Multipole Expansion of Atomic Electron Density Fluctuation Interactions in the Density-Functional Tight-Binding Method.

The accuracy of the density-functional tight-binding (DFTB) method in describing noncovalent interactions is limited due to its reliance on monopole-based spherical charge densities. In this study, we present a multipole-extended second-order DFTB (mDFTB2) method that takes into account atomic dipole and quadrupole interactions. Furthermore, we combine the multipole expansion with the monopole-based third-order contribution, resulting in the mDFTB3 method. To assess the accuracy of mDFTB2 and mDFTB3, we evaluate their performance in describing noncovalent interactions, proton transfer barriers, and dipole moments. Our benchmark results show promising improvements even when using the existing electronic parameters optimized for the original DFTB3 model. Both mDFTB2 and mDFTB3 outperform their monopole-based counterparts, DFTB2 and DFTB3, in terms of accuracy. While mDFTB2 and mDFTB3 perform comparably for neutral and positively charged systems, mDFTB3 exhibits superior performance over mDFTB2 when dealing with negatively charged systems and proton transfers. Overall, the incorporation of the multipole expansion significantly enhances the accuracy of the DFTB method in describing noncovalent interactions and proton transfers.

A Perspective on Sustainable Computational Chemistry Software Development and Integration.

The power of quantum chemistry to predict the ground and excited state properties of complex chemical systems has driven the development of computational quantum chemistry software, integrating advances in theory, applied mathematics, and computer science. The emergence of new computational paradigms associated with exascale technologies also poses significant challenges that require a flexible forward strategy to take full advantage of existing and forthcoming computational resources. In this context, the sustainability and interoperability of computational chemistry software development are among the most pressing issues. In this perspective, we discuss software infrastructure needs and investments with an eye to fully utilize exascale resources and provide unique computational tools for next-generation science problems and scientific discoveries.

Shadow Molecular Dynamics and Atomic Cluster Expansions for Flexible Charge Models.

A shadow molecular dynamics scheme for flexible charge models is presented where the shadow Born-Oppenheimer potential is derived from a coarse-grained approximation of range-separated density functional theory. The interatomic potential, including the atomic electronegativities and the charge-independent short-range part of the potential and force terms, is modeled by the linear atomic cluster expansion (ACE), which provides a computationally efficient alternative to many machine learning methods. The shadow molecular dynamics scheme is based on extended Lagrangian (XL) Born-Oppenheimer molecular dynamics (BOMD) [Eur. Phys. J. B 2021, 94, 164]. XL-BOMD provides stable dynamics while avoiding the costly computational overhead associated with solving an all-to-all system of equations, which normally is required to determine the relaxed electronic ground state prior to each force evaluation. To demonstrate the proposed shadow molecular dynamics scheme for flexible charge models using atomic cluster expansion, we emulate the dynamics generated from self-consistent charge density functional tight-binding (SCC-DFTB) theory using a second-order charge equilibration (QEq) model. The charge-independent potentials and electronegativities of the QEq model are trained for a supercell of uranium oxide (UO2) and a molecular system of liquid water. The combined ACE+XL-QEq molecular dynamics simulations are stable over a wide range of temperatures both for the oxide and for the molecular systems and provide a precise sampling of the Born-Oppenheimer potential energy surfaces. Accurate ground Coulomb energies are produced by the ACE-based electronegativity model during an NVE simulation of UO2, predicted to be within 1 meV of those from SCC-DFTB on average during comparable simulations.

Semi-Empirical Shadow Molecular Dynamics: A PyTorch Implementation.

Extended Lagrangian Born-Oppenheimer molecular dynamics (XL-BOMD) in its most recent shadow potential energy version has been implemented in the semiempirical PyTorch-based software PySeQM. The implementation includes finite electronic temperatures, canonical density matrix perturbation theory, and an adaptive Krylov subspace approximation for the integration of the electronic equations of motion within the XL-BOMB approach (KSA-XL-BOMD). The PyTorch implementation leverages the use of GPU and machine learning hardware accelerators for the simulations. The new XL-BOMD formulation allows studying more challenging chemical systems with charge instabilities and low electronic energy gaps. The current public release of PySeQM continues our development of modular architecture for large-scale simulations employing semi-empirical quantum-mechanical treatment. Applied to molecular dynamics, simulation of 840 carbon atoms, one integration time step executes in 4 s on a single Nvidia RTX A6000 GPU.

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.

Graph-based quantum response theory and shadow Born-Oppenheimer molecular dynamics.

Graph-based linear scaling electronic structure theory for quantum-mechanical molecular dynamics simulations [A. M. N. Niklasson et al., J. Chem. Phys. 144, 234101 (2016)] is adapted to the most recent shadow potential formulations of extended Lagrangian Born-Oppenheimer molecular dynamics, including fractional molecular-orbital occupation numbers [A. M. N. Niklasson, J. Chem. Phys. 152, 104103 (2020) and A. M. N. Niklasson, Eur. Phys. J. B 94, 164 (2021)], which enables stable simulations of sensitive complex chemical systems with unsteady charge solutions. The proposed formulation includes a preconditioned Krylov subspace approximation for the integration of the extended electronic degrees of freedom, which requires quantum response calculations for electronic states with fractional occupation numbers. For the response calculations, we introduce a graph-based canonical quantum perturbation theory that can be performed with the same natural parallelism and linear scaling complexity as the graph-based electronic structure calculations for the unperturbed ground state. The proposed techniques are particularly well-suited for semi-empirical electronic structure theory, and the methods are demonstrated using self-consistent charge density-functional tight-binding theory both for the acceleration of self-consistent field calculations and for quantum-mechanical molecular dynamics simulations. Graph-based techniques combined with the semi-empirical theory enable stable simulations of large, complex chemical systems, including tens-of-thousands of atoms.

Quantum Perturbation Theory Using Tensor Cores and a Deep Neural Network.

Time-independent quantum response calculations are performed using Tensor cores. This is achieved by mapping density matrix perturbation theory onto the computational structure of a deep neural network. The main computational cost of each deep layer is dominated by tensor contractions, i.e., dense matrix-matrix multiplications, in mixed-precision arithmetics, which achieves close to peak performance. Quantum response calculations are demonstrated and analyzed using self-consistent charge density-functional tight-binding theory as well as coupled-perturbed Hartree-Fock theory. For linear response calculations, a novel parameter-free convergence criterion is presented that is well-suited for numerically noisy low-precision floating point operations and we demonstrate a peak performance of almost 200 Tflops using the Tensor cores of two Nvidia A100 GPUs.

Quantum-Based Molecular Dynamics Simulations Using Tensor Cores.

Tensor cores, along with tensor processing units, represent a new form of hardware acceleration specifically designed for deep neural network calculations in artificial intelligence applications. Tensor cores provide extraordinary computational speed and energy efficiency but with the caveat that they were designed for tensor contractions (matrix-matrix multiplications) using only low-precision floating-point operations. Despite this perceived limitation, we demonstrate how tensor cores can be applied with high efficiency to the challenging and numerically sensitive problem of quantum-based Born-Oppenheimer molecular dynamics, which requires highly accurate electronic structure optimizations and conservative force evaluations. The interatomic forces are calculated on-the-fly from an electronic structure that is obtained from a generalized deep neural network, where the computational structure naturally takes advantage of the exceptional processing power of the tensor cores and allows for high performance in excess of 100 Tflops on a single Nvidia A100 GPU. Stable molecular dynamics trajectories are generated using the framework of extended Lagrangian Born-Oppenheimer molecular dynamics, which combines computational efficiency with long-term stability, even when using approximate charge relaxations and force evaluations that are limited in accuracy by the numerically noisy conditions caused by the low-precision tensor core floating-point operations. A canonical ensemble simulation scheme is also presented, where the additional numerical noise in the calculated forces is absorbed into a Langevin-like dynamics.

The Middle Science: Traversing Scale In Complex Many-Body Systems.

A roadmap is developed that integrates simulation methodology and data science methods to target new theories that traverse the multiple length- and time-scale features of many-body phenomena.

Forces Required for Isolated Malleus Shaft Fractures.

BACKGROUND AND HYPOTHESIS: Isolated malleus shaft fractures are rare cases. A commonly reported cause is a finger pulled out from a wet outer ear canal after a shower or bath. The objective was to investigate experimentally the mechanism and forces needed to establish an isolated malleus shaft fracture. METHODS: Ten fresh-frozen human temporal bones were adapted to allow visual inspection of the structures involved while negative pressure trauma was applied. Thirty malleus bones were broken and the required forces were measured. Measurements from 60 adult test subjects were used to create mathematical and physical models to calculate and measure the forces necessary for generating trauma. To calculate the maximum muscle force developed by the tensor tympani muscle, the muscle area and fiber type composition were determined. RESULTS: The temporal bone experiments showed that applied negative pressure in a wet ear canal could not fracture the malleus shaft with only passive counterforce from supporting structures, although the forces exceeded what was required for a malleus shaft fracture. When adding calculated counteracting forces from the tensor tympani muscles, which consisted of 87% type II fibers, we estimate that a sufficient force is generated to cause a malleus fracture. CONCLUSION: The combination of a negative pressure created by a finger pulling outward in a wet ear canal and a simultaneous counteracting reflexive force by the tensor tympani muscle were found to be sufficient to cause an isolated malleus fracture with an intact tympanic membrane.

Mixed Precision Fermi-Operator Expansion on Tensor Cores from a Machine Learning Perspective.

We present a second-order recursive Fermi-operator expansion scheme using mixed precision floating point operations to perform electronic structure calculations using tensor core units. A performance of over 100 teraFLOPs is achieved for half-precision floating point operations on Nvidia's A100 tensor core units. The second-order recursive Fermi-operator scheme is formulated in terms of a generalized, differentiable deep neural network structure, which solves the quantum mechanical electronic structure problem. We demonstrate how this network can be accelerated by optimizing the weight and bias values to substantially reduce the number of layers required for convergence. We also show how this machine learning approach can be used to optimize the coefficients of the recursive Fermi-operator expansion to accurately represent the fractional occupation numbers of the electronic states at finite temperatures.

Extended Lagrangian Born-Oppenheimer molecular dynamics for orbital-free density-functional theory and polarizable charge equilibration models.

Extended Lagrangian Born-Oppenheimer molecular dynamics (XL-BOMD) [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] is formulated for orbital-free Hohenberg-Kohn density-functional theory and for charge equilibration and polarizable force-field models that can be derived from the same orbital-free framework. The purpose is to introduce the most recent features of orbital-based XL-BOMD to molecular dynamics simulations based on charge equilibration and polarizable force-field models. These features include a metric tensor generalization of the extended harmonic potential, preconditioners, and the ability to use only a single Coulomb summation to determine the fully equilibrated charges and the interatomic forces in each time step for the shadow Born-Oppenheimer potential energy surface. The orbital-free formulation has a charge-dependent, short-range energy term that is separate from long-range Coulomb interactions. This enables local parameterizations of the short-range energy term, while the long-range electrostatic interactions can be treated separately. The theory is illustrated for molecular dynamics simulations of an atomistic system described by a charge equilibration model with periodic boundary conditions. The system of linear equations that determines the equilibrated charges and the forces is diagonal, and only a single Ewald summation is needed in each time step. The simulations exhibit the same features in accuracy, convergence, and stability as are expected from orbital-based XL-BOMD.

Graphics Processing Unit-Accelerated Semiempirical Born Oppenheimer Molecular Dynamics Using PyTorch.

A new open-source high-performance implementation of Born Oppenheimer molecular dynamics based on semiempirical quantum mechanics models using PyTorch called PYSEQM is presented. PYSEQM was designed to provide researchers in computational chemistry with an open-source, efficient, scalable, and stable quantum-based molecular dynamics engine. In particular, PYSEQM enables computation on modern graphics processing unit hardware and, through the use of automatic differentiation, supplies interfaces for model parameterization with machine learning techniques to perform multiobjective training and prediction. The implemented semiempirical quantum mechanical methods (MNDO, AM1, and PM3) are described. Additional algorithms include a recursive Fermi-operator expansion scheme (SP2) and extended Lagrangian Born Oppenheimer molecular dynamics allowing for rapid simulations. Finally, benchmark testing on the nanostar dendrimer and a series of polyethylene molecules provides a baseline of code efficiency, time cost, and scaling and stability of energy conservation, verifying that PYSEQM provides fast and accurate computations.

Density-Matrix Based Extended Lagrangian Born-Oppenheimer Molecular Dynamics.

Extended Lagrangian Born-Oppenheimer molecular dynamics [ Phys. Rev. Lett. 2008, 100, 123004] is presented for Hartree-Fock theory, where the extended electronic degrees of freedom are represented by a density matrix, including fractional occupation numbers at elevated electronic temperatures. In contrast to regular direct Born-Oppenheimer molecular dynamics simulations, no iterative self-consistent field optimization is required prior to the force evaluations. To sample regions of the potential energy landscape where the gap is small or vanishing, which leads to particular convergence problems in regular direct Born-Oppenheimer molecular dynamics simulations, an adaptive integration scheme for the extended electronic degrees of freedom is presented. The integration scheme is based on a tunable, low-rank approximation of a fourth-order kernel, [Formula: see text], that determines the metric tensor, [Formula: see text], used in the extended harmonic oscillator of the Lagrangian that generates the dynamics of the electronic degrees of freedom. The formulation and algorithms provide a general guide to implement extended Lagrangian Born-Oppenheimer molecular dynamics for quantum chemistry, density functional theory, and semiempirical methods using a density matrix formalism.

A New, Promising Experimental Ossicular Prosthesis: A Human Temporal Bone Study With Laser Doppler Vibrometry.

OBJECTIVE: We compared the sound transmission using different types of total ossicular replacement prostheses (TORP); we then studied the performance of a new TORP that we designed inspired by the columella, the single ossicle found in birds. METHODS: Stapedial vibrations were measured on nine freshly frozen human temporal bones with laser Doppler vibrometry. We then compared the performances of eight common TORP positions or designs as well as the new silver prototype of bird-type prosthesis, designed also according to our digital holography patterns of the human tympanic membrane (TM). RESULTS: The TORPs placed in lateral contact with both the TM and the malleus handle outperformed, at most frequencies, those placed only in contact with the TM.The new bird-type prosthesis performed equally well or better than all other prostheses. CONCLUSION: If the malleus handle can be retained when placing a TORP, the best sound transmission can be achieved by placing the TORP in contact with both the distal part of the malleus handle and the TM. The good performance of our bird-type prosthesis suggests that there is still room for future improvement of prosthesis design to further optimize hearing outcomes after surgery.

Extended Lagrangian Born-Oppenheimer molecular dynamics using a Krylov subspace approximation.

It is shown how the electronic equations of motion in extended Lagrangian Born-Oppenheimer molecular dynamics simulations [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008); J. Chem. Phys. 147, 054103 (2017)] can be integrated using low-rank approximations of the inverse Jacobian kernel. This kernel determines the metric tensor in the harmonic oscillator extension of the Lagrangian that drives the evolution of the electronic degrees of freedom. The proposed kernel approximation is derived from a pseudoinverse of a low-rank estimate of the Jacobian, which is expressed in terms of a generalized set of directional derivatives with directions that are given from a Krylov subspace approximation. The approach allows a tunable and adaptive approximation that can take advantage of efficient preconditioning techniques. The proposed kernel approximation for the integration of the electronic equations of motion makes it possible to apply extended Lagrangian first-principles molecular dynamics simulations to a broader range of problems, including reactive chemical systems with numerically sensitive and unsteady charge solutions. This can be achieved without requiring exact full calculations of the inverse Jacobian kernel in each time step or relying on iterative non-linear self-consistent field optimization of the electronic ground state prior to the force evaluations as in regular direct Born-Oppenheimer molecular dynamics. The low-rank approximation of the Jacobian is directly related to Broyden's class of quasi-Newton algorithms and Jacobian-free Newton-Krylov methods and provides a complementary formulation for the solution of nonlinear systems of equations.

Linear Scaling Pseudo Fermi-Operator Expansion for Fractional Occupation.

Recursive Fermi-operator expansion methods for the calculation of the idempotent density matrix are valid only at zero electronic temperature with integer occupation numbers. We show how such methods can be modified to include fractional occupation numbers of an approximate or pseudo Fermi-Dirac distribution and how the corresponding entropy term of the free energy is calculated. The proposed methodology is demonstrated and evaluated for different electronic structure methods, including density functional tight-binding theory, Kohn-Sham density functional theory using numerical orbitals, and quantum chemistry Hartree-Fock theory using Gaussian basis functions.

Higher-Order Extended Lagrangian Born-Oppenheimer Molecular Dynamics for Classical Polarizable Models.

Generalized extended Lagrangian Born-Oppenheimer molecular dynamics (XLBOMD) methods provide a framework for fast iteration-free simulations of models that normally require expensive electronic ground state optimizations prior to the force evaluations at every time step. XLBOMD uses dynamically driven auxiliary degrees of freedom that fluctuate about a variationally optimized ground state of an approximate "shadow" potential which approximates the true reference potential. While the requirements for such shadow potentials are well understood, constructing such potentials in practice has previously been ad hoc, and in this work, we present a systematic development of XLBOMD shadow potentials that match the reference potential to any order. We also introduce a framework for combining friction-like dissipation for the auxiliary degrees of freedom with general-order integration, a combination that was not previously possible. These developments are demonstrated with a simple fluctuating charge model and point induced dipole polarization models.

An Optimal Partial Ossicular Prosthesis Should Connect Both to the Tympanic Membrane and Malleus: A Temporal Bone Study Using Laser Doppler Vibrometry.

OBJECTIVE: To compare stapes vibrations in different partial ossicular replacement prosthesis (PORP) applications. METHODS: Stapedial vibrations were measured on fresh frozen human temporal bones with laser Doppler vibrometry. Eight different types of common ossiculoplasty methods were compared regarding recovery of stapes vibrations in relation with the normal ossicular chain. The PORPs were divided into three groups: 1) PORPs with the lateral contact only with the tympanic membrane, 2) PORPs with lateral contact only to the malleus handle, and 3) PORPs with lateral contact with both the malleus handle and the tympanic membrane. RESULTS: The PORPs with lateral contact only to the malleus handle performed better than the PORPs with lateral contact to the tympanic membrane only at 2 kHZ, but the best recovery was found in the group with contact both to the malleus handle and the tympanic membrane. CONCLUSION: The best sound transmission might be achieved by placing a PORP in contact with both the tympanic membrane and the handle of the malleus.

Next generation extended Lagrangian first principles molecular dynamics.

Extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] is formulated for general Hohenberg-Kohn density-functional theory and compared with the extended Lagrangian framework of first principles molecular dynamics by Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)]. It is shown how extended Lagrangian Born-Oppenheimer molecular dynamics overcomes several shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while improving or maintaining important features of Car-Parrinello simulations. The accuracy of the electronic degrees of freedom in extended Lagrangian Born-Oppenheimer molecular dynamics, with respect to the exact Born-Oppenheimer solution, is of second-order in the size of the integration time step and of fourth order in the potential energy surface. Improved stability over recent formulations of extended Lagrangian Born-Oppenheimer molecular dynamics is achieved by generalizing the theory to finite temperature ensembles, using fractional occupation numbers in the calculation of the inner-product kernel of the extended harmonic oscillator that appears as a preconditioner in the electronic equations of motion. Material systems that normally exhibit slow self-consistent field convergence can be simulated using integration time steps of the same order as in direct Born-Oppenheimer molecular dynamics, but without the requirement of an iterative, non-linear electronic ground-state optimization prior to the force evaluations and without a systematic drift in the total energy. In combination with proposed low-rank and on the fly updates of the kernel, this formulation provides an efficient and general framework for quantum-based Born-Oppenheimer molecular dynamics simulations.