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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Extended Lagrangian Born–Oppenheimer molecular dynamics for orbital-free density-functional theory and polarizable charge equilibration models

We report extended Lagrangian Born–Oppenheimer molecular dynamics (XL-BOMD) is formulated for orbital-free Hohenberg–Kohn density-functional theory and for charge equilibration and polarizable force-field models that can be derived from the same orbital-free framework. The purpose is to introduce the most recent features of orbital-based XL-BOMD to molecular dynamics simulations based on charge equilibration and polarizable force-field models. These features include a metric tensor generalization of the extended harmonic potential, preconditioners, and the ability to use only a single Coulomb summation to determine the fully equilibrated charges and the interatomic forces in each time step for the shadow Born–Oppenheimer potential energy surface. The orbital-free formulation has a charge-dependent, short-range energy term that is separate from long-range Coulomb interactions. This enables local parameterizations of the short-range energy term, while the long-range electrostatic interactions can be treated separately. The theory is illustrated for molecular dynamics simulations of an atomistic system described by a charge equilibration model with periodic boundary conditions. The system of linear equations that determines the equilibrated charges and the forces is diagonal, and only a single Ewald summation is needed in each time step. The simulations exhibit the same features in accuracy, convergence, and stability as are expected from orbital-based XL-BOMD.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Shadow molecular dynamics and atomic cluster expansions for flexible charge models

A shadow molecular dynamics scheme for flexible charge models is presented, where the shadow Born-Oppenheimer potential is derived from a coarse-grained approximation of range-separated density functional theory. The interatomic potential, including the atomic electronegativities and the charge-independent short-range part of the potential and force terms, are modeled by the linear atomic cluster expansion (ACE), which provides a computationally efficient alternative to many machine learning methods. The shadow molecular dynamics scheme is based on extended Lagrangian (XL) Born-Oppenheimer molecular dynamics (BOMD) [Eur. Phys. J. B 94, 164 (2021)]. XL-BOMD provides a stable dynamics, while avoiding the costly computational overhead associated with solving an all-to-all system of equations, which normally is required to determine the relaxed electronic ground state prior to each force evaluation. To demonstrate the proposed shadow molecular dynamics scheme for flexible charge models using the atomic cluster expansion, we emulate the dynamics generated from self-consistent charge density functional tight-binding (SCC-DFTB) theory using a second-order charge equilibration (QEq) model. The charge-independent potentials and electronegativities of the QEq model are trained for a supercell of uranium oxide (UO2) and a molecular system of liquid water. The combined ACE + XL-QEq dynamics are stable over a wide range of temperatures both for the oxide and the molecular systems, and provide a precise sampling of the Born-Oppenheimer potential energy surfaces. Accurate ground Coulomb energies are produced by the ACE-based electronegativity model during an NVE simulation of UO 2 , predicted to be within 1 meV of those from SCC-DFTB on average during comparable simulations.

74 ATOMIC AND MOLECULAR PHYSICS↗
NASA NTRS1995

Experimental Aerodynamic Characteristics of the Pegasus Air-Launched Booster and Comparisons with Predicted and Flight Results

Experimental longitudinal and lateral-directional aerodynamic characteristics were obtained for the Pegasus and Pegasus XL configurations over a Mach number range from 1.6 to 6 and angles of attack from -4 to +24 degrees. Angle of sideslip was varied from -6 to +6 degrees, and control surfaces were deflected to obtain elevon, aileron, and rudder effectiveness. Experimental data for the Pegasus configuration are compared with engineering code predictions performed by Nielsen Engineering & Research, Inc. (NEAR) in the aerodynamic design of the Pegasus vehicle, and with results from the Aerodynamic Preliminary Analysis System (APAS) code. Comparisons of experimental results are also made with longitudinal flight data from Flight #2 of the Pegasus vehicle. Results show that the longitudinal aerodynamic characteristics of the Pegasus and Pegasus XL configurations are similar, having the same lift-curve slope and drag levels across the Mach number range. Both configurations are longitudinally stable, with stability decreasing towards neutral levels as Mach number increases. Directional stability is negative at moderate to high angles of attack due to separated flow over the vertical tail. Dihedral effect is positive for both configurations, but is reduced 30-50 percent for the Pegasus XL configuration because of the horizontal tail anhedral. Predicted longitudinal characteristics and both longitudinal and lateral-directional control effectiveness are generally in good agreement with experiment. Due to the complex leeside flowfield, lateral-directional characteristics are not as well predicted by the engineering codes. Experiment and flight data are in good agreement across the Mach number range.

Rhode, M. N.↗
DOE OSTI2025

Quantitative Comparisons of Image Quality for Flash X-Ray Detectors

Due to X-rays’ ability to penetrate materials, flash X-ray radiography can be used for high-speed measurements where direct optical access is not possible. Choice of detector has a pronounced impact on resulting image quality. Four different detector systems were evaluated with a 450kVp flash source to quantitatively compare image quality metrics. The scintillating digital detector had less image noise than the three different storage phosphor computed radiography detectors across all transmission levels, but lacked the spatial resolution of the computed radiography detectors. For the screens tested here, the HPX-DR digital system had the highest signal to noise ratio of 68.24 and contrast to noise ratio of 35.53, but had the lowest spatial resolution, resolving 2.5 line pairs per millimeter at 1.78% contrast. At a value of 37.59, the Flex GP imaging plate had a signal to noise value above its storage phosphor counterparts under a 450kVp flash source. For radiographic setups typically used for dynamic experiments, the Flex XL Blue and Flex HR detectors had signal to noise ratios of 18.44 and 26.56 respectively. The highest resolved spatial frequencies of the Flex GP, Flex XL Blue, and Flex HR with the flash source are 3.85, 5.00, and 3.85 line pairs per millimeter, respectively. In conclusion, the Flex GP detector had the best combination of signal to noise ratio, contrast to noise ratio, and spatial resolution under a flash source.

computed radiography↗
DOE OSTI2024

The impact of hot-press conditions on the durability of polymer electrolyte membrane fuel cells

The proton exchange membrane integrity can be compromised during hot-press fabrication of membrane electrode assemblies (MEAs) causing premature cell failures during operation. In this work, infrared (IR) thermography was used as a diagnostic tool to spatially visualize hydrogen (H 2 ) crossover and identify process-induced-membrane irregularities (PIMs). These irregularities were identified as seed locations for MEA failures. Fine tuning of hot-press conditions was used to mitigate premature cell failures informed by accelerated stress testing (AST). The impact of PIMs on the initial performance, high-frequency resistances, open-circuit voltage, and H 2 crossover are reported. Nafion XL and 212 membranes, hot-pressed with a force of 16 kg/cm 2 and temperature of 120°C, were found to be consistently irregularity-free. Irregularity-free MEAs using Nafion 211, 212, and XL membranes demonstrated AST lifetime improvements of 58, 64 and 400%, respectively, compared to those fabricated with non-optimized conditions. In conclusion, this work highlights the importance of fabrication parameters on premature cell failures.

08 HYDROGEN↗
DOE OSTI2025

Asymptotic-preserving dynamical low-rank method for the stiff nonlinear Boltzmann equation

In kinetic theory, numerically solving the full Boltzmann equation is extremely expensive. This is because the Boltzmann collision operator involves a high-dimensional, nonlinear integral that must be evaluated at each spatial grid point and every time step. The challenge becomes even more pronounced in the fluid (strong collisionality) regime, where the collision operator exhibits strong stiffness, causing explicit time integrators to impose severe stability restrictions. In this paper, we propose addressing this problem through a dynamical low-rank (DLR) approximation. The resulting algorithm requires evaluating the Boltzmann collision operator only r 2 times, where r, the rank of the approximation, is much smaller than the number of spatial grid points. We propose a novel DLR integrator, called the XL integrator, which reduces the number of steps compared to the available alternatives (such as the projector splitting or basis update & Galerkin (BUG) integrator). For a class of problems including the Boltzmann collision operator which enjoys a separation property between physical and velocity space, we further propose a specialized version of the XL integrator, called the sXL integrator. This version requires solving only one differential equation to update the low-rank factors. Furthermore, the proposed low-rank schemes are asymptotic-preserving, meaning they can capture the asymptotic fluid limit in the case of strong collisionality. Our numerical experiments demonstrate the efficiency and accuracy of the proposed methods across a wide range of regimes, from non-stiff (kinetic) to stiff (fluid).

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Combining Reactive Quantum-Mechanical Molecular-Dynamics Simulations with Mutagenesis, Crystallography, and Enzyme Kinetics to Reveal Plausible Steps of Isocyanide Hydratase Catalysis

A complete understanding of enzyme mechanisms requires atomistic details of chemical reactions. Quantum-based molecular dynamics simulations (QMD) are a potential source of this information, but trade-offs between accuracy and computational cost have limited their use. We previously developed extended Lagrangian Born–Oppenheimer molecular dynamics (XL-BOMD) methods that leverage a negligible compromise in accuracy to substantially decrease the cost of QMD simulations. Here, we develop a reactive QMD approach using the latest XL-BOMD formulation, which enables efficient simulations of highly reactive systems, and use it to investigate mechanisms of intermediate formation in isocyanide hydratase (ICH) catalysis. In QMD simulations, molecular analogs of ICH active site residues reacted with para-nitrophenyl isocyanide, forming a thioimidate. Analysis of simulated atomic configurational and charge dynamics revealed a pathway where protonation of the isocyanide carbon occurs prior to thioimidate formation and suggested a possible role of Asp17 as a proton donor in the early phase of ICH catalysis. To test whether the pathway seen using the reactive QMD approach might be relevant to ICH catalysis, we performed X-ray crystallography and pre-steady-state enzyme kinetics studies of wild-type and D17N mutant ICH. Both the structure and kinetics are sensitive to the D17N mutation in a manner that is consistent with the order of the reaction steps seen in the simulations. Mobile protons play essential roles in many enzymes, yet they are difficult to observe experimentally, making the ordering of proton-dependent steps ambiguous in many enzyme mechanisms. The ability to directly simulate model reactions for the design of experiments that provide information about enzyme mechanisms involving mobile protons demonstrates the significance of our reactive QMD approach and motivates further biological applications.

36 MATERIALS SCIENCE↗
DOE OSTI2026

High-Performance Semiempirical Excited-State Molecular Dynamics Powered by Graphics Processing Units

Here, this Letter introduces excited-state molecular dynamics in PYSEQM, a GPU-accelerated semiempirical quantum chemistry engine implemented in PyTorch. The new module enables Born–Oppenheimer molecular dynamics (BOMD) using configuration-interaction singles and random phase approximation for excited states, allowing long trajectories and large statistical ensembles to be simulated efficiently on a single GPU. We also implement an extended Lagrangian excited-state BOMD (XL-ESMD) scheme that propagates auxiliary electronic variables, enabling relaxed ground and excited-state convergence thresholds without compromising energy conservation. The excited-state BOMD implementation scales smoothly from small chromophores to a nearly 900-atom dendrimer (taking 6.5 s per MD step). PYSEQM also supports batched execution, allowing many geometries or trajectories to be evaluated in a single GPU launch, substantially increasing throughput and making ensemble-based protocols routine. As a demonstration, we compute absorption, emission, and infrared spectra from trajectories propagated on the ground and first excited states. The XL-ESMD scheme yields identical spectra at significantly lower computational cost, establishing the role of extended Lagrangian based dynamics for efficient excited-state BOMD simulations. Beyond raw performance, PYSEQM’s PyTorch foundation provides automatic differentiation for forces, efficient GPU batching, and seamless interfacing with machine learning models. These capabilities position PYSEQM as a practical platform for machine learning-augmented excited-state dynamics and lay the foundation for future data-driven nonadiabatic excited-state dynamics modeling of ultrafast spectroscopic probes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Orbital stability analysis and photometric characterization of the second Earth Trojan asteroid 2020 XL5

Trojan asteroids are small bodies orbiting around the L 4 or L 5 Lagrangian points of a Sun-planet system. Due to their peculiar orbits, they provide key constraints to the Solar System evolution models. Despite numerous dedicated observational efforts in the last decade, asteroid 2010 TK 7 has been the only known Earth Trojan thus far. Here we confirm that the recently discovered 2020 XL 5 is the second transient Earth Trojan known. To study its orbit, we used archival data from 2012 to 2019 and observed the object in 2021 from three ground-based observatories. Our study of its orbital stability shows that 2020 XL 5 will remain in L 4 for at least 4 000 years. With a photometric analysis we estimate its absolute magnitude to be ${H}_{r}=18.5{8}_{-0.15}^{+0.16}$, and color indices suggestive of a C-complex taxonomy. Assuming an albedo of 0.06 ± 0.03, we obtain a diameter of 1.18 ± 0.08 km, larger than the first known Earth Trojan asteroid.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Photolytic activation of Ni (II) X 2 L explains how Ni-mediated cross coupling begins

Nickel photocatalysis has recently become vital to organic synthesis, but how the Ni (II) X 2 L pre-catalyst (X = Cl, Br; L = bidentate ligand) becomes activated to Ni (I) XL has remained puzzling and is typically addressed on a case-by-case basis. Here, we reveal a general mechanism where light induces photolysis of the Ni (II) -X bond, either via direct excitation or triplet energy transfer. Photolysis produces Ni (I) XL and a halogen radical, X*. Subsequent hydrogen atom abstraction, often from the solvent, produces a C(sp 3 ) radical, R*, that recombines with Ni (I) to form organonickel(II) complexes, Ni (II) XRL. Rather than acting as a loss pathway, Ni (II) XRL behaves as a light-activated reservoir of Ni (I) via photolysis of the Ni (II) -C bond. These results explain the role of the solvent in protecting the catalyst from off-cycle dimerization, demonstrate that two photons are often required to drive the reaction, and show how tuning the ligand can control the concentration of active Ni (I) species.

08 HYDROGEN↗
DOE OSTI2021

SURFACE FINISHING AND ELECTROLESS NICKEL PLATING OF ADDITIVELY MANUFACTURED (AM) METAL COMPONENTS

This study investigates the application of electroless nickel deposition on additively manufactured stainless steel samples. Current additive manufacturing (AM) technologies produce metal components with a rough surface. Rough surfaces generally exhibit fatigue characteristics, increasing the probability of initiating a crack or fracture to the printed part. For this reason, the direct use of as-produced parts in a finished product cannot be actualized, which presents a challenge. Post-processing of the AM parts is therefore required to smoothen the surface. This study analyzes chempolish (CP) and electropolish (EP) surface finishing techniques for post-processing AM stainless steel components CP has a great advantage in creating uniform, smooth surfaces regardless of size or part geometry EP creates an extremely smooth surface, which reduces the surface roughness to the sub-micrometer level. In this study, we also investigate nickel deposition on EP, CP, and as-built AM components using electroless nickel solutions. Electroless nickel plating is a method of alloy treatment designed to increase manufactured component's hardness and surface resistance to the unrelenting environment. The electroless nickel plating process is more straightforward than its counterpart electroplating.. We use low-phosphorus (2-5% P), medium-phosphorus (6-9% P), and high-phosphorus (10-13% P). These Ni deposition experiments were optimized using the L9 Taguchi design of experiments (TDOE), which compromises the prosperous content in the solution, surface finish, plane of the geometry, and bath temperature. The pre-and post-processed surface of the AM parts was characterized by KEYENCE Digital MicroscopeVHX-7000 and Phenom XL Desktop SEM. The experimental results show that electroless nickel deposition produces uniform Ni coating on the additively manufactured components up to 20 μm per hour. Mechanical properties of as-built and Ni coated AM samples were analyzed by applying a standard 10 N scratch test. Nickel coated AM samples were up to two times scratch resistant compared to the as-built samples. This study suggests electroless nickel plating is a robust viable option for surface hardening and finishing AM components for various applications and operating conditions.

Keywords: additive manufacturing, fatigue, chempol↗
NASA NTRS1996

Biomechanically Induced and Controller Coupled Oscillations Experienced on the F-16XL Aircraft During Rolling Maneuvers

During rapid rolling maneuvers, the F-16 XL aircraft exhibits a 2.5 Hz lightly damped roll oscillation, perceived and described as 'roll ratcheting.' This phenomenon is common with fly-by-wire control systems, particularly when primary control is derived through a pedestal-mounted side-arm controller. Analytical studies have been conducted to model the nature of the integrated control characteristics. The analytical results complement the flight observations. A three-degree-of-freedom linearized set of aerodynamic matrices was assembled to simulate the aircraft plant. The lateral-directional control system was modeled as a linear system. A combination of two second-order transfer functions was derived to couple the lateral acceleration feed through effect of the operator's arm and controller to the roll stick force input. From the combined systems, open-loop frequency responses and a time history were derived, describing and predicting an analogous in-flight situation. This report describes the primary control, aircraft angular rate, and position time responses of the F-16 XL-2 aircraft during subsonic and high-dynamic-pressure rolling maneuvers. The analytical description of the pilot's arm and controller can be applied to other aircraft or simulations to assess roll ratcheting susceptibility.

Smith, John W.↗
NASA NTRS2007

Integration and Testing Challenges of Small Satellite Missions: Experiences from the Space Technology 5 Project

The Space Technology 5(ST5) payload was successfully carried into orbit on an OSC Pegasus XL launch vehicle, which was carried aloft and dropped from the OSC Lockheed L-1011 from Vandenberg Air Force Base March 22,2006, at 9:03 am Eastern time, 6:03 am Pacific time. In order to reach the completion of the development and successful launch of ST 5, the systems integration and test(I&T) team determined that a different approach was required to meet the project requirements rather than the standard I&T approach used for single, room-sized satellites. The ST5 payload, part of NASA's New Millennium Program headquartered at JPL, consisted of three micro satellites (approximately 30 kg each) and the Pegasus Support Structure (PSS), the system that connected the spacecrafts to the launch vehicle and deployed the spacecrafts into orbit from the Pegasus XL launch vehicle. ST5 was a technology demonstration payload, intended to test six (6) new technologies for potential use for future space flights along with demonstrating the ability of small satellites to perform quality science. The main technology was a science grade magnetometer designed to take measurements of the earth's magnetic field. The three spacecraft were designed, integrated, and tested at NASA Goddard Space Flight Center with integration and environmental testing occurring in the Bldg. 7-1 0-15-29. The three spacecraft were integrated and tested by the same I&T team. The I&T Manager determined that there was insufficient time in the schedule to perform the three I&T spacecraft activities in series used standard approaches. The solution was for spacecraft #1 to undergo integration and test first, followed by spacecraft #2 and #3 simultaneously. This simultaneous integration was successful for several reasons. Each spacecraft had a Lead Test Conductor who planned and coordinated their spacecraft through its integration and test activities. One team of engineers and technicians executed the integration of all three spacecraft, learning and gaining knowledge and efficiency as spacecraft #1 integration and testing progressed. They became acutely familiar with the hardware, operation and processes for I&T, thus each team member had the experience and knowledge to safely execute I&T for spacecraft #2 and #3 together. The integration team was very versatile and each member could perform many different activities or work any spacecraft, when needed. Daily meetings between the three Lead TCs and technician team allowed the team to plan and implement activities efficiently. The three (3) spacecraft and PSS were successfully integrated and tested, shipped to the launch site, and ready for launch per the I&T schedule that was planned three years previously.

Sauerwein, Timothy A.↗
NASA NTRS2008

Radio-sensitization of Prostate Cancer Cells by Monensin Treatment and its associated Gene Expression Profiling Changes

Radio-resistant or recurrent prostate cancer represents a serious health risk for approximately 20%-30% of patients treated with primary radiation therapy for clinically localized prostate cancer. Here, we investigated the effect of monensin on sensitizing radiation mediated cell killing of two radio-resistant prostate cell lines Lncap (P53+ and AR+) and PC3 (P53- and AR-). Treatment with monensin alone (5 micromoles-20 micromoles) showed a significant direct cell killing of Lncap (10-30%), but not PC3 cells. Monensin was also shown to successfully sensitize Lncap cells to X-ray radiation (2Gy-10Gy) mediated cell death, up to 50% of killing with the combined treatment. To better understand the mechanisms of radio-resistance of these two cell lines and their different response to monensin, the apoptosis related gene expression profiles in both cell lines were analyzed using cDNA PCR array. Without any treatment, PC3 showed a much higher expression level of antiapoptosis genes than Lncap in the BCL2 family, the caspase/card family and the TNF ligand/receptor family. At 2 hr after 20 micormolar monensin treatment alone, only the TRAF and CIDE family showed a greater induction in Lncap cells than in PC3. Exposures to 10 Gy X-rays alone of Lncap cells significantly induced gene expression levels in the death and death receptor domain family, the TNF ligand and receptor family, and apoptotic group of BCL2 family; whereas exposures of PC3 induced only the expression of genes in the anti-apoptosis group of CASP and CARD family. Furthermore, we selectively suppressed the expression of several anti-apoptosis genes (BCL-xl, Bcl2A1, BIRC2, BIRC3 and CASP2) in PC3 cells by using the siRNA treatment. Exposure to 10Gy X-rays alone showed an enhanced cell killing (about 15%) in BCL-x1 silenced cells, but not in cells with siRNA treatment targeting other anti-apoptosis genes. We also exposed PC3 cells to protons in the Bragg peak region to compare the effectiveness of cell killing of X-rays. Interestingly, in comparison to X-rays, protons significantly reduced the gene expression in the anti-apoptosis family, suggesting that proton treatment may be more effective for PC3 cells. As a conclusion, monensin was found to sensitize Lncap cells, but not PC3, and over-expression of Bcl-xl cells may be responsible for the radio- or chemo-resistance characteristics of PC3 cells.

Zhang Ye↗
DOE OSTI2025

An Analysis of Input Parameters for Film-Based Flash X-Ray Radiography

Flash X-ray radiography (flash) is a commonly used diagnostic technique in dynamic experiments. An analysis of the effects of input parameters on resulting metrics of image quality can aid the experimentalist in configuring the X-ray input parameters to produce the highest quality radiograph for a given experiment. Here, a flash X-ray test bed with HS800 film and a LANEX Medium F intensifier screen was used with an L3 450 kVp pulser and Scandiflash X-ray tube for this study. Input parameters including charge voltage, source filtering, and film-pack assembly were investigated for their impact on contrast-to-noise ratio (CNR), contrast, and contrast transfer function (CTF). Using VIDAR’s NDT Pro industrial film digitizer, scanner parameters such as optical density range, pixel spacing, scan mode, and digital bit-depth were also examined for their impact on image quality metrics. The highest CNR values were found with two LANEX intensifiers and no filtering. Charge voltage had no direct impact on CNR values. LANEX screen count and filtering resulted both in direct effects on CNR and interaction effects with each other and CNR value. Uncertainty bounds for CNR comparisons and repeatability of CTF evaluations are also discussed. Finally, the film results are compared with a previous study using other detector types, specifically Carestream INDUSTREX Flex GP, Flex HR, Flex XL Blue, and HPX-DR 3543.

dynamic radiography↗
DOE OSTI2022

Mitigating cerium migration for perfluorosulfonic acid membranes using organic ligands

Improving the electrochemical stability of proton exchange membranes is a pressing priority for heavy-duty fuel cell vehicles. The lifetime of the most widely used perfluorosulfonic acid membranes is limited by reactive free radicals generated inside the system. Cerium has been found to reduce the chemical degradation of the membranes. However, cerium migration during fuel cell operation limits the chemical durability enhancement effect expected from the radical scavenging activity of cerium. Here we investigate a wide range of organic immobilizers for cerium, measuring their suitability concerning cerium retention, radical scavenging activity, and fuel cell performance. Further, we report that partially fluorinated phosphonic acids enhance cerium retention up to 45 times and reduce fluoride emission rate by 38% compared to the commercial Nafion™ XL membrane pre-impregnated with cerium. The energetics of cerium-phosphonic acid complex systems by density functional theory calculations rationalizes effective cerium immobilization.

25 ENERGY STORAGE↗
DOE OSTI2023

Enabling Fortran Standard Parallelism in GAMESS for Accelerated Quantum Chemistry Calculations

The performance of Fortran 2008 DO CONCURRENT (DC) relative to OpenACC and OpenMP target offloading (OTO) with different compilers is studied for the GAMESS quantum chemistry application. Specifically, DC and OTO are used to offload the Fock build, which is a computational bottleneck in most quantum chemistry codes, to GPUs. The DC Fock build performance is studied on NVIDIA A100 and V100 accelerators and compared with the OTO versions compiled by the NVIDIA HPC, IBM XL, and Cray Fortran compilers. The results show that DC can speed up the Fock build by 3.0× compared with that of the OTO model. Finally, with similar offloading efforts, DC is a compelling programming model for offloading Fortran applications to GPUs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Molecular architecture and functional dynamics of the pre-incision complex in nucleotide excision repair

Nucleotide excision repair (NER) is vital for genome integrity. Yet, our understanding of the complex NER protein machinery remains incomplete. Combining cryo-EM and XL-MS data with AlphaFold2 predictions, we build an integrative model of the NER pre-incision complex(PInC). Here TFIIH serves as a molecular ruler, defining the DNA bubble size and precisely positioning the XPG and XPF nucleases for incision. Using simulations and graph theoretical analyses, we unveil PInC’s assembly, global motions, and partitioning into dynamic communities. Remarkably, XPG caps XPD’s DNA-binding groove and bridges both junctions of the DNA bubble, suggesting a novel coordination mechanism of PInC’s dual incision. XPA rigging interlaces XPF/ERCC1 with RPA, XPD, XPB, and 5' ssDNA, exposing XPA’s crucial role in licensing the XPF/ERCC1 incision. Mapping disease mutations onto our models reveals clustering into distinct mechanistic classes, elucidating xeroderma pigmentosum and Cockayne syndrome disease etiology.

60 APPLIED LIFE SCIENCES↗