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Mean ionic activity coefficients in aqueous NaCl solutions from molecular dynamics simulations
The mean ionic activity coefficients of aqueous NaCl solutions of varying concentrations at 298.15 K and 1 bar have been obtained from molecular dynamics simulations by gradually turning on the interactions of an ion pair inserted into the solution. Several common non-polarizable water and ion models have been used in the simulations. Gibbs-Duhem equation calculations of the thermodynamic activity of water are used to confirm the thermodynamic consistency of the mean ionic activity coefficients. While the majority of model combinations predict the correct trends in mean ionic activity coefficients, they overestimate their values at high salt concentrations. The solubility predictions also suffer from inaccuracies, with all models underpredicting the experimental values, some by large factors. These results point to the need for further ion and water model development.
Development of a model electronic Hamiltonian for understanding electronic relaxation dynamics of [Fe(bpy){sub 3}]{sup 2+} through molecular dynamics simulations
A model electronic Hamiltonian of [Fe(bpy){sub 3}]{sup 2+}, which was recently refined for use in molecular dynamics simulations, is reviewed with some additional results. In particular, the quality of the refined model Hamiltonian is examined in terms of the vibrational frequencies and solvation structures of the lowest singlet and quintet states.
Understanding misfit strain releasing mechanisms via molecular dynamics simulations of CdTe growth on {112}zinc-blende CdS
Molecular dynamics simulations have been used to analyse microstructures of CdTe films grown on {112} surfaces of zinc-blende CdS. Interestingly, CdTe films grow in <331> orientations as opposed to <112> epitaxial orientations. At the CdTe-{331}/CdS-{112} interface, however, there exists an axis that is parallel to the <110> orientation of both CdS and CdTe. It is the direction orthogonal to this <110> that becomes different, being <116> for CdTe and <111> for CdS, respectively. Missing CdTe-{110} planes are found along the <110> axis, suggesting that the misfit strain is released by the conventional misfit dislocation mechanism along this axis. In the orthogonal axis, the misfit strain is found to be more effectively released by the new grain orientation mechanism. Our finding is supported by literature experimental observations of the change of growth direction when Cd 0.96 Zn 0.04 Te films are deposited on GaAs. Lastly the analyses of energetics clearly demonstrate the cause for the formation of the new orientation, and the insights gained from our studies can help understand the grain structures experimentally observed in lattice mismatched systems.
System-size corrections for self-diffusion coefficients calculated from molecular dynamics simulations: The case of CO{sub 2}, n-alkanes, and poly(ethylene glycol) dimethyl ethers
Molecular dynamics simulations were carried out to study the self-diffusion coefficients of CO{sub 2}, methane, propane, n-hexane, n-hexadecane, and various poly(ethylene glycol) dimethyl ethers (glymes in short, CH{sub 3}O–(CH{sub 2}CH{sub 2}O){sub n}–CH{sub 3} with n = 1, 2, 3, and 4, labeled as G1, G2, G3, and G4, respectively) at different conditions. Various system sizes were examined. The widely used Yeh and Hummer [J. Phys. Chem. B 108, 15873 (2004)] correction for the prediction of diffusion coefficient at the thermodynamic limit was applied and shown to be accurate in all cases compared to extrapolated values at infinite system size. The magnitude of correction, in all cases examined, is significant, with the smallest systems examined giving for some cases a self-diffusion coefficient approximately 15% lower than the infinite system-size extrapolated value. The results suggest that finite size corrections to computed self-diffusivities must be used in order to obtain accurate results.
Dynamic mapping of conical intersection seams: A general method for incorporating the geometric phase in adiabatic dynamics in polyatomic systems
The incorporation of the geometric phase in single-state adiabatic dynamics near a conical intersection (CI) seam has so far been restricted to molecular systems with high symmetry or simple model Hamiltonians. This is due to the fact that the ab initio determined derivative coupling (DC) in a multi-dimensional space is not curl-free, thus making its line integral path dependent. In a recent work [C. L. Malbon et al. , J. Chem. Phys. 145, 234111 (2016)], we proposed a new and general approach based on an ab initio determined diabatic representation consisting of only two electronic states, in which the DC is completely removable, so that its line integral is path independent in the simply connected domains that exclude the CI seam. Then with the CIs included, the line integral of the single-valued DC can be used to construct the complex geometry-dependent phase needed to exactly eliminate the double-valued character of the real-valued adiabatic electronic wavefunction. This geometry-dependent phase gives rise to a vector potential which, when included in the adiabatic representation, rigorously accounts for the geometric phase in a system with an arbitrary locus of the CI seam and an arbitrary number of internal coordinates. Here, we demonstrate this approach in a three-dimensional treatment of the tunneling facilitated dissociation of the S 1 state of phenol, which is affected by a C s symmetry allowed but otherwise accidental seam of CI. Here, since the space is three-dimensional rather than two-dimensional, the seam is a curve rather than a point. The nodal structure of the ground state vibronic wavefunction is shown to map out the seam of CI.
The role of sub-surface hydrogen on CO 2 reduction and dynamics on Ni(110): An ab initio molecular dynamics study
The catalytic reduction of carbon dioxide is a crucial step in many chemical industrial reactions, such as methanol synthesis, the reverse water-gas shift reaction (rWGS) and formic acid synthesis. Here, we investigate the role of bulk hydrogen, where hydrogen atoms are found deep inside a metal surface as opposed to subsurface ones, upon CO 2 reduction over a Ni(110) surface using density functional theory (DFT) and ab initio molecular dynamics (AIMD) simulations. While it has previously been shown that subsurface hydrogen stabilizes CO 2 and can aid in overcoming reaction barriers, the role of bulk hydrogen is less studied and thus unknown with regard to CO 2 reduction. Furthermore, we find that the presence of bulk hydrogen can significantly alter the electronic structure of the Ni(110) surface, particularly the work function and d-band center, such that CO 2 adsorbs more strongly to the surface and is more easily reduced. Our results show an enhanced CO 2 dissociation in the presence of bulk hydrogen, shedding light on a hitherto underappreciated mechanistic pathway for CO 2 reduction on metal surfaces.
Lattice dynamics of BaFe2X3(X = S, Se) compounds
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Trion formation dynamics in monolayer transition metal dichalcogenides
Here, we report charged exciton (trion) formation dynamics in doped monolayer transition metal dichalcogenides, specifically molybdenum diselenide (MoSe 2 ), using resonant two-color pump-probe spectroscopy. When resonantly pumping the exciton transition, trions are generated on a picosecond time scale through exciton-electron interaction. As the pump energy is tuned from the high energy to low energy side of the inhomogeneously broadened exciton resonance, the trion formation time increases by ~50%. This feature can be explained by the existence of both localized and delocalized excitons in a disordered potential and suggests the existence of an exciton mobility edge in transition metal dichalcogenides.
Anisotropic fluid dynamics for Gubser flow
Investigating a variety of closing schemes to the infinite hierarchy of momentum moments of the exactly solvable Boltzmann equation for systems undergoing Gubser flow, we study the precision with which the resulting hydrodynamic equations reproduce the exact evolution of hydrodynamic moments of the distribution function. We find that anisotropic hydrodynamics, obtained by expanding the distribution function around a dynamically evolving locally anisotropic background whose evolution is matched to exactly reproduce the macroscopic pressure anisotropy caused by the different longitudinal and transverse expansion rates in Gubser ow, provides the most accurate macroscopic description of the microscopic kinetic evolution. This confirms a similar earlier finding for Bjorken ow [Molnar, Niemi and Rischke, Phys. Rev. D 94, 125003 (2016)]. Also, we explain the physics behind this optimal matching procedure and show that one can efficiently correct for a nonoptimized matching choice by adding a residual shear stress to the energy-momentum tensor whose evolution is again determined by the Boltzmann equation. Further insights to guide the optimal choice of a macroscopic anisotropic hydrodynamic framework for strongly-coupled systems that do not admit a microscopic kinetic description are reported.
Data-Driven Analysis of Multipactor Dynamics via Dynamic Mode Decomposition
Multipactor effect is a performance-limiting kinetic plasma effect that can occur in high-power microwave and radio frequency (RF) devices. Multipactor effect is of special concern in vacuum or near-vacuum conditions such as those in particle accelerators and spaceborne devices. In this work, we present a data-driven reduced-order model (ROM) based on dynamic mode decomposition (DMD) for modeling of multipactor effects. We study multipactor effects and the resulting nonlinear harmonic generation by processing high-fidelity data generated from electromagnetic particle-in-cell (EMPIC) simulations using the DMD algorithm. We also investigate time-delay embedding extensions of DMD with improved generalizability and accuracy for modeling the electron plasma current density behavior. Here, the results show that DMD provides valuable insights into multipactor phenomena by extracting relevant modal spatiotemporal patterns and frequencies. In addition, DMD offers the potential to time extrapolate EMPIC simulations at a minimal cost, thereby reducing overall simulation time.
The Dynamic Conformational Cycle of the Group I Chaperonin C-Termini Revealed via Molecular Dynamics Simulation
Chaperonins are large ring shaped oligomers that facilitate protein folding by encapsulation within a central cavity. All chaperonins possess flexible C-termini which protrude from the equatorial domain of each subunit into the central cavity. Biochemical evidence suggests that the termini play an important role in the allosteric regulation of the ATPase cycle, in substrate folding and in complex assembly and stability. Despite the tremendous wealth of structural data available for numerous orthologous chaperonins, little structural information is available regarding the residues within the C-terminus. Herein, molecular dynamics simulations are presented which localize the termini throughout the nucleotide cycle of the group I chaperonin, GroE, from Escherichia coli. The simulation results predict that the termini undergo a heretofore unappreciated conformational cycle which is coupled to the nucleotide state of the enzyme. As such, these results have profound implications for the mechanism by which GroE utilizes nucleotide and folds client proteins.
Advances in Plasma Dynamics, American Institute of Aeronautics and Astronautics, and Northwestern University, Biennial Gas Dynamics Symposium, 6th, Evanston, Ill., August 25-27, 1965, Proceedings.
Plasma dynamics - AIAA and Northwestern University Conference, Evanston, August 1965
Dynamic scaling for earth based testing of Mars terminal descent dynamics
The purpose of this paper is to outline the derivation and limitations of a dynamic scaling law for Earth based testing of this type of Mars terminal descent system.
A New Algorithmic Framework for Robot Dynamics Analysis with Application to Space Robots Dynamics Simulation
In this paper a new algorithm for fast serial and parallel dynamics simulation of space robots as characterized by serial chain systems with a floating base is presented.
Transforming Energy Through Computational Excellence: NREL Computational Fluid Dynamics Modeling Complex, Dynamic Systems
Computational fluid dynamics (CFD) enables modeling, analysis, and visualization of phenomena that would usually be impossible or extremely expensive to measure experimentally.