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Susan R. Atlas

Publications and source records attributed to Susan R. Atlas.

10 recordsLinked to original sources

Latent space design of interatomic potentials

The advent of neural-network-based deep learning techniques has led to the emergence of increasingly sophisticated numerical interatomic potentials, including graph neural networks and large language-motivated foundation models. Parameterized to reproduce large, precomputed quantum mechanical training datasets for molecules and materials, models can be fine-tuned for greater accuracy on specific problems. Despite notable successes, machine learning (ML) models of potentials still face intrinsic challenges due to the combinatoric complexity of the underlying quantum chemical interactions, the existence of as-yet-undiscovered but potentially relevant bonding motifs absent from training datasets, and the need for post-prediction interpretability analysis. Drawing inspiration from autoencoder methods, we propose a constructive approach to interatomic potential design. In standard autoencoder architectures, a ML model self-organizes numerical training data in an unsupervised manner to discover underlying patterns and construct a compressed representation or latent space embedding model of the data, which is then used for prediction and inference. In the present work, we describe how latent space patterns and associated quantum embeddings can be constructed using first-principles methods based on theorems of density functional theory (DFT) and known, analytic constraints. This enables a parsimonious, physics-based representation of energies and densities, formally coupling the electronic and atomic length scales through the electron density, and linking ground, excited, and charge-transfer states of the interacting atoms. We describe the complete set of latent space components providing the foundation for a recently-proposed ensemble charge-transfer potential, and discuss opportunities for synergy in the design and explainability of contemporary machine-learned interatomic potentials.

physics.chem-ph

Information encoding in spherical DFT

Spherical density functional theory (DFT) is a reformulation of the classic theorems of DFT, in which the role of the total density of a many-electron system is replaced by a set of sphericalized densities, constructed by spherically-averaging the total electron density about each atomic nucleus. In Hohenberg-Kohn DFT and its constrained-search generalization, the electron density suffices to reconstruct the spatial locations and atomic numbers of the constituent atoms, and thus the external potential. However, the original proofs of spherical DFT require knowledge of the atomic locations at which each sphericalized density originates, in addition to the set of sphericalized densities themselves. In the present work, we utilize formal results from geometric algebra -- in particular, the subfield of distance geometry -- to show that for Coulombic systems this spatial information is encoded within the ensemble of sphericalized densities themselves, and does not require independent specification. Consequently, the set of sphericalized densities uniquely determines the total external potential of the system, exactly as in Hohenberg-Kohn DFT. This theoretical result is illustrated through numerical examples for LiF and for glycine, the simplest amino acid. In addition to establishing a sound practical foundation for spherical DFT as applied to Coulombic systems, the extended theorem provides a rationale for the use of sphericalized atomic basis densities -- rather than orientation-dependent basis functions -- when designing classical or machine-learned potentials for atomistic simulation.

physics.chem-ph

Elastic tensor-derived properties of composition-dependent disordered refractory binary alloys using DFPT

The elastic tensor provides valuable insight into the mechanical behavior of a material with lattice strain, such as disordered binary alloys. Traditional stress-strain methods have made it possible to compute elastic constants for ordered structures and individually tailored alloy compositions. However, this approach depends on predetermined or iteratively-chosen strain tensors. This poses a significant challenge for systematic, composition-dependent studies of disordered materials with low symmetry. DFPT provides a compelling alternative to stress-strain methods: it allows for an unbiased determination of the elastic tensor, as well as access to local field data derived from the underlying general response function framework. Despite its intrinsic flexibility and efficiency, DFPT has seen limited application to the study of disordered systems. At the same time, there is a growing need for expanded quantum mechanical data to improve predictive modeling of complex disordered material properties. Here we present results for the rigid-ion and relaxed-ion elastic tensors computed using DFPT, for a comprehensive set of structural refractory BCC binary alloys of Mo, Nb, Ta, and W. We map the quantum-driven heterogeneity in elastic properties, and associated relaxation fields at each disordered structure lattice site, by computing the force response internal strain tensor and displacement response internal strain tensors. Derived properties -- the bulk modulus ($B$), shear modulus ($G$), Young's modulus ($E$), Poisson's ratio ($\nu$), Pugh's ratio ($B/G$), Cauchy pressure and elastic anisotropy -- are reported as a function of composition for all refractory binaries. The DFPT-computed mechanical properties data for the refractory binary alloys at systematically-varied Mo, Nb, Ta, and W compositions are in excellent agreement with available experimental data.

cond-mat.mtrl-sci

Embedding quantum statistical excitations in a classical force field

Quantum-mechanically-driven charge polarization and charge transfer are ubiquitous in biomolecular systems, controlling reaction rates, allosteric interactions, ligand-protein binding, membrane transport, and dynamically-driven structural transformations. Molecular dynamics (MD) simulations of these processes require quantum mechanical (QM) information in order to accurately describe their reactive dynamics. However, current techniques -- empirical force fields, subsystem approaches, ab initio MD, and machine learning -- vary in their ability to achieve a consistent chemical description across multiple atom types, and at scale. Here we present a physics-based, atomistic force field, the ensemble DFT charge-transfer embedded-atom method, in which QM forces are described at a uniform level of theory across all atoms, avoiding the need for explicit solution of the Schrödinger equation or large, precomputed training datasets. Coupling between the electronic and atomistic length scales is effected through an ensemble density functional theory formulation of the embedded atom method originally developed for elemental materials. Charge transfer is expressed in terms of ensembles of ionic states basis densities of individual atoms, and charge polarization, in terms of atomic excited state basis densities. This provides a highly compact yet general representation of the force field, encompassing both local and system-wide effects. Charge rearrangement is realized through the evolution of ensemble weights, adjusted at each dynamical timestep via chemical potential equalization.

physics.chem-ph

Simulating collective neutrinos oscillations on the Intel Many Integrated Core (MIC) architecture

We evaluate the second-generation Intel Xeon Phi coprocessor based on the Intel Many Integrated Core (MIC) architecture, aka the Knights Landing or KNL, for simulating neutrino oscillations in (core-collapse) supernovae. For this purpose we have developed a numerical code XFLAT which is optimized for the MIC architecture and which can run on both the homogeneous HPC platform with CPUs or Xeon Phis only and the hybrid platform with both CPUs and Xeon Phis. To efficiently utilize the SIMD (vector) units of the MIC architecture we implemented a design of Structure of Array (SoA) in the low-level module of the code. We benchmarked the code on the NERSC Cori supercomputer which is equipped with dual 68-core 7250 Xeon Phis. We find that compare to the first generation of the Xeon Phi (Knights Corner a.k.a KNC) the performance improves by many folds. Some of the problems that we encountered in this work may be solved with the advent of the new supernova model for neutrino oscillations and the next-generation Xeon Phi.

physics.comp-ph

Performance Analysis of an Astrophysical Simulation Code on the Intel Xeon Phi Architecture

We have developed the astrophysical simulation code XFLAT to study neutrino oscillations in supernovae. XFLAT is designed to utilize multiple levels of parallelism through MPI, OpenMP, and SIMD instructions (vectorization). It can run on both CPU and Xeon Phi co-processors based on the Intel Many Integrated Core Architecture (MIC). We analyze the performance of XFLAT on configurations with CPU only, Xeon Phi only and both CPU and Xeon Phi. We also investigate the impact of I/O and the multi-node performance of XFLAT on the Xeon Phi-equipped Stampede supercomputer at the Texas Advanced Computing Center (TACC).

cs.DC

Environment Dependent Charge Potential for Water

We present a new interatomic potential for water captured in a charge-transfer embedded atom method (EAM) framework. The potential accounts for explicit, dynamical charge transfer in atoms as a function of the local chemical environment. As an initial test of the charge-transfer EAM approach for a molecular system, we have constructed a relatively simple version of the potential and examined its ability to model the energetics of small water clusters. The excellent agreement between our results and current experimental and higher-level quantum computational data signifies a successful first step towards developing a unified charge-transfer potential capable of accurately describing the polymorphs, dynamics, and complex thermodynamic behavior of water.

cond-mat.mtrl-sci

Energy dependence on fractional charge for strongly interacting subsystems

The energies of a pair of strongly-interacting subsystems with arbitrary noninteger charges are examined from closed and open system perspectives. An ensemble representation of the charge dependence is derived, valid at all interaction strengths. Transforming from resonance-state ionicity to ensemble charge dependence imposes physical constraints on the occupation numbers in the strong-interaction limit. For open systems, the chemical potential is evaluated using microscopic and thermodynamic models, leading to a novel correlation between ground-state charge and an electronic temperature.

cond-mat.other

Regularization Strategies for Hyperplane Classifiers: Application to Cancer Classification with Gene Expression Data

Linear discrimination, from the point of view of numerical linear algebra, can be treated as solving an ill-posed system of linear equations. In order to generate a solution that is robust in the presence of noise, these problems require regularization. Here, we examine the ill-posedness involved in the linear discrimination of cancer gene expression data with respect to outcome and tumor subclasses. We show that a filter factor representation, based upon Singular Value Decomposition, yields insight into the numerical ill-posedness of the hyperplane-based separation when applied to gene expression data. We also show that this representation yields useful diagnostic tools for guiding the selection of classifier parameters, thus leading to improved performance.

q-bio.GN

An Empirical Charge Transfer Potential with Correct Dissociation Limits

The empirical valence bond (EVB) method [J. Chem. Phys. 52, 1262 (1970)] has always embodied charge transfer processes. The mechanism of that behavior is examined here and recast for use as a new empirical potential energy surface for large-scale simulations. A two-state model is explored. The main features of the model are: (1) Explicit decomposition of the total system electron density is invoked; (2) The charge is defined through the density decomposition into constituent contributions; (3) The charge transfer behavior is controlled through the resonance energy matrix elements which cannot be ignored; and (4) A reference-state approach, similar in spirit to the EVB method, is used to define the resonance state energy contributions in terms of "knowable" quantities. With equal validity, the new potential energy can be expressed as a nonthermal ensemble average with a nonlinear but analytical charge dependence in the occupation number. Dissociation to neutral species for a gas-phase process is preserved. A variant of constrained search density functional theory is advocated as the preferred way to define an energy for a given charge.

physics.chem-ph