Minimal Basis Research Articles

Can one hear the shape of a crystal?

Isospectrality is a general fundamental concept often involving whether various operators can have identical spectra, i.e., the same set of eigenvalues. In the context of the Laplacian operator, the famous question “Can one hear the shape of a drum?” concerns whether different shaped drums can have the same vibrational modes. The isospectrality of a lattice in d-dimensional Euclidean space Rd is a tantamount to whether it is uniquely determined by its theta series, i.e., the radial distribution function g2(r). While much is known about the isospectrality of Bravais lattices across dimensions, little is known about this question of more general crystal (periodic) structures with an n-particle basis (n≥2). Here, we ask what is nmin(d), the minimum value of n for inequivalent (i.e., unrelated by isometric symmetries) crystals with the same theta function in space dimension d? To answer these questions, we use rigorous methods as well as a precise numerical algorithm that enables us to determine the minimum multiparticle basis of inequivalent isospectral crystals. Our algorithm identifies isospectral four-, three- and two-particle bases in one, two, and three spatial dimensions, respectively. For many of these isospectral crystals, we rigorously show that they indeed possess identically the same g2(r)'s for all values of r. Based on our analyses, we conjecture that nmin(d)=4, 3, 2 for d=1, 2, 3, respectively. The identification of isospectral crystals enables one to study the degeneracy of the ground-state under the action of isotropic pair potentials. Indeed, using inverse statistical-mechanical techniques, we find an isotropic pair potential whose low-temperature configurations in two dimensions obtained via simulated annealing can lead to both of two isospectral crystal structures with n=3, the proportion of which can be controlled by the cooling rate. Our findings provide general insights into the structural and ground-state degeneracies of crystal structures as determined by radial pair information. Published by the American Physical Society 2024

Variational Hirshfeld Partitioning: General Framework and the Additive Variational Hirshfeld Partitioning Method.

We introduce the general mathematical framework of variational Hirshfeld partitioning, wherein the best possible approximation to a molecule's electron density is obtained by minimizing the f-divergence between the molecular density and a non-negative linear combination of (normalized) basis functions. This framework subsumes several existing methods that variationally optimize their pro-atoms, like (Gaussian) iterative stockholder analysis (ISA and GISA) and minimal basis iterative stockholder partitioning (MBIS), and provides a solid foundation for developing mathematically rigorous partitioning schemes. In this paper, we delve into the mathematical underpinnings of Hirshfeld-inspired partitioning schemes and show that among all the valid f-divergence measures only the extended Kullback-Leibler is a suitable choice. This led us to develop a novel partitioning scheme, called additive variational Hirshfeld (AVH), which constructs the pro-molecular density as a convex linear combination of the densities from selected states of isolated atoms and atomic ions. The AVH method is size-consistent with a unique solution and provides a straightforward approach for adding constraints for fragment properties. It also results in an intuitively appealing valence-bond-like decomposition of the molecular density as a weighted average of the densities of the atomic states in the molecule; that is, the AVH atomic density is a minimal deformation of the corresponding isolated atomic reference state's density. Compared to other variational Hirshfeld variants, our numerical results show that AVH yields chemically interpretable and sensible atomic charges that are not excessively large and demonstrate computational robustness.

A Study of Bases, Continuity and Homeomorphism in Hausdorff Topology

This paper surveys the essential concepts of bases, continuity, and homeomorphism within the context of Hausdorff topology. We examine the characterization of Hausdorff spaces through various types of bases, including minimal generative bases, which serve to illuminate the intrinsic properties of these spaces. The interplay between bases and morphisms is explored, emphasizing how morphisms facilitate continuity of mappings between Hausdorff spaces and their quotient images. We investigate the implications of these relationships for determining homeomorphisms, establishing conditions under which two Hausdorff spaces can be deemed equivalent. Key results include the construction of quotient images using equivalence relations, as well as criteria for continuity and homeomorphism that are uniquely suited to Hausdorff spaces. The findings on bases also demonstrate that a topological space X is Hausdorff if and only if there exists a minimal generative base BM for X such that for any Subfamily B′M of BM that is also a base for X, every element of BM can be expressed as a union of elements from B′M . This result provides an important tool for studying the properties of Hausdorff spaces and their relationships with other topological spaces.

Challenges in Maritime Cybersecurity Training and Compliance

The implementation of cybersecurity standards and directives in the maritime sector plays a crucial role in protecting critical maritime infrastructures from cyber threats. The level of protection depends heavily on humans. However, the effectiveness of cybersecurity training and compliance programmes, an essential component of these standards, is often hindered by challenges related to the sector’s environment, including the established technologies, practices, and norms. This paper aims to identify these challenges through a literature review and set the basis for more effective human risk minimization, responses, and training. We identify 17 challenges and validate them with an online survey (N = 205) capturing real-world perspectives from maritime-related stakeholders. Our findings contribute to enhancing the effectiveness of maritime cybersecurity training and compliance programmes, ultimately strengthening the maritime cybersecurity posture.

Some counterexamples in surface homology

We present four counterexamples in surface homology. The first example shows that even if the loops inducing a homology basis intersect each other at most once, they still may separate the surface into two parts. The other three examples show some difficulties in working with minimal homology bases. Introducing hyperbolic ribbon graphs we modify the examples so as to have a hyperbolic metric.

SUPOUT TOPOLOGY ON DIRECTED FUZZY GRAPHS

In this work, we introduce a topology, called supout topology and denoted $\mathcal{F}^{o}_{\mathcal{G}}$, for a fuzzy directed graph. We study some properties of this topology and give some examples of open and closed sets. We demonstrate that two isomorphic fuzzy directed graphs have homeomorphic supout topologies. In addition, we prove that this topology is an Alexandroff one and then use minimal basis to characterize homeomorphic fuzzy directed graphs. Finally, we investigate the connectedness of this topology vs. the connectivity of the graph.

Non-covalent interactions and charge transfer in the CO activation by low-valent group 14 complexes.

The CO activation by low-valent group 14 catalysts encompasses the rupture of varied covalent bonds in a single transition state through a concerted pathway. The bond between the central main group atom and the hydride in the complex is elongated to trigger the formation of the C-H bond with CO accompanied by the concomitant formation of the E-O bond between the complex and CO to lead the corresponding formate product. Prior studies have established that besides the apolar nature of CO , its initial interaction with the complex is primarily governed by electrostatic interactions. Notably, other stabilizing interactions and the transfer of charge between catalysts and CO during the initial phases of the reaction have been ignored. In this study, we have quantified the non-covalent interactions and charge transfer that facilitate the activation of CO by group 14 main group complex. Our findings indicate that electrostatic interactions predominantly stabilize the complex and CO in the reactant region. However, induction energy becomes the main stabilizing force as the reaction progresses towards the transition state, surpassing electrostatics. Induction contributes about 50% to the stabilization at the transition state, followed by electrostatics (40%) and dispersion interactions (10%). Atomic charges calculated with the minimal basis iterative stockholder (MBIS) method reveal larger charge transfer for the back-side reaction path in which CO approaches the catalysts in contrast to the front-side approach. Notably, it was discovered that a minor initial bending of CO to approximately initiates the charge transfer process for all systems. Furthermore, our investigation of group 14 elements demonstrates a systematic reduction in both activation energies and charge transfer to CO while descending in group 14. All studied reactions were characterized along the reaction coordinate obtained with the intrinsic reaction coordinate (IRC) methodology at the M06-2X/6-31g(d,p) level of theory. Gibbs free energy in toluene was computed using electronic energies at the DLPNO-CCSD(T)/cc-pVTZ-SSD(E) level of theory. Vibrational and translational entropy corrections were applied to provide a more accurate description of the obtained Gibbs free energies. To better characterize the changes in the reaction coordinate for all reactions, the reaction force analysis (RFA) has been employed. It enables the partition of the reaction coordinate into the reactant, transition state, and product regions where different stages of the mechanism occur. A detailed characterization of the main non-covalent driving forces in the initial stages of the activation of CO by low-valent group 14 complexes was performed using symmetry-adapted perturbation theory (SAPT). The SAPT0-CT/def2-SVP method was employed for these computations. Charge transfer descriptors based on atomic population using the MBIS scheme were also obtained to complement the SAPT analyses.

Snap-through and indirect reduced-order modelling

Snap-through is a nonlinear jump phenomenon that is increasingly being designed into engineering structures. The rich and varied dynamics of snap-through present a significant bottleneck in the design process as costly dynamic simulations are required to ensure predictable behaviour. The purpose of this research is to investigate the use of a recent projection-based, reduced-order modelling technique, namely, implicit condensation and expansion with inertial compensation, to reproduce the snap-through behaviours found in bistable finite element systems in analogous models with minimal degrees of freedom. In this work, the free response of a simple mass-spring oscillator is used to differentiate different types of snap-through. This provides a framework for discussing the dynamics of a family of buckled beams. The ability of the reduced-order models to faithfully reproduce these dynamics is investigated by testing the existence and stability of predicted periodic orbits. It is shown that the minimum projection basis required to capture snap-through accurately can be found through considering the minimum energy required for different types of snap-through. For bistable beams, this can be further simplified to just requiring an eigenvalue analysis at the most unstable equilibrium.

Density functional theory (DFT) study of water autoionization in solvated clusters.

We have implemented a cluster-continuum method using density functional theory to model water clusters and various charged species derived from water. The two aims of this study are to determine the minimal basis required for proper modeling of water autoionization and to determine the minimum number of explicit water molecules required to properly model the energetics of solvation. The thermodynamics of water autoionization converge following a modified power law to deliver chemically accurate values of the Gibbs energy change for autoionization with tractably small clusters. Convergence is slower and not exponential as assumed in previous work. We identify the n = 21 set of clusters as the first effectively bulk water like clusters that can capture the energetic influence of both the first and second solvation shells. In this cluster, a water molecule is encapsulated in the center of a closed shell of other water molecules that hydrogen bond to form five-membered rings. The total energy change for clusters with n ≥ 21 calculated using both the RPBE-D3 and ωB97X-D exchange-correlation functionals with the 6-311+G** basis set is shown to deliver good approximations to the free energy change at 298K. This is true even though neither functional models the individual enthalpy or entropy contributions particularly well.

Partial density of states representation for accurate deep neural network predictions of X-ray spectra.

The performance of a machine learning (ML) algorithm for chemistry is highly contingent upon the architect's choice of input representation. This work introduces the partial density of states (p-DOS) descriptor: a novel, quantum-inspired structural representation which encodes relevant electronic information for machine learning models seeking to simulate X-ray spectroscopy. p-DOS uses a minimal basis set in conjunction with a guess (non-optimised) electronic configuration to extract and then discretise the density of states (DOS) of the absorbing atom to form the input vector. We demonstrate that while the electronically-focused p-DOS performs well in isolation, optimal performance is achieved when supplemented with nuclear structural information imparted via a geometric representation. p-DOS provides a description of the key electronic properties of a system which is not only concise and computationally efficient, but also independent of molecular size or choice of basis set. It can be rapidly generated, facilitating its application with large training sets. Its performance is demonstrated using a wide variety of examples at the sulphur K-edge, including the prediction of ultrafast X-ray spectroscopic signal associated with photoexcited 2(5H)-thiophenone. These results highlight the potential for ML models developed using p-DOS to contribute to the interpretation and prediction of experimental results e.g. in operando measurements of batteries and/or catalysts and femtosecond time-resolved studies, especially those made possible by emergent cutting-edge technologies, especially X-ray free electron lasers.

Two Improved Algorithms to Compute the Minimal Bases of Univariate Matrices

Two Improved Algorithms to Compute the Minimal Bases of Univariate Matrices

Converging Time-Dependent Density Functional Theory Calculations in Five Iterations with Minimal Auxiliary Preconditioning.

Eigenvalue problems and linear systems of equations involving large symmetric matrices are commonly solved in quantum chemistry using Krylov space methods, such as the Davidson algorithm. The preconditioner is a key component of Krylov space methods that accelerates convergence by improving the quality of new guesses at each iteration. We systematically design a new preconditioner for time-dependent density functional theory (TDDFT) calculations based on the recently introduced TDDFT-ris semiempirical model by retuning the empirical scaling factor and the angular momenta of a minimal auxiliary basis. The final preconditioner produced includes up to d-functions in the auxiliary basis and is named "rid". The rid preconditioner converges excitation energies and polarizabilities in 5-6 iterations on average, a factor of 2-3 faster than the conventional diagonal preconditioner, without changing the converged results. Thus, the rid preconditioner is a broadly applicable and efficient preconditioner for TDDFT calculations.

Targeting spectroscopic accuracy for dispersion bound systems from abinitio techniques: Translational eigenstates of Ne@C70.

We investigate the endofullerene system Ne@C70 by constructing a three-dimensional Potential Energy Surface (PES) describing the translational motion of the Ne atom. This is constructed from electronic structure calculations from a plethora of methods, including MP2, SCS-MP2, SOS-MP2, RPA@PBE, and C(HF)-RPA, which were previously used for He@C60 in Panchagnula et al. [J. Chem. Phys. 160, 104303 (2024)], alongside B86bPBE-25X-XDM and B86bPBE-50X-XDM. The reduction in symmetry moving from C60 to C70 introduces a double well potential along the anisotropic direction, which forms a test of the sensitivity and effectiveness of the electronic structure methods. The nuclear Hamiltonian is diagonalized using a symmetrized double minimum basis set outlined in Panchagnula and Thom [J. Chem. Phys. 159, 164308 (2023)], with translational energies having error bars ±1 and ±2 cm-1. We find no consistency between electronic structure methods as they find a range of barrier heights and minima positions of the double well and different translational eigenspectra, which also differ from the Lennard-Jones (LJ) PES given in Mandziuk and Bačić [J. Chem. Phys. 101, 2126-2140 (1994)]. We find that generating effective LJ parameters for each electronic structure method cannot reproduce the full PES nor recreate the eigenstates, and this suggests that the LJ form of the PES, while simple, may not be best suited to describe these systems. Even though MP2 and RPA@PBE performed best for He@C60, due to the lack of concordance between all electronic structure methods, we require more experimental data in order to properly validate the choice.

Fast Algorithms for Minimum Homology Basis

Fast Algorithms for Minimum Homology Basis

An effective cosmological collider

Effective field theories (EFTs) of heavy particles coupled to the inflaton are rife with operator redundancies, frequently obscured by sensitivity to both boundary terms and field redefinitions. We initiate a systematic study of these redundancies by establishing a minimal operator basis for an archetypal example, the abelian gauge-Higgs-inflaton EFT. Working up to dimension 9, we show that certain low-dimensional operators are entirely redundant and identify new non-redundant operators with potentially interesting cosmological collider signals. Our methods generalize straightforwardly to other EFTs of heavy particles coupled to the inflaton.

On the cardinality of irredundant and minimal bases of finite permutation groups

Given a finite permutation group G with domain Ω\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\Omega $$\\end{document}, we associate two subsets of natural numbers to G, namely I(G,Ω)\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${\\mathcal {I}}(G,\\Omega )$$\\end{document} and M(G,Ω)\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${\\mathcal {M}}(G,\\Omega )$$\\end{document}, which are the sets of cardinalities of all the irredundant and minimal bases of G, respectively. We prove that I(G,Ω)\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${\\mathcal {I}}(G,\\Omega )$$\\end{document} is an interval of natural numbers, whereas M(G,Ω)\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${\\mathcal {M}}(G,\\Omega )$$\\end{document} may not necessarily form an interval. Moreover, for a given subset of natural numbers X⊆N\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$X \\subseteq {\\mathbb {N}}$$\\end{document}, we provide some conditions on X that ensure the existence of both intransitive and transitive groups G such that I(G,Ω)=X\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${\\mathcal {I}}(G,\\Omega ) = X$$\\end{document} and M(G,Ω)=X\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${\\mathcal {M}}(G,\\Omega ) = X$$\\end{document}.

Chemical simulations of quantum systems using quantum computers - review of algorithms and their experimental verification

Computer simulations using ever-increasing computing power and machine learning techniques allow advanced molecular modelling, molecular dynamics simulations and studies of intermolecular interactions. However, due to the complexity of biological systems and chemical processes at the molecular level, their accurate representation using classical computer models and techniques has faced a number of significant limitations for many years. A new and promising direction for the development of computational science and its potential applications in biochemistry is quantum computing and its integration with classical high-performance supercomputing systems. This article responds to the growing interest in the use of available quantum computers in exemplary applications. In this paper, we aim to provide an overview of the basic notions involved in the development of quantum algorithms and simulations related to issues at the interface of quantum chemistry and biochemistry. In addition, the article introduces the basic principles of performing simulations using the state-of-the-art quantum computers in the era of Noisy Intermediate-Scale Quantum (NISQ). Experimental results of the classical-quantum algorithm Variational Quantum Eigensolver (VQE) for example molecules H2 and CH+ are also presented. Despite the many shortcomings of currently available quantum computers, the analysed VQE algorithm proved to be effective in approximating the ground state of molecules using a minimal functional basis.

Four-derivative Yang-Mills couplings in heterotic theory through T-duality

This study delves into the dimensional reduction of the classical effective action of heterotic string theory on a circle, along with its T-duality symmetry, with the aim of identifying the bosonic couplings. To achieve this, we propose a truncation scheme for the generalized Buscher rules and the reduced action, specifically targeting the truncation of the nonlinear appearance of the scalar component of the Yang-Mills field in the base space. By imposing this truncated T-duality on the reduced action, we successfully determine the four- derivative bosonic couplings in the minimal basis, where field redefinition is imposed. Notably, these couplings, which are associated with the Lorentz Chern-Simons coupling HΩ, exhibit an exact correspondence with the NS-NS couplings found in the Metsaev-Tseytlin action.Furthermore, we investigate the bosonic couplings in the maximal basis, where field redefinition is not imposed. In this scenario, the truncated T-duality fixes the effective action up to 17 arbitrary parameters. By assigning specific values to these parameters, we establish a framework in which the NS-NS couplings align with those in the Meissner action. Remarkably, within this scheme, the Yang-Mills couplings precisely coincide with those obtained through the S-matrix method.

Obtaining Robust Density Functional Tight-Binding Parameters for Solids across the Periodic Table.

The density functional tight-binding (DFTB) approach allows electronic structure-based simulations at length and time scales far beyond what is possible with first-principles methods. This is achieved by using minimal basis sets and empirical approximations. Unfortunately, the sparse availability of parameters across the periodic table is a significant barrier to the use of DFTB in many cases. We therefore propose a workflow that allows the robust and consistent parametrization of DFTB across the periodic table. Importantly, our approach requires no element-pairwise parameters so that the parameters can be used for all element combinations and are readily extendable. This is achieved by parametrizing all elements on a consistent set of artificial homoelemental crystals, spanning a wide range of coordination environments. The transferability of the resulting periodic table baseline parameters to multielement systems and unknown structures is explored and the model is extensively benchmarked against previous specialized and general DFTB parametrizations.

Assessment of Embedding Schemes in a Hybrid Machine Learning/Classical Potentials (ML/MM) Approach.

Machine learning (ML) methods have reached high accuracy levels for the prediction of in vacuo molecular properties. However, the simulation of large systems solely through ML methods (such as those based on neural network potentials) is still a challenge. In this context, one of the most promising frameworks for integrating ML schemes in the simulation of complex molecular systems are the so-called ML/MM methods. These multiscale approaches combine ML methods with classical force fields (MM), in the same spirit as the successful hybrid quantum mechanics-molecular mechanics methods (QM/MM). The key issue for such ML/MM methods is an adequate description of the coupling between the region of the system described by ML and the region described at the MM level. In the context of QM/MM schemes, the main ingredient of the interaction is electrostatic, and the state of the art is the so-called electrostatic-embedding. In this study, we analyze the quality of simpler mechanical embedding-based approaches, specifically focusing on their application within a ML/MM framework utilizing atomic partial charges derived in vacuo. Taking as reference electrostatic embedding calculations performed at a QM(DFT)/MM level, we explore different atomic charges schemes, as well as a polarization correction computed using atomic polarizabilites. Our benchmark data set comprises a set of about 80k small organic structures from the ANI-1x and ANI-2x databases, solvated in water. The results suggest that the minimal basis iterative stockholder (MBIS) atomic charges yield the best agreement with the reference coupling energy. Remarkable enhancements are achieved by including a simple polarization correction.