Localized Quantum Chemistry on Quantum Computers
Not Available
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
SEARCH · Search NASA
Results for “computational chemistry”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
ChemComp: A Compilation Framework for Computing with Chemical Reaction Networks
The acceleration of scientific computation, data analytics, and artificial intelligence is driving a surge in computational requirements. Yet, state-of-the-art high-performance computing systems are approaching physical limitations that impede further significant improvements in energy efficiency. As we move towards post-exascale computing systems, innovative approaches are necessary to overcome this barrier in power consumption. Novel analog and hybrid digital-analog architectures hold promise for enhancing energy efficiency by several orders of magnitude. Biochemical computation stands out among the various solutions being explored due to its potential to enable new classes of devices with immense computational capabilities. These devices can capitalize on the inherent efficacy of biological cells in solving optimization problems and are scalable through increasing reaction system size or vessel capacity, potentially satisfying scientific computing's high-performance requirements. Nonetheless, several theoretical and practical limitations persist, including problem formulation and mapping to chemical reaction networks (CRNs) and implementation of actual CRN devices. In this paper, we propose a framework for biochemical computation using systems chemistry. We present the initial components of our approach: an abstract chemical reaction dialect implemented as a multi-level intermediate representation (MLIR) compiler extension and a pathway to represent mathematical problems with CRNs. To showcase the potential of this approach, we emulate a simplified chemical reservoir device. This work lays the groundwork for leveraging chemistry's computing potential in creating energy-efficient, high-performance computing systems tailored to contemporary computational needs.
artificial intelligence↗
Significance of Energy Conservation in Coupled-Trajectory Approaches to Nonadiabatic Dynamics
Practical methods for simulating photo-induced dynamics of molecules often rely on a trajectory-description of the nuclear dynamics, incorporating approximate electron-nuclear feedback. Through approximating electron–nuclear correlation terms in the exact factorization approach, trajectory-based methods have been derived and successfully applied to the dynamics of a variety of light-induced molecular processes, capturing quantum (de)coherence effects rigorously. These terms account for the coupling among the trajectories, recovering the nonlocal nature of quantum nuclear dynamics that is completely overlooked in traditional independent-trajectory algorithms. Nevertheless, some of the approximations introduced in the derivation of some of these methods do not conserve the total energy. We analyze energy conservation in the coupled trajectory mixed quantum-classical (CTMQC) algorithm and explore the performance of a modified algorithm, CTMQC-E, where some of the terms are redefined to restore energy conservation. Here, a set of molecular models is used as a test, namely, 2-cis-penta-2,4-dienimium cation, bis(methylene) adamantyl radical cation, butatriene cation, uracil radical cation, and neutral pyrazine.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Permutationally Invariant Networks for Enhanced Sampling (PINES): Discovery of Multimolecular and Solvent-Inclusive Collective Variables
The typically rugged nature of molecular free energy landscapes can frustrate efficient sampling of the thermodynamically relevant phase space due to the presence of high free energy barriers. Enhanced sampling techniques can improve phase space exploration by accelerating sampling along particular collective variables (CVs). A number of techniques exist for data-driven discovery of CVs parameterizing the important large scale motions of the system. A challenge to CV discovery is learning CVs invariant to symmetries of the molecular system, frequently rigid translation, rigid rotation, and permutational relabeling of identical particles. Of these, permutational invariance has proved a persistent challenge in frustrating the data-driven discovery of multi-molecular CVs in systems of self-assembling particles and solvent-inclusive CVs for solvated systems. In this work, we integrate Permutation Invariant Vector (PIV) featurizations with autoencoding neural networks to learn nonlinear CVs invariant to translation, rotation, and permutation, and perform interleaved rounds of CV discovery and enhanced sampling to iteratively expand sampling of configurational phase space and obtain converged CVs and free energy landscapes. Here, we demonstrate the Permutationally Invariant Network for Enhanced Sampling (PINES) approach in applications to the self-assembly of a 13-atom Argon cluster, association/dissociation of a NaCl ion pair in water, and hydrophobic collapse of a C 45 H 92 n-pentatetracontane polymer chain. We make the approach freely available as a new module within the PLUMED2 enhanced sampling libraries.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
E(3)-equivariant graph neural networks for data-efficient and accurate interatomic potentials
Abstract This work presents Neural Equivariant Interatomic Potentials (NequIP), an E(3)-equivariant neural network approach for learning interatomic potentials from ab-initio calculations for molecular dynamics simulations. While most contemporary symmetry-aware models use invariant convolutions and only act on scalars, NequIP employs E(3)-equivariant convolutions for interactions of geometric tensors, resulting in a more information-rich and faithful representation of atomic environments. The method achieves state-of-the-art accuracy on a challenging and diverse set of molecules and materials while exhibiting remarkable data efficiency. NequIP outperforms existing models with up to three orders of magnitude fewer training data, challenging the widely held belief that deep neural networks require massive training sets. The high data efficiency of the method allows for the construction of accurate potentials using high-order quantum chemical level of theory as reference and enables high-fidelity molecular dynamics simulations over long time scales.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Energy–Geometry Dependency of Molecular Structures: A Multistep Machine Learning Approach
There is growing interest in estimating quantum observables while circumventing expensive computational overhead for facile in silico materials screening. Machine learning (ML) methods are implemented to perform such calculations in shorter times. In this paper, we introduce a multistep method based on machine learning algorithms to estimate total energy on the basis of spatial coordinates and charges for various chemical structures, including organic molecules, inorganic molecules, and ions. This method quickly calculates total energy with 0.76 au in root-mean-square error (RMSE) and 1.5% in mean absolute percent error (MAPE) when tested on a database of optimized and unoptimized structures. Using similar molecular representations, experimental thermochemical properties were estimated, with MAPE as low as 6% and RMSE of 8 cal/mol·K for heat capacity in a 10-fold cross-validation.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A generative artificial intelligence framework based on a molecular diffusion model for the design of metal-organic frameworks for carbon capture
Metal-organic frameworks (MOFs) exhibit great promise for CO 2 capture. However, finding the best performing materials poses computational and experimental grand challenges in view of the vast chemical space of potential building blocks. Here, we introduce GHP-MOFassemble, a generative artificial intelligence (AI), high performance framework for the rational and accelerated design of MOFs with high CO 2 adsorption capacity and synthesizable linkers. GHP-MOFassemble generates novel linkers, assembled with one of three pre-selected metal nodes (Cu paddlewheel, Zn paddlewheel, Zn tetramer) into MOFs in a primitive cubic topology. GHP-MOFassemble screens and validates AI-generated MOFs for uniqueness, synthesizability, structural validity, uses molecular dynamics simulations to study their stability and chemical consistency, and crystal graph neural networks and Grand Canonical Monte Carlo simulations to quantify their CO 2 adsorption capacities. We present the top six AI-generated MOFs with CO 2 capacities greater than 2m mol g -1 , i.e., higher than 96.9% of structures in the hypothetical MOF dataset.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Nanoparticle Tracking to Probe Transport in Porous Media
From the granular and fractured subsurface environment to highly engineered polymer membranes used in pharmaceutical purification, porous materials are ubiquitous in nature and industrial applications. In particular, porous media are used extensively in processes including water treatment, pharmaceutical sterilization, food/beverage processing and heterogeneous catalysis, where hindered mass transport is either essential to the process or a necessary, but undesirable limitation. Unfortunately, there are currently no universal models capable of predicting mass transport based on a description of the porous material because real porous materials are complex, and because many coupled dynamic mechanisms (e.g. adsorption, steric effects, hydrodynamic effects, electrostatic interactions, etc.) give rise to the observed macroscopic transport phenomena. While classical techniques, like nuclear magnetic resonance and dynamic light scattering, provide useful information about mass transport in porous media at the ensemble level, they provide limited insight into the microscopic mechanisms that give rise to complex phenomena such as anomalous diffusion, hindered pore-space accessibility, and unexpected retention under flow, among many others. To address this issue, we have developed refractive index matching imaging systems, combined with single-particle tracking methods, allowing the direct visualization of single particle motion within a variety of porous materials. Here, we summarize our recent efforts to advance the understanding of nanoparticle transport in porous media using single-particle tracking methods in both fundamental and applied scenarios. First, we describe the basic principles for two-dimensional and three-dimensional single-particle tracking in porous materials. Then, we describe concrete examples of nanoparticle transport in porous materials from two perspectives: (1) understanding fundamental elementary particle transport processes in porous media, including pore accessibility and cavity escape, which limit transport in porous media; (2) facilitating applications in industrial processes, e.g. by understanding the mechanisms of particle fouling and remobilization in filtration membranes. Finally, we provide an outlook of opportunities associated with investigating other types of mass transport in confined environments using single-particle tracking methods, including electrophoretic and self-propelled motion.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Protein Surface Printer for Exploring Protein Domains
The surface of proteins is vital in determining protein functions. Herein, a program, Protein Surface Printer (PSP), is built that performs multiple functions in quantifying protein surface domains. Two proteins, PETase and cytochrome P450, are used to validate that the program supports atomistic simulations with different combinations of programs and force fields. A case study is conducted on the structural analysis of the spike proteins of SARS-CoV-2 and SARS-CoV and the human cell receptor ACE2. Although the surface domains of both spike proteins are highly similar, their receptor-binding domains (RBDs) and the O-linked glycan domains are structurally different. The O-linked glycan domain of SARS-CoV-2 is highly positively charged, which may promote binding to negatively charged human cells.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
OpenMSCG: A Software Tool for Bottom-Up Coarse-Graining
Not Available
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Using Machine Learning to Understand the Causes of Quantum Decoherence in Solution-Phase Bond-Breaking Reactions
Not Available
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Can electric fields drive chemistry for an aqueous microdroplet?
Abstract Reaction rates of common organic reactions have been reported to increase by one to six orders of magnitude in aqueous microdroplets compared to bulk solution, but the reasons for the rate acceleration are poorly understood. Using a coarse-grained electron model that describes structural organization and electron densities for water droplets without the expense of ab initio methods, we investigate the electric field distributions at the air-water interface to understand the origin of surface reactivity. We find that electric field alignments along free O–H bonds at the surface are ~16 MV/cm larger on average than that found for O–H bonds in the interior of the water droplet. Furthermore, electric field distributions can be an order of magnitude larger than the average due to non-linear coupling of intramolecular solvent polarization with intermolecular solvent modes which may contribute to even greater surface reactivity for weakening or breaking chemical bonds at the droplet surface.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Materials Graph Library (MatGL), an open-source graph deep learning library for materials science and chemistry
Graph deep learning models, which incorporate a natural inductive bias for atomic structures, are of immense interest in materials science and chemistry. Here, we introduce the Materials Graph Library (MatGL), an open-source graph deep learning library for materials science and chemistry. Built on top of the popular Deep Graph Library (DGL) and Python Materials Genomics (Pymatgen) packages, MatGL is designed to be an extensible “batteries-included” library for developing advanced model architectures for materials property predictions and interatomic potentials. At present, MatGL has efficient implementations for both invariant and equivariant graph deep learning models, including the Materials 3-body Graph Network (M3GNet), MatErials Graph Network (MEGNet), Crystal Hamiltonian Graph Network (CHGNet), TensorNet and SO3Net architectures. MatGL also provides several pre-trained foundation potentials (FPs) with coverage of the entire periodic table, and property prediction models for out-of-box usage, benchmarking and fine-tuning. Finally, MatGL integrates with PyTorch Lightning to enable efficient model training.
chemistry↗
A quantum eigenvalue solver based on tensor networks
Electronic ground states are of central importance in chemical simulations, but have remained beyond the reach of efficient classical algorithms except in cases of weak electron correlation or one-dimensional spatial geometry. We introduce a hybrid quantum-classical eigenvalue solver that constructs a wavefunction ansatz from a linear combination of matrix product states in rotated orbital bases, enabling the characterization of strongly correlated ground states with arbitrary spatial geometry. The energy is converged via a gradient-free generalized sweep algorithm based on quantum subspace diagonalization, with a potentially exponential speedup in the off-diagonal matrix element contractions upon translation into compact quantum circuits of linear depth in the number of qubits. Chemical accuracy is attained in numerical experiments for both a stretched water molecule and an octahedral arrangement of hydrogen atoms, achieving substantially better correlation energies compared to a unitary coupled-cluster benchmark, with orders of magnitude reductions in quantum resource estimates and a surprisingly high tolerance to shot noise. This proof-of-concept study suggests a promising new avenue for scaling up simulations of strongly correlated chemical systems on near-term quantum hardware.
chemistry↗
Quantum chemical calculations for over 200,000 organic radical species and 40,000 associated closed-shell molecules
Not Available
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Dependency of solvation effects on metal identity in surface reactions
Solvent interactions with adsorbed moieties involved in surface reactions are often believed to be similar for different metal surfaces. However, solvents alter the electronic structures of surface atoms, which in turn affects their interaction with adsorbed moieties. To reveal the importance of metal identity on aqueous solvent effects in heterogeneous catalysis, we studied solvent effects on the activation free energies of the O–H and C–H bond cleavages of ethylene glycol over the (111) facet of six transition metals (Ni, Pd, Pt, Cu, Ag, Au) using an explicit solvation approach based on a hybrid quantum mechanical/molecular mechanical (QM/MM) description of the potential energy surface. A significant metal dependence on aqueous solvation effects was observed that suggests solvation effects must be studied in detail for every reaction system. The main reason for this dependence could be traced back to a different amount of charge-transfer between the adsorbed moieties and metals in the reactant and transition states for the different metal surfaces.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Precision Polishing of Ablator Capsules via in situ Process Monitoring and Machine Learning–Based Optimization
In inertial confinement fusion (ICF) experiments seeking output gains of unity and beyond, the quality of the ablator capsule is paramount for minimizing the hydrodynamic mix that quenches the central hot spot. Defects in the form of foreign particles or missing mass on the surface and within the wall of the capsule are primary offenders. High-density carbon capsules made for ICF experiments at the National Ignition Facility are precision polished to achieve surface smoothness on the order of a few nanometers as well as to minimize isolated defects in the form of pits. Given the critical role of this process, we are developing smart manufacturing techniques with the goal of elevating the efficiency of this process. Our approach is to use MEMS (micro-electromechanical systems)–based sensors to capture the fine vibration signals generated during the polishing process and combine them with synchronized visual feedback as needed. Beyond using these sensors for process monitoring, we use specific deep learning methods to analyze the data and extract correlations with both the process parameters and the final performance of the polishing run. Here, in this work, we describe the multiple fronts we have explored in this regard and the results we have gotten so far. This approach promises to have the potential to ultimately provide real-time feedback that can be used to ensure the progress of the run as well as a means for faster optimization.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗