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Results for “combinatorial optimization”

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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280 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Universal machine learning framework for defect predictions in zinc blende semiconductors

Our article introduces a universal predictive framework for point defect formation energies and charge transition levels in a wide chemical space of zinc blende semiconductors and possible impurity atoms selected from across the periodic table. This framework was developed by leveraging high-throughput quantum mechanical simulations benchmarked using some experimental data from the literature, as well as machine learning (ML)-based regressions techniques that map unique materials descriptors to computed defect properties and yield optimized and generalizable models. Furthermore, the power and utility of these models is revealed through quick predictions for thousands of new defects and screening of low-energy impurities, which may tune the equilibrium conductivity in the semiconductor. This work presents, to our knowledge, the largest density functional theory (DFT) dataset of defect properties in semiconductors and the largest DFT+ML-based screening of point defects in semiconductors to date.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Scaling Out a Combinatorial Algorithm for Discovering Carcinogenic Gene Combinations to Thousands of GPUs

Cancer is a leading cause of death in the US, second only to heart disease. It is primarily a result of a combination of an estimated two-nine genetic mutations (multi-hit combinations). Although a body of research has identified hundreds of cancer-causing genetic mutations, we don’t know the specific combination of mutations responsible for specific instances of cancer for most cancer types. An approximate algorithm for solving the weighted set cover problem was previously adapted to identify combinations of genes with mutations that may be responsible for individual instances of cancer. However, the algorithm’s computational requirement scales exponentially with the number of genes, making it impractical for identifying more than three-hit combinations, even after the algorithm was parallelized and scaled up to a V100 GPU. Since most cancers have been estimated to require more than three hits, we scaled out the algorithm to identify combinations of four or more hits using 1000 nodes (6000 V100 GPUs with ≈48×106 processing cores) on the Summit supercomputer at Oak Ridge National Laboratory. Efficiently scaling out the algorithm required a series of algorithmic innovations and optimizations for balancing an exponentially divergent workload across processors and for minimizing memory latency and inter-node communication. We achieved an average strong scaling efficiency of 90.14% (80.96%–97.96% for 200 to 1000 nodes), compared to a 100 node run, with 84.18% scaling efficiency for 1000 nodes. With experimental validation, the multi-hit combinations identified here could provide further insight into the etiology of different cancer subtypes and provide a rational basis for targeted combination therapy.

Dash, Sajal↗
DOE OSTI2017

Transcriptional reprogramming in yeast using dCas9 and combinatorial gRNA strategies

Background Transcriptional reprogramming is a fundamental process of living cells in order to adapt to environmental and endogenous cues. In order to allow flexible and timely control over gene expression without the interference of native gene expression machinery, a large number of studies have focused on developing synthetic biology tools for orthogonal control of transcription. Most recently, the nuclease-deficient Cas9 (dCas9) has emerged as a flexible tool for controlling activation and repression of target genes, by the simple RNA-guided positioning of dCas9 in the vicinity of the target gene transcription start site. Results In this study we compared two different systems of dCas9-mediated transcriptional reprogramming, and applied them to genes controlling two biosynthetic pathways for biobased production of isoprenoids and triacylglycerols (TAGs) in baker’s yeast Saccharomyces cerevisiae . By testing 101 guide-RNA (gRNA) structures on a total of 14 different yeast promoters, we identified the best-performing combinations based on reporter assays. Though a larger number of gRNA-promoter combinations do not perturb gene expression, some gRNAs support expression perturbations up to ~threefold. The best-performing gRNAs were used for single and multiplex reprogramming strategies for redirecting flux related to isoprenoid production and optimization of TAG profiles. From these studies, we identified both constitutive and inducible multiplex reprogramming strategies enabling significant changes in isoprenoid production and increases in TAG. Conclusion Taken together, we show similar performance for a constitutive and an inducible dCas9 approach, and identify multiplex gRNA designs that can significantly perturb isoprenoid production and TAG profiles in yeast without editing the genomic context of the target genes. We also identify a large number of gRNA positions in 14 native yeast target pomoters that do not affect expression, suggesting the need for further optimization of gRNA design tools and dCas9 engineering.

Biotechnology & Applied Microbiology↗
DOE OSTI2020

On the Solution of ℓ 0 -Constrained Sparse Inverse Covariance Estimation Problems

The sparse inverse covariance matrix is used to model conditional dependencies between variables in a graphical model to fit a multivariate Gaussian distribution. Estimating the matrix from data are well known to be computationally expensive for large-scale problems. Sparsity is employed to handle noise in the data and to promote interpretability of a learning model. Although the use of a convex ℓ 1 regularizer to encourage sparsity is common practice, the combinatorial ℓ 0 penalty often has more favorable statistical properties. In this paper, we directly constrain sparsity by specifying a maximally allowable number of nonzeros, in other words, by imposing an ℓ 0 constraint. Here, we introduce an efficient approximate Newton algorithm using warm starts for solving the nonconvex ℓ 0 -constrained inverse covariance learning problem. Numerical experiments on standard data sets show that the performance of the proposed algorithm is competitive with state-of-the-art methods.

$\ell_0$-Constrained↗
DOE OSTI2022

Quantum Distributed Unit Commitment: An Application in Microgrids

The dawn of quantum computing brings on a revolution in the way combinatorially complex power system problems such as Unit Commitment are solved. The Unit Commitment problem complexity is expected to increase in the future because of the trend toward the increase of penetration of intermittent renewables. Even though quantum computing has proven effective for solving a host of problems, its applications for power systems’ problems have been rather limited. Here, in this paper, a quantum unit commitment is innovatively formulated and the quantum version of the decomposition and coordination alternate direction method of multipliers (ADMM) is established. The above is achieved by devising quantum algorithms and by exploiting the superposition and entanglement of quantum bits (qubits) for solving subproblems, which are then coordinated through ADMM to obtain feasible solutions. The main contributions of this paper include: 1) the innovative development of a quantum model for Unit Commitment; 2) development of decomposition and coordination-supported framework which paves the way for the utilization of limited quantum resources to potentially solve the large-scale discrete optimization problems; 3) devising the novel quantum distributed unit commitment (QDUC) to solve the problem in a larger scale than currently available quantum computers are capable of solving. The QDUC results are compared with those from its classical counterpart, which validate the efficacy of quantum computing.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Coupled Microbial-Conversion and Computational-Fluid-Dynamics (CFD) Models for Butanediol Production in Micro-Aerated Reactors

Microbial conversion of substrates to macromolecules has been widely used in the synthesis of value-added products in pharmaceutical and biotechnology industries. These bioreactions are also being investigated in the production of low-value commodities such as biofuels [1]. Gas-liquid mass-transfer and transport-reaction coupling are important challenges when designing and scaling up these reactor systems. Experiments in wellmixed small-scale reactors have enabled characterization of microbial reactivity, while their coupling with macroscale transport remains relatively unexplored. In this work, we use a coupled metabolic-CFD model to study the action of a genetically engineered microbe Zymomonas mobilis [2] on sugars to produce 2,3-Butanediol (BDO). BDO is an important hydrocarbon intermediate that can be catalytically upgraded to several fuels and chemicals [3]. An important aspect to this particular microbial conversion is the need for micro-aerated environments as opposed to traditional aerobic fermentation. Slight variations in oxygen concentration can result in competing reaction pathways that disable BDO production. Hence, gas-liquid mass transfer and transport need to be optimized in large-scale reactors to maximize BDO production, for which CFD is a valuable tool. The aerobic-fermentation CFD model previously developed by the authors [5] for simulating bubble-column and airlift reactors at scale was used in this study. The Reynolds-averaged mass, momentum and energy transport equations for interpenetrating gas and liquid phase are solved in this model along with the transport and interphase mass transfer of oxygen. Our previous work used a phenomenological model for microbial oxygen uptake that neglected microbial growth and other reaction pathways. In this work, a detailed metabolic model enabled prediction of product formation and inhibition pathways. In order to manage computational cost, we used a subcycling technique [6] that takes advantage of the clear separation in transport (~ 200 sec) and reaction (~ 2-3 hours) timescales. The CFD model is first solved to steady state, after which the metabolic model is advanced at every cell in the computational domain using the local oxygen concentration. The CFD model is then run to achieve a new steady state that provides a new oxygen distribution for the metabolic model. This process, where reaction and fluid updates are interleaved together, is iterated until reactants are completely exhausted. This work will examine the performance of different reactor designs such as bubble column and airlift reactors at scale (250-500 m3). Oxygen mass-transfer coefficient and distribution are critically analyzed among reactors, and optimization studies pertaining to aeration is presented. Furthermore, it has been observed in experiments that high BDO production may be achieved by manipulating the aerobic environment over the course of reaction, such that oxygen concentration is high during the growth phase, and very low as sugar is depleted. This characteristic will be addressed by our simulations for which a timedependent scheduling strategy for aeration is presented that maximizes BDO production. [1] Humbird, D., Davis, R., and McMillan, J., Aeration costs in stirred-tank and bubble column bioreactors, Biochemical Engineering Journal, 127, 161—166, 2017 [2] Yang, S., Mohagheghi, A., Franden, M. A., Chou, Y.-C., Chen, X., Dowe, N., Himmel, M. E., and Zhang, M., Metabolic engineering of zymomonas mobilis for 2, 3-butanediol production from lignocellulosic biomass sugars. Biotechnology for biofuels, 9(1):189, 2016 [3] Kim, S. J., Sim, H. J., Kim, J. W., Lee, Y. G., Park, Y. C., and Seo, J. H., Enhanced production of 2,3-butanediol from xylose by combinatorial engineering of xylose metabolic pathway and cofactor regeneration in pyruvate decarboxylase-deficient Saccharomyces cerevisiae. Bioresource Technology, 245:1551–1557, 2017 [4] Weller, H., Tabor, G., Jasak, H. and Fureby, C., A tensorial approach to computational continuum mechanics using object-oriented techniques, Computers in physics, 12, 6, 620--631, 1998

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2024

DyG-DPCD: A Distributed Parallel Community Detection Algorithm for Large-Scale Dynamic Graphs

Dynamic (Temporal) graphs capture the valuable evolution of real-world systems, from the continuously evolving patterns of social interactions and genetic pathways to the dynamic fluctuations of economic forces. Detecting communities for such evolving networks poses unique challenges. Detecting and analyzing the evolution of communities within dynamic graphs unlocks valuable insights into the underlying structural and temporal patterns of real-world systems. However, the sheer volume of modern graph data and the inherent complexity of the temporal dimension pose significant challenges to scalable community detection algorithms. Addressing this gap, our work explores the limited landscape of scalable distributed-memory parallel methods specifically designed for dynamic network community detection. We propose a novel parallel algorithm, DyG-DPCD (Dynamic Graph Distributed Parallel Community Detection), to detect communities in dynamic networks using the Message Passing Interface (MPI) framework. We present a vertex-centric approach, allowing us to detect communities through local optimization. Furthermore, we enhance our baseline algorithm by incorporating three heuristics, which improve the algorithm’s performance significantly while maintaining the quality of the solutions. We demonstrate the efficiency of our algorithm by experimenting on several real-world large-scale networks with hundreds of millions of edges spanning diverse domains. Notably, DyG-DPCD achieves speedups between 25× and 30× for large networks that we experimented on using NERSC compute nodes. In conclusion, our algorithm outperforms the STINGER parallel re-agglomeration algorithm by 30×.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Combinatorial design of multimeric chelating peptoids for selective metal coordination

Current methods for metal chelation are generally based on multidentate organic ligands, which are generated through cumbersome multistep synthetic processes that lack flexibility for systematically varying metal-binding motifs. Octadentate ligands incorporating hydroxypyridinone or catecholamide binding moieties onto a spermine scaffold are known to display some of the highest affinities towards f-elements. Enhancing binding affinity for specific lanthanide or actinide ions however, necessitates ligand architectures that allow for modular and high throughput synthesis. Here we introduce a high-throughput combinatorial library of 16 tetrameric N -substituted glycine oligomers (peptoids) containing hydroxypyridinone or catecholamide chelating units linked via an ethylenediamine bridge and, for comparison, we also synthesized the corresponding mixed ligands derived from the spermine scaffold: 3,4,3-LI(1,2-HOPO) 2 (CAM) 2 and 3,4,3-LI(CAM) 2 (1,2-HOPO) 2 . Coordination-based luminescence studies were carried out with Eu 3+ and Tb 3+ to begin probing the properties of the new ligand architecture and revealed higher sensitization efficiency with the spermine scaffold as well as different spectroscopic features among the structural peptoid isomers. Solution thermodynamic properties of selected ligands revealed different coordination properties between the spermine and peptoid analogues with Eu 3+ stability constants log β 110 ranging from 28.88 ± 3.45 to 43.97 ± 0.49. The general synthetic strategy presented here paves the way for precision design of new specific and versatile ligands, with a variety of applications tailored towards the use of f-elements, including separations, optical device optimization, and pharmaceutical development.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Development of solar fuels photoanodes through combinatorial integration of Ni–La–Co–Ce oxide catalysts on BiVO 4

The development of an efficient photoanode remains the primary materials challenge in the establishment of a scalable technology for solar water splitting. The typical photoanode architecture consists of a semiconductor light absorber coated with a metal oxide that serves a combination of functions, including corrosion protection, electrocatalysis, light trapping, hole transport, and elimination of deleterious recombination sites. To date, such coatings have been mostly limited to simple materials such as TiO 2 and Co-Pi, with extensive experimental and theoretical effort required to provide an understanding of the physics and chemistry of the semiconductor-coating interface. In order to provide a more efficient exploration of metal oxide coatings for a given light absorber, we introduce a high throughput methodology wherein a uniform BiVO 4 thin film is coated with 858 unique metal oxides covering a range of metal oxide loadings and the full Ni–La–Co–Ce oxide quaternary composition space. Photoelectrochemical characterization of each photoanode reveals that approximately one third of the coatings lower the photoanode performance while select combinations of metal oxide composition and loading provide up to a 14-fold increase in the maximum photoelectrochemical power generation for oxygen evolution in pH 13 electrolyte. Particular Ce-rich coatings also exhibit an anti-reflection effect that further amplifies the performance, yielding a 20-fold enhancement in power conversion efficiency compared to bare BiVO 4 . By use of in situ optical spectroscopy and comparisons between the metal oxide coatings and their extrinsic optical and electrocatalytic properties, we present a suite of data-driven discoveries, including composition regions which form optimal interfaces with BiVO 4 and photoanodes that are suitable for integration with a photocathode due to their excellent power conversion and solar transmission efficiencies. The high throughput experimentation and informatics provides a powerful platform for both identifying the pertinent interfaces for further study and discovering high performance photoanodes for incorporation into efficient water splitting devices.

10 SYNTHETIC FUELS↗
DOE OSTI2020

A combined machine learning and density functional theory study of binary Ti-Nb and Ti-Zr alloys: Stability and Young’s modulus

The multicomponent Ti alloys, specifically the -phase, have experienced a strong growth over the last decades, due to their outstanding properties of ultra-high strength and low Young’s modulus. These properties play a significant role in many aerospace and biomedical applications. Selection and optimization of multicomponent alloys is challenging due to the vast chemical and compositional space. Here we investigate the use of machine learning techniques informed by density functional calculations to guide the selection of Nb- and Zr-based Ti binary alloys. From the cubic structures obtained from high throughput calculations and literature, we identify several structures with Young’s moduli below 40 GPa. The multivariant decision tree methods provide efficient surrogate models to identify structure variables have high influences on the energetic stability and Young’s modulus. Furthermore, we implement a workflow of incorporating DFT provided results and machine learning method to explore the chemical and composition space of other binary and multicomponent alloys, to eventually accelerate the material design via taking advantages of identified key variables.

36 MATERIALS SCIENCE↗