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Journal of Chemical Physics

Jeppe C Dyre
This article gives an overview of excess-entropy scaling, the 1977 discovery by Rosenfeld that entropy determines properties of liquids like viscosity, diffusion constant, and heat conductivity. We give examples from computer simulations confirming this intriguing connection between dynamics and thermodynamics, counterexamples, and experimental validations. Recent uses in application-related contexts are reviewed, and theories proposed for the origin of excess-entropy scaling are briefly summarized. It is shown that if two thermodynamic state points of a liquid have the same microscopic dynamics, they must have the same excess entropy...
December 7, 2018: Journal of Chemical Physics
Junhao Li, Matthew Otten, Adam A Holmes, Sandeep Sharma, C J Umrigar
This paper presents in detail our fast semistochastic heat-bath configuration interaction (SHCI) method for solving the many-body Schrödinger equation. We identify and eliminate computational bottlenecks in both the variational and perturbative steps of the SHCI algorithm. We also describe the parallelization and the key data structures in our implementation, such as the distributed hash table. The improved SHCI algorithm enables us to include in our variational wavefunction two orders of magnitude more determinants than has been reported previously with other selected configuration interaction methods...
December 7, 2018: Journal of Chemical Physics
Norikazu Ohtori, Hikaru Uchiyama, Yoshiki Ishii
The Stokes-Einstein (SE) relation is examined for hard-sphere (HS) and Weeks-Chandler-Andersen (WCA) fluids by the molecular dynamics method on temperatures and densities corresponding to the saturated vapor line of Lennard-Jones (LJ) liquids. While the self-diffusion coefficient, D , and shear viscosity, η sv , increases and decreases, respectively, with increasing steepness in interaction potentials, the same SE relation holds for HS and WCA fluids as that obtained for LJ liquids, i.e., Dη sv = ( k B T / C )( N / V )1/3 , where k B is the Boltzmann constant, T is the temperature, and N is the particle number included in the system volume V ...
December 7, 2018: Journal of Chemical Physics
Hannah K Wayment-Steele, Vijay S Pande
As deep Variational Auto-Encoder (VAE) frameworks become more widely used for modeling biomolecular simulation data, we emphasize the capability of the VAE architecture to concurrently maximize the time scale of the latent space while inferring a reduced coordinate, which assists in finding slow processes as according to the variational approach to conformational dynamics. We provide evidence that the VDE framework [Hernández et al. , Phys. Rev. E 97 , 062412 (2018)], which uses this autocorrelation loss along with a time-lagged reconstruction loss, obtains a variationally optimized latent coordinate in comparison with related loss functions...
December 7, 2018: Journal of Chemical Physics
De-Wen Sun, Marcus Müller
Besides dictating the equilibrium phase diagram, the rugged free-energy landscape of AB block copolymers gives rise to a multitude of non-equilibrium phenomena. Self-consistent field theory (SCFT) can be employed to calculate the mean-field free energy, <mml:math xmlns:mml=""> <mml:mi>F</mml:mi> <mml:mrow> <mml:mo>[</mml:mo> <mml:mrow> <mml:msubsup> <mml:mrow> <mml:mi>ϕ</mml:mi> </mml:mrow> <mml:mrow> <mml:mi>A</mml:mi> </mml:mrow> <mml:mrow> <mml:mi>t</mml:mi> <mml:mi>a</mml:mi> <mml:mi>r</mml:mi> <mml:mi>g</mml:mi> <mml:mi>e</mml:mi> <mml:mi>t</mml:mi> </mml:mrow> </mml:msubsup> </mml:mrow> <mml:mo>]</mml:mo> </mml:mrow> </mml:math> , of a non-equilibrium unstable state that is characterized by a given spatial density distribution, <mml:math xmlns:mml="http://www...
December 7, 2018: Journal of Chemical Physics
R Holomb, O Kondrat, V Mitsa, M Veres, A Czitrovszky, A Feher, N Tsud, M Vondráček, K Veltruská, V Matolín, K C Prince
The super-bandgap laser irradiation of the in situ prepared As-S chalcogenide films was found to cause drastic structural transformations and unexpected selective diffusion processes, leading to As enrichment on the nanolayer surface. Excitation energy dependent synchrotron radiation photoelectron spectroscopy showed complete reversibility of the molecular transformations and selective laser-driven mass transport during "laser irradiation"-"thermal annealing" cycles. Molecular modeling and density functional theory calculations performed on As-rich cage-like clusters built from basic structural units indicate that the underlying microscopic mechanism of laser induced transformations is connected with the realgar-pararealgar transition in the As-S structure...
December 7, 2018: Journal of Chemical Physics
M Kar, T Körzdörfer
We aim to find homovalent alternatives for lead and iodine in CH3 NH3 PbI3 perovskites that show bandgaps suitable for building novel perovskite-perovskite tandem solar cells. To this end, we employ a computational screening for materials with a bandgap between 1.0 eV and 1.9 eV, using density functional theory calculations at the Perdew-Burke-Ernzerhof and Heyd-Scuseria-Ernzerhof levels of theory. The room-temperature stability of the materials and their phases that satisfy the bandgap criteria is evaluated based on the empirical Goldschmidt tolerance factor...
December 7, 2018: Journal of Chemical Physics
Nancy Makri
In a recent communication [N. Makri, J. Chem. Phys. 148 , 101101 (2018)], it was shown that the locality of interactions in many systems of interest allows a decomposition of the path integral and its evaluation via sequential linking of the paths of relatively small "modules" (e.g., chemical groups or monomers). The present paper describes the modular path integral methodology for simulating dynamical properties by propagating the density matrix in real time. The procedure is first presented for the simple topology of a single-file arrangement of units interacting via nearest neighbor couplings and subsequently extended to the calculation of two-particle correlations in arrays that may also contain some long-range interactions, to the treatment of systems with side chains or cyclic structures, to the simulation of internal dynamics in long organic molecules, and to the modifications required for coupling of one or several units of a system to dissipative environments...
December 7, 2018: Journal of Chemical Physics
Erik Thoms, Sławomir Kołodziej, Michał Wikarek, Stefan Klotz, Sebastian Pawlus, Marian Paluch
We report a striking anomaly in the pressure dependent Debye-relaxation time of the branched monohydroxy alcohol 2-butyl-1-octanol. Evidence of a crossover from slower to faster than exponential pressure dependency was obtained at different temperatures via high pressure broadband dielectric spectroscopy. At the same time, viscosity measurements reveal similar behavior in the viscosity, respectively, the structural relaxation time, indicating a similar origin of the phenomena.
December 7, 2018: Journal of Chemical Physics
J-M Hartmann, C Boulet, H Zhang, F Billard, O Faucher, B Lavorel
We present the first quantum mechanical model of the collisional dissipation of the alignment of a gas of symmetric-top molecules (ethane) impulsively induced by a linearly polarized non-resonant laser field. The approach is based on use of the Bloch model and of the Markov and secular approximations in which the effects of collisions are taken into account through the state-to-state rates associated with exchanges among the various rotational states. These rates are constructed using the Energy Corrected Sudden (ECS) approximation with (a few) input parameters obtained independently from fits of the pressure-broadening coefficients of ethane absorption lines...
December 7, 2018: Journal of Chemical Physics
Russell K W Spencer, Mark W Matsen
No abstract text is available yet for this article.
December 7, 2018: Journal of Chemical Physics
Bo Peng, Karol Kowalski
In this paper, we analyze new approximations of the Green's function coupled cluster (GFCC) method where locations of poles are improved by extending the excitation level of inner auxiliary operators. These new GFCC approximations can be categorized as the GFCC-i( n , m ) method, where the excitation level of the inner auxiliary operators ( m ) used to describe the ionization potential and electron affinity effects in the N - 1 and N + 1 particle spaces is higher than the excitation level ( n ) used to correlate the ground-state coupled cluster wave function for the N -electron system...
December 7, 2018: Journal of Chemical Physics
E M Isaac Moreira, B G A Brito, J Higino Damasceno, J N Teixeira Rabelo, G-Q Hai, L Cândido
The valence electron binding energies and the aromaticity of neutral and charged small boron clusters with three and four atoms are investigated using a combination of the fixed-node diffusion quantum Monte Carlo (FN-DMC) method, the density functional theory, and the Hartree-Fock approximation. The obtained electron binding energies such as the adiabatic detachment energy, vertical detachment energy, adiabatic ionization potential, and the vertical ionization potential are in excellent agreement with available experimental measurements...
December 7, 2018: Journal of Chemical Physics
P Honvault, G Guillon, R Kochanov, V Tyuterev
The isotopic exchange reaction, 16 O + 18 O18 O → 16 O18 O + 18 O, involving excited ozone, <mml:math xmlns:mml=""> <mml:msubsup> <mml:mrow> <mml:mi>O</mml:mi> </mml:mrow> <mml:mrow> <mml:mn>3</mml:mn> </mml:mrow> <mml:mrow> <mml:mo>*</mml:mo> </mml:mrow> </mml:msubsup> </mml:math> , as intermediate complex, was investigated by means of a time independent quantum mechanical approach using the TKTHS potential energy surface (PES) [V...
December 7, 2018: Journal of Chemical Physics
T Palm, P Nalbach
Quantum systems are typically subject to various environmental noise sources. Treating these environmental disturbances with a system-bath approach beyond weak coupling, one must refer to numerical methods as, for example, the numerically exact quasi-adiabatic path integral approach. This approach, however, cannot treat baths which couple to the system via operators, which do not commute. We extend the quasi-adiabatic path integral approach by determining the time discrete influence functional for such non-commuting fluctuations and by modifying the propagation scheme accordingly...
December 7, 2018: Journal of Chemical Physics
Ignacio Loaiza, Artur F Izmaylov
Due to a continuum of electronic states present in periodic systems, the description of molecular dynamics on surfaces poses a serious computational challenge. One of the most used families of approaches in these settings are friction theories, which up to a random fluctuating force term are based on the Ehrenfest approach. Yet, a mean-field treatment of electronic degrees of freedom in the Ehrenfest method makes this approach inaccurate in some cases. Our aim is to clarify when Ehrenfest breaks down for molecular dynamics on surfaces...
December 7, 2018: Journal of Chemical Physics
Maximilian Beyer, Frédéric Merkt
Ab initio calculations of the energy level structure of <mml:math xmlns:mml=""> <mml:msubsup> <mml:mrow> <mml:mi>H</mml:mi> </mml:mrow> <mml:mrow> <mml:mn>2</mml:mn> </mml:mrow> <mml:mrow> <mml:mo>+</mml:mo> </mml:mrow> </mml:msubsup> </mml:math> that include relativistic and radiative corrections to nonrelativistic energies and the diagonal part of the hyperfine interaction have predicted the existence of four bound rovibrational levels [( v = 0, N = 0 - 2) and ( v = 1, N = 0)] of the first electronically excited ( <mml:math xmlns:mml="http://www...
December 7, 2018: Journal of Chemical Physics
Ilya G Ryabinkin, Scott N Genin, Artur F Izmaylov
For quantum computing applications, the electronic Hamiltonian for the electronic structure problem needs to be unitarily transformed into a qubit form. We found that mean-field procedures on the original electronic Hamiltonian and on its transformed qubit counterpart can give different results. We establish conditions of when fermionic and qubit mean fields provide the same or different energies. In cases when the fermionic mean-field (Hartree-Fock) approach provides an accurate description (electronic correlation effects are small), the choice of molecular orbitals for the electron Hamiltonian representation becomes the determining factor in whether the qubit mean-field energy will be equal to or higher than that of the fermionic counterpart...
December 7, 2018: Journal of Chemical Physics
William Barford, Jonathan R Mannouch
We develop a model of excitons coupled to the rotational motion of monomers to study the torsionally induced relaxation and decoherence of excitons in π -conjugated polymers. The model assumes that the monomer units are described by elastically uncoupled harmonic oscillators and that there is a linear exciton-roton coupling. Although the rotational degrees of freedom are much slower than the exciton, so that the adiabatic approximation is generally expected to be valid, we also investigate possible quantized roton corrections via coupled time evolving block decimation-Ehrenfest equations of motion...
December 7, 2018: Journal of Chemical Physics
Walter Malone, Johnathan von der Heyde, Abdelkader Kara
We explore the adsorption of pyridine on Cu, Ag, Au, and Pt(110) surfaces using density functional theory. To account for the van der Waals interaction, we use the optB86b-vdW, optB88-vdW, optPBE-vdW, revPBE-vdW, and rPW86-vdW2 functionals. For comparison, we also run calculations using the generalized gradient approximation-PBE (Perdew-Burke-Ernzerhof) functional. We find the most stable adsorption site to depend on both metal and functional, with two energetically favorable adsorption sites, namely, a vertically oriented site and a flat pyridine site...
December 7, 2018: Journal of Chemical Physics
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