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NASA NTRS1993

Applicability of PM3 to transphosphorylation reaction path: Toward designing a minimal ribozyme

A growing body of evidence shows that RNA can catalyze many of the reactions necessary both for replication of genetic material and the possible transition into the modern protein-based world. However, contemporary ribozymes are too large to have self-assembled from a prebiotic oligonucleotide pool. Still, it is likely that the major features of the earliest ribozymes have been preserved as molecular fossils in the catalytic RNA of today. Therefore, the search for a minimal ribozyme has been aimed at finding the necessary structural features of a modern ribozyme (Beaudry and Joyce, 1990). Both a three-dimensional model and quantum chemical calculations are required to quantitatively determine the effects of structural features of the ribozyme on the reaction it catalyzes. Using this model, quantum chemical calculations must be performed to determine quantitatively the effects of structural features on catalysis. Previous studies of the reaction path have been conducted at the ab initio level, but these methods are limited to small models due to enormous computational requirements. Semiempirical methods have been applied to large systems in the past; however, the accuracy of these methods depends largely on a simple model of the ribozyme-catalyzed reaction, or hydrolysis of phosphoric acid. We find that the results are qualitatively similar to ab initio results using large basis sets. Therefore, PM3 is suitable for studying the reaction path of the ribozyme-catalyzed reaction.

Manchester, John I.↗

DOE OSTI2024

In situ tumor model for longitudinal in silico imaging trials

Abstract Objective.In this article, we introduce a computational model for simulating the growth of breast cancer lesions accounting for the stiffness of surrounding anatomical structures.Approach.In our model, ligaments are classified as the most rigid structures while the softer parts of the breast are occupied by fat and glandular tissues As a result of these variations in tissue elasticity, the rapidly proliferating tumor cells are met with differential resistance. It is found that these cells are likely to circumvent stiffer terrains such as ligaments, instead electing to proliferate preferentially within the more yielding confines of the breast’s soft topography. By manipulating the interstitial tumor pressure in direct proportion to the elastic constants of the tissues surrounding the tumor, this model thus creates the potential for realizing a database of unique lesion morphology sculpted by the distinctive topography of each local anatomical infrastructure. We modeled the growth of simulated lesions within volumes extracted from fatty breast models, developed by Graffet alwith a resolution of 50μm generated with the open-source and readily available Virtual Imaging Clinical Trials for Regulatory Evaluation (VICTRE) imaging pipeline. To visualize and validate the realism of the lesion models, we leveraged the imaging component of the VICTRE pipeline, which replicates the siemens mammomat inspiration mammography system in a digital format. This system was instrumental in generating digital mammogram (DM) images for each breast model containing the simulated lesions.Results.By utilizing the DM images, we were able to effectively illustrate the imaging characteristics of the lesions as they integrated with the anatomical backgrounds. Our research also involved a reader study that compared 25 simulated DM regions of interest (ROIs) with inserted lesions from our models with DM ROIs from the DDSM dataset containing real manifestations of breast cancer. In general the simulation time for the lesions was approximately 2.5 hours, but it varied depending on the lesion’s local environment.Significance.The lesion growth model will facilitate and enhance longitudinal in silico trials investigating the progression of breast cancer.

Engineering↗

DOE OSTI2025

Verifying LLM generative agents reflect human behavior in contested information environments to effectively simulate disinformation campaigns (Proteus)

Disinformation poses a significant and evolving threat to today’s online environment. Individuals encounter challenges in detecting disinformation, subsequently influencing their behavior and decision-making processes. Our research examines the potential use of large language model (LLM) generative agents (LGAs) to replicate human behavior to better understand how disinformation is spread in online environments. Using human subjects research, we first investigate how personality traits, individual differences, and demographic factors relate to decision-making in simulated online disinformation environments. Then, we examine whether LGAs can effectively replicate human responses in the same simulated online environments when assigned personality traits, demographic characteristics and behavioral attributes. Our findings indicate that LGAs can align with human decisions in these scenarios; however, alignment is contingent upon scenario context, persona settings and LLM selection. Results provide valuable insights for methodology refinement in future research and in utilizing LGAs to model complex national security challenges such as disinformation campaigns.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1999

Motion sickness and proprioceptive aftereffects following virtual environment exposure

To study the potential aftereffects of virtual environments (VE), tests of visually guided behavior and felt limb position (pointing with eyes open and closed) along with self-reports of motion sickness-like discomfort were administered before and after 30 min exposure of 34 subjects. When post- discomfort was compared to a pre-baseline, the participants reported more sickness afterward (p < 0.03). The change in felt limb position resulted in subjects pointing higher (p < 0.038) and slightly to the left, although the latter difference was not statistically significant (p = 0.08). When findings from a second study using a different VE system were compared, they essentially replicated the results of the first study with higher sickness afterward (p < 0.001) and post- pointing errors were also up (p < 0.001) and to the left (p < 0.001). While alternative explanations (e.g. learning, fatigue, boredom, habituation, etc.) of these outcomes cannot be ruled out, the consistency of the post- effects on felt limb position changes in the two VE implies that these recalibrations may linger once interaction with the VE has concluded, rendering users potentially physiologically maladapted for the real world when they return. This suggests there may be safety concerns following VE exposures until pre-exposure functioning has been regained. The results of this study emphasize the need for developing and using objective measures of post-VE exposure aftereffects in order to systematically determine under what conditions these effects may occur.

NASA Discipline Neuroscience↗

DOE OSTI2025

Accelerating discoveries at DIII-D with the Integrated Research Infrastructure

DIII-D research is being accelerated by leveraging high performance computing (HPC) and data resources available through the National Energy Research Scientific Computing Center (NERSC) Superfacility initiative. As part of this initiative, a high-resolution, fully automated, whole discharge kinetic equilibrium reconstruction workflow was developed that runs at the NERSC for most DIII-D shots in under 20 min. This has eliminated a long-standing research barrier and opened the door to more sophisticated analyses, including plasma transport and stability. These capabilities would benefit from being automated and executed within the larger Department of Energy Advanced Scientific Computing Research program’s Integrated Research Infrastructure (IRI) framework. The goal of IRI is to empower researchers to meld DOE’s world-class research tools, infrastructure, and user facilities seamlessly and securely in novel ways to radically accelerate discovery and innovation. For transport, we are looking at producing flux matched profiles and also using particle tracing to predict fast ion heat deposition from neutral beam injection before a shot takes place. Our starting point for evaluating plasma stability focuses on the pedestal limits that must be navigated to achieve better confinement. This information is meant to help operators run more effective experiments, so it needs to be available rapidly inside the DIII-D control room. So far this has been achieved by ensuring the data is available with existing tools, but as more novel results are produced new visualization tools must be developed. In addition, all of the high-quality data we have generated has been collected into databases that can unlock even deeper insights. This has already been leveraged for model and code validation studies as well as for developing AI/ML surrogates. The workflows developed for this project are intended to serve as prototypes that can be replicated on other experiments and can be run to provide timely and essential information for ITER, as well as next stage fusion power plants.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2020

Customizable Scale-Out Key-Value Stores

Enterprise KV stores are often not well suited for HPC applications, and thus cumbersome end-to-end KV design customization is required to meet the needs of modern HPC applications. To this end, in this article we present bespoKV, an adaptive, extensible, and scale-out KV store framework. bespoKV decouples the KV store design into the control plane for distributed management and the data plane for local data store. For the control plane, bespoKVprovides pre-built modules, called controlets, supporting common distributed functionalities (e.g., replication, consistency, and topology) and their various combinations. This decoupling allows bespoKV to take a user-provided single-server KV store, called a datalet, and transparently enables a scalable and fault-tolerant distributed KV store service. The resulting distributed stores are also adaptive to consistency or topology requirement changes and can be easily extended for new types of services. Such specializations enable innovative uses of KV stores in HPC applications, especially for emerging applications that utilize KV-friendly workloads. We evaluate bespoKV in a local testbed as well as in a public cloud settings. Experiments show that bespoKV-enabled distributed KV stores scale horizontally to a large number of nodes, and performs comparably and sometimes 1.2× to 2.6× better than the state-of-the-art systems.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2005

VERSE - Virtual Equivalent Real-time Simulation

Distributed real-time simulations provide important timing validation and hardware in the- loop results for the spacecraft flight software development cycle. Occasionally, the need for higher fidelity modeling and more comprehensive debugging capabilities - combined with a limited amount of computational resources - calls for a non real-time simulation environment that mimics the real-time environment. By creating a non real-time environment that accommodates simulations and flight software designed for a multi-CPU real-time system, we can save development time, cut mission costs, and reduce the likelihood of errors. This paper presents such a solution: Virtual Equivalent Real-time Simulation Environment (VERSE). VERSE turns the real-time operating system RTAI (Real-time Application Interface) into an event driven simulator that runs in virtual real time. Designed to keep the original RTAI architecture as intact as possible, and therefore inheriting RTAI's many capabilities, VERSE was implemented with remarkably little change to the RTAI source code. This small footprint together with use of the same API allows users to easily run the same application in both real-time and virtual time environments. VERSE has been used to build a workstation testbed for NASA's Space Interferometry Mission (SIM PlanetQuest) instrument flight software. With its flexible simulation controls and inexpensive setup and replication costs, VERSE will become an invaluable tool in future mission development.

virtual real time↗

DOE OSTI2024

A Molecular View of Methane Activation on Ni(111) through Enhanced Sampling and Machine Learning

A combination of machine learned interatomic potentials (MLIPs) and enhanced sampling simulations is used to investigate the activation of methane on a Ni(111) surface. The work entails the development and iterative refinement of MLIPs, initially trained on a dataset constructed via ab initio molecular dynamics (AIMD) simulations, supplemented by adaptive biasing forces, to enrich the sampling of catalytically relevant configurations. Our results reveal that by incorporating collective variables that capture the behavior of the reactant molecule, as well as additional frames that describe the dynamic response of the catalytic surface, it is possible to enhance considerably the accuracy of predicted energies and forces. By employing enhanced sampling schemes in the refinement of the MLIP, we systematically explore the potential energy surface, leading to a refined MLIP capable of predicting DFT-level energies and forces and replicating key geometric characteristics of the catalytic system. The resulting free energy landscapes at several temperatures provide a detailed view of the thermodynamics and dynamics of methane activation. Specifically, as methane approaches and dissociates on the catalytic surface, the process involves the dynamic interplay of CH 4 and the Ni catalyst that includes both enthalpic and entropic contributions. The progression towards the transition state involves an CH 4 moiety that is increasingly restrained in its ability to rotate or translate, while the stage following the transition state is characterized by a notable rise of the Ni atom that interacts with the cleaved C–H bond. Furthermore, this leads to an increase in the mobility of the adsorbed species, a feature that becomes more pronounced at higher temperatures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

SAS4A/SASSYS-1 Lead Verification Test Suite

SAS4A/SASSYS-1 is a simulation tool used to perform deterministic analyses of anticipated events as well as design basis and beyond design basis accidents for advanced liquid-metal-cooled nuclear reactors. With its origin as SAS1A in the late 1960s, the SAS series of codes has been under continuous use and development for over forty-five years and represents a critical investment in safety analysis capabilities for the U.S. Department of Energy. Although SAS4A/SASSYS-1 was developed to support the analysis of any liquid-metal-cooled nuclear reactor, it has primarily been utilized to design and analyze Sodium Fast Reactors (SFRs). As a result, most of the verification basis for SAS4A/SASSYS-1 utilizes sodium as a coolant and geometry descriptions that are typical of a SFR facility. In this work, new verification problems are defined to extend the applicability of the SAS4A/SASSYS-1 verification basis into Lead Fast Reactor (LFR) design space. A review of the existing SAS4A/SASSYS-1 SFR verification test suite is performed to determine the number of test cases that are SFR specific. SFR specific test cases are replicated using lead as a coolant and system layouts that are representative of LFRs. This report provides definitions and reference solutions for seven new test cases that scope lead-specific features and capabilities of the software. For a verification test to be considered acceptable, comparisons of analytical solutions to SAS4A/SASSYS-1 predictions must produce negligible or justifiable errors. All LFR specific test cases are found to be acceptable.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2022

Dry in-pile fracture test (DRIFT) for separate-effects validation of ceramic fuel fracture models

Fracture is an important component of nuclear fuel behavior, and significant efforts have been invested into developing fuel performance models that are capable of accurately representing fracture. Usable data on the process of fracture propagation in nuclear fuel under realistic service conditions are very limited. To address this need, a series of separate-effects experiments were developed and performed at Idaho National Laboratory's Transient Reactor Test (TREAT) facility. These experiments employ a heat sink to radially remove heat from the fuel in a manner that approximates the effect of coolant in an operating light-water reactor (LWR). The test holder for these experiments is known as the Dry In-pile Fracture Test (DRIFT). A series of experiments employing DRIFT and TREAT were performed to provide data on the extent and nature of fracture in fresh fuel at various points during a ramp to full power. Novel aspects of these experiments include the way they employ a heat sink to replicate steady-state LWR conditions, as well as the use of fiber optic sensors for in-reactor thermal instrumentation. Details on the development of this experiment, experimental conditions, and resulting data (including in situ thermal measurements and post-irradiation imaging of fracture) are provided in this work. LWR-equivalent powers ranging from 10 to 25 kW/m were tested using this apparatus. Cracking was visible at all power levels, with increasing cracking extent as the power level increased, although there was little difference in the cracking between the two highest-power tests, which had LWR-equivalent powers of 20 and 25 kW/m.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2023

A physics-driven Σ-Y atomization model for heavy-duty engine simulations

The atomization of a liquid jet is a multi-scale and multi-physics problem of interest for many engineering applications. Particularly, it drives the fuel-oxidizer mixing and dictates the efficiency of combustion engines. High-fidelity multi-phase simulations remain challenging due to the excessive computational cost required to capture all the atomization scales. Thus, atomization models are necessary to represent sub-grid liquid structures. Here, in this work, a modified Σ-Y model in the context of Eulerian-Lagrangian Spray Atomization (ELSA) is used to transport the surface area density of the spray. The model's predictive performance is assessed under various operating conditions relevant to heavy-duty engines using the Engine Combustion Network (ECN) Spray C and Spray D research-grade injectors. The classic droplet collision formulation of the Σ-Y model alone does not replicate the response of the measured spray surface area to changes in injector, ambient pressure, and injection pressure, requiring individual tuning of the model's parameters. Instead, a transition between dense and dilute spray breakup mechanisms is proposed in terms of the average droplet spacing. The collision breakup mechanism represents the dilute spray, whereas the droplet size in the dense spray is driven by a competition between the integral scale of turbulence and the balance between the turbulent kinetic energy and the surface energy of the droplets. Such an approach minimizes the requirements for model tuning. Moreover, the role of the constants of a compressible standard k-ε RANS model is assessed in the injector's internal flow and external spray simulation framework, and an updated set is proposed. The results are validated against x-ray radiography and Ultra-Small Angle X-ray Scattering (USAXS) data and highlight the predictive capabilities of the proposed physics-driven Σ-Y model, which is compatible with engine simulation turnaround times.

42 ENGINEERING↗

NASA NTRS2015

The Hopper: A Wearable Robotic Device Testbed for Micro-Gravity Bone-Loading Proof-of-Concept

Wearable robotic systems are showing increased potential for addressing crew countermeasures needs. Wearable robots offer a compactness, programmability, and eccentric loading capability not present in more conventional exercise equipment. Correspondingly, advancements in the man to machine interface has progressed, allowing for higher loads to be applied directly to the person in new and novel ways. Recently, the X1 exoskeleton, a lower extremity wearable robot originally designed for mobility assistance and rehabilitation, underwent human subject testing to assess its potential as a knee dynamometer. This was of interest to NASA physiologists because currently strength is not assessed in flight due to hardware limitations, and thus there is a poor understanding of the time course of in-flight changes to muscle strength. The study concluded that the X1 compared well with the Biodex, the "gold standard" in terrestrial dynamometry, with coefficients of variation less than 6.0%. In a following study, the X1 powered ankle was evaluated for its efficacy in exercising calf muscles. Current on-orbit countermeasures equipment does not adequately protect the calf from atrophy. The results of this study were also positive (targeted muscle activity demonstrated via comparing pre- and post-exercise magnetic resonance imaging T2 measurements), again showing the efficacy of wearable robotic devices for addressing the countermeasure needs of our astronauts. Based on these successes and lessons learned, the Grasshopper was co-developed between IHMC (Florida Institute for Human and Machine Cognition) and NASA. The Grasshopper, or the Hopper for short, is a wearable robotic device designed to address muscle and bone density loss for astronauts spending extended periods of time in micro-gravity. The Grasshopper connects to the user's torso like a hiking backpack, over the shoulders and around the waist. At the feet are footplates that strap to the user. There are two actuators, one at each "knee" joint, which are capable of high fidelity torque control. Because the Hopper uses motors instead of gravity to create the load on the user, the device is suited for use on space missions. Exercise in zero-gravity conditions is critical to maintain muscle strength and bone mass. In operation, the actuators try to fold up, or collapse, the device, putting a compressive load between the user's feet and torso. This force is similar to carrying a heavy backpack. The user then bends and extends his or her knees, replicating a weightlifting squat exercise. The applied load is precisely controlled by a computer, and can be programmed to simulate gravitation loads or any desired load prescription, such as free-weight squat exercise. It is even possible to perform eccentric exercises, or negatives, without the need for a spotter. Because the hip joints, as well as the spine and long leg bones, are in the applied load path, there is the potential to stimulate bone growth, countering the typical bone loss when astronauts return from extended duration space travel.

Beck, C. E.↗

DOE OSTI2023

Degree-preserving graph dynamics: a versatile process to construct random networks

Real-world networks evolve over time via the addition or removal of vertices and edges. In current network evolution models, vertex degree varies or grows arbitrarily. A recently introduced degree-preserving network growth (DPG) family of models preserves vertex degree, resulting in structures significantly different from and more diverse than previous models. Despite its degree preserving property, the DPG model is able to replicate the output of several well-known real-world network growth models. Simulations showed that many real-world networks can also be constructed from small seed graphs via the DPG process. Here, we start the development of a rigorous mathematical theory underlying the DPG family of network growth models. We prove that the degree sequence of the output of some of the well-known, real-world network growth models can be reconstructed via the DPG process, using proper parametrization. We also show that the general problem of deciding whether a simple graph can be obtained via the DPG process from a small seed (DPG feasibility) is, however, NP-complete. In conclusion, it is an intriguing open problem to uncover whether there is a structural reason behind the DPG-constructability of real-world networks.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1991

A physical control interface with proprioceptive feedback and multiple degrees of freedom

The use of the drug thalidomide by pregnant mothers in Britain resulted in a variety of deformities including the birth of children having no arms. Such children were provided with powered artificial arms with up to five degrees of freedom simultaneously controlled in real time by shoulder movement. The physiological sense of proprioception was extended from the user into the device, reducing the need for visual feedback and conscious control. With the banning of thalidomide, this technique fell into disuse but it is now being re-examined as a control mechanism for other artificial limbs and it may have other medical applications to allow patients to control formerly paralyzed limbs moved by electrical stimulation. It may also have commercial applications in robotic manipulation or physical interaction with virtual environments. To allow it to be investigated further, the original pneumatic control system has recently been converted to an electrical analogue to allow interfacing to electronic and computer-assisted systems. A harness incorporates force-sensitive resistors and linear potentiomenters for sensing position and force at the interface with the skin, and miniature electric motors and lead screws for feeding back to the user the position of the robotic arm and the forces applied to it. In the present system, control is applied to four degrees of freedom using elevation/depression and protraction/reaction of each shoulder so that each collar bone emulates a joystick. However, both electrical and mechanical components have been built in modular form to allow rapid replication and testing of a variety of force and position control strategies.

Creasey, G. H.↗

NASA NTRSDate not supplied

Particle Interaction Physics Model Formulation for Plume-Surface Interaction Erosion and Cratering

As part of the Game Changing Development (GCD) Program, funded by NASA’s Space Technology Mission Directorate (STMD), the development of simulation capability for the prediction of extra-terrestrial Plume Surface Interaction (PSI) environments has been undertaken by the Fluid Dynamics Branch at NASA/MSFC. The Predictive Simulation Capability (PSC) Element is focused on creating simulation capability for the reliable and accurate prediction of PSI in Martian (~650 Pa) and Lunar (vacuum) ambient environments. In addition to the predictive simulation capability, the GCD Program also contains a companion Ground Testing Element for development of focused datasets for validation of predictive capability as well as a Flight-focused Instrumentation Element. This paper will present the status of implementing and maturing particle-particle interaction constituent physics models essential in simulating the landing surface granular material flow under PSI effects. This gas-particle multi-phase interaction modeling of plume impingement flow on the extra-terrestrial soil material is performed with the Gas-Granular Flow Solver (GGFS) addressed in a companion paper. The response of regolith particle flow induced by lander PSI requires accurate representation of the regolith granular material fluidic behavior and gas-granular interactions. The lunar regolith, as the extreme example, is poorly sorted with broad particle size distributions and large fines content. It has significant cohesion, due to interlocking particle shapes for the very jagged particles. The combination of particle shape and size distribution has been identified as major drivers in the complex particle flow response and resulting crater shape characteristics of extraterrestrial granular material. Constituent models for spherical particles can be formulated directly from particle kinetics theory. Complex particle shapes can be modeled by gluing together elemental spherical shapes into composite particles, requiring a Discrete Element Model (DEM) particle kinetics modeling approach to extract data and formulate constituent models. Mixture constituent models for poly-disperse mixtures (i.e, containing distribution of particle sizes) have recently been developed. The required non-spherical particle mixture granular material response closure models are then obtained through small-scale unit physics DEM simulations for the range of particle shapes, mixtures and packing densities. The granular material response closure models are then implemented in the Eulerian granular flow formulation. This DEM-based constituent model extraction process and formulation of poly-disperse particle mixtures has been successfully developed by small business and academic partners in the development of the Gas-Granular Flow Solver (GGFS) simulation program simulation framework. The currently implemented capabilities have reached the capability level of modeling bi-disperse, non-spherical particle mixtures is being continuously extended towards computational modeling of full range irregular particle mixtures. Under the GCD project, this technology is being further developed, transferred to NASA analysts, and matured towards application readiness. The predictive simulation capability team under the GCD project has acquired the modeling tools and processes of the DEM based constituent model formulation from the GGFS development team and is developing the capability to replicate the existing process. This is the first important step towards the ability of the NASA team to independently perform such model development in a production setting. Further efforts are underway to migrate the DEM based model simulation process performed with the academic based tools to more capable Open Source, highly parallelized simulation tools for efficient operation on NASA HPC assets. Evaluation of the currently implemented (such as mono-disperse and bi-disperse spherical and irregular shape particle constituent model applications) and continuously evolving full-range particle physics models in the GGFS tool is performed by the NASA team to advance application readiness of the simulations. Application testing for complex PSI erosions and cratering scenarios such as the Apollo LM is performed for axi-symmetric and full 3D simulations to aid the tool developers in achieving practical application readiness for NASA projects. Important validation and application testing will further be performed against experimental data generated under the GCD PSI project experimental component.

Peter A Liever↗

DOE OSTI2021

Early Drug Discovery and Development of Novel Cancer Therapeutics Targeting DNA Polymerase Eta (POLH)

Polymerase eta (or Pol η or POLH) is a specialized DNA polymerase that is able to bypass certain blocking lesions, such as those generated by ultraviolet radiation (UVR) or cisplatin, and is deployed to replication foci for translesion synthesis as part of the DNA damage response (DDR). Inherited defects in the gene encoding POLH (a.k.a., XPV) are associated with the rare, sun-sensitive, cancer-prone disorder, xeroderma pigmentosum, owing to the enzyme’s ability to accurately bypass UVR-induced thymine dimers. In standard-of-care cancer therapies involving platinum-based clinical agents, e.g., cisplatin or oxaliplatin, POLH can bypass platinum-DNA adducts, negating benefits of the treatment and enabling drug resistance. POLH inhibition can sensitize cells to platinum-based chemotherapies, and the polymerase has also been implicated in resistance to nucleoside analogs, such as gemcitabine. POLH overexpression has been linked to the development of chemoresistance in several cancers, including lung, ovarian, and bladder. Co-inhibition of POLH and the ATR serine/threonine kinase, another DDR protein, causes synthetic lethality in a range of cancers, reinforcing that POLH is an emerging target for the development of novel oncology therapeutics. Using a fragment-based drug discovery approach in combination with an optimized crystallization screen, we have solved the first X-ray crystal structures of small novel drug-like compounds, i.e., fragments, bound to POLH, as starting points for the design of POLH inhibitors. The intrinsic molecular resolution afforded by the method can be quickly exploited in fragment growth and elaboration as well as analog scoping and scaffold hopping using medicinal and computational chemistry to advance hits to lead. An initial small round of medicinal chemistry has resulted in inhibitors with a range of functional activity in an in vitro biochemical assay, leading to the rapid identification of an inhibitor to advance to subsequent rounds of chemistry to generate a lead compound. Importantly, our chemical matter is different from the traditional nucleoside analog-based approaches for targeting DNA polymerases.

60 APPLIED LIFE SCIENCES↗

NASA NTRS2021

Pretest Computational Assessment of Boundary Layer Transition in the NASA Juncture Flow Model with an NACA 0015-Based Wing

The first two phases of the NASA Juncture Flow experiment were carried out on a DLR-F6 swept-wing model and were designed to provide “CFD validation-quality” data toward the assessment and improvement of existing CFD turbulence models in predicting onset and extent of three-dimensional separated flow near the wing-juncture trailing-edge region. The next phase of experiments will involve an NACA 0015-based swept wing, as prior risk reduction experiments had indicated that this wing shape resulted in reduced separation near the juncture region than the DLR-F6 wing, thus providing a better option to evaluate the ability of CFD models to predict incipient turbulent separation. The NACA 0015 measurements will also include IR thermography to infer the variation of transition front with respect to an increasing angle of attack. The primary objective of this work is to computationally make a preliminary assessment of the transition front on both surfaces of the NACA 0015 wing at a crank-chord-based Reynolds number of 2.4 x 106 for four different angles of attack, (0°, 2.5°, 5°, and 7.5°) and to determine the dominant mechanisms responsible for transition. This assessment includes both RANS-based transition models from NASA’s OVERFLOW 2.3b flow solver and linear parabolized stability equations (PSE) stability analysis based on the Langley Stability and Transition Analysis code, LASTRAC. Linear PSE results indicate that the upper surface of the wing is dominated by Tollmien- Schlichting (TS) instabilities, and that the laminar flow region shrinks from about 50% chord to a very small region just downstream of the attachment line as the angle of attack is increased from 0° to 7.5°. Consequently, the transition fronts predicted by the Spalart- Allmaras-based amplification factor transport (AFT-2017b) equation model (which accounts for the TS instabilities alone) and the Menter’s shear-stress transport equation (SST2003)- based Langtry-Menter transition model with ability to account for both TS and crossflow effects (LM2015) compare well with those predicted using linear PSE. On the lower surface of the wing, stationary crossflow (CF) instabilities begin to appear on the inboard portion of the wing in addition to the TS-instabilities for the larger angles of attack (5° and 7.5°), further reducing the laminar flow extent within the inboard region. The LM2015 model that accounts for CF effects is able to replicate this trend but appears to predict a slightly earlier transition. The outcome of this effort will inform the experiment and, when the actual experimental data become available, provide further opportunity to assess and improve the various transition models.

CFD modeling↗

DOE OSTI2020

Consistency and reproducibility in atomic layer deposition

Atomic layer deposition (ALD) is a thin film synthesis technique that can provide exquisite accuracy and precision in film thickness and composition even on complex, large area substrates. Based on self-limiting surface chemistry, ALD can be insensitive to process conditions and reactor designs, allowing an ALD process developed in one lab to be easily reproduced in other labs. In practice, however, ALD is sometimes difficult to reproduce or replicate, and the results can vary substantially between ALD reactors and between labs. This is exemplified by large deviations in reports on the growth of, e.g., Al2O3, FeOx, and TiO2 given the same precursors under similar conditions. Furthermore, the problem of irreproducibility seems to be growing as ALD is adopted by more researchers and integrated into new applications. In this article, the authors highlight some of the major sources of variations and errors and common misconceptions related to ALD. In particular, the authors focus on issues related to precursors, substrates, and deposition tools. The authors illustrate these problems through examples from the literature, and they present results from numerical simulations that describe how nonidealities would manifest in thickness profiles in a typical cross-flow reactor. They also describe how reproducibility in ALD is linked to consistent experimental practice and reporting between labs. The authors’ hope is that by educating newcomers to ALD and advocating for consistent reporting of deposition conditions, they can minimize irreproducibility and enable ALD practitioners to realize the full potential afforded by self-limiting surface chemistry.

36 MATERIALS SCIENCE↗