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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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At least 541 records · Page 30
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Collective motion conceals fitness differences in crowded cellular populations

Many cellular populations are tightly packed, such as microbial colonies and biofilms, or tissues and tumours in multicellular organisms. The movement of one cell in these crowded assemblages requires motion of others, so that cell displacements are correlated over many cell diameters. Whenever movement is important for survival or growth, these correlated rearrangements could couple the evolutionary fate of different lineages. However, little is known about the interplay between mechanical forces and evolution in dense cellular populations. Here, by tracking slower-growing clones at the expanding edge of yeast colonies, we show that the collective motion of cells prevents costly mutations from being weeded out rapidly. Joint pushing by neighbouring cells generates correlated movements that suppress the differential displacements required for selection to act. This mechanical screening of fitness differences allows slower-growing mutants to leave more descendants than expected under non-mechanical models, thereby increasing their chance for evolutionary rescue. Our work suggests that, in crowded populations, cells cooperate with surrounding neighbours through inevitable mechanical interactions. This effect has to be considered when predicting evolutionary outcomes, such as the emergence of drug resistance or cancer evolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Fine-scale contemporary recombination variation and its fitness consequences in adaptively diverging stickleback fish

Despite deep evolutionary conservation, recombination rates vary greatly across the genome and among individuals, sexes and populations. Yet the impact of this variation on adaptively diverging populations is not well understood. Here we characterized fine-scale recombination landscapes in an adaptively divergent pair of marine and freshwater populations of threespine stickleback from River Tyne, Scotland. Through whole-genome sequencing of large nuclear families, we identified the genomic locations of almost 50,000 crossovers and built recombination maps for marine, freshwater and hybrid individuals at a resolution of 3.8 kb. We used these maps to quantify the factors driving variation in recombination rates. We found strong heterochiasmy between sexes but also differences in recombination rates among ecotypes. Hybrids showed evidence of significant recombination suppression in overall map length and in individual loci. Recombination rates were lower not only within individual marine–freshwater-adaptive loci, but also between loci on the same chromosome, suggesting selection on linked gene ‘cassettes’. Through temporal sampling along a natural hybrid zone, we found that recombinants showed traits associated with reduced fitness. Our results support predictions that divergence in cis-acting recombination modifiers, whose functions are disrupted in hybrids, may play an important role in maintaining differences among adaptively diverging populations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Arbuscular mycorrhizal fungi equalize differences in plant fitness and facilitate plant species coexistence through niche differentiation

Mycorrhizal fungi are essential to the establishment of the vast majority of plant species but are often conceptualized with contradictory roles in plant community assembly. On the one hand, host-specific mycorrhizal fungi may allow a plant to be competitively dominant by enhancing growth. On the other hand, host-specific mycorrhizal fungi with different functional capabilities may increase nutrient niche partitioning, allowing plant species to coexist. Here, to resolve the balance of these two contradictory forces, we used a controlled greenhouse study to manipulate the presence of two main types of mycorrhizal fungus, ectomycorrhizal fungi and arbuscular mycorrhizal fungi, and used a range of conspecific and heterospecific competitor densities to investigate the role of mycorrhizal fungi in plant competition and coexistence. We find that the presence of arbuscular mycorrhizal fungi equalizes fitness differences between plants and stabilizes competition to create conditions for host species coexistence. Furthermore, our results show how below-ground mutualisms can shift outcomes of plant competition and that a holistic view of plant communities that incorporates their mycorrhizal partners is important in predicting plant community dynamics.

09 BIOMASS FUELS↗
DOE OSTI2022

Learning protein fitness models from evolutionary and assay-labeled data

Machine learning-based models of protein fitness typically learn from either unlabeled, evolutionarily related sequences or variant sequences with experimentally measured labels. For regimes where only limited experimental data are available, recent work has suggested methods for combining both sources of information. Toward that goal, we propose a simple combination approach that is competitive with, and on average outperforms more sophisticated methods. Our approach uses ridge regression on site-specific amino acid features combined with one probability density feature from modeling the evolutionary data. Within this approach, we find that a variational autoencoder-based probability density model showed the best overall performance, although any evolutionary density model can be used. Moreover, our analysis highlights the importance of systematic evaluations and sufficient baselines.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

VarIabiLity seLection of AstrophysIcal sources iN PTF (VILLAIN): I. Structure function fits to 71 million objects

Light-curve variability is well-suited to characterizing objects in surveys with high cadence and a long baseline. This is especially relevant in view of the large datasets to be produced by the Vera C. Rubin Observatory Legacy Survey of Space and Time (LSST). We aim to determine variability parameters for objects in the Palomar Transient Factory (PTF) and explore differences between quasars (QSOs), stars, and galaxies. We relate variability and colour information in preparation for future surveys. We fit joint likelihoods to structure functions (SFs) of 71 million PTF light curves with a Markov chain Monte Carlo method. For each object, we assume a power-law SF and extract two parameters: the amplitude on timescales of one year, A, and a power-law index, γ. With these parameters and colours in the optical (Pan-STARRS1) and mid-infrared (WISE), we identify regions of parameter space dominated by different types of spectroscopically confirmed objects from SDSS. Candidate QSOs, stars, and galaxies are selected to show their parameter distributions. QSOs show high-amplitude variations in the R band, and the highest γ values. Galaxies have a broader range of amplitudes and their variability shows relatively little dependency on timescale. With variability and colours, we achieve a photometric selection purity of 99.3% for QSOs. Even though hard cuts in monochromatic variability alone are not as effective as seven-band magnitude cuts, variability is useful in characterizing object subclasses. Through variability, we also find QSOs that were erroneously classified as stars in the SDSS. We discuss perspectives and computational solutions in view of the upcoming LSST.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

Atomistic force field for alumina fit to density functional theory

We present a force field for bulk alumina (Al{sub 2}O{sub 3}), which has been parametrized by fitting the energies, forces, and stresses of a large database of reference configurations to those calculated with density functional theory (DFT). We use a functional form that is simpler and computationally more efficient than some existing models of alumina parametrized by a similar technique. Nevertheless, we demonstrate an accuracy of our potential that is comparable to those existing models and to DFT. We present calculations of crystal structures and energies, elastic constants, phonon spectra, thermal expansion, and point defect formation energies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Permutation invariant polynomial neural network approach to fitting potential energy surfaces. II. Four-atom systems

A rigorous, general, and simple method to fit global and permutation invariant potential energy surfaces (PESs) using neural networks (NNs) is discussed. This so-called permutation invariant polynomial neural network (PIP-NN) method imposes permutation symmetry by using in its input a set of symmetry functions based on PIPs. For systems with more than three atoms, it is shown that the number of symmetry functions in the input vector needs to be larger than the number of internal coordinates in order to include both the primary and secondary invariant polynomials. This PIP-NN method is successfully demonstrated in three atom-triatomic reactive systems, resulting in full-dimensional global PESs with average errors on the order of meV. These PESs are used in full-dimensional quantum dynamical calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Electrically detected magnetic resonance modeling and fitting: An equivalent circuit approach

The physics of electrically detected magnetic resonance (EDMR) quadrature spectra is investigated. An equivalent circuit model is proposed in order to retrieve crucial information in a variety of different situations. This model allows the discrimination and determination of spectroscopic parameters associated to distinct resonant spin lines responsible for the total signal. The model considers not just the electrical response of the sample but also features of the measuring circuit and their influence on the resulting spectral lines. As a consequence, from our model, it is possible to separate different regimes, which depend basically on the modulation frequency and the RC constant of the circuit. In what is called the high frequency regime, it is shown that the sign of the signal can be determined. Recent EDMR spectra from Alq{sub 3} based organic light emitting diodes, as well as from a-Si:H reported in the literature, were successfully fitted by the model. Accurate values of g-factor and linewidth of the resonant lines were obtained.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Cholesky-decomposed density MP2 with density fitting: Accurate MP2 and double-hybrid DFT energies for large systems

Our recently developed QQR-type integral screening is introduced in our Cholesky-decomposed pseudo-densities Møller-Plesset perturbation theory of second order (CDD-MP2) method. We use the resolution-of-the-identity (RI) approximation in combination with efficient integral transformations employing sparse matrix multiplications. The RI-CDD-MP2 method shows an asymptotic cubic scaling behavior with system size and a small prefactor that results in an early crossover to conventional methods for both small and large basis sets. We also explore the use of local fitting approximations which allow to further reduce the scaling behavior for very large systems. The reliability of our method is demonstrated on test sets for interaction and reaction energies of medium sized systems and on a diverse selection from our own benchmark set for total energies of larger systems. Timings on DNA systems show that fast calculations for systems with more than 500 atoms are feasible using a single processor core. Parallelization extends the range of accessible system sizes on one computing node with multiple cores to more than 1000 atoms in a double-zeta basis and more than 500 atoms in a triple-zeta basis.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Robust and efficient variational fitting of Fock exchange

We propose a new variational fitting approach for Fock exchange that requires only the calculation of analytical three-center electron repulsion integrals. It relies on localized molecular orbitals and Hermite Gaussian auxiliary functions. The working equations along with a detailed description of the implementation are presented. The computational performance of the new algorithm is analyzed by benchmark calculations on systems with different dimensionality. Comparison with standard four-center and three-center electron repulsion integral Hartree-Fock calculations shows an excellent accuracy-performance relation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Electronic coupling calculations with transition charges, dipoles, and quadrupoles derived from electrostatic potential fitting

A transition charge, dipole, and quadrupole from electrostatic potential (TrESP-CDQ) method for electronic coupling calculations is proposed. The TrESP method is based on the classical description of electronic Coulomb interaction between transition densities for individual molecules. In the original TrESP method, only the transition charge interactions were considered as the electronic coupling. In the present study, the TrESP method is extended to include the contributions from the transition dipoles and quadrupoles as well as the transition charges. Hence, the self-consistent transition density is employed in the ESP fitting procedure. To check the accuracy of the present approach, several test calculations are performed to a helium dimer, a methane dimer, and an ethylene dimer. As a result, the TrESP-CDQ method gives a much improved description of the electronic coupling, compared with the original TrESP method. The calculated results also show that the self-consistent treatment to the transition densities contributes significantly to the accuracy of the electronic coupling calculations. Based on the successful description of the electronic coupling, the contributions to the electronic coupling are also analyzed. This analysis clearly shows a negligible contribution of the transition charge interaction to the electronic coupling. Hence, the distribution of the transition density is found to strongly influence the magnitudes of the transition charges, dipoles, and quadrupoles. The present approach is useful for analyzing and understanding the mechanism of excitation-energy transfer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Effect of Sn on the optical band gap determined using absorption spectrum fitting method

We report the preparation and the optical studies on tellurium rich glasses thin films. The thin films of Se{sub 30}Te{sub 70-x} Sn{sub x} system for x= 0, 1.5, 2.5 and 4.5 glassy alloys prepared by melt quenching technique are deposited on the glass substrate using vacuum thermal evaporation technique. The analysis of absorption spectra in the spectral range 400nm–4000 nm at room temperature obtained from UV-VIS-NIR spectrophotometer [Perkin Elmer Lamda-750] helps us in the optical characterization of the thin films under study. The absorption spectrum fitting method is applied by using the Tauc’s model for estimating the optical band gap and the width of the band tail of the thin films. The optical band gap is calculated and is found to decrease with the Sn content.

36 MATERIALS SCIENCE↗
DOE OSTI2015

On the use of Abelian point group symmetry in density-fitted local MP2 using various types of virtual orbitals

Electron correlation methods based on symmetry-adapted canonical Hartree-Fock orbitals can be speeded up significantly in the well known group theoretical manner, using the fact that integrals vanish unless the integrand is totally symmetric. In contrast to this, local electron correlation methods cannot benefit from such simplifications, since the localized molecular orbitals (LMOs) generally do not transform according to irreducible representations of the underlying point group symmetry. Instead, groups of LMOs become symmetry-equivalent and this can be exploited to accelerate local calculations. We describe an implementation of such a symmetry treatment for density-fitted local Møller-Plesset perturbation theory, using various types of virtual orbitals: Projected atomic orbitals, orbital specific virtuals, and pair natural orbitals. The savings by the symmetry treatment are demonstrated by calculations for several large molecules having different point group symmetries. Benchmarks for the parallel execution efficiency of our method are also presented.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Determination of vibrational and rotational temperatures in highly constricted nitrogen plasmas by fitting the second positive system of N{sub 2} molecules

Highly constricted plasmas are an active research area because of their ability to generate high activity of plasma beams, which exhibit potential in applications of material processing and film deposition. In this study, optical emission spectroscopy was used to study the highly constricted nitrogen plasma created at low pressure. The vibrational and rotational temperatures of molecules were determined by fitting the second positive system of nitrogen molecule. Under the conditions of the power densities as high as 7 ∼ 85 W/cm{sup 3} and the pressures of 2 ∼ 200 Pa, the determined rotational temperature was found to be relatively low, increasing from 350 to 700 K and the vibrational temperature keeping at ∼ 5000 K. The analysis of dissipated power revealed that ∼ 80 % of input power is dissipated for the nitrogen molecule dissociation and the creation/loss of ions at the tube wall, producing an as high as 10{sup 12} ∼ 10{sup 13} cm{sup −3} plasma with the nitrogen dissociation degrees of 2%∼15%. With the increase in the discharge pressure, more input power was found to be dissipated in the dissociation of nitrogen molecules instead of creation of ions, resulting in a higher density of radicals.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Phase change alloy viscosities down to T{sub g} using Adam-Gibbs-equation fittings to excess entropy data: A fragile-to-strong transition

A striking anomaly in the viscosity of Te{sub 85}Ge{sub 15} alloys noted by Greer and coworkers from the work of Neumann et al. is reminiscent of the equally striking comparison of liquid tellurium and water anomalies documented long ago by Kanno et al. In view of the power laws that are used to fit the data on water, we analyze the data on Te{sub 85}Ge{sub 15} using the Speedy-Angell power-law form, and find a good account with a singularity T{sub s} only 25 K below the eutectic temperature. However, the heat capacity data in this case are not diverging, but instead exhibit a sharp maximum like that observed in fast cooling in the Molinero-Moore model of water. Applying the Adam-Gibbs viscosity equation to these calorimetric data, we find that there must be a fragile-to-strong liquid transition at the heat capacity peak temperature, and then predict the 'strong' liquid course of the viscosity down to T{sub g} at 406 K (403.6 K at 20 K min{sup −1} in this study). Since crystallization can be avoided by moderately fast cooling in this case, we can check the validity of the extrapolation by making a direct measurement of fragility at T{sub g}, using differential scanning calorimetric techniques, and then comparing with the value from the extrapolated viscosity at T{sub g}. The agreement is encouraging, and prompts discussion of relations between water and phase change alloy anomalies.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Analytical gradients of the state-average complete active space self-consistent field method with density fitting

An efficient implementation of the state-averaged complete active space self-consistent field (SA-CASSCF) gradients employing density fitting (DF) is presented. The DF allows a reduction both in scaling and prefactors of the different steps involved. The performance of the algorithm is demonstrated on a set of molecules ranging up to an iron-Heme b complex which with its 79 atoms and 811 basis functions is to our knowledge the largest SA-CASSCF gradient computed. For smaller systems where the conventional code could still be used as a reference, both the linear response calculation and the gradient formation showed a clear timing reduction and the overall cost of a geometry optimization is typically reduced by more than one order of magnitude while the accuracy loss is negligible.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Determination of morphological characteristics of metallic nanoparticles based on modified Maxwell-Garnett fitting of optical responses

A modified effective medium theory (MEMT) is introduced to determine morphological characteristics and the volume fraction of colloidal metallic nanoparticles. By analyzing the optical absorption spectra of gold nanoparticles (NPs), this model is used to determine the distribution of prolate and oblate NPs and to demonstrate the presence of spherical NPs. In addition to interband transition, the model takes into account the longitudinal and transversal surface plasmon resonances. The results predicted by the MEMT theory were found to be in very good agreement with the shape distributions obtained by transmission electron microscopy. We found that fitting optical absorption spectra using MEMT provides a robust tool for measuring the shape and concentration of metallic NPs.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

On the elimination of the electronic structure bottleneck in on the fly nonadiabatic dynamics for small to moderate sized (10-15 atom) molecules using fit diabatic representations based solely on ab initio electronic structure data: The photodissociation of phenol

In this work, we demonstrate that for moderate sized systems, here a system with 13 atoms, global coupled potential energy surfaces defined for several electronic states over a wide energy range and for distinct regions of nuclear coordinate space characterized by distinct electron configurations, can be constructed with precise energetics and an excellent description of non-adiabatic interactions in all regions. This is accomplished using a recently reported algorithm for constructing quasi-diabatic representations, H{sup d}, of adiabatic electronic states coupled by conical intersections. In this work, the algorithm is used to construct an H{sup d} to describe the photodissociation of phenol from its first and second excited electronic states. The representation treats all 33 internal degrees of freedom in an even handed manner. The ab initio adiabatic electronic structure data used to construct the fit are obtained exclusively from multireference configuration interaction with single and double excitation wave functions comprised of 88 × 10{sup 6} configuration state functions, at geometries determined by quasi-classical trajectories. Since the algorithm uses energy gradients and derivative couplings in addition to electronic energies to construct H{sup d}, data at only 7379 nuclear configurations are required to construct a representation, which describes all nuclear configurations involved in H atom photodissociation to produce the phenoxyl radical in its ground or first excited electronic state, with a mean unsigned energy error of 202.9 cm{sup −1} for electronic energies <60 000 cm{sup −1}.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗