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  • Articles  (23,658)
  • 2010-2014  (23,658)
  • Journal of Chemical Physics  (10,392)
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  • Articles  (23,658)
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  • 1
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    Stochastic algorithm for size-extensive vibrational self-consistent field methods on fully anharmonic potential energy surfaces (2014)
    American Institute of Physics (AIP)
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    Publication Date: 2014-12-31
    Description: A stochastic algorithm based on Metropolis Monte Carlo (MC) is presented for the size-extensive vibrational self-consistent field methods (XVSCF( n ) and XVSCF[ n ]) for anharmonic molecular vibrations. The new MC-XVSCF methods substitute stochastic evaluations of a small number of high-dimensional integrals of functions of the potential energy surface (PES), which is sampled on demand, for diagrammatic equations involving high-order anharmonic force constants. This algorithm obviates the need to evaluate and store any high-dimensional partial derivatives of the potential and can be applied to the fully anharmonic PES without any Taylor-series approximation in an intrinsically parallelizable algorithm. The MC-XVSCF methods reproduce deterministic XVSCF calculations on the same Taylor-series PES in all energies, frequencies, and geometries. Calculations using the fully anharmonic PES evaluated on the fly with electronic structure methods report anharmonic effects on frequencies and geometries of much greater magnitude than deterministic XVSCF calculations, reflecting an underestimation of anharmonic effects in a Taylor-series approximation to the PES.
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
    Published by American Institute of Physics (AIP)
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  • 2
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    A systematic way for the cost reduction of density fitting methods (2014)
    American Institute of Physics (AIP)
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    Publication Date: 2014-12-31
    Description: We present a simple approach for the reduction of the size of auxiliary basis sets used in methods exploiting the density fitting (resolution of identity) approximation for electron repulsion integrals. Starting out of the singular value decomposition of three-center two-electron integrals, new auxiliary functions are constructed as linear combinations of the original fitting functions. The new functions, which we term natural auxiliary functions (NAFs), are analogous to the natural orbitals widely used for the cost reduction of correlation methods. The use of the NAF basis enables the systematic truncation of the fitting basis, and thereby potentially the reduction of the computational expenses of the methods, though the scaling with the system size is not altered. The performance of the new approach has been tested for several quantum chemical methods. It is demonstrated that the most pronounced gain in computational efficiency can be expected for iterative models which scale quadratically with the size of the fitting basis set, such as the direct random phase approximation. The approach also has the promise of accelerating local correlation methods, for which the processing of three-center Coulomb integrals is a bottleneck.
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    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
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  • 3
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    Viscoelasticity of model interphase chromosomes (2014)
    American Institute of Physics (AIP)
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    Publication Date: 2014-12-31
    Description: We investigated the viscoelastic response of model interphase chromosomes by tracking the three-dimensional motion of hundreds of dispersed Brownian particles of sizes ranging from the thickness of the chromatin fiber up to slightly above the mesh size of the chromatin solution. In agreement with previous computational studies on polymer solutions and melts, we found that the large-time behaviour of the diffusion coefficient and the experienced viscosity of moving particles as functions of particle size deviate from the traditional Stokes-Einstein relation and agree with a recent scaling theory of diffusion of non-sticky particles in polymer solutions. Interestingly, we found that at short times large particles are temporarily “caged” by chromatin spatial constraints, which thus form effective domains whose sizes match remarkably well with recent experimental results for micro-tracers inside interphase nuclei. Finally, by employing a known mathematical relation between the time mean-square displacement of tracked particles and the complex shear modulus of the surrounding solution, we calculated the elastic and viscous moduli of interphase chromosomes.
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    Topics: Chemistry and Pharmacology , Physics
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  • 4
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    Excellence of numerical differentiation method in calculating the coefficients of high temperature series expansion of the free energy and convergence problem of the expansion (2014)
    American Institute of Physics (AIP)
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    Publication Date: 2014-12-31
    Description: In this paper, it is shown that the numerical differentiation method in performing the coupling parameter series expansion [S. Zhou, J. Chem. Phys. 125 , 144518 (2006); AIP Adv. 1 , 040703 (2011)] excels at calculating the coefficients a i of hard sphere high temperature series expansion ( HS-HTSE ) of the free energy. Both canonical ensemble and isothermal-isobaric ensemble Monte Carlo simulations for fluid interacting through a hard sphere attractive Yukawa ( HSAY ) potential with extremely short ranges and at very low temperatures are performed, and the resulting two sets of data of thermodynamic properties are in excellent agreement with each other, and well qualified to be used for assessing convergence of the HS-HTSE for the HSAY fluid. Results of valuation are that (i) by referring to the results of a hard sphere square well fluid [S. Zhou, J. Chem. Phys. 139 , 124111 (2013)], it is found that existence of partial sum limit of the high temperature series expansion series and consistency between the limit value and the true solution depend on both the potential shapes and temperatures considered. (ii) For the extremely short range HSAY potential, the HS-HTSE coefficients a i falls rapidly with the order i , and the HS-HTSE converges from fourth order; however, it does not converge exactly to the true solution at reduced temperatures lower than 0.5, wherein difference between the partial sum limit of the HS-HTSE series and the simulation result tends to become more evident. Something worth mentioning is that before the convergence order is reached, the preceding truncation is always improved by the succeeding one, and the fourth- and higher-order truncations give the most dependable and qualitatively always correct thermodynamic results for the HSAY fluid even at low reduced temperatures to 0.25.
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    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
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  • 5
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    Accurate nonrelativistic ground-state energies of 3d transition metal atoms (2014)
    American Institute of Physics (AIP)
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    Publication Date: 2014-12-31
    Description: We present accurate nonrelativistic ground-state energies of the transition metal atoms of the 3 d series calculated with Fixed-Node Diffusion Monte Carlo (FN-DMC). Selected multi-determinantal expansions obtained with the CIPSI (Configuration Interaction using a Perturbative Selection made Iteratively) method and including the most prominent determinants of the full configuration interaction expansion are used as trial wavefunctions. Using a maximum of a few tens of thousands determinants, fixed-node errors on total DMC energies are found to be greatly reduced for some atoms with respect to those obtained with Hartree-Fock nodes. To the best of our knowledge, the FN-DMC/(CIPSI nodes) ground-state energies presented here are the lowest variational total energies reported so far. They differ from the recently recommended non-variational values of McCarthy and Thakkar [J. Chem. Phys. 136 , 054107 (2012)] only by a few percents of the correlation energy. Thanks to the variational property of FN-DMC total energies, our results provide exact lower bounds for the absolute value of all-electron correlation energies, | E c |.
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    Topics: Chemistry and Pharmacology , Physics
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  • 6
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    Coil-to-globule transitions of homopolymers and multiblock copolymers (2014)
    American Institute of Physics (AIP)
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    Publication Date: 2014-12-31
    Description: We study the coil-to-globule transitions of both homopolymers and multiblock copolymers using integrated tempering sampling method, which is a newly proposed enhanced sampling method that can efficiently sample the energy space with low computational costs. For homopolymers, the coil-to-globule structure transition temperatures ( T tr ) are identified by the radius of gyration of the chain. The transition temperature shows a primary scaling dependence on the chain length ( N ) with T tr ∼ N −1/2 . For multiblock copolymers, the coil-to-globule transition can be identified as first order, depending on the block size and the difference in attractive interactions of blocks. The influence of mutating a small portion of strongly attractive blocks to weakly attractive blocks on the coil-to-globule transition is found to be related to the position of the mutation.
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    Topics: Chemistry and Pharmacology , Physics
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  • 7
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    Effects of reactant rotational excitations on H2 + NH2 → H + NH3 reactivity (2014)
    American Institute of Physics (AIP)
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    Publication Date: 2014-12-31
    Description: Rotational mode specificity of the title reaction is examined using an initial state selected time-dependent wave packet method on an accurate ab initio based global potential energy surface. This penta-atomic reaction presents an ideal system to test several dynamical approximations, which might be useful for future quantum dynamics studies of polyatomic reactions, particularly with rotationally excited reactants. The first approximation involves a seven-dimensional (7D) model in which the two non-reactive N–H bonds are fixed at their equilibrium geometry. The second is the centrifugal sudden (CS) approximation within the 7D model. Finally, the J -shifting ( J S) model is tested, again with the fixed N–H bonds. The spectator-bond approximation works very well in the energy range studied, while the centrifugal sudden and J -shifting integral cross sections (ICSs) agree satisfactorily with the coupled-channel counterparts in the low collision energy range, but deviate at the high energies. The calculated integral cross sections indicate that the rotational excitation of H 2 somewhat inhibits the reaction while the rotational excitations of NH 2 have little effect. These findings are compared with the predictions of the sudden vector projection model. Finally, a simple model is proposed to predict rotational mode specificity using K -averaged reaction probabilities.
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    Topics: Chemistry and Pharmacology , Physics
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  • 8
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    Two-phase flow in a chemically active porous medium (2014)
    American Institute of Physics (AIP)
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    Publication Date: 2014-12-31
    Description: We study the problem of the transformation of a given reactant species into an immiscible product species, as they flow through a chemically active porous medium. We derive the equation governing the evolution of the volume fraction of the species, in a one-dimensional macroscopic description, identify the relevant dimensionless numbers, and provide simple models for capillary pressure and relative permeabilities, which are quantities of crucial importance when tackling multiphase flows in porous media. We set the domain of validity of our models and discuss the importance of viscous coupling terms in the extended Darcy’s law. We investigate numerically the steady regime and demonstrate that the spatial transformation rate of the species along the reactor is non-monotonous, as testified by the existence of an inflection point in the volume fraction profiles. We obtain the scaling of the location of this inflection point with the dimensionless lengths of the problem. Eventually, we provide key elements for optimization of the reactor.
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    Topics: Chemistry and Pharmacology , Physics
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  • 9
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    New observation and combined analysis of the Cs20g−, 0u+, and 1g states at the asymptotes 6S1/2 + 6P1/2 and 6S1/2 + 6P3/2 (2014)
    American Institute of Physics (AIP)
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    Publication Date: 2014-12-31
    Description: We report on new observations of the photoassociation spectroscopy of ultracold cesium molecules using a highly sensitive detection technique and a combined analysis with all observed electronic states. The technique is achieved by directly modulating the frequency of the trapping lasers of a magneto-optical trap. New observations of the Cs 2 0 g − , 0 u + , and 1 g states at the asymptotes 6 S 1/2 + 6 P 1/2 and 6 S 1/2 + 6 P 3/2 are reported. The spectral range is extended to the red detuning of 112 cm −1 below the 6 S 1/2 + 6 P 3/2 dissociation limit. Dozens of vibrational levels of the ultracold Cs 2 0 g − , 0 u + , and 1 g states are observed for the first time. The available experimental binding energies of these states are analyzed simultaneously in a framework of the generalized LeRoy–Bernstein theory and the almost degenerate perturbation theory by Marinescu and Dalgarno [Phys. Rev. A: At., Mol., Opt. Phys. 52 , 311 (1995)]. The unique atomic-related parameter c 3 governing the dispersion forces of all the molecular states is estimated as (10.29 ± 0.05) a.u.
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  • 10
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    Direct path integral estimators for isotope fractionation ratios (2014)
    American Institute of Physics (AIP)
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    Publication Date: 2014-12-31
    Description: Fractionation of isotopes among distinct molecules or phases is a quantum effect which is often exploited to obtain insights on reaction mechanisms, biochemical, geochemical, and atmospheric phenomena. Accurate evaluation of isotope ratios in atomistic simulations is challenging, because one needs to perform a thermodynamic integration with respect to the isotope mass, along with time-consuming path integral calculations. By re-formulating the problem as a particle exchange in the ring polymer partition function, we derive new estimators giving direct access to the differential partitioning of isotopes, which can simplify the calculations by avoiding thermodynamic integration. We demonstrate the efficiency of these estimators by applying them to investigate the isotope fractionation ratios in the gas-phase Zundel cation, and in a few simple hydrocarbons.
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    Topics: Chemistry and Pharmacology , Physics
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