Six-site Model Research Articles

Towards string order melting of spin-1 particle chains in superconducting transmons using optimal control

Utilizing optimal control to simulate a model Hamiltonian is an emerging strategy that leverages the intrinsic physics of a device with digital quantum simulation methods. Here we evaluate optimal control for probing the nonequilibrium properties of symmetry-protected topological (SPT) states simulated with superconducting hardware. Assuming a tunable transmon architecture, we cast the evolution of these SPT states as a series of one- and two-site pulse optimization problems that are solved in the presence of leakage constraints. From the generated pulses, we classically simulate the time-dependent melting of the perturbed SPT string order across a six-site model with an average state infidelity of ${10}^{\ensuremath{-}3}$. The feasibility of these pulses as well as their efficient application indicate that high-fidelity simulations of string order melting are within reach of current quantum computing systems.

Systematic evaluation and refinement of existing all-atom force fields for the simulation of liquid acetonitrile.

The reliability of a molecular dynamics (MD) simulation study mainly depends on the accuracy of the applied force field. Unlike the ability of some potential models for reasonably predicting the thermodynamic properties of acetonitrile (ACN), simulated dynamical properties such as self-diffusion are generally underestimated compared to experimental values. The present work focuses on the evaluation and refinement of several available all-atom force fields for ACN and proposes a refined flexible six-site potential model. The main modification is related to the reduction of intermolecular LJ parameters (σ and ɛ) for hydrogen atoms, especially ɛ, significantly affecting the dynamical behavior. Besides, the adjustment of σ and ɛ for nitrile carbon and nitrogen atoms helps reach optimum results. Our refined model shows an excellent agreement with the experiment for self-diffusion coefficient and thermodynamic quantities as well as providing a qualitative description of the microscopic structure of liquid ACN. © 2018 Wiley Periodicals, Inc.

Methylammonium Cation Dynamics in Methylammonium Lead Halide Perovskites: A Solid-State NMR Perspective.

In light of the intense recent interest in the methylammonium lead halides, CH3NH3PbX3 (X = Cl, Br, and I) as sensitizers for photovoltaic cells, the dynamics of the methylammonium (MA) cation in these perovskite salts has been reinvestigated as a function of temperature via 2H, 14N, and 207Pb NMR spectroscopy. In the cubic phase of all three salts, the MA cation undergoes pseudoisotropic tumbling (picosecond time scale). For example, the correlation time, τ2, for the C-N axis of the iodide salt is 0.85 ± 0.30 ps at 330 K. The dynamics of the MA cation are essentially continuous across the cubic ↔ tetragonal phase transition; however, 2H and 14N NMR line shapes indicate that subtle ordering of the MA cation occurs in the tetragonal phase. The temperature dependence of the cation ordering is rationalized using a six-site model, with two equivalent sites along the c-axis and four equivalent sites either perpendicular or approximately perpendicular to this axis. As the cubic ↔ tetragonal phase transition temperature is approached, the six sites are nearly equally populated. Below the tetragonal ↔ orthorhombic phase transition, 2H NMR line shapes indicate that the C-N axis is essentially frozen.

Anisotropy in geometrically rough structure of ice prismatic plane interface during growth: Development of a modified six-site model of H2O and a molecular dynamics simulation.

This paper presents a modified version of the six-site model of H2O [H. Nada and J. P. J. M. van der Eerden, J. Chem. Phys. 118, 7401 (2003)]. Although the original six-site model was optimized by assuming the cut-off of the Coulomb interaction at an intermolecular distance of 10 Å, the modified model is optimized by using the Ewald method for estimating the Coulomb interaction. Molecular dynamics (MD) simulations of an ice-water interface suggest that the melting point of ice at 1 atm in the modified model is approximately 274.5 K, in good agreement with the real melting point of 273.15 K. MD simulations of bulk ice and water suggest that the modified model reproduces not only the structures and density curves of ice and water, but also the diffusion coefficient of water molecules in water near the melting point at 1 atm. Using the modified model, a large-scale MD simulation of the growth at an ice-water interface of the prismatic plane is performed to elucidate the anisotropy in the interface structure during growth. Simulation results indicate that the geometrical roughness of the ice growth front at the interface is greater in the c-axis direction than in the direction normal to the c-axis when it is analyzed along the axes parallel to the prismatic plane. In addition, during the growth at the interface, the transient appearance of specific crystallographic planes, such as a {202¯1} pyramidal plane, occurs preferentially at the ice growth front. The effect of different ensembles with different simulation systems on the anisotropy in the interface structure is also investigated.

Effect of solvent composition on the structural and dynamical properties of sodium chloride solutions in water-methanol mixtures

Molecular dynamics (MD) simulations have been performed on sodium chloride solutions in water-methanol mixtures under ambient conditions with methanol mole fractions (xm) ranging from 0.09 to 0.87. MD simulations are performed with the flexible SPC water model and the flexible six-site model for methanol. The ions are modeled as charged Lennard–Jones spheres. The structural properties of the solutions are discussed on the basis of radial distribution functions. A chain cluster of methanol is predominant in the mixture where xm exceeds 0.7. The number of methanol molecules are higher than water molecules in the first coordination shell of sodium and chloride ions beyond xm=0.5 and 0.48 respectively. With increasing xm, the diffusion coefficients for water (DH2O) and for methanol (DCH3OH) initially decrease. From xm=0.29 DCH3OH increases while DH2O rises only from about 0.7. The two diffusion coefficients are equal at xm=0.8. The deduced first and second reorientational correlation times for the OH and the dipole moment vectors for water speed up with increasing xm. Through the τ1/τ2 ratio, the reorientational motion of water molecules can be entirely ascribed to a jump. OH methanol vector reorientational occurs by a mechanism similar to that of water.

Water dynamics on ice and hydrate lattices studied by second-order central-line stimulated-echo oxygen-17 nuclear magnetic resonance.

Oxygen-17 stimulated-echo spectroscopy is a novel nuclear magnetic resonance (NMR) technique that allows one to investigate the time scale and geometry of ultraslow molecular motions in materials containing oxygen. The method is based on detecting orientationally encoded frequency changes within oxygen's central-transition NMR line that are caused by second-order quadrupolar interactions. In addition to the latter, the present theoretical analysis of various two-pulse echo and stimulated-echo pulse sequences takes also heteronuclear dipolar interactions into account. As an experimental example, the ultraslow water motion in polycrystals of tetrahydrofuran clathrate hydrate is studied via two-time oxygen-17 stimulated-echo correlation functions. The resulting correlation times and those of hexagonal ice are similar to those from previous deuteron NMR measurements. Calculations of the echo functions' final-state correlations for various motional models are compared with the experimental data of the clathrate hydrate. It is found that a six-site model including the oxygen-proton dipolar interaction describes the present results.

Determination of New Cu+, Cu2+, and Zn2+ Lennard-Jones Ion Parameters in Acetonitrile

We present new Lennard-Jones (LJ) parameters for Cu(+), Cu(2+), and Zn(2+) ion-acetonitrile interactions. The adjustment of ion parameters is made to reproduce simultaneously experimental solvation free energy and structural properties, namely ion-N distance and coordination numbers. Initially, the methodology has been validated deriving parameters for well-studied Na(+) and Cl(-) ions in acetonitrile being compared with experimental and theoretical data. The transferability of parameters is checked by the calculation of thermodynamic and structural properties with three different acetonitrile models. The results obtained for transition metal ions show an overall agreement with reference values. The solvation free energy calculated with new LJ trained parameters using a six-site acetonitrile model, and two older three- and six-site acetonitrile models presents, respectively, percent differences of 0.4, 4.8, and 7.3% when compared with experimental values.

Six-site polarizable model of water based on the classical Drude oscillator

A polarizable water model, SWM6, was developed and optimized for liquid phase simulations under ambient conditions. Building upon the previously developed SWM4-NDP model, additional sites representing oxygen lone-pairs were introduced. The geometry of the sites is assumed to be rigid. Considering the large number of adjustable parameters, simulated annealing together with polynomial fitting was used to facilitate model optimization. The new water model was shown to yield the correct self-diffusion coefficient after taking the system size effect into account, and the dimer geometry is better reproduced than in the SWM4 models. Moreover, the experimental oxygen-oxygen radial distribution is better reproduced, indicating that the new model more accurately describes the local hydrogen bonding structure of bulk phase water. This was further validated by its ability to reproduce the experimental nuclear magnetic shielding and related chemical shift of the water hydrogen in the bulk phase, a property sensitive to the local hydrogen bonding structure. In addition, comparison of the liquid properties of the SWM6 model is made with those of a number of widely used additive and polarizable models. Overall, improved balance between the description of monomer, dimer, clustered, and bulk phase water is obtained with the new model compared to its SWM4-NDP polarizable predecessor, though application of the model requires an approximately twofold increase on computational resources.

Coherent exciton transport driven by torsional dynamics: a quantum dynamical study of phenylene-vinylene type conjugated systems

We present a quantum dynamical study of exciton transfer across a torsional defect that locally breaks the pi-conjugation in an oligo-(p-phenylene vinylene) (OPV) fragment. A site-based vibronic coupling Hamiltonian is used which is formulated in a comparative fashion (i) for a Frenkel exciton basis, assuming localized electron-hole pairs whose superposition yields a delocalized exciton, and (ii) more accurately, for a Merrifield type exciton basis including spatially separated electron-hole pairs. Starting from a partially delocalized ("spectroscopic unit") initial condition, the observed transfer dynamics is found to involve two characteristic time scales: (i) a very rapid, coherent transient on a 10-100 femtosecond scale, largely determined by Rabi type oscillations modulated by bond-length-alternation modes, and (ii) a slower time scale involving the planarization of the torsional coordinates that determines the onset of a quasi-stationary exciton-polaron state, and in the process leads to a "healing" of the torsional defect within - 500 femtoseconds. The dynamics obtained from the full electron-hole basis vs. Frenkel basis are in good agreement. In the full electron-hole dynamics, the transients are found to involve a rapid expansion and subsequent contraction of the electron-hole coherence size. Quantum dynamical simulations for a minimal six-site model involving 36 states and 22 vibrational modes, were carried out using the multiconfiguration time dependent Hartree (MCTDH) method.

Simulations of nuclear spin relaxation in liquid acetonitrile

Molecular dynamics simulations at 298 and 273 K were carried out in order to explore the ability of calculations to predict NMR spin–lattice relaxation rates of the protons of liquid acetonitrile. The six-site model of Nikitin and Lyubartsev (J. Computat. Chem. 28 (2007), pp. 2020–2026) was used with systems containing up to 13,824 molecules. The effects of employing a cut-off for intermolecular interactions were explored. It was found that the model and procedures used predict intramolecular and intermolecular spin–lattice relaxation rates that are within ∼25% of experimental values at both temperatures.

Molecular Dynamics Simulations of Ice Nucleation by Electric Fields

Molecular dynamics simulations are used to investigate heterogeneous ice nucleation in model systems where an electric field acts on water molecules within 10-20 Å of a surface. Two different water models (the six-site and TIP4P/Ice models) are considered, and in both cases, it is shown that a surface field can serve as a very effective ice nucleation catalyst in supercooled water. Ice with a ferroelectric cubic structure nucleates near the surface, and dipole disordered cubic ice grows outward from the surface layer. We examine the influences of temperature and two important field parameters, the field strength and distance from the surface over which it acts, on the ice nucleation process. For the six-site model, the highest temperature where we observe field-induced ice nucleation is 280 K, and for TIP4P/Ice 270 K (note that the estimated normal freezing points of the six-site and TIP4P/Ice models are ∼289 and ∼270 K, respectively). The minimum electric field strength required to nucleate ice depends a little on how far the field extends from the surface. If it extends 20 Å, then a field strength of 1.5 × 10(9) V/m is effective for both models. If the field extent is 10 Å, then stronger fields are required (2.5 × 10(9) V/m for TIP4P/Ice and 3.5 × 10(9) V/m for the six-site model). Our results demonstrate that fields of realistic strength, that act only over a narrow surface region, can effectively nucleate ice at temperatures not far below the freezing point. This further supports the possibility that local electric fields can be a significant factor influencing heterogeneous ice nucleation in physical situations. We would expect this to be especially relevant for ice nuclei with very rough surfaces where one would expect local fields of varying strength and direction.

SAFT-γ Force Field for the Simulation of Molecular Fluids. 1. A Single-Site Coarse Grained Model of Carbon Dioxide

An application of the "top-down" concept for the development of accurate coarse-grained intermolecular potentials of complex fluids is presented. With the more common "bottom-up" procedure, coarse-grained models are constructed from a suitable simplification of a detailed atomistic representation, and small adjustments to the intermolecular parameters are made by comparison with limited experimental data where necessary. In contrast, in the top-down approach, a molecular-based equation of state is used to obtain an effective coarse-grained intermolecular potential that reproduces the macroscopic experimental thermophysical properties over a wide range of conditions. These coarse-grained intermolecular potentials can then be used in conventional molecular simulation to obtain properties (such as structure or dynamics) that are not directly accessible from the equation of state or at extreme conditions where the theory is expected to fail. To demonstrate our procedure, a coarse-grained model for carbon dioxide (CO(2)) is obtained from a recent implementation of the statistical associating fluid theory of variable range (SAFT-VR) employing a Mie (generalized Lennard-Jones) potential; the parameters of this single-site Mie model of CO(2) are estimated by optimizing the equation of state's description of the experimental vapor-pressure and saturated liquid density data. This approach is only viable because of the excellent agreement of the SAFT-VR Mie EoS with simulation data. Our single-site SAFT-γ coarse-grained model for CO(2) is used in Monte Carlo molecular simulation to assess the adequacy of the description of the fluid-phase behavior and properties that were not used to develop the potential model such as the enthalpy of vaporization, interfacial tension, density profiles, supercritical densities, and second-derivative thermodynamic properties (thermal expansivity, isothermal compressibility, heat capacity, Joule-Thompson coefficient, and speed of sound). The accuracy of the description with the single-site SAFT-γ model of CO(2) is found to be of similar quality to that of more sophisticated intermolecular potentials such as a six-site (three LJ centers and three charged sites) all-atom model. The SAFT-γ top-down approach to coarse-graining resolves a key challenge with coarse-graining techniques: the provision of a direct robust link between the microscopic and macroscopic scales.

Arrhenius analysis of anisotropic surface self-diffusion on the prismatic facet of ice

We present an Arrhenius analysis of self-diffusion on the prismatic surface of ice calculated from molecular dynamics simulations. The six-site water model of Nada and van der Eerden was used in combination with a structure-based criterion for determining the number of liquid-like molecules in the quasi-liquid layer. Simulated temperatures range from 230 K-287 K, the latter being just below the melting temperature of the model, 289 K. Calculated surface diffusion coefficients agree with available experimental data to within quoted precision. Our results indicate a positive Arrhenius curvature, implying a change in the mechanism of self-diffusion from low to high temperature, with a concomitant increase in energy of activation from 29.1 kJ mol(-1) at low temperature to 53.8 kJ mol(-1) close to the melting point. In addition, we find that the surface self-diffusion is anisotropic at lower temperatures, transitioning to isotropic in the temperature range of 240-250 K. We also present a framework for self-diffusion in the quasi-liquid layer on ice that aims to explain these observations.

Groundwater Level Prediction Using SOM-RBFN Multisite Model

In this paper, a groundwater level forecasting model is proposed by combining the theory of self-organizing map (SOM) and radial basis function network (RBFN). The proposed model is referred to as SOM-RBFN model. Recently, RBFN has been applied in time series forecasting. Traditionally, the number of hidden units and the positioning of the radial basis centers are crucial problems for establishing RBFN. The proposed model can decide the number of RBFN’s hidden units with using the two-dimensional feature map which is constructed by SOM, and then it can determine the positioning of the radial basis centers easily. The proposed model is applied to actual groundwater level data in southern Taiwan from 1997 to 2003. It is found that the multisite model can predict the 1 month ahead groundwater level more precisely than the single-site model. Moreover, it is also found that the four-site model is more competent in predicting groundwater level as compared to the single-site model and six-site model. Therefore, ...

Calculation of the crystal-melt interfacial free energy of succinonitrile from molecular simulation

The crystal-metal interfacial free energy for a six-site model of succinonitrile [N triple bond C-(CH(2))(2)-C triple bond N] has been calculated using molecular-dynamics simulation from the power spectrum of capillary fluctuations in interface position. The orientationally averaged magnitude of the interfacial free energy is determined to be (7.0+/-0.4)x10(-3) J m(-2). This value is in agreement (within the error bars) with the experimental value [(7.9+/-0.8)x10(-3) J m(-2)] of Marasli et al. [J. Cryst. Growth 247, 613 (2003)], but is about 20% lower than the earlier experimental value [(8.9+/-0.5)x10(-3) J m(-2)] obtained by Schaefer et al. [Philos. Mag. 32, 725 (1975)]. In agreement with the experiment, the calculated anisotropy of the interfacial free energy of this body-centered-cubic material is small. In addition, the Turnbull coefficient from our simulation is also in agreement with the experiment. This work demonstrates that the capillary fluctuation method of Hoyt et al. [Phys. Rev. Lett. 86, 5530 (2001)] can be successfully applied to determine the crystal-melt interfacial free energy of molecular materials.

Anisotropy in growth kinetics at interfaces between proton-disordered hexagonal ice and water: A molecular dynamics study using the six-site model of H2O

Molecular dynamics simulations of interfaces between proton-disordered hexagonal ice and water are carried out at a temperature near the melting point and a pressure of 1 atm using the six-site model of H2O, which was recently proposed for simulation studies of ice and water near the melting point. The simulations are performed for the interfaces of basal, prismatic and {112¯0} planes of ice. The growth process of ice is clearly observed on all planes. It is observed, during growth on the {112¯0} plane, the {112¯0} plane disappears and prismatic planes appear instead. The result suggests that the growth velocity at the interface is larger for the {112¯0} plane than for the prismatic plane. The structure of each interface and growth kinetics at each interface are analyzed on a molecular scale. Simulations show the interfaces of the prismatic and the {112¯0} planes have a geometrically rough structure, whereas the interface of the basal plane has a molecularly flat structure. The simulations also show, that on all planes, growth occurs by reorganization of the hydrogen-bonded network in water near the interface. The reorganization occurs three-dimensionally on the prismatic and the {112¯0} planes, whereas two-dimensionally on the basal plane. The anisotropy in the growth velocity, which is obtained in the present study, is qualitatively consistent with previous experiments. It is shown that the present results on the anisotropy in the interface structure and growth kinetics qualitatively explain the macroscopic shape of ice growing from water in a real system.

A clear observation of crystal growth of ice from water in a molecular dynamics simulation with a six-site potential model of H 2O

We demonstrate that a six-site potential model of H 2O, which we proposed recently, is suitable for simulation works on the crystal growth of ice from water. Using the model, a molecular dynamics simulation of a system including interfaces between the prismatic face of the proton-disordered hexagonal ice and water is carried out at a supercooled state and a pressure of 1 atm. The results clearly indicate that the ice grows at the interfaces continuously during the simulation. Moreover, the growth kinetics at the interfaces is analyzed on a molecular scale.

Molecular dynamics simulations of acetonitrile/dimethyl sulfoxide liquid mixtures.

Binary liquid mixtures of dimethyl sulfoxide and acetonitrile at the three molar fractions 0.25, 0.50, and 0.75 have been investigated by molecular dynamics computer simulations. Thermodynamic states corresponding to liquid-vapor coexistence at a temperature of 298 K were considered. Intermolecular interactions were described by potential models of the site-site (12-6) Lennard-Jones plus Coulomb type that have been developed for the description of the pure liquids. Dimethyl sulfoxide has been represented by four interactions sites and acetonitrile by a three- as well as a six-site potential model. We have calculated thermodynamic properties and the intermolecular pair distribution functions. Intermolecular interaction energies indicate deviations from the behavior of ideal mixtures. The local mole fraction analysis demonstrates that dimethyl sulfoxide is preferentially solvated by acetonitrile and that the first solvation shell surrounding acetonitrile molecules is significantly enriched by dimethyl sulfoxide. The nonideal behavior in the mixtures is not affected by the choice of the three- or the six-site potential model for acetonitrile. Orientational correlations of dipole vectors within the first solvation shells indicate that the relative molecular orientations found in pure acetonitrile and dimethyl sulfoxide are maintained in the mixtures. Parallel and antiparallel dipole-dipole configurations determine first shell acetonitrile-dimethyl sulfoxide configurations. Dynamical features of the mixtures are discussed in terms of diffusion constants and orientational correlation times as obtained from the time correlation functions for linear velocities and molecular dipole moments, respectively. Computed relaxation times indicate faster reorientational motion for dimethyl sulfoxide if acetonitrile is added. In contrast, the orientational dynamics of acetonitrile becomes stronger correlated upon dilution with dimethyl sulfoxide. The diffusion coefficients for both compounds follow this tendency.

An intermolecular potential model for the simulation of ice and water near the melting point: A six-site model of H2O

An intermolecular potential model of H2O with six interaction sites is proposed. The model is developed for the simulation of ice and water near the melting point. Parameters in the potential are determined to reproduce the real melting point of ice, and densities of ice and water near the melting point, which are predicted by calculating derivatives of the free energies and volumes of ice and water against potential parameters. Free energy calculations are carried out for several ice structures and water, and the results are compared with those obtained in four- and five-site models, which are currently in use. It is shown that, only in the present six-site model, the proton-disordered hexagonal ice is the stable structure at the melting point, as in real ice. The melting point of the proton-disordered hexagonal ice at 1 atm is estimated to be 271±9 K in the present model, which is in good agreement with the real melting point of 273.15 K. Moreover, results of Monte Carlo simulations of ice and water show that the present six-site model reproduces well the real structural and thermodynamic properties of ice and water near the melting point.

Molecular dynamics simulation studies of liquid acetonitrile: New six‐site model

Molecular dynamics (MD) simulations are carried out for liquid acetonitrile using a new six-site model for the solvent molecules. The recent force field of Cornell et al. ( J Am Chem Soc, 1995, 117, 5179) was used under the RESP approach to obtain the atomic charges. A new flexible all-atom solvent model was achieved whose density, heat of vaporization, and isothermal compressibility values are in good agreement with available experimental data, especially for a generic force field. Radial distribution functions are calculated and discussed to study the liquid structure in detail. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 901–908, 2000