arXiv subjects

Daniel S. Levine

Publications and source records attributed to Daniel S. Levine.

15 recordsLinked to original sources

arXiv2026

Quantum-accurate atomistic modeling of enzyme catalysis using a machine learned potential

Electronic rearrangements associated with bond forming/breaking in catalytic enzymes require quantum mechanical (QM) treatment beyond classical molecular mechanics (MM). Hybrid QM/MM methods enable tractable simulations but require system-specific setup and are sensitive to the QM region choice and treatment of the QM/MM interface. We demonstrate quantum-accurate treatment of all-atom, complete enzymes in explicit solvent comprising up to 54k atoms and 1 microsecond of total simulation time using the machine-learned interatomic potential (MLIP) eSEN-omol. We reproduce experimental barrier trends for Claisen rearrangement in chorismate mutase, resolve critical intermediate states in PETase catalyzed polymer depolymerization, and distinguish mechanistic alternatives for metal-activated phosphoryl transfer in nucleoside diphosphate kinase. We realize 1000x speedups relative to typical QM/MM calculations without system-specific tuning. These results establish MLIPs as a practical route to QM-accurate simulations of enzyme catalysis.

physics.chem-ph↗

arXiv2026

FastCSP: Accelerated Molecular Crystal Structure Prediction with Universal Model for Atoms

Molecular crystal structure prediction (CSP) is essential for applications in pharmaceuticals and organic electronics. However, CSP remains challenging and computationally intensive due to the need to explore a large search space with sub-kJ/mol accuracy to distinguish between competing polymorphs. While dispersion-inclusive density functional theory (DFT) offers the necessary precision, its computational cost is impractical for a large number of putative structures. Here, we present FastCSP, an open-source, end-to-end CSP workflow driven entirely by a single pretrained universal machine learning interatomic potential (MLIP), the Universal Model for Atoms (UMA), without any system-specific fine-tuning or DFT calculations. FastCSP integrates conformer generation, random structure generation via Genarris 3, geometry optimization, free energy evaluation, and conformer energy corrections, all powered by UMA. Benchmarked on 28 semi-rigid and 10 flexible molecules spanning 74 experimental polymorphs, FastCSP reliably recovers all known structures, ranking them within 9 kJ/mol of the global minimum. UMA reproduces dispersion-inclusive DFT results with high fidelity across chemically diverse compounds. Conformer corrections are particularly beneficial for flexible compounds with conformational polymorphism, such as ROY. UMA's accuracy, transferability, and computational cost thus eliminate the need for classical force fields in early-stage screening and DFT-based re-ranking in CSP workflows. The open-source release of the entire FastCSP workflow lowers the barrier to accessing CSP, enabling both pharmaceutical-grade and high-throughput polymorph screening within practical computational reach.

physics.chem-ph↗

arXiv2026

Insights into CO dimerization at electrified Cu interfaces from large-scale machine learning simulations

Catalysis at solid-liquid interfaces underpins many energy technologies, yet ab initio simulations that capture interfacial dynamics remain prohibitively expensive. Here we introduce Open Catalyst 2025 (OC25), the largest dataset for solid-liquid interfaces. To demonstrate OC25-trained models as practical tools for electrocatalysis, we investigate CO dimerization on Cu surfaces, a key step in CO$_2$ electroreduction. Using large cells (>800 atoms) and enhanced sampling up to 7 ns - the largest explicit-solvent CO dimerization study to date - we compute free-energy profiles under varied surface charge, cation identity, and surface facet. We find that dimerization is weakly sensitive to charge and cation identity, with appreciable stabilization only at the most negative charge densities, while extension to stepped Cu(310) reveals a more favorable pathway at modest reducing potentials. Our results demonstrate that OC25-trained models provide a scalable tool for investigating electrocatalytic transformations at solid-liquid interfaces, enabling simulations orders of magnitude beyond ab initio methods.

cond-mat.mtrl-sci↗

arXiv2026

The Open Molecules 2025 (OMol25) Dataset, Evaluations, and Models

Machine learning (ML) models hold the promise of transforming atomic simulations by delivering quantum chemical accuracy at a fraction of the computational cost. Realization of this potential would enable high-throughout, high-accuracy molecular screening campaigns to explore vast regions of chemical space and facilitate ab initio simulations at sizes and time scales that were previously inaccessible. However, a fundamental challenge to creating ML models that perform well across molecular chemistry is the lack of comprehensive data for training. Despite substantial efforts in data generation, no large-scale molecular dataset exists that combines broad chemical diversity with a high level of accuracy. To address this gap, Meta FAIR introduces Open Molecules 2025 (OMol25), a large-scale dataset composed of more than 100 million density functional theory (DFT) calculations at the $ω$B97M-V/def2-TZVPD level of theory, representing billions of CPU core-hours of compute. OMol25 uniquely blends elemental, chemical, and structural diversity including: 83 elements, a wide-range of intra- and intermolecular interactions, explicit solvation, variable charge/spin, conformers, and reactive structures. There are ~83M unique molecular systems in OMol25 covering small molecules, biomolecules, metal complexes, and electrolytes, including structures obtained from existing datasets. OMol25 also greatly expands on the size of systems typically included in DFT datasets, with systems of up to 350 atoms. In addition to the public release of the data, we provide baseline models and a comprehensive set of model evaluations to encourage community engagement in developing the next-generation ML models for molecular chemistry.

physics.chem-ph↗

arXiv2026

UMA: A Family of Universal Models for Atoms

The ability to quickly and accurately compute properties from atomic simulations is critical for advancing a large number of applications in chemistry and materials science including drug discovery, energy storage, and semiconductor manufacturing. To address this need, Meta FAIR presents a family of Universal Models for Atoms (UMA), designed to push the frontier of speed, accuracy, and generalization. UMA models are trained on half a billion unique 3D atomic structures (the largest training runs to date) by compiling data across multiple chemical domains, e.g. molecules, materials, and catalysts. We develop empirical scaling laws to help understand how to increase model capacity alongside dataset size to achieve the best accuracy. The UMA small and medium models utilize a novel architectural design we refer to as mixture of linear experts that enables increasing model capacity without sacrificing speed. For example, UMA-medium has 1.4B parameters but only ~50M active parameters per atomic structure. We evaluate UMA models on a diverse set of applications across multiple domains and find that, remarkably, a single model without any fine-tuning can perform similarly or better than specialized models. We are releasing the UMA code, weights, and associated data to accelerate computational workflows and enable the community to continue to build increasingly capable AI models.

cs.LG↗

arXiv2026

The Open Polymers 2026 (OPoly26) Dataset and Evaluations

Polymers-macromolecular systems composed of repeating chemical units-constitute the molecular foundation of living organisms, while their synthetic counterparts drive transformative advances across medicine, consumer products, and energy technologies. While machine learning (ML) models have been trained on millions of quantum chemical atomistic simulations for materials and/or small molecular structures to enable efficient, accurate, and transferable predictions of chemical properties, polymers have largely not been included in prior datasets due to the computational expense of high quality electronic structure calculations on representative polymeric structures. Here, we address this shortcoming with the creation of the Open Polymers 2026 (OPoly26) dataset, which contains more than 6.57 million density functional theory (DFT) calculations on up to 360 atom clusters derived from polymeric systems, comprising over 1.2 billion total atoms. OPoly26 captures the chemical diversity that makes polymers intrinsically tunable and versatile materials, encompassing variations in monomer composition, degree of polymerization, chain architectures, and solvation environments. We show that augmenting ML model training with the OPoly26 dataset improves model performance for polymer prediction tasks. We also publicly release the OPoly26 dataset to help further the development of ML models for polymers, and more broadly, strive towards universal atomistic models.

physics.chem-ph↗

arXiv2026

Quantum-Enhanced Neural Exchange-Correlation Functionals

Kohn-Sham Density Functional Theory (KS-DFT) provides the exact ground state energy and electron density of a molecule, contingent on the as-yet-unknown universal exchange-correlation (XC) functional. Recent research has demonstrated that neural networks can efficiently learn to represent approximations to that functional, offering accurate generalizations to molecules not present during the training process. With the latest advancements in quantum-enhanced machine learning (ML), evidence is growing that Quantum Neural Network (QNN) models may offer advantages in ML applications. In this work, we explore the use of QNNs for representing XC functionals, enhancing and comparing them to classical ML techniques. We present QNNs based on differentiable quantum circuits (DQCs) as quantum (hybrid) models for XC in KS-DFT, implemented across various architectures. We assess their performance on 1D and 3D systems. To that end, we expand existing differentiable KS-DFT frameworks and propose strategies for efficient training of such functionals, highlighting the importance of fractional orbital occupation for accurate results. Our best QNN-based XC functional yields energy profiles of the H$_2$ and planar H$_4$ molecules that deviate by no more than 1 mHa from the reference DMRG and FCI/6-31G results, respectively. Moreover, they reach chemical precision on a system, H$_2$H$_2$, not present in the training dataset, using only a few variational parameters. This work lays the foundation for the integration of quantum models in KS-DFT, thereby opening new avenues for expressing XC functionals in a differentiable way and facilitating computations of various properties.

quant-ph↗

arXiv2025

Learning from the electronic structure of molecules across the periodic table

Machine-Learned Interatomic Potentials (MLIPs) require vast amounts of atomic structure data to learn forces and energies, and their performance continues to improve with training set size. Meanwhile, the even greater quantities of accompanying data in the Hamiltonian matrix H behind these datasets has so far gone unused for this purpose. Here, we provide a recipe for integrating the orbital interaction data within H towards training pipelines for atomic-level properties. We first introduce HELM ("Hamiltonian-trained Electronic-structure Learning for Molecules"), a state-of-the-art Hamiltonian prediction model which bridges the gap between Hamiltonian prediction and universal MLIPs by scaling to H of structures with 100+ atoms, high elemental diversity, and large basis sets including diffuse functions. To accompany HELM, we release a curated Hamiltonian matrix dataset, 'OMol_CSH_58k', with unprecedented elemental diversity (58 elements), molecular size (up to 150 atoms), and basis set (def2-TZVPD). Finally, we introduce 'Hamiltonian pretraining' as a method to extract meaningful descriptors of atomic environments even from a limited number atomic structures, and repurpose this shared embedding space to improve performance on energy-prediction in low-data regimes. Our results highlight the use of electronic interactions as a rich and transferable data source for representing chemical space.

physics.chem-ph↗

arXiv2025

Open Molecular Crystals 2025 (OMC25) Dataset and Models

The development of accurate and efficient machine learning models for predicting the structure and properties of molecular crystals has been hindered by the scarcity of publicly available datasets of structures with property labels. To address this challenge, we introduce the Open Molecular Crystals 2025 (OMC25) dataset, a collection of over 27 million molecular crystal structures containing 12 elements and up to 300 atoms in the unit cell. The dataset was generated from dispersion-inclusive density functional theory (DFT) relaxation trajectories of over 230,000 randomly generated molecular crystal structures of around 50,000 organic molecules. OMC25 comprises diverse chemical compounds capable of forming different intermolecular interactions and a wide range of crystal packing motifs. We provide detailed information on the dataset's construction, composition, structure, and properties. To demonstrate the quality and use cases of OMC25, we further trained and evaluated state-of-the-art open-source machine learning interatomic potentials. By making this dataset publicly available, we aim to accelerate the development of more accurate and efficient machine learning models for molecular crystals.

physics.chem-ph↗

arXiv2025

Learning Smooth and Expressive Interatomic Potentials for Physical Property Prediction

Machine learning interatomic potentials (MLIPs) have become increasingly effective at approximating quantum mechanical calculations at a fraction of the computational cost. However, lower errors on held out test sets do not always translate to improved results on downstream physical property prediction tasks. In this paper, we propose testing MLIPs on their practical ability to conserve energy during molecular dynamic simulations. If passed, improved correlations are found between test errors and their performance on physical property prediction tasks. We identify choices which may lead to models failing this test, and use these observations to improve upon highly-expressive models. The resulting model, eSEN, provides state-of-the-art results on a range of physical property prediction tasks, including materials stability prediction, thermal conductivity prediction, and phonon calculations.

physics.comp-ph↗

arXiv2020

The Ground State Electronic Energy of Benzene

We report on the findings of a blind challenge devoted to determining the frozen-core, full configuration interaction (FCI) ground state energy of the benzene molecule in a standard correlation-consistent basis set of double-$ζ$ quality. As a broad international endeavour, our suite of wave function-based correlation methods collectively represents a diverse view of the high-accuracy repertoire offered by modern electronic structure theory. In our assessment, the evaluated high-level methods are all found to qualitatively agree on a final correlation energy, with most methods yielding an estimate of the FCI value around $-863$ m$E_{\text{H}}$. However, we find the root-mean-square deviation of the energies from the studied methods to be considerable (1.3 m$E_{\text{H}}$), which in light of the acclaimed performance of each of the methods for smaller molecular systems clearly displays the challenges faced in extending reliable, near-exact correlation methods to larger systems. While the discrepancies exposed by our study thus emphasize the fact that the current state-of-the-art approaches leave room for improvement, we still expect the present assessment to provide a valuable community resource for benchmark and calibration purposes going forward.

physics.chem-ph↗

arXiv2020

CASSCF with Extremely Large Active Spaces using the Adaptive Sampling Configuration Interaction Method

The complete active space self-consistent field (CASSCF) method is the principal approach employed for studying strongly correlated systems. However, exact CASSCF can only be performed on small active spaces of ~20 electrons in ~20 orbitals due to exponential growth in the computational cost. We show that employing the Adaptive Sampling Configuration Interaction (ASCI) method as an approximate Full CI solver in the active space allows CASSCF-like calculations within chemical accuracy (<1 kcal/mol for relative energies) in active spaces with more than ~50 active electrons in ~50 active orbitals, significantly increasing the sizes of systems amenable to accurate multiconfigurational treatment. The main challenge with using any selected CI-based approximate CASSCF is the orbital optimization problem; they tend to exhibit large numbers of local minima in orbital space due to their lack of invariance to active-active rotations (in addition to the local minima that exist in exact CASSCF). We highlight methods that can avoid spurious local extrema as a practical solution to the orbital optimization problem. We employ ASCI-SCF to demonstrate lack of polyradical character in moderately sized periacenes with up to 52 correlated electrons and compare against heat-bath CI on an iron porphyrin system with more than 40 correlated electrons.

physics.comp-ph↗

arXiv2019

Modern Approaches to Exact Diagonalization and Selected Configuration Interaction with the Adaptive Sampling CI Method

Recent advances in selected CI, including the adaptive sampling configuration interaction (ASCI) algorithm and its heat bath extension, have made the ASCI approach competitive with the most accurate techniques available, and hence an increasingly powerful tool in solving quantum Hamiltonians. In this work, we show that a useful paradigm for generating efficient selected CI/exact diagonalization algorithms is driven by fast sorting algorithms, much in the same way iterative diagonalization is based on the paradigm of matrix vector multiplication. We present several new algorithms for all parts of performing a selected CI, which includes new ASCI search, dynamic bit masking, fast orbital rotations, fast diagonal matrix elements, and residue arrays. The algorithms presented here are fast and scalable, and we find that because they are built on fast sorting algorithms they are more efficient than all other approaches we considered. After introducing these techniques we present ASCI results applied to a large range of systems and basis sets in order to demonstrate the types of simulations that can be practically treated at the full-CI level with modern methods and hardware, presenting double- and triple-zeta benchmark data for the G1 dataset. The largest of these calculations is Si$_{2}$H$_{6}$ which is a simulation of 34 electrons in 152 orbitals. We also present some preliminary results for fast deterministic perturbation theory simulations that use hash functions to maintain high efficiency for treating large basis sets.

physics.comp-ph↗

arXiv2018

Postponing the orthogonality catastrophe: efficient state preparation for electronic structure simulations on quantum devices

Despite significant work on resource estimation for quantum simulation of electronic systems, the challenge of preparing states with sufficient ground state support has so far been largely neglected. In this work we investigate this issue in several systems of interest, including organic molecules, transition metal complexes, the uniform electron gas, Hubbard models, and quantum impurity models arising from embedding formalisms such as dynamical mean-field theory. Our approach uses a state-of-the-art classical technique for high-fidelity ground state approximation. We find that easy-to-prepare single Slater determinants such as the Hartree-Fock state often have surprisingly robust support on the ground state for many applications of interest. For the most difficult systems, single-determinant reference states may be insufficient, but low-complexity reference states may suffice. For this we introduce a method for preparation of multi-determinant states on quantum computers.

quant-ph↗

arXiv2018

An efficient deterministic perturbation theory for selected configuration interaction methods

The interplay between advances in stochastic and deterministic algorithms has recently led to development of interesting new selected configuration interaction (SCI) methods for solving the many body Schrödinger equation. The performance of these SCI methods can be greatly improved with a second order perturbation theory (PT2) correction, which is often evaluated in a stochastic or hybrid-stochastic manner. In this work, we present a highly efficient, fully deterministic PT2 algorithm for SCI methods and demonstrate that our approach is orders of magnitude faster than recent proposals for stochastic SCI+PT2. We also show that it is important to have a compact reference SCI wave function, in order to obtain optimal SCI+PT2 energies. This indicates that it advantageous to use accurate search algorithms such as 'ASCI search' rather than more approximate approaches. Our deterministic PT2 algorithm is based on sorting techniques that have been developed for modern computing architectures and is inherently straightforward to use on parallel computing architectures. Related architectures such as GPU implementations can be also used to further increase the efficiency. Overall, we demonstrate that the algorithms presented in this work allow for efficient evaluation of trillions of PT2 contributions with modest computing resources.

cond-mat.str-el↗