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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 1,531 records · Page 85
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Formulation and Assessment of a Wash-Primer Containing Lanthanum “Tannate” for Steel Temporary Protection

Tannins are polyphenols synthesized by plants and useful for the coating industry as corrosion inhibitors. In addition, lanthanum salts have a great inhibitory effect on steel corrosion. The aim of this study was to obtain lanthanum “tannate” with adequate solubility to be incorporated as the corrosion inhibitor in a wash-primer. The “tannate” was obtained from commercial “Quebracho” tannin and 0.1 M La(NO{sub 3}){sub 3}. The soluble tannin was determined by the Folin–Denis reagent, while the concentration of Lanthanum was obtained by a gravimetric procedure. The protective action of “tannate” on SAE 1010 steel was evaluated by linear polarization curves and corrosion potential measurements. Lanthanum “tannate” was incorporated in a wash-primer formulation and tested by corrosion potential and ionic resistance measurements. The corrosion rate was also determined by the polarization resistance technique. Besides, the primer was incorporated in an alkyd paint system and its anticorrosion performance assessed in the salt spray cabinet and by electrochemical impedance spectroscopy. Results showed that lanthanum “tannate” primer inhibits the development of deleterious iron oxyhydroxides on the steel substrate and incorporated into a paint system had a similar behavior to the primer formulated with zinc tetroxychromate.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Are current effectiveness criteria fit for purpose? Using a controversial strategic assessment as a test case

Highlights: • The effectiveness framework of Bond et al. (2015) is tested on a case study. • The strategic assessment of the proposed Browse LNG Precinct is evaluated. • The effectiveness framework is modified as a result of the analysis. • “Legitimacy” encompasses both pluralism and normative effectiveness. • Substantive effectiveness should include consideration of unintended consequences. - Abstract: The aim of this paper is to test the broader utility of the sustainability assessment effectiveness framework of Bond et al. (2015) by applying it to a controversial strategic assessment case study. The effectiveness framework comprises six dimensions: procedural effectiveness, substantive effectiveness, transactive effectiveness, normative effectiveness, pluralism, and knowledge and learning. It was originally developed to evaluate sustainability assessment at a system-wide level and it has not been previously applied to a specific case study. The analysis was conducted through document review and the first-hand experience of two of the authors who were involved in the case study in different capacities. The case study selected was the strategic assessment of the proposed Browse Liquefied Natural Gas (LNG) Precinct in Western Australia, which was conducted over the period 2007–2015 under the strategic assessment provisions of both the Western Australian and Australian Commonwealth environmental legislation. The framework provided a useful structure within which this complex case study could be explored, its strengths and weaknesses brought to light, and the interactions between the dimensions highlighted. We also found opportunities for refinement of the framework. As a result of this analysis we propose to replace the final three dimensions of the framework with legitimacy, where a legitimate process is one which all stakeholders agree is fair and which delivers an acceptable outcome for all parties, though we acknowledge the need for further conceptualisation of this dimension. We also suggest that the concept of substantive effectiveness should be expanded to incorporate the unintended consequences of impact assessment. Our research thus makes both a useful addition to the literature already published on the Browse case study, as well as to the literature on impact assessment effectiveness.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2022

Recovery of DNA from fired and unfired cartridge casings: comparison of two DNA collection methods

For over 10 years, various studies have attempted to increase the recovery of DNA from ammunition by modifying the DNA collection, extraction, purification, and amplification procedures, with varying levels of success. This study focused on the “soaking” method of Montpetit & O’Donnell [1] and the “rinse-and-swab" method of Bille et al. [2]. First, testing for the presence of exogenous DNA, 210 boxed cartridges (brass, steel, and nickel-plated) from nine manufacturers were swabbed and DNA was extracted, concentrated, and quantified. Extracts that quantified > 0 ng/µL (44 of 210) were amplified and genotyped with GlobalFiler™. Of those, only one extract yielded two alleles indicating that the manufacturing and packaging of ammunition was virtually DNA free. Next, to obtain a baseline comparison of two DNA collection methods on a non-metallic substrate and identify a suitable number of cells to spot on cartridges, different DNA input amounts of primary human adult epidermal keratinocytes (HEKa) were tested. Thereafter, 300 brass and 300 nickel-plated, cartridges were spotted with HEKa cells containing ~5 ng of DNA, fired or unfired, and processed with either method. Finally, five methods representing hybrids of the soaking and rinse-and-swab methods were tested to determine if variations of those methods could be used to increase DNA yield and recovery. The results show that the soaking method consistently yielded more DNA than the rinse-and-swab method from a non-metallic substrate. However, the comparison study demonstrated that both methods performed comparably for cartridges. On average, the soaking method recovered 0.25 ng of DNA (5.1% recovery) and the rinse-and-swab method recovered 0.28 ng (5.8% recovery). However, average recoveries were significantly different among three analysts and considerable variation in yields were observed, possibly due to storage time. Furthermore, consistent with prior reports, the DNA recovered from brass casings was only 16% of that recovered from nickel-plated casings and the average yield of DNA from fired casings was reduced to 67% of unfired casings. Moreover, DNA extracts from brass or nickel-plated casings did not appear to contain amplification inhibitors and only 30/596 appeared severely degraded. Finally, both the published rinse-and-swab and soaking methods yielded more DNA than all modifications of the two methods. Overall, both methods yielded equivalent DNA quantities. Additionally, recovery of DNA from any given cartridge casing may be dependent on storage time as well as the skill, proficiency, and experience of the analyst and may reflect stochastic effects, particularly for casings containing low copy and/or degraded DNA.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

A high-order discontinuous Galerkin method for fluid–structure interaction with efficient implicit–explicit time stepping

We present a high-order accurate scheme for coupled fluid–structure interaction problems. The fluid is discretized using a discontinuous Galerkin method on unstructured tetrahedral meshes, and the structure uses a high-order volumetric continuous Galerkin finite element method. Standard radial basis functions are used for the mesh deformation. The time integration is performed using a partitioned approach based on implicit–explicit Runge–Kutta methods. The resulting scheme fully decouples the implicit solution procedures for the fluid and the solid parts, which we perform using two separate efficient parallel solvers. We demonstrate up to fifth order accuracy in time on a non-trivial test problem, on which we also show that additional subiterations are not required. We solve a benchmark problem of a cantilever beam in a shedding flow, and show good agreement with other results in the literature. Finally, we solve for the flow around a thin membrane at a high angle of attack in both 2D and 3D, and compare with the results obtained with a rigid plate.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

A fast Fourier transform-based mesoscale field dislocation mechanics study of grain size effects and reversible plasticity in polycrystals

A numerical implementation of a non-local polycrystal plasticity theory based on a mesoscale version of the field dislocation mechanics theory (MFDM) of Acharya and Roy (2006) is presented using small-strain elasto-viscoplastic fast Fourier transform-based (EVPFFT) algorithm developed by Lebensohn et al. (2012). In addition to considering plastic flow and hardening only due to SSDs (statistically stored dislocations) as in the classic EVPFFT framework, the proposed method accounts for the evolution of GND (geometrically necessary dislocations) densities solving a hyperbolic-type partial differential equation, and GND effects on both plastic flow and hardening. This allows consideration of an enhanced strain-hardening law that includes the effect of the GND density tensor. The numerical implementation of a reduced version of the MFDM is presented in the framework of the FFT-based augmented Lagrangian procedure of Michel et al. (2001). A Finite Differences scheme combined with discrete Fourier transforms is applied to solve both incompatibility and equilibrium equations. The numerical procedure named MFDM-EVPFFT is used to perform full field simulations of polycrystal plasticity considering different grain sizes and their mechanical responses during monotonic tensile and reversible tension-compression tests. Using Voronoi tessellation and periodic boundary conditions, voxelized representative volume elements (RVEs) with different grain sizes are generated. With MFDM-EVPFFT, a Hall-Petch type scaling law is obtained in contrast with the conventional crystal plasticity EVPFFT. In the case of reversible plasticity, a stronger Bauschinger effect is observed with the MFDM-EVPFFT approach in comparison with conventional EVPFFT. Here, the origin of these differences is analyzed in terms of heterogeneity, GND density and stress evolutions during the compression stage.

36 MATERIALS SCIENCE↗
DOE OSTI2013

The renormalization scale-setting problem in QCD

A key problem in making precise perturbative QCD predictions is to set the proper renormalization scale of the running coupling. The conventional scale-setting procedure assigns an arbitrary range and an arbitrary systematic error to fixed-order pQCD predictions. In fact, this ad hoc procedure gives results which depend on the choice of the renormalization scheme, and it is in conflict with the standard scale-setting procedure used in QED. Predictions for physical results should be independent of the choice of the scheme or other theoretical conventions. We review current ideas and points of view on how to deal with the renormalization scale ambiguity and show how to obtain renormalization scheme- and scale-independent estimates. We begin by introducing the renormalization group (RG) equation and an extended version, which expresses the invariance of physical observables under both the renormalization scheme and scale-parameter transformations. The RG equation provides a convenient way for estimating the scheme- and scale-dependence of a physical process. We then discuss self-consistency requirements of the RG equations, such as reflexivity, symmetry, and transitivity, which must be satisfied by a scale-setting method. Four typical scale setting methods suggested in the literature, i.e., the Fastest Apparent Convergence (FAC) criterion, the Principle of Minimum Sensitivity (PMS), the Brodsky–Lepage–Mackenzie method (BLM), and the Principle of Maximum Conformality (PMC), are introduced. Basic properties and their applications are discussed. We pay particular attention to the PMC, which satisfies all of the requirements of RG invariance. Using the PMC, all non-conformal terms associated with the β-function in the perturbative series are summed into the running coupling, and one obtains a unique, scale-fixed, scheme-independent prediction at any finite order. The PMC provides the principle underlying the BLM method, since it gives the general rule for extending BLM up to any perturbative order; in fact, they are equivalent to each other through the PMC–BLM correspondence principle. Thus, all the features previously observed in the BLM literature are also adaptable to the PMC. The PMC scales and the resulting finite-order PMC predictions are to high accuracy independent of the choice of the initial renormalization scale, and thus consistent with RG invariance. The PMC is also consistent with the renormalization scale-setting procedure for QED in the zero-color limit. The use of the PMC thus eliminates a serious systematic scale error in perturbative QCD predictions, greatly improving the precision of empirical tests of the Standard Model and their sensitivity to new physics.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

CODEX: Role of velocity substructure in the scaling relations of galaxy clusters

The use of galaxy clusters as cosmological probes relies on a detailed understanding of their properties. They define cluster selection and ranking linked to a cosmologically significant cluster mass function. Previous studies have employed small samples of clusters, concentrating on achieving the first calibrations of cluster properties with mass, while the diversity of cluster properties has been revealed via detailed studies. The large spectroscopic follow-up on the CODEX cluster sample with SDSS and NOT enables a detailed study of hundreds of clusters, lifting the limitations of previous samples. We aim to update the spectroscopic cluster identification of CODEX by running the spectroscopic group finder on the follow-up spectroscopy results and connecting the dynamical state of clusters to their scaling relations. We implemented a reproducible spectroscopic membership determination and cleaning procedures, based on the redMaPPer membership, running the spectroscopic group finder on the follow-up spectroscopy results and cleaning the membership for spectroscopic outliers. We applied the Anderson-Darling test for velocity substructure and analysed its influence on the scaling relations. We also tested the effect of the X-ray-to-optical centre offset on the scaling relations. We report on the scaling relations between richness, X-ray luminosity, and velocity dispersion for a complete sample of clusters with at least 15 members. Clusters with velocity substructure exhibit enhanced velocity dispersion for a given richness and are characterized by 2.5 times larger scatter. Clusters that have a strong offset in X-ray-to-optical centres have comparable scaling relations as clusters with substructure. We demonstrate that there is a consistency in the parameters of the scaling relations for the low- and high-richness galaxy clusters. Splitting the clusters by redshift, we note a decrease in scatter with redshift in all scaling relations. We localize the redshift range where a high scatter is observed to z < 0.15, which is in agreement with the literature results on the scatter. We note that the increase in scatter for both high- and low-luminosity clusters is z < 0.15, suggesting that both cooling and the resulting active galactic nucleus feedback are at the root of this scatter.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

Study on the ultrasonic inspection method using the full matrix capture for the in service railway wheel

The quality of wheel is especially important for the safety of high speed railway. In this paper, a new ultrasonic array inspection method, the Full Matrix Capture (FMC) has been studied and applied to the high speed railway wheel inspection, especially in the wheel web from the tread. Firstly, the principle of FMC and TFM algorithm is discussed, and then the new optimization is applied to the standard FMC; Secondly the fundamentals of optimization is described in detail and the performance is analyzed. Finally, the experiment has been built with a standard phased array block and railway wheel, and then the testing results are discussed and analyzed. It is demonstrated that this change for the ultrasonic data acquisition and image reconstruction has higher efficiency and lower cost comparing to the FMC's procedure.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

On the analysis and comparison of conformer-specific essential dynamics upon ligand binding to a protein

The native state of a protein consists of an equilibrium of conformational states on an energy landscape rather than existing as a single static state. The co-existence of conformers with different ligand-affinities in a dynamical equilibrium is the basis for the conformational selection model for ligand binding. In this context, the development of theoretical methods that allow us to analyze not only the structural changes but also changes in the fluctuation patterns between conformers will contribute to elucidate the differential properties acquired upon ligand binding. Molecular dynamics simulations can provide the required information to explore these features. Its use in combination with subsequent essential dynamics analysis allows separating large concerted conformational rearrangements from irrelevant fluctuations. We present a novel procedure to define the size and composition of essential dynamics subspaces associated with ligand-bound and ligand-free conformations. These definitions allow us to compare essential dynamics subspaces between different conformers. Our procedure attempts to emphasize the main similarities and differences between the different essential dynamics in an unbiased way. Essential dynamics subspaces associated to conformational transitions can also be analyzed. As a test case, we study the glutaminase interacting protein (GIP), composed of a single PDZ domain. Both GIP ligand-free state and glutaminase L peptide-bound states are analyzed. Our findings concerning the relative changes in the flexibility pattern upon binding are in good agreement with experimental Nuclear Magnetic Resonance data.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Cosmic shear measurements with Dark Energy Survey Science Verification data

Here, we present measurements of weak gravitational lensing cosmic shear two-point statistics using Dark Energy Survey Science Verification data. We also demonstrate that our results are robust to the choice of shear measurement pipeline, either ngmix or im3shape, and robust to the choice of two-point statistic, including both real and Fourier-space statistics. Our results pass a suite of null tests including tests for B-mode contamination and direct tests for any dependence of the two-point functions on a set of 16 observing conditions and galaxy properties, such as seeing, airmass, galaxy color, galaxy magnitude, etc. We furthermore use a large suite of simulations to compute the covariance matrix of the cosmic shear measurements and assign statistical significance to our null tests. We find that our covariance matrix is consistent with the halo model prediction, indicating that it has the appropriate level of halo sample variance. We also compare the same jackknife procedure applied to the data and the simulations in order to search for additional sources of noise not captured by the simulations. We find no statistically significant extra sources of noise in the data. We determined that the overall detection significance with tomography for our highest source density catalog is 9.7 σ. Cosmological constraints from the measurements in this work are presented in a companion paper [DES et al., Phys. Rev. D 94, 022001 (2016).].

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

(2 + δ)-dimensional theory of the electromechanics of lipid membranes: Electrostatics

The coupling of electric fields to the mechanics of lipid membranes gives rise to intriguing electromechanical behavior, as, for example, evidenced by the deformation of lipid vesicles in external electric fields. Electromechanical effects are relevant for many biological processes, such as the propagation of action potentials in axons and the activation of mechanically gated ion channels. Currently, a theoretical framework describing the electromechanical behavior of arbitrarily curved and deforming lipid membranes does not exist. Purely mechanical models commonly treat lipid membranes as two-dimensional surfaces, ignoring their finite thickness. While holding analytical and numerical merit, this approach cannot describe the coupling of lipid membranes to electric fields and is thus unsuitable for electromechanical models. In a sequence of articles, we derive an effective surface theory of the electromechanics of lipid membranes, called the (2 + δ)-dimensional theory, which has the advantages of surface descriptions while accounting for finite thickness effects. The present article proposes a generic dimension reduction procedure relying on low-order spectral expansions. This procedure is applied to the electrostatics of lipid membranes to obtain the (2 + δ)-dimensional theory that captures potential differences across and electric fields within lipid membranes. Finally, this model is tested on different geometries relevant for lipid membranes, showing good agreement with the corresponding three-dimensional electrostatics theory.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

TU-FG-201-01: 18-Month Clinical Experience of a Linac Daily Quality Assurance (QA) Solution Using Only EPID and OBI

Purpose: To describe the clinical use of a Linear Accelerator (Linac) DailyQA system with only EPID and OBI. To assess the reliability over an 18-month period and improve the robustness of this system based on QA failure analysis. Methods: A DailyQA solution utilizing an in-house designed phantom, combined EPID and OBI image acquisitions, and a web-based data analysis and reporting system was commissioned and used in our clinic to measure geometric, dosimetry and imaging components of a Varian Truebeam Linac. During an 18-month period (335 working days), the Daily QA results, including the output constancy, beam flatness and symmetry, uniformity, TPR20/10, MV and KV imaging quality, were collected and analyzed. For output constancy measurement, an independent monthly QA system with an ionization chamber (IC) and annual/incidental TG51 measurements with ADCL IC were performed and cross-compared to Daily QA system. Thorough analyses were performed on the recorded QA failures to evaluate the machine performance, optimize the data analysis algorithm, adjust the tolerance setting and improve the training procedure to prevent future failures. Results: A clinical workflow including beam delivery, data analysis, QA report generation and physics approval was established and optimized to suit daily clinical operation. The output tests over the 335 working day period cross-correlated with the monthly QA system within 1.3% and TG51 results within 1%. QA passed with one attempt on 236 days out of 335 days. Based on the QA failures analysis, the Gamma criteria is revised from (1%, 1mm) to (2%, 1mm) considering both QA accuracy and efficiency. Data analysis algorithm is improved to handle multiple entries for a repeating test. Conclusion: We described our 18-month clinical experience on a novel DailyQA system using only EPID and OBI. The long term data presented demonstrated the system is suitable and reliable for Linac daily QA.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Reliable and practical computational description of molecular crystal polymorphs

Reliable prediction of the polymorphic energy landscape of a molecular crystal would yield profound insight into drug development in terms of the existence and likelihood of late-appearing polymorphs. However, the computational prediction of molecular crystal polymorphs is highly challenging due to the high dimensionality of conformational and crystallographic space accompanied by the need for relative free energies to within 1 kJ/mol per molecule. In this study, we combine the most successful crystal structure sampling strategy with the most successful first-principles energy ranking strategy of the latest blind test of organic crystal structure prediction methods. Specifically, we present a hierarchical energy ranking approach intended for the refinement of relative stabilities in the final stage of a crystal structure prediction procedure. Such a combined approach provides excellent stability rankings for all studied systems and can be applied to molecular crystals of pharmaceutical importance.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Validating Synthetic Galaxy Catalogs for Dark Energy Science in the LSST Era

Large simulation efforts are required to provide synthetic galaxy catalogs for ongoing and upcoming cosmology surveys. These extragalactic catalogs are being used for many diverse purposes covering a wide range of scientific topics. In order to be useful, they must offer realistically complex information about the galaxies they contain. Hence, it is critical to implement a rigorous validation procedure that ensures that the simulated galaxy properties faithfully capture observations and delivers an assessment of the level of realism attained by the catalog. We present here a suite of validation tests that have been developed by the Rubin Observatory Legacy Survey of Space and Time (LSST) Dark Energy Science Collaboration (DESC). We discuss how the inclusion of each test is driven by the scientific targets for static ground-based dark energy science and by the availability of suitable validation data. The validation criteria that are used to assess the performance of a catalog are flexible and depend on the science goals. We illustrate the utility of this suite by showing examples for the validation of cosmoDC2, the extragalactic catalog recently released for the LSST DESC second Data Challenge.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2019

Low Cost High Efficiency Magnetrons for Accelerator Applications

High efficiency, low cost RF sources are required for proton, ion, and muon accelerators. These sources must be compact and provide precise control of the output power and phase. Currently only large, expensive klystrons can provide this performance. Calabazas Creek Research Inc. proposes to develop a phase locked magnetron-based system that has phase and amplitude control via a low power amplifier. The system uses phase modulation to control the RF power. The efficiency can exceed 80% and the cost is expected to be less than $3/Watt, significantly lower than other high power amplifiers. CCR originally proposed to develop a magnetron with a grid for control of phase and amplitude. Detailed simulations showed that this was not a promising approach. The grid was found to be viable only in magnetrons with low duty cycle, and amplitude control was demonstrated; but the grid was found to be not effective for phase locking. Attention was turned to a concept from Fermilab, which is very promising for both amplitude and phase control and does not require a grid. CCR will develop an RF system providing phase and amplitude control of a 100 kW peak, 10 kW average 1.3 GHz magnetron. Procedures and techniques will be applicable to design of systems at other frequencies and power levels. The program will include development of the magnetron and locking electronics. The system will be tested at Fermilab. Commercial Applications and Other Benefits Magnetrons can provide high levels of RF power at very high efficiency at low cost. As oscillators, however, their applications are limited. Magnetrons with more precise control of the output power and control of the phase could find wide application in accelerators and colliders. They would also provide improved performance for high resolution radar.

43 PARTICLE ACCELERATORS↗
DOE OSTI2020

Multiphysics Coupling of PROTEUS-NODAL and SAM for Molten Salt Reactor Simulation

The purpose of this report is to document the new features and capabilities that have been implemented in the PROTEUS-NODAL code and the coupling procedure of PROTEUS-NODAL with SAM to analyze MSRs. This report is organized as follows. Section 2 presents the variational nodal P 1 solver for cylindrical geometries and its verification test results. Section 3 discusses the transient analysis capability implemented in the P 1 solvers of PROTEUS-NODAL. The solution methods for the coupled system of TFSP and precursor drift equations, the coarse mesh finite difference (CMFD) acceleration, the kinetics parameter evaluation method, and the thermal feedback are discussed. The verification test results against the SP 3 solutions are also discussed. Section 4 describes the coupling scheme of PROTEUS-NODAL and SAM under the MOOSE framework for MSR applications. The developed MOOSE applications named “TreeFrog” and “TreeKangaroo” are discussed. Verification test results for the coupled system are also discussed by comparing the MSFR steady state solution with that obtained from a manually coupled PROTEUS-NODAL and ANSYS CFX computational fluid dynamics (CFD) calculations and the MSFR transient analysis results with the open literature solutions and the PROTEUS-NODAL solutions obtained with the standalone thermal-hydraulics solver. Section 5 provides conclusions and future works.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2022

Estimation of High-Altitude Electromagnetic Pulse Signal Leakage into Power Generation Facilities: Simulations and Measurements

The coupling of early-time high-altitude electromagnetic pulse signals into a power generation facility was investigated. This study encompasses both electromagnetic simulation and on-site experimental efforts that are relevant to shielding effectiveness estimation with a passive technique. As an initial step in understanding the attenuation models involved, simulations were carried out as a function of frequency, building properties, and signal incidence angle. Testing was then performed at the US Department of Energy’s Oak Ridge National Laboratory campus to identify the equipment needed for signal collection and to fine-tune the experimental procedure. Finally, as an application of the models and methods presented, measurements were conducted at a power generation plant to derive the field transfer functions and coupled high-altitude electromagnetic pulse waveforms for various locations within the facility.

42 ENGINEERING↗
DOE OSTI2022

On the Rapid Calculation of Binding Affinities for Antigen and Antibody Design and Affinity Maturation Simulations

The accurate and efficient calculation of protein-protein binding affinities is an essential component in antibody and antigen design and optimization, and in computer modeling of antibody affinity maturation. Such calculations remain challenging despite advances in computer hardware and algorithms, primarily because proteins are flexible molecules, and thus, require explicit or implicit incorporation of multiple conformational states into the computational procedure. The astronomical size of the amino acid sequence space further compounds the challenge by requiring predictions to be computed within a short time so that many sequence variants can be tested. In this study, we compare three classes of methods for antibody/antigen (Ab/Ag) binding affinity calculations: (i) a method that relies on the physical separation of the Ab/Ag complex in equilibrium molecular dynamics (MD) simulations, (ii) a collection of 18 scoring functions that act on an ensemble of structures created using homology modeling software, and (iii) methods based on the molecular mechanics-generalized Born surface area (MM-GBSA) energy decomposition, in which the individual contributions of the energy terms are scaled to optimize agreement with the experiment. When applied to a set of 49 antibody mutations in two Ab/HIV gp120 complexes, all of the methods are found to have modest accuracy, with the highest Pearson correlations reaching about 0.6. In particular, the most computationally intensive method, i.e., MD simulation, did not outperform several scoring functions. The optimized energy decomposition methods provided marginally higher accuracy, but at the expense of requiring experimental data for parametrization. Within each method class, we examined the effect of the number of independent computational replicates, i.e., modeled structures or reinitialized MD simulations, on the prediction accuracy. We suggest using about ten modeled structures for scoring methods, and about five simulation replicates for MD simulations as a rule of thumb for obtaining reasonable convergence. We anticipate that our study will be a useful resource for practitioners working to incorporate binding affinity calculations within their protein design and optimization process.

59 BASIC BIOLOGICAL SCIENCES↗