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DOE OSTI2024

Predictive Phenomics Initiative Project Dataset Catalog Collection

The Predictive Phenomics Science & Technology Initiative (PPI) at Pacific Northwest National Laboratory are tackling the grand challenge of understanding and predicting phenotype by identifying the molecular basis of function and enable function-driven design and control of biological systems. Research projects within this initiative are divided into three Thrust Areas (TAs): TA1) Enhancing Multi-Scale Phenomics Measurements, TA2) Identifying Molecular Patterns of Biological Function, and TA3) Computational Methods - Phenotypic Signatures. In efforts to enable discovery, reproducibility, and reuse of PPI-funded digital research data generated or used through the course of the proposed research-funded lifecycles, all corresponding digital data assets conducted under the Laboratory Directed Research and Development Program at PNNL are linked to this PPI dataset catalog collection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

An EvoDevo Study of Salmonid Visual Opsin Dynamics and Photopigment Spectral Sensitivity

Salmonids are ideal models as many species follow a distinct developmental program from demersal eggs and a large yolk sac to hatching at an advanced developmental stage. Further, these economically important teleosts inhabit both marine- and freshwaters and experience diverse light environments during their life histories. At a genome level, salmonids have undergone a salmonid-specific fourth whole genome duplication event (Ss4R) compared to other teleosts that are already more genetically diverse compared to many non-teleost vertebrates. Thus, salmonids display phenotypically plastic visual systems that appear to be closely related to their anadromous migration patterns. This is most likely due to a complex interplay between their larger, more gene-rich genomes and broad spectrally enriched habitats; however, the molecular basis and functional consequences for such diversity is not fully understood. This study used advances in genome sequencing to identify the repertoire and genome organization of visual opsin genes (those primarily expressed in retinal photoreceptors) from six different salmonids [Atlantic salmon ( Salmo salar ), brown trout ( Salmo trutta ), Chinook salmon ( Oncorhynchus tshawytcha ), coho salmon ( Oncorhynchus kisutch ), rainbow trout ( Oncorhynchus mykiss ), and sockeye salmon ( Oncorhynchus nerka )] compared to the northern pike ( Esox lucius ), a closely related non-salmonid species. Results identified multiple orthologues for all five visual opsin classes, except for presence of a single short-wavelength-sensitive-2 opsin gene. Several visual opsin genes were not retained after the Ss4R duplication event, which is consistent with the concept of salmonid rediploidization. Developmentally, transcriptomic analyzes of Atlantic salmon revealed differential expression within each opsin class, with two of the long-wavelength-sensitive opsins not being expressed before first feeding. Also, early opsin expression in the retina was located centrally, expanding dorsally and ventrally as eye development progressed, with rod opsin being the dominant visual opsin post-hatching. Modeling by spectral tuning analysis and atomistic molecular simulation, predicted the greatest variation in the spectral peak of absorbance to be within the Rh2 class, with a ∼40 nm difference in λ max values between the four medium-wavelength-sensitive photopigments. Overall, it appears that opsin duplication and expression, and their respective spectral tuning profiles, evolved to maximize specialist color vision throughout an anadromous lifecycle, with some visual opsin genes being lost to tailor marine-based vision.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Cholesky-based experimental design for Gaussian process and kernel-based emulation and calibration.

Gaussian processes and other kernel-based methods are used extensively to construct approximations of multivariate data sets. The accuracy of these approximations is dependent on the data used. This paper presents a computationally efficient algorithm to greedily select training samples that minimize the weighted L p error of kernel-based approximations for a given number of data. The method successively generates nested samples, with the goal of minimizing the error in high probability regions of densities specified by users. The algorithm presented is extremely simple and can be implemented using existing pivoted Cholesky factorization methods. Training samples are generated in batches which allows training data to be evaluated (labeled) in parallel. For smooth kernels, the algorithm performs comparably with the greedy integrated variance design but has significantly lower complexity. Numerical experiments demonstrate the efficacy of the approach for bounded, unbounded, multi-modal and non-tensor product densities. We also show how to use the proposed algorithm to efficiently generate surrogates for inferring unknown model parameters from data using Bayesian inference.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1989

Frequency response modeling and control of flexible structures: Computational methods

The dynamics of vibrations in flexible structures can be conventiently modeled in terms of frequency response models. For structural control such models capture the distributed parameter dynamics of the elastic structural response as an irrational transfer function. For most flexible structures arising in aerospace applications the irrational transfer functions which arise are of a special class of pseudo-meromorphic functions which have only a finite number of right half place poles. Computational algorithms are demonstrated for design of multiloop control laws for such models based on optimal Wiener-Hopf control of the frequency responses. The algorithms employ a sampled-data representation of irrational transfer functions which is particularly attractive for numerical computation. One key algorithm for the solution of the optimal control problem is the spectral factorization of an irrational transfer function. The basis for the spectral factorization algorithm is highlighted together with associated computational issues arising in optimal regulator design. Options for implementation of wide band vibration control for flexible structures based on the sampled-data frequency response models is also highlighted. A simple flexible structure control example is considered to demonstrate the combined frequency response modeling and control algorithms.

Bennett, William H.↗
NASA NTRS1981

Theoretical Treatment of the X(sup 1)Sigma(sup +), A(sup 1)Sigma(sup +), and B(sup 1)Pi states of LiH

Ab initio self-consistent-field plus configuration-interaction calculations are reported for the X(sup 1)Sigma(sup +), A(sup 1)Sigma(sup +), and B(sup 1)Pi states of LiH using a 22(sugma)12(pi)7(delta) function Slater basis set. The resulting dissociation energies, with the experimental values in parentheses, are D(sub e)(X(sup 1)Sigma(sup +)) = 19 972 (20288)/ cm, and D(sub e)(A(sup 1)Sigma(sup +)) = 9042 (8682)/ cm, and D(sup e)(B(sup 1)Pi) = 284 (288) /cm. This is the first ab initio treatment to quantitatively account for the binding in the B(sup 1)Pi state. Calculated dipole moments and electronic transition moments for the X(sup 1)Sigma(sup+)-A(sup 1)Sigma(sup +), X(sup 1)Sigma(sup +)-B((sup 1)Pi, and A(sup 1)Sigma(sup +)- B(sup 1)PI band systems are in excellent agreement with existing theoretical and experimental data. Radiative transition probabilities and lifetimes, including both the bound-bound and bound-free contributions, are computed for all vibrational levels of the A(sup 1)Sigma(sup+) and B(sup 1)Pi states. Comparison with previous results using experimentally based potentials provides insight into the sensitivity of the radiative lifetimes to the detailed nature of the uppermost region of the potentials. Our calculated lifetimes for the lower vibrational levels of the A(sup 1)Sigma(sup +) state are within the experimental uncertainty. Our calculated lifetimes for the three vibrational levels of the B(sup 1)Pi state are in excellent agreement with those of Zemke and Stwalley (values in parentheses), increasing with (upsilon)' from 11.3 (11.3) nsec at (upsilon)' = 0, to 17.0 (17.0) nsec at (upsilon)' = 1, and then to 23.5 (24.0) nsec at (upsilon)' = 2.

Partridge, Harry↗
NASA NTRS1989

The dissociation energy of N2

The requirements for very accurate ab initio quantum chemical prediction of dissociation energies are examined using a detailed investigation of the nitrogen molecule. Although agreement with experiment to within 1 kcal/mol is not achieved even with the most elaborate multireference CI (configuration interaction) wave functions and largest basis sets currently feasible, it is possible to obtain agreement to within about 2 kcal/mol, or 1 percent of the dissociation energy. At this level it is necessary to account for core-valence correlation effects and to include up to h-type functions in the basis. The effect of i-type functions, the use of different reference configuration spaces, and basis set superposition error were also investigated. After discussing these results, the remaining sources of error in our best calculations are examined.

Almloef, Jan↗
NASA NTRS1989

The dissociation energy of N2

The requirements for very accurate ab initio quantum chemical prediction of dissociation energies are examined using a detailed investigation of the nitrogen molecule. Although agreement with experiment to within 1 kcal/mol is not achieved even with the most elaborate multireference CI (configuration interaction) wave functions and largest basis sets currently feasible, it is possible to obtain agreement to within about 2 kcal/mol, or 1 percent of the dissociation energy. At this level it is necessary to account for core-valence correlation effects and to include up to h-type functions in the basis. The effect of i-type functions, the use of different reference configuration spaces, and basis set superposition error were also investigated. After discussing these results, the remaining sources of error in our best calculations are examined.

Almlof, Jan↗
NASA NTRS2011

An Estimate of the Size and Shape of Sunspot Cycle 24 Based on its Early Cycle Behavior using the Hathaway-Wilson-Reichmann Shape-Fitting Function

On the basis of 12-month moving averages (12-mma) of monthly mean sunspot number (R), sunspot cycle 24 had its minimum amplitude (Rm = 1.7) in December 2008. At 12 mo past minimum, R measured 8.3, and at 18 mo past minimum, it measured 16.4. Thus far, the maximum month-to-month rate of rise in 12-mma values of monthly mean sunspot number (AR(t) max) has been 1.7, having occurred at elapsed times past minimum amplitude (t) of 14 and 15 mo. Compared to other sunspot cycles of the modern era, cycle 24?s Rm and AR(t) max (as observed so far) are the smallest on record, suggesting that it likely will be a slow-rising, long-period sunspot cycle of below average maximum amplitude (RM). Supporting this view is the now observed relative strength of cycle 24?s geomagnetic minimum amplitude as measured using the 12-mma value of the aa-geomagnetic index (aam = 8.4), which also is the smallest on record, having occurred at t equals 8 and 9 mo. From the method of Ohl (the inferred preferential association between RM and aam), one predicts RM = 55 +/- 17 (the ?1 se prediction interval) for cycle 24. Furthermore, from the Waldmeier effect (the inferred preferential association between the ascent duration (ASC) and RM) one predicts an ASC longer than 48 mo for cycle 24; hence, maximum amplitude occurrence should be after December 2012. Application of the Hathaway-Wilson-Reichmann shape-fitting function, using an RM = 70 and ASC = 56 mo, is found to adequately fit the early sunspot number growth of cycle 24.

Wilson, Robert M.↗
DOE OSTI2021

Improving scalability of electronic structure code for molecular simulations in the presence of environment

A scalable density functional electronic code with Gaussian basis set, called UTEP-NRLMOL, is developed to perform simulations of molecular systems in the presence of the environment with particular attention to the memory requirements. In the electronic structure calculations, the memory and computation time are proportional to the number of atoms. Memory requirements for density functional calculations scale as N*N, where N is the number of atoms. While the recent advances in HPC offer platforms with large numbers of cores, the limited amount of memory available on a given node and poor scalability of the electronic structure codes hinder their efficient usage of these platforms. We have introduced new scaling and parallelization paradigms using MPI-3 shared-memory functionality combined with usage of sparse algebra and storage of matrices in sparse format. This extends the range of applicability of the UTEP-NRLMOL code to large systems over 10,000 atoms, or using up to 67,000 basis functions, and making use of HPC architectures using over 6,000 processors utilizing all available cores. We have also interfaced code with effective fragment potential and polarizable continuum model libraries. The code was used in simulations of several applications which are published in reputed scientific journals.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Forces from Stochastic Density Functional Theory under Nonorthogonal Atom-Centered Basis Sets

We develop a formalism for calculating forces on the nuclei within the linear-scaling stochastic density functional theory (sDFT) in a nonorthogonal atom-centered basis set representation (Fabian et al. Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2019, 9, e1412, 10.1002/wcms.1412) and apply it to the Tryptophan Zipper 2 (Trp-zip2) peptide solvated in water. We use an embedded-fragment approach to reduce the statistical errors (fluctuation and systematic bias), where the entire peptide is the main fragment and the remaining 425 water molecules are grouped into small fragments. We analyze the magnitude of the statistical errors in the forces and find that the systematic bias is of the order of 0.065 eV/Å (~1.2 × 10 -3 E h / a 0 ) when 120 stochastic orbitals are used, independently of system size. This magnitude of bias is sufficiently small to ensure that the bond lengths estimated by stochastic DFT (within a Langevin molecular dynamics simulation) will deviate by less than 1% from those predicted by a deterministic calculation.

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

A Theoretical Benchmark of the Geometric and Optical Properties for 3d Transition Metal Nanoclusters via Density Functional Theory

Understanding structure–property relationships in atomically precise metal nanoclusters is vital in finding selective and tunable catalysts. Here, in this study, density functional theory (DFT) was used to benchmark seven exchange correlation functionals at different basis sets for 17 atomically precise nanoclusters against experimentally determined geometries, band gaps, and optical gaps. The set contains both monometallic and bimetallic clusters that possess at least two types of 3d transition metals (specifically, Cu, Ni, Fe, or Co). The benchmark highlights that PBE0 is a good functional to use regardless of the basis set, and Minnesota functionals do well with respect to specific metals. Further, while long-range corrected functionals overestimate band and optical gaps, they model absorption features better than the other considered functionals. The study additionally looks at the photoinduced hydrogen evolution reaction (HER) and the CO 2 reduction mechanism on nanoclusters reported from the literature.

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

Exploring metastable states in UO 2 using hybrid functionals and dynamical mean field theory

A detailed exploration of the f-atomic orbital occupancy space for UO2 is performed using a first principles approach based on density functional theory (DFT), employing a full hybrid functional within a systematic basis set. Specifically, the PBE0 functional is combined with an occupancy biasing scheme implemented in a wavelet-based algorithm which is adapted to large supercells. The results are compared with previous DFT + U calculations reported in the literature, while dynamical mean field theory is also performed to provide a further base for comparison. This work shows that the computational complexity of the energy landscape of a correlated f-electron oxide is much richer than has previously been demonstrated. The resulting calculations provide evidence of the existence of multiple previously unexplored metastable electronic states of UO 2 , including those with energies which are lower than previously reported ground states.

36 MATERIALS SCIENCE↗
DOE OSTI2020

The role of high-order electron correlation effects in a model system for non-valence correlation-bound anions

The diffusion Monte Carlo (DMC), auxiliary field quantum Monte Carlo (AFQMC), and equation-of-motion coupled cluster (EOM-CC) methods are used to calculate the electron binding energy (EBE) of the non-valence anion state of a model (H2O)4 cluster. Two geometries are considered, one at which the anion is unbound and the other at which it is bound in the Hartree–Fock (HF) approximation. It is demonstrated that DMC calculations can recover from the use of a HF trial wave function that has collapsed onto a discretized continuum solution, although larger EBEs are obtained when using a trial wave function for the anion that provides a more realistic description of the charge distribution and, hence, of the nodal surface. For the geometry at which the cluster has a non-valence correlation-bound anion, both the inclusion of triples in the EOM-CC method and the inclusion of supplemental diffuse d functions in the basis set are important. DMC calculations with suitable trial wave functions give EBE values in good agreement with our best estimate EOM-CC result. AFQMC using a trial wave function for the anion with a realistic electron density gives a value of the EBE nearly identical to the EOM-CC result when using the same basis set. For the geometry at which the anion is bound in the HF approximation, the inclusion of triple excitations in the EOM-CC calculations is much less important. The best estimate EOM-CC EBE value is in good agreement with the results of DMC calculations with appropriate trial wave functions.

Upadhyay, Shiv (ORCID:0000000285010501)↗
NASA NTRS1978

Calculation of electrostatic fields in periodic structures of complex shape

A universal algorithm is presented for calculating electrostatic fields in an infinite periodic structure consisting of electrodes of arbitrary shape which are located in mirror-symmetrical manner along the axis of electron-beam propagation. The method is based on the theory of R-functions, and the differential operators which are derived on the basis of the functions. Numerical results are presented and the accuracy of the results is examined.

Kravchenko, V. F.↗
DOE OSTI2023

Exchange correlation potentials from full configuration interaction in a Slater orbital basis

Ryabinkin–Kohut–Staroverov (RKS) theory builds a bridge between wave function theory and density functional theory by using quantities from the former to produce accurate exchange-correlation potentials needed by the latter. In this work, the RKS method is developed and tested alongside Slater atomic orbital basis functions for the first time. To evaluate this approach, full configuration interaction computations in the Slater orbital basis are employed to give quality input to RKS, allowing full correlation to be present along with correct nuclei cusps and asymptotic decay of the wavefunction. SlaterRKS is shown to be an efficient algorithm to arrive at exchange-correlation potentials without unphysical artifacts in moderately-sized basis sets. Furthermore, enforcement of the nuclear cusp conditions will be shown to be vital for the success of the Slater-basis RKS method. As a result, examples of weakly and strongly correlated molecular systems will demonstrate the main features of SlaterRKS.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Influence of the complete basis set approximation, tight weighted-core, and diffuse functions on the DLPNO-CCSD(T1) atomization energies of neutral H,C,O-compounds

The impact of complete basis set extrapolation schemes (CBS), diffuse functions, and tight weighted core functions on enthalpies of formation predicted via the DLPNO-CCSD(T1) reduced Feller Peterson-Dixon approach has been examined for neutral H,C,O-compounds. All tested three-point (TZ/QZ/5Z) extrapolation schemes result in mean unsigned deviation (MUD) below 2 kJ mol -1 relative to the experiment. Here, the two-point QZ/5Z and TZ/QZ CBS 1/$l^3_{max}$ extrapolation schemes are inferior to their inverse power counterpart (1/($l_{max}$ + 1/2) 4 ) by 1.3 and 4.3 kJ mol -1 . The CBS extrapolated frozen core atomization energies are insensitive (within 1 kJ mol -1 ) to augmentation of the basis set with tight weighted core functions. The core-valence correlation effects converge already at triple-ζ, although double- ζ/triple- ζ CBS extrapolation performs better and is recommended. The effect of diffuse function augmentation converges slowly, and cannot be reproduced with double- ζ or triple- ζ calculations as these are plagued with basis set superposition and incompleteness errors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1987

On the bond distance in methane

The equilibrium bond distance in methane was optimized using coupled-pair functional and contracted CI wave functions, and a Gaussian basis that includes g-type functions on carbon and d-type functions on hydrogen. The resulting bond distance, when corrected for core-valence correlation effects, agrees with the experimental value of 2.052 a(0) to within the experimental uncertainty of 0.002 a(0). The main source of error in the best previous studies, which showed discrepancies with experiment of 0.007 a(0) is shown to be basis set incompleteness. In particular, it is important that the basis set be close to saturation, at least for the lower angular quantum numbers.

Bowen-Jenkins, Philippa↗