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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 415 records · Page 23
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Control, Fault Management, and Grid Support Functionality of an MV AC-DC Solid State Transformer based EV Extreme Fast Charging Station

Electric vehicles (EVs) have become increasingly popular in recent times while revolutionizing the consumer and commercial transportation market. The development of charging infrastructure has become one of the priorities for increasing the adoption of EVs. Extreme fast charging (XFC) technology can reduce the so-called ’range anxiety’ of consumers as they significantly reduce the charging time. With the advent of wide band-gap (WBG) power devices and improvement in power electronic converters, medium voltage (MV) solid state transformer (SST) based XFC system has the potential to replace the traditional XFC stations because of the lower footprint, ease of installation, enhanced control feature, and better system efficiency. The control system design is one of the critical aspects of the SST development process. Careful consideration and detailed analysis are required to find out suitable control method for the SST based on its topology among different centralized and decentralized control architectures. Also, the control parameters selection and potential improvement to the transient response of the controller ought to be investigated. Another major concern of the SST is different types of internal fault which reduces the overall reliability of the XFC system. As a result, designing a robust protection system is essential. Among different fault modes, open circuit switch faults have received significant attention as an active research area because of their likelihood and severe effects on converters. Therefore, the power stages used in the XFC system require functional and accurate open circuit switch fault management methods. An equally significant aspect of this SST based XFC is its compatibility in a microgrid where there is no synchronous generator present. When the grid is not available, the XFC SSTs can provide grid forming capability and continue supplying the critical loads in islanded mode. The transition between grid connected and islanded mode, especially the grid resynchronization process has to be carefully performed for the safety of the microgrid components. The challenges posed by the aforementioned issues have inspired the work done in this dissertation. Here, a 13.2 kV, 1 MVA, AC/DC SST for the XFC system is examined and a comparative analysis is conducted to select the control architecture based on feasibility of implementation and performance. A detailed control parameter design process is demonstrated considering the sensor dynamics and delay. The selected decentralized control method is augmented by introducing a novel sensor-less load current feedforward method to provide better voltage regulation at the DC bus during a change of load. Next, in the fault management section, a hierarchical failure mode effect analysis (FMEA) is proposed to enable a systematic design of the internal fault protection of the XFC SST as there are limited examples in the literature regarding the analysis of the safety and design of the protection of a power electronic converter system. Novel open circuit switch fault management methods for the converters in the system are presented. Finally, XFC SST based MV microgrid operations in grid connected mode and islanded mode are explored. A secondary control method for grid resynchronization is presented and a design process of control parameters is shown to ensure the stability of the secondary voltage and frequency regulation.

30 DIRECT ENERGY CONVERSION↗
DOE OSTI2021

Upgrades and redesign of the National Ignition Facility’s soft x-ray opacity spectrometer (OpSpec)

The soft x-ray Opacity Spectrometer (OpSpec) used on the National Ignition Facility (NIF) has recently incorporated an elliptically shaped crystal. The original OpSpec used two convex cylindrical crystals for time-integrated measurements of point-projection spectra from 540 to 2100 eV. However, with the convex geometry, the low-energy portion of the spectrum suffered from high backgrounds due to scattered x-rays as well as reflections from alternate crystal planes. An elliptically shaped crystal allows an acceptance aperture at the crossover focus between the crystal and the detector, which reduces background and eliminates nearly all reflections from alternate crystal planes. The current elliptical design is an improvement from the convex cylindrical design but has a usable energy range from 900 to 2100 eV. In addition, OpSpec is currently used on 18 NIF shots/year, in which both crystals are typically damaged beyond reuse, so efficient production of 36 crystals/year is required. Design efforts to improve the existing system focus on mounting reliability, reducing crystal strain to increase survivability between mounting and shot time, and extending the energy range of the instrument down to 520 eV. The elliptical design, results, and future options are presented.

Wallace, M. S. (ORCID:0000000310871216)↗
DOE OSTI2023

Cyber-Informed Engineering Guidance—Implementing CIE in Early Systems Engineering Lifecycle Stages

Traditionally, cybersecurity is not considered in the design process. Design engineers typically focus on building safety and reliability into their products and applications. Security against malicious cyber incidents is often an afterthought, resulting in deployment of security solutions during installation or operation. Unfortunately, waiting to consider cybersecurity until later in the systems engineering lifecycle often results in less effective and more expense security. Idaho National Laboratory (INL) developed the concept of Cyber-Informed Engineering (CIE) in 2015 to provide a framework that enables cybersecurity to be built into systems beginning at the conceptual design stage. In addition to ongoing research by INL, the U.S. Department of Energy (DOE) Office of Cybersecurity, Energy Security, and Emergency Response has recently developed a National CIE Strategy document for incorporating CIE into the design and operation of infrastructure systems reliant on digital monitoring or controls. This paper provides a brief review of this National CIE Strategy as well as a roadmap to historical, current, and future CIE research by INL through the U.S. DOE Office of Nuclear Energy (NE) Cybersecurity Crosscutting Technology Development Program. A near-term focus of the DOE-NE’s research and development is to extend the foundational CIE work into detailed guidance for implementation during initial systems engineering stages in nuclear digital instrumentation and control projects and to demonstrate use of the guidance in an integrated energy systems project.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2025

Automating Testing of DUNE Electronics via a Finite State Machine

The Deep Underground Neutrino Experiment (DUNE) is a flagship international collaboration designed to study neutrinos tiny, nearly massless particles that may hold answers to fundamental questions about the Universe. Fermilab s Robotic Test Stand (RTS) plays a critical role in ensuring the quality of approximately 50,000 Application-Specific Integrated Circuit (ASIC) chips that will be used in DUNE s massive liquid argon detectors. These electronics will be inside the cryostat; therefore, they will need to have a high yield of working chips and low noise. To improve the automation and reliability of the RTS, this project focused on designing and implementing a Python-based finite state machine (FSM) to manage chip handling workflows. The FSM was developed as a modular software framework to coordinate robotic arm movements, manage chip tray positions, and monitor system states during testing. Key features include robust error handling routines, a pause/resume system for safe mid-cycle interruptions, and a simulation mode for iterative testing without hardware dependencies. The system was designed to prepare for seamless integration with RTS hardware components such as the robotic arm and vision system. This integration will streamline collaboration and enable efficient deployment of updates across the six total institutions performing testing. The outcomes of this internship contribute to Fermilab s mission to advance high-energy physics and support the DOE s national goals by directly improving the testing of equipment to be used in DUNE. The project also provided valuable experience in software design and contributing to the success of DUNE.

Kang, Caleb [William Rainey Harper Coll.]↗
DOE OSTI2025

Automating Testing of DUNE Electronics via a Finite State Machine

The Deep Underground Neutrino Experiment (DUNE) is a flagship international collaboration designed to study neutrinos—tiny, nearly massless particles that may hold answers to fundamental questions about the Universe. Fermilab’s Robotic Test Stand (RTS) plays a critical role in ensuring the quality of approximately 50,000 Application-Specific Integrated Circuit (ASIC) chips that will be used in DUNE’s massive liquid argon detectors. These electronics will be inside the cryostat; therefore, they will need to have a high yield of working chips and low noise. To improve the automation and reliability of the RTS, this project focused on designing and implementing a Python-based finite state machine (FSM) to manage chip handling workflows. The FSM was developed as a modular software framework to coordinate robotic arm movements, manage chip tray positions, and monitor system states during testing. Key features include robust error handling routines, a pause/resume system for safe mid-cycle interruptions, and a simulation mode for iterative testing without hardware dependencies. The system was designed to prepare for seamless integration with RTS hardware components such as the robotic arm and vision system. This integration will streamline collaboration and enable efficient deployment of updates across the six institutions performing testing. The outcomes of this internship contribute to Fermilab’s mission to advance high-energy physics and support the DOE’s national goals by directly improving the testing of equipment to be used in DUNE. The project also provided valuable experience in software design and contributing to the success of DUNE.

Kang, Caleb [Fermilab]↗
DOE OSTI2023

Automotive Silicon Carbide Power Module Cooling With A Novel Modular Manifold And Embedded Heat Sink

The next generation of integrated power electronics packages will implement wide-bandgap devices with ultrahigh device heat fluxes. Although jet impingement has received attention for power electronics thermal management, it is not used in commercial electric vehicles (EVs) because of the associated pressure drop and reliability concerns. Here, in this paper, we present a modular thermal management system designed for automotive power electronics. The system achieves superior thermal performance to benchmarked EVs, while adhering to reliability standards and with low pumping power. The system utilizes a low-cost and lightweight plastic manifold to generate jets over an optimized heat sink, which is embedded in the direct-bonded-copper (DBC) substrate. The embedded heat sink concept leverages additive manufacturing to add elliptical pin fins to the DBC substrate. The heat sink geometry is optimized for submerged jet impingement using a unit-cell model and an exhaustive search algorithm. The model predictions are validated using unit-cell experiments. A full-scale power module model is then used to compare the DBC-embedded heat sink against direct DBC cooling and baseplate-integrated heat sinks for single-sided (SS) and double-sided (DS) cooling concepts. Using the SS and DS DBC-embedded cooling concepts, the models predict a thermal resistance that represents a reduction of 75% and 85% compared to the 2015 BMW i3, respectively, for the same water-ethylene glycol inverter flow rate. We have shown that an inverter with a 100-kilo-Watt-per-liter power density is achievable with the proposed design.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2025

Convergent Manufacturing of Large-Scale Components for Nuclear Applications, via Additive Manufacturing and Powder Metallurgy Hot Isostatic Pressing

Powder metallurgy (PM)–hot isostatic pressing (PM-HIP) has long been recognized as a powerful route for producing fully dense, near net shape metallic components. By consolidating powders under high temperature and pressure, HIP provides isotropic properties, uniform microstructures, and scalability to complex geometries that are vital for sectors such as aerospace, energy, and nuclear power. Yet despite these advantages, the technology has remained constrained by costly trial and error canister fabrication, limitations of conventional forging, and incomplete knowledge about how the canister design influences final part properties. Additive manufacturing (AM), by contrast, thrives on design freedom and geometric flexibility but struggles with speed, scalability, and cost when applied to very large structures. The research presented in this report investigated how a convergent manufacturing approach, combining AM with PM-HIP, can merge the strengths of both technologies, leveraging AM’s flexibility for canister design and HIP’s consolidation capability to deliver reliable, large, and complex parts. The work progressed through three case studies that built on one another in scale and complexity. Small cylindrical canisters fabricated by conventional methods, laser powder bed fusion, and directed energy deposition were filled with stainless steel powders and subjected to HIP. The resulting parts demonstrated near-full density and mechanical properties on par with wrought stainless steel, showing for the first time that AM canisters can be a direct substitute for conventional ones without sacrificing quality. The next step involved a medium-scale, noncentrosymmetric T-valve, which is an enclosed, multibranch geometry that tested the limits of AM + PM-HIP integration. The T-valve achieved predictable shrinkage and uniform densification, confirming feasibility for enclosed designs. However, this study also revealed oxide inclusions and interfacial challenges at the AM + HIP boundary, underscoring the critical importance of controlling interface chemistry and employing robust, in situ strategies, such as melt pool monitoring and thermal monitoring, coupled with nondestructive evaluation techniques such as x-ray computed tomography. Finally, the effort culminated in fabricating a large-scale impeller weighing nearly 2000 lb and spanning 5 ft in diameter. Produced via multirobot wire arc AM and hot isostatic pressed to near-full density, the impeller validated industrial-scale feasibility. Predictive models closely matched experimental shrinkage, tensile properties were spatially uniform across the component, and the AM + PM-HIP interface proved mechanically sound despite the presence of oxide-decorated prior particle boundaries. This large-scale demonstration is a major milestone, showing that hybrid AM + PM‑HIP can reliably deliver components at reactor-relevant scales. Collectively, these studies charted a logical pathway: small-scale work built scientific confidence, medium-scale work highlighted opportunities and challenges, and large-scale work proved industrial impact. The overarching conclusion of this report is that AM + PM-HIP should not be seen as a replacement for forging but as a complementary pathway that provides the US with flexibility, resilience, and new options for manufacturing nuclear-grade components. Looking ahead, several directions emerge as critical to sustaining progress. Predictive modeling must become faster, more accessible, and more accurate, with digital twins and machine learning reducing reliance on trial and error. Powders and alloys must be optimized for HIP, with improved cleanliness, reduced oxides, and tailored chemistries that enhance creep, fatigue, and irradiation resistance. Interfaces between AM and HIP regions must be better engineered through coatings, machining strategies, and surface treatments to mitigate oxide formation and ensure reliable bonding to explore opportunities for HIP of targeted compositional parts, as well as multimaterial HIP cladding applications. Monitoring and nondestructive evaluation need to expand, incorporating multimodal sensors, x-ray computed tomography, and real-time data integration through platforms such as Pelican. At the same time, the pathway to industrial adoption requires techno-economic analysis, machinability studies, and qualification frameworks aligned with industry and regulatory standards. Finally, workforce and academic engagement must be strengthened. Programs that train technicians and engineers for US Navy and US Department of Energy manufacturing challenges should be paired with academic partnerships to support fundamental research, with open sharing of non-export-controlled data to accelerate innovation and build the next generation of experts. In conclusion, this report demonstrates that hybrid AM + PM-HIP is scientifically viable and strategically important. By combining the design agility of AM with the consolidation strength of HIP and embedding modeling, monitoring, and workforce development, this approach provided a transformative new capability for US manufacturing. The path forward is clear: hybrid AM + PM-HIP is not just a promising research direction but is also potentially an industrially relevant pathway that can reshape how nuclear-grade components are designed, qualified, and deployed.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Next Generation Solid Oxide Fuel Cell Module Development

The overall objective of this project was to develop a transformative Solid Oxide Fuel Cell (SOFC) building block configuration comprised of multi-stack arrays that can be utilized in large-scale power plants. This transformative design signified the benefits of lower performance degradation coupled with improved reliability, low cost, smaller packaging for easier transport and installation, and improved maintenance and field serviceability characteristics. The project goal was to design and fabricate a scalable hot module for housing an array of SOFC stacks and to demonstrate the characteristics of the module gas distribution, insulation and instrumentation, and DC power take-off. The approach was to validate the design of a stack prototype scalable to megawatt (MW) class systems using FuelCell Energy’s Compact SOFC Architecture (CSA) stacks. The scope of work was intended to design, build, and test a compact and low-cost multi-stack sub-module with flexibility to house CSA stacks and scalable to 350 kW which could ultimately be deployed in construction of MW-class systems.

20 FOSSIL-FUELED POWER PLANTS↗
DOE OSTI2023

Optimizing design and dispatch of a resilient renewable energy microgrid for a South African hospital

Lack of access to reliable energy is a major concern for countries in sub-Saharan Africa. The national grids are unable to consistently satisfy demand. Therefore, users turn to distributed generation systems in the form of back-up generators. However, such systems are usually designed based on a rule of thumb. We employ a mixed-integer linear programming model that considers several options such as renewable energy, combined heat and power, and storage technologies, in addition to those on-site, to provide optimal design and dispatch decisions that minimize total cost. We apply this model to a case study for a hospital in South Africa, considering its need for reliable electricity in light of multiple outages that might occur over the course of a year, as well as its high heating and cooling loads. Our results show that optimal design and dispatch decisions for the distributed generation system address reliability challenges, regardless of the time at which they occur. And, these solutions yield millions of dollars in savings, suggesting that technologies such as the absorption chiller may be overlooked in typical designs; its integration can reduce demand charges even in the absence of combined heat and power. We show that total cost is most sensitive to changes in site electrical demand, followed by capital cost, fuel cost, photovoltaic production, and monthly demand charges; changes in fuel cost primarily affect system sizes of combined heat and power and the absorption chiller, while photovoltaic system size is more sensitive to the changes in capital and fuel costs, photovoltaic resource availability, and hourly electrical demand. Finally, an outage simulator demonstrates the ability of our optimized system to sustain with no interruptions in power five-hour outages with probability 1.0 and ten-hour outages with probability 0.65, significant improvements over 0.5 and 0.0, respectively, under a business-as-usual case.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2026

Failure Mode and Effects Analysis (FMEA) for Photovoltaic Inverter

Photovoltaic (PV) inverters are critical yet vulnerable components in modern energy systems, often acting as reliability bottlenecks that increase the levelized cost of energy (LCOE). To address this, this paper presents a comprehensive Failure Mode and Effects Analysis (FMEA) tailored for PV inverters. Leveraging field data and literature, we identify failure-prone components, such as capacitors,, and relays, and prioritize their risks based on quantitative Risk Priority Numbers (RPNs). The analysis reveals that surge-induced MOV short circuits, capacitor degradation, and environmental cooling fan failures dominate the risk profile. These findings provide a targeted framework for reliability improvement, guiding future efforts in predictive diagnostics, design optimization, and accelerated life testing strategies.

14 SOLAR ENERGY↗
DOE OSTI2022

Structure- and Interaction-Based Design of Anti-SARS-CoV-2 Aptamers

Aptamer selection against novel infections is a complicated and time-consuming approach. Synergy can be achieved by using computational methods together with experimental procedures. In this study, we aim to develop a reliable methodology for a rational aptamer in silico et vitro design. The new approach combines multiple steps: (1) Molecular design, based on screening in a DNA aptamer library and directed mutagenesis to fit the protein tertiary structure; (2) 3D molecular modeling of the target; (3) Molecular docking of an aptamer with the protein; (4) Molecular dynamics (MD) simulations of the complexes; (5) Quantum-mechanical (QM) evaluation of the interactions between aptamer and target with further analysis; (6) Experimental verification at each cycle for structure and binding affinity by using small-angle X-ray scattering, cytometry, and fluorescence polarization. By using a new iterative design procedure, structure- and interaction-based drug design (SIBDD), a highly specific aptamer to the receptor-binding domain of the SARS-CoV-2 spike protein, was developed and validated. The SIBDD approach enhances speed of the high-affinity aptamers development from scratch, using a target protein structure. The method could be used to improve existing aptamers for stronger binding. This approach brings to an advanced level the development of novel affinity probes, functional nucleic acids. It offers a blueprint for the straightforward design of targeting molecules for new pathogen agents and emerging variants.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Integrating Transactive Energy into Reliability Evaluation for a Self-healing Distribution System with Microgrid

Non-utility owned distributed energy resources (DERs) are mostly untapped currently, but they can provide many grid services such as voltage regulation and service restoration, if properly controlled, and can improve the distribution systems reliability when coordinated with utility-owned assets such as self-healing control and microgrids. This paper integrates transactive energy control into the distribution system reliability evaluation to quantitatively assess the impact of non-utility owned DERs on reliability improvement. Here, a transactive reactive power control strategy is designed to incentivize the DERs to provide reactive power support for improving voltage profiles thus enabling additional customer load restoration during an outage. Also, an operational sequence to coordinate the non-utility owned DERs with the utility owned self-healing control and utility owned microgrids is designed and integrated into the service restoration process with the operational constraints guaranteed by checking the three-phase unbalanced power flow for post-fault network reconfiguration. The reliability indices are then calculated through a Monte Carlo simulation. The transactive reactive power control strategy is tested on a four-feeder distribution system operated by Duke Energy in the U.S. Results demonstrate that the non-utility owned DERs with the transactive control improve the reliability of both the system and critical loads by more than 30%.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2022

Cost Efficient-by-Design Microreactors: Trade-offs between cost, technical, and regulatory factors

This research evaluates a cost reduction investigation through adoption of a functional containment approach on the microreactor system and structure. Trade-offs between microreactor system designs, fuels and reactor module sizes are evaluated based on performance-based and risk-informed design procedures. Cost savings are evaluated against trade-offs in the reliability of passive heat removal systems, reactivity control, and radioactive material containment. Results can inform the Microreactor Program and reactor designs on “sweet spots” for microreactors that are cost-efficient while meeting required safety limits.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2020

Validating Extreme Scale Resilience with Veracity (Final Project Report)

As semiconductor technology continues to scale to smaller dimensions and as power-consumption of processor chips continues to increase in importance, there is significant uncertainty about the reliability of future large-scale computers. This uncertainty impacts algorithm design and application development, as well as decisions about system operation policy and provisioning decisions. The Veracity endeavored to answer pertinent questions regarding system reliability and resilience with the goal of enabling reliable science on future leadership machines while keeping overprovisioning low.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Progress in development of pulsed resonant charging power supply for the Spallation Neutron Source extraction kicker PFN system

A conceptual design of the pulsed resonant charging power supply (RCPS) for the beam extraction system of the Spallation Neutron Source (SNS) at the Oak Ridge National Laboratory (ORNL) was previously reported at the 2019 IEEE Pulsed Power & Plasma Science Conference (PPPS 2019) [1]. Development and testing of the prototype supply continued through the year to finalize the design ahead of the Proton Power Upgrade (PPU). Testing revealed reliability issues with the original resonant charging scheme related to the step-up transformer core. Additional components were incorporated into the system, and some of the original prototype components were replaced to improve performance and reliability of the power supply. This paper describes the changes in the resonant charging scheme, presents the results of testing of the improved prototype at full power level, and shows the final design of the RCPS.

Peplov, Vladimir↗
DOE OSTI2022

Dynamic Material Flow Analysis of Silicon Photovoltaic Modules to Support a Circular Economy Transition

Solar photovoltaics (PV) are the fastest growing renewable energy technologies for clean, cheap, and sustainable electricity generation. To prepare for rapid scale-up, the PV industry needs to project material requirements to build out all aspects of the supply chain appropriately and plan to handle large volumes of module waste. Impacts of deploying different material circularity strategies to reduce waste and conserve primary resources need to be quantified to inform sustainable material management. Here, we introduce the photovoltaic dynamic material flow analysis (PV DMFA) model based on PV electricity generation. The model quantifies material flows and stocks in the cradle-to-cradle life cycles of utility-scale c-Si PV systems in the United States through 2100. We present case studies for solar flat glass and aluminum frame materials under various scenarios to project the impacts of PV performance, reliability, and processing parameters, material circularity strategies, and module design shifts. In the absence of circularity measures, ~100 million MT of flat glass and ~12 million MT of aluminum would be needed for PV installations by 2100 to meet projected growth in domestic utility PV demand to nearly 1000 TWh in 2100. With optimistic but feasible improvements in efficiency, reliability, and circularity, material intensity and waste could be reduced by nearly 50%. Efficient module collection, minimally intrusive recycling, and careful scrap handling and cleaning could improve material circularity in the PV value chain. This model serves as a sustainability data support tool that may aid in the circular economy transition for PV systems.

circular economy↗
DOE OSTI2020

Innovation in Radiological Security, Part 2 of 2 – Insights into Developing a Cloud-hosted Security Technology

A Sentry Remote Monitoring System (Sentry-RMS) is a stand-alone security system that provides detection, assessment, and communication of priority alarms as an additional means of thwarting internal and external threats to sites that maintain radiological material. The SEntry-RMS CommUnications and REsponse (Sentry-SECURE) platform is an optional feature of the Sentry-RMS that relays priority alarm information to the identified response stakeholders. Sentry-SECURE is hosted in a cloud environment that abstracts the data owner’s and data consumer’s platforms to allow for greater information sharing. This promotes situational awareness amongst authorized users and enables future innovation among modern response platforms. When securely architecting a cloud solution such as this, the use of design paradigms can be an effective tool to increase the accuracy and reliability of cyber- and information-security-related decisions made throughout the development process. This approach also supports the categorization of design considerations into three levels: industry concepts, project approaches, and data protections for digital processes. Industry concepts consist of the notional underpinnings that guide or motivate a security process, system, or design but often lack any tangible attributes. Project approaches represent decisions made during the design and development process to prioritize a solution, method, or practice above another that may provide a comparable functional output but lacks a desired security benefit. Data protections for digital processes represent the selection, integration, and implementation of specific controls for a given asset. This paper will explore specific examples of how Sentry-SECURE has been designed to account for considerations at each of these three levels, while balancing the operational intent of the platform with the security enhancements necessary to maintain data integrity, availability, and confidentiality.

assessment, RMS, security, physical, cloud, Cyber ↗
DOE OSTI2023

Evaluating the active site-substrate interplay between x-ray crystal structure and molecular dynamics in chorismate mutase

Designing realistic quantum mechanical (QM) models of enzymes is dependent on reliably discerning and modeling residues, solvents, and cofactors important in crafting the active site microenvironment. Interatomic van der Waals contacts have previously demonstrated usefulness toward designing QM-models, but their measured values (and subsequent residue importance rankings) are expected to be influenceable by subtle changes in protein structure. Using chorismate mutase as a case study, this work examines the differences in ligand-residue interatomic contacts between an x-ray crystal structure and structures from a molecular dynamics simulation. Select structures are further analyzed using symmetry adapted perturbation theory to compute ab initio ligand-residue interaction energies. The findings of this study show that ligand-residue interatomic contacts measured for an x-ray crystal structure are not predictive of active site contacts from a sampling of molecular dynamics frames. In addition, the variability in interatomic contacts among structures is not correlated with variability in interaction energies. However, the results spotlight using interaction energies to characterize and rank residue importance in future computational enzymology workflows.

Chemistry↗