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At least 811 records · Page 45

BMX: Biological modelling and interface exchange

Abstract High performance computing has a great potential to provide a range of significant benefits for investigating biological systems. These systems often present large modelling problems with many coupled subsystems, such as when studying colonies of bacteria cells. The aim to understand cell colonies has generated substantial interest as they can have strong economic and societal impacts through their roles in in industrial bioreactors and complex community structures, called biofilms, found in clinical settings. Investigating these communities through realistic models can rapidly exceed the capabilities of current serial software. Here, we introduce BMX, a software system developed for the high performance modelling of large cell communities by utilising GPU acceleration. BMX builds upon the AMRex adaptive mesh refinement package to efficiently model cell colony formation under realistic laboratory conditions. Using simple test scenarios with varying nutrient availability, we show that BMX is capable of correctly reproducing observed behavior of bacterial colonies on realistic time scales demonstrating a potential application of high performance computing to colony modelling. The open source software is available from the zenodo repository https://doi.org/10.5281/zenodo.8084270 under the BSD-2-Clause licence.

97 MATHEMATICS AND COMPUTING↗

Potential energy profile for the Cl + (H 2 O) 3 → HCl + (H 2 O) 2 OH reaction. A CCSD(T) study

Four different reaction pathways are initially located for the reaction of Cl atom plus water trimer Cl + (H 2 O) 3 → HCl + (H 2 O) 2 OH using a standard DFT method. As found for the analogous fluorine reaction, the geometrical and energetic results for the four chlorine pathways are closely related. However, the energetics for the Cl reaction are very different from those for fluorine. Here in this paper, we investigate the lowest-energy chlorine pathway using the “gold standard” CCSD(T) method in conjunction with correlation-consistent basis sets up to cc-pVQZ. Structurally, the stationary points for the water trimer reaction Cl + (H 2 O) 3 may be compared to those for the water monomer reaction Cl + H 2 O and water dimer reaction Cl + (H 2 O) 2 . Based on the CCSD(T) energies, the title reaction is endothermic by 19.3 kcal mol -1 , with a classical barrier height of 16.7 kcal mol -1 between the reactants and the exit complex. There is no barrier for the reverse reaction. The Cl … (H 2 O) 3 entrance complex lies 5.3 kcal mol -1 below the separated reactants. The HCl … (H 2 O) 2 OH exit complex is bound by 8.6 kcal mol -1 relative to the separated products. The Cl + (H 2 O) 3 reaction is somewhat similar to the analogous Cl + (H 2 O) 2 reaction, but qualitatively different from the Cl + H 2 O reaction. It is reasonable to expect that the reactions between the chlorine atom and larger water clusters may be similar to the Cl + (H 2 O) 3 reaction. The potential energy profile for the Cl + (H 2 O) 3 reaction is radically different from that for the valence isoelectronic F + (H 2 O) 3 system, which may be related to the different bond energies between HCl and HF.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Graphical Gaussian Process Regression Model for Aqueous Solvation Free Energy Prediction of Organic Molecules in Redox Flow Battery

The solvation free energy of organic molecules is a critical parameter in determining emergent properties such as solubility, liquid-phase equilibrium constants, and pKa and redox potentials in an organic redox flow battery. In this work, we present a machine learning (ML) model that can learn and predict the aqueous solvation free energy of an organic molecule using Gaussian process regression method based on a new molecular graph kernel. To investigate the performance of the ML model on electrostatic interaction, the nonpolar interaction contribution of solvent and the conformational entropy of solute in solvation free energy, three data sets with implicit or explicit water solvent models, and contribution of conformational entropy of solute are tested. We demonstrate that our ML model can predict the solvation free energy of molecules at chemical accuracy with a mean absolute error of less than 1 kcal/mol for subsets of the QM9 dataset and the Freesolv database. To solve the general data scarcity problem for a graph-based ML model, we propose a dimension reduction algorithm based on the distance between molecular graphs, which can be used to examine the diversity of the molecular data set. It provides a promising way to build a minimum training set to improve prediction for certain test sets where the space of molecular structures is predetermined.

25 ENERGY STORAGE↗

Exact restoration of Galilei invariance in density functional calculations with quantum Monte Carlo

We investigate some aspects of the connection between mean-field and ab-initio calculations for any-nucleon systems employing the Gogny effective interaction. In particular, we present variational Monte Carlo calculations of 4 He and 16 O, for which we extended the formalism of the linear method to the case of a density-dependent Hamiltonian. Monte Carlo calculations using an uncorrelated basis reduce to Hartree-Fock ones, but Galilean invariance can be preserved, contrary to the usual treatment. An analysis of the results obtained with the Gogny force when used in conjunction with correlated wave functions has also been performed. Here, the calculations show the collapse of the deuteron, leading to a set of unphysical predictions for the structure of heavier nuclei. This behavior remarks the different role of the Gogny effective interaction as compared to bare interactions typically used in fully microscopic calculations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Displacement driven balancing of a diamond turning machine flycutter

The spindle balancing operation is critical to the performance of precision lathes and should be conducted anytime the configuration of the spindle or its tooling is modified such that an unbalanced condition may occur. Within the machine tool community, accelerometers are typically used as the feedback device during the balancing operation. At Lawrence Livermore National Laboratory (LLNL), we have nearly 40 years of history using displacement sensors, such as capacitance gauges, in place of accelerometers when balancing precision spindles. The process of balancing a precision machine spindle using displacement sensors is presented in the context of two work examples. In this case, the details of the one-dimensional balancing operation performed after replacing a flycutter on the spindles of two unique large optic diamond turning machines is discussed. The pros and cons of accelerometer driven balancing and displacement driven balancing are also presented. In the accelerometer context, the level of balance achieved for our work example is less than 100 micro-g or a total indicator reading (TIR) of 1.6 µm. The process of balancing has been enhanced over the years as advances have been made in software, data acquisition systems, and instrumentation. The balancing system is described including details about instrumentation, set-up, how phase and spindle structure stiffness is calculated, and how the LLNL developed software that guides the user through the process by suggesting corrective action.

42 ENGINEERING↗

Engineered living materials for capture, conversion, and recycling technologies

Continued dependence on crude oil and natural gas resources for fossil fuels has caused global atmospheric carbon dioxide (CO 2 ) emissions to increase to record-setting proportions. There is an urgent need for efficient and inexpensive carbon sequestration systems to mitigate large-scale CO 2 emissions from industrial flue gas. Carbonic anhydrase (CA) has shown high potential for enhanced CO 2 capture applications compared to conventional absorption-based methods currently utilized in various industrial settings. This study aims to understand structural aspects that contribute to the stability of CA enzymes critical for their applications in industrial processes, which require the ability to withstand conditions different from their native environments. Here, we evaluated the thermostability and enzyme activity of mesophilic and thermophilic CA variants at different temperature conditions and in the presence of atmospheric gas pollutants like nitrogen oxides (NO x ) and sulphur oxides (SO x ). Based on our enzyme activity assays and molecular dynamics simulations, we see increased conformational stability and CA activity levels in thermostable CA variants incubated week-long at different temperature conditions. The thermostable CA variants also retained high levels of CA activity despite changes in solution pH due to increasing NO x and SO x concentrations. Furthermore, a loss of CA activity was observed only at high concentrations of NO x /SO x that possibly can be minimized with appropriate buffered solutions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

ASSESSMENT OF HIGH-VOLUME HARVESTED FLY ASH BLENDS FOR USE IN PRECAST CONSTRUCTION

Declining supplies of fresh fly ashes in some regions have further driven the importance of using harvested fly ash as a supplementary cementitious material and thus replacement for more energy-intensive ordinary Portland cement (OPC). Higher replacement rates of OPC with fly ash in general has traditionally been limited in precast operations due to stringent early-age strength requirements necessitated by initial prestress and lifting/handling of hardened components – often well within 24 hours after fresh concrete placement. Therefore, a series of mix designs were developed, as part of a larger framework for reassessing high-volume fly ash (HVFA) use in the context of precast construction, to demonstrate the feasibility of using larger fractions of harvested fly ash in concrete formulations suitable for precast fabrication demands. More specifically, a target minimum 24-hour compressive strength of 24.1 MPa (3500 psi) was set, in accordance with conventional precast structural design checks, while increasing the fly ash content to 40% replacement of OPC – at least a 15% increase above the traditional limit of 25%. The effect of using more sustainable Type IL cement in contrast to conventional Type III Portland cement (the traditional standard for precast use) – both in conjunction with HVFA use – was also examined. Early-age mechanical properties including compressive strength, modulus of rupture, and modulus of elasticity were evaluated within the aforementioned early-age window. Lastly, corresponding design equations were then reassessed for their applicability with respect to the high-early strength HVFA mixes examined herein.

Gombeda, Matthew J.↗

Combined Experimental and Computational Efforts to Establish Ion Mobility, Solubility and Stability of Functional Liquids for Electrochemical Energy Storage

This work provides a computation-driven investigation of the stability of organic electrolytes for lithium-air batteries. Electrolyte instability is currently a key challenge that limits practical use of aprotic Li-air batteries, and the chemical processes that cause this instability are often kinetically-driven. Computational screening for kinetic stability involves the determination of reaction barriers for the numerous potential reaction mechanisms, barriers that are challenging to calculate due to the difficulty of locating transition state structures. Here we screen a broad set of substituted electrolytes for susceptibility to nucleophilic attack by superoxide. We find that carbonates are not typically expected to be stable and that sulfones are generally stable, validating literature trends. We study the effects of chemical functionalization with electron-donating and withdrawing groups and their interplay with steric factors, identifying functional groups and other chemical modifications that increase stability in these groups. User-input driven transition state identification is used for these initial calculations, and an automated computational pipeline is subsequently presented and validated as a means to perform further high-throughput searches across mechanisms and chemistries. The pipeline integrates cheminformatics-based reaction encoding, relaxed potential energy scans, and nudged elastic band calculations for an end-to-end approach to barrier calculations. We review this automated search approach and its current limitations, and discuss challenges and further work.

25 ENERGY STORAGE↗

Financial Analysis of the Smallmouth Bass Flows implemented at the Glen Canyon Dam during Water Year 2024

The Glen Canyon Dam (GCD) is a Colorado River Storage Project (CRSP) power resource that is a component of the Salt Lake City Area Integrated Projects (SLCA/IP). The 2016 record of decision (ROD) for the GCD long-term experimental and management plan (LTEMP) final Environmental Impact Statement (EIS) specifies criteria for GCD monthly water releases, daily and hourly operating limits, and experimental releases. This report presents a financial analysis of the Smallmouth bass (Micropterus dolomieu) (SMB) flows implemented at GCD during Water Year (WY) 2024. These bypass flows were introduced by the U.S. Bureau of Reclamation (USBR) as an emergency response to the growing threat posed by invasive SMB in the Colorado River ecosystem downstream of the dam. SMB are a non-native predatory species that pose a significant threat to native fish populations, including the endangered humpback chub (Gila cypha). The thermal regime below GCD, typically cold due to hypolimnetic releases from Lake Powell, has historically served as a thermal barrier limiting SMB establishment. However, persistently low reservoir levels in recent years have reduced stratification in Lake Powell, allowing warmer water to be released downstream. This has enabled SMB to spawn successfully below the dam, prompting urgent ecological concerns. To mitigate the risk of SMB proliferation, the USBR implemented a series of bypass flows in WY 2024. Drawn from a lower elevation than the penstocks, the bypass structures released cooler water downstream. These short-duration bypass flows aimed to keep temperatures cool enough to prevent SMB from spawning, thereby reducing the ecological threat posed by this invasive species. Although motivated by ecological objectives, these bypass flows came with financial tradeoffs. Releasing water through the bypass structures instead of the turbines at GCD reduced hydropower generation, resulting in a significantly lower financial position for Western Area Power Administration (WAPA), which is responsible for marketing the electricity produced by the GCD Powerplant. This report analyzes the financial impact of the SMB flows implemented from July to November 2024. These experimental releases led to an estimated financial cost of approximately $18.9 million, primarily driven by the substantial volume of water diverted through the bypass structures. This study applies an integrated set of tools to estimate WAPA financial impacts by simulating GCD under two types of cases; namely, (1) a “With Experiment” case that mimics the water operations that actually occurred, including the SMB bypass flows, and (2) a “Without Experiment” case that simulates operations under the assumption that the SMB flows did not occur. Both cases comply with LTEMP hourly and daily operating criteria, and the monthly water release volumes are assumed to be identical under both cases. The Colorado River Storage Project Python-based model (CRiSPPy) model was the main modeling tool used to simulate the dispatch of the GCD hydropower plant and associated water releases from Lake Powell. In the modeling process, the research team used extensive data sets and historical information on SLCA/IP power plant characteristics, hydrologic conditions, and WAPA’s power purchases and sales prices.

13 HYDRO ENERGY↗

Population Structure of White Sturgeon (Acipenser transmontanus) in the Columbia River Inferred from Single-Nucleotide Polymorphisms

White sturgeon (Acipenser transmontanus) are the largest freshwater fish in North America, with reproducing populations in the Sacramento-San Joaquin, Fraser, and Columbia River Basins. Of these, the Columbia River is the largest, but it is also highly fragmented by hydroelectric dams, and many segments are characterized by declining abundance and persistent recruitment failure. Efforts to conserve and supplement these fish requires an understanding of their spatial genetic structure. Here, we assembled a large set of samples from throughout the Columbia River Basin, along with representative collections from adjacent basins, and genotyped them using a panel of 325 single-nucleotide markers. Results from individual- and group-based analyses of these data indicate that white sturgeon in the uppermost Columbia River Basin, in the Kootenai and upper Snake Rivers, are the most distinct, while the remaining populations downstream in the basin can be described as a genetic gradient consistent with an isolation-by-distance effect. Notably, the population in the lowest reaches of the Columbia River is more distinct from the middle or upper reaches than from outside basins, and suggests historically a higher or more recent gene exchange through coastal routes than with populations in the interior Columbia Basin. Nonetheless, proximal reaches were generally only marginally or non-significantly divergent, suggesting that transplanting larvae or juveniles from nearby sources poses relatively little risk of outbreeding depression. Indeed, we inferred examples of dispersal between reaches via close-kin mark-recapture and genetic mark-recapture that indicate movement between nearby reaches is not unusual. Samples from the Kootenai and upper Snake Rivers exhibited notably lower genetic diversity than the remaining samples as a result of population bottlenecks, genetic drift, and/or historical divergence. Conservation actions, such as supplementation, are underway to maintain population viability and will require balanced efforts to increase demographic abundance while maintaining genetic diversity.

Willis, Stuart C.↗

Geology of selected lava tubes in the Bend Area, Oregon

Longitudinal profiles representing 5872.5 m of mapped lava tubes and a photogeologic map relating lava tubes to surface geology, regional structure and topography are presented. Three sets of lava tubes were examined: (1) Arnold Lava Tube System (7km long) composed of collapsed and uncollapsed tube segments and lava ponds, (2) Horse Lava Tube System (11 km long) composed of parallel and anastomosing lava tube segments, and (3) miscellaneous lava tubes. Results of this study tend to confirm the layered lava hypothesis of Ollier and Brown (1965) for lava tube formation; however, there are probably several modes of formation for lava tubes in general. Arnold System is a single series of tubes apparently formed in a single basalt flow on a relatively steep gradient. The advancing flow in which the tubes formed was apparently temporarily halted, resulting in the formation of lava ponds which were inflated and later drained by the lava tube system. Horse System probably formed in multiple, interconnected flows. Pre-flow gradient appears to have been less than for Arnold System, and resulted in meandrous, multiple tube networks.

Greely, R.↗

Decomposition-aggregation stability analysis of the spinning Skylab

Stability of an 11-th order linear model of the spinning Skylab is determined by the decomposition-aggregation method based upon the comparison principle and vector Liapunov functions. To reduce the inherent conservativeness of the method an optimization problem is formulated and resolved producing the optimum comparison system. The system provides the best estimate of the stability region of the important structural parameter - asymmetry in the boom settings.

Cuk, S. M.↗

The development of an engineering computer graphics laboratory

Hardware and software systems developed to further research and education in interactive computer graphics were described, as well as several of the ongoing application-oriented projects, educational graphics programs, and graduate research projects. The software system consists of a FORTRAN 4 subroutine package, in conjunction with a PDP 11/40 minicomputer as the primary computation processor and the Imlac PDS-1 as an intelligent display processor. The package comprises a comprehensive set of graphics routines for dynamic, structured two-dimensional display manipulation, and numerous routines to handle a variety of input devices at the Imlac.

Anderson, D. C.↗

Covariance analyses of satellite-derived mesoscale wind fields

Statistical structure functions have been computed independently for nine satellite-derived mesoscale wind fields that were obtained on two different days. Small cumulus clouds were tracked at 5 min intervals, but since these clouds occurred primarily in the warm sectors of midlatitude cyclones the results cannot be considered representative of the circulations within cyclones in general. The field structure varied considerably with time and was especially affected if mesoscale features were observed. The wind fields on the 2 days studied were highly anisotropic with large gradients in structure occurring approximately normal to the mean flow. Structure function calculations for the combined set of satellite winds were used to estimate random error present in the fields. It is concluded for these data that the random error in vector winds derived from cumulus cloud tracking using high-frequency satellite data is less than 1.75 m/s. Spatial correlation functions were also computed for the nine data sets. Normalized correlation functions were considerably different for u and v components and decreased rapidly as data point separation increased for both components. The correlation functions for transverse and longitudinal components decreased less rapidly as data point separation increased.

Maddox, R. A.↗

Characteristics of 30-centimeter mercury ion thrusters

The technology development of the 30-cm J-series mercury ion thruster for prime propulsion application in solar electric propulsion systems has been conducted at NASA-Lewis Research Center. This development included the fabrication and testing of the 30-cm thruster. The present J-series thruster design is the result of an intensive effort to eliminate real and potential design deficiencies that were uncovered during initial endurance, structural, and performance tests. A standardized set of test and data recording procedure was formulated to allow for the characterization of the J-series thruster. This paper briefly reviews the design of the J-series thruster and presents a compilation of recent test results that define the J-series thruster characteristics.

Maloy, J. E.↗

Workshop rationale

The problems involved in processing remotely sensed data are defined within the contex of the total information system structure. The correlation of various data sets through georeferencing and cataloging is emphasized along with geometric rectification. The sources and types of possible geometric errors are outlined.

Billingsley, F. C.↗

Radar cross section studies

The ultimate goal is to generate experimental techniques and computer codes of rather general capability that would enable the aerospace industry to evaluate the scattering properties of aerodynamic shapes. Another goal involves developing an understanding of scattering mechanisms so that modification of the vehicular structure could be introduced within constraints set by aerodynamics. The development of indoor scattering measurement systems with special attention given to the compact range is another goal. There has been considerable progress in advancing state-of-the-art scattering measurements and control and analysis of the electromagnetic scattering from general targets.

Burnside, W. D.↗