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At least 1,495 records · Page 83
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Synthetic communities as a model for determining interactions between a biofertilizer chassis organism and native microbial consortia

Biofertilizers are critical for sustainable agriculture because they can replace ecologically disruptive chemical fertilizers while improving the trajectory of soil and plant health. However, for improving deployment, the persistence of biofertilizers within native soil consortia must be elucidated and enhanced. In this study we characterized a high-throughput, modular, and automation-friendly in vitro approach to screen for biofertilizer persistence within soil-derived consortia after co-cultivation with stable synthetic soil microbial communities (SynComs) obtained through a top-down cultivation process. Here, we profiled ~1200 SynComs isolated from various soil sources and cultivated in divergent media types, and we detected significant phylogenetic diversity (e.g. Shannon index >4) and richness (observed richness >400) across these communities. We observed high reproducibility in SynCom community structure from common soil and media types, which provided a testbed for assessing biofertilizer persistence within representative native consortia. Furthermore, we demonstrated that the screening method described herein can be coupled with microbial engineering to efficiently identify soil-derived SynComs in which an engineered biofertilizer organism (i.e. Bacillus subtilis) persists. Accordingly, we discovered that B. subtilis persisted in ~10% of SynComs that generally followed the diversity–invasion principle. Additionally, our approach enabled analysis of the ecological impact of B. subtilis inoculation on SynCom structure and profile alterations in community diversity and richness associated with the presence of a genetically modified model bacterium. Ultimately, this work has established a modular pipeline that could be integrated into a variety of microbiology/microbiome-relevant workflows or related applications that would benefit from assessment of the persistence of a specific organism of interest and its interaction with native consortia.

biofertilizers↗
DOE OSTI2022

ClusterCAD 2.0: an updated computational platform for chimeric type I polyketide synthase and nonribosomal peptide synthetase design

Abstract Megasynthase enzymes such as type I modular polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) play a central role in microbial chemical warfare because they can evolve rapidly by shuffling parts (catalytic domains) to produce novel chemicals. If we can understand the design rules to reshuffle these parts, PKSs and NRPSs will provide a systematic and modular way to synthesize millions of molecules including pharmaceuticals, biomaterials, and biofuels. However, PKS and NRPS engineering remains difficult due to a limited understanding of the determinants of PKS and NRPS fold and function. We developed ClusterCAD to streamline and simplify the process of designing and testing engineered PKS variants. Here, we present the highly improved ClusterCAD 2.0 release, available at https://clustercad.jbei.org. ClusterCAD 2.0 boasts support for PKS-NRPS hybrid and NRPS clusters in addition to PKS clusters; a vastly enlarged database of curated PKS, PKS-NRPS hybrid, and NRPS clusters; a diverse set of chemical ‘starters’ and loading modules; the new Domain Architecture Cluster Search Tool; and an offline Jupyter Notebook workspace, among other improvements. Together these features massively expand the chemical space that can be accessed by enzymes engineered with ClusterCAD.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Network portal: a database for storage, analysis and visualization of biological networks

The ease of generating high-throughput data has enabled investigations into organismal complexity at the systems level through the inference of networks of interactions among the various cellular components (genes, RNAs, proteins and metabolites). The wider scientific community, however, currently has limited access to tools for network inference, visualization and analysis because these tasks often require advanced computational knowledge and expensive computing resources. We have designed the network portal (http://networks.systemsbiology.net) to serve as a modular database for the integration of user uploaded and public data, with inference algorithms and tools for the storage, visualization and analysis of biological networks. The portal is fully integrated into the Gaggle framework to seamlessly exchange data with desktop and web applications and to allow the user to create, save and modify workspaces, and it includes social networking capabilities for collaborative projects. While the current release of the database contains networks for 13 prokaryotic organisms from diverse phylogenetic clades (4678 co-regulated gene modules, 3466 regulators and 9291 cis-regulatory motifs), it will be rapidly populated with prokaryotic and eukaryotic organisms as relevant data become available in public repositories and through user input. The modular architecture, simple data formats and open API support community development of the portal.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Abiotic Stress Reorganizes Rhizosphere and Endosphere Network Structure of Sorghum bicolor

Sorghum bicolor is a promising bioenergy feedstock with high biomass production and unusual tolerance for stresses, such as water and nutrient limitation. Although the membership of the sorghum microbiome in response to stress has been explored, relatively little is known about how microbe–microbe networks change under water- or nutrient-limited conditions. This is important because network changes can indicate impacts on the functionality and stability of microbial communities. We performed network-based analysis on the core bacterial and archaeal community of an agronomically promising high biomass bioenergy genotype, Grassl, grown under nitrogen and water stress. Stress caused relatively minor changes in bacterial abundances within soil, rhizosphere, and endosphere communities but led to significant changes in bacterial network structure and modularity. We found a complete reorganization of network roles in all plant compartments, as well as an increase in the modularity and proportion of positive associations, which potentially could represent coexistence and cooperation in the sorghum bacterial/archaeal community under stress. Although stressors are often believed to be destabilizing, we found stressed networks were as or more stable than non-stressed networks, likely due to their redundancy and compartmentalization. Together, these findings support the idea that both sorghum and its bacterial/archaeal community can be resilient to future environmental stressors.

09 BIOMASS FUELS↗
DOE OSTI2021

Simulating non-native cubic interactions on noisy quantum machines

As a milestone for general-purpose computing machines, we demonstrate that quantum processors can be programed to efficiently simulate dynamics that are not native to the hardware. Moreover, on noisy devices without error correction, we show that simulation results are significantly improved when the quantum program is compiled using modular gates instead of a restricted set of standard gates. We demonstrate the general methodology by solving a cubic interaction problem, which appears in nonlinear optics, gauge theories, as well as plasma and fluid dynamics. To encode the non-native Hamiltonian evolution, we decompose the Hilbert space into a direct sum of invariant subspaces in which the nonlinear problem is mapped to a finite-dimensional Hamiltonian simulation problem. Furthermore, in a three-states example, the resultant unitary evolution is realized by a product of approximately 20 standard gates, using which approximately ten simulation steps can be carried out on state-of-the-art quantum hardware before results are corrupted by decoherence. In comparison, the simulation depth is improved by more than an order of magnitude when the unitary evolution is realized as a single cubic gate, which is compiled directly using optimal control. Alternatively, parametric gates may also be compiled by interpolating control pulses. Modular gates thus obtained provide high-fidelity building blocks for quantum Hamiltonian simulations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2017

Multistage Monte Carlo simulation of jet modification in a static medium

In this work, the modification of hard jets in an extended static medium held at a fixed temperature is studied using three different Monte Carlo event generators: linear Boltzmann transport (LBT), modular all twist transverse-scattering elastic-drag and radiation (MATTER), and modular algorithm for relativistic treatment of heavy-ion interactions (MARTINI). Each event generator contains a different set of assumptions regarding the energy and virtuality of the partons within a jet versus the energy scale of the medium and, hence, applies to a different epoch in the space-time history of the jet evolution. Here modeling is developed where a jet may sequentially transition from one generator to the next, on a parton-by-parton level, providing a detailed simulation of the space-time evolution of medium modified jets over a much broader dynamic range than has been attempted previously in a single calculation. Comparisons are carried out for different observables sensitive to jet quenching, including the parton fragmentation function and the azimuthal distribution of jet energy around the jet axis. The effect of varying the boundary between different generators is studied and a theoretically motivated criterion for the location of this boundary is proposed. Lastly, the importance of such an approach with coupled generators to the modeling of jet quenching is discussed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2012

Conventions and workflows for using Situs

Recent developments of the Situs software suite for multi-scale modeling are reviewed. Typical workflows and conventions encountered during processing of biophysical data from electron microscopy, tomography or small-angle X-ray scattering are described. Situs is a modular program package for the multi-scale modeling of atomic resolution structures and low-resolution biophysical data from electron microscopy, tomography or small-angle X-ray scattering. This article provides an overview of recent developments in the Situs package, with an emphasis on workflows and conventions that are important for practical applications. The modular design of the programs facilitates scripting in the bash shell that allows specific programs to be combined in creative ways that go beyond the original intent of the developers. Several scripting-enabled functionalities, such as flexible transformations of data type, the use of symmetry constraints or the creation of two-dimensional projection images, are described. The processing of low-resolution biophysical maps in such workflows follows not only first principles but often relies on implicit conventions. Situs conventions related to map formats, resolution, correlation functions and feature detection are reviewed and summarized. The compatibility of the Situs workflow with CCP4 conventions and programs is discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Dispersive X-ray absorption spectroscopy using independent grazing-incidence focusing and convexly bent Bragg-crystal dispersing optics

We present a modular instrument for dispersive X-ray absorption spectroscopy (DXAS) developed for the Advanced Spectroscopy Beamline at Sector 25 of the Advanced Photon Source. The setup employs a double-multilayer monochromator to provide X-rays with a broad energy bandwidth, Kirkpatrick–Baez mirrors for focusing, a convexly bent Bragg-crystal polychromator for energy dispersion, and a pixel-array detector to resolve all X-ray energies and collect their intensity simultaneously, thereby enabling acquisition of a full X-ray absorption spectrum in a single shot. The use of separate optics for X-ray focusing and energy dispersion provides high spatial resolution and avoids chromatic aberrations inherent in focusing bent-crystal optics, and a modular design makes implementation of the technique at other beamlines possible without requiring modifications to the upstream beamline configurations. Theoretical calculations are performed to determine optimal instrument operating parameters and demonstrate that an energy resolution better than the K-edge core-hole lifetime broadening can be maintained while providing a sufficient bandwidth for X-ray absorption near-edge structure spectroscopy through the full operating range of 5–11 keV. Additionally, instrument design, data analysis methods, and initial DXAS results on lithium–manganese–nickel oxide laminates are presented.

47 OTHER INSTRUMENTATION↗
DOE OSTI2019

Adaptation of Commercial Current-Controlled Inverters for Operation with Virtual Oscillator Control

Virtual oscillator control (VOC) is a decentralized time-domain control technique for ac microgrids where inverters are regulated to emulate the dynamics of weakly nonlinear oscillators. VOC enables the design of modular and scalable systems where inverters can synchronize and share power without communication and in near real-time. In this paper, we show how off-the-shelf commercial inverters with current control can be reprogrammed to behave as voltage sources with virtual oscillator dynamics for deployment in islanded settings. We focus on commercial grid-tied inverters that have an inner current-control loop and show how the outer-loop controls can be straightforwardly modified to enable voltage-control-mode operation. To illustrate the practicality and ease of our approach, the proposed strategy was implemented on a 3.2 kVA experimental test bed composed of 10 SunPower-brand micro-inverters with special firmware for VOC implementation. Results from the experiments not only demonstrate feasibility of the proposed dual-loop VOC architecture on a hardware setup but also show improved voltage regulation due to the additional voltage control loop.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2023

Medium Voltage Solid State Transformer for Extreme Fast Charging Applications

A modular and scalable solid state transformer (SST) with direct medium voltage (MV) AC connectivity is proposed to enable DC extreme fast charging (XFC) of electric vehicles. Single-phase-modules (SPMs), each consisting of an active-front-end (AFE) stage and an isolated DC-DC stage, are connected in input-series-output-parallel (ISOP) configuration. The modular hardware is co-designed with decentralized control of the DC-DC stages where voltage and power balancing are achieved by each SPM using only its local sensor feedback; a centralized controller (CC) regulates the low voltage (LV) DC bus through the AFE stages without any sensor feedback form the SPMs. The controller architecture contrasts sharply with the prior art for MV AC to LV DC SSTs where high-speed bidirectional communication among SPMs and a CC are required for module-level voltage and power balancing, which severely limits the scalability and practical realization of higher voltage and higher power units. Detailed small-signal analysis and controller design guidelines are developed. Furthermore, a soft start-up strategy is presented. The proposed converter and control structure are validated through simulation and experimental results.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2024

Exploring the Landscape of Distributed Graph Clustering on Leadership Supercomputers

The rapid growth of large-scale datasets in fields like biology and social networks has driven the need for advanced graph analytics techniques. Community detection, a fundamental task in graph analytics, identifies closely connected groups of nodes within a network, providing valuable insights across various disciplines. This study focuses on two classic community detection methods, the Louvain algorithm and Markov Clustering (MCL), and evaluates the performance of two prominent distributed community detection algorithms: HiPDPL-GPU, our prior implementation, and HipMCL. We conduct experiments on GPU-accelerated heterogeneous HPC systems, Summit and Frontier, to assess their performance under varying conditions. Our objective is to identify the strengths and weaknesses of these algorithms in terms of scalability, and quality of solutions. We evaluate these algorithms on a diverse set of 70+ networks spanning 13 domains, with sizes ranging up to 4.2 billion edges. Our results demonstrate that HiPDPL-GPU consistently outperforms HipMCL, especially for large-scale networks. HiPDPL-GPU achieves significantly faster runtimes (47x to 1439x), higher modularity scores, and improved scalability. These findings highlight HiPDPL-GPU as a promising solution for efficient and effective large-scale graph analytics in diverse application domains, and provide insights into the feasibility of using MCL-based approaches for certain application domains.

Community detection, graph algorithms↗
DOE OSTI2014

A Runtime Environment for Supporting Research in Resilient HPC System Software & Tools

The high-performance computing (HPC) community continues to increase the size and complexity of hardware platforms that support advanced scientific workloads. The runtime environment (RTE) is a crucial layer in the software stack for these large-scale systems. The RTE manages the interface between the operating system and the application running in parallel on the machine. The deployment of applications and tools on large-scale HPC computing systems requires the RTE to manage process creation in a scalable manner, support sparse connectivity, and provide fault tolerance. We have developed a new RTE that provides a basis for building distributed execution environments and developing tools for HPC to aid research in system software and resilience. This paper describes the software architecture of the Scalable runTime Component Infrastructure (STCI), which is intended to provide a complete infrastructure for scalable start-up and management of many processes in large-scale HPC systems. We highlight features of the current implementation, which is provided as a system library that allows developers to easily use and integrate STCI in their tools and/or applications. The motivation for this work has been to support ongoing research activities in fault-tolerance for large-scale systems. We discuss the advantages of the modular framework employed and describe two use cases that demonstrate its capabilities: (i) an alternate runtime for a Message Passing Interface (MPI) stack, and (ii) a distributed control and communication substrate for a fault-injection tool.

Computer Science↗
DOE OSTI2017

Dissipativity-based design of local and wide-area DER controls for large-scale power systems with high penetration of renewables

In this paper, an integrated and modular control design is developed for distributed energy resources (DERs) to stabilize power systems and minimize effects of load variations and intermittent generation. Traditionally, the droop control of each generator (or virtual power plant) works as a local feedback loop to track frequency during load disturbance, whereas automatic generation control (AGC) calculates control signals and sends them to each generator with the goal of matching the total generation and load in the overall system. The droop control and the AGC work separately, therefore the two controls often conflict each other. The proposed design enables us to modularly synthesize an integrated control for each of the DERs by using both local and wide-area measurements so that the controls work together in enhancing stability and performance of the power system. The design methodology admits the full nonlinear power flow equations, and it results in a data-driven control that in real-time takes into account the nonlinear power flow interactions (in terms of current angle measurements) and adaptively adjusts parameters of the controls that operate the DERs. The design framework uses the concept of passivity-short systems to analyze individual DERs and quantify their dynamic responses in such a way that the resulting system-wide implementation becomes plug-and-play. Simulations are done to demonstrate the effectiveness of the proposed methodology and design.

Harvey, Roland↗
DOE OSTI2019

Decentralized Carrier Interleaving in Cascaded Multilevel DC-AC Converters: Preprint

Cascaded dc-ac converters with interleaved carriers are commonly used in applications where elevated voltages and low-distortion multilevel waveforms are needed. Example applications include modular multilevel converters and solid-state transformers. In such systems, carrier interleaving is generally achieved via communication among the stacked converters or a centralized controller. Due to the large number of converters in such a system, existing approaches entail significant wiring complexity and communication may limit resilience to failures. In this paper, we introduce a control strategy which achieves communication-free carrier interleaving among series-connected converters. The proposed controller is embedded within each converter control loop and only requires measurements available at each set of converter terminals. We formulate a dynamic system model and show that the system converges to the interleaved condition irrespective of the number of converters in the stack. After outlining a practical method for digital implementation, experiments are shown on a hardware-in-the-loop setup.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2017

Design Considerations of a Transverse Flux Machine for Direct-Drive Wind Turbine Applications

This paper presents the design considerations of a double-sided transverse flux machine (TFM) for direct-drive wind turbine applications. The TFM has a modular structure with quasi-U stator cores and ring windings. The rotor is constructed with ferrite magnets in a flux-concentrating arrangement to achieve high air gap flux density. The design considerations for this TFM with respect to initial sizing, pole number selection, key design ratios, and pole shaping are presented in this paper. Pole number selection is critical in the design process of a TFM because it affects both the torque density and power factor under fixed magnetic and changing electrical loading. Several key design ratios are introduced to facilitate the design procedure. The effect of pole shaping on back-emf and inductance is also analyzed. These investigations provide guidance toward the required design of a TFM for direct-drive applications. The analyses are carried out using analytical and three-dimensional finite element analysis. A prototype is under construction for experimental verification.

17 WIND ENERGY↗
DOE OSTI2023

Design, Optimization, and Validation of GaN-Based DAB Converter for Active Cell Balancing in BTMS Applications

This paper focuses on the design of a bidirectional dual active bridge (DAB) DC/DC converter that utilizes Gallium Nitride (GaN) switches as active components. In the existing literature, MOSFET-based DAB for active cell balancing is available, but GaN-based DAB converter for active cell balancing is still new. The proposed modular isolated GaN-based DAB converter is designed as an individual module of active cell balancing for behind-the-meter storage (BTMS) applications, targeting high-power charging stations. Modular isolated converters are connected to each cell (low voltage bus), and each cell is connected in series to build up a battery module. According to the reference current command of supervisory control, each DAB converter can transfer power back and forth through the high voltage (HV) bus to balance the State of Charge (SoC) between the cells. Each module DAB converter is designed at a 50 W power rating. Switch power and transformer losses are analyzed for different switching frequencies, showing the optimum switching frequency for minimum losses. Furthermore, the procedure to select the required gate driver and the PCB layout optimization are discussed. Finally, the DAB performance analysis of GaN-based DAB and Si-based DAB is provided for a battery module operating with a LiFeMnPO4 prismatic cell with 3.2V 20Ah rated values.

active cell balancing↗
DOE OSTI2021

Automated Generation of Integrated Digital and Spiking Neuromorphic Machine Learning Accelerators

The growing numbers of application areas for artificial intelligence (AI) methods have led to an explosion of domain-specific accelerators that could support every new machine learning (ML) algorithm advancement, clearly highlighting the need for a capability to quickly and automatically transition from algorithm definition to hardware implementation and explore design space along a variety of SWaP (size, weight and Power). The software defined architectures (SODA) synthesizer implements a compiler-based modular infrastructure for the end-to-end generation of machine learning accelerators from high-level frameworks to hardware description language. At the same time, neuromorphic computing, by mimicking how the brain operates, promises to perform artificial intelligence tasks at efficiencies orders of magnitude higher than the current conventional tensor-processing based accelerators, as demonstrated by a variety of specialized designs leveraging Spiking Neural Networks (SNNs). Nevertheless, the mapping of an artificial neural network (ANN) to solutions supporting SNNs is still a non-trivial and very device-specific task, and completely lack the possibility to design hybrid systems that integrate conventional and spiking neural models. In this paper we discuss the support for such an integrated generation leveraging the SODA Synthesizer framework and its modular structure. In particular, we present a new MLIR dialect (part of the SODA frontend) that allows expressing spiking neural network features (e.g., available resources, spiking sequences, analog signal reading, etc.) and illustrate how it enables mapping to Spiking Neurons and deployment to the related specialized hardware (which, in the digital domain, could be generated through the other existing layers of the SODA Synthesizer). We then discuss the opportunities for even deeper integration afforded by the hardware compilation infrastructure, providing a path towards the generation of complex heterogeneous artificial intelligence systems.

Curzel, Serena↗
DOE OSTI2024

Balancing Charging Station Utilization and Throughput in Electric Vehicle Charging Stations with Queuing Theory

The rapid increase in electric vehicle (EV) adoption demands enhancements in the efficiency and adaptability of EV supply equipment (EVSE). Traditional EVSE systems often fail to optimize power delivery to meet the variable acceptance rates of EV batteries, resulting in significant energy wastage and reduced operational efficiency. This research addresses these challenges by integrating queuing theory with modular EVSE architectures, offering a dual strategy to optimize the operation of EV charging stations. A simulation model was developed to assess various configurations of charger capacities and outlet numbers. This model aimed to identify the optimal setup that maximizes station utilization while minimizing charging times and maximizing throughput. The model focused on charger capacities ranging from 50 to 250 kW and analyzed the different capacities’ effects on charging times and the number of vehicles served. The results indicate that a charger capacity of 125 kW is optimal, striking a balance between the charging time and the number of EVs served per hour, thus achieving the highest station utilization rate. This capacity allows for servicing a significant number of EVs with moderate increases in charging times. Lower capacities, although capable of serving more vehicles, lead to longer charging times and decreased throughput efficiency. The study underscores the effectiveness of combining queuing theory with flexible, modular charging systems that can dynamically adjust to EV charging demands.

Kumar, Praveen↗