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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

CoMet

CoMet is an application for finding epistatic and pleiotropic relationships from large quantities of genomic data. It solves these large combinatorial problems on GPU-accelerated systems with thousands of compute nodes. Its methods include the 2-way Proportional Similarity method, the Custom Correlation Coefficient and the DUO method. CoMet was developed at the Oak Ridge Leadership Computing Facility in collaboration with the Computational Biology and Bioinformatics Group at Oak Ridge National Laboratory.

Joubert, WayneD↗
DOE OSTI2024

Automating data analysis for hydrogen/deuterium exchange mass spectrometry using data-independent acquisition methodology

We present a hydrogen/deuterium exchange workflow coupled to tandem mass spectrometry (HX-MS 2 ) that supports the acquisition of peptide fragment ions alongside their peptide precursors. The approach enables true auto-curation of HX data by mining a rich set of deuterated fragments, generated by collisional-induced dissociation (CID), to simultaneously confirm the peptide ID and authenticate MS 1 -based deuteration calculations. The high redundancy provided by the fragments supports a confidence assessment of deuterium calculations using a combinatorial strategy. The approach requires data-independent acquisition (DIA) methods that are available on most MS platforms, making the switch to HX-MS 2 straightforward. Importantly, we find that HX-DIA enables a proteomics-grade approach and wide-spread applications. Considerable time is saved through auto-curation and complex samples can now be characterized and at higher throughput. We illustrate these advantages in a drug binding analysis of the ultra-large protein kinase DNA-PKcs, isolated directly from mammalian cells.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1987

The 3-D world modeling with updating capability based on combinatorial geometry

A 3-D world modeling technique using range data is discribed. Range data quantify the distances from the sensor focal plane to the object surface, i.e., the 3-D coordinates of discrete points on the object surface are known. The approach proposed herein for 3-D world modeling is based on the Combinatorial Geometry (CG) method which is widely used in Monte Carlo particle transport calculations. First, each measured point on the object surface is surrounded by a small sphere with a radius determined by the range to that point. Then, the 3-D shapes of the visible surfaces are obtained by taking the (Boolean) union of all the spheres. The result is an unambiguous representation of the object's boundary surfaces. The pre-learned partial knowledge of the environment can be also represented using the CG Method with a relatively small amount of data. Using the CG type of representation, distances in desired directions to boundary surfaces of various objects are efficiently calculated. This feature is particularly useful for continuously verifying the world model against the data provided by a range finder, and for integrating range data from successive locations of the robot during motion. The efficiency of the proposed approach is illustrated by simulations of a spherical robot in a 3-D room in the presence of moving obstacles and inadequate prelearned partial knowledge of the environment.

Goldstein, M.↗
DOE OSTI2023

On relaxations of the max k -cut problem formulations

Here, a tight continuous relaxation is a crucial factor in solving mixed integer formulations of many NP-hard combinatorial optimization problems. The (weighted) max k-cut problem is a fundamental combinatorial optimization problem with multiple notorious mixed integer optimization formulations. In this paper, we explore four existing mixed integer optimization formulations of the max k-cut problem. Specifically, we show that the continuous relaxation of a binary quadratic optimization formulation of the problem is: (i) stronger than the continuous relaxation of two mixed integer linear optimization formulations and (ii) at least as strong as the continuous relaxation of a mixed integer semidefinite optimization formulation. We also conduct a set of experiments on multiple sets of instances of the max k-cut problem using state-of-the-art solvers that empirically confirm the theoretical results in item (i). Furthermore, these numerical results illustrate the advances in the efficiency of global non-convex quadratic optimization solvers and more general mixed integer nonlinear optimization solvers. As a result, these solvers provide a promising option to solve combinatorial optimization problems. Our codes and data are available on GitHub.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

High-throughput screening of tribological properties of monolayer films using molecular dynamics and machine learning

Monolayer films have shown promise as a lubricating layer to reduce friction and wear of mechanical devices with separations on the nanoscale. These films have a vast design space with many tunable properties that can affect their tribological effectiveness. For example, terminal group chemistry, film composition, and backbone chemistry can all lead to films with significantly different tribological properties. This design space, however, is very difficult to explore without a combinatorial approach and an automatable, reproducible, and extensible workflow to screen for promising candidate films. Here, using the Molecular Simulation Design Framework (MoSDeF), a combinatorial screening study was performed to explore 9747 unique monolayer films (116 964 total simulations) and a machine learning (ML) model using a random forest regressor, an ensemble learning technique, to explore the role of terminal group chemistry and its effect on tribological effectiveness. The most promising films were found to contain small terminal groups such as cyano and ethylene. The ML model was subsequently applied to screen terminal group candidates identified from the ChEMBL small molecule library. Approximately 193 131 unique film candidates were screened with approximately a five order of magnitude speed-up in analysis compared to simulation alone. The ML model was thus able to be used as a predictive tool to greatly speed up the initial screening of promising candidate films for future simulation studies, suggesting that computational screening in combination with ML can greatly increase the throughput in combinatorial approaches to generate in silico data and then train ML models in a controlled, self-consistent fashion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Combinatorial Evaluation of Physical Feature Engineering, Classical Machine Learning, and Deep Learning Models for Synchrophasor Data at Scale

A major objective of the project was to train and evaluate the effectiveness of multiple event and anomaly detection, identification and classification deep temporal learning models for processing of real-time phasor measurement unit (PMU) data streams. A vast dataset, consisting of two years of phasor measurements from all three U.S. Interconnections, was curated and released by the Department of Energy (DOE) through Pacific Northwest National Laboratory (PNNL). The dataset also included an event log that provided event times and types (e.g. generator trips, line trips, planned service events, transformer operations, etc.). Our analysis of this dataset addressed six (6) of the eleven (11) research priorities identified in Funding Opportunity Announcement (FOA) DE-FOA-0001861 “Big Data Analysis of Synchrophasor Data” (FOA 1861). Rather than being limited to pre-determined specific algorithms, this project relied on the uniquely structured, highly performant underlying time series database capabilities of the PredictiveGrid platform to assess the vast dataset utilizing a wide variety of algorithms.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2019

Co-location Pattern Mining of Geosocial Data to Characterize Urban Functional Spaces

Spatial Co-location Pattern (SCP) mining continues to play a critical role in understanding the morphology of urban functional spaces of world cities. It requires a large amount of fine-granular data and computing efficiency to handle the combinatorial explosion of co-location patterns. To this end, this work has two main contributions - i) We showcase a novel approach to perform SCP mining to characterize intra-city scale structure of urban functionality or co-located activity patterns using geosocial Points-of-Interest (POI) vector data. ii) We present a generalized and optimized parallel/distributed SCP mining algorithm implemented on a Hadoop MapReduce system and demonstrate the utility of our approach using the city of Berlin (Germany) as an example. The SCPs tend to vary across Berlin's municipal boroughs and at different spatial scales. Our findings on Berlin's functional structure conform to existing urban geography models. Such a data-driven exploration of massive urban POIs using distributed computing is first of its kind and can help better understand the changing dynamics of urban functionality, as well as physical, and social network structure around the world.

Masrur, Arif↗
NASA NTRS2017

Initial Results of Heuristic Guided Orbit Selection for a Low Frequency Radio Interferometric Spacecraft Constellation

A constellation of radio telescope spacecraft can leverage interferometry to accurately image distant objects throughout the universe, but mission design must balance among many interrelated constraints. In particular, the number of craft and the selection of time-varying orbital parameters play a pivotal role in determining what interferometric baselines are feasible with respect to different targets, and thus drives the breadth and quality of data available to the constellation. The large combinatorial orbit configuration space and competing concerns present a challenging problem that is not well addressed by traditional mission design processes. This paper describes application of automated optimization methods to help direct mission design effort to the most promising dynamic constellation geometries: those that achieve broad interferometric coverage but remain cost-effective and resilient to failures. Several automatic heuristic-driven optimization algorithms representing complementary search strategies were created to explore among concrete constellation configuration plans. Evaluation of each candidate constellation plan was accelerated by efficiently combining precomputed caches of orbital and interferometric data. Results indicate that leveraging automated optimization for constellation mission design is both practical and illuminating: generated solutions provided both evidence for existing design intuitions as well as fresh insights into novel configurations.

Hernandez, Sonia↗
DOE OSTI2025

Tropical amplitudes for colored Lagrangians

Recently a new formulation for scattering amplitudes in Tr(Φ 3 ) theory has been given based on simple combinatorial ideas in the space of kinematic data. This allows all-loop integrated amplitudes to be expressed as “curve integrals” defined using tropical building blocks — the “headlight functions”. This paper shows how the formulation extends to the amplitudes of more general Lagrangians. We will present a number of different ways of introducing tropical “numerator functions” that allow us to describe general Lagrangian interactions. The simplest family of these “tropical numerators” computes the amplitudes of interesting Lagrangians with infinitely many interactions. We also describe methods for tropically formulating the amplitudes for general Lagrangians. One uses a variant of “Wick contraction” to glue together numerator factors for general interaction vertices. Another uses a natural characterization of polygons on surfaces to give a novel combinatorial description of all possible diagrams associated with arbitrary valence interactions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Engineering of increased L-Threonine production in bacteria by combinatorial cloning and machine learning

The goal of this study is to develop a general strategy for bacterial engineering using an integrated synthetic biology and machine learning (ML) approach. This strategy was developed in the context of increasing L-threonine production in Escherichia coli ATCC 21277. A set of 16 genes was initially selected based on metabolic pathway relevance to threonine biosynthesis and used for combinatorial cloning to construct a set of 385 strains to generate training data (i.e., a range of L-threonine titers linked to each of the specific gene combinations). Hybrid (regression/classification) deep learning (DL) models were developed and used to predict additional gene combinations in subsequent rounds of combinatorial cloning for increased L-threonine production based on the training data. As a result, E. coli strains built after just three rounds of iterative combinatorial cloning and model prediction generated higher L-threonine titers (from 2.7 g/L to 8.4 g/L) than those of patented L-threonine strains being used as controls (4-5 g/L). Interesting combinations of genes in L-threonine production included deletions of the tdh, metL, dapA, and dhaM genes as well as overexpression of the pntAB, ppc, and aspC genes. Mechanistic analysis of the metabolic system constraints for the best performing constructs offers ways to improve the models by adjusting weights for specific gene combinations. Graph theory analysis of pairwise gene modifications and corresponding levels of L-threonine production also suggests additional rules that can be incorporated into future ML models.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Measurements of Beam Spin Asymmetries in p+p0 and p´p0 Dihadron Production at CLAS12

Semi-Inclusive Deep Inelastic Scattering (SIDIS) is a powerful experimental tool for studying the internal structure and dynamics of the proton, revealing how quarks and gluons are distributed and interact within it. SIDIS describes a process where an elec tron scatters off one of the constituent quarks within the proton, causing it to undergo hadronization, creating multiple hadrons in the final state. Through factorization, the full process can be split into probabilistic components: one which describes the internal structure of the proton using Parton Distribution Functions (PDFs), and another which describes the hadronization process using Fragmentation Functions (FFs). These functions are non-perturbative quantities of Quantum Chromodynamics (QCD), meaning they cannot be calculated directly from first principles and must instead be extracted from experimental measurements. Acommon approach for accessing PDFs and FFs using SIDIS is to measure asymmetries. In this context, asymmetries correspond to subtle differences in the angular distribution of outgoing particles that arise when the spin orientation of the incoming beam or target is reversed. Because many of these effects only appear when spin is involved, they isolate specific, nuanced properties of the proton’s spin-structure that are otherwise hidden in spin averaged measurements. In practice, they show up as specific azimuthal modulations (e.g., sin ¿R, sin(¿h ´ ¿R)), whose amplitudes isolate convolutions of PDFs and FFs at leading and subleading twist. Non-zero asymmetries of these angular distributions can be traced back to unique combinations of PDFs and FFs, offering a way to probe them directly. In this work, we measure SIDIS by analyzing high energy electron-proton scattering events using the CLAS12 detector at Jefferson Lab. This study focuses on subset of SIDIS referred to as dihadron SIDIS, where pairs of hadrons — here p+p0 and p´p0 — are observed. We analyzed these dihadrons using detector data collected during Fall 2018 and Spring 2019, where longitudinally polarized electrons from the CEBAF accelerator were incident on a liquid hydrogen target. A photon classifier using a Gradient Boosted Trees (GBTs) architecture was trained using Monte Carlo simulations to reduce the amount of iv false combinatorial background p0’s. When deployed on experimental data, the model in creases our dihadron statistics by up to five-fold compared to previous CLAS12 p0 analyses. This work reports the first measurements of beam spin asymmetries for p+p0 and p´p0 dihadron production in SIDIS. The measured asymmetries offer new insights to the spin-dependent structure and dynamics within the proton, as well as the spin-dependent properties of quark fragmentation. Non-zero twist-3 sin¿R amplitudes are observed, pro viding sensitivity to the subleading twist PDF e(x). The PDF e(x) encodes quark-gluon correlations within the proton — a property that is otherwise inaccessible at leading twist. Additionally, this work measured significant twist-2 modulations carried by sin(¿h ´ ¿R) and sin(2¿h ´2¿R), providing experimental access to the helicity dihadron fragmentation function (DiFF) GK 1 . Because there is no equivalent quark helicity-dependent FF in single pion SIDIS, the DiFF GK 1 offers a unique lens into novel spin-dependent fragmentation. For instance, the twist-2 modulations observed in this study are enhanced by vector mesons created during fragmentation — a behavior predicted by phenomenological models. This study broadens our understanding of dihadron fragmentation, revealing new details about the flavor and charge dependence of hadronization.

Matousek, Gregory [Duke Univ., Durham, NC (United ↗
NASA NTRS2010

Random vs. Combinatorial Methods for Discrete Event Simulation of a Grid Computer Network

This study compared random and t-way combinatorial inputs of a network simulator, to determine if these two approaches produce significantly different deadlock detection for varying network configurations. Modeling deadlock detection is important for analyzing configuration changes that could inadvertently degrade network operations, or to determine modifications that could be made by attackers to deliberately induce deadlock. Discrete event simulation of a network may be conducted using random generation, of inputs. In this study, we compare random with combinatorial generation of inputs. Combinatorial (or t-way) testing requires every combination of any t parameter values to be covered by at least one test. Combinatorial methods can be highly effective because empirical data suggest that nearly all failures involve the interaction of a small number of parameters (1 to 6). Thus, for example, if all deadlocks involve at most 5-way interactions between n parameters, then exhaustive testing of all n-way interactions adds no additional information that would not be obtained by testing all 5-way interactions. While the maximum degree of interaction between parameters involved in the deadlocks clearly cannot be known in advance, covering all t-way interactions may be more efficient than using random generation of inputs. In this study we tested this hypothesis for t = 2, 3, and 4 for deadlock detection in a network simulation. Achieving the same degree of coverage provided by 4-way tests would have required approximately 3.2 times as many random tests; thus combinatorial methods were more efficient for detecting deadlocks involving a higher degree of interactions. The paper reviews explanations for these results and implications for modeling and simulation.

Kuhn, D. Richard↗
DOE OSTI2024

Surfaceology for colored Yukawa theory

Arkani-Hamed and collaborators have recently shown that scattering amplitudes for colored theories can be expressed as integrals over combinatorial objects simply constructed from surfaces decorated by kinematic data. In this paper we extend the curve integral formalism to theories with colored fermionic matter and present a compact formula for the all-loop, all-genus, all-multiplicity amplitude integrand of a colored Yukawa theory. The curve integral formalism makes certain properties of the amplitudes manifest and repackages non-trivial numerators into a single combinatorial object. We also present an efficient formula for L-loop integrated amplitudes in terms of a sum over 2 L combinatorial determinants.

1/N Expansion↗
DOE OSTI2023

Towards scanning nanostructure X-ray microscopy

This article demonstrates spatial mapping of the local and nanoscale structure of thin film objects using spatially resolved pair distribution function (PDF) analysis of synchrotron X-ray diffraction data. This is exemplified in a lab-on-chip combinatorial array of sample spots containing catalytically interesting nanoparticles deposited from liquid precursors using an ink-jet liquid-handling system. A software implementation is presented of the whole protocol, including an approach for automated data acquisition and analysis using the atomic PDF method. The protocol software can handle semi-automated data reduction, normalization and modeling, with user-defined recipes generating a comprehensive collection of metadata and analysis results. By slicing the collection using included functions, it is possible to build images of different contrast features chosen by the user, giving insights into different aspects of the local structure.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Improving Data and Prediction Quality of High-Throughput Perovskite Synthesis with Model Fusion

Combinatorial fusion analysis (CFA) is an approach for combining multiple scoring systems using the rank-score characteristic function and cognitive diversity measure. One example is to combine diverse machine learning models to achieve better prediction quality. In this work, we apply CFA to the synthesis of metal halide perovskites containing organic ammonium cations via inverse temperature crystallization. Using a data set generated by high-throughput experimentation, four individual models (support vector machines, random forests, weighted logistic classifier, and gradient boosted trees) were developed. We characterize each of these scoring systems and explore 66 possible combinations of the models. When measured by the precision on predicting crystal formation, the majority of the combination models improves the individual model results. The best combination models outperform the best individual models by 3.9 percentage points in precision. In addition to improving prediction quality, we demonstrate how the fusion models can be used to identify mislabeled input data and address issues of data quality. In particular, we identify example cases where all single models and all fusion models do not give the correct prediction. Experimental replication of these syntheses reveals that these compositions are sensitive to modest temperature variations across the different locations of the heating element that can hinder or enhance the crystallization process. In summary, we demonstrate that model fusion using CFA can not only identify a previously unconsidered influence on reaction outcome but also be used as a form of quality control for high-throughput experimentation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1991

Combinatorial FSK modulation for power-efficient high-rate communications

Deep-space and satellite communications systems must be capable of conveying high-rate data accurately with low transmitter power, often through dispersive channels. A class of noncoherent Combinatorial Frequency Shift Keying (CFSK) modulation schemes is investigated which address these needs. The bit error rate performance of this class of modulation formats is analyzed and compared to the more traditional modulation types. Candidate modulator, demodulator, and digital signal processing (DSP) hardware structures are examined in detail. System-level issues are also discussed.

Wagner, Paul K.↗