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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 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

PHANOTATE: a novel approach to gene identification in phage genomes

Motivation: Currently there are no tools specifically designed for annotating genes in phages. Several tools are available that have been adapted to run on phage genomes, but due to their underlying design, they are unable to capture the full complexity of phage genomes. Phages have adapted their genomes to be extremely compact, having adjacent genes that overlap and genes completely inside of other longer genes. This non-delineated genome structure makes it difficult for gene prediction using the currently available gene annotators. Here we present PHANOTATE, a novel method for gene calling specifically designed for phage genomes. Although the compact nature of genes in phages is a problem for current gene annotators, we exploit this property by treating a phage genome as a network of paths: where open reading frames are favorable, and overlaps and gaps are less favorable, but still possible. We represent this network of connections as a weighted graph, and use dynamic programing to find the optimal path. Results: We compare PHANOTATE to other gene callers by annotating a set of 2133 complete phage genomes from GenBank, using PHANOTATE and the three most popular gene callers. We found that the four programs agree on 82% of the total predicted genes, with PHANOTATE predicting more genes than the other three. We searched for these extra genes in both GenBank’s non-redundant protein database and all of the metagenomes in the sequence read archive, and found that they are present at levels that suggest that these are functional protein-coding genes. Availability and implementation: https://github.com/deprekate/PHANOTATE. Supplementary information: Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Adaptive PID Gain Scheduling Control for Hydropower Turbine Using Neural CDE and Stochastic Distribution Shaping

This paper introduces a gain-scheduling PID controller design strategy for hydroturbine frequency control mode. This scheme first uses real data to learn the nonlinear dynamics of the hydroturbine using neural controlled differential equations and then perturbs the obtained nonlinear system at different equilibrium points, based on which a static output feedback adaptive dynamic programming algorithm is then used to optimize the PID gains for each equilibrium point. Moreover, a continuous-time version of stochastic distribution control is proposed to further fine-tune the optimized PID gains. Finally, the controller is obtained by implementing linear interpolation between the optimized PID control gains. The simulation results show that the proposed gain-scheduling PID controller can control a larger range of operation points compared with the given fixed PID controller and the baseline method. Compared with the given fixed PID controller, the proposed gain-scheduling PID controller can regulate hydroturbine frequency against disturbances induced by power-load variation with over 50% less overshoot for some operation points.

13 HYDRO ENERGY↗
DOE OSTI2020

CoSim: A Simulator for Co-Scheduling of Batch and On-Demand Jobs in HPC Datacenters

The increasing scale and complexity of scientific applications are rapidly transforming the ecosystem of tools, methods, and workflows adopted by the high-performance computing (HPC) community. Big data analytics and deep learning are gaining traction as essential components in this ecosystem in a variety of scenarios, such as, steering of experimental instruments , acceleration of high-fidelity simulations through surrogate computations, and guided ensemble searches. In this context, the batch job model traditionally adopted by the supercomputing in-frastructures needs to be complemented with support to schedule opportunistic on-demand analytics jobs, leading to the problem of efficient preemption of batch jobs with minimum loss of progress. In this paper, we design and implement a simulator, CoSim, that enables on-the-fly analysis of the trade-offs arising between delaying the start of opportunistic on-demand jobs, which leads to longer analytics latency, and loss of progress due to preemption of batch jobs, which is necessary to make room for on-demand jobs. To this end, we propose an algorithm based on dynamic programming with predictable performance and scalability that enables supercomputing infrastructure schedulers to analyze the aforementioned trade-off and take decisions in near real-time. Compared with other state-of-art approaches using traces of the Theta pre-Exascale machine, our approach is capable of finding the optimal solution, while achieving high performance and scalability.

batch job preemption↗
DOE OSTI2022

Optimal Coordination of Distributed Energy Resources Using Deep Deterministic Policy Gradient

Recent studies showed that reinforcement learning (RL) is a promising approach for coordination and control of distributed energy resources (DER) under uncertainties. Many existing RL approaches, including Q-learning and approximate dynamic programming, are based on lookup table methods, which become inefficient when the problem size is large and infeasible when continuous states and actions are involved. In addition, when modeling battery energy storage system (BESS), the loss of life is not reasonably considered into the decision-making process. This paper proposes an innovative deep RL method for DER coordination considering BESS degradation. The proposed deep RL is designed based on an adaptive actor-critic architecture and employs an off-policy deterministic policy gradient method for determining the dispatch operation that minimizes the operation cost and BESS life loss. Case studies were performed to validate the proposed method and demonstrate the effects of incorporating degradation models into control design.

Das, Avijit↗
DOE OSTI2020

Optimal Eco-Driving Control of Connected and Autonomous Vehicles Through Signalized Intersections

This article focuses on the speed planning problem for connected and automated vehicles (CAVs) communicating to traffic lights. The uncertainty of traffic signal timing for signalized intersections on the road is considered. The eco-driving problem is formulated as a data-driven chance-constrained robust optimization problem. Effective red-light duration (ERD) is defined as a random variable, and describes the feasible passing time through the signalized intersections. Usually, the true probability distribution for ERD is unknown. Consequently, a data-driven approach is adopted to formulate chance constraints based on empirical sample data. This incorporates robustness into the eco-driving control problem with respect to uncertain signal timing. Dynamic programming (DP) is employed to solve the optimization problem. The simulation results demonstrate that the proposed method can generate optimal speed reference trajectories with 40% less vehicle fuel consumption, while maintaining the arrival time at a similar level compared to a modified intelligent driver model (IDM). The proposed control approach significantly improves the controller's robustness in the face of uncertain signal timing, without requiring to know the distribution of the random variable a priori.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2020

Value Gradient Learning Approach in Power and Frequency Regulation of Grid-Connected Synchronverters

In this paper, a neural network adaptive critic design (ACD) method based on value gradient learning (VGL) is used to optimally control a grid-connected synchronverter. The main drawback of the traditional synchronverters is their infeasibility to face non-inductive grids. To be able to implement a synchronverter technique in any impedance angle, a neural network-based adaptive controller is used. The advantage of adaptive dynamic programing is its ability to adjust itself when it faces changes and uncertainties in the power system. The proposed VGL consists of two subnetworks: the critic network and the action network. The action network is trained during the operation, and the critic network can be pretrained offline or can be simultaneously trained with the action network. To compare the effectiveness of the traditional synchronverter to the VGL-based synchronverter, the simulation results are provided.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2022

Superconvergence of Online Optimization for Model Predictive Control

We develop a one-Newton-step-per-horizon, online, lag-L, model predictive control (MPC) algorithm for solving discrete-time, equality-constrained, nonlinear dynamic programs. Based on recent sensitivity analysis results for the target problems class, we prove that the approach exhibits a behavior that we call superconvergence; that is, the tracking error with respect to the full horizon solution is not only stable for successive horizon shifts, but also decreases with increasing shift order to a minimum value that decays exponentially in the length of the receding horizon. The key analytical step is the decomposition of the one-step error recursion of our algorithm into algorithmic error and perturbation error. We show that the perturbation error decays exponentially with the lag between two consecutive receding horizons, while the algorithmic error, determined by Newton’s method, achieves quadratic convergence instead. Overall this approach induces our local exponential convergence result in terms of the receding horizon length for suitable values of L. In conclusion, numerical experiments validate our theoretical findings.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Optimal Load Ensemble Control in Chance-Constrained Optimal Power Flow

Distribution system operators (DSOs) world-wide foresee a rapid roll-out of distributed energy resources. From the system perspective, their reliable and cost effective integration requires accounting for their physical properties in operating tools used by the DSO. This work describes an decomposable approach to leverage the dispatch flexibility of thermostatically controlled loads (TCLs) for operating distribution systems with a high penetration level of photovoltaic resources. Each TCL ensemble is modeled using the Markov Decision Process (MDP). The MDP model is then integrated with a chance constrained optimal power flow that accounts for the uncertainty of PV resources. Since the integrated optimization model cannot be solved efficiently by existing dynamic programming methods or off-the-shelf solvers, this paper proposes an iterative Spatio-Temporal Dual Decomposition algorithm (ST-D2). Finally, we demonstrate the merits of the proposed integrated optimization and ST-D2 algorithm on the IEEE 33-bus test system.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2020

A Deep Generative Model for Non-Intrusive Identification of EV Charging Profiles

The proliferation of electric vehicles (EVs) brings environmental benefits and technical challenges to power grids. An identification algorithm which can accurately extract individual EV charging profiles out of widely available smart meter measurements has attracted great interests. This paper proposes a non-intrusive identification framework for EV charging profile extraction, which is driven by deep generative models (DGM). First, the proposed DGM is designed as a representation layer embedded into the Markov process and used to model the joint probability distribution of available time-series data. A novel contribution is to approximate posterior distributions by neural networks whose parameters are obtained by variational inference and supervised learning. Second, the EV charging status is inferred from the DGM via dynamic programming. Lastly, the desired EV charging profile can be reconstructed by the rated power of EV models and inferred status. Compared with the benchmark Hidden Markov Models, the proposed framework can better handle noise in data with less computational complexity and better overall accuracy performances with smaller recall. The proposed framework is validated by numerical experiments on the Pecan Street dataset.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2019

Formulation and Comparison of Two Real-Time Predictive Gear Shift Algorithms for Connected/Automated Heavy-Duty Vehicles

Our work investigates the problem of predictive gear scheduling for fuel consumption minimization in connected/automated heavy trucks. The literature highlights the fuel economy benefits of such predictive scheduling, but there is a need to optimize such scheduling online, in real time. To address this need, we begin by using dynamic programming (DP) to schedule gear shifting offline, in a manner that achieves a globally optimal Pareto tradeoff between the conflicting objectives of minimizing fuel consumption and shift frequency. The computational cost of DP is unfavorable for online implementation, but we present two algorithms addressing this issue. Both algorithms rely on the fact that in the Pareto limit where fuel consumption minimization is the sole objective, DP furnishes a simple static shift map . Our first algorithm trains a recurrent neural network to prune the shift schedule generated by this map. The second algorithm performs this pruning in a direct manner tailored to reduce the schedule's rain flow count. We simulate these algorithms for different drive cycles. Both algorithms achieve a reasonable tradeoff between fuel consumption and gear shift frequency. Yet, the rain flow count algorithm is both more effective in approaching the DP-based Pareto front and more computationally efficient.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2023

Integrated Optimization of Powertrain Energy Management and Vehicle Motion Control for Autonomous Hybrid Electric Vehicles

Hybrid Electric Vehicles (HEVs) and autonomous vehicles have been widely studied recently for on-road transportation. In the study of autonomous HEVs, the control of the vehicle's external dynamics and powertrain dynamics are often treated separately. Optimizing these two problems together can significantly improve fuel economy. In this paper, an autonomous HEV following a leader is considered. First, the augmented model to integrate the abovementioned dynamics is presented. Second, the optimization problem is defined to find the optimum fuel consumption of the follower in pursuit of a leader in a drive cycle. A customized control strategy based on Approximate Dynamic Programming (ADP) is then explored in which the optimal cost-to-go at each time step is approximated using neural networks. Also, the accuracy of the optimization solution is enhanced by applying the concept of the reachable sets. At last, three case studies show that the examined integrated control strategy outperforms the one with the separated optimization method by an additional 7.4%, 4.6%, and 11.8% improvement in fuel consumption, respectively.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2023

Design Considerations and Analysis of Multi-Level Erasure Coding in Large-Scale Data Centers

Multi-level erasure coding (MLEC) has seen large deployments in the field, but there is no in-depth study of design considerations for MLEC at scale. In this paper, we provide comprehensive design considerations and analysis of MLEC at scale. We introduce the design space of MLEC in multiple dimensions, including various code parameter selections, chunk placement schemes, and various repair methods. We quantify their performance and durability, and show which MLEC schemes and repair methods can provide the best tolerance against independent/correlated failures and reduce repair network traffic by orders of magnitude. To achieve this, we use various evaluation strategies including simulation, splitting, dynamic programming, and mathematical modeling. We also compare the performance and durability of MLEC with other EC schemes such as SLEC and LRC and show that MLEC can provide high durability with higher encoding throughput and less repair network traffic over both SLEC and LRC.

Wang, Meng↗
DOE OSTI2020

ADEPT: a domain independent sequence alignment strategy for gpu architectures

Bioinformatic workflows frequently make use of automated genome assembly and protein clustering tools. At the core of most of these tools, a significant portion of execution time is spent in determining optimal local alignment between two sequences. This task is performed with the Smith-Waterman algorithm, which is a dynamic programming based method. With the advent of modern sequencing technologies and increasing size of both genome and protein databases, a need for faster Smith-Waterman implementations has emerged. Multiple SIMD strategies for the Smith-Waterman algorithm are available for CPUs. However, with the move of HPC facilities towards accelerator based architectures, a need for an efficient GPU accelerated strategy has emerged. Existing GPU based strategies have either been optimized for a specific type of characters (Nucleotides or Amino Acids) or for only a handful of application use-cases. In this paper, we present ADEPT, a new sequence alignment strategy for GPU architectures that is domain independent, supporting alignment of sequences from both genomes and proteins. Our proposed strategy uses GPU specific optimizations that do not rely on the nature of sequence. We demonstrate the feasibility of this strategy by implementing the Smith-Waterman algorithm and comparing it to similar CPU strategies as well as the fastest known GPU methods for each domain. ADEPT’s driver enables it to scale across multiple GPUs and allows easy integration into software pipelines which utilize large scale computational systems. We have shown that the ADEPT based Smith-Waterman algorithm demonstrates a peak performance of 360 GCUPS and 497 GCUPs for protein based and DNA based datasets respectively on a single GPU node (8 GPUs) of the Cori Supercomputer. Overall ADEPT shows 10x faster performance in a node-to-node comparison against a corresponding SIMD CPU implementation. ADEPT demonstrates a performance that is either comparable or better than existing GPU strategies. We demonstrated the efficacy of ADEPT in supporting existing bionformatics software pipelines by integrating ADEPT in MetaHipMer a high-performance denovo metagenome assembler and PASTIS a high-performance protein similarity graph construction pipeline. Our results show 10% and 30% boost of performance in MetaHipMer and PASTIS respectively.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

The Ramping Polytope and Cut Generation for the Unit Commitment Problem

We present a perfect formulation for a single generator in the unit commitment problem, inspired by the dynamic programming approach taken by Frangioni and Gentile. This generator can have characteristics such as ramp-up/ramp-down constraints, time-dependent start-up costs, and start-up/shut-down limits. To develop this perfect formulation, we extend the result of Balas on unions of polyhedra to present a framework allowing for flexible combinations of polyhedra using indicator variables. Here, we use this perfect formulation to create a cut-generating linear program, similar in spirit to lift-and-project cuts, and demonstrate computational efficacy of these cuts in a utility-scale unit commitment problem.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Kraken2 Metagenomic Virus Database

The Database: Kraken2 [1] database built from a classification tree containing over 700k metagenomic viruses from JGI IMG/VR [2]. (1) Wood, D. E., Lu, J., and Langmead, B. (2019). Improved metagenomic analysis with Kraken 2. Genome Biol., 20(1), 1–13. doi: 10.1186/s13059-019-1891-0 (2) Paez-Espino D, Chen I-MA, Palaniappan K, Ratner A, Chu K, Szeto E, et al. IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses. Nucleic Acids Res. 2017;45:D457-65. For Paper: Title: A k-mer based approach for virus classification in metatranscriptomic and metagenomic samples identifies viral associations in the Populus phytobiome and autism brains Abstract Background Viruses are an underrepresented taxa in the study and identification of microbiome constituents; however, they play an important role in health, microbiome regulation, and transfer of genetic material. Only a few thousand viruses have been isolated, sequenced, and assigned a taxonomy, which further limits the ability to identify and quantify viruses in the microbiome. Additionally, the vast diversity of viruses represents a challenge for classification, not only in constructing a viral taxonomy, but also in identifying similarities between a virus' genotype and its phenotype. However, the diversity of viral sequences can be leveraged to classify their sequences in metagenomic and metatranscriptomic samples. Methods To identify viruses in transcriptomic and genomic samples, we developed a dynamic programming algorithm for creating a classification tree out of 715,672 metagenome viruses. To create the classification tree, we clustered proportional similarity scores generated from the k-mer profiles of each of the metagenome viruses. We then integrated the viral classification tree with the NCBI taxonomy for use with ParaKraken, a metagenomic/transcriptomic classifier. Results To illustrate the breadth of our utility for classifying viruses with ParaKraken, we analyzed data from a plant metagenome study identifying the differences between two Populus genotypes in three different compartments and on a human metatranscriptome study identifying the differences between Autism Spectrum Disorder patients and controls in post mortem brain biopsies. In the Populus study, we identified genotype and compartment specific viral signatures, while in the Autism study we identified a significant increased abundance of eight viral sequences in Autism brain biopsies. Conclusion Viruses represent an important aspect of the microbiome. The ability to classify viruses represents the first step in being able to better understand their role in the microbiome. The viral classification method presented here allows for more complete identification of viral sequences for use in identifying associations between viruses and the host and viruses and other microbiome members. Acknowledgements and Funding This research used resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725. This research was also supported by the Plant-Microbe Interfaces Scientific Focus Area in the Genomic Science Program, the Office of Biological and Environmental Research (BER) in the U.S. Department of Energy Office of Science, and by the Department of Energy, Laboratory Directed Research and Development funding (ProjectID 8321), at the Oak Ridge National Laboratory. Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the US DOE under contract DE-AC05-00OR22725. This research used resources of the Compute and Data Environment for Science (CADES).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

SIERRA/Aero Theory Manual (V.4.54)

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment.

42 ENGINEERING↗
DOE OSTI2019

SIERRA/Aero User Manual (V.4.54)

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment.

42 ENGINEERING↗