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NASA NTRS2003

Structure, Function, Self-Assembly and Origin of Simple Membrane Proteins

Integral membrane proteins perform such essential cellular functions as transport of ions, nutrients and waste products across cell walls, transduction of environmental signals, regulation of cell fusion, recognition of other cells, energy capture and its conversion into high-energy compounds. In fact, 30-40% of genes in modem organisms codes for membrane proteins. Although contemporary membrane proteins or their functional assemblies can be quite complex, their transmembrane fragments are usually remarkably simple. The most common structural motif for these fragments is a bundle of alpha-helices, but occasionally it could be a beta-barrel. In a series of molecular dynamics computer simulations we investigated self-organizing properties of simple membrane proteins based on these structural motifs. Specifically, we studied folding and insertion into membranes of short, nonpolar or amphiphatic peptides. We also investigated glycophorin A, a peptide that forms sequence-specific dimers, and a transmembrane aggregate of four identical alpha-helices that forms an efficient and selective voltage-gated proton channel was investigated. Many peptides are attracted to water-membrane interfaces. Once at the interface, nonpolar peptides spontaneously fold to a-helices. Whenever the sequence permits, peptides that contain both polar and nonpolar amino also adopt helical structures, in which polar and nonpolar amino acid side chains are immersed in water and membrane, respectively. Specific identity of side chains is less important. Helical peptides at the interface could insert into the membrane and adopt a transmembrane conformation. However, insertion of a single helix is unfavorable because polar groups in the peptide become completely dehydrated upon insertion. The unfavorable free energy of insertion can be regained by spontaneous association of peptides in the membrane. The first step in this process is the formation of dimers, although the most common are aggregates of 4-7 helices. The helices could arrange themselves such that they formed pores capable of transporting ions and small molecules across membranes. Stability of transmembrane aggregates of simple proteins is often only marginal and, therefore, it can be regulated by environmental signals or small sequence modifications in the region of interhelical interactions. A key step in the earliest evolution of membrane proteins was the emergence of selectivity for specific substrates. Many channels could become selective if one or only a few properly chosen amino acids are properly placed along the channel, acting as filters or gates. This is a convenient evolutionary solution because it does not require imposing conditions on the whole sequence.

Pohorille, Andrew↗

DOE OSTI2025

DEVELOPMENT AND APPLICATION OF RISK ANALYSIS TOOLKIT FOR PLANT RESOURCE OPTIMIZATION

This paper presents the development of methods and tools that are being designed to optimize plant operations (e.g., maintenance/replacement schedules and optimal maintenance postures for plant components) in a manner that is more cost effective than current approaches and makes better use of available component health and cost data. These methods include both data- and model-based optimization methods. Model-based optimization methods directly include reliability and cost models to determine an optimal plant operational strategy. We consider gradient-based and evolutionary (based on genetic algorithms) optimization methods. The second class of methods target more specific use cases (e.g., project schedule optimization) and are not based on reliability models directly, but they require specific component reliability and cost data. This class of methods is based on variants of the knapsack problem with an aim to determine an optimal project schedule that maximizes the overall NPV. This paper also presents multi-objective methods designed to identify an optimal maintenance posture based on a Pareto frontier analysis. Rather than dictating the “right” tradeoff (i.e., identify the absolute best posture), we show how it is possible to perform a trade space exploration approach (i.e., identify value and costs of several postures and let the analysis account for desired value and cost metrics). This is performed by identifying maintenance postures that maximize value (e.g., system availability) and minimize operational costs, i.e., the Pareto frontier in a value-cost trade space. For all these methods we present detailed applicative examples that show their validity from a decision-making perspective.

97 - MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Online evolutionary neural architecture search for multivariate non-stationary time series forecasting

Time series forecasting (TSF) is one of the most important tasks in data science. TSF models are usually pre-trained with historical data and then applied on future unseen datapoints. However, real-world time series data is usually non-stationary and models trained offline usually face problems from data drift. Models trained and designed in an offline fashion can not quickly adapt to changes quickly or be deployed in real-time. To address these issues, this work presents the Online NeuroEvolution-based Neural Architecture Search (ONE-NAS) algorithm, which is a novel neural architecture search method capable of automatically designing and dynamically training recurrent neural networks (RNNs) for online forecasting tasks. Without any pre-training, ONE-NAS utilizes populations of RNNs that are continuously updated with new network structures and weights in response to new multivariate input data. ONE-NAS is tested on real-world, large-scale multivariate wind turbine data as well as the univariate Dow Jones Industrial Average (DJIA) dataset. These results demonstrate that ONE-NAS outperforms traditional statistical time series forecasting methods, including online linear regression, fixed long short-term memory (LSTM) and gated recurrent unit (GRU) models trained online, as well as state-of-the-art, online ARIMA strategies. Additionally, results show that utilizing multiple populations of RNNs which are periodically repopulated provide significant performance improvements, allowing this online neural network architecture design and training to be successful.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

A deep dilated convolutional residual network for predicting interchain contacts of protein homodimers

Abstract Motivation Deep learning has revolutionized protein tertiary structure prediction recently. The cutting-edge deep learning methods such as AlphaFold can predict high-accuracy tertiary structures for most individual protein chains. However, the accuracy of predicting quaternary structures of protein complexes consisting of multiple chains is still relatively low due to lack of advanced deep learning methods in the field. Because interchain residue–residue contacts can be used as distance restraints to guide quaternary structure modeling, here we develop a deep dilated convolutional residual network method (DRCon) to predict interchain residue–residue contacts in homodimers from residue–residue co-evolutionary signals derived from multiple sequence alignments of monomers, intrachain residue–residue contacts of monomers extracted from true/predicted tertiary structures or predicted by deep learning, and other sequence and structural features. Results Tested on three homodimer test datasets (Homo_std dataset, DeepHomo dataset and CASP-CAPRI dataset), the precision of DRCon for top L/5 interchain contact predictions (L: length of monomer in a homodimer) is 43.46%, 47.10% and 33.50% respectively at 6 Å contact threshold, which is substantially better than DeepHomo and DNCON2_inter and similar to Glinter. Moreover, our experiments demonstrate that using predicted tertiary structure or intrachain contacts of monomers in the unbound state as input, DRCon still performs well, even though its accuracy is lower than using true tertiary structures in the bound state are used as input. Finally, our case study shows that good interchain contact predictions can be used to build high-accuracy quaternary structure models of homodimers. Availability and implementation The source code of DRCon is available at https://github.com/jianlin-cheng/DRCon. The datasets are available at https://zenodo.org/record/5998532#.YgF70vXMKsB. Supplementary information Supplementary data are available at Bioinformatics online.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Reference-free structural variant detection in microbiomes via long-read co-assembly graphs

Motivation: The study of bacterial genome dynamics is vital for understanding the mechanisms underlying microbial adaptation, growth, and their impact on host phenotype. Structural variants (SVs), genomic alterations of 50 base pairs or more, play a pivotal role in driving evolutionary processes and maintaining genomic heterogeneity within bacterial populations. While SV detection in isolate genomes is relatively straightforward, metagenomes present broader challenges due to the absence of clear reference genomes and the presence of mixed strains. In response, our proposed method rhea, forgoes reference genomes and metagenome-assembled genomes (MAGs) by encompassing all metagenomic samples in a series (time or other metric) into a single co-assembly graph. The log fold change in graph coverage between successive samples is then calculated to call SVs that are thriving or declining. Results: We show rhea to outperform existing methods for SV and horizontal gene transfer (HGT) detection in two simulated mock metagenomes, particularly as the simulated reads diverge from reference genomes and an increase in strain diversity is incorporated. We additionally demonstrate use cases for rhea on series metagenomic data of environmental and fermented food microbiomes to detect specific sequence alterations between successive time and temperature samples, suggesting host advantage. Our approach leverages previous work in assembly graph structural and coverage patterns to provide versatility in studying SVs across diverse and poorly characterized microbial communities for more comprehensive insights into microbial gene flux.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

StructuredFuzzer: Fuzzing Structured Text-Based Control Logic Applications

Rigorous testing methods are essential for ensuring the security and reliability of industrial controller software. Fuzzing, a technique that automatically discovers software bugs, has also proven effective in finding software vulnerabilities. Unsurprisingly, fuzzing has been applied to a wide range of platforms, including programmable logic controllers (PLCs). However, current approaches, such as coverage-guided evolutionary fuzzing implemented in the popular fuzzer American Fuzzy Lop Plus Plus (AFL++), are often inadequate for finding logical errors and bugs in PLC control logic applications. They primarily target generic programming languages like C/C++, Java, and Python, and do not consider the unique characteristics and behaviors of PLCs, which are often programmed using specialized programming languages like Structured Text (ST). Furthermore, these fuzzers are ill suited to deal with complex input structures encapsulated in ST, as they are not specifically designed to generate appropriate input sequences. This renders the application of traditional fuzzing techniques less efficient on these platforms. To address this issue, this paper presents a fuzzing framework designed explicitly for PLC software to discover logic bugs in applications written in ST specified by the IEC 61131-3 standard. The proposed framework incorporates a custom-tailored PLC runtime and a fuzzer designed for the purpose. We demonstrate its effectiveness by fuzzing a collection of ST programs that were crafted for evaluation purposes. We compare the performance against a popular fuzzer, namely, AFL++. The proposed fuzzing framework demonstrated its capabilities in our experiments, successfully detecting logic bugs in the tested PLC control logic applications written in ST. On average, it was at least 83 times faster than AFL++, and in certain cases, for example, it was more than 23,000 times faster.

47 OTHER INSTRUMENTATION↗

DOE OSTI2020

Inference of Chromosome-Length Haplotypes Using Genomic Data of Three or a Few More Single Gametes

Compared with genomic data of individual markers, haplotype data provide higher resolution for DNA variants, advancing our knowledge in genetics and evolution. Although many computational and experimental phasing methods have been developed for analyzing diploid genomes, it remains challenging to reconstruct chromosome-scale haplotypes at low cost, which constrains the utility of this valuable genetic resource. Gamete cells, the natural packaging of haploid complements, are ideal materials for phasing entire chromosomes because the majority of the haplotypic allele combinations has been preserved. Therefore, compared with the current diploid-based phasing methods, using haploid genomic data of single gametes may substantially reduce the complexity in inferring the donor’s chromosomal haplotypes. In this study, we developed the first easy-to-use R package, Hapi, for inferring chromosome-length haplotypes of individual diploid genomes with only a few gametes. Hapi outperformed other phasing methods when analyzing both simulated and real single gamete cell sequencing data sets. The results also suggested that chromosome-scale haplotypes may be inferred by using as few as three gametes, which has pushed the boundary to its possible limit. The single gamete cell sequencing technology allied with the cost-effective Hapi method will make large-scale haplotype-based genetic studies feasible and affordable, promoting the use of haplotype data in a wide range of research.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

A User’s Guide to the PLTEMP/ANL Code

PLTEMP/ANL V4.4 is a program that obtains a steady-state flow and temperature solution, in geometrical extent, for a nuclear reactor core, or a single fuel assembly, including the effect of manufacturing and modelling uncertainties by the means of hot channel factors. It is based on an evolutionary sequence of codes originally used for calculating plate temperatures, hence “PLTEMP”, developed at Argonne National Laboratory over the past 30 years. Fueled and non-fueled regions are modeled. Each fuel assembly consists of one or more plates or tubes separated by coolant channels. The fuel plates may have one to five layers of different materials, each with heat generation. The width of a fuel plate may be divided into multiple longitudinal stripes, each with its own axial power shape. Depending upon the heat transfer method selected, the temperature solution is effectively 2-dimensional or 3-dimensional. The geometry may be either slab or radial, corresponding to fuel assemblies made of a series of flat (or slightly curved) plates, or of nested tubes. A variety of thermal-hydraulic correlations are available to determine safety margins such as onset of nucleate boiling ratio (ONBR), departure from nucleate boiling ratio (DNBR), and onset of flow instability ratio (OFIR). Coolant properties for either light or heavy water are obtained from FORTRAN functions rather than from tables. The code is intended for thermal-hydraulic analysis of research reactor performance in the sub-cooled boiling regime. Both turbulent and laminar flow regimes can be modeled. Options to calculate both forced flow and natural circulation are available. A general search capability for select design and safety parameters is available to greatly reduce the reactor analyst’s time.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2022

End-to-end learning of multiple sequence alignments with differentiable Smith–Waterman

Abstract Motivation Multiple sequence alignments (MSAs) of homologous sequences contain information on structural and functional constraints and their evolutionary histories. Despite their importance for many downstream tasks, such as structure prediction, MSA generation is often treated as a separate pre-processing step, without any guidance from the application it will be used for. Results Here, we implement a smooth and differentiable version of the Smith–Waterman pairwise alignment algorithm that enables jointly learning an MSA and a downstream machine learning system in an end-to-end fashion. To demonstrate its utility, we introduce SMURF (Smooth Markov Unaligned Random Field), a new method that jointly learns an alignment and the parameters of a Markov Random Field for unsupervised contact prediction. We find that SMURF learns MSAs that mildly improve contact prediction on a diverse set of protein and RNA families. As a proof of concept, we demonstrate that by connecting our differentiable alignment module to AlphaFold2 and maximizing predicted confidence, we can learn MSAs that improve structure predictions over the initial MSAs. Interestingly, the alignments that improve AlphaFold predictions are self-inconsistent and can be viewed as adversarial. This work highlights the potential of differentiable dynamic programming to improve neural network pipelines that rely on an alignment and the potential dangers of optimizing predictions of protein sequences with methods that are not fully understood. Availability and implementation Our code and examples are available at: https://github.com/spetti/SMURF. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Deep Learning and Likelihood Approaches for Viral Phylogeography Converge on the Same Answers Whether the Inference Model Is Right or Wrong

Abstract Analysis of phylogenetic trees has become an essential tool in epidemiology. Likelihood-based methods fit models to phylogenies to draw inferences about the phylodynamics and history of viral transmission. However, these methods are often computationally expensive, which limits the complexity and realism of phylodynamic models and makes them ill-suited for informing policy decisions in real-time during rapidly developing outbreaks. Likelihood-free methods using deep learning are pushing the boundaries of inference beyond these constraints. In this paper, we extend, compare, and contrast a recently developed deep learning method for likelihood-free inference from trees. We trained multiple deep neural networks using phylogenies from simulated outbreaks that spread among 5 locations and found they achieve close to the same levels of accuracy as Bayesian inference under the true simulation model. We compared robustness to model misspecification of a trained neural network to that of a Bayesian method. We found that both models had comparable performance, converging on similar biases. We also implemented a method of uncertainty quantification called conformalized quantile regression that we demonstrate has similar patterns of sensitivity to model misspecification as Bayesian highest posterior density (HPD) and greatly overlap with HPDs, but have lower precision (more conservative). Finally, we trained and tested a neural network against phylogeographic data from a recent study of the SARS-Cov-2 pandemic in Europe and obtained similar estimates of region-specific epidemiological parameters and the location of the common ancestor in Europe. Along with being as accurate and robust as likelihood-based methods, our trained neural networks are on average over 3 orders of magnitude faster after training. Our results support the notion that neural networks can be trained with simulated data to accurately mimic the good and bad statistical properties of the likelihood functions of generative phylogenetic models.

Evolutionary Biology↗

DOE OSTI2020

A User’s Guide to the PLTEMP/ANL Code

PLTEMP/ANL V4.3 is a program that obtains a steady-state flow and temperature solution for a nuclear reactor core, or for a single fuel assembly. It is based on an evolutionary sequence of codes originally used for plate temperatures, hence “PLTEMP”, developed at Argonne National Laboratory over several decades. Fueled and non-fueled regions are modeled. Each fuel assembly consists of one or more plates or tubes separated by coolant channels. The fuel plates may have one to five layers of different materials, each with heat generation. The width of a fuel plate may be divided into multiple longitudinal stripes, each with its own axial power shape. Depending upon the heat transfer method selected, the temperature solution is effectively 2-dimensional or 3-dimensional (Appendix XV). It begins with a solution across all coolant channels and fuel plates or tubes within a given fuel assembly, at the entrance to the assembly. The temperature solution is repeated for each axial node along the length of the fuel assembly. The geometry may be either slab or radial, corresponding to fuel assemblies made of a series of flat (or slightly curved) plates, or of nested tubes. A variety of thermal-hydraulic correlations are available to determine safety margins such as onset-of-nucleate boiling ratio(ONBR), departure from nucleate boiling ratio (DNBR), and onset of flow instability ratio (OFIR). Coolant properties for either light or heavy water are obtained from FORTRAN functions rather than from tables. The code is intended for thermal-hydraulic analysis of research reactor performance in the sub-cooled boiling regime. Both turbulent and laminar flow regimes can be modeled. Options to calculate both forced flow and natural circulation are available. A general search capability is available (Appendix XII) to greatly reduce the reactor analyst’s time.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2021

A User’s Guide to the PLTEMP/ANL Code (V.4.3)

PLTEMP/ANL V4.3 is a program that obtains a steady-state flow and temperature solution for a nuclear reactor core, or for a single fuel assembly. It is based on an evolutionary sequence of codes originally used for plate temperatures, hence “PLTEMP”, developed at Argonne National Laboratory over several decades. Fueled and non-fueled regions are modeled. Each fuel assembly consists of one or more plates or tubes separated by coolant channels. The fuel plates may have one to five layers of different materials, each with heat generation. The width of a fuel plate may be divided into multiple longitudinal stripes, each with its own axial power shape. Depending upon the heat transfer method selected, the temperature solution is effectively 2-dimensional or 3-dimensional (Appendix XV). It should be noted that for a 3-dimensional solution the axial power shape is modeled without accounting for axial heat conduction. It begins with a solution across all coolant channels and fuel plates or tubes within a given fuel assembly, at the entrance to the assembly. The temperature solution is repeated for each axial node along the length of the fuel assembly. The geometry may be either slab or radial, corresponding to fuel assemblies made of a series of flat (or slightly curved) plates, or of nested tubes. A variety of thermal-hydraulic correlations are available to determine safety margins such as onset-of-nucleate boiling ratio(ONBR), departure from nucleate boiling ratio (DNBR), and onset of flow instability ratio (OFIR). Coolant properties for either light or heavy water are obtained from FORTRAN functions rather than from tables. The code is intended for thermal-hydraulic analysis of research reactor performance in the sub-cooled boiling regime. Both turbulent and laminar flow regimes can be modeled. Options to calculate both forced flow and natural circulation are available. A general search capability is available (Appendix XII) to greatly reduce the reactor analyst’s time.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2025

A haplotype‐resolved reference genome of Quercus alba sheds light on the evolutionary history of oaks

Summary White oak ( Quercus alba ) is an abundant forest tree species across eastern North America that is ecologically, culturally, and economically important. We report the first haplotype‐resolved chromosome‐scale genome assembly of Q. alba and conduct comparative analyses of genome structure and gene content against other published Fagaceae genomes. We investigate the genetic diversity of this widespread species and the phylogenetic relationships among oaks using whole genome data. Despite strongly conserved chromosome synteny and genome size across Quercus , certain gene families have undergone rapid changes in size, including defense genes. Unbiased annotation of resistance (R) genes across oaks revealed that the overall number of R genes is similar across species – as are the chromosomal locations of R gene clusters – but, gene number within clusters is more labile. We found that Q. alba has high genetic diversity, much of which predates its divergence from other oaks and likely impacts divergence time estimations. Our phylogenetic results highlight widespread phylogenetic discordance across the genus. The white oak genome represents a major new resource for studying genome diversity and evolution in Quercus . Additionally, we show that unbiased gene annotation is key to accurately assessing R gene evolution in Quercus .

Larson, Drew A. [Department of Biology Indiana Uni↗

NASA NTRSDate not supplied

High-Order Methods in NASA’s Next Generation of Computational Fluid Dynamics Tools

The missions of the National Aeronautics and Space Administration (NASA) routinely produce unique requirements and challenges for development and application of Computational Fluid Dynamics (CFD) methods. NASA presently embodies four distinct Mission Directorates: Aeronautics Research, Exploration Systems, Science, and Space Operations. These missions generate requirements for systems that operate in a wide variety of environments. They range from the high-speed flight of aerodynamically optimized vehicles operating in the earth’s atmosphere to spacecraft designed for missions that don’t favor aerodynamic optimization, some operating in the atmosphere of planets and planetary moons such as Mars and Venus or Saturn’s moon Titan. Systems supporting these vehicles, such as rocket and jet propulsion, reaction control systems, fluid and thermal transfer systems, etc. can also generate their own unique set of flow phenomena that challenge today’s CFD methodology. Through the NASA Engineering and Safety Center (NESC), NASA annually conducts state-of-the-discipline assessments in fifteen distinct engineering disciplines. These assessments are performed by the NASA Technical Fellows that lead Technical Discipline Teams (TDT) of recognized experts in these fifteen areas. In the Aerosciences discipline, three topics have been identified as the top challenges for the discipline: aero-plume interaction prediction, unsteady separated flows, and aerothermodynamic prediction. These challenge areas are defined by the Agency’s high-risk projects and problems on which the NESC is requested to perform independent testing, analysis, and assessments. When viewed as a whole, these tests, analyses, and assessments provide a clear view of the recurring technical challenges facing Agency engineers and researchers and can be used to guide future research and technology development. The present state-of-the-art in the application of CFD at NASA is the use of Reynolds-Averaged Navier- Stokes (RANS) solvers, primarily executed in a steady-state mode of operation. In isolated cases, Unsteady RANS (URANS) solvers have been employed when steady RANS solutions produce poorly converging or oscillating results or in cases, such as aeroelastic analysis, which require unsteady aerodynamic simulation. For most traditional external and internal aerodynamic flows, structured overset grids or unstructured grids are employed to minimize geometric modeling and grid generation times. Grid adaptation, primarily as a series of coarse-grain intermediate processing steps is also seeing use on particularly complex flow problems and configurations. In the case of aerothermodynamic flows, engineers have been forced to continue to employ structured grid techniques as the present unstructured grid methodology has proven inadequate in the prediction of surface heating. In the area of aero-plume interaction modeling, two-gas, frozen chemistry simulation is generally the state-of-the- art, with some production solvers capable of predicting flows with only a single gas component. Prediction of flows falling into the afore-mentioned top Aerosciences technical challenges have severely stressed the present state-of-the-art in CFD prediction and for some problems, such as unsteady separated flows and aero-plume interaction cases, engineers have begun employing Large Eddy Simulation (LES) and Hybrid RANS/LES techniques. In some isolated aero-propulsion interaction cases, chemically reacting flow simulations have been applied. These methods are highly evolutionary and engineers have little experience in their application, so they cannot be heavily relied upon in today’s application environment. Therefore, this leads one to muse over which numerical technologies will be included in the CFD tools that will be employed 30 years in the future. This presentation will describe specific technical problems that have stressed NASA’s traditional CFD methods to their breaking point and will link these issues to the Agency’s top Aerosciences technical challenges. The discussion will then shift to the characteristics of future CFD solvers that will be required to attack these challenges and how these characteristics differ from the present state-of-the- art. High-order methods certainly appear to have a place in the development of future CFD tools and some of the physical characteristics of our most challenging problems suggest that high-order methods are the only way to effectively solve them. But there are some relatively severe implementation issues that face these methods, particularly in the area of general applicability and robust operation as an engineering tool. Desired characteristics of next-generation CFD solvers will be discussed and the author’s view of which emerging numerical technologies might be employed to address these attributes will also be presented

David M Schuster↗