Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “GENETICS”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 631 records · Page 35
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Finite-Temperature Structures of Supported Subnanometer Catalysts Inferred via Statistical Learning and Genetic Algorithm-Based Optimization

Single-atom catalysts (SACs) minimize noble metal utilization and can alter the activity and selectivity of supported metal nanoparticles. However, the morphology of active centers, including single atoms and subnanometer clusters of a few atoms, remains elusive due to experimental challenges. The computational cost to describe numerous cluster shapes and sizes makes direct first-principles calculations impractical. We present a computational framework to enable structure determination for single-atom and subnanometer cluster catalysts. As a case study, we obtained the low energy structures of Pd n (n = 1-21) clusters supported on CeO 2 (111), which are critical components of automobile three-way catalysts. Trained on density functional theory data, a three-dimensional cluster expansion is established using statistical learning to describe the Hamiltonian and predict energies of supported Pdn clusters of any structure. Low energy stable and metastable structures are identified using a Metropolis Monte Carlo-based genetic algorithm in the canonical ensemble at 300 K. We observe that supported single atoms sinter to form bilayer clusters and large cluster isomers share similarities in both shape and energy, and elucidate the significance of the support and microstructure on cluster stability. We discovered a simple surrogate structure-energy model, where the energy per atom scales with the square root of the average first coordination number, which can be used to estimate energies and compare the stability of clusters. Our framework, applicable to any metal/support system, fills an important methodological gap to predict the stability of supported metal catalysts in the subnanometer regime.

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

Adsorption Hysteresis Under Control: Tuning Host–Guest Interactions via a Genetic Algorithm

Mesoporous adsorbent materials offer a large volumetric capacity; however, cyclic adsorption/desorption processes in these systems often suffer from hysteresis and may require a significant pressure swing to access this capacity. To mitigate hysteresis, a proposed strategy is to include nucleation sites on the walls of the mesoporous material to facilitate droplet and bubble formation, lowering the free energy barriers to the respective phase transitions. It is unclear, however, what combination of adsorbate− adsorbent interactions and spatial patterning would be beneficial for a given application, considering that improvements to some sorption properties may come at the expense of other attributes. To understand these interconnected observables, we examine two model systems, planar-slit and cylindrical pores with tunable interaction sites, using GPU-accelerated transition matrix Monte Carlo simulations. The simulations provide a free energy map of the pressure−adsorption space in a matter of minutes, which we use to track adsorption isotherm characteristics as a function of adsorbent properties. We then leverage the rapid acquisition of simulation data to construct a genetic algorithm to iteratively modify interaction sites of the slit-pore wall to minimize the hysteresis of this system without sacrificing uptake. We find that the adsorption branch of the isotherm is easily modulated via the average host−guest interaction strength, but desorption is only adjustable if there is a suitable bubble nucleation site. Within the context of a slit-pore system, we identify relative interaction strengths and patch sizes required to gain control over both branches of the hysteresis loop.

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

Modeling Wavelength Dependent Mid-infrared (5.5–25 μm) Optical Constants of Silicate Glasses: A Genetic Algorithm Approach

Wavelength-dependent mid-infrared (400–1,800 cm -1 ; 5.56–25 μm) optical constants (real and imaginary indices of refraction; n and k) are determined using reflectance spectra at a spectral sampling of 4 cm -1 for several silicate glasses of varying SiO 2 wt% which include (a) basaltic volcanic glass from Kilauea, Hawaii, (b) synthetic andesite, (c) two synthetic dacites, (d) obsidian volcanic glass from Mount Lassen, California, (e) synthetic rhyodacite, and (f) rhyolitic volcanic glass from Mexico. Because glasses are optically isotropic, no specific orientation was required for spectral measurements, and polished glass samples were measured at random orientations using micro-FTIR spectrometer. Lorentz-Lorenz dispersion theory and Fresnel reflectance model for high symmetry materials were used to model the optical constants by optimizing oscillator parameters in modeled spectra to match laboratory spectra. A genetic algorithm (GA) approach automatically finds the natural oscillators and their parameters for each spectrum, and then uses these parameters in a non-linear least squares optimization routine. The study compared spectral parameters such as Christiansen feature, reststrahlen bands (RBs), and the peaks centered around 860–1,100 (peak 1) and 400–480 cm -1 (peak 2) of n and k to their respective SiO 2 wt% of the glasses. CF, RBs, peak 1 of n and k, and peak 2 of n shift to higher wavenumbers with increased SiO 2 wt%, whereas peak 2 of k shifts to lower wavenumbers with increased SiO 2 wt%. Derived optical constants of these glasses will improve quantitative abundance mapping of volcanic materials on the surfaces of silicate targets in the Solar System.

58 GEOSCIENCES↗
DOE OSTI2019

Hair Proteome Variation at Different Body Locations on Genetically Variant Peptide Detection for Protein-Based Human Identification

Abstract Human hair contains minimal intact nuclear DNA for human identification in forensic and archaeological applications. In contrast, proteins offer a pathway to exploit hair evidence for human identification owing to their persistence, abundance, and derivation from DNA. Individualizing single nucleotide polymorphisms (SNPs) are often conserved as single amino acid polymorphisms in genetically variant peptides (GVPs). Detection of GVP markers in the hair proteome via high-resolution tandem mass spectrometry permits inference of SNPs with known statistical probabilities. To adopt this approach for forensic investigations, hair proteomic variation and its effects on GVP identification must first be characterized. This research aimed to assess variation in single-inch head, arm, and pubic hair, and discover body location-invariant GVP markers to distinguish individuals. Comparison of protein profiles revealed greater body location-specific variation in keratin-associated proteins and intracellular proteins, allowing body location differentiation. However, robust GVP markers derive primarily from keratins that do not exhibit body location-specific differential expression, supporting GVP identification independence from hair proteomic variation at the various body locations. Further, pairwise comparisons of GVP profiles with 8 SNPs demonstrated greatest interindividual variation and high intraindividual consistency, enabling similar differentiative potential of individuals using single hairs irrespective of body location origin.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Transitions in genetic toggle switches driven by dynamic disorder in rate coefficients

In biochemical systems, intrinsic noise may drive the system switch from one stable state to another. We investigate how kinetic switching between stable states in a bistable network is influenced by dynamic disorder, i.e., fluctuations in the rate coefficients. Using the geometric minimum action method, we first investigate the optimal transition paths and the corresponding minimum actions based on a genetic toggle switch model in which reaction coefficients draw from a discrete probability distribution. For the continuous probability distribution of the rate coefficient, we then consider two models of dynamic disorder in which reaction coefficients undergo different stochastic processes with the same stationary distribution. In one, the kinetic parameters follow a discrete Markov process and in the other they follow continuous Langevin dynamics. We find that regulation of the parameters modulating the dynamic disorder, as has been demonstrated to occur through allosteric control in bistable networks in the immune system, can be crucial in shaping the statistics of optimal transition paths, transition probabilities, and the stationary probability distribution of the network.

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

Determining best practices for using genetic algorithms in molecular discovery

Genetic algorithms (GAs) are a powerful tool to search large chemical spaces for inverse molecular design. However, GAs have multiple hyperparameters that have not been thoroughly investigated for chemical space searches. In this tutorial, we examine the general effects of a number of hyperparameters, such as population size, elitism rate, selection method, mutation rate, and convergence criteria, on key GA performance metrics. Here, we show that using a self-termination method with a minimum Spearman’s rank correlation coefficient of 0.8 between generations maintained for 50 consecutive generations along with a population size of 32, a 50% elitism rate, three-way tournament selection, and a 40% mutation rate provides the best balance of finding the overall champion, maintaining good coverage of elite targets, and improving relative speedup for general use in molecular design GAs.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Multi-Objective Optimization of Uranium Target Assembly–3: A Comparison of Genetic and Traditional Methods

Commonly produced as a byproduct of uranium fission, 99 Mo is a key medical isotope that is in high demand in the United States. An international goal is to switch from medical isotope production technologies that require highly enriched uranium to medical isotope production technologies that require only low-enriched uranium. Niowave Inc. is contributing to this goal by developing an accelerator-driven subcritical assembly called the Uranium Target Assembly (UTA). This work compares the performance of Dakota’s Multi-Objective Genetic Algorithm (MOGA) against traditional sensitivity analysis in the neutronic optimization of the UTA-3 system. The design objectives are k-eigenvalue (k eff ) and natural uranium fission power, which are directly correlated with the amount of 99 Mo produced. Dakota:MOGA did not perform as well as human engineering ingenuity in optimization studies with high numbers of input parameters, such as fuel rod type selection and fuel rod placement. However, Dakota:MOGA did outperform traditional sensitivity analysis in optimization studies with fewer than 20 parameters and revealed the degree to which each parameter influences the optimal design space for k eff and natural uranium fission power (to a lesser extent). As the design model became more complex in the final stage of design, the computational resources required to calculate the design objective values in the Monte Carlo N-Particle transport code from selected input parameter combinations limited Dakota:MOGA’s performance, and, unfortunately, human intervention was required to discern the optimal design space. In conclusion, future work will attempt to reduce computational resource constraints by incorporating areduced-order neutronics model into the optimization cycle.

Accelerator-driven systems↗
DOE OSTI2025

Genetic programming for the nuclear many-body problem: a guide

Genetic Programming (GP) is an evolutionary algorithm that generates computer programs, or mathematical expressions, to solve complex problems. In this Guide, we demonstrate how to use GP to develop surrogate models to mitigate the computational costs of modeling atomic nuclei with ever increasing complexity. The computational burden escalates when uncertainty quantification is pursued, or when observables must be globally computed for thousands of nuclei. By studying three models in which the mean field depends on the total particle density self-consistently, we show that by constructing reduced order models supported by GP one can speed up many-body computations by several orders of magnitude with a negligible loss in accuracy.

dimensionality reduction↗
DOE OSTI2021

Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases

Abstract Online, open access databases for biological knowledge serve as central repositories for research communities to store, find and analyze integrated, multi-disciplinary datasets. With increasing volumes, complexity and the need to integrate genomic, transcriptomic, metabolomic, proteomic, phenomic and environmental data, community databases face tremendous challenges in ongoing maintenance, expansion and upgrades. A common infrastructure framework using community standards shared by many databases can reduce development burden, provide interoperability, ensure use of common standards and support long-term sustainability. Tripal is a mature, open source platform built to meet this need. With ongoing improvement since its first release in 2009, Tripal provides full functionality for searching, browsing, loading and curating numerous types of data and is a primary technology powering at least 31 publicly available databases spanning plants, animals and human data, primarily storing genomics, genetics and breeding data. Tripal software development is managed by a shared, inclusive governance structure including both project management and advisory teams. Here, we report on the most important and innovative aspects of Tripal after 11 years development, including integration of diverse types of biological data, successful collaborative projects across member databases, and support for implementing FAIR principles.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Genetic mapping and prediction of flowering time and plant height in a maize Stiff Stalk MAGIC population

Abstract The Stiff Stalk heterotic pool is a foundation of US maize seed parent germplasm and has been heavily utilized by both public and private maize breeders since its inception in the 1930s. Flowering time and plant height are critical characteristics for both inbred parents and their test crossed hybrid progeny. To study these traits, a 6-parent multiparent advanced generation intercross population was developed including maize inbred lines B73, B84, PHB47 (B37 type), LH145 (B14 type), PHJ40 (novel early Stiff Stalk), and NKH8431 (B73/B14 type). A set of 779 doubled haploid lines were evaluated for flowering time and plant height in 2 field replicates in 2016 and 2017, and a subset of 689 and 561 doubled haploid lines were crossed to 2 testers, respectively, and evaluated as hybrids in 2 locations in 2018 and 2019 using an incomplete block design. Markers were derived from a practical haplotype graph built from the founder whole genome assemblies and genotype-by-sequencing and exome capture-based sequencing of the population. Genetic mapping utilizing an update to R/qtl2 revealed differing profiles of significant loci for both traits between 635 of the DH lines and 2 sets of 570 and 471 derived hybrids. Genomic prediction was used to test the feasibility of predicting hybrid phenotypes based on the per se data. Predictive abilities were highest on direct models trained using the data they would predict (0.55–0.63), and indirect models trained using per se data to predict hybrid traits had slightly lower predictive abilities (0.49–0.55). Overall, this finding is consistent with the overlapping and nonoverlapping significant quantitative trait loci found within the per se and hybrid populations and suggests that selections for phenology traits can be made effectively on doubled haploid lines before hybrid data is available.

Genetics & Heredity↗
DOE OSTI2025

Decoding crops one cell at a time: from cell atlases to single-cell genetics

Understanding the mechanisms underlying key agricultural traits remains a central challenge in crop research, but recent advances in technologies are providing powerful tools to address this issue. Among these, single-cell and spatial transcriptomics have revealed tissue heterogeneity and spatial organization, offering unique insights into cellular gene expression dynamics and the coordinated activity of multiple cell types. These approaches help uncover how specific cell types contribute to agricultural traits and refine candidate loci lists through integration with trait-associated loci. Additionally, single-cell and spatial transcriptomics have the potential to serve as cell-level readout platforms integrating cellular perturbations, enabling high-throughput discovery of causal relationships between genotype and gene expression at the cellular level in plants. Successful implementation will accelerate the identification of key genetic variants for crop improvement. Furthermore we review lessons learned from application of single-cell screening in mammalian cells, highlight major technical and biological barriers to its use in plants, and outline potential strategies to overcome these challenges. Together, the widespread application and integration of single-cell and spatial transcriptomics with other technologies enable not only the descriptive cataloging of cell states but also the causal interrogation of sequence functions and regulatory networks at cell type resolution, ultimately advancing gene function studies and accelerating crop improvement.

Cellular heterogeneity↗
DOE OSTI2025

Targeted genetic manipulation and yeast-like evolutionary genomics in the green alga Auxenochlorella

Auxenochlorella spp. are diploid oleaginous green algae whose streamlined genomes can be readily manipulated by homologous recombination, making them highly amenable to discovery research and bioengineering. Vegetatively diploid organisms experience specific evolutionary phenomena, including allodiploid hybridization, mitotic recombination, loss-of-heterozygosity, and aneuploidy; however, studies of these forces have largely focused on yeasts. Here, we present a telomere-to-telomere phased diploid genome assembly of Auxenochlorella UTEX 250-A (haploid length 22 Mb) and introduce a genetic toolkit for site-specific manipulation of the nuclear genome in multiple strains, featuring several selectable markers, inducible promoters, and fluorescent reporters for protein localization. UTEX 250-A is an allodiploid hybrid of Auxenochlorella protothecoides and Auxenochlorella symbiontica, two species differentiated by extensive chromosomal rearrangements. UTEX 250-A haplotypes are a mosaic of each parental species following mitotic recombination, and two chromosomes are trisomic. Loss-of-heterozygosity events are pervasive across Auxenochlorella and can evolve rapidly in the laboratory. High-quality structural annotation yielded ∼7,500 genes per haplotype. Auxenochlorella have experienced gene family loss and reduction, including core photosynthesis genes, and exhibit periodic adenine and cytosine methylation at promoters and gene bodies, respectively. Approximately 10% of genes, especially those involved in DNA repair and sex, overlap antisense long noncoding RNAs, which may participate in a regulatory mechanism. We demonstrate the utility of Auxenochlorella for fundamental research by knockout of a chlorophyll biosynthesis enzyme, and confirm one trisomy by allele-specific transformation. These results demonstrate the generality of several evolutionary forces associated with vegetative diploidy and provide a foundation for the use of Auxenochlorella as a reference organism.

CHL27↗
DOE OSTI2021

The genetic basis of phage susceptibility, cross-resistance and host-range in Salmonella

Though bacteriophages (phages) are known to play a crucial role in bacterial fitness and virulence, our knowledge about the genetic basis of their interaction, cross-resistance and host-range is sparse. Here, we employed genome-wide screens in Salmonella enterica serovar Typhimurium to discover host determinants involved in resistance to eleven diverse lytic phages including four new phages isolated from a therapeutic phage cocktail. We uncovered 301 diverse host factors essential in phage infection, many of which are shared between multiple phages demonstrating potential cross-resistance mechanisms. We validate many of these novel findings and uncover the intricate interplay between RpoS, the virulence-associated general stress response sigma factor and RpoN, the nitrogen starvation sigma factor in phage cross-resistance. Finally, the infectivity pattern of eleven phages across a panel of 23 genome sequenced Salmonella strains indicates that additional constraints and interactions beyond the host factors uncovered here define the phage host range.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

A novel synthetic-genetic-array–based yeast one-hybrid system for high discovery rate and short processing time

Eukaryotic gene expression is often tightly regulated by interactions between transcription factors (TFs) and their DNA cis targets. Yeast one-hybrid (Y1H) is one of the most extensively used methods to discover these interactions. We developed a high-throughput meiosis-directed yeast one-hybrid system using the Magic Markers of the synthetic genetic array analysis. The system has a transcription factor–DNA interaction discovery rate twice as high as the conventional diploid-mating approach and a processing time nearly one-tenth of the haploid-transformation method. The system also offers the highest accuracy in identifying TF–DNA interactions that can be authenticated in vivo by chromatin immunoprecipitation. With these unique features, this meiosis-directed Y1H system is particularly suited for constructing novel and comprehensive genome-scale gene regulatory networks for various organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Direct structural retrieval from gas-phase ultrafast diffraction data using a genetic algorithm

Ultrafast scattering techniques such as ultrafast electron diffraction and ultrafast x-ray diffraction have been utilized to elucidate the structural dynamics, reaction intermediates, and final products in molecular reactions following photoexcitation. The time-dependent structures are typically not directly retrieved from the experimental data, but they rely on comparison with calculations. The genetic algorithm (GA), a global optimization strategy, can be used to retrieve the molecular structures directly from diffraction patterns without any theoretical input. However, the robustness of the GA with respect to real experimental conditions such as a limited momentum transfer range, noise, and artifacts has not been studied in detail. In this work, we characterize the performance of the GA with simulated data that mimic realistic experimental conditions. We have developed and implemented a variant of the GA specific to diffraction measurements which performs better in the presence of imperfect data compared to the standard implementation of the GA. We demonstrate this method with both synthetic data and experimental ultrafast electron diffraction data on the UV-induced photodissociation of trifluoroiodomethane (C⁢F 3⁡ I) molecules.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Experimental demonstration of coupled multi-peak Bragg coherent diffraction imaging with genetic algorithms

Bragg coherent diffraction imaging has the potential to provide significant insight into the structure-properties relationship for crystalline materials by imaging, with nanoscale resolution, three-dimensional strain fields within individual grains and nanoparticles. The capability of present-day synchrotrons to locate and measure a multiplicity of Bragg reflections from a single grain makes it possible to recover the full strain tensor with nanometer resolution. Recent methods for coupling reconstructions from several peaks to determine the strain tensor have been developed and applied to synthetic data, but have not been applied to experimental data. Here, using a coupled genetic reconstruction algorithm, we reconstruct an experimental data set and demonstrate improvements in the ability to resolve vector-valued displacement fields internal to the particle as compared to what is achieved with a noncoupled approach. The coupled approach developed in this work was also validated on simulated data sets. In both simulated and experimental data, reconstructions from our coupled Bragg peak algorithm show improvements over the noncoupled independent reconstruction method of 5% in terms of accuracy and 53% in terms of consistency.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Genetic Algorithm-Based Commutation Angle Control for Torque Ripple Mitigation in Switched Reluctance Motor Drives

This work addresses the application of the Genetic Algorithm (GA) technique to optimize the commutation angles of a 2 kW 8/6 switched reluctance machine (SRM). The primary goal is to reduce the well-known drawback of SRMs: the torque ripple. Firstly, the machine was modeled in Matlab /Simulink ® using lookup tables obtained via finite element method (FEM) simulations. Subsequently, the model was used to perform the GA routine aiming to find the optimal phase commutation angles that minimize the torque ripple factor. Notably, the torque performance of the SRM was significantly affected by the commutation angles during the search for the optimal solution. Afterwards, the GA results for four different operation points were verified experimentally through a developed drive platform with digital signal processor-based (DSP) control and an asymmetric bridge converter. As showed by the experiments, the proposed approach was suitable to reduce the torque ripple by more than 50% for one of the evaluated operating points. Furthermore, it was confirmed that the torque ripple mitigation led to acoustic noise improvement.

42 ENGINEERING↗
DOE OSTI2021

Comprehensive Efficiency Analysis of Current Source Inverter Based on CSI-Type Double Pulse Test and Genetic Algorithm

A current-source inverter (CSI) has a natural output voltage boost feature that can be advantageous for traction applications. Switching frequency is one of the easily-controlled variables that can be adjusted to improve the CSI efficiency at different operating points when the boost function is used. This paper investigates a CSI-based double-pulse test (DPT) measurement that mimics normal operation of the CSI. A loss model of the CSI is developed based on the CSI-type DPT experimental results. The impacts of the switching frequency and voltage boost ratio on the CSI efficiency and output voltage ripple are investigated. Based on the loss model, a genetic algorithm has been introduced that makes it possible to optimize the CSI's switching frequency and modulation index to maximize its efficiency under any desired operating condition.

current-source inverter, genetic algorithm, SPM ma↗