Full Calculations Research Articles

Ab initio electron-lattice downfolding: Potential energy landscapes, anharmonicity, and molecular dynamics in charge density wave materials

The interplay of electronic and nuclear degrees of freedom presents an outstanding problem in condensed matter physics and chemistry. Computational challenges arise especially for large systems, long time scales, in nonequilibrium, or in systems with strong correlations. In this work, we show how downfolding approaches facilitate complexity reduction on the electronic side and thereby boost the simulation of electronic properties and nuclear motion-in particular molecular dynamics (MD) simulations. Three different downfolding strategies based on constraining, unscreening, and combinations thereof are benchmarked against full density functional calculations for selected charge density wave (CDW) systems, namely 1H-TaS_22, 1T-TiSe_22, 1H-NbS_22, and a one-dimensional carbon chain. We find that the downfolded models can reproduce potential energy surfaces on supercells accurately and facilitate computational speedup in MD simulations by about five orders of magnitude in comparison to purely ab initio calculations. For monolayer 1H-TaS_22 we report classical and path integral replica exchange MD simulations, revealing the impact of thermal and quantum fluctuations on the CDW transition.

Optic Nerve Head and Retinal Nerve Fiber Layer Analysis in Emmetropic Malay Children.

The study aims to investigate the normal reference values for optic nerve head (ONH) and retinal nerve fiber layer (RNFL) parameters in emmetropic Malay children, utilizing measurements obtained through Cirrus SD-OCT (Carl Zeiss Meditec, Dublin, CA). A cross-sectional study was conducted on 95 Malay children, aged between seven and 17 years, with no ocular abnormalities. It was held at Hospital Universiti Sains Malaysia, Malaysia, from January 2014 to December 2015. All children underwent a full ocular examination, including refraction and calculation of axial length. ONH and retinal nerve fiber layer thickness (RNFLT) parameters were measured using the Cirrus SD-OCT machine. One eye of each subject was selected randomly for study. The associations between the parameters and the effect of age, gender,axial length, and spherical equivalent (SE) on the measurements were statistically validated. Ninety-five children were involved in the study, with 65 females (68.4%) and 30 males (31.6%). The mean age was 10.6 (2.82) years, the mean intraocular pressure (IOP) was 14.8 (2.81) mmHg, the mean SE-refraction was 0.12 (0.28) diopters, and the mean axial length was 23.03 (0.76) mm. The mean disc area, rim area, and cup volume were 2.32 (0.40) mm2, 1.53 (0.33) mm2, and 0.204 (0.16) mm3, respectively. The average cup-to-disc ratio (SD) (CDR) and the vertical CDR were 0.55 (0.13) and 0.50(0.14). Mean (SD) RNFLT was 102.08 (11.08) μm for all patients. There was a strong positive correlation between the average, superior, and inferior RNFLT with the optical disc area. The rim area and the average, superior, inferior, and nasal RNFLT alsoshowed a significant correlation. The inferiorRNFLT was negatively correlated with the average CDR. There was also a major influence of gender on the disc area. There were no major age, axial length, and SE influences on the measurements. This study provided normative information for ONH and RNFLT parameters in emmetropic Malay children. It was observed that emmetropic Malay males exhibited a significantly larger optical disc area. The increase in RNFLT is correlated with a significant increase in disc and rim areas.

Crossover from attractive to repulsive induced interactions and bound states of two distinguishable Bose polarons

We study the impact of induced correlations and quasiparticle properties by immersing two distinguishable impurities in a harmonically trapped bosonic medium. It is found that when the impurities couple both either repulsively or attractively to their host, the latter mediates a two-body correlated behavior between them. In the reverse case, namely the impurities interact oppositely with the host, they feature anti-bunching. Monitoring the impurities relative distance and constructing an effective two-body model to be compared with the full many-body calculations, we are able to associate the induced (anti-) correlated behavior of the impurities with the presence of attractive (repulsive) induced interactions. Furthermore, we capture the formation of a bipolaron and a trimer state in the strongly attractive regime. The trimer refers to the correlated behavior of two impurities and a representative atom of the bosonic medium and it is characterized by an ellipsoidal shape of the three-body correlation function. Our results open the way for controlling polaron induced correlations and creating relevant bound states.

Are we really Bayesian? Probabilistic inference shows sub-optimal knowledge transfer.

Numerous studies have found that the Bayesian framework, which formulates the optimal integration of the knowledge of the world (i.e. prior) and current sensory evidence (i.e. likelihood), captures human behaviours sufficiently well. However, there are debates regarding whether humans use precise but cognitively demanding Bayesian computations for behaviours. Across two studies, we trained participants to estimate hidden locations of a target drawn from priors with different levels of uncertainty. In each trial, scattered dots provided noisy likelihood information about the target location. Participants showed that they learned the priors and combined prior and likelihood information to infer target locations in a Bayes fashion. We then introduced a transfer condition presenting a trained prior and a likelihood that has never been put together during training. How well participants integrate this novel likelihood with their learned prior is an indicator of whether participants perform Bayesian computations. In one study, participants experienced the newly introduced likelihood, which was paired with a different prior, during training. Participants changed likelihood weighting following expected directions although the degrees of change were significantly lower than Bayes-optimal predictions. In another group, the novel likelihoods were never used during training. We found people integrated a new likelihood within (interpolation) better than the one outside (extrapolation) the range of their previous learning experience and they were quantitatively Bayes-suboptimal in both. We replicated the findings of both studies in a validation dataset. Our results showed that Bayesian behaviours may not always be achieved by a full Bayesian computation. Future studies can apply our approach to different tasks to enhance the understanding of decision-making mechanisms.

A proposed refueling scheme for the modular pebble bed reactor

In this paper, a suggested design of the fuel pebble and loading pattern in the MIT Modular Pebble Bed HTGR (MPBR) using thorium (232Th) is presented. Using the MCNP5 code model for the MPBR reactor, different compositions of Thorium Low Enriched Uranium (ThLEU) with different Heavy Metal (HM) loading and 235U enrichment were investigated to achieve the maximum thorium utilization with relatively minimum reactivity insertion in case of water ingress accident. Using pure Low Enriched Uranium (LEU) pebbles and ThLEU pebbles with the same HM loading and 235U enrichment, different pebbles loading patterns were studied. One loading pattern was selected to achieve the criticality with enough excess reactivity compensating for the poisoning effect of xenon build-up at the startup of the reactor operation and the negative effect of fuel and reflector temperature coefficients of reactivity. This loading pattern aims also to reduce the radial power peaking in the core and to minimize the axial Power Peaking Factor (PPF) in the central hot channel, with a minimum number of pure LEU fuel batches. A calculation procedure was developed that combines fuel pebble depletion and full core calculations to investigate the impact of a proposed online refueling scheme for the MPBR reactor and to simulate the multicycle refueling mechanism. Using SERPENT 1.1.7, the nuclide concentrations were calculated as a function of pebble burnup for both LEU and ThLEU pebbles. A multicycle online refueling scheme was proposed and the average number of passes required for LEU and ThLEU pebbles to reach their maximum burnup was estimated.

A Novel Fission-Matrix Based Radial Boundary Correction Methodology and its Implementation into the RAPID Code System

The RAPID code system utilizes a novel combined fission matrix methodology to rapidly solve the whole-core eigenvalue problem. To represent axial and radial reflector regions, the fission density distribution in the boundary assemblies, a fission density correction factor methodology was devised and demonstrated. Although, accurate results were achieved, because of the need for a full core Monte Carlo calculation, this technique requires significant computing resources. To address this issue, this paper introduces a novel FM based methodology, which achieves accurate results, however at very small computing expense. The methodology has been implemented into the RAPID code system, and successfully demonstrated for the Watts Bar whole core OECD/NEA

Influence of tip clearance on internal energy loss characteristics of axial flow pumps under different operating conditions

Axial flow pumps possess a unique structure where there must be clearances between the impeller and the piping wall, usually not exceeding 0.1% of the impeller diameter. Despite the small size of the clearance, the internal micro-vortex structures have a non-negligible impact on the main flow field of the impeller. Under the action of the pressure difference between the suction and pressure surfaces of blades, some fluids form high-energy jets in the tip clearance area, known as tip leakage vortices (TLVs). TLV interacts with the flow of the main flow field, exerting a significant impact on the internal flow state, energy loss, and hydraulic performance of the pump. To identify the influence of TLVs on the internal flow field and energy loss of axial flow pumps, this work uses a modified partially averaged Navier–Stokes (PANS) model to perform full flow field numerical calculations for a certain axial flow pump and conducts a comparative analysis of the internal flow field energy dissipation, unsteady vortex structures, energy loss, and other characteristics under three different tip clearances: 0.2 mm (0.05%D), 0.6 mm (0.15%D), and 1.0 mm (0.25%D) based on the energy transport theory. The results indicate that at optimal operating conditions, the internal energy distribution of the fluid in each flow passage is uniform, and the energy loss is primarily caused by axial backflow in the tip area; under critical rotating stall conditions, clearance size affects the distribution state of enstrophy in the guide vane flow passage, leading to average enstrophy being highest at the rim area and the most uneven distribution of enstrophy, inducing larger energy loss in the impeller; during deep stall conditions, the unevenness of internal energy distribution is stronger than that under critical stall conditions, but the overall energy loss within the impeller flow area is lower than that under critical stall conditions, while energy unevenness is mitigated as the tip clearance size increases.

Asymmetric rectified electric fields: nonlinearities and equivalent circuits.

Recent experiments [S. H. Hashemi et al., Phys. Rev. Lett., 2018, 121, 185504] have shown that a long-ranged steady electric field emerges when applying an oscillating voltage over an electrolyte with unequal mobilities of cations and anions confined between two planar blocking electrodes. To explain this effect we analyse full numerical calculations based on the Poisson-Nernst-Planck equations by means of analytically constructed equivalent electric circuits. Surprisingly, the resulting equivalent circuit has two capacitive elements, rather than one, which introduces a new timescale for electrolyte dynamics. We find a good qualitative agreement between the numerical results and our simple analytic model, which shows that the long-range steady electric field emerges from the different charging rates of cations and anions in the electric double layers.

Bottom-hadron production in high-energy pp and heavy-ion collisions

The hadro-chemistry of bottom quarks produced in hadronic collisions encodes valuable information on the mechanism of color-neutralization in these reactions. We first compute the chemistry of bottom-hadrons in high-energy pp collisions employing statistical hadronization with a largely augmented set of states beyond the currently measured spectrum. This enables a comprehensive prediction of fragmentation fractions of weakly decaying bottom hadrons for the first time and a satisfactory explanation of the existing measurements in pp collisions at the LHC. Utilizing the bottom hadro-chemistry thus obtained as the baseline, we then perform transport simulations of bottom quarks in the hot QCD matter created in PbPb collisions at the LHC energy and calculate the pertinent bottom-hadron observables. The transverse momentum (pT) dependent modifications of the bottom baryon-to-meson ratio (Λb0/B-) relative to their pp counterparts are highlighted as a result of bottom quark diffusion and hadronization in the Quark-Gluon Plasma (QGP). We finally summarize the heavy quark (charm vs bottom) diffusion coefficients as extracted from transport simulations and compare them to result from recent full lattice QCD computations.

(Invited) Study of Electrochemical Interfaces Using DFT and the Classical Liquid Theory Hybrid Simulations

Understanding the properties of electrochemical interfaces leads to improving the efficiency and durability of energy and structural materials such as secondary batteries, fuel cells, catalysts, and corrosion. First-principles calculations based on the density functional theory (DFT) are useful simulation technique to those materials and are widely used to understand physicochemical phenomena such as charge and electron transfer and reaction kinetics. However, the simulation costs for the full DFT calculation are quite large. Thus, we need to reduce it to obtain as many results as possible within the limited calculation resources. Combining the DFT and the classical liquid theory is one of a possible way to reduce the costs. We have been developed a series of simulation techniques to hybridize the DFT and the reference interaction site model (RISM) [1-4]. In the presentation, after providing a brief introduction of our simulation technique, we will show the simulation results for electrolyte decompositions and battery degradation [5], a confined effect of water molecule in the MXene electrode [6], and a water dissociation reaction on Cu surface using an automated reaction path search method [7,8].

SVM-based fast 3D pore-scale rock-typing and permeability upscaling for complex rocks using Minkowski functionals

The rapid advancement of digital core analysis has greatly promoted the research progress of flow and transport in porous media. However, complex analytical process with exceeding computational load impedes the application on large data volume. Considering the strong heterogeneity of the underground porous media, the integration of pore-scale information into continuum scale is widely concerned for the future development of digital physical analysis. For hierarchical porous structures, pore-scale rock-typing and upscaling of petrophysical properties is a promising solution towards the issue, and morphological and topological descriptors associating data clustering methods are popularly utilized. However, the size of the regional support through which the parameter fields are generated heavily affects the descriptive capacities of the parameters and the following partitioning process. We propose in this work a robust integrated pore-scale rock-typing and upscaling technology for 3D porous structures which uses Minkowski functionals as the descriptive parameters. A fast-computational method utilising fast Fourier transform has been applied for efficient generation of the parameter fields. A comparative study between the two different classification methods of Support Vector Machine (SVM) and Gaussian Mixture Model (GMM) has been conducted on two complex artificial porous systems and a laminated sandstone through various regional support sizes. Throughout the test, SVM has illustrated obvious advantage of overcoming regional support size effect even with limited labelling information. The Upscaling of permeability on the natural sandstone sample based on the rock type distribution has demonstrated excellent accuracy comparing with full scale direct computation.

Isotopic Analysis of Lead at Ultratrace Levels Using Thermal Ionization Mass Spectrometry (TIMS) Coupled with the Continuous Heating Method: Optimization of the Data Integration Range and Method.

This study systematically and experimentally evaluates data integration methods for the isotopic analysis of Pb at ultratrace levels using thermal ionization mass spectrometry (TIMS) with a continuous heating method. The evaluation utilized a certified reference material of Pb (SRM 981). The experimental evaluations encompass different data calculation methods (methods I, II, and III) and integration ranges (full, over 1%, 25%, and 75%). Method I, in which isotope ratios were calculated based on summed ion signal intensities compensating for mass fractionation, was consistent with the certified values for 10 and 1 ng standard samples across all integration ranges. For 100 pg samples, full range calculations failed for specific isotope ratios, but reduced ranges (over 1%, 25%, and 75%) yielded values overlapping with certified ones. Method II, in which isotope ratios were calculated by averaging the precalculated isotope ratios, exhibited inferior performance compared to method I. Method III, using weighted averaging to reduce anomalous values, showed results consistent with those of method I but was recommended only for single measurements. An integration range of over 1% or 25% is preferred to exclude anomalies while compensating for mass fractionation. The optimized method was validated by comparing two different instruments used for the isotopic analysis of the reference material. The enhanced accuracy and precision provide valuable insights for researchers working in ultratrace-level Pb isotopic analysis using TIMS.

Vibrationally correlated calculations in polyspherical coordinates: Taylor expansion-based kinetic energy operators.

The efficiency of quantum chemical simulations of nuclear motion can in many cases greatly benefit from the application of curvilinear coordinate systems. This is rooted in the fact that a set of smartly selected curvilinear coordinates may represent the motion naturally well, thus decreasing the couplings between motions in these coordinates. In this study, we assess the validity of different Taylor expansion-based approximations of kinetic energy operators in a (curvilinear) polyspherical parametrization. To this end, we investigate the accuracy as well as the numerical performance of the approximations in time-independent vibrational coupled cluster and full vibrational interaction calculations for several test cases ranging from tri- to penta-atomic molecules. We find that several of the proposed schemes reproduce the vibrational ground state and excitation energies to a decent accuracy, justifying their application in future investigations. Furthermore, due to the restricted mode coupling and their inherent sum-of-products form, the new approximations open up the possibility of treating large molecular systems with efficient vibrational coupled cluster schemes in general coordinates.

Superdense Hexagonal BP and AlP with Quartz Topology: Crystal Chemistry and DFT Study

The superdense hexagonal phosphides BP and AlP, whose structures are formed by distorted tetrahedra and characterized by quartz-derived (qtz) topology, were predicted from crystal chemistry and first principles as potential high-pressure phases. From full geometry structure relaxations and ground state energy calculations based on quantum density functional theory (DFT), qtz BP and AlP were found to be less cohesive than the corresponding cubic zinc-blende (zb) phases with diamond-like (dia) topology, but were confirmed to be mechanically (elastic constants) and dynamically (phonons) stable. From the energy–volume equations of state, qtz phases were found to be energetically favorable at small volumes (high pressures), with zb-to-qtz transition pressures of 144 GPa for BP and 28 GPa for AlP. According to the electronic band structures and the site projected density of states, both phosphides exhibit larger band gaps of the zinc-blende phases compared to the qtz phases; the smaller values for the latter result from the smaller volumes per formula unit, leading to increased covalence.

Lift analysis and anti-rolling control system design of Magnus rotating roll stabilizer at full speed range

To analyze the impact of the operating mode of the Magnus rotating roll stabilizer on anti-rolling performance, a full speed range lift calculation method is proposed. By combining the micro-element approach with the mechanism of the Magnus effect force, the lift law of the rotating stabilizer in different modes could be obtained theoretically. Subsequently, correction factors are fitted for various operating conditions to correct the full speed range lift model through hydrodynamic simulation analysis of the stabilizer. In addition, RBF neural networks are introduced to approximate uncertain ship models under different modes to achieve anti-rolling control of the Magnus rotating stabilizer in various operating modes. When the stabilizer switches operating mode, this network provides a corresponding adaptive ship model for the sliding mode controller to optimize the anti-rolling effect of the sliding mode controller. The simulation shows that the corrected lift model has good predictive performance. Compared to traditional fin stabilizers and rotating stabilizers, the sliding mode control algorithm based on the RBF neural network can maintain excellent anti-rolling performance at full speed range, with a maximum anti-roll efficiency of over 93%.

Introducing the embedded random phase approximation: H2 dissociative adsorption on Cu(111) as an exemplar

The random phase approximation (RPA) as a means of treating electron correlation recently has been shown to outperform standard density functional theory (DFT) approximations in a variety of cases. However, the computational cost of the RPA is substantially more than DFT, especially when aiming to study extended surfaces. Properly accounting for sufficient surface ensemble size, Brillouin zone sampling, and vacuum separation of periodic images in standard periodic-planewave-based DFT code raises the cost to achieve converged results. Here, we show that sub-system embedding schemes enable use of the RPA for modeling heterogeneous reactions at reduced computational cost. We explore two different embedded RPA (emb-RPA) approaches, periodic emb-RPA and cluster emb-RPA. We use the (experimentally and theoretically) well-studied H2 dissociative adsorption on Cu(111) as our exemplar, and first perform full periodic RPA calculations as a benchmark. The full RPA results match well the semi-empirical barrier fit to experimental observables and others derived from high-level computations, e.g., from recent embedded n-electron valence second order perturbation theory [Zhao et al., J. Chem. Theory Comput. 16(11), 7078–7088 (2020)] and quantum Monte Carlo [Doblhoff-Dier et al., J. Chem. Theory Comput. 13(7), 3208–3219 (2017)] simulations. Among the two emb-RPA approaches tested, the cluster emb-RPA accurately reproduces the energy profile (maximum error of 50 meV along the reaction pathway) while reducing the computational cost by approximately two orders of magnitude. We therefore expect that the embedded cluster approach will enable wider RPA implementation in heterogeneous catalysis.

REAlgo: Rapid and efficient algorithm for estimating MP2/CCSD energy gradients for large molecular clusters.

This work reports the development of an algorithm for rapid and efficient evaluation of energy gradients for large molecular clusters employing correlated methods viz. second-order Møller-Plesset perturbation theory (MP2) theory and couple cluster singles and doubles (CCSD). The procedure segregates the estimation of Hartree-Fock (HF) and correlation components. The HF energy and gradients are obtained by performing a full calculation. The correlation energy is approximated as the corresponding two-body interaction energy. Correlation gradients for each monomer are approximated from the respective monomer-centric fragments comprising its immediate neighbours. The programmed algorithm is explored for the geometry optimization of large molecular clusters using the BERNY optimizer as implemented in the Gaussian suite of software. The accuracy and efficacy of the method are critically probed for a variety of large molecular clusters containing up to 3000 basis functions, in particular large water clusters. The CCSD level geometry optimization of molecular clusters containing ∼800 basis functions employing a modest hardware is also reported.

Sensitivity of cirrus and contrail radiative effect on cloud microphysical and environmental parameters

Abstract. Natural cirrus clouds and contrails cover about 30 % of the Earth's mid-latitudes and up to 70 % of the tropics. Due to their widespread occurrence, cirrus clouds have a considerable impact on the Earth energy budget, which, on average, leads to a warming net radiative effect (solar + thermal infrared). However, whether the instantaneous radiative effect (RE), which in some cases corresponds to a radiative forcing, of natural cirrus or contrails is positive or negative depends on their microphysical, macrophysical, and optical properties, as well as the radiative properties of the environment. This is further complicated by the fact that the actual ice crystal shape is often unknown, and thus, ice clouds remain one of the components that are least understood in the Earth's radiative budget. The present study aims to investigate the dependency of the effect on cirrus RE on eight parameters, namely solar zenith angle, ice water content, ice crystal effective radius, cirrus temperature, surface albedo, surface temperature, cloud optical thickness of an underlying liquid water cloud, and three ice crystal shapes. In total, 283 500 plane-parallel radiative transfer simulations have been performed, not including three-dimensional scattering effects. Parameter ranges are selected that are typically associated with natural cirrus and contrails. In addition, the effect of variations in the relative humidity profile and the ice cloud geometric thickness have been investigated for a sub-set of the simulations. The multi-dimensionality and complexity of the eight-dimensional parameter space makes it impractical to discuss all potential configurations in detail. Therefore, specific cases are selected and discussed. For a given parameter combination, the largest impact on solar, thermal-infrared (TIR), and net RE is related to the ice crystal effective radius. The second most important parameter is ice water content, which equally impacts the solar and terrestrial RE. The solar RE of cirrus is also determined by solar zenith angle, surface albedo, liquid cloud optical thickness, and ice crystal shape (in descending priority). RE in the TIR spectrum is dominated by surface temperature, ice cloud temperature, liquid water cloud optical thickness, and ice crystal shape. Net RE is controlled by surface albedo, solar zenith angle, and surface temperature in decreasing importance. The relative importance of the studied parameters differs, depending on the ambient conditions. Furthermore, and during nighttime the net RE is equal to the TIR RE. The data set generated in this work is publicly available. It can be used as a lookup table to extract the RE of cirrus clouds, contrails, and contrail cirrus instead of full radiative transfer calculations.

From ray to spray: augmenting amplitudes and taming fast oscillations in fully numerical neutrino codes

In this note we describe how to complement the neutrino evolution matrix calculated at a given energy and trajectory with additional information which allows to reliably extrapolate it to nearby energies or trajectories without repeating the full computation. Our method works for arbitrary matter density profiles, can be applied to any propagation model described by an Hamiltonian, and exactly guarantees the unitarity of the evolution matrix. As a straightforward application, we show how to enhance the calculation of the theoretical predictions for experimentally measured quantities, so that they remain accurate even in the presence of fast neutrino oscillations. Furthermore, the ability to “move around” a given energy and trajectory opens the door to precise interpolation of the oscillation amplitudes within a grid of tabulated values, with potential benefits for the computation speed of Monte-Carlo codes. We also provide a set of examples to illustrate the most prominent features of our approach.

Stability of electroweak vacuum and supersymmetric contribution to muon g − 2

We study the stability of the electroweak vacuum in the supersymmetric (SUSY) standard model (SM), paying particular attention to its relation to the SUSY contribution to the muon anomalous magnetic moment aμ. If the SUSY contribution to aμ is sizable, the electroweak vacuum may become unstable because of enhanced trilinear scalar interactions. With aμ being fixed, larger slepton masses require more enhanced trilinear couplings, which make the electroweak vacuum more unstable. Thus, assuming SUSY contribution to aμ being sizable, an upper bound on the slepton masses is obtained. We give a detailed prescription to perform a full one-loop calculation of the decay rate of the electroweak vacuum for the case that the SUSY contribution to aμ is enhanced. We also give an upper bound on the slepton masses as a function of the SUSY contribution to aμ.