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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.
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Exploiting a Shortcoming of Coupled-Cluster Theory: The Extent of Non-Hermiticity as a Diagnostic Indicator of Computational Accuracy
The fundamental non-Hermitian nature of the forms of the coupled-cluster (CC) theory widely used in quantum chemistry has usually been viewed as a negative, but the present paper shows how this can be used to an advantage. Specifically, the non-symmetric nature of the reduced one-particle density matrix (in the molecular orbital basis) is advocated as a diagnostic indicator of computational quality. In the limit of the full coupled-cluster theory [which is equivalent to full configuration interaction (FCI)], the electronic wave function and correlation energy are exact within a given one-particle basis set, and the symmetric character of the exact density matrix is recovered. The extent of the density matrix asymmetry is shown to provide a measure of “how difficult the problem is” (like the well-known T 1 diagnostic), but its variation with the level of theory also gives information about “how well this particular method works”, irrespective of the difficulty of the problem at hand. The proposed diagnostic is described and applied to a select group of small molecules, and an example of its overall utility for the practicing quantum chemist is illustrated through its application to the beryllium dimer (Be 2 ). Future application of this idea to excited states, open-shell systems, and symmetry-breaking problems and an extension of the method to the two-particle density are then proposed.
Machine Learning Enables Prediction of Halide Perovskites’ Optical Behavior with >90% Accuracy
Not Available
A Transferable Force Field for Predicting Adsorption and Diffusion of Water in Cationic Zeolites with Coupled Cluster Accuracy
We present a transferable force field for water in proton-exchanged, alkali (Li, Na, K, Rb, and Cs) metal-exchanged, and alkaline-earth (Mg, Ca, Sr, and Ba) metal-exchanged zeolites. The fitting methodology is based on adsorbate–adsorbent interaction energies obtained from periodic density functional theory calculations and corrected using the coupled-cluster method applied to small model clusters. To ensure an accurate prediction of both adsorption and diffusion properties of water, sets of configurations that sample both adsorption sites and intracrystalline hopping transition states were used in the fitting. The quality of the force field is assessed for a wide range of zeolites with different topologies and chemical compositions, demonstrating good agreement between theoretical predictions and experimental measurements of water adsorption and diffusion.
Using Multiple Signatures to Improve Accuracy of Substorm Identification
Abstract We have developed a new procedure for combining lists of substorm onset times from multiple sources. We apply this procedure to observational data and to magnetohydrodynamic (MHD) model output from 1–31 January 2005. We show that this procedure is capable of rejecting false positive identifications and filling data gaps that appear in individual lists. The resulting combined onset lists produce a waiting time distribution that is comparable to previously published results, and superposed epoch analyses of the solar wind driving conditions and magnetospheric response during the resulting onset times are also comparable to previous results. Comparison of the substorm onset list from the MHD model to that obtained from observational data reveals that the MHD model reproduces many of the characteristic features of the observed substorms, in terms of solar wind driving, magnetospheric response, and waiting time distribution. Heidke skill scores show that the MHD model has statistically significant skill in predicting substorm onset times.
Performance and Accuracy Implications of Parallel Split Physics-Dynamics Coupling in the Energy Exascale Earth System Atmosphere Model
Simultaneous calculation of atmospheric processes is faster than calculating processes one at a time. This type of parallelism is beneficial or perhaps even necessary to provide good performance on modern supercomputers, which achieve faster performance through increased processor count rather than improved clock speed. The scalability of the Energy Exascale Earth System Model (E3SM) Atmosphere Model (EAM) is limited by the fluid dynamics which scales up to the number of mesh cells in the global mesh. In contrast, the suite of physics parameterizations in EAM is scalable up to the total number of physics columns, which is an order of magnitude greater than the number of mesh cells. A proposed solution to unlocking the greater potential performance from the physics suite is to solve the physics and dynamics in parallel. This work represents a first attempt at parallel splitting of the grid-scale fluid dynamics model and the subgrid-scale physics parameterizations in a global atmosphere model. We will demonstrate that switching to parallel physics-dynamics coupling extends the scalability of the EAM to up to 3 times the previous peak scalability limit and is up to 20% faster than the sequentially split coupling at the highest core counts and the same time step. Decadal simulations of both coupling approaches show very little impact to the model climate. This improved performance does not come without drawbacks, however. Parallel splitting requires a shorter time step and other modifications which largely offset performance gains. A mass fixer is required for conservation. Techniques for mitigating these issues are also discussed.
Differentiable, Learnable, Regionalized Process-Based Models With Multiphysical Outputs can Approach State-Of-The-Art Hydrologic Prediction Accuracy
Predictions of hydrologic variables across the entire water cycle have significant value for water resources management as well as downstream applications such as ecosystem and water quality modeling. Recently, purely data-driven deep learning models like long short-term memory (LSTM) showed seemingly insurmountable performance in modeling rainfall runoff and other geoscientific variables, yet they cannot predict untrained physical variables and remain challenging to interpret. Here, we show that differentiable, learnable, process-based models (called δ models here) can approach the performance level of LSTM for the intensively observed variable (streamflow) with regionalized parameterization. We use a simple hydrologic model HBV as the backbone and use embedded neural networks, which can only be trained in a differentiable programming framework, to parameterize, enhance, or replace the process-based model's modules. Without using an ensemble or post-processor, δ models can obtain a median Nash-Sutcliffe efficiency of 0.732 for 671 basins across the USA for the Daymet forcing data set, compared to 0.748 from a state-of-the-art LSTM model with the same setup. For another forcing data set, the difference is even smaller: 0.715 versus 0.722. Meanwhile, the resulting learnable process-based models can output a full set of untrained variables, for example, soil and groundwater storage, snowpack, evapotranspiration, and baseflow, and can later be constrained by their observations. Both simulated evapotranspiration and fraction of discharge from baseflow agreed decently with alternative estimates. The general framework can work with models with various process complexity and opens up the path for learning physics from big data.
Future Climate Projections for South Florida: Improving the Accuracy of Air Temperature and Precipitation Extremes With a Hybrid Statistical Bias Correction Technique
Projecting future climate variables is essential for comprehending the potential impacts on hydroclimatic hazards like floods and droughts. Evaluating these impacts is challenging due to the coarse spatial resolution of global climate models (GCMs); therefore, bias correction is widely used. Here, we applied two statistical methods—standard empirical quantile mapping (EQM) and a hybrid approach, EQM with linear correction (EQM-LIN)—to bias correct precipitation and air temperature simulated by nine GCMs. We used historical observations from 20 weather stations across South Florida to project future climate under three shared socioeconomic pathways (SSPs). Compared to the EQM, the hybrid EQM-LIN method improved R 2 of daily quantiles by up to 30% over the historical period and improved MAE up to 70% in months that contain most extreme values. Projected extreme precipitation at the weather stations showed that, compared to the EQM-LIN, the EQM method underestimates the high quantiles by up to 26% in SSP585. The projected changes in annual maximum precipitation from historical period (1985–2014) to near future (2040–2069) and far future (2070–2100) were between 2% and 16% across the study area. Projected future precipitation suggested a slight decrease during summer but an increase in fall. This, along with rising summer temperatures, suggested that South Florida can experience rapid oscillations from warmer summers and increased flooding in fall under future climate. Additionally, our comparative analyses with globally and nationally downscaled studies showed that such coarse scale studies do not represent the climatic extremes well, particularly for high quantile precipitation.
Prediction of organic homolytic bond dissociation enthalpies at near chemical accuracy with sub-second computational cost
Bond dissociation enthalpies (BDEs) of organic molecules play a fundamental role in determining chemical reactivity and selectivity. However, BDE computations at sufficiently high levels of quantum mechanical theory require substantial computing resources. In this paper, we develop a machine learning model capable of accurately predicting BDEs for organic molecules in a fraction of a second. We perform automated density functional theory (DFT) calculations at the M06-2X/def2-TZVP level of theory for 42,577 small organic molecules, resulting in 290,664 BDEs. A graph neural network trained on a subset of these results achieves a mean absolute error of 0.58 kcal mol-1 (vs DFT) for BDEs of unseen molecules. We further demonstrate the model on two applications: first, we rapidly and accurately predict major sites of hydrogen abstraction in the metabolism of drug-like molecules, and second, we determine the dominant molecular fragmentation pathways during soot formation.
Metaplastic and energy-efficient biocompatible graphene artificial synaptic transistors for enhanced accuracy neuromorphic computing
CMOS-based computing systems that employ the von Neumann architecture are relatively limited when it comes to parallel data storage and processing. In contrast, the human brain is a living computational signal processing unit that operates with extreme parallelism and energy efficiency. Although numerous neuromorphic electronic devices have emerged in the last decade, most of them are rigid or contain materials that are toxic to biological systems. In this work, we report on biocompatible bilayer graphene-based artificial synaptic transistors (BLAST) capable of mimicking synaptic behavior. The BLAST devices leverage a dry ion-selective membrane, enabling long-term potentiation, with ~50 aJ/µm 2 switching energy efficiency, at least an order of magnitude lower than previous reports on two-dimensional material-based artificial synapses. The devices show unique metaplasticity, a useful feature for generalizable deep neural networks, and we demonstrate that metaplastic BLASTs outperform ideal linear synapses in classic image classification tasks. With switching energy well below the 1 fJ energy estimated per biological synapse, the proposed devices are powerful candidates for bio-interfaced online learning, bridging the gap between artificial and biological neural networks.
Extending quantum-mechanical benchmark accuracy to biological ligand-pocket interactions
Predicting the binding affinity of ligands to protein pockets is key in the drug design pipeline. The flexibility of ligand-pocket motifs arises from a range of attractive and repulsive electronic interactions during binding. Accurately accounting for all interactions requires robust quantum-mechanical (QM) benchmarks, which are scarce for ligand-pocket systems. Additionally, disagreement between “gold standard” Coupled Cluster (CC) and Quantum Monte Carlo (QMC) methods casts doubt on many benchmarks for larger non-covalent systems. We introduce the “QUantum Interacting Dimer” (QUID) benchmark framework containing 170 non-covalent (non-)equilibrium systems modeling chemically and structurally diverse ligand-pocket motifs. Symmetry-adapted perturbation theory shows that QUID broadly covers non-covalent binding motifs and energetic contributions. Robust binding energies are obtained using complementary CC and QMC methods, achieving agreement of 0.5 kcal/mol. The benchmark data analysis reveals that several dispersion-inclusive density functional approximations provide accurate energy predictions, though their atomic van der Waals forces differ in magnitude and orientation. Contrarily, semiempirical methods and empirical force fields require improvements in capturing non-covalent interactions (NCIs) for out-of-equilibrium geometries. The wide span of NCIs, highly accurate interaction energies, and analysis of molecular properties take QUID beyond the “gold standard” for QM benchmarks of ligand-protein systems.
Adaptive finite differencing in high accuracy electronic structure calculations
Abstract A multi-order Adaptive Finite Differencing (AFD) method is developed for the kinetic energy operator in real-space, grid-based electronic structure codes. It uses atomic pseudo orbitals produced by the corresponding pseudopotential codes to optimize the standard finite difference (SFD) operators for improved precision. Results are presented for a variety of test systems and Bravais lattice types, including the well-known Δ test for 71 elements in the periodic table, the Mott insulator NiO, and borax decahydrate, which contains covalent, ionic, and hydrogen bonds. The tests show that an 8th-order AFD operator leads to the same average Δ value as that achieved by plane-wave codes and is typically far more accurate and has a much lower computational cost than a 12th-order SFD operator. The scalability of real-space electronic calculations is demonstrated for a 2016-atom NiO cell, for which the computational time decreases nearly linearly when scaled from 18 to 144 CPU-GPU nodes.
acCRISPR: an activity-correction method for improving the accuracy of CRISPR screens
Abstract High throughput CRISPR screens are revolutionizing the way scientists unravel the genetic underpinnings of engineered and evolved phenotypes. One of the critical challenges in accurately assessing screening outcomes is accounting for the variability in sgRNA cutting efficiency. Poorly active guides targeting genes essential to screening conditions obscure the growth defects that are expected from disrupting them. Here, we develop acCRISPR, an end-to-end pipeline that identifies essential genes in pooled CRISPR screens using sgRNA read counts obtained from next-generation sequencing. acCRISPR uses experimentally determined cutting efficiencies for each guide in the library to provide an activity correction to the screening outcomes via calculation of an optimization metric, thus determining the fitness effect of disrupted genes. CRISPR-Cas9 and -Cas12a screens were carried out in the non-conventional oleaginous yeast Yarrowia lipolytica and acCRISPR was used to determine a high-confidence set of essential genes for growth under glucose, a common carbon source used for the industrial production of oleochemicals. acCRISPR was also used in screens quantifying relative cellular fitness under high salt conditions to identify genes that were related to salt tolerance. Collectively, this work presents an experimental-computational framework for CRISPR-based functional genomics studies that may be expanded to other non-conventional organisms of interest.
Real-time prediction of 1 H and 13 C chemical shifts with DFT accuracy using a 3D graph neural network
From quantum chemical and experimental NMR data, a 3D graph neural network, CASCADE, has been developed to predict carbon and proton chemical shifts. Stereoisomers and conformers of organic molecules can be correctly distinguished.
Examining the accuracy of methods for obtaining pressure dependent rate coefficients
In this work we benchmark the performance of various methods for obtaining pressure-dependent phenomenological rate coefficients against direct numerical simulations and propose a new method called simulation least-squares.
Optimizing the accuracy of viscoelastic characterization with AFM force–distance experiments in the time and frequency domains
Atomic Force Microscopy (AFM) force-distance (FD) experiments have emerged as an attractive alternative to traditional micro-rheology measurement techniques owing to their versatility of use in materials of a wide range of mechanical properties. Here, we show that the range of time dependent behaviour which can reliably be resolved from the typical method of FD inversion (fitting constitutive FD relations to FD data) is inherently restricted by the experimental parameters: sampling frequency, experiment length, and strain rate. Specifically, we demonstrate that violating these restrictions can result in errors in the values of the parameters of the complex modulus. In the case of complex materials, such as cells, whose behaviour is not specifically understood a priori, the physical sensibility of these parameters cannot be assessed and may lead to falsely attributing a physical phenomenon to an artifact of the violation of these restrictions. We use arguments from information theory to understand the nature of these inconsistencies as well as devise limits on the range of mechanical parameters which can be reliably obtained from FD experiments. The results further demonstrate that the nature of these restrictions depends on the domain (time or frequency) used in the inversion process, with the time domain being far more restrictive than the frequency domain. Lastly, we demonstrate how to use these restrictions to better design FD experiments to target specific timescales of a material's behaviour through our analysis of a polydimethylsiloxane (PDMS) polymer sample.
Greater transferability and accuracy of norm-conserving pseudopotentials using nonlinear core corrections
We investigate the transferability of NLCC pseudopotentials (PPs) using the GTH protocol with various functionals (GGA, meta-GGA, hybrid), exploring their effects on thermochemical and non-thermochemical properties.