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At least 1,585 records · Page 88

Accelerating Multivariate Functional Approximation Computation with Domain Decomposition Techniques⋆

Modeling large datasets through Multivariate Functional Approximations (MFA) provide an elegant way to handle many visualization and scientific analysis workflows. The process necessitates scalable data partitioning methods to compute MFA representations efficiently without compromising the accuracy or continuity of the reconstructed solution. We propose a domain -decomposed method for computing the MFA with B -spline bases, which reduces the total work per task and uses a restricted Additive Schwarz (RAS) method to converge the control point data degrees -of -freedom along subdomain boundaries. We provide an in-depth analysis of the parallel approach with domain decomposition solvers, aiming to minimize local subdomain error residuals and recover high -order continuity at subdomain interfaces with appropriate choices of knot overlaps. The communication cost, determined by the overlap regions in the RAS implementation, is optimized to recover the numerical error profile of the single subdomain case. Our proposed method stands in contrast to previous methods, which typically only recover either C 0 or at best C 1 continuity for arbitrary B -spline degree expansions, or those that require post -processing to blend discontinuities in the reconstructed data. We demonstrate the effectiveness of our approach using analytical and real -world datasets in 1D, 2D, and 3D through both strong and weak scaling studies. The performance results indicate that the overall cost of computing the approximation is directly proportional to the underlying nearest -neighbor communication implementation, and is only weakly dependent on the overlap region size that determines the size of the messages. This finding underscores the efficiency and scalability of our proposed method, making it a promising solution for handling large datasets in scientific workflows.

additive Schwarz solvers↗

Plug & play directed evolution of proteins with gradient-based discrete MCMC

Abstract A long-standing goal of machine-learning-based protein engineering is to accelerate the discovery of novel mutations that improve the function of a known protein. We introduce a sampling framework for evolving proteins in silico that supports mixing and matching a variety of unsupervised models, such as protein language models, and supervised models that predict protein function from sequence. By composing these models, we aim to improve our ability to evaluate unseen mutations and constrain search to regions of sequence space likely to contain functional proteins. Our framework achieves this without any model fine-tuning or re-training by constructing a product of experts distribution directly in discrete protein space. Instead of resorting to brute force search or random sampling, which is typical of classic directed evolution, we introduce a fast Markov chain Monte Carlo sampler that uses gradients to propose promising mutations. We conduct in silico directed evolution experiments on wide fitness landscapes and across a range of different pre-trained unsupervised models, including a 650 M parameter protein language model. Our results demonstrate an ability to efficiently discover variants with high evolutionary likelihood as well as estimated activity multiple mutations away from a wild type protein, suggesting our sampler provides a practical and effective new paradigm for machine-learning-based protein engineering.

59 BASIC BIOLOGICAL SCIENCES↗

Updated analyses of gluon distribution functions for the pion and kaon from the gauge-invariant nonlocal chiral quark model

In this work, we investigate the gluon distribution functions for the pion and kaon, in addition to the improved result of the valence-quark ones, in the gauge-invariant nonlocal chiral-quark model, in which the momentum dependence of the quark interactions is properly taken into account. We then analyze the gluon distribution functions, generated dynamically through the splitting functions in the Dokshitzer-Gribov-Lipatov-Altarelli-Parisi QCD evolution. By comparing with the recent lattice QCD results and Jefferson Lab angular momentum global analyses, it is found that the present numerical results for the gluon parton distribution functions for the pion exhibit a good agreement and the valence up-quark distribution results for the pion by reproducing the reanalyzed experimental data with a remarkable agreement. Our prediction on the gluon distribution functions for the kaon is also consistent with the recent lattice data for the kaon within the errors. Published by the American Physical Society 2024

Hutauruk, Parada. T. P. (ORCID:0000000242257109)↗

Self-similar Reynolds-averaged mechanical–scalar turbulence models for Rayleigh–Taylor mixing induced by power-law accelerations in the small Atwood number limit

Analytical self-similar solutions to two-, three-, and four-equation Reynolds-averaged mechanical–scalar turbulence models describing turbulent Rayleigh–Taylor mixing driven by a temporal power-law acceleration are derived in the small Atwood number (Boussinesq) limit. The solutions generalize those previously derived for constant acceleration Rayleigh–Taylor mixing for models based on the turbulent kinetic energy K and its dissipation rate ε, together with the scalar variance S and its dissipation rate χ [O. Schilling, “Self-similar Reynolds-averaged mechanical–scalar turbulence models for Rayleigh–Taylor, Richtmyer–Meshkov, and Kelvin–Helmholtz instability-induced mixing in the small Atwood number limit,” Phys. Fluids 33, 085129 (2021)]. The turbulent fields are expressed in terms of the model coefficients and power-law exponent, with their temporal power-law scalings obtained by requiring that the self-similar equations are explicitly time-independent. Mixing layer growth parameters and other physical observables are obtained explicitly as functions of the model coefficients and parameterized by the exponent of the power-law acceleration. Values for physical observables in the constant acceleration case are used to calibrate the two-, three-, and four-equation models, such that the self-similar solutions are consistent with experimental and numerical simulation data corresponding to a canonical (i.e., constant acceleration) Rayleigh–Taylor turbulent flow. The calibrated four-equation model is then used to numerically reconstruct the mean and turbulent fields, and turbulent equation budgets across the mixing layer for several values of the power-law exponent. Finally, the reference solutions derived here can be used to understand the model predictions for strongly accelerated or decelerated Rayleigh–Taylor mixing in the large Reynolds number limit.

42 ENGINEERING↗

Modeling the Deep Space Network costs for future space missions by using major cost drivers

This paper develops a cost model to do long range planning cost estimates for Deep Space Network (DSN) support of future space missions. The model is a function of eight major mission cost drivers such as uplink frequency upgrade, telemetry upgrade, and antenna gain/noise temperature upgrade. This paper focuses on the costs required to modify and/or enhance the DSN to prepare for supporting future space missions. Two models are derived from actual cost data from three space missions: Voyager (Uranus), Voyager (Neptune), and Magellan. Model A makes it possible to estimate the total cost, and Model B makes it possible to estimate the time profile cost and total cost for DSN support of a similar future space mission. The models were back tested against the total cost and the time profile cost for DSN support of the three projects, and gave cost estimates which range from 17 percent below to 19 percent above actual costs for Model A, and 22.5 percent below to 17.5 percent above for Model B. The total cost Model A was also applied to estimate the total costs for DSN support of two other independent projects: Mariner Jupiter/Saturn (MJS later became Voyager), and Viking. This model gave total cost estimates for DSN support which range from 15 percent to 4 percent above actual total costs for MJS and Viking, respectively.

Remer, Donald S.↗

State-Based Behavior Modeling of the Integrated SLS-MPCV System

In NASA's effort to foster a human spaceflight capability beyond Earth's orbit, two space systems are being developed - the Space Launch System (SLS) and the Multi-Purpose Crew Vehicle (MPCV). As of this time, the interactions between the two systems during launch are not fully detailed. To remedy this situation, a Systems Engineering approach utilizing models was developed to investigate the behavior of the integrated SLS-MPCV stack during ascent and abort situations. Specifically, this innovative approach combines aspects of Model-Based Systems Engineering (MBSE) and state analysis to simultaneously model the physical, functional, and behavioral aspects of systems. This approach focuses solely on the interactions between the systems, leaving much of the internal workings of either system at a logical level (i.e., black box). By utilizing this newly defined approach, a behavior model for the integrated SLS-MPCV stack was developed, emphasizing only the subset of interactions between the systems that impact behavior. Finally, analysis is performed within the model to investigate requirements gaps and examine the execution times of key behaviors related to various ascent phases and abort scenarios. The work described in this paper is merely a portion of the outlined effort being undertaken for this project; only a segment of the SLS-MPCV system behavior will be described.

Space Launch System (SLS)↗

Modeling plasma-induced surface charge effects on CO 2 activation by single atom catalysts supported on reducible and irreducible metal oxides

Abstract The accumulation of negative surface charge on catalytic surfaces in the presence of low-temperature plasma (LTP) could influence catalytic performance. However, it is difficult to disentangle the role of surface charging and other LTP catalytic effects in experiment. Herein, we use density functional theory (DFT) modeling to understand the effect of plasma-induced surface charging on CO 2 activation by atomically dispersed single atom (SA) catalysts on both reducible and irreducible metal oxide supports. We model CO 2 adsorption strength and CO 2 dissociation barriers for Co 1 , Ni 1 , Cu 1 , Rh 1 , Pd 1 , and Ag 1 SAs on both reducible and irreducible supports, namely, CeO 2 (100), TiO 2 (101), and γ -Al 2 O 3 (110), to elucidate trends. We find that accumulated surface charge on the SA increases the CO 2 adsorption strength and decreases the CO 2 dissociation barrier for all studied SA/support combinations. For both charged and uncharged (neutral) systems, SAs on the reducible CeO 2 (100) support generally adsorb CO 2 more weakly compared to when on irreducible supports like γ -Al 2 O 3 (110). SAs on γ -Al 2 O 3 (110) typically have larger barriers for CO 2 dissociation for both charged and uncharged systems compared to TiO 2 (101) and CeO 2 (100). The magnitude of surface charging effects on CO 2 binding energies and dissociation barriers depends sensitively on both the SA and the support. In some cases, the CO 2 activation trends qualitatively change between neutral and charged systems for a fixed SA across different supports. This DFT modeling study demonstrates that surface charging should be considered in strong electric fields because it can have a large effect on molecule adsorption and bond-breaking on catalytic surfaces.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Clinical Decision Support Software: Modeling and Capabilities

With its distance from Earth and communication delays, exploration space flight will place new demands for crew autonomy. Crewmembers operating during such missions require a dedicated Clinical Decision Support System (CDSS) that enhances their earth independence by augmenting their knowledge, skills, and abilities in different medical scenarios. A CDSS is a software application that must function optimally in diverse and varied scenarios (while interfacing with and providing actionable information to appropriate vehicle systems) to augment crew performance by enhancing or adding knowledge, skills, and abilities that preserve health and wellness and ultimately helping to ensure mission success. In addition, the software tool should provide various functions and computational models to meet the demands of astronauts beyond low earth orbit.

B Russell↗

A computational study of complex three-dimensional compressible turbulent flow fields

Solutions of the time dependent, Reynolds-averaged, Navier-Stokes equations are presented and are compared with a family of experimental results for the three-dimensional interaction of a shock wave with a turbulent boundary layer. The solutions correctly predict the major features of the flow field independent of the shock strength and the extent of separation when using a two-equation turbulence model with wall functions. The experimentally observed boundary between cylindrical and conical flow regimes is also predicted. However, for the flow fields with large separated zones, the details of the measured pressure distributions are not accurately computed, which indicates a need for improved turbulence modeling and/or grid resolution.

Horstman, C. C.↗

FPA Depot - Web Application

Lines of code (LOC) analysis is one of the methods used to measure programmer productivity and estimate schedules of programming projects. The Launch Control System (LCS) had previously used this method to estimate the amount of work and to plan development efforts. The disadvantage of using LOC as a measure of effort is that one can only measure 30% to 35% of the total effort of software projects involves coding [8]. In the application, instead of using the LOC we are using function point for a better estimation of hours in each software to develop. Because of these disadvantages, Jamie Szafran of the System Software Branch of Control And Data Systems (NE-C3) at Kennedy Space Canter developed a web application called Function Point Analysis (FPA) Depot. The objective of this web application is that the LCS software architecture team can use the data to more accurately estimate the effort required to implement customer requirements. This paper describes the evolution of the domain model used for function point analysis as project managers continually strive to generate more accurate estimates.

Avila, Edwin M. Martinez↗

Correction to Reconciling Work Functions and Adsorption Enthalpies for Implicit Solvent Models: A Pt (111)/Water Interface Case Study

This errata is to correct the acknowledgment in the original published article. G.B. (partial support), V.-A.G., M.-T.N., and R.R. were supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division. Computer resources were provided by Research Computing at Pacific Northwest National Laboratory and the National Energy Research Scientific Computing Center (NERSC), a U.S. Department of Energy Office of Science User Facility operated under Contract No. DE-AC02-05CH11231. PNNL is operated by Battelle for the U.S. Department of Energy under Contract DE-AC05-76RL01830. G.B. acknowledges the EPSRC for partial support in PhD funding. The authors acknowledge the use of the IRIDIS High Performance Computing Facility (IRIDIS 5) and associated support services at the University of Southampton in the completion of this work. We are grateful to the UK Materials and Molecular Modeling Hub (Thomas HPC) for computational resources, which is partially funded by EPSRC (EP/P020194/1).

continuum solvation, metal/water interfaces, ab in↗

Describing adsorption of benzene, thiophene, and xenon on coinage metals by using the Zaremba–Kohn theory-based model

Semilocal (SL) density functional approximations (DFAs) are widely applied but have limitations due to their inability to incorporate long-range van der Waals (vdW) interaction. Non-local functionals (vdW-DF, VV10, and rVV10) or empirical methods (DFT+D, DFT+vdW, and DFT+MBD) are used with SL-DFAs to account for such missing interaction. The physisorption of a molecule on the surface of the coinage metals (Cu, Ag, and Au) is a typical example of systems where vdW interaction is significant. However, it is difficult to find a general method that reasonably describes both adsorption energy and geometry of even the simple prototypes of cyclic and heterocyclic aromatic molecules such as benzene (C 6 H 6 ) and thiophene (C 4 H 4 S), respectively, with reasonable accuracy. Here, we present an alternative scheme based on Zaremba–Kohn theory, called DFT+vdW-dZK. We show that unlike other popular methods, DFT+vdW-dZK and particularly SCAN+vdW-dZK give an accurate description of the physisorption of a rare-gas atom (xenon) and two small albeit diverse prototype organic molecules on the (111) surfaces of the coinage metals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

In situ measurement of damage evolution in shocked magnesium as a function of microstructure

Accurate modeling and prediction of damage induced by dynamic loading in materials have long proved to be a difficult task. Examination of postmortem recovered samples cannot capture the time-dependent evolution of void nucleation and growth, and attempts at analytical models are hindered by the necessity to make simplifying assumptions, because of the lack of high-resolution, in situ, time-resolved experimental data. We use absorption contrast imaging to directly image the time evolution of spall damage in metals at ~1.6-μm spatial resolution. We observe a dependence of void distribution and size on time and microstructure. The insights gained from these data can be used to validate and improve dynamic damage prediction models, which have the potential to lead to the design of superior damage-resistant materials.

36 MATERIALS SCIENCE↗

A Field-Deployable Magnetic Resonance Imaging Rhizotron for Modeling and Enhancing Root Growth and Biogeochemical Function

A collaborative team from Texas A&M AgriLife Research, ABQMR Inc., the Soil Health Institute, the Athinoula A. Martinos Center for Biomedical Imaging, and NIST developed low-field magnetic resonance imaging (LF-MRI) instrumentation capable of imaging intact soil-root systems. The system measured root biomass, architecture, 3D mass distribution, and growth rates, providing a non-destructive means to evaluate ideal plant characteristics based on root metrics. It also successfully generated three-dimensional images of soil water content, a key property influencing root growth and exploration. Operating much like an MRI used in a medical setting, the system functioned in field conditions without damaging plants, overcoming the limitations of traditional methods such as trenching, soil coring, and root excavation. Over the course of the project, the team designed and built three functional prototype systems. These prototypes provided new insights into root–water–soil interactions that drive processes such as nutrient uptake, water use, and carbon management. This information contributed to efforts to optimize plants for carbon sequestration without sacrificing economic yield. The project also supported the identification of desirable traits for energy sorghum, including high root growth rates, more vertical root angles, and enhanced drought resilience under water-limiting conditions.

09 BIOMASS FUELS↗