-Khanh, Theoretical and Applied Fracture Mechanics 40, 75 (2003); L. E. Govaert, H. G. H. van Melick, and H. E. H. Meijer, Polymer 42, 1271 (2001)] and on metallic glasses [W. L. Johnson, J. Lu, and M. D. Demetriou, Intermetallics 10, 1039 (2002)]. In addition to the very observation of the yield stress which is an important feature seen in experiments on complex systems like pastes, dense colloidal suspensions [F. Da Cruz, F. Chevoir, D. Bonn, and P. Coussot, Phys. Rev. E 66, 051305 (2002)] and foams [G. Debrégeas, H. Tabuteau, and J.-M. di Meglio, Phys. Rev. Lett. 87, 178305 (2001)], further links between our model and soft glassy materials are found. An example is the existence of hysteresis loops in the system response to a varying imposed stress. Finally, we measure the static yield stress for our model and study its dependence on temperature. We find that for temperatures far below the mode coupling critical temperature of the model (T[sub c]=0.435 in Lennard-Jones units), σ[sub y] decreases slowly upon heating followed by a stronger decrease as T[sub c] is approached. We discuss the reliability of results on the static yield stress and give a criterion for its validity in terms of the time scales relevant to the problem. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

As it was shown from molecular dynamics of two-dimensional hard needles [Phys. Rev. E 66, 012201 (2002)], the uniaxial velocity autocorrelation function (VACF) of this system exhibits a two time scale character. This corresponds to the symmetry of the particles. In this paper we provide a theory of the Enskog type that corroborates the idea that the VACF can be successfully described as a sum of two single decays. From the comparison between molecular dynamics and theoretical results, we show that the Enskog approach is a satisfactory kinetic theory, which functions as well in the nematic as in the isotropic phase. Different properties of VACFs have been investigated, in particular, the dependence on the orientational order, temperature, and particles’ inertness. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Point polarizable molecules at fixed spatial positions have solvable electrostatic properties in classical approximation, the most familiar being the Clausius–Mossotti (CM) formula. This paper generalizes the model and imagines various applications to nanosystems. The behavior is worked out for a sequence of octahedral fragments of simple cubic crystals, and the crossover to the bulk CM law is found. Some relations to fixed moment systems are discussed and exploited. The one-dimensional dipole stack is introduced as an important model system. The energy of interaction of parallel stacks is worked out, and clarifies the diverse behavior found in different crystal structures. It also suggests patterns of self-organization which polar molecules in solution might adopt. A sum rule on the stack interaction is found and tested. Stability of polarized states under thermal fluctuations is discussed, using the one-dimensional domain wall as an example. Possible structures for polar hard ellipsoids are considered. An idea is formulated for enhancing polarity of nanosystems by intentionally adding metallic coatings. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

A second order method is developed for determining steepest descent lines of potential energy surfaces by following steepest curves of successive local quadratic surface approximations. The basic principle is similar to that of a previously developed method where, however, the availability of analytically calculated exact Hessians was assumed wherever needed. By contrast, only the analytically calculated exact values of the energy and its gradient are used here and this difference entails marked changes in strategy. Applications to the Gonzalez–Schlegel and the Müller–Brown surfaces show that the method compares favorably with existing methods. [ABSTRACT FROM AUTHOR]

A single vibrational coherence state can be created by using either vibrationally resonant infrared field-matter interactions or Raman transitions induced by the electronically off-resonant fields. Then, the two-dimensional (2D) vibrational coherence created by two such interactions can be probed by using electronically off-resonant optical pulse via scattering by the 2D transient grating. However, due to the off-resonant field-matter interactions during the probing process, the signal intensity is likely to be small. Thus, in this paper, the cases when the 2D transient grating is probed by electronically resonant optical pulse are theoretically considered and the associated nonlinear response functions are investigated. It turns out that these novel 2D vibrational spectroscopic methods utilizing an electronically resonant probe pulse can be used to study both the linear and quadratic vibronic coupling strengths of molecules in either isotropic or anisotropic condensed phases, in addition to the vibrational anharmonicity and nonlinearity of the coordinate dependencies of the dipole moment, polarizability, and hyperpolarizability. © 2000 American Institute of Physics. [ABSTRACT FROM AUTHOR]

We propose a direct method for reducing the dimension of the space of orbital products that occur, for example, in the calculation of time dependent density functional theory linear response and in Hedin’s GW approximation to the electron propagator. We do this by defining, within the linear space of orbital products, a subspace of dominant directions that are associated with a certain eigenvalue problem. These directions span the entire linear space of products with an error that decreases approximately exponentially with their number. Our procedure works best for atomic orbitals of finite range and it avoids the use of extra sets of auxiliary fit functions. [ABSTRACT FROM AUTHOR]

Selected configuration interaction (SCI) for atomic and molecular electronic structure calculations is reformulated in a general framework encompassing all CI methods. The linked cluster expansion is used as an intermediate device to approximate CI coefficients BK of disconnected configurations (those that can be expressed as products of combinations of singly and doubly excited ones) in terms of CI coefficients of lower-excited configurations where each K is a linear combination of configuration-state-functions (CSFs) over all degenerate elements of K. Disconnected configurations up to sextuply excited ones are selected by Brown’s energy formula, ΔEK=(E-HKK)BK2/(1-BK2), with BK determined from coefficients of singly and doubly excited configurations. The truncation energy error from disconnected configurations, ΔEdis, is approximated by the sum of ΔEKs of all discarded Ks. The remaining (connected) configurations are selected by thresholds based on natural orbital concepts. Given a model CI space M, a usual upper bound ES is computed by CI in a selected space S, and EM=ES+ΔEdis+δE, where δE is a residual error which can be calculated by well-defined sensitivity analyses. An SCI calculation on Ne ground state featuring 1077 orbitals is presented. Convergence to within near spectroscopic accuracy (0.5 cm-1) is achieved in a model space M of 1.4×109 CSFs (1.1×1012 determinants) containing up to quadruply excited CSFs. Accurate energy contributions of quintuples and sextuples in a model space of 6.5×1012 CSFs are obtained. The impact of SCI on various orbital methods is discussed. Since ΔEdis can readily be calculated for very large basis sets without the need of a CI calculation, it can be used to estimate the orbital basis incompleteness error. A method for precise and efficient evaluation of ES is taken up in a companion paper. [ABSTRACT FROM AUTHOR]

We review the force-extension behavior of polymers collapsed in poor solvent, modified to include the effects of semiflexibility and considered for globules with “ordered” and “disordered” internal structures. A series of ordered globules is used as a model for the unbinding of a disordered globule beneath its glass transition and for multiple-repeat proteins such as the poly-Ig-domain titin used in atomic force microscopy studies. These single-chain results form the foundation for the treatment of cross-linked networks of globular polymers. [ABSTRACT FROM AUTHOR]

Intra- and interpolyad structures are investigated in the vibrational energy pattern of acetylene, using the spectroscopic Hamiltonian presented in previous papers in this series [see El Idrissi et al., J. Chem. Phys. 110, 2074 (1999)]. The existence of two constants of the motion is shown to generate very regular patterns in the manifold of vibrational energy levels. Distinct regular and oscillatory contributions are evidenced in the number of vibrational levels in the main polyads, which are fully reproduced using the generating function presented in Sadovskií and Zhilinskií [J. Chem. Phys. 103, 10520 (1995)]. Further developments of this approach are outlined. © 2000 American Institute of Physics. [ABSTRACT FROM AUTHOR]

A quantum-mechanical model is designed for the calculation of termolecular association reaction rate coefficients in the low-pressure fall-off regime. The dynamics is set up within the energy transfer mechanism and the kinetic scheme is the steady-state approximation. We applied this model to the formation of ozone O+O[sub 2]+M→O[sub 3]+M for M=Ar, making use of semiquantitative potential energy surfaces. The stabilization process is treated by means of the vibrational close-coupling infinite order sudden scattering theory. Major approximations include the neglect of the O[sub 3] vibrational bending mode and rovibrational couplings. We calculated individual isotope-specific rate constants and rate constant ratios over the temperature range 10–1000 K and the pressure fall-off region 10[sup -7]–10[sup 2] bar. The present results show a qualitative and semiquantitative agreement with available experiments, particularly in the temperature region of atmospheric interest. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Assesses the importance of the empirical corrections in first-principle ab initio model chemistries. Success of the Gaussian (G2) model and its derivatives in reproducing a variety of experimental values; Expression of the higher-level correction (HLC) in terms of the number of alpha and beta valence electrons; Importance of the empirical corrections for G2 methods.

Presents a model of exit-channel corrected state distributions in the products of three-atom barrierless unimolecular reactions. Variational determination of transition state (TS); Transfer of energy between rotational and translational motions on the way from the TS to the products; Derivation of free-path integration model.

It was previously reported that the reaction products from the synthesis of ozone in an electric discharge through molecular oxygen display a non-mass-dependent (NoMaDic) oxygen isotope effect. In this paper, we report a detailed characterization of the isotope effect, including the effect of molecular oxygen pressure, and the presence of a chemically inert third body (helium). The NoMaDic effect is due to an isotopically selective stabilization of the O3 formation reaction intermediate, possibly resulting from the ability of the different isotopomers to exhibit different molecular symmetries. [ABSTRACT FROM AUTHOR]

In this Reply, we respond to the issue raised in Taylor’s Comment [J. Chem. Phys.123, 167101 (2005), preceding paper] on our previous article [J. A. Porter and J. E. G. Lipson, J. Chem. Phys.122, 094906 (2005)] and show that the predictions of the Born-Green-Yvon theory are in qualitative agreement with simulation trends for all chain lengths studied. In addition, we comment on Taylor’s simulation results and discuss why the points raised in Taylor’s Comment do not affect the conclusions reached in our earlier article. [ABSTRACT FROM AUTHOR]

A new ionothermal synthesis utilizing 1-alkyl-pyridinium hexafluorophosphates [CxPy][PF6] (x = 2, 4, 6) led to the formation of highly crystalline single-phase ammonium cobalt trifluoride, (NH4)CoF3. Although ammonium transition-metal fluorides have been extensively studied with respect to their structural and magnetic properties, multiple aspects remain unclear. For that reason, the obtained (NH4)CoF3 has been investigated over a broad temperature range by means of single-crystal and powder x-ray diffraction as well as magnetization and specific heat measurements. In addition, energy-dispersive x-ray and vibrational spectroscopy as well as thermal analysis measurements were undertaken. (NH4)CoF3 crystallizes in the cubic perovskite structure and undergoes a structural distortion to a tetragonal phase at 127.7 K, which also is observable in the magnetic susceptibility measurements, which has not been observed before. A second magnetic phase transition occurring at 116.9 K is of second-order character. The bifurcation of the susceptibility curves indicates a canted antiferromagnetic ordering. At 2.5 K, susceptibility measurements point to a third phase change for (NH4)CoF3. [ABSTRACT FROM AUTHOR]

Advances in nanophotonics, quantum optics, and low-dimensional materials have enabled precise control of light–matter interactions down to the nanoscale. Combining concepts from each of these fields, there is now an opportunity to create and manipulate photonic matter via strong coupling of molecules to the electromagnetic field. Toward this goal, here we demonstrate a first principles framework to calculate polaritonic excited-state potential-energy surfaces, transition dipole moments, and transition densities for strongly coupled light–matter systems. In particular, we demonstrate the applicability of our methodology by calculating the polaritonic excited-state manifold of a formaldehyde molecule strongly coupled to an optical cavity. This proof-of-concept calculation shows how strong coupling can be exploited to alter photochemical reaction pathways by influencing avoided crossings with tuning of the cavity frequency and coupling strength. Therefore, by introducing an ab initio method to calculate excited-state potential-energy surfaces, our work opens a new avenue for the field of polaritonic chemistry. [ABSTRACT FROM AUTHOR]

It is well established that the chemistry in microdroplets has been found to be radically different from reactions in bulk, particularly in the case of water. It has also been established that there is a threshold size for microdroplets to behave differently than droplets near the 10 µm diameter range. We present a three-dimensional electrostatic treatment in the spirit of the Gouy–Chapman model for double layers at interfaces. Our treatment predicts a strong concentration of charged molecules toward the surface of the droplet. As the droplet size deceases, the majority of the volume of the liquid experiences a large DC electric field. Such electric fields are highly unusual in a conducting fluid such as water. We believe that this unique environment helps to explain the reaction rate acceleration and new chemistry that have been observed in microdroplets compared to bulk phase. [ABSTRACT FROM AUTHOR]

The master equation for a chemical hyperchaos model has been studied by stochastic simulations in this paper. It was revealed that intrinsic fluctuations have intensive effect on hyperchaos, having dramatically altered the dynamics and phase space portrait of the deterministic hyperchaos. This is remarkable because the drastic effect displayed by internal noises on hyperchaos is in considerable contrast with the case of simple type chaos where the effect of intrinsic fluctuations is trivial. © 2001 American Institute of Physics. [ABSTRACT FROM AUTHOR]

To what extent can a 'bottom-up' mesoscale fluid model developed through systematic coarse-graining techniques recover the physical properties of a molecular scale system? In a previous paper [C.-C. Fu, P. M. Kulkarni, M. S. Shell, and L. G. Leal, J. Chem. Phys. 137, 164106 (2012)], we addressed this question for thermodynamic properties through the development of coarse-grained (CG) fluid models using modified iterative Boltzmann inversion methods that reproduce correct pair structure and pressure. In the present work we focus on the dynamic behavior. Unlike the radial distribution function and the pressure, dynamical properties such as the self-diffusion coefficient and viscosity in a CG model cannot be matched during coarse-graining by modifying the pair interaction. Instead, removed degrees of freedom require a modification of the equations of motion to simulate their implicit effects on dynamics. A simple but approximate approach is to introduce a friction coefficient, γ, and random forces for the remaining degrees of freedom, in which case γ becomes an additional parameter in the coarse-grained model that can be tuned. We consider the non-Galilean-invariant Langevin and the Galilean-invariant dissipative particle dynamics (DPD) thermostats with CG systems in which we can systematically tune the fraction [lowercase_phi_synonym] of removed degrees of freedom. Between these two choices, only DPD allows both the viscosity and diffusivity to match a reference Lennard-Jones liquid with a single value of γ for each degree of coarse-graining [lowercase_phi_synonym]. This friction constant is robust to the pressure correction imposed on the effective CG potential, increases approximately linearly with [lowercase_phi_synonym], and also depends on the interaction cutoff length, rcut, of the pair interaction potential. Importantly, we show that the diffusion constant and viscosity are constrained by a simple scaling law that leads to a specific choice of DPD friction coefficient for a given degree of coarse-graining. Moreover, we find that the pair interaction distance cutoffs used for DPD random and dissipative forces should be considered separately from that of the conservative interaction potential. [ABSTRACT FROM AUTHOR]

Modeling the bridge function in the reference-hypernetted chain equation with that of a hard-sphere fluid has proven to be highly successful for simple liquids, particularly when the reference-hard-sphere diameter is treated as an adjustable parameter. In this paper, we examine the generalization of this technique to liquids of diatomic molecules, with the reference bridge function taken from that of the corresponding hard-diatomic-molecule fluid. Specifically, the diatomic molecules of the system of interest interact through an atom–atom Lennard-Jones potential while the hard-diatomic-reference model is solved in Percus–Yevick approximation. We find that variation of the sphere diameter of the hard-diatomic molecule makes possible excellent agreement with simulation results for the two-center Lennard-Jones fluid, just as it does for simple fluids. [ABSTRACT FROM AUTHOR]

Although molecular dynamics simulations have become a useful tool in essentially all fields of chemistry, condensed matter physics, materials science, and biology, there is still a large gap between the time scale which can be reached in molecular dynamics simulations and that observed in experiments. To address the problem, many enhanced sampling methods were introduced, which effectively extend the time scale being approached in simulations. In this perspective, we review a variety of enhanced sampling methods. We first discuss collective-variables-based methods including metadynamics and variationally enhanced sampling. Then, collective variable free methods such as parallel tempering and integrated tempering methods are presented. At last, we conclude with a brief introduction of some newly developed combinatory methods. We summarize in this perspective not only the theoretical background and numerical implementation of these methods but also the new challenges and prospects in the field of the enhanced sampling. [ABSTRACT FROM AUTHOR]

In this paper, we report the measurements of the third-order susceptibilities of new dithienylethylenes in solutions using the degenerate four-wave mixing technique at λ=532 nm in the picosecond regime. From these measurements we deduced the second-order hyperpolarizabilities γ values, which are about 10[sup 3] larger than the γ value of CS[sub 2] and are comparable with the corresponding values for the new synthesized diphenylpolyene derivatives. We also determined the optical power limiting properties of the mentioned compounds using nanosecond laser pulses in the visible range. The dispersion of nonlinear absorption coefficients is obtained in the framework of Gaussian collimated beam propagation in sample. Kerr ellipsometry measurements are responsible for the excited absorption cross section and are spectrally shifted comparing with the optical limiting processes (up to 50 nm). The appropriate quantum chemical calculations are done. The contributions of electronic and vibration subsystems as well as contribution of the particular parts of each molecule into the output third nonlinear optical response are given. © 2001 American Institute of Physics. [ABSTRACT FROM AUTHOR]