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Results for “algorithmic structures”

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 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

BCL::MP-fold: Membrane protein structure prediction guided by EPR restraints

For many membrane proteins, the determination of their topology remains a challenge for methods like X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy. Electron paramagnetic resonance (EPR) spectroscopy has evolved as an alternative technique to study structure and dynamics of membrane proteins. The present study demonstrates the feasibility of membrane protein topology determination using limited EPR distance and accessibility measurements. The BCL::MP-Fold (BioChemical Library membrane protein fold) algorithm assembles secondary structure elements (SSEs) in the membrane using a Monte Carlo Metropolis (MCM) approach. Sampled models are evaluated using knowledge-based potential functions and agreement with the EPR data and a knowledge-based energy function. Twenty-nine membrane proteins of up to 696 residues are used to test the algorithm. The RMSD100 value of the most accurate model is better than 8 Å for 27, better than 6 Å for 22, and better than 4 Å for 15 of the 29 proteins, demonstrating the algorithms' ability to sample the native topology. The average enrichment could be improved from 1.3 to 2.5, showing the improved discrimination power by using EPR data. Proteins 2015; 83:1947–1962. © 2015 Wiley Periodicals, Inc

Biochemistry & Molecular Biology↗
DOE OSTI2018

pnnl/chgl

CHGL is a hypergraph computation library for Chapel. It's primary contributions are data structures for hypergraphs and the algorithms to operate on these data structures.

Jenkins, Louis↗
DOE OSTI2020

Benchmarking materials property prediction methods: the Matbench test set and Automatminer reference algorithm

Abstract We present a benchmark test suite and an automated machine learning procedure for evaluating supervised machine learning (ML) models for predicting properties of inorganic bulk materials. The test suite, Matbench, is a set of 13 ML tasks that range in size from 312 to 132k samples and contain data from 10 density functional theory-derived and experimental sources. Tasks include predicting optical, thermal, electronic, thermodynamic, tensile, and elastic properties given a material’s composition and/or crystal structure. The reference algorithm, Automatminer, is a highly-extensible, fully automated ML pipeline for predicting materials properties from materials primitives (such as composition and crystal structure) without user intervention or hyperparameter tuning. We test Automatminer on the Matbench test suite and compare its predictive power with state-of-the-art crystal graph neural networks and a traditional descriptor-based Random Forest model. We find Automatminer achieves the best performance on 8 of 13 tasks in the benchmark. We also show our test suite is capable of exposing predictive advantages of each algorithm—namely, that crystal graph methods appear to outperform traditional machine learning methods given ~10 4 or greater data points. We encourage evaluating materials ML algorithms on the Matbench benchmark and comparing them against the latest version of Automatminer.

36 MATERIALS SCIENCE↗
DOE OSTI2018

An approach based on dwindling filter method for positive definite generalized eigenvalue problem

In this paper, we present a new spectral residual method for solving large-scale positive definite generalized eigenvalue problems. The proposed algorithm is equipped with a dwindling multidimensional nonmonotone filter, in which the envelope dwindles as the step length decreases. We have also employed a relaxed nonmonotone line search technique in the structure of the algorithm which allows it to enjoy the nonmonotonicity from scratch. Under some mild and standard assumptions, the global convergence property of the proposed algorithm is established. An implementation of the new algorithm on some test problems shows the efficiency and effectiveness of the proposed algorithm in practice.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Design of intrinsically disordered protein variants with diverse structural properties

Intrinsically disordered proteins (IDPs) perform a broad range of functions in biology, suggesting that the ability to design IDPs could help expand the repertoire of proteins with novel functions. Computational design of IDPs with specific conformational properties has, however, been difficult because of their substantial dynamics and structural complexity. We describe a general algorithm for designing IDPs with specific structural properties. We demonstrate the power of the algorithm by generating variants of naturally occurring IDPs that differ in compaction, long-range contacts, and propensity to phase separate. We experimentally tested and validated our designs and analyzed the sequence features that determine conformations. We show how our results are captured by a machine learning model, enabling us to speed up the algorithm. Our work expands the toolbox for computational protein design and will facilitate the design of proteins whose functions exploit the many properties afforded by protein disorder.

Science & Technology - Other Topics↗
DOE OSTI2026

VoroClust: Scalable Clustering for Remote Sensing

Although supervised machine learning provides a powerful framework for image classification and segmentation, it requires comprehensive consistent datasets, which are not available for many remote-sensing applications. Remote-sensing datasets are expensive to collect, and each is acquired under different environmental conditions or with significant variations in system operating parameters. Unsupervised clustering algorithms analyze the structure of each dataset independently, rather than drawing on similarities with existing “training” examples, and are thus well suited for practical remote-sensing applications. We introduce VoroClust, a fast density-based unsupervised clustering algorithm applicable to high-resolution and high-dimensional data. VoroClust runs as fast as distance-based clustering methods, while capturing complex regional geometries at least as well as current-density-based methods. It uses a data-centered sphere cover to reduce computational demands, while still capturing data topology. It then propagates clusters outward from local peaks in density. We show that VoroClust provides fast state-of-the-art clustering for both high-resolution polarimetric synthetic aperture radar and high-dimensional hyperspectral imaging datasets.

42 ENGINEERING↗
DOE OSTI2014

Design Optimization of Structural Health Monitoring Systems

Sensor networks drive decisions. Approach: Design networks to minimize the expected total cost (in a statistical sense, i.e. Bayes Risk) associated with making wrong decisions and with installing maintaining and running the sensor network itself. Search for optimal solutions using Monte-Carlo-Sampling-Adapted Genetic Algorithm. Applications include structural health monitoring and surveillance.

42 ENGINEERING↗
DOE OSTI2020

Black-Box Optimization for Design of Concentrating Solar Power and Photovoltaic Hybrid Systems with Optimal Dispatch Decisions

The hybridization of concentrating solar power (CSP) and photovoltaics (PV) can enable dispatchable renewable electricity generation at a lower price than current stand-alone CSP systems. However, designing a CSP-PV hybrid system can be challenging because of the many degrees of freedom in design that affect the internal and external system interactions and trade-offs. We develop a methodology to determine optimal designs for CSP-PV hybrids by implementing NLopt's derivative-free, or “black-box,” algorithms around pre-existing CSP-PV hybrid simulation software that utilizes the National Renewable Energy Laboratory’s System Advisor Model (SAM); we then employ a dispatch optimization model to determine operational decisions that maximize a plant’s profits. We present optimal designs for CSP-PV hybrid systems dispatching against four time-of-delivery (ToD) pricing structures. NLopt’s algorithms can improve the base case design’s power purchase agreement (PPA) price by 15% to 21%, depending on the ToD pricing structure. In addition, we present the resulting optimal CSP-PV hybrid design’s annual performance metrics, which tend to have capacity factors between 50% and 62%, but are able to generate electricity during the year’s highest-valued periods about 90% of the time. Lastly, we investigate the trade-offs between capacity factor and PPA price using Pareto fronts and demonstrate that, for some ToD pricing structures, the system capacity factor can increase by 20% but at the expense of a 2% increase in PPA price.

black-box↗
DOE OSTI2021

Gate-free state preparation for fast variational quantum eigensolver simulations

Abstract The variational quantum eigensolver is currently the flagship algorithm for solving electronic structure problems on near-term quantum computers. The algorithm involves implementing a sequence of parameterized gates on quantum hardware to generate a target quantum state, and then measuring the molecular energy. Due to finite coherence times and gate errors, the number of gates that can be implemented remains limited. In this work, we propose an alternative algorithm where device-level pulse shapes are variationally optimized for the state preparation rather than using an abstract-level quantum circuit. In doing so, the coherence time required for the state preparation is drastically reduced. We numerically demonstrate this by directly optimizing pulse shapes which accurately model the dissociation of H 2 and HeH + , and we compute the ground state energy for LiH with four transmons where we see reductions in state preparation times of roughly three orders of magnitude compared to gate-based strategies.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2026

Symmetry dilemmas in quantum computing for chemistry: A comprehensive analysis

Symmetry adaptation, universality, and gate efficiency are central but often competing requirements in quantum algorithms for electronic structure and many-body physics. For example, fully symmetry-adapted universal operator pools typically generate long and deep quantum circuits; gate-efficient universal operator pools generally break symmetries; and gate-efficient, fully symmetry-adapted operator pools may not be universal. In this work, we analyze such symmetry dilemmas both theoretically and numerically. On the theory side, we prove that the popular, gate-efficient operator pool consisting of singlet spin-adapted singles and perfect-pairing doubles is not universal when spatial symmetry is enforced. To demonstrate the strengths and weaknesses of the three types of pools, we perform numerical simulations using an adaptive algorithm paired with operator pools that are (i) fully symmetry-adapted and universal, (ii) fully symmetry-adapted and non-universal, and (iii) breaking a single symmetry and universal. Our numerical simulations encompass three physically relevant scenarios in which the target state is (i) the global ground state, (ii) the ground state crossed by a state differing in multiple symmetry properties, and (iii) the ground state crossed by a state differing in a single symmetry property. Our results show when symmetry-breaking but universal pools can be used safely, when enforcing at least one distinguishing symmetry suffices, and when a particular symmetry must be rigorously preserved to avoid variational collapse. Together, the formal and numerical analyses provide a practical guide for designing and benchmarking symmetry-adapted operator pools that balance universality, resource requirements, and robust state targeting in quantum simulations for chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

A General Sparse Tensor Framework for Electronic Structure Theory

Linear-scaling algorithms must be developed in order to extend the domain of applicability of electronic structure theory to molecules of any desired size. But, the increasing complexity of modern linear-scaling methods makes code development and maintenance a significant challenge. A major contributor to this difficulty is the lack of robust software abstractions for handling block-sparse tensor operations. We therefore report the development of a highly efficient symbolic block-sparse tensor library in order to provide access to high-level software constructs to treat such problems. Our implementation supports arbitrary multi-dimensional sparsity in all input and output tensors. We then avoid cumbersome machine-generated code by implementing all functionality as a high-level symbolic C++ language library and demonstrate that our implementation attains very high performance for linear-scaling sparse tensor contractions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Comparing crystal structures with symmetry and geometry

Abstract Measuring the similarity between two arbitrary crystal structures is a common challenge in crystallography and materials science. Although there are an infinite number of ways to mathematically relate two crystal structures, only a few are physically meaningful. Here we introduce both a geometry-based and a symmetry-adapted similarity metric to compare crystal structures. Using crystal symmetry and combinatorial optimization we describe an algorithm to arrive at the structural relationship that minimizes these similarity metrics across all possible maps between any pair of crystal structures. The approach makes it possible to (i) identify pairs of crystal structures that are identical, (ii) quantitatively measure the similarity between crystal structures, and (iii) find and rank structural transformation pathways between any pair of crystal structures. We discuss the advantages of using the symmetry-adapted cost metric over the geometric cost. Finally, we show that all known structural transformation pathways between common crystal structures are recovered with the mapping algorithm. The methodology presented in this study will be of value to efforts that seek to catalogue crystal structures, identify structural transformation pathways or prune large first-principles datasets used to parameterize on-lattice Hamiltonians.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Structural search for stable Mg–Ca alloys accelerated with a neural network interatomic model

Here, we have combined a neural network formalism with metaheuristic structural global search algorithms to systematically screen the Mg–Ca binary system for new (meta)stable alloys. The combination of these methods allows for an efficient exploration of the potential energy surface beyond the possibility of the traditional searches based on ab initio energy evaluations. The identified pool of low-enthalpy structures was complemented with special quasirandom structures (SQS) at different stoichiometries. In addition to the only Mg–Ca phase known to form under standard synthesis conditions, C14-Mg 2 Ca, the search has uncovered several candidate materials that could be synthesized under elevated temperatures or pressures. We demonstrate that the vibrational entropy lowers the relative free energy of several phases with magnesium kagome layers: C15 and C36 Laves structures at the 2:1 composition and an orthorhombic oS36 structure at the 7:2 composition. The estimated phase transition temperatures close to the melting point leave open the possibility of synthesizing the predicted materials at high temperatures. At high pressures up to 10 GPa, two new phases at the 1:1 and 3:1 Mg:Ca stoichiometries become thermodynamically stable and should form in multi-anvil experiments.

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

SU-F-18C-15: Model-Based Multiscale Noise Reduction On Low Dose Cone Beam Projection

Purpose: To improve image quality of low dose cone beam CT for patient positioning in radiation therapy. Methods: In low dose cone beam CT (CBCT) imaging systems, Poisson process governs the randomness of photon fluence at x-ray source and the detector because of the independent binomial process of photon absorption in medium. On a CBCT projection, the variance of fluence consists of the variance of noiseless imaging structure and that of Poisson noise, which is proportional to the mean (noiseless) of the fluence at the detector. This requires multiscale filters to smoothen noise while keeping the structure information of the imaged object. We used a mathematical model of Poisson process to design multiscale filters and established the balance of noise correction and structure blurring. The algorithm was checked with low dose kilo-voltage CBCT projections acquired from a Varian OBI system. Results: From the investigation of low dose CBCT of a Catphan phantom and patients, it showed that our model-based multiscale technique could efficiently reduce noise and meanwhile keep the fine structure of the imaged object. After the image processing, the number of visible line pairs in Catphan phantom scanned with 4 ms pulse time was similar to that scanned with 32 ms, and soft tissue structure from simulated 4 ms patient head-and-neck images was also comparable with scanned 20 ms ones. Compared with fixed-scale technique, the image quality from multiscale one was improved. Conclusion: Use of projection-specific multiscale filters can reach better balance on noise reduction and structure information loss. The image quality of low dose CBCT can be improved by using multiscale filters.

60 APPLIED LIFE SCIENCES↗