Effective Potential Method Research Articles

Dispersion Interactions in Water Clusters.

The importance of dispersion forces in water clusters is examined using the effective fragment potential (EFP) method. Since the original EFP1 water potential does not include dispersion, a dispersion correction to the EFP1 potential (EFP1-D) was derived and implemented. The addition of dispersion to the EFP1 potential yields improved geometries for water clusters that contain 2-6 molecules. The importance of the odd E7 contribution to the dispersion energy is investigated. The E7 dispersion term is repulsive for all of the water clusters studied here and can have a magnitude that is as large as half of the E6 value. The E7 term therefore contributes to larger intermolecular distances for the optimized geometries. Inclusion of many-body effects and/or higher order terms may be necessary to further improve dispersion energies and optimized geometries.

Physicochemical and Fatty Acid Profile of Fish Oil from Head of Tuna (Thunnus albacares) Extracted from Various Extraction Method

By-product of tuna fish processing industry has the potential to be developed into fish oil rich in omega. Fish by-products are the main natural source of omega-3 polyunsaturated fatty acids, EPA (eicosapentaenoic acid) and DHA (docosahexaenoic acid) with a great importance in food industry and pharmacy. The purpose of this research is to see the effect of fish oil extracting method from the head of tuna fish as by-product of tuna fish processing industry to the physicochemical properties and the profile of fatty acid fish oil. There are several methods of extraction to produce of fish oil. This research was run in triplicate with a completely randomized design (CRD) with three treatments: pre-cooked wet rendering, acid silage, and solvent extraction. It can be concluded that the extraction method has an effect on physicochemical properties and fatty acid profile of fish oil. The wet rendering extraction method is the most effective and most potential extraction method to be applied because it produces the highest yield (12.80%) compared to the silage process (6.16%) and solvent extraction method (8.49%). PUFA produced from wet rendering was 44.34%, statistically not different with solvent extraction method (44.49%), but it higher than silage process method (32.77%).

Higgs boson mass corrections in the μνSSM with effective potential methods

To solve the $\mu$ problem of the MSSM, the $\mu$ from $\nu$ Supersymmetric Standard Model ($\mu\nu$SSM) introduces three singlet right-handed neutrino superfields $\hat{\nu}_i^c$, which lead to the mixing of the neutral components of the Higgs doublets with the sneutrinos, producing a relatively large CP-even neutral scalar mass matrix. In this work, we analytically diagonalize the CP-even neutral scalar mass matrix and analyze in detail how the mixing impacts the lightest Higgs boson mass. We also give an approximate expression for the lightest Higgs boson mass. Simultaneously, we consider the radiative corrections to the Higgs boson masses with effective potential methods.

Light rings and light points of boson stars

This work is devoted to the study of photon trajectories around rotating boson stars. The basic properties of boson star models are given with a particular emphasis on the high compactness those objects can have. Using an effective potential method, circular orbits of photons around rotating boson stars are then obtained, at least for relativistic enough configurations. A particular class of light rings, in which the photons are at rest on a stable orbit, is exhibited. By this one means that the associated worldline is collinear to the Killing vector corresponding to the asymptotic time translation symmetry. It is proposed to call those orbits light points. Their existence is very specific to boson stars and the link between light points and ergoregions is investigated.

Motion of spin-half particles in the axially symmetric field of naked singularities of the static q-metric

Quantum-mechanical motion of a half-spin particle was examined in the axially symmetric field of static naked singularities formed by mass distribution with quadrupole moment (q-metric). The analysis was performed by means of the method of effective potentials of the Dirac equation generalized for the case when radial and angular variables are not separated. As $-1<q<q_{lim}, |q_{lim}|<<1 $ the naked singularities do not except the existence of stationary bound states of Dirac particles for a prolate mass distribution in the q-metric along the axial axis. For the oblate mass distribution, the naked singularities of the q-metric are separated from the Dirac particle by infinitely large repulsive barriers with the subsequent potential well deepening while moving along the angle from the equator (or from $\theta=\theta_{min}, \theta=\pi-\theta_{min}$) towards poles. The exception are the poles and, as $0<q<q*$, some points $\theta_{i}$ for the states of the particle with j>=3/2.

Potato feature prediction based on machine vision and 3D model rebuilding

Machine vision based on color, multispectral, and hyperspectral cameras to develop potato quality grading can be used to predict length, width, and mass, as well as defects on the interior and exterior of a sample. However, the images obtained by these cameras are limited by two-dimensional shape information, including width, length, and boundary. Other vital elements of appearance data related to potato mass and quality, including thickness, volume, and surface gradient changes are difficult to detect due to slight surface color differences and device limitations. In this study, we recorded the depth images of 110 potatoes using a depth camera, including samples with uniform shapes or with deformations (e.g., bumps and divots). A novel method was developed for estimating potato mass and shape information and three-dimensional models were built utilizing a new image processing algorithm for depth images. Other features, including length, width, thickness, and volume were also calculated as mass prediction related factors. Experimental results indicate that the proposed models accurately predict potato length, width, and thickness; the mean absolute errors for these predictions were 2.3mm, 2.1mm, and 2.4mm, respectively, while the mean percentage errors were 2.5%, 3.5%, and 4.4%. Mass prediction based on a 3D volume model for both normal and deformed potato samples proved to be more accurate compared to models based on area calculation. Thus 93% of samples were graded by the correct size group using the volume density model while only 73% were graded correctly using the area density. This depth image processing is an effective potential method for future non-destructive post-harvesting grading, especially for products where size, shape, and surface condition are important factors.

Water Solvent Effect on Theoretical Evaluation of 1H NMR Chemical Shifts: o-Methyl-Inositol Isomer.

In this paper, density functional theory calculations of nuclear magnetic resonance (NMR) chemical shifts for l-quebrachitol isomer, previously studied in our group, are reported with the aim of investigating in more detail the water solvent effect on the prediction of 1H NMR spectra. In order to include explicit water molecules, 20 water-l-quebrachitol configurations obtained from Monte Carlo simulation were selected to perform geometry optimizations using the effective fragment potential method encompassing 60 water molecules around the solute. The solvated solute optimized geometries were then used in B3LYP/6-311+G(2d,p) NMR calculations with PCM-water. The inclusion of explicit solvent in the B3LYP NMR calculations resulted in large changes in the 1H NMR profiles. We found a remarkable improvement in the agreement with experimental NMR profiles when the explicit hydrated l-quebrachitol structure is used in B3LYP 1H NMR calculations, yielding a mean absolute error (MAE) of only 0.07 ppm, much lower than reported previously for the gas phase optimized structure (MAE = 0.11 ppm). In addition, a very improved match between theoretical and experimental 1H NMR spectrum measured in D2O was achieved with the new hydrated optimized l-quebrachitol structure, showing that a fine-tuning of the theoretical NMR spectra can be accomplished once solvent effects are properly considered.

Phonon spectra of plutonium at high temperatures

Ab initio molecular dynamics calculations are used to investigate the vibrational properties of the high-temperature $\ensuremath{\delta}$ and $\ensuremath{\epsilon}$ phases of plutonium. We combine the local-density approximation (LDA)$+U$ for strong electron correlations and the temperature-dependent effective potential method in order to calculate the phonon spectra of the two phases, as well as their dependence on temperature. Our results show that the $\ensuremath{\epsilon}$ phase can only be stabilized when temperature and correlations are simultaneously accounted for. We are also able to quantify the degree of anharmonicity of the two phases. While the $\ensuremath{\delta}$ phase is fairly harmonic up to 1000 K, we find that the $\ensuremath{\epsilon}$ phase is strongly anharmonic, which explains why this structure dominates the phase diagram at high temperature.

Computational Study of the Malonic Acid Tautomerization Products in Highly Concentrated Particles.

Knowing the tautomeric form of malonic acid (MA) in concentrated particles is critical to understanding its effect on the atmosphere. Energies and vibrational modes of hydrated MA particles were calculated using density functional theory (DFT) at the B3LYP/6-31G(d,p) level and the effective fragment potential (EFP) method. Visualization of the keto and enol isomer vibrational modes enabled the assignment of keto isomer peaks in the 1710-1750 cm-1 range, and previously unidentified experimental IR peaks in the 1690-1710 cm-1 can now be attributed to the enol isomer. Comparison of calculated spectra of pure hydrated enol or keto isomers confirm recent experimental evidence, presented by Ghorai et al. ( J. Phys. Chem. A 2011 , 115 , 4373 - 4380 ) of a shift in the keto-enol tautomer equilibrium when MA exists as concentrated particles.

Multipole Moments in the Effective Fragment Potential Method.

In the effective fragment potential (EFP) method the Coulomb potential is represented using a set of multipole moments generated by the distributed multipole analysis (DMA) method. Misquitta, Stone, and Fazeli recently developed a basis space-iterated stockholder atom (BS-ISA) method to generate multipole moments. This study assesses the accuracy of the EFP interaction energies using sets of multipole moments generated from the BS-ISA method, and from several versions of the DMA method (such as analytic and numeric grid-based), with varying basis sets. Both methods lead to reasonable results, although using certain implementations of the DMA method can result in large errors. With respect to the CCSD(T)/CBS interaction energies, the mean unsigned error (MUE) of the EFP method for the S22 data set using BS-ISA-generated multipole moments and DMA-generated multipole moments (using a small basis set and the analytic DMA procedure) is 0.78 and 0.72 kcal/mol, respectively. The MUE accuracy is on the same order as MP2 and SCS-MP2. The MUEs are lower than in a previous study benchmarking the EFP method without the EFP charge transfer term, demonstrating that the charge transfer term increases the accuracy of the EFP method. Regardless of the multipole moment method used, it is likely that much of the error is due to an insufficient short-range electrostatic term (i.e., charge penetration term), as shown by comparisons with symmetry-adapted perturbation theory.

Exploring the Solvatochromism of Betaine 30 with Ab Initio Tools: From Accurate Gas-Phase Calculations to Implicit and Explicit Solvation Models.

Betaine 30 is known for the extraordinary solvatochromism of its visible absorption band that goes from λ=882 nm in tetrachloromethane to λ=453 nm in water (Δλ=-429 nm). This large blueshift partly originates from a dramatic decrease of the dipole moment upon excitation. Despite several decades of research, experimental works still disagree on the exact value of the excess dipole moment, the orientation of the dipole moment of the excited-state, the role and amplitude of the change of the polarisability upon excitation as well as on the gas-phase excitation energy. In this work, we present an in-depth theoretical investigation. First, we carefully tested several levels of theory on the model system and next calculated the electric properties of betaine 30 at the CC2 level. Our best estimates are Δμ=-7 D for the excess dipole moment, that is, a significant decrease but no change of direction, a Δα value of -120 a.u. and a gas-phase vertical excitation energy of 1.127 eV. The implicit solvation models are able to reproduce the experimental trends, with large correlation coefficients for non-hydrogen-bond-donating solvents, the smallest root-mean-square deviation error being reached with the vertical excitation model (VEM). The explicit effective fragment potential method combined with time-dependent density functional theory (TD-DFT) in a QM/MM framework provides accurate estimates for hydrogen-bond-donating solvents, whereas the addition of a dispersion correction is needed to restore the correct solvatochromic direction in tetrachloromethane.

Electronic Polarization Effect of the Water Environment in Charge-Separated Donor-Acceptor Systems: An Effective Fragment Potential Model Study.

The electronic polarization (POL) of the surrounding environment plays a crucial role in the energetics of charge-separated systems. Here, the mechanism of POL in charge-separated systems is studied using a combined quantum mechanical and effective fragment potential (QM/EFP) method. In particular, the POL effect caused by charge separation (CS) is investigated at the atomic level by decomposition into the POL at each polarizability point. The relevance of the electric field generated by the CS is analyzed in detail. The model systems investigated are Na+-Cl- and guanine-thymine solvated in water. The dominant part of the POL arises from solvent molecules close to the donor (D) and acceptor (A) units. At short D-A distances, the electric field shows both positive and negative interferences. The former case enhances the POL energy. At longer distances, the interference is weakened, and the local electric field determines the POL energy.

Diffusion in dense non-isothermal Coulomb plasma

We generalize our previous work on diffusion of ions in isothermal plasmas to handle non-isothermal systems. This approach, combined with the method of effective potentials for computing diffusion coefficients, allows us to formulate the diffusion problem in Coulomb systems of arbitrary coupling. The results are applied to study heat-blanketing envelopes of neutron stars in diffusive equilibrium.

Highly Efficient Free Energy Calculations of the Fe Equation of State Using Temperature-Dependent Effective Potential Method.

Free energy calculations at finite temperature based on ab initio molecular dynamics (AIMD) simulations have become possible, but they are still highly computationally demanding. Besides, achieving simultaneously high accuracy of the calculated results and efficiency of the computational algorithm is still a challenge. In this work we describe an efficient algorithm to determine accurate free energies of solids in simulations using the recently proposed temperature-dependent effective potential method (TDEP). We provide a detailed analysis of numerical approximations employed in the TDEP algorithm. We show that for a model system considered in this work, hcp Fe, the obtained thermal equation of state at 2000 K is in excellent agreement with the results of standard calculations within the quasiharmonic approximation.

Optimized effective potentials at a glance: the effective exchange potential of Becke–Johnson applied to molecules

A brief review of the optimized effective potential method in density functional theory is outlined. Some implications of replacing the true Kohn–Sham potential by a functional derivative with respect to the Kohn–Sham one-electron orbitals are revisited in regard to functionals beyond the generalized gradient approximation level. Focusing on the simple but accurate effective exchange potential proposed by Becke and Johnson, sample tests of its self-consistent implementation are presented on a set of atoms and molecules with thoughts of how to improve its efficiency for molecular applications.

Implementation Strategies for Orbital-dependent Density Functionals

The development of density functional theory (DFT) has been focused primarily on two main pillars: (1) the pursuit of more accurate exchange-correlation (XC) density functionals; (2) the feasibility of computational implementation when dealing with many-body systems. In this context, this work is aimed on using one-dimensional quantum systems as theoretical laboratories to investigate the implementation of orbital functionals (OFs) of density. By definition, OFs are those which depend only implicitly on the density, via an explicit formulation in terms of Kohn-Sham orbitals. Typical examples are the XC functionals arising from the Perdew-Zunger self-interaction correction (PZSIC). Formally, via Kohn-Sham equations, the implementation of OFs must be performed by means of the optimized effective potential method (OEP), which is known by requiring an excessive computational effort even when dealing with few electrons systems. Here, we proceed a systematical investigation aiming to simplify or avoid the OEP procedure, taking as reference the implementation of the PZSIC correction applied to one-dimensional Hubbard chains.

Bose and Fermi statistics and the regularization of the nonrelativistic Jacobian for the scale anomaly

We regulate in Euclidean space the Jacobian under scale transformations for two-dimensional nonrelativistic fermions and bosons interacting via contact interactions and compare the resulting scaling anomalies. For fermions, Grassmannian integration inverts the Jacobian: however, this effect is cancelled by the regularization procedure and a result similar to that of bosons is attained. We show the independence of the result with respect to the regulating function, and show the robustness of our methods by comparing the procedure with an effective potential method using both cutoff and $\zeta$-function regularization.

Extension of the Effective Fragment Potential Method to Macromolecules.

The effective fragment potential (EFP) approach, which can be described as a nonempirical polarizable force field, affords an accurate first-principles treatment of noncovalent interactions in extended systems. EFP can also describe the effect of the environment on the electronic properties (e.g., electronic excitation energies and ionization and electron-attachment energies) of a subsystem via the QM/EFP (quantum mechanics/EFP) polarizable embedding scheme. The original formulation of the method assumes that the system can be separated, without breaking covalent bonds, into closed-shell fragments, such as solvent and solute molecules. Here, we present an extension of the EFP method to macromolecules (mEFP). Several schemes for breaking a large molecule into small fragments described by EFP are presented and benchmarked. We focus on the electronic properties of molecules embedded into a protein environment and consider ionization, electron-attachment, and excitation energies (single-point calculations only). The model systems include chromophores of green and red fluorescent proteins surrounded by several nearby amino acid residues and phenolate bound to the T4 lysozyme. All mEFP schemes show robust performance and accurately reproduce the reference full QM calculations. For further applications of mEFP, we recommend either the scheme in which the peptide is cut along the Cα-C bond, giving rise to one fragment per amino acid, or the scheme with two cuts per amino acid, along the Cα-C and Cα-N bonds. While using these fragmentation schemes, the errors in solvatochromic shifts in electronic energy differences (excitation, ionization, electron detachment, or electron-attachment) do not exceed 0.1 eV. The largest error of QM/mEFP against QM/EFP (no fragmentation of the EFP part) is 0.06 eV (in most cases, the errors are 0.01-0.02 eV). The errors in the QM/molecular mechanics calculations with standard point charges can be as large as 0.3 eV.

Accurate Kohn-Sham ionization potentials from scaled-opposite-spin second-order optimized effective potential methods.

One important property of Kohn-Sham (KS) density functional theory is the exact equality of the energy of the highest occupied KS orbital (HOMO) with the negative ionization potential of the system. This exact feature is out of reach for standard density-dependent semilocal functionals. Conversely, accurate results can be obtained using orbital-dependent functionals in the optimized effective potential (OEP) approach. In this article, we investigate the performance, in this context, of some advanced OEP methods, with special emphasis on the recently proposed scaled-opposite-spin OEP functional. Moreover, we analyze the impact of the so-called HOMO condition on the final quality of the HOMO energy. Results are compared to reference data obtained at the CCSD(T) level of theory. © 2016 Wiley Periodicals, Inc.

Multi-configurational explicitly correlated wave functions for the study of confined many electron atoms

Explicitly correlated wave functions to study confined atoms under impenetrable spherical walls have been obtained. Configuration mixing and a correlation factor are included in the variational ansatz. The behaviors of the ground state and some low-lying excited states of He, Be, B and C atoms with the confinement size are analyzed. Level crossing with confinement is found for some cases. This effect is analyzed in terms of the single particle energy of the occupied orbitals. The multi-configuration parameterized optimized effective potential method is employed with a cut-off factor to account for Dirichlet boundary conditions. The variational Monte Carlo method is used to deal with explicitly correlated wave functions.