DFT+U and quantum Monte Carlo study of electronic and optical properties of AgNiO2 and AgNi1-xCoxO2 delafossite.

As the only semimetallic d10-based delafossite, AgNiO2 has received a great deal of attention due to both its unique semimetallicity and its antiferromagnetism in the NiO2 layer that is coupled with a lattice distortion. In contrast, other delafossites such as AgCoO2 are insulating. Here we study how the electronic structure of AgNi1-xCoxO2 alloys vary with Ni/Co concentration, in order to investigate the electronic properties and phase stability of the intermetallics. While the electronic and magnetic structure of delafossites have been studied using density functional theory (DFT), earlier studies have not included corrections for strong on-site Coulomb interactions. In order to treat these interactions accurately, in this study we use Quantum Monte Carlo (QMC) simulations to obtain accurate estimates for the electronic and magnetic properties of AgNiO2. By comparison to DFT results we show that these electron correlations are critical to account for. We show that Co doping on the magnetic Ni sites results in a metal-insulator transition near x ∼0.33, and reentrant behavior near x ∼ 0.66.

Deciphering chemical order/disorder and material properties at the single-atom level.

Perfect crystals are rare in nature. Real materials often contain crystal defects and chemical order/disorder such as grain boundaries, dislocations, interfaces, surface reconstructions and point defects. Such disruption in periodicity strongly affects material properties and functionality. Despite rapid development of quantitative material characterization methods, correlating three-dimensional (3D) atomic arrangements of chemical order/disorder and crystal defects with material properties remains a challenge. On a parallel front, quantum mechanics calculations such as density functional theory (DFT) have progressed from the modelling of ideal bulk systems to modelling 'real' materials with dopants, dislocations, grain boundaries and interfaces; but these calculations rely heavily on average atomic models extracted from crystallography. To improve the predictive power of first-principles calculations, there is a pressing need to use atomic coordinates of real systems beyond average crystallographic measurements. Here we determine the 3D coordinates of 6,569 iron and 16,627 platinum atoms in an iron-platinum nanoparticle, and correlate chemical order/disorder and crystal defects with material properties at the single-atom level. We identify rich structural variety with unprecedented 3D detail including atomic composition, grain boundaries, anti-phase boundaries, anti-site point defects and swap defects. We show that the experimentally measured coordinates and chemical species with 22 picometre precision can be used as direct input for DFT calculations of material properties such as atomic spin and orbital magnetic moments and local magnetocrystalline anisotropy. This work combines 3D atomic structure determination of crystal defects with DFT calculations, which is expected to advance our understanding of structure-property relationships at the fundamental level.

Evaluation of the excitation spectra with diffusion Monte Carlo on an auxiliary bosonic ground state.

We aim to improve upon the variational Monte Carlo (VMC) approach for excitations replacing the Jastrow factor by an auxiliary bosonic (AB) ground state and multiplying it by a fermionic component factor. The instantaneous change in imaginary time of an arbitrary excitation in the original interacting fermionic system is obtained by measuring observables via the ground-state distribution of walkers of an AB system that is subject to an auxiliary effective potential. The effective potential is used to (i) drive the AB system's ground-state configuration space toward the configuration space of the excitations of the original fermionic system and (ii) subtract from a diffusion Monte Carlo (DMC) calculation contributions that can be included in conventional approximations, such as mean-field and configuration interaction (CI) methods. In this novel approach, the AB ground state is treated statistically in DMC, whereas the fermionic component of the original system is expanded in a basis. The excitation energies of the fermionic eigenstates are obtained by sampling a fermion-boson coupling term on the AB ground state. We show that this approach can take advantage of and correct for approximate eigenstates obtained via mean-field calculations or truncated interactions. We demonstrate that the AB ground-state factor incorporates the correlations missed by standard Jastrow factors, further reducing basis truncation errors. Relevant parts of the theory have been tested in soluble model systems and exhibit excellent agreement with exact analytical data and CI and VMC approaches. In particular, for limited basis set expansions and sufficient statistics, AB approaches outperform CI and VMC in terms of basis size for the same systems. The implementation of this method in current codes, despite being demanding, will be facilitated by reusing procedures already developed for calculating ground-state properties with DMC and excitations with VMC.

The TIR-domain containing effectors BtpA and BtpB from Brucella abortus impact NAD metabolism.

Brucella species are facultative intracellular Gram-negative bacteria relevant to animal and human health. Their ability to establish an intracellular niche and subvert host cell pathways to their advantage depends on the delivery of bacterial effector proteins through a type IV secretion system. Brucella Toll/Interleukin-1 Receptor (TIR)-domain-containing proteins BtpA (also known as TcpB) and BtpB are among such effectors. Although divergent in primary sequence, they interfere with Toll-like receptor (TLR) signaling to inhibit the innate immune responses. However, the molecular mechanisms implicated still remain unclear. To gain insight into the functions of BtpA and BtpB, we expressed them in the budding yeast Saccharomyces cerevisiae as a eukaryotic cell model. We found that both effectors were cytotoxic and that their respective TIR domains were necessary and sufficient for yeast growth inhibition. Growth arrest was concomitant with actin depolymerization, endocytic block and a general decrease in kinase activity in the cell, suggesting a failure in energetic metabolism. Indeed, levels of ATP and NAD+ were low in yeast cells expressing BtpA and BtpB TIR domains, consistent with the recently described enzymatic activity of some TIR domains as NAD+ hydrolases. In human epithelial cells, both BtpA and BtpB expression reduced intracellular total NAD levels. In infected cells, both BtpA and BtpB contributed to reduction of total NAD, indicating that their NAD+ hydrolase functions are active intracellularly during infection. Overall, combining the yeast model together with mammalian cells and infection studies our results show that BtpA and BtpB modulate energy metabolism in host cells through NAD+ hydrolysis, assigning a novel role for these TIR domain-containing effectors in Brucella pathogenesis.

Surrogate Hessian accelerated structural optimization for stochastic electronic structure theories.

We present an efficient energy-based method for structural optimization with stochastic electronic structure theories, such as diffusion quantum Monte Carlo (DMC). This method is based on robust line-search energy minimization in reduced parameter space, exploiting approximate but accurate Hessian information from a surrogate theory, such as density functional theory. The surrogate theory is also used to characterize the potential energy surface, allowing for simple but reliable ways to maximize statistical efficiency while retaining controllable accuracy. We demonstrate the method by finding the minimum DMC energy structures of the selected flake-like aromatic molecules, such as benzene, coronene, and ovalene, represented by 2, 6, and 19 structural parameters, respectively. In each case, the energy minimum is found within two parallel line-search iterations. The method is near-optimal for a line-search technique and suitable for a broad range of applications. It is easily generalized to any electronic structure method where forces and stresses are still under active development and implementation, such as diffusion Monte Carlo, auxiliary-field Monte Carlo, and stochastic configuration interaction, as well as deterministic approaches such as the random-phase approximation. Accurate and efficient means of geometry optimization could shed light on a broad class of materials and molecules, showing high sensitivity of induced properties to structural variables.

Exascale applications: skin in the game.

As noted in Wikipedia, skin in the game refers to having 'incurred risk by being involved in achieving a goal', where 'skin is a synecdoche for the person involved, and game is the metaphor for actions on the field of play under discussion'. For exascale applications under development in the US Department of Energy Exascale Computing Project, nothing could be more apt, with the skin being exascale applications and the game being delivering comprehensive science-based computational applications that effectively exploit exascale high-performance computing technologies to provide breakthrough modelling and simulation and data science solutions. These solutions will yield high-confidence insights and answers to the most critical problems and challenges for the USA in scientific discovery, national security, energy assurance, economic competitiveness and advanced healthcare. This article is part of a discussion meeting issue 'Numerical algorithms for high-performance computational science'.

Perspectives on van der Waals Density Functionals: The Case of TiS2.

The van der Waals interaction is of foundational importance for a wide variety of physical systems. In particular, van der Waals forces lie at the heart of potential device technologies that may be realized from the functional organization of layered two-dimensional (2D) nanomaterials. For intermediate to large-scale applications modeling, van der Waals density functionals have become the de facto choice for first-principles calculations. In particular, the vdW-DF family of functionals have provided a systematic approach to this theoretically challenging problem. While much progress has been made, there remains room for improvement in the microscopic description of vdW forces from these density functionals. In this work, we compute benchmark results for the binding energy and the electronic density response to binding in TiS2 via accurate diffusion quantum Monte Carlo calculations. We compare these benchmark data to results obtained from local, semilocal, and van der Waals functionals. In particular, we gauge the quality of the original vdW-DF/vdW-DF2 functionals, as well as updated variants such as vdW-DF-C09, vdW-DF-optB88, vdW-DF-optB86b, and vdW-DF2-B86R. We find a close relationship between the accuracy of predicted interlayer separation distances and binding energies for TiS2, with the vdW-DF-optB88 functional performing very well in terms of both quantities. In general, the more recently developed functionals are systematic improvements over older ones. However, when considering the response of the electron density to binding, we find that local-density approximation (LDA) and PBEsol generally outperform the vdW-DF functionals in describing the interlayer charge accumulation with vdW-DF-C09 variants performing the best overall.

Toward a systematic improvement of the fixed-node approximation in diffusion Monte Carlo for solids-A case study in diamond.

While Diffusion Monte Carlo (DMC) is in principle an exact stochastic method for ab initio electronic structure calculations, in practice, the fermionic sign problem necessitates the use of the fixed-node approximation and trial wavefunctions with approximate nodes (or zeros). This approximation introduces a variational error in the energy that potentially can be tested and systematically improved. Here, we present a computational method that produces trial wavefunctions with systematically improvable nodes for DMC calculations of periodic solids. These trial wavefunctions are efficiently generated with the configuration interaction using a perturbative selection made iteratively (CIPSI) method. A simple protocol in which both exact and approximate results for finite supercells are used to extrapolate to the thermodynamic limit is introduced. This approach is illustrated in the case of the carbon diamond using Slater-Jastrow trial wavefunctions including up to one million Slater determinants. Fixed-node DMC energies obtained with such large expansions are much improved, and the fixed-node error is found to decrease monotonically and smoothly as a function of the number of determinants in the trial wavefunction, a property opening the way to a better control of this error. The cohesive energy extrapolated to the thermodynamic limit is in close agreement with the estimated experimental value. Interestingly, this is also the case at the single-determinant level, thus, indicating a very good error cancellation in carbon diamond between the bulk and atomic total fixed-node energies when using single-determinant nodes.

Correction: The TIR Homologue Lies near Resistance Genes in Staphylococcus aureus, Coupling Modulation of Virulence and Antimicrobial Susceptibility.

[This corrects the article DOI: 10.1371/journal.ppat.1006092.].

Hybrid DFT investigation of the energetics of Mg ion diffusion in α-MoO3.

Rechargeable batteries that utilize divalent Mg ions as the charge carrier species can in principle achieve substantially greater volumetric energy densities than conventional Li-ion batteries. One significant impediment to the development of commercially viable Mg-ion batteries is the slow rate of Mg ion diffusion through otherwise promising cathode materials. Accurate prediction of the activation energies associated with this diffusion process using density functional theory (DFT) is especially challenging due to self-interaction errors intrinsic to DFT that lead to over-delocalization of the d-electrons. One effective but highly computationally demanding approach to reducing self-interaction errors is the use of hybrid functionals, which incorporate a fraction of exact Hartree-Fock exchange. In this work, we assess the effects of exact exchange on computed activation energies for ion diffusion in one potential cathode material, α-MoO3. In contrast to previous studies that primarily utilize non-hybrid functionals, we perform nudged elastic band calculations in which the nuclear coordinates are fully converged using both hybrid functionals and k-point sampling. It is found that while non-hybrid functionals indicate the existence of thermodynamically accessible channels for bulk Mg ion diffusion in all three dimensions, hybrid functionals predict that some of these channels are largely inaccessible under typical charge/discharge conditions. Furthermore, it is demonstrated that certain commonly used approximations for incorporating the effects of Hartree-Fock exchange are inadequate for this system, including DFT+U calculations and the use of single-point hybrid calculations using atomic positions obtained using non-hybrid functionals.

An efficient hybrid orbital representation for quantum Monte Carlo calculations.

The scale and complexity of the quantum system to which real-space quantum Monte Carlo (QMC) can be applied in part depends on the representation and memory usage of the trial wavefunction. B-splines, the computationally most efficient basis set, can have memory requirements exceeding the capacity of a single computational node. This situation has traditionally forced a difficult choice of either using slow internode communication or a potentially less accurate but smaller basis set such as Gaussians. Here, we introduce a hybrid representation of the single particle orbitals that combine a localized atomic basis set around atomic cores and B-splines in the interstitial regions to reduce the memory usage while retaining the high speed of evaluation and either retaining or increasing overall accuracy. We present a benchmark calculation for NiO demonstrating a superior accuracy while using only one eighth of the memory required for conventional B-splines. The hybrid orbital representation therefore expands the overall range of systems that can be practically studied with QMC.

A comparative study of surface energies and water adsorption on Ce-bastnäsite, La-bastnäsite, and calcite via density functional theory and water adsorption calorimetry.

Bastnäsite, a fluoro-carbonate mineral, is the single largest mineral source of light rare earth elements (REE), La, Ce and Nd. Enhancing the efficiency of separation of the mineral from gangue through froth flotation is the first step towards meeting an ever increasing demand for REE. To design and evaluate collector molecules that selectively bind to bastnäsite, a fundamental understanding of the structure and surface properties of bastnäsite is essential. In our earlier work (J. Phys. Chem. C, 2016, 120, 16767), we carried out an extensive study of the structure, surface stability and water adsorption energies of La-bastnäsite. In this work, we make a comparative study of the surface properties of Ce-bastnäsite, La-bastnäsite, and calcite using a combination of density functional theory (DFT) and water adsorption calorimetry. Spin polarized DFT+U calculations show that the exchange interaction between the electrons in Ce 4f orbitals is negligible and that these orbitals do not participate in bonding with the oxygen atom of the adsorbed water molecule. In agreement with calorimetry, DFT calculations predict larger surface energies and stronger water adsorption energies on Ce-bastnäsite than on La-bastnäsite. The order of stabilities for stoichiometric surfaces is as follows: [101[combining macron]0] > [101[combining macron]1] > [101[combining macron]2] > [0001] > [112[combining macron]2] > [101[combining macron]4] and the most favorable adsorption sites for water molecules are the same as for La-bastnäsite. In agreement with water adsorption calorimetry, at low coverage water molecules are strongly stabilized via coordination to the surface Ce3+ ions, whereas at higher coverage they are adsorbed less strongly via hydrogen bonding interaction with the surface anions. Due to similar water adsorption energies on bastnäsite [101[combining macron]1] and calcite [101[combining macron]4] surfaces, the design of collector molecules that selectively bind to bastnäsite over calcite must exploit the structural differences in the predominantly exposed facets of these minerals.

Combining configurational energies and forces for molecular force field optimization.

While quantum chemical simulations have been increasingly used as an invaluable source of information for atomistic model development, the high computational expenses typically associated with these techniques often limit thorough sampling of the systems of interest. It is therefore of great practical importance to use all available information as efficiently as possible, and in a way that allows for consistent addition of constraints that may be provided by macroscopic experiments. Here we propose a simple approach that combines information from configurational energies and forces generated in a molecular dynamics simulation to increase the effective number of samples. Subsequently, this information is used to optimize a molecular force field by minimizing the statistical distance similarity metric. We illustrate the methodology on an example of a trajectory of configurations generated in equilibrium molecular dynamics simulations of argon and water and compare the results with those based on the force matching method.

Diffusion quantum Monte Carlo calculations of SrFeO3 and LaFeO3.

The equations of state, formation energy, and migration energy barrier of the oxygen vacancy in SrFeO3 and LaFeO3 were calculated with the diffusion quantum Monte Carlo (DMC) method. Calculations were also performed with various Density Functional Theory (DFT) approximations for comparison. DMC reproduces the measured cohesive energies of these materials with errors below 0.23(5) eV and the structural properties within 1% of the experimental values. The DMC formation energies of the oxygen vacancy in SrFeO3 and LaFeO3 under oxygen-rich conditions are 1.3(1) and 6.24(7) eV, respectively. Similar calculations with semi-local DFT approximations for LaFeO3 yielded vacancy formation energies 1.5 eV lower. Comparison of charge density evaluated with DMC and DFT approximations shows that DFT tends to overdelocalize the electrons in defected SrFeO3 and LaFeO3. Calculations with DMC and local density approximation yield similar vacancy migration energy barriers, indicating that steric/electrostatic effects mainly determine migration barriers in these materials.

Incidence of severe diarrhoea due to Vibrio cholerae in the catchment area of six surveillance hospitals in Bangladesh.

Cholera is an important public health problem in Bangladesh. Interventions to prevent cholera depend on their cost-effectiveness which in turn depends on cholera incidence. Hospital-based diarrhoeal disease surveillance has been ongoing in six Bangladeshi hospitals where a systematic proportion of patients admitted with diarrhoea were enrolled and tested for Vibrio cholerae. However, incidence calculation using only hospital data underestimates the real disease burden because many ill persons seek treatment elsewhere. We conducted a healthcare utilization survey in the catchment areas of surveillance hospitals to estimate the proportion of severe diarrhoeal cases that were admitted to surveillance hospitals and estimated the population-based incidence of severe diarrhoea due to V. cholerae by combining both hospital surveillance and catchment area survey data. The estimated incidence of severe diarrhoea due to cholera ranged from 0.3 to 4.9/1000 population in the catchment area of surveillance hospitals. In children aged <5 years, incidence ranged from 1.0 to 11.0/1000 children. Diarrhoeal deaths were most common in the Chhatak Hospital's catchment area (18.5/100 000 population). This study provides a credible estimate of the incidence of severe diarrhoea due to cholera in Bangladesh, which can be used to assess the cost-effectiveness of cholera prevention activities.

Competitive lithium solvation of linear and cyclic carbonates from quantum chemistry.

The composition of the lithium cation (Li(+)) solvation shell in mixed linear and cyclic carbonate-based electrolytes has been re-examined using Born-Oppenheimer molecular dynamics (BOMD) as a function of salt concentration and cluster calculations with ethylene carbonate:dimethyl carbonate (EC:DMC)-LiPF6 as a model system. A coordination preference for EC over DMC to a Li(+) was found at low salt concentrations, while a slightly higher preference for DMC over EC was found at high salt concentrations. Analysis of the relative binding energies of the (EC)n(DMC)m-Li(+) and (EC)n(DMC)m-LiPF6 solvates in the gas-phase and for an implicit solvent (as a function of the solvent dielectric constant) indicated that the DMC-containing Li(+) solvates were stabilized relative to (EC4)-Li(+) and (EC)3-LiPF6 by immersing them in the implicit solvent. Such stabilization was more pronounced in the implicit solvents with a high dielectric constant. Results from previous Raman and IR experiments were reanalyzed and reconciled by correcting them for changes of the Raman activities, IR intensities and band shifts for the solvents which occur upon Li(+) coordination. After these correction factors were applied to the results of BOMD simulations, the composition of the Li(+) solvation shell from the BOMD simulations was found to agree well with the solvation numbers extracted from Raman experiments. Finally, the mechanism of the Li(+) diffusion in the dilute (EC:DMC)LiPF6 mixed solvent electrolyte was studied using the BOMD simulations.

Quantum Monte Carlo analysis of a charge ordered insulating antiferromagnet: the Ti4O7 Magnéli phase.

The Magnéli phase Ti4O7 is an important transition metal oxide with a wide range of applications because of its interplay between charge, spin, and lattice degrees of freedom. At low temperatures, it has non-trivial magnetic states very close in energy, driven by electronic exchange and correlation interactions. We have examined three low-lying states, one ferromagnetic and two antiferromagnetic, and calculated their energies as well as Ti spin moment distributions using highly accurate quantum Monte Carlo methods. We compare our results to those obtained from density functional theory-based methods that include approximate corrections for exchange and correlation. Our results confirm the nature of the states and their ordering in energy, as compared with density-functional theory methods. However, the energy differences and spin distributions differ. A detailed analysis suggests that non-local exchange-correlation functionals, in addition to other approximations such as LDA+U to account for correlations, are needed to simultaneously obtain better estimates for spin moments, distributions, energy differences and energy gaps.

Cohesive energy and structural parameters of binary oxides of groups IIA and IIIB from diffusion quantum Monte Carlo.

We have applied the diffusion quantum Monte Carlo (DMC) method to calculate the cohesive energy and the structural parameters of the binary oxides CaO, SrO, BaO, Sc2O3, Y2O3, and La2O3. The aim of our calculations is to systematically quantify the accuracy of the DMC method to study this type of metal oxides. The DMC results were compared with local, semi-local, and hybrid Density Functional Theory (DFT) approximations as well as with experimental measurements. The DMC method yields cohesive energies for these oxides with a mean absolute deviation from experimental measurements of 0.18(2) eV, while with local, semi-local, and hybrid DFT approximations, the deviation is 3.06, 0.94, and 1.23 eV, respectively. For lattice constants, the mean absolute deviations in DMC, local, semi-local, and hybrid DFT approximations are 0.017(1), 0.07, 0.05, and 0.04 Å, respectively. DMC is a highly accurate method, outperforming the DFT approximations in describing the cohesive energies and structural parameters of these binary oxides.

Structural stability and defect energetics of ZnO from diffusion quantum Monte Carlo.

We have applied the many-body ab initio diffusion quantum Monte Carlo (DMC) method to study Zn and ZnO crystals under pressure and the energetics of the oxygen vacancy, zinc interstitial, and hydrogen impurities in ZnO. We show that DMC is an accurate and practical method that can be used to characterize multiple properties of materials that are challenging for density functional theory (DFT) approximations. DMC agrees with experimental measurements to within 0.3 eV, including the band-gap of ZnO, the ionization potential of O and Zn, and the atomization energy of O2, ZnO dimer, and wurtzite ZnO. DMC predicts the oxygen vacancy as a deep donor with a formation energy of 5.0(2) eV under O-rich conditions and thermodynamic transition levels located between 1.8 and 2.5 eV from the valence band maximum. Our DMC results indicate that the concentration of zinc interstitial and hydrogen impurities in ZnO should be low under n-type and Zn- and H-rich conditions because these defects have formation energies above 1.4 eV under these conditions. Comparison of DMC and hybrid functionals shows that these DFT approximations can be parameterized to yield a general correct qualitative description of ZnO. However, the formation energy of defects in ZnO evaluated with DMC and hybrid functionals can differ by more than 0.5 eV.

Role of surface structure on Li-ion energy storage capacity of two-dimensional transition-metal carbides.

A combination of density functional theory (DFT) calculations and experiments is used to shed light on the relation between surface structure and Li-ion storage capacities of the following functionalized two-dimensional (2D) transition-metal carbides or MXenes: Sc2C, Ti2C, Ti3C2, V2C, Cr2C, and Nb2C. The Li-ion storage capacities are found to strongly depend on the nature of the surface functional groups, with O groups exhibiting the highest theoretical Li-ion storage capacities. MXene surfaces can be initially covered with OH groups, removable by high-temperature treatment or by reactions in the first lithiation cycle. This was verified by annealing f-Nb2C and f-Ti3C2 at 673 and 773 K in vacuum for 40 h and in situ X-ray adsorption spectroscopy (XAS) and Li capacity measurements for the first lithiation/delithiation cycle of f-Ti3C2. The high-temperature removal of water and OH was confirmed using X-ray diffraction and inelastic neutron scattering. The voltage profile and X-ray adsorption near edge structure of f-Ti3C2 revealed surface reactions in the first lithiation cycle. Moreover, lithiated oxygen terminated MXenes surfaces are able to adsorb additional Li beyond a monolayer, providing a mechanism to substantially increase capacity, as observed mainly in delaminated MXenes and confirmed by DFT calculations and XAS. The calculated Li diffusion barriers are low, indicative of the measured high-rate performance. We predict the not yet synthesized Cr2C to possess high Li capacity due to the low activation energy of water formation at high temperature, while the not yet synthesized Sc2C is predicted to potentially display low Li capacity due to higher reaction barriers for OH removal.