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At least 505 records · Page 28
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Multitask Machine Learning of Collective Variables for Enhanced Sampling of Rare Events

Computing accurate reaction rates is a central challenge in computational chemistry and biology because of the high cost of free energy estimation with unbiased molecular dynamics. In this work, a data-driven machine learning algorithm is devised to learn collective variables with a multitask neural network, where a common upstream part reduces the high dimensionality of atomic configurations to a low dimensional latent space and separate downstream parts map the latent space to predictions of basin class labels and potential energies. Here, the resulting latent space is shown to be an effective low-dimensional representation, capturing the reaction progress and guiding effective umbrella sampling to obtain accurate free energy landscapes. This approach is successfully applied to model systems including a 5D Müller Brown model, a 5D three-well model, the alanine dipeptide in vacuum, and an Au(110) surface reconstruction unit reaction. It enables automated dimensionality reduction for energy controlled reactions in complex systems, offers a unified and data-efficient framework that can be trained with limited data, and outperforms single-task learning approaches, including autoencoders.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Unsupervised atomic data mining via multi-kernel graph autoencoders for machine learning force fields

Constructing a chemically diverse dataset while avoiding sampling bias is critical to training efficient and generalizable force fields. However, in computational chemistry and materials science, many common dataset generation techniques are prone to oversampling regions of the potential energy surface. Furthermore, these regions can be difficult to identify and isolate from each other or may not align well with human intuition, making it challenging to systematically remove bias in the dataset. While traditional clustering and pruning (down-sampling) approaches can be useful for this, they can often lead to information loss or a failure to properly identify distinct regions of the potential energy surface due to difficulties associated with the high dimensionality of atomic descriptors. In this work, we introduce the Multi-kernel Edge Attention-based Graph Autoencoder (MEAGraph) model, an unsupervised approach for analyzing atomic datasets. MEAGraph combines multiple linear kernel transformations with attention-based message passing to capture geometric sensitivity and enable effective dataset pruning without relying on labels or extensive training. Demonstrated applications on niobium, tantalum, and iron datasets show that MEAGraph efficiently groups similar atomic environments, allowing for the use of basic pruning techniques for removing sampling bias. This approach provides an effective method for representation learning and clustering that can be used for data analysis, outlier detection, and dataset optimization.

Materials science↗
DOE OSTI2024

Analytic Nuclear Gradients for Complete Active Space Linearized Pair-Density Functional Theory

Accurately modeling photochemical reactions is difficult due to the presence of conical intersections and locally avoided crossings, as well as the inherently multiconfigurational character of excited states. As such, one needs a multistate method that incorporates state interaction in order to accurately model the potential energy surface at all nuclear coordinates. The recently developed linearized pair-density functional theory (L-PDFT) is a multistate extension of multiconfiguration PDFT, and it has been shown to be a cost-effective post-MCSCF method (as compared to more traditional and expensive multireference many-body perturbation methods or multireference configuration interaction methods) that can accurately model potential energy surfaces in regions of strong nuclear–electronic coupling in addition to accurately predicting Franck–Condon vertical excitations. Here, in this paper, we report the derivation of analytic gradients for L-PDFT and their implementation in the PySCF-forge software, and we illustrate the utility of these gradients for predicting ground- and excited-state equilibrium geometries and adiabatic excitation energies for formaldehyde, s-trans-butadiene, phenol, and cytosine.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Ultrafast lattice disordering can be accelerated by electronic collisional forces

In the prevalent picture of ultrafast structural phase transitions, the atomic motion occurs in a slowly varying potential energy surface determined adiabatically by the fast electrons. However, this ignores non-conservative forces caused by electron-lattice collisions, which can significantly influence atomic motion. Most ultrafast techniques only probe the average structure and are less sensitive to random displacements, and therefore do not detect the role played by non-conservative forces in phase transitions. Here we show that the lattice dynamics of the prototypical insulator-to-metal transition of VO 2 cannot be described by a potential energy alone. We use the sample temperature to control the preexisting lattice disorder before ultrafast photoexcitation across the phase transition and our ultrafast diffuse scattering experiments show that the fluctuations characteristic of the rutile metal develop equally fast (120 fs) at initial temperatures of 100 K and 300 K. This indicates that additional non-conservative forces are responsible for the increased lattice disorder. In conclusion, these results highlight the need for more sophisticated descriptions of ultrafast phenomena beyond the Born-Oppenheimer approximation as well as ultrafast probes of spatial fluctuations beyond the average unit cell measured by diffraction.

36 MATERIALS SCIENCE↗
NASA NTRSDate not supplied

Quantum Hardware-Enabled Molecular Dynamics via Transfer Learning

The ability to perform ab initio molecular dynamics simulations using potential energy surfaces provided by quantum computers would open the door to virtually exact dynamics for a variety of chemical and biochemical systems, with impacts on catalysis and biophysics. Nonetheless, performing molecular dynamics on surfaces produced by quantum hardware has been hampered by the noisy energies typically produced by quantum computers and challenges associated with computing gradients and scaling to large systems interest. A recent set of advances in machine learning, known as transfer learning, provides a new path forward for molecular dynamics simulations on quantum hardware. Transfer learning offers a workaround, where one first trains models on larger, less accurate classical datasets and then refines them on smaller, more accurate quantum datasets. We explore this approach by training machine learning models to predict a molecule's potential energy based on its geometric structure using Behler-Parrinello neural networks. When successfully trained, the model enables energy gradient predictions necessary for dynamic simulations. To reduce the quantum resources needed, the model is initially trained with data derived from classical density functional theory and subsequently refined with a smaller dataset obtained from a variational quantum eigensolver optimization of the unitary coupled cluster ansatz. We show that this approach significantly reduces the size of the needed quantum training dataset while capturing the high accuracies needed within quantum chemistry simulations. The success of this two-step training method opens more opportunities to apply machine learning models on quantum data, a significant stride towards efficient quantum-classical hybrid computational models.

quantum computing↗
DOE OSTI2024

Conical Intersection Accessibility Dictates Brightness in Red Fluorescent Proteins

Red fluorescent protein (RFP) variants are highly sought after for in-vivo imaging since longer wavelengths improve depth and contrast in fluorescence imaging. However, the lower energy emission wavelength usually correlates with a lower fluorescent quantum yield compared to their green emitting counterparts. To guide the rational design of bright variants, we have theoretically assessed two variants (mScarlet and mRouge) which are reported to have very different brightness. Using an α-CASSCF QM/MM framework (chromophore and all protein residues within 6 Å of it in the QM region, for a total of more than 450 QM atoms), we identify key points on the ground and first excited state potential energy surfaces. The brighter variant mScarlet has a rigid scaffold, and the chromophore stays largely planar on the ground state. The dimmer variant mRouge shows more flexibility and can accommodate a pre-twisted chromophore conformation which provides easier access to conical intersections. Notably, the main difference between the variants lies in the intersection seam regions, which appear largely inaccessible in mScarlet but partially accessible in mRouge. This observation is mainly related with changes in the cavity charge distribution, the hydrogen-bonding network involving the chromophore and a key ARG/THR mutation (which changes both charge and steric hindrance).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1990

Ballooning mode instability at the plasmapause

The ballooning mode instability, which can excite hydromagnetic waves at the plasmapause, is studied in the presence of azimuthal plasma flows induced during geomagnetically disturbed periods. A general sufficient criterion for the ballooning mode stability is derived, for a change in the potential energy greater than or equal to 0, which involves the integration over an entire field line. A local stability analysis at the equatorial plasmapause region shows that the ballooning modes could be spontaneously generated via instability under at least two conditions: one is similar to the usual interchange condition, and the second to the quasi-interchange modes. Both of these local instability conditions can be derived from the general stability criterion. Finally an exact solution for the equilibrium state with flow is derived analytically, and the change in the potential energy is computed numerically. It is found that, in the cases studied, the flow does not spontaneously excite the ballooning modes; it only further stabilizes (or destabilizes) the ballooning spectrum if originally the system is stable (or unstable). The analysis would be useful for the interpretation of some of the low-frequency modes observed at the ground and near the equatorial plasmapause.

Lakhina, G. S.↗
DOE OSTI2024

Ab initio exploration of low–lying electronic states of linear and bent MNX + (M = Ca, Sr, Ba, Ra; X = O, S, Se, Te, Po) and their origins

High-level multireference and coupled cluster quantum calculations were employed to analyze low-lying electronic states of linear-MNX + and side-bonded-M[NX] + (M = Ca, Sr, Ba, Ra; X = O, S, Se, Te, Po) species. Their full potential energy curves (PECs), dissociation energies (D e s), geometric parameters, excitation energies (T e s), and harmonic vibrational frequencies (ω e s) are reported. The first three chemically bound electronic states of MNX + and M[NX] + are 3 Σ – , 1 Δ, 1 Σ + and 3 A", 1 A', 1 A", respectively. The 3 Σ – , 1 Δ, 1 Σ + of MNX + originate from the M + ( 2 D) + NX( 2 Π) fragments, whereas the 3 A", 1 A', 1A" states of M[NX] + dissociate to M + ( 2 S) + NX( 2 Π) as a result of avoided crossings. The MNX + and M[NX] + are real minima on the potential energy surface and their interconversions are possible. The M 2+ NX – /M 2+ [NX] – ionic structure is an accurate representation for their low-lying electronic states. The D e s of MNX + species were found to depend on the dipole moment (μ) of the corresponding NX ligands and a linear relationship between these two parameters was observed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Improvements to the macroscopic-microscopic approach of nuclear fission

The well-established macroscopic-microscopic (mac-mic) description of nuclear fission enables the prediction of fission-fragment yields for a broad range of fissioning systems. In this work, we present several key enhancements to this approach. We improve upon the microscopic sector of nuclear potential-energy surfaces by magnifying the resolution of the Lipkin-Nogami equations and strengthening the Strutinsky procedure, thus reducing spurious effects from the continuum. We further present a novel deterministic method for calculating fission dynamics under the assumption of strongly damped nucleonic motion. Our technique directly determines the evolution of the scissioned shape distribution according to the number of random-walk steps rather than the statistical accumulation of fission events. We show that our new technique is equivalent to the Metropolis random walk pioneered over the past decade by Randrup and colleagues. It further improves upon it because we remove the need for altering the nuclear landscape via a biased potential. With our final improvement, we calculate fission fragments mass and charge distributions using particle number projection, which affords the simultaneous calculation of both mass- and charge-yield distributions. Fission fragments are thus calculated from the quantum-mechanical A -body states of the potential-energy surface rather than from the collective mass asymmetry variable α g of the finite-range liquid-drop model used in past work. We highlight the success of our enhancements by predicting the odd-even staggering and the charge polarization for the neutron-induced fission of 233 U and 235 U .

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
NASA NTRS2011

Surface Modeling to Support Small-Body Spacecraft Exploration and Proximity Operations

In order to simulate physically plausible surfaces that represent geologically evolved surfaces, demonstrating demanding surface-relative guidance navigation and control (GN&C) actions, such surfaces must be made to mimic the geological processes themselves. A report describes how, using software and algorithms to model body surfaces as a series of digital terrain maps, a series of processes was put in place that evolve the surface from some assumed nominal starting condition. The physical processes modeled in this algorithmic technique include fractal regolith substrate texturing, fractally textured rocks (of empirically derived size and distribution power laws), cratering, and regolith migration under potential energy gradient. Starting with a global model that may be determined observationally or created ad hoc, the surface evolution is begun. First, material of some assumed strength is layered on the global model in a fractally random pattern. Then, rocks are distributed according to power laws measured on the Moon. Cratering then takes place in a temporal fashion, including modeling of ejecta blankets and taking into account the gravity of the object (which determines how much of the ejecta blanket falls back to the surface), and causing the observed phenomena of older craters being progressively buried by the ejecta of earlier impacts. Finally, regolith migration occurs which stratifies finer materials from coarser, as the fine material progressively migrates to regions of lower potential energy.

Riedel, Joseph E.↗
NASA NTRS1996

Theoretical Studies of the HO/HO2 Catalytic Cycle for Ozone Destruction

Recently it has been determined that the HO/HO2 catalytic cycle accounts for nearly one-half of the total ozone depletion in the lower stratosphere. The catalytic cycle is: (1) HO + O3 yields HO2 + O2; (2) HO2 + O3 yields HO + O2 + O2. The net reaction is 2O3 yields 3O2. The rate limiting step in this process is the reaction of HO2 with ozone. There is a problem extending the experimental measurement of the rate of this reaction over the range 233-400 K down to stratospheric temperatures of 210-220 K. Therefore we have undertaken a project to determine the temperature dependence of the rate constant for this reaction in the low temperature region. The first step in this project, which is described in this poster, is the determination of the relevant potential energy surfaces. The calculations use CASSCF/derivative methods to define the pathways followed by CASSCF/ACPF to determine the energetics. The HO + O3 reaction is found to proceed through an HO4 complex, which is unstable with respect to HO2 + O2. The HO2 +O3 reaction is more complex. One pathway, which has been characterized, is the formation of an HO5 complex which decomposes to HO3 + O2 and subsequently to HO + O2 + O2. Another pathway, which is believed to also play a role, is hydrogen abstraction to give O2 + HO3 and subsequent decomposition of HO3 to HO + O2. Isotopic labeling experiments indicate that the later pathway is dominant. However, so far attempts to locate the saddle point for this pathway have not been successful. We have also characterized the potential energy surfaces for a number of species involved in these reactions, including HO3 and triplet O4. The triplet O4 species is probably involved in the reaction of vibrationally excited O2 with ground state O2 leading to O3 + O. The latter reaction is believed to be important as an additional source of stratospheric ozone.

Walch, Stephen P.↗
DOE OSTI2020

Coupled cluster spectroscopic properties of the coinage metal nitrosyls, M–NO (M = Cu, Ag, Au)

Ab initio near-equilibrium potential energy and dipole moment surfaces for the bent CuNO, AgNO, and AuNO molecules have been calculated under the Feller-Peterson-Dixon (FPD) composite framework at the coupled cluster level of theory including complete basis set extrapolation, outer-core correlation, scalar relativistic effects, and spin-orbit coupling. The Brueckner coupled cluster doubles with perturbative triples method, BCCD(T), was used to greatly improve upon CCSD(T), which was particularly problematic for CuNO. In the latter case the BCCD(T) vibrational frequencies showed significant differences compared to CCSD(T), e.g., nearly 65 cm -1 for the NO stretching frequency, and BCCD(T) also resulted in much better agreement with the available experimental frequencies. A full range of ro-vibrational spectroscopic constants are given for all three molecules of this study using the accurate composite potential energy functions and employing 2nd-order vibrational perturbation theory.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

How well are hazards associated with derechos reproduced in regional climate simulations?

Abstract. A 15-member ensemble of convection-permitting regional simulations of the fast-moving and destructive derecho of 29–30 June 2012 that impacted the northeastern urban corridor of the USA is presented. This event generated 1100 reports of damaging winds, generated significant wind gusts over an extensive area of up to 500 000 km2, caused several fatalities, and resulted in widespread loss of electrical power. Extreme events such as this are increasingly being used within pseudo-global-warming experiments to examine the sensitivity of historical, societally important events to global climate non-stationarity and how they may evolve as a result of changing thermodynamic and dynamic contexts. As such it is important to examine the fidelity with which such events are described in hindcast experiments. The regional simulations presented herein are performed using the Weather Research and Forecasting (WRF) model. The resulting ensemble is used to explore simulation fidelity relative to observations for wind gust magnitudes, spatial scales of convection (as is manifest in high composite reflectivity, cREF), and both rainfall and hail production as a function of model configuration (microphysics parameterization, lateral boundary conditions (LBCs), start date, use of nudging, compiler choice, damping, and number of vertical levels). We also examine the degree to which each ensemble member differs with respect to key mesoscale drivers of convective systems (e.g., convective available potential energy and vertical wind shear) and critical manifestations of deep convection, e.g., vertical velocities, cold-pool generation, and how those properties relate to the correct characterization of the associated atmospheric hazards (wind gusts and hail). Use of a double-moment, seven-class scheme with number concentrations for all species (including hail and graupel) results in the greatest fidelity of model-simulated wind gusts and convective structure to the observations of this event. All ensemble members, however, fail to capture the intensity of the event in terms of the spatial extent of convection and the production of high near-surface wind gusts. We further show very high sensitivity to the LBCs employed and specifically that simulation fidelity is higher for simulations nested within ERA-Interim compared to ERA5. Excess convective available potential energy (CAPE) in all ensemble members after the derecho passage leads to excess production of convective cells, wind gusts, cREF > 40 dBZ, and precipitation during a frontal passage on the subsequent day. This event proved very challenging to forecast in real time and to reproduce in the 15-member hindcast simulation ensemble presented here. Future work could examine if simulations with other initial and lateral boundary conditions can achieve greater fidelity.

Shepherd, Tristan (ORCID:0000000186276419)↗
NASA NTRS2002

Equivalent-Continuum Modeling With Application to Carbon Nanotubes

A method has been proposed for developing structure-property relationships of nano-structured materials. This method serves as a link between computational chemistry and solid mechanics by substituting discrete molecular structures with equivalent-continuum models. It has been shown that this substitution may be accomplished by equating the vibrational potential energy of a nano-structured material with the strain energy of representative truss and continuum models. As important examples with direct application to the development and characterization of single-walled carbon nanotubes and the design of nanotube-based devices, the modeling technique has been applied to determine the effective-continuum geometry and bending rigidity of a graphene sheet. A representative volume element of the chemical structure of graphene has been substituted with equivalent-truss and equivalent continuum models. As a result, an effective thickness of the continuum model has been determined. This effective thickness has been shown to be significantly larger than the interatomic spacing of graphite. The effective thickness has been shown to be significantly larger than the inter-planar spacing of graphite. The effective bending rigidity of the equivalent-continuum model of a graphene sheet was determined by equating the vibrational potential energy of the molecular model of a graphene sheet subjected to cylindrical bending with the strain energy of an equivalent continuum plate subjected to cylindrical bending.

Odegard, Gregory M.↗
NASA NTRS2003

Reactive Resonances in N+N2 Exchange Reaction

Rich reactive resonances are found in a 3D quantum dynamics study of the N + N2 exchange reaction using a recently developed ab initio potential energy surface. This surface is characterized by a feature in the interaction region called Lake Eyring , that is, two symmetric transition states with a shallow minimum between them. An L2 analysis of the quasibound states associated with the shallow minimum confirms that the quasibound states associated with oscillations in all three degrees of freedom in Lake Eyring are responsible for the reactive resonances in the state-to-state reaction probabilities. The quasibound states, mostly the bending motions, give rise to strong reasonance peaks, whereas other motions contribute to the bumps and shoulders in the resonance structure. The initial state reaction probability further proves that the bending motions are the dominating factors of the reaction probability and have longer life times than the stretching motions. This is the first observation of reactive resonances from a "Lake Eyring" feature in a potential energy surface.

Wang, Dunyou↗
DOE OSTI2024

Pairing a Global Optimization Algorithm with EXAFS to Characterize Lanthanide Structure in Solution

Ensemble-average sampling of structures from ab initio molecular dynamics (AIMD) simulations can be used to predict theoretical extended X-ray absorption fine structure (EXAFS) signals that closely match experimental spectra. However, AIMD simulations are time-consuming and resource-intensive, particularly for solvated lanthanide ions, which often form multiple nonrigid geometries with high coordination numbers. Here, to accelerate the characterization of lanthanide structures in solution, we employed the Northwest Potential Energy Surface Search Engine (NWPEsSe), an adaptive-learning global optimization algorithm, to efficiently screen first-shell structures. As case studies, we examine two systems: Eu(NO 3 ) 3 dissolved in acetonitrile with a terpyridine ligand (terpyNO 2 ), and Nd(NO 3 ) 3 dissolved in acetonitrile. The theoretical spectra for structures identified by NWPEsSe were compared to both experimental and AIMD-derived EXAFS spectra. The NWPEsSe algorithm successfully identified the proper solvation structure for both Eu(NO 3 ) 3 (terpyNO 2 ) and Nd(NO 3 )(acetonitrile) 3 , with the calculated EXAFS signals closely matching the experimental spectra for the Eu-ligand complex and showing good similarity for the Nd salt; the better agreement with the ligand-containing structure is attributed to a less dynamic coordination environment due to the rigid ligand. The key advantage of the global optimization algorithm lies in its ability to sample the coordination environment across the potential energy surface and reduce the time required to identify structures from generally a month to within a week. Additionally, this approach is versatile and can be adapted to characterize main-group metal complexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Data-Driven Many-Body Models for Molecular Fluids: CO 2 /H 2 O Mixtures as a Case Study

In this study, we extend the scope of the many-body TTM-nrg and MB-nrg potential energy functions (PEFs), originally introduced for halide ion–water and alkali-metal ion–water interactions, to the modeling of carbon dioxide (CO2) and water (H2O) mixtures as prototypical examples of molecular fluids. Both TTM-nrg and MB-nrg PEFs are derived entirely from electronic structure data obtained at the coupled cluster level of theory and are, by construction, compatible with MB-pol, a many-body PEF that has been shown to accurately reproduce the properties of water. Although both TTM-nrg and MB-nrg PEFs adopt the same functional forms for describing permanent electrostatics, polarization, and dispersion, they differ in the representation of short-range contributions, with the TTM-nrg PEFs relying on conventional Born–Mayer expressions and the MB-nrg PEFs employing multidimensional permutationally invariant polynomials. By providing a physically correct description of many-body effects at both short and long ranges, the MB-nrg PEFs are shown to quantitatively represent the global potential energy surfaces of the CO 2 –CO 2 and CO 2 –H 2 O dimers and the energetics of small clusters, as well as to correctly reproduce various properties in both gas and liquid phases. Furthermore, building upon previous studies of aqueous systems, our analysis provides further evidence for the accuracy and efficiency of the MB-nrg framework in representing molecular interactions in fluid mixtures at different temperature and pressure conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Remote Influence of Andean Convection on Amazonian Rainfall and Its Mechanisms

Models from Coupled Model Intercomparison Project Phase 6 produce too much precipitation over the Andes but too little over the Amazon or the Wet Andes-Dry Amazon (WADA) bias pattern. Unlike the conventional view that convection parameterization and land model deficiencies can contribute to Amazonian rainfall biases, we approach this long-standing biased model behavior through the lens of Andean convection. Using Community Earth System Model v1.1 and focusing on the wet season, our mechanism-denial experiments demonstrate that Andean convection notably reduces precipitation over the Amazon during austral summer. The Andean forced Amazonian response operates on weather timescale. Furthermore, the reduction of Amazonian rainfall is detectable within a few hours after initial Andean forcing. The precipitation response is primarily driven by variations in the moisture budget and is moderated by changes in convective available potential energy over the Amazon. Changes in the total advection of moisture over the Amazon are dominated by the vertical advection term and can be attributed to discrepancies in the dynamic omega field. In the experiments, the Andean east flank region is scrutinized where the vertical velocity and moisture fields play an intermediary role for the Andean driven WADA connection. The Andean forcing induces descending anomalies on the Andean east flank. The disturbances of wind and geopotential fields over the Andean east flank propagate eastward via Kelvin waves. Over the Amazon, descending anomalies and advective drying lead to reduction of mid-to-high level cloud, increase of shortwave cloud forcing and surface net radiation, and enhancement of themodynamic stability and rainfall reduction.

58 GEOSCIENCES↗