Self-consistent Procedure Research Articles

Coupled Perturbed Approach to Dual Basis Sets for Molecules and Solids. II: Energy and Band Corrections for Periodic Systems.

When trying to reach convergence of quantum chemical calculations toward the complete basis set limit, crystalline solids generally prove to be more challenging than molecules. This is due both to the closer packing of atoms─hence, to linear dependencies─and to the problematic behavior of Ewald techniques used for dealing with the infinite character of Coulomb sums. Thus, a dual basis set approach is even more desirable for periodic systems than for molecules. In such an approach, the self-consistent procedure is implemented in a small basis set, and the effect of the enlargement of the basis set is estimated a posteriori. In this paper, we extend to crystalline solids our previous coupled perturbed dual basis set approach [J. Chem. Theory Comput. 2020, 16, 1, 340-353] in which the basis set enlargement is treated as a perturbation. Among the notable features of this approach are (i) the possibility of obtaining not only a correction to the energy but also to energy bands and electron density; (ii) the absence of a diagonalization step for the full Fock matrix in the large basis set; and (iii) the possibility of extrapolating low order perturbation energy corrections to infinite order. We also present here the first periodic implementation of the dual basis set method of Liang and Head-Gordon [J. Phys. Chem. A 2004, 108, 3206-3210]. The effectiveness of both approaches is, then, compared on a small, but representative, set of solids.

Deformation behavior of aluminum alloy rivets for aerospace applications

For many decades, solid rivets made of high-strength aluminum alloys have been used for mechanical joining of aircraft structures. For numerical modeling of riveting processes the detailed description of the deformation behavior of the rivets is of utmost importance; however, only very little reliable material data are available. Therefore, this study reviews and investigates the deformation behavior of commercial MS20426AD3-5 countersunk rivets made of aluminum alloy AA-2117-T4 as typically used in aerospace applications. The self-consistent procedure for determining the material-specific flow curve includes (i) the exact preparation of cylindrical samples, (ii) compression testing of the samples at testing speeds of 0.05 mm/s, 0.5 mm/s and 5 mm/s, and (iii) inverse numerical modeling of the testing procedure. In general, the compliance of the testing setup must be considered for obtaining reliable flow curves, especially when testing small samples. The determined flow curve of aluminum alloy AA-2117-T4 showed higher yield stress and more distinct initial strain hardening than most of the flow curves published in literature. Although the flow curve did not show any significant strain rate dependency, notable softening due to deformation-induced adiabatic heating of the compressed sample was observed at the highest testing speed. However, the fracture strain seems to be strain rate-dependent, because samples deformed at the low testing speed did not show any signs of macroscopic fracture, whereas local fracture occurred in samples deformed at the medium and high testing speeds.

Beyond monopole electrostatics in regulating conformations of intrinsically disordered proteins.

Conformations and dynamics of an intrinsically disordered protein (IDP) depend on its composition of charged and uncharged amino acids, and their specific placement in the protein sequence. In general, the charge (positive or negative) on an amino acid residue in the protein is not a fixed quantity. Each of the ionizable groups can exist in an equilibrated distribution of fully ionized state (monopole) and an ion-pair (dipole) state formed between the ionizing group and its counterion from the background electrolyte solution. The dipole formation (counterion condensation) depends on the protein conformation, which in turn depends on the distribution of charges and dipoles on the molecule. Consequently, effective charges of ionizable groups in the IDP backbone may differ from their chemical charges in isolation-a phenomenon termed charge-regulation. Accounting for the inevitable dipolar interactions, that have so far been ignored, and using a self-consistent procedure, we present a theory of charge-regulation as a function of sequence, temperature, and ionic strength. The theory quantitatively agrees with both charge reduction and salt-dependent conformation data of Prothymosin-alpha and makes several testable predictions. We predict charged groups are less ionized in sequences where opposite charges are well mixed compared to sequences where they are strongly segregated. Emergence of dipolar interactions from charge-regulation allows spontaneous coexistence of two phases having different conformations and charge states, sensitively depending on the charge patterning. These findings highlight sequence dependent charge-regulation and its potential exploitation by biological regulators such as phosphorylation and mutations in controlling protein conformation and function.

Depletion potential, correlation functions and demixing transition in model colloid-polymer mixtures

We describe a theoretical framework to calculate depletion potential between colloid particles induced by non-adsorbing ideal polymer chains (s-species) and correlation functions in a coarse-grained one-component system of colloids (c-species). A Padé approximant is used to express the depletion potential as a pair potential with many-body contributions subsumed in it. The depletion potential and correlation functions of c-species are calculated using a self-consistent procedure. Results for several values of size ratio q=σsσc (σs and σc are, respectively diameters of the polymer chain and a colloid particle) and packing fractions of s- and c-species are reported. The spinodal curve and critical point of demixing transition are determined for several values of q. Calculated values are compared with values found from other theories and simulations.

Amber free energy tools: Interoperable software for free energy simulations using generalized quantum mechanical/molecular mechanical and machine learning potentials

We report the development and testing of new integrated cyberinfrastructure for performing free energy simulations with generalized hybrid quantum mechanical/molecular mechanical (QM/MM) and machine learning potentials (MLPs) in Amber. The Sander molecular dynamics program has been extended to leverage fast, density-functional tight-binding models implemented in the DFTB+ and xTB packages, and an interface to the DeePMD-kit software enables the use of MLPs. The software is integrated through application program interfaces that circumvent the need to perform “system calls” and enable the incorporation of long-range Ewald electrostatics into the external software’s self-consistent field procedure. The infrastructure provides access to QM/MM models that may serve as the foundation for QM/MM–ΔMLP potentials, which supplement the semiempirical QM/MM model with a MLP correction trained to reproduce ab initio QM/MM energies and forces. Efficient optimization of minimum free energy pathways is enabled through a new surface-accelerated finite-temperature string method implemented in the FE-ToolKit package. Furthermore, we interfaced Sander with the i-PI software by implementing the socket communication protocol used in the i-PI client–server model. The new interface with i-PI allows for the treatment of nuclear quantum effects with semiempirical QM/MM–ΔMLP models. The modular interoperable software is demonstrated on proton transfer reactions in guanine-thymine mispairs in a B-form deoxyribonucleic acid helix. The current work represents a considerable advance in the development of modular software for performing free energy simulations of chemical reactions that are important in a wide range of applications.

Computing the committor with the committor to study the transition state ensemble.

The study of the kinetic bottlenecks that hinder the rare transitions between long-lived metastable states is a major challenge in atomistic simulations. Here we propose a method to explore the transition state ensemble, which is the distribution of configurations that the system passes through as it translocates from one metastable basin to another. We base our method on the committor function and the variational principle that it obeys. We find its minimum through a self-consistent procedure that starts from information limited to the initial and final states. Right from the start, our procedure allows the sampling of very many transition state configurations. With the help of the variational principle, we perform a detailed analysis of the transition state ensemble, ranking quantitatively the degrees of freedom mostly involved in the transition and enabling a systematic approach for the interpretation of simulation results and the construction of efficient physics-informed collective variables.

Spurious Oscillations Caused by Density Functional Approximations: Who is to Blame? Exchange or Correlation?

We analyze the varying susceptibilities of different density functional approximations (DFAs) to present spurious oscillations on the profiles of several vibrational properties. Among other problems, these spurious oscillations cause significant errors in harmonic and anharmonic IR and Raman frequencies and intensities. This work hinges on a judicious strategy to dissect the exchange and correlation components of DFAs and pinpoint the origins of these oscillations. We identify spurious oscillations in derivatives of all energy components with respect to nuclear displacements, including those energy terms that do not involve numerical integrations. These indirect spurious oscillations are attributed to suboptimal electron densities resulting from a self-consistent field procedure using a DFA that exhibits direct spurious oscillations. Direct oscillations stem from inaccurate numerical integration of the exchange and correlation energy density functionals. A thorough analysis of direct spurious oscillations reveals that only a handful of exchange and correlation components are insensitive to spurious oscillations, giving rise to three families of functionals, BH&H, LSDA, and BLYP. Among the functionals in these families, we encounter four widespread DFAs: BLYP, B3LYP, LC-BLYP, and CAM-B3LYP. Certain DFAs like PBE appear less sensitive to spurious oscillations due to compensatory cancellations between their energy components. Additionally, we found non-negligible but small oscillations in PBE and TPSS, which could be safely employed provided a sufficiently large integration grid is used in the calculations. These findings hint at the key components of current approximations to be improved and emphasize the necessity to develop accurate DFAs suitable for studying molecular spectroscopies.

Machine learning nuclear orbital-free density functional based on Thomas–Fermi approach

Orbital-free density functional theory (DFT) is much more efficient than the orbital-dependent Kohn–Sham DFT due to the avoidance of the auxiliary one-body orbitals. The machine learning approach has been applied to build nuclear orbital-free DFT recently [Wu et al., Phys. Rev. C 105 (2022) L031303] and achieved more precise descriptions for nuclei than existing orbital-free DFTs. Here, improved machine learning nuclear orbital-free density functional is built by including the Thomas–Fermi approach as a basement. Performances of the functional are compared in detail with the ones based on the pure machine learning approach. It is found that with the Thomas–Fermi functional included, the machine-learning-based functional can achieve better performance in directly predicting the kinetic energies and in providing the ground-state properties by the self-consistent procedures.

GradDFT. A software library for machine learning enhanced density functional theory.

Density functional theory (DFT) stands as a cornerstone method in computational quantum chemistry and materials science due to its remarkable versatility and scalability. Yet, it suffers from limitations in accuracy, particularly when dealing with strongly correlated systems. To address these shortcomings, recent work has begun to explore how machine learning can expand the capabilities of DFT: an endeavor with many open questions and technical challenges. In this work, we present GradDFT a fully differentiable JAX-based DFT library, enabling quick prototyping and experimentation with machine learning-enhanced exchange-correlation energy functionals. GradDFT employs a pioneering parametrization of exchange-correlation functionals constructed using a weighted sum of energy densities, where the weights are determined using neural networks. Moreover, GradDFT encompasses a comprehensive suite of auxiliary functions, notably featuring a just-in-time compilable and fully differentiable self-consistent iterative procedure. To support training and benchmarking efforts, we additionally compile a curated dataset of experimental dissociation energies of dimers, half of which contain transition metal atoms characterized by strong electronic correlations. The software library is tested against experimental results to study the generalization capabilities of a neural functional across potential energy surfaces and atomic species, as well as the effect of training data noise on the resulting model accuracy.

Liquid crystal resonator as a nonlinear reflector for passive Q-switching and mode locking

We carry out a theoretical study of a Fabry–Perot resonator with a central layer of nematic liquid crystal as a nonlinear polarization rotation (NPR) device for passive Q-switching and mode locking. We develop a self-consistent procedure for calculating the device dynamical response as a function of the input light intensity and polarization. We show how a positive feedback effect for the optical reorientation of the liquid crystal director makes the resonator abruptly switch to high-reflectivity state. We demonstrate that the time-delay between the pulse initiation and the resonator switch can be avoided by tilted liquid crystal molequles at the resonator boundaries. We show that such a NPR optical device is suitable for Q-switching operation with μs pulses and hundreds of kHz repetition rates. Further decrease of pulse duration and increase of the pulse repetition rate is possible by either increasing the pulse power or by increasing the Fabry–Perot resonator finesse. Finally, we show that the same Fabry–Perot resonator can be used for Q-switching and mode locking at tens of MHz repetition rates and ns pulse durations by using an electro-optic uniaxial–biaxial transition as an alternative to NPR in order to reduce pulse duration and increase repetition rate.

Electron Scattering from 1-Methyl-5-Nitroimidazole: Cross-Sections for Modeling Electron Transport through Potential Radiosensitizers.

In this study, we present a complete set of electron scattering cross-sections from 1-Methyl-5-Nitroimidazole (1M5NI) molecules for impact energies ranging from 0.1 to 1000 eV. This information is relevant to evaluate the potential role of 1M5NI as a molecular radiosensitizers. The total electron scattering cross-sections (TCS) that we previously measured with a magnetically confined electron transmission apparatus were considered as the reference values for the present analysis. Elastic scattering cross-sections were calculated by means of two different schemes: The Schwinger multichannel (SMC) method for the lower energies (below 15 eV) and the independent atom model-based screening-corrected additivity rule with interferences (IAM-SCARI) for higher energies (above 15 eV). The latter was also applied to calculate the total ionization cross-sections, which were complemented with experimental values of the induced cationic fragmentation by electron impact. Double differential ionization cross-sections were measured with a reaction microscope multi-particle coincidence spectrometer. Using a momentum imaging spectrometer, direct measurements of the anion fragment yields and kinetic energies by the dissociative electron attachment are also presented. Cross-sections for the other inelastic channels were derived with a self-consistent procedure by sampling their values at a given energy to ensure that the sum of the cross-sections of all the scattering processes available at that energy coincides with the corresponding TCS. This cross-section data set is ready to be used for modelling electron-induced radiation damage at the molecular level to biologically relevant media containing 1M5NI as a potential radiosensitizer. Nonetheless, a proper evaluation of its radiosensitizing effects would require further radiobiological experiments.

Quark-antiquark states of the lightest scalar mesons within the Nambu-Jona-Lasinio model with flavor-dependent coupling constants

The quark-antiquark components of the U(3) lightest scalar meson nonet are investigated by considering the Nambu-Jona-Lasinio model with flavor-dependent coupling constants that were derived by considering (non-perturbative) gluon exchange. The strange quark effective mass () is varied such that the strangeness content of these scalar mesons can be analyzed further. The neutral states S 0, S 8, and S 3 are adopted as the most relevant quark-antiquark components, respectively, of the σ(500), f 0(980) and mesons. As a result, the mass hierarchy between states S 0 and S 8, and mesons, can be, respectively, inverted and corrected for quite low values of the strange quark constituent mass. In addition, for some particular values of , the masses of σ(500) and f 0(980) can also be obtained by considering the mixing coupling constant G 08. However, the masses of all the nine mesons are not described simultaneously in a self-consistent procedure and this goes along with the need of non-quark-antiquark states to completely describe their masses. A neutral-meson mixing matrix is defined and the leading mixing angle is found by fitting a correct value of the σ(500) − f 0(980) mass difference. Two different estimates for the strengths of the mixings and are proposed, leading to somewhat different behaviors. First by assuming leading transitions to intermediary flavor eigenstates and second by considering a dynamical evolution. The results may be in good agreement with experimental values from BESS-III depending on the value of the strange quark effective mass.

Design of superconducting tokamak magnet systems and applications to HTS

In this paper we illustrate a self-consistent procedure to design the superconducting Toroidal Field (TF) and Central Solenoid (CS) magnet systems starting from the basic plasma dimensioning parameters. By defining the plasma major radius and minor radii, as well as the inboard TF coil neutron shielding radial built, we proceed by sizing the TF Winding Pack (WP), its case and the CS modules. The ITER magnets design philosophy and criteria are adopted throughout the study. A key outcome of this work is to illustrate the inter-play between machine size, magnetic field and availability of inductive flux for burn. In doing so we investigate the advantages brought by high field tokamak design compared the more conventional (ITER-like) Nb3Sn based magnet design solutions.

Josephson diode based on conventional superconductors and a chiral quantum dot

We propose theoretically a Josephson diode consisting of the conventional superconductors with the plain $s$-wave pairing and a chiral quantum dot. When an external magnetic field is exerted on the quantum dot, the critical current of the Josephson structure is different for the opposite directions of current flow. The strong nonreciprocity can be obtained in a large area of the parameter space. The inversion and the on/off state of the nonreciprocity can be conveniently regulated by adjusting the direction of the external field. The dependencies of the nonreciprocal behaviors on the hopping amplitude, the magnitude of the magnetic field, and the energy level of the quantum dot are investigated in details using the Keldysh nonequilibrium Green's function formalism under the self-consistent procedure. The symmetric and the antisymmetric properties of the nonreciprocity are analyzed from symmetries satisfied by the superconductors. The proposed diode effect also applies to other chiral conductors as interlayer. Its formation has no restriction on the type of the current-phase difference relations. The generality and flexibility of our proposed diode effect provides more possibilities for the design of the dissipationless diode devices.

Shadow energy functionals and potentials in Born-Oppenheimer molecular dynamics.

In Born-Oppenheimer molecular dynamics (BOMD) simulations based on the density functional theory (DFT), the potential energy and the interatomic forces are calculated from an electronic ground state density that is determined by an iterative self-consistent field optimization procedure, which, in practice, never is fully converged. The calculated energies and forces are, therefore, only approximate, which may lead to an unphysical energy drift and instabilities. Here, we discuss an alternative shadow BOMD approach that is based on backward error analysis. Instead of calculating approximate solutions for an underlying exact regular Born-Oppenheimer potential, we do the opposite. Instead, we calculate the exact electron density, energies, and forces, but for an underlying approximate shadow Born-Oppenheimer potential energy surface. In this way, the calculated forces are conservative with respect to the approximate shadow potential and generate accurate molecular trajectories with long-term energy stabilities. We show how such shadow Born-Oppenheimer potentials can be constructed at different levels of accuracy as a function of the integration time step, δt, from the constrained minimization of a sequence of systematically improvable, but approximate, shadow energy density functionals. For each energy functional, there is a corresponding ground state Born-Oppenheimer potential. These pairs of shadow energy functionals and potentials are higher-level generalizations of the original "zeroth-level" shadow energy functionals and potentials used in extended Lagrangian BOMD [Niklasson, Eur. Phys. J. B 94, 164 (2021)]. The proposed shadow energy functionals and potentials are useful only within this extended dynamical framework, where also the electronic degrees of freedom are propagated as dynamical field variables together with the atomic positions and velocities. The theory is quite general and can be applied to MD simulations using approximate DFT, Hartree-Fock, or semi-empirical methods, as well as to coarse-grained flexible charge models.

Self-Consistent Study of the Superconducting Gap in the Strontium-doped Lanthanum Cuprate

This work is aimed at numerically investigating the behavior of the Fermi energy in Strontium-doped Lanthanum Cuprate, using a numerical zero temperature elastic scattering cross-section procedure in the unitary collision regime. The main task is to vary the zero temperature superconducting energy gap from its zero value in the normal state, to the highest value of 60 meV. We find that there are two different reduced phase space regimes for the first harmonic line node's order parameter. The first one, represented by a Fermi energy with a value of - 0.4 meV, where the rest of the material parameters, and the degrees of freedom of the normal to the superconducting phase transition are not sensitive to the self-consistent variation of the zero temperature superconducting energy gap. A different case is found when in the self-consistent numerical procedure, the Fermi energy takes a value of - 0.04 meV, indicating that the fermion-dressed quasiparticles have material parameters strongly sensitive to the numerical changes in the zero temperature gap, resulting in a reduced phase space, where the input and output zero superconducting energy values, and the degrees of freedom are separated by the self-consistent numerical analysis. The first scenario considers that when the Fermi energy and the nearest hopping terms have the same order of magnitude, the physics can be described by a picture given by nonequilibrium statistical mechanics. A second scenario indicates, that when the Fermi energy parameter and the hopping term have different order of magnitude; the physical picture tends to be related to the nonrelativistic quantum mechanical degrees of freedom coming from quasi-stationary quantum energy levels, with a damping term seen in the probability density distribution function, that is described in the configuration space. Henceforth, it is concluded that the use of the zero temperature elastic scattering cross-section links the phase and configuration spaces through the inverse scattering lifetime, and helps to clarify the role of the degrees of freedom in Strontium-doped Lanthanum Cuprate. Finally, we think that the self-consistent numerical procedure with the reduced phase space, induces nonlocality in the inverse scattering lifetime.

Effect of Confinement and Coulomb Interactions on the Electronic Structure of the (111) LaAlO3/SrTiO3 Interface.

A tight binding supercell approach is used for the calculation of the electronic structure of the (111) LaAlO3/SrTiO3 interface. The confinement potential at the interface is evaluated solving a discrete Poisson equation by means of an iterative method. In addition to the effect of the confinement, local Hubbard electron-electron terms are included at the mean-field level within a fully self-consistent procedure. The calculation carefully describes how the two-dimensional electron gas arises from the quantum confinement of electrons near the interface due to the band bending potential. The resulting electronic sub-bands and Fermi surfaces show full agreement with the electronic structure determined by angle-resolved photoelectron spectroscopy experiments. In particular, we analyse how the effect of local Hubbard interactions change the density distribution over the layers from the interface to the bulk. Interestingly, the two-dimensional electron gas at the interface is not depleted by local Hubbard interactions which indeed induce an enhancement of the electron density between the first layers and the bulk.

Ab-initio calculations of temperature dependent electronic structures of inorganic halide perovskite materials.

Despite wide interest in halide perovskite materials, it is still challenging to accurately calculate their electronic structure and its temperature dependence. In this work, we present ab-initio calculations of the temperature dependence of the electronic structure of CsPbX3 materials (X = Cl, Br or I) in the cubic form and of the zero temperature electronic structure of the orthorhombic phase of these materials. Phonon-induced temperature dependent band energy renormalization was calculated within the framework of Allen-Heine-Cardona theory, where we exploited the self-consistent procedure to determine both the energy level shifts and their broadenings. The phonon spectrum of the materials was obtained using the self-consistent phonon method since standard density functional perturbation theory calculations in harmonic approximation yield phonon modes with imaginary frequencies due to the fact that the cubic structure is not stable at zero temperature. Our results suggest that low energy phonon modes mostly contribute to phonon-induced band energy renormalization. The calculated values of the band gaps at lowest temperature where the material exhibits a cubic structure are in good agreement with experimental results from the literature. The same is the case for the slope of the temperature dependence of the band gap for the CsPbI3 material where reliable experimental data are available in the literature. We also found that phonon-induced temperature dependence of the band gap is most pronounced for the conduction band minimum and valence band maximum, while other bands exhibit a weaker dependence.

Analysis of planar waveguides with a thin overlayer and nonlinear cladding

The aim of this paper is to analyse a planar optical waveguide with Kerr-type nonlinear cladding and a thin linear overlayer separating the cladding and the guiding core. The results of numerical calculations show that the bistable behaviour of the nonlinear waveguides can be easily controlled by changing the parameters of this additional layer. The analysis is based on the self-consistent iteration procedure which provides relevant dispersion characteristics limited to physically stable solutions.

Cluster Amplitudes and Their Interplay with Self-Consistency in Density Functional Methods.

Density functional theory (DFT) provides convenient electronic structure methods for the study of molecular systems and materials. Regular Kohn-Sham DFT calculations rely on unitary transformations to determine the ground-state electronic density, ground state energy, and related properties. However, for dissociation of molecular systems into open-shell fragments, due to the self-interaction error present in a large number of density functional approximations, the self-consistent procedure based on the this type of transformation gives rise to the well-known charge delocalization problem. To avoid this issue, we showed previously that the cluster operator of coupled-cluster theory can be utilized within the context of DFT to solve in an alternative and approximate fashion the ground-state self-consistent problem. This work further examines the application of the singles cluster operator to molecular ground state calculations. Two approximations are derived and explored: i) A linearized scheme of the quadratic equation used to determine the cluster amplitudes. ii) The effect of carrying the calculations in a non-self-consistent field fashion. These approaches are found to be capable of improving the energy and density of the system and are quite stable in either case. The theoretical framework discussed in this work could be used to describe, with an added flexibility, quantum systems that display challenging features and require expanded theoretical methods.