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Journal of Chemical Physics

Tao Chen, Hu-Jun Qian, Zhong-Yuan Lu
No abstract text is available yet for this article.
September 14, 2016: Journal of Chemical Physics
A Zaccone, I Terentjev, T W Herling, T P J Knowles, A Aleksandrova, E M Terentjev
While a significant body of investigations have been focused on the process of protein self-assembly, much less is understood about the reverse process of a filament breaking due to thermal motion into smaller fragments, or depolymerization of subunits from the filament ends. Indirect evidence for actin and amyloid filament fragmentation has been reported, although the phenomenon has never been directly observed either experimentally or in simulations. Here we report the direct observation of filament depolymerization and breakup in a minimal, calibrated model of coarse-grained molecular simulation...
September 14, 2016: Journal of Chemical Physics
Jorge Adrián Perera-Burgos, José Miguel Méndez-Alcaraz, Gabriel Pérez-Ángel, Ramón Castañeda-Priego
Depletion forces are a particular class of effective interactions that have been mainly investigated in binary mixtures of hard-spheres in bulk. Although there are a few contributions that point toward the effects of confinement on the depletion potential, little is known about such entropic potentials in two-dimensional colloidal systems. From theoretical point of view, the problem resides in the fact that there is no general formulation of depletion forces in arbitrary dimensions and, typically, any approach that works well in three dimensions has to be reformulated for lower dimensionality...
September 14, 2016: Journal of Chemical Physics
Giorgio Pessot, Hartmut Löwen, Andreas M Menzel
In the perspective of developing smart hybrid materials with customized features, ferrogels and magnetorheological elastomers allow a synergy of elasticity and magnetism. The interplay between elastic and magnetic properties gives rise to a unique reversible control of the material behavior by applying an external magnetic field. Albeit few works have been performed on the time-dependent properties so far, understanding the dynamic behavior is the key to model many practical situations, e.g., applications as vibration absorbers...
September 14, 2016: Journal of Chemical Physics
Vipin Agrawal, Pedro Peralta, Yiyang Li, Jay Oswald
We investigate the thermomechanical response of semi-crystalline polyethylene under shock compression by performing molecular dynamics (MD) simulations using a new coarse-graining scheme inspired by the embedded atom method. The coarse-graining scheme combines the iterative Boltzmann inversion method and least squares optimization to parameterize interactions between coarse-grained sites, including a many-body potential energy designed to improve the representability of the model across a wide range of thermodynamic states...
September 14, 2016: Journal of Chemical Physics
Heurison S Silva, Fábio J S Lopes, Paulo B Miranda
Molecular orientation within azopolymer thin films is important for their nonlinear optical properties and photonic applications. We have used optical second-harmonic generation (SHG) to study the molecular orientation of Layer-by-Layer (LbL) films of a cationic polyelectrolyte (poly(allylamine hydrochloride)) and an anionic polyelectrolyte containing azochromophore side groups (MA-co-DR13) on a glass substrate. The SHG measurements indicate that there is a preferential orientation of the azochromophores in the film, leading to a significant optical nonlinearity...
September 14, 2016: Journal of Chemical Physics
Mircea Galiceanu, Aurel Jurjiu
We focus on the relaxation dynamics of multilayer polymer structures having, as underlying topology, the Husimi cactus. The relaxation dynamics of the multilayer structures is investigated in the framework of generalized Gaussian structures model using both Rouse and Zimm approaches. In the Rouse type-approach, we determine analytically the complete eigenvalues spectrum and based on it we calculate the mechanical relaxation moduli (storage and loss modulus) and the average monomer displacement. First, we monitor these physical quantities for structures with a fixed generation number and we increase the number of layers, such that the linear topology will smoothly come into play...
September 14, 2016: Journal of Chemical Physics
Donghua Xu, Alicia Certain, Hyon-Jee Lee Voigt, Todd Allen, Brian D Wirth
Studies of solute precipitation and precipitate phase stability in nuclear structural materials under concurrent irradiation and heat often lead to contradictory results due to the complex nature of the phenomena which is far from well understood. Here, we present a comprehensive atomistically based continuum model for the copper precipitation and re-dissolution kinetics in an ion irradiated and thermally annealed Fe-0.78 at. % Cu alloy. Our model incorporates thermal and irradiation enhanced diffusion of atomic Cu, clustering of Cu into sub-nanometer and nanometer sized precipitates, thermal dissociation of the precipitates and, in particular, a cascade re-dissolution parameter that has been made available by recent molecular dynamics simulations...
September 14, 2016: Journal of Chemical Physics
Rebecca Schmitz, Niels Müller, Svenja Ullmann, Michael Vogel
We perform molecular dynamics simulations to investigate structural and dynamical properties of ethylene glycol-water (EG-WA) mixtures in mesoporous silica. To obtain comprehensive insights into the dependence of liquid behaviors on the confinement features, we exploit that straightforward modification of the force field parameters allows us to vary the properties of the hydrogen-bond network of the confined liquid, we alter the polarity of the silica surface, and we consider amorphous as well as crystalline matrices...
September 14, 2016: Journal of Chemical Physics
M Tie, A-A Dhirani
Strong electron-electron interactions experienced by electrons as they delocalize are widely believed to play a key role in a range of remarkable phenomena such as high Tc superconductivity, colossal magnetoresistance, and others. Strongly correlated electrons are often described by the Hubbard model, which is the simplest description of a correlated system and captures important gross features of phase diagrams of strongly correlated materials. However, open challenges in this field include experimentally mapping correlated electron phenomena beyond those captured by the Hubbard model, and extending the model accordingly...
September 14, 2016: Journal of Chemical Physics
Rengin Peköz, Davide Donadio
The adsorption of phenol and phenoxy on the (111) surface of Au and Pt has been investigated by density functional theory calculations with the conventional PBE functional and three different non-local van der Waals (vdW) exchange and correlation functionals. It is found that both phenol and phenoxy on Au(111) are physisorbed. In contrast, phenol on Pt(111) presents an adsorption energy profile with a stable chemisorption state and a weakly metastable physisorbed precursor. While the use of vdW functionals is essential to determine the correct binding energy of both chemisorption and physisorption states, the relative stability and existence of an energy barrier between them depend on the semi-local approximations in the functionals...
September 14, 2016: Journal of Chemical Physics
D M Heyes, D Dini, E R Smith
System property fluctuations increasingly dominate a physical process as the sampling volume decreases. The purpose of this work is to explore how the fluctuation statistics of various thermodynamic properties depend on the sampling volume, using molecular dynamics (MD) simulations. First an examination of various expressions for calculating the bulk pressure of a bulk liquid is made, which includes a decomposition of the virial expression into two terms, one of which is the Method of Planes (MOP) applied to the faces of the cubic simulation cell...
September 14, 2016: Journal of Chemical Physics
Yuan-Chao Hu, Bao-Shuang Shang, Peng-Fei Guan, Yong Yang, Hai-Yang Bai, Wei-Hua Wang
A ternary metallic glass-forming liquid is found to be not strongly correlating thermodynamically, but its average dynamics, dynamic heterogeneities including the high order dynamic correlation length, and static structure are still well described by thermodynamic scaling with the same scaling exponent γ. This may indicate that the metallic liquid could be treated as a single-parameter liquid. As an intrinsic material constant stemming from the fundamental interatomic interactions, γ is theoretically predicted from the thermodynamic fluctuations of the potential energy and the virial...
September 14, 2016: Journal of Chemical Physics
Simon Schreck, Philippe Wernet
The effects of isotope substitution in liquid water are probed by x-ray absorption spectroscopy at the O K-edge as measured in transmission mode. Confirming earlier x-ray Raman scattering experiments, the D2O spectrum is found to be blue shifted with respect to H2O, and the D2O spectrum to be less broadened. Following the earlier interpretations of UV and x-ray Raman spectra, the shift is related to the difference in ground-state zero-point energies between D2O and H2O, while the difference in broadening is related to the difference in ground-state vibrational zero-point distributions...
September 14, 2016: Journal of Chemical Physics
Maryna Vlasiuk, Federico Frascoli, Richard J Sadus
The thermodynamic, structural, and vapor-liquid equilibrium properties of neon are comprehensively studied using ab initio, empirical, and semi-classical intermolecular potentials and classical Monte Carlo simulations. Path integral Monte Carlo simulations for isochoric heat capacity and structural properties are also reported for two empirical potentials and one ab initio potential. The isobaric and isochoric heat capacities, thermal expansion coefficient, thermal pressure coefficient, isothermal and adiabatic compressibilities, Joule-Thomson coefficient, and the speed of sound are reported and compared with experimental data for the entire range of liquid densities from the triple point to the critical point...
September 14, 2016: Journal of Chemical Physics
Po-Yu Tsai
Electrostatic hexapole state-selector is a versatile tool in experimental stereodynamics. The requirement of appropriate models to correctly predict the behavior of molecules in the hexapole motivated us to realize a treatment that predicts the Stark effect of linear triatomic molecules with rotational doublet states. Various perturbative approximations are conventionally adopted to obtain analytic Stark energy derivatives of a truncated Hamiltonian matrix, without utilizing numerical diagonalization of the full Hamiltonian matrix...
September 14, 2016: Journal of Chemical Physics
Lisa A Fredin, Petter Persson
The rapidly growing interest in photocatalytic systems for direct solar fuel production such as hydrogen generation from water splitting is grounded in the unique opportunity to achieve charge separation in molecular systems provided by electron transfer processes. In general, both photoinduced and catalytic processes involve complicated dynamics that depend on both structural and electronic effects. Here the excited state landscape of metal centered light harvester-catalyst pairs is explored using density functional theory calculations...
September 14, 2016: Journal of Chemical Physics
Vasyl Yatsyna, Daniël J Bakker, Raimund Feifel, Anouk M Rijs, Vitali Zhaunerchyk
Delocalized molecular vibrations in the far-infrared and THz ranges are highly sensitive to the molecular structure, as well as to intra- and inter-molecular interactions. Thus, spectroscopic studies of biomolecular structures can greatly benefit from an extension of the conventional mid-infrared to the far-infrared wavelength range. In this work, the conformer-specific gas-phase far-infrared spectra of two aromatic molecules containing the peptide -CO-NH- link, namely, 2- and 4-Methylacetanilide, are investigated...
September 14, 2016: Journal of Chemical Physics
R Słupski, K Jankowski, J R Flores
Accurate Møller-Plesset (MP2) correlation energies calculated by means of the variational-perturbation and the finite-element methods are presented for several members of the Cu(+) isoelectronic series (N = 28), which represent closed-shell systems containing for the first time the 3d(10)-electron configuration and, consequently, closed M-shell. Total MP2 energies as well as their inner- and inter-shell components are reported for Cu(+), Zn(2+), Ge(4+), Kr(8+), Sr(10+), and Cd(20+). We found that for these ions the Z-dependence of the total MP2 energies is significantly weaker than for the members of the Ar-like series...
September 14, 2016: Journal of Chemical Physics
Hongwei Li, Nathanael M Kidwell, Xiaohong Wang, Joel M Bowman, Marsha I Lester
The unimolecular dissociation dynamics of the dimethyl-substituted Criegee intermediate (CH3)2COO is examined experimentally using velocity map imaging to ascertain the translational and internal energy distributions of the OH and H2CC(CH3)O radical products. The energy profile of key features along the reaction coordinate is also evaluated theoretically. Unimolecular decay of (CH3)2COO is initiated by vibrational activation in the CH stretch overtone region and the resultant OH X(2)Π3/2 (v = 0) products are state-selectively ionized and imaged...
September 14, 2016: Journal of Chemical Physics
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