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Results for “Aggregation ability”

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 OSTI2014

Inhibition of cell proliferation, migration and invasion of B16-F10 melanoma cells by α-mangostin

Highlights: • We studied the anticancer potential of a new emerging molecule, α-mangostin (α-M). • We provide first evidences on the effects of α-M on transglutaminase activity. • We deeply examined the antimetastatic effects of α-M through many in vitro assays. • Proteomic analysis revealed that α-M promotes a reorganization at cellular level. - Abstract: In this study, we have evaluated the potential antineoplastic effects of α-mangostin (α-M), the most representative xanthone in Garcinia mangostana pericarp, on melanoma cell lines. This xanthone markedly inhibits the proliferation of high-metastatic B16-F10 melanoma cells. Furthermore, by deeply analyzing which steps in the metastatic process are influenced by xanthone it was observed that α-M strongly interferes with homotypic aggregation, adhesion, plasticity and invasion ability of B16-F10 cells, probably by the observed reduction of metalloproteinase-9 activity. The antiproliferative and antimetastatic properties of α-M have been established in human SK-MEL-28 and A375 melanoma cells. In order to identify pathways potentially involved in the antineoplastic properties of α-M, a comparative mass spectrometry proteomic approach was employed. These findings may improve our understanding of the molecular mechanisms underlying the anti-cancer effects of α-M on melanoma.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Mercury Removal from Contaminated Water by Wood-Based Biochar Depends on Natural Organic Matter and Ionic Composition

Biochars can remove potentially toxic elements, such as inorganic mercury [Hg(II)] from contaminated waters. However, their performance in complex water matrices is rarely investigated, and the combined roles of natural organic matter (NOM) and ionic composition in the removal of Hg(II) by biochar remain unclear. Here, we investigate the influence of NOM and major ions such as chloride (Cl – ), nitrate (NO 3 – ), calcium (Ca 2+ ), and sodium (Na + ) on Hg(II) removal by a wood-based biochar (SWP700). Multiple sorption sites containing sulfur (S) were located within the porous SWP700. In the absence of NOM, Hg(II) removal was driven by these sites. Ca 2+ bridging was important in enhancing removal of negatively charged Hg(II)-chloro complexes. In the presence of NOM, formation of soluble Hg-NOM complexes (as seen from speciation calculations), which have limited access to biochar pores, suppressed Hg(II) removal, but Cl – and Ca 2+ could still facilitate it. The ability of Ca 2+ to aggregate NOM, including Hg-NOM complexes, promoted Hg(II) removal from the dissolved fraction (<0.45 μm). Hg(II) removal in the presence of Cl – followed a stepwise mechanism. Weakly bound oxygen functional groups in NOM were outcompeted by Cl – , forming smaller-sized Hg(II)-chloro complexes, which could access additional intraparticle sorption sites. Therein, Cl – was outcompeted by S, which finally immobilized Hg(II) in SWP700 as confirmed by extended X-ray absorption fine structure spectroscopy. We conclude that in NOM containing oxic waters, with relatively high molar ratios of Cl – : NOM and Ca 2+ : NOM, Hg(II) removal can still be effective with SWP700.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Identifying Cu( ii )–amyloid peptide binding intermediates in the early stages of aggregation by resonance Raman spectroscopy: a simulation study

The aggregation of amyloid beta (Aβ) peptides plays a crucial role in the pathology and etiology of Alzheimer's disease. Experimental evidence shows that copper ion is an aggregation-prone species with the ability to coordinately bind to Aβ and further induce the formation of neurotoxic Aβ oligomers. However, the detailed structures of Cu(II)–Aβ complexes have not been illustrated, and the kinetics and dynamics of the Cu(II) binding are not well understood. Two Cu(II)–Aβ complexes have been proposed to exist under physiological conditions, and another two might exist at higher pH values. By using ab initio simulations for the spontaneous resonance Raman and time domain stimulated resonance Raman spectroscopy signals, we obtained the characteristic Raman vibronic features of each complex. Finally, these signals contain rich structural information with high temporal resolution, enabling the characterization of transient states during the fast Cu–Aβ binding and interconversion processes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Decentralized Carrier Phase Shifting for Optimal Harmonic Minimization in Asymmetric Parallel-Connected Inverters

This paper presents a carrier phase shifting technique for minimizing the aggregate harmonics in networks of asymmetric parallel-connected inverters for distributed power generation system applications. The proposed technique is: 1) implemented in a decentralized manner, relying only on local voltage and current measurements, and 2) optimal in the sense that it minimizes a cost function representing the carrier-frequency current harmonics. The analysis indicates that the proposed optimal carrier phase shifting technique can enable order-of-magnitude reductions in harmonic power, and also universal improvements compared to symmetric carrier interleaving for asymmetric inverter networks. Moreover, compared to existing methods that require either centralized communication or information exchange between inverters to coordinate carriers, the proposed technique is completely decentralized, which provides important practical benefits for implementation, including improved robustness and reduced cost. The technique is experimentally validated on a network of three single-phase 2-kW inverters and demonstrates a 36.5% reduction in the weighted total harmonic distortion factor of the aggregate inverter current, and the ability to converge to the optimal carrier phase spacing dynamically in less than one line frequency cycle (16.7 ms) in steady state and transient operating conditions.

42 ENGINEERING↗
DOE OSTI2022

Securing Solar for the Grid: Extreme Control Whitepaper

Emerging standards outlining desired behaviors for Distributed Energy Resources (DER), such as IEEE 1547-2018, define several device-level control functions to regulate DER power injections/consumptions in response to locally sensed grid conditions. The ability to adjust settings of aggregations of DER with standardized embedded control functionality constitutes a mechanism which can, potentially, create undesirable or deleterious effects on the power grid. The purpose of this white paper is to highlight unintended effects stemming from improperly tuned embedded control functions in Distributed Energy Resources (DER), which could be exploited by a malicious entity as a means to attack the power grid.

14 SOLAR ENERGY↗
NASA NTRS2001

Validation of Ocean Color Satellite Data Products in Under Sampled Marine Areas

The planktonic marine cyanobacterium, Trichodesmium sp., is broadly distributed throughout the oligotrophic marine tropical and sub-tropical oceans. Trichodesmium, which typically occurs in macroscopic bundles or colonies, is noteworthy for its ability to form large surface aggregations and to fix dinitrogen gas. The latter is important because primary production supported by N2 fixation can result in a net export of carbon from the surface waters to deep ocean and may therefore play a significant role in the global carbon cycle. However, information on the distribution and density of Trichodesmium from shipboard measurements through the oligotrophic oceans is very sparse. Such estimates are required to quantitatively estimate total global rates of N2 fixation. As a result current global rate estimates are highly uncertain. Thus in order to understand the broader biogeochemical importance of Trichodesmium and N2 fixation in the oceans, we need better methods to estimate the global temporal and spatial variability of this organism. One approach that holds great promise is satellite remote sensing. Satellite ocean color sensors are ideal instruments for estimating global phytoplankton biomass, especially that due to episodic blooms, because they provide relatively high frequency synoptic information over large areas. Trichodesmium has a combination of specific ultrastructural and biochemical features that lend themselves to identification of this organism by remote sensing. Specifically, these features are high backscatter due to the presence of gas vesicles, and absorption and fluorescence of phycoerythrin. The resulting optical signature is relatively unique and should be detectable with satellite ocean color sensors such as the Sea-Viewing Wide Field-of-view Sensor (SeaWiFS).

Subramaniam, Ajit↗
DOE OSTI2015

Discovery of an Inhibitor of Z-Alpha1 Antitrypsin Polymerization

Polymerization of the Z variant alpha-1-antitrypsin (Z-α1AT) results in the most common and severe form of α1AT deficiency (α1ATD), a debilitating genetic disorder whose clinical manifestations range from asymptomatic to fatal liver and/or lung disease. As the altered conformation of Z-α1AT and its attendant aggregation are responsible for pathogenesis, the polymerization process per se has become a major target for the development of therapeutics. Based on the ability of Z-alpha 1AT to aggregate by recruiting the reactive center loop (RCL) of another Z-α1AT into its s4A cavity, we developed a high-throughput screening assay that uses a modified 6-mer peptide mimicking the RCL to screen for inhibitors of Z-α1AT polymer growth. We used a subset of compounds from the Library of Pharmacologically Active Compounds (LOPAC) with molecular weights ranging from 300 to 700 Da, to evaluate the assay's capabilities. The inhibitor S-(4-nitrobenzyl)-6-thioguanosine was identified as a lead compound and its ability to prevent Z-α1AT polymerization confirmed by secondary assays. In order to further investigate the binding location of S-(4-nitrobenzyl)-6-thioguanosine, an in silico strategy was pursued and the intermediate alpha 1AT M* state modeled to allow molecular docking simulations and explore various potential binding sites. Docking results predict that S-(4-nitrobenzyl)-6-thioguanosine can bind at the s4A cavity and at the edge of beta-sheet A. The former binding site would directly block RCL insertion whereas the latter site would prevent beta-sheet A from expanding between s3A/s5A, and thus indirectly impede RCL insertion. Our investigations have revealed a novel compound that inhibits the formation of Z-α1AT polymers, as well as in vitro and in silico strategies for identifying and characterizing additional blocking molecules of Z-α1AT polymerization.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1993

The C-terminal region of alpha-crystallin: involvement in protection against heat-induced denaturation

Recent studies have demonstrated that the alpha-crystallins can protect other proteins against heat-induced denaturation and aggregation. To determine the possible involvement of the C-terminal region in this activity, the alpha-crystallins were subjected to limited tryptic digestion, and the amount of cleavage from the N-terminal and C-terminal regions of the alpha-A and alpha-B crystallin chains was assessed using antisera specific for these regions. Limited tryptic digestion resulted in cleavage only from the C-terminal region of alpha-A crystallin. This trypsin-treated alpha-A crystallin preparation showed a decreased ability to protect proteins from heat-induced aggregation using an in vitro assay. Together, these results demonstrate that the C-terminal region of alpha-A crystallin is important for its ability to protect against heat-induced aggregation, which is consistent with the hypothesis that post-translational changes that are known to occur at the C-terminal region may have significant effects on the ability of alpha-A crystallin to protect against protein denaturation in vivo.

NASA Discipline Cell Biology↗
NASA NTRS2019

Method for Tracking and Communicating Aggregate Risk Through the Use of Model-Based Systems Engineering (MBSE) Tools

Large, complex projects can identify a significant number and variety of risks, throughout the project life cycle. These risks are analyzed, mitigated, closed or accepted as independent uncertainties. Once closed or accepted, it is easy for projects to lose awareness of their impact. In reality, each of these risks contributes some amount to the overall risk posture of the project. The ability to track and effectively communicate this aggregate risk has represented a challenge to project management. There have been previous attempts to create a schema to communicate the aggregate effect of risks, without notable success. Most of these attempts have centered on some additive metric derived from the scoring of likelihood and consequence values. This, in and of itself, is a logical approach, but all too often the scores were then aggregated to a level where all context was lost. One weakness has been a lack of attempt to create linkages or logical groups of the risks upon which useful aggregation could then occur. The overall move to model-based (systems) engineering (MBSE) has opened up a vast frontier of opportunities to better integrate all project data. MBSE provides an underlying layer that links data items to each other. Objectives link to requirements, which then link to functions, functions to physical architecture items, and so on, as far down as projects want to model. While it started with a focus on modeling requirements based on things like use cases, efforts are now underway to integrate safety and mission assurance (S&MA) information and analyses, such as risks. This effort, called Model Based Mission Assurance (MBMA), is yielding models that are more useful and are a more accurate representations of the systems. MBSE models, with this ability to link related items, provide a new means of tracking and communicating aggregate risks. In the proposed method, risks are added into the models as distinct items, having attributes that communicate a scoring derived from the likelihood and consequence values as charted on the standard NASA 5x5 risk matrix. Like earlier efforts, each box in the 5x5 has an associated scoring, which may include both a current score and potential post-mitigation/control score. The risk items are then linked to elements of the model, such as system objectives/goals, requirements, functions, or physical architecture items, with "Risk to" relationships. These risks will then be communicated by use of reports generated from the model, detailing all risks and/or hazards linked to model elements. These reports can include aggregate impacts, including a current scoring and potential future state scoring based on the planned mitigations and/or controls. These reports will show all risks, open, accepted, and closed, linked to project objectives or requirements. When run as part of an upcoming risk acceptance discussion, these reports will serve to remind the team of all previous risks that relate to the effected portion of the system. When included as part of periodic program or project reviews, risk reviews, and safety reviews, this method can improve the overall understanding of the system's true risk posture. This proposed method takes full advantage of the advances that modern modeling techniques provide, with a minimal investment of additional time. Utilizing the model environment also enables a near constant access to current state of aggregate risks.

model based mission assurance↗
DOE OSTI2023

Elucidating the speciation of extracted lanthanides by diglycolamides

Many studies over the past few decades have been devoted to addressing the application of diglycolamides (DGAs) for hydrometallurgical-based, f-element separations. Work to date has shown the molecular structure of a DGA derivative can have a significant impact on intra-lanthanide partitioning patterns. More recent studies have pushed towards probing the structure function relationship of the lanthanide-DGA complex to enable the design of more efficient lanthanide separation systems. Spectroscopic techniques, such as UV–Visible, Fourier Transformed Infrared Spectroscopy (FT-IR), Nuclear Magnetic Resonance (NMR), and Extended X-ray Absorption Fine Structure (EXAFS), provide information regarding the inner-sphere coordination of a given lanthanide-DGA complex. Scattering techniques, such as Dynamic Light Scattering (DLS), Small-Angle X-ray Scattering (SAXS), and Small-Angle Neutron Scattering (SANS), address nanoscale structures including aggregate sizes and morphology. Here, this review assesses the current state-of-knowledge regarding lanthanide-DGA hydrometallurgical (i.e., solvent extraction systems) interrogated using spectroscopic and scattering techniques to characterize the extracted Ln 3+ DGA species. Of particular interest to this review is the impact of varied diluents, inclusion and variation of phase modifiers, and DGA derivatization on system characteristics. While there has been extensive literature on the application of DGAs for f-element separations, the literature lacks a collective assessment of the speciation of Ln 3+ in the organic phase. This review provides new insights into the field of DGA separations, explicitly with an application to intra-lanthanide separations. Specifically, this review illustrates the importance of both the co-extraction anion (Cl - , NO 3 - , or ClO 4 - ) as it pertains to both the aggregate size and Ln 3+ distribution coefficient. It is evident the ability of the anion to disrupt the hydrogen bonding network limits both aggregate size and distribution coefficients according to the Hoffmeister series. This suggests the importance of the large, softer anions with a low charge-to-surface area ratio on encouraging hydrogen bond interactions. In addition, the co-extracted cation (H + vs Na + ) is important for mitigating transfer of Ln 3+ from the aqueous to the organic phase through extensive hydrogen bonding networks. These networks are responsible for forming supramolecular aggregates where a change in morphology is observed with increasing concentrations of H + and/or Ln 3+ in the organic phase.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Design of non-aggregating variants of Aβ peptide

Highlights: • Non-aggregating, non-toxic variants of Aβ peptide were designed using Aβ structure. • Mutations reduce aggregation by stabilising Aβ into small non-toxic oligomers. • Identification of these residues will assist the design of future therapeutic peptides. - Abstract: Self association of the amyloid-β (Aβ{sub 42}) peptide into oligomers, high molecular weight forms, fibrils and ultimately neuritic plaques, has been correlated with progressive cognitive decline in Alzheimer’s disease. Thus, insights into the drivers of the aggregation pathway have the capacity to significantly contribute to our understanding of disease mechanism. Functional assays and a three-dimensional crystal structure of the P3 amyloidogenic region 18–41 of Aβ were used to identify residues important in self-association and to design novel non-aggregating variants of the peptide. Biophysical studies (gel filtration, SDS–PAGE, dynamic light scattering, thioflavin T assay, and electron microscopy) demonstrate that in contrast to wild type Aβ these targeted mutations lose the ability to self-associate. Loss of aggregation also correlates with reduced neuronal toxicity. Our results highlight residues and regions of the Aβ peptide important for future targeting agents aimed at the amelioration of Alzheimer’s disease.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Inline small-angle X-ray scattering-coupled chromatography under extreme hydrostatic pressure

As continuing discoveries highlight the surprising abundance and resilience of deep ocean and subsurface microbial life, the effects of extreme hydrostatic pressure on biological structure and function have attracted renewed interest. Biological small-angle X-ray scattering (BioSAXS) is a widely used method of obtaining structural information from biomolecules in solution under a wide range of solution conditions. Due to its ability to reduce radiation damage, remove aggregates, and separate monodisperse components from complex mixtures, size-exclusion chromatography-coupled SAXS (SEC-SAXS) is now the dominant form of BioSAXS at many synchrotron beamlines. While BioSAXS can currently be performed with some difficulty under pressure with non-flowing samples, it has not been clear how, or even if, continuously flowing SEC-SAXS, with its fragile media-packed columns, might work in an extreme high-pressure environment. Here we show, for the first time, that reproducible chromatographic separations coupled directly to high-pressure BioSAXS can be achieved at pressures up to at least 100 MPa and that pressure-induced changes in folding and oligomeric state and other properties can be observed. Further, the apparatus described here functions at a range of temperatures (0°C–50°C), expanding opportunities for understanding biomolecular rules of life in deep ocean and subsurface environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

J-domain proteins interaction with neurodegenerative disease-related proteins

HSP70 chaperones, J-domain proteins (JDPs) and nucleotide exchange factors (NEF) form functional networks that have the ability to prevent and reverse the aggregation of proteins associated with neurodegenerative diseases. JDPs can interact with specific substrate proteins, hold them in a refolding-competent conformation and target them to specific HSP70 chaperones for remodeling. Thereby, JDPs select specific substrates and constitute an attractive target for pharmacological intervention of neurodegenerative diseases. This, under the condition that the exact mechanism of JDPs interaction with specific substrates is unveiled. In this review, we provide an overview of the structural and functional variety of JDPs that interact with neurodegenerative disease-associated proteins and we highlight those studies that identified specific residues, domains or regions of JDPs that are crucial for substrate binding.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Exciton Delocalization in Indolenine Squaraine Aggregates Templated by DNA Holliday Junction Scaffolds

Exciton delocalization plays a prominent role in the photophysics of molecular aggregates, ultimately governing their particular function or application. DNA is a compelling scaffold in which to template molecular aggregates and promote exciton delocalization. As individual dye molecules are the basis of exciton delocalization in molecular aggregates, their judicious selection is important. Motivated by their excellent photostability and spectral properties, here we examine the ability of squaraine dyes to undergo exciton delocalization when aggregated via a DNA Holliday junction (HJ) template. A commercially available indolenine squaraine dye was chosen for the study given its strong structural resemblance to Cy5, a commercially available cyanine dye previously shown to undergo exciton delocalization in DNA HJs. Three types of DNA-dye aggregate configurations—transverse dimer, adjacent dimer, and tetramer—were investigated. Signatures of exciton delocalization were observed in all squaraine-DNA aggregates. Specifically, strong blue shift and Davydov splitting were observed in steady-state absorption spectroscopy and exciton-induced features were evident in circular dichroism spectroscopy. Strongly suppressed fluorescence emission provided additional, indirect evidence for exciton delocalization in the DNA-templated squaraine dye aggregates. To quantitatively evaluate and directly compare the excitonic Coulombic coupling responsible for exciton delocalization, the strength of excitonic hopping interactions between the dyes were obtained by simultaneous fitting the experimental steady-state absorption and CD spectra via a Holstein-like Hamiltonian in which, following the theoretical approach of Kühn, Renger, and May, the dominant vibrational mode is explicitly considered. The excitonic hopping strength within indolenine squaraines was found to be comparable to that of the analogous Cy5 DNA-templated aggregate. The squaraine aggregates adopted primarily an H-type (dyes oriented parallel to each other) spatial arrangement. Extracted geometric details of dye mutual orientation in the aggregates enabled close comparison of aggregate configurations and the elucidation of the influence of dye angular relationship on excitonic hopping interactions in squaraine aggregates. Furthermore, these results encourage the application of squaraine-based aggregates in next generation systems driven by molecular excitons.

36 MATERIALS SCIENCE↗
DOE OSTI2018

The Building ENergy Demand (BEND) Model: A Comprehensive Composite Building Energy Modeling Framework

The Building ENergy Demand (BEND) model was developed at Pacific Northwest National Laboratory (PNNL) to simulate climate-dependent hourly building energy demand with the ability to disaggregate down to or aggregate up to any geographic area of interest, including counties, states, electric utility service territories, and census regions. The BEND modeling framework is designed to study the effects of climate change, economics, technology advancement, and various mitigation policies on aggregate building energy demand. To make the process computationally feasible, BEND reduces granularity in building characteristics and weather forcing while maintaining enough detail to minimize systematic differences (biases) between BEND results and data from the Energy Information Administration (EIA). Based on the Commercial Building Energy Consumption Survey (CBECS) and Residential Energy Consumption Survey (RECS) databases, BEND establishes a set of representative buildings with predefined sets of building types, sizes, and vintages. These representative buildings are defined for each of the four U.S. census regions and the five climate zones used by the EIA for building surveys (hereafter “EIA climate zones”). BEND’s representative buildings are based on a statistical analysis of the CBECS and RECS databases that infers detailed parameters such as construction type, thermal properties, internal loads, equipment and mechanical systems, and operation schedules from the high-level descriptors in those databases (building type, vintage, size, and location). The representative buildings are simplified and consolidated into a set of prototype buildings for the purpose of simulating building energy demand. Combining the prototype buildings with weather files from selected locations and years, BEND creates a set of simulation-ready building models to be run using the EnergyPlus simulation engine (EnergyPlus). The base spatial unit of each BEND simulation is a subregion that is the intersection of an International Energy Conservation Code climate zone, a census region, and an EIA climate zone; analysis for each spatial unit is influenced by the weather file BEND selects to represent the climate-similar area. The major simulation outputs of interest to BEND are hourly energy consumption values for each simulated year, possibly for multiple fuel types. Based on building-stock weights derived from the CBECS/RECS data, the hourly output streams are aggregated to a single, 8760-hour load profile for each of the major building categories—residential and commercial—with the possibility of segregating by fuel types. To correct for biases inherent in the use of a limited suite of representative buildings, BEND is calibrated against observational targets of total annual building energy consumption and hourly load profiles (including peak demand) obtained for the decision-relevant geographic scales of interest (e.g., total electric load data for individual balancing authorities available from EIA). Based on available data such as population distribution, BEND is able to aggregate both up and down scales, allowing the study of building energy demand over a range of spatial scales (e.g., states or counties within the Western Electricity Coordinating Council, Eastern Interconnection, or the entire U.S.) and/or subsets of building types (e.g., office buildings with particular size ranges).

24 POWER TRANSMISSION AND DISTRIBUTION↗
NASA NTRS2001

Physical State of Ices in the Outer Solar System

Comparison of the identity and abundances of ices observed around protostars and those associated with comets clearly suggests that comets preserve the heritage of the interstellar materials that aggregated to form them. However, the ability to identify these same species on icy satellites in the outer solar system is a complex function of the composition of the original ices, their subsequent thermal histories, and their exposure to various radiation environments. Our ability to identify the ices currently present on objects in the outer solar system relies upon observational and laboratory, and theoretical efforts. To date there is ample observational evidence for crystalline water ice throughout the outer solar system. In addition, there is growing evidence that amorphous ice may be present on some bodies. More volatile ices, e.g. N2, CH4. CO, and other species, e.g. ammonia hydrate, are identified on objects lying at and beyond Uranus. Both photolysis and radiolysis play important roles in altering the original surfaces due to chemical reactions and erosion of the surface. Ultraviolet photolysis appears to dominate alteration of the upper few hundred Angstroms, although sputtering the surface can sometimes be a significantly competitative process; dominating on icy surfaces embedded in a strong planetary magnetospheric field. There is growing observational evidence that the by-products of photolysis and radiolysis, suggested on a theoretical basis, are present on icy surfaces.

Roush, Ted L.↗
NASA NTRS2019

Using Graph Coloring to Compute Total Derivatives More Efficiently in OpenMDAO

When they are applicable, gradient based optimization algorithms are the most efficient way to solve design optimization problems. Although gradient based methods are generally efficient, they can be made significantly more so through the usage of analytic techniques to compute the necessary total derivatives. The traditional forward (direct) and reverse (adjoint) analytic techniques have computational costs that scale linearly with the number of design variables and the number of constraints, respectively. In this work, we present an application of a graph coloring algorithm to the analytic techniques for computing total derivative Jacobians in order to achieve much better computational scaling than the pure analytic methods can provide alone. A detailed theoretical explanation of how coloring algorithms interact with analytic derivative methods is presented that illustrates specific types of sparsity patterns that must be present in total derivative Jacobians in order for this coloring technique to be effective. The new technique has been implemented as a feature in the OpenMDAO framework and the implementation is demonstrated on two example problems. The performance on the example problems up to 50% reduction in compute cost for optimizations with bi-directional coloring compared to traditional constraint aggregation. Additionally, the results show how coloring technique alleviates some of the numerical difficulties that constraint aggregation can cause, leading to the ability to solve larger problems. It is expected that the new method will have wide applicability to multidisciplinary optimization problems, and that its availability in OpenMDAO will offer significant computational savings for users without the need for them to implement the coloring algorithm themselves.

Trajectory↗