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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

A new multi-scale structure finding algorithm to identify cosmological structure

We introduce a new structure finding algorithm that self-consistently parses large scale cosmological structure into clusters, filaments and voids. This structure finding algorithm probes the structure at multiple scales and classifies the appropriate regions with the most probable structure type and size. We show that it can identify the baryon fraction of intercluster medium and cosmological voids.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Repetitive proteins that undergo large conformational changes evade structural prediction algorithms

Protein structure prediction algorithms, such as AlphaFold, have accelerated protein design and advanced the understanding of the relationship between amino acid sequence and protein structure. However, these algorithms are limited in their ability to predict the structures of conformationally dynamic, intrinsically disordered, and stimuli-responsive proteins. To evaluate sequence-to-structure predictions of such challenging proteins, we explored a class of conformationally dynamic, repeats-in-toxin (RTX) proteins. RTX proteins adopt intrinsically disordered conformations in the absence of calcium and undergo reversible folding into β-roll structures upon binding to calcium. RTX proteins are characterized by tandem repeats of the sequence GGXGXDXUX, in which X can be any amino acid and U is an aliphatic amino acid. We designed RTX sequence variants with global substitutions of nonconserved amino acids, tandem repeats of consensus sequences GGAGXDTLY, and tandem repeats of scrambled sequences GGAGXDTYL. AlphaFold2 and AlphaFold3 predicted that all of these RTX variants adopt β-roll structures, characteristic of wild-type RTX bound to calcium. However, modeling the predicted structures with molecular dynamics simulations and characterizing the protein variants with circular dichroism spectroscopy, small-angle x-ray scattering, and x-ray crystallography revealed that variants adopt diverse, sequence-dependent structures in the absence and presence of calcium. To better design proteins for applications in biotechnology and sustainability, it is critical to build predictive tools that consider intrinsically disordered protein states and validate these tools with multi-mode, multi-scale experimental data.

Chang, Marina P. [Stanford Univ., CA (United State↗
DOE OSTI2018

Prediction of novel high-pressure H 2 O -NaCl and carbon oxide compounds with a symmetry-driven structure search algorithm

Crystal structure prediction with theoretical methods is particularly challenging when unit cells with many atoms need to be considered. Here we employ a symmetry-driven structure search (SYDSS) method and combine it with density functional theory (DFT) to predict novel crystal structures at high pressure. We sample randomly from all 1,506 Wyckoff positions of the 230 space groups to generate a set of initial structures. During the subsequent structural relaxation with DFT, existing symmetries are preserved, but the symmetries and the space group may change as atoms move to more symmetric positions. By construction, our algorithm generates symmetric structures with high probability without excluding any configurations. This improves the search efficiency, especially for large cells with 20 atoms or more. We apply our SYDSS algorithm to identify stoichiometric (H 2 O) n -(NaCl) m and C n O m compounds at high pressure. We predict a novel H 2 O-NaCl structure with Pnma symmetry to form at 3.4 Mbar, which is within the range of diamond anvil experiments. In addition, we predict a novel C 2 O structure at 19.8 Mbar and C4O structure at 44.0 Mbar with Pbca and C2/m symmetry respectively.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Canonical symplectic structure and structure-preserving geometric algorithms for Schrödinger–Maxwell systems

An infinite dimensional canonical symplectic structure and structure-preserving geometric algorithms are developed for the photon–matter interactions described by the Schrödinger–Maxwell equations. The algorithms preserve the symplectic structure of the system and the unitary nature of the wavefunctions, and bound the energy error of the simulation for all time-steps. This new numerical capability enables us to carry out first-principle based simulation study of important photon–matter interactions, such as the high harmonic generation and stabilization of ionization, with long-term accuracy and fidelity.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2017

Structure and structure-preserving algorithms for plasma physics

Hamiltonian and action principle (HAP) formulations of plasma physics are reviewed for the purpose of explaining structure preserving numerical algorithms. Geometric structures associated with and emergent from HAP formulations are discussed. These include conservative integration, which exactly conserves invariants, symplectic integration, which exactly preserves the Hamiltonian geometric structure, and other Hamiltonian integration techniques. Basic ideas of variational integration and Poisson integration, which can preserve the noncanonical Hamiltonian structure, are discussed. Metriplectic integration, which preserves the structure of conservative systems with both Hamiltonian and dissipative parts, is proposed. Two kinds of simulated annealing, a relaxation technique for obtaining equilibrium states, are reviewed: one that uses metriplectic dynamics, which maximizes an entropy at fixed energy, and the other that uses double bracket dynamics, which preserves Casimir invariants. Throughout, applications to plasma systems are emphasized. The paper concludes with a discussion of geometric electromagnetic particle-in-cell [Kraus et al., J. Plasma Phys. (to be published); e-print arXiv:1609.03053v1 [math.NA]], a particle in cell code that incorporates Hamiltonian and geometrical structure preserving properties.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2015

WE-AB-BRA-08: Results of a Multi-Institutional Study for the Evaluation of Deformable Image Registration Algorithms for Structure Delineation Via Computational Phantoms

Purpose: To investigate the accuracy of various algorithms for deformable image registration (DIR), to propagate regions of interest (ROIs) in computational phantoms based on patient images using different commercial systems. This work is part of an Italian multi-institutional study to test on common datasets the accuracy, reproducibility and safety of DIR applications in Adaptive Radiotherapy. Methods: Eleven institutions with three available commercial solutions provided data to assess the agreement of DIR-propagated ROIs with automatically drown ROIs considered as ground-truth for the comparison. The DIR algorithms were tested on real patient data from three different anatomical districts: head and neck, thorax and pelvis. For every dataset two specific Deformation Vector Fields (DVFs) provided by ImSimQA software were applied to the reference data set. Three different commercial software were used in this study: RayStation, Velocity and Mirada. The DIR-mapped ROIs were then compared with the reference ROIs using the Jaccard Conformity Index (JCI). Results: More than 600 DIR-mapped ROIs were analyzed. Putting together all JCI data of all institutions for the first DVF, the mean JCI was 0.87 ± 0.7 (1 SD) while for the second DVF JCI was 0.8 ± 0.13 (1 SD). Several considerations on different structures are available from collected data: the standard deviation among different institutions on specific structure raise as the larger is the applied DVF. The higher value is 10% for bladder. Conclusion: Although the complexity of deformation of human body is very difficult to model, this work illustrates some clinical scenarios with well-known DVFs provided by specific software. CI parameter gives the inter-user variability and may put in evidence the need of improving the working protocol in order to reduce the inter-institution JCI variability.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Tensor hypercontracted ppRPA: Reducing the cost of the particle-particle random phase approximation from O(r {sup 6}) to O(r {sup 4})

In recent years, interest in the random-phase approximation (RPA) has grown rapidly. At the same time, tensor hypercontraction has emerged as an intriguing method to reduce the computational cost of electronic structure algorithms. In this paper, we combine the particle-particle random phase approximation with tensor hypercontraction to produce the tensor-hypercontracted particle-particle RPA (THC-ppRPA) algorithm. Unlike previous implementations of ppRPA which scale as O(r{sup 6}), the THC-ppRPA algorithm scales asymptotically as only O(r{sup 4}), albeit with a much larger prefactor than the traditional algorithm. We apply THC-ppRPA to several model systems and show that it yields the same results as traditional ppRPA to within mH accuracy. Our method opens the door to the development of post-Kohn Sham functionals based on ppRPA without the excessive asymptotic cost of traditional ppRPA implementations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Simulation of unsteady blood flows in a patient-specific compliant pulmonary artery with a highly parallel monolithically coupled fluid-structure interaction algorithm

Computational fluid dynamics (CFD) is increasingly used to study blood flows in patient-specific arteries for understanding certain cardiovascular diseases. The techniques work quite well for relatively simple problems, but need improvements when the problems become harder in the case when (1) the geometry becomes complex (from a few branches to a full pulmonary artery), (2) the model becomes more complex (from fluid-only calculation to coupled fluid-structure interaction calculation), (3) both the fluid and wall models become highly nonlinear, and (4) the computer on which we run the simulation is a supercomputer with tens of thousands of processor cores. To push the limit of CFD in all four fronts, in this paper, we develop and study a highly parallel algorithm for solving a monolithically coupled fluid-structure system for the modeling of the interaction of the blood flow and the arterial wall. As a case study, we consider a patient-specific, full size pulmonary artery obtained from CT (Computed Tomography) images, with an artificially added layer of wall with a fixed thickness. The fluid is modeled with a system of incompressible Navier-Stokes equations and the wall is modeled by a geometrically nonlinear elasticity equation. As far as we know this is the first time the unsteady blood flow in a full pulmonary artery is simulated without assuming a rigid wall. We report the proposed numerical algorithm and software scale well beyond 10,000 processor cores on a supercomputer for solving the fluid-structure interaction problem discretized with a stabilized finite element method in space and an implicit scheme in time involving hundreds of millions of unknowns.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2013

Hierarchical Petascale Simulation Framework For Stress Corrosion Cracking

A number of major accomplishments resulted from the project. These include: • Data Structures, Algorithms, and Numerical Methods for Reactive Molecular Dynamics. We have developed a range of novel data structures, algorithms, and solvers (amortized ILU, Spike) for use with ReaxFF and charge equilibration. • Parallel Formulations of ReactiveMD (Purdue ReactiveMolecular Dynamics Package, PuReMD, PuReMD-GPU, and PG-PuReMD) for Messaging, GPU, and GPU Cluster Platforms. We have developed efficient serial, parallel (MPI), GPU (Cuda), and GPU Cluster (MPI/Cuda) implementations. Our implementations have been demonstrated to be significantly better than the state of the art, both in terms of performance and scalability. • Comprehensive Validation in the Context of Diverse Applications. We have demonstrated the use of our software in diverse systems, including silica-water, silicon-germanium nanorods, and as part of other projects, extended it to applications ranging from explosives (RDX) to lipid bilayers (biomembranes under oxidative stress). • Open Source Software Packages for Reactive Molecular Dynamics. All versions of our soft- ware have been released over the public domain. There are over 100 major research groups worldwide using our software. • Implementation into the Department of Energy LAMMPS Software Package. We have also integrated our software into the Department of Energy LAMMPS software package.

36 MATERIALS SCIENCE↗
DOE OSTI2016

An added-mass partition algorithm for fluid–structure interactions of compressible fluids and nonlinear solids

We describe an added-mass partitioned (AMP) algorithm for solving fluid–structure interaction (FSI) problems involving inviscid compressible fluids interacting with nonlinear solids that undergo large rotations and displacements. The computational approach is a mixed Eulerian–Lagrangian scheme that makes use of deforming composite grids (DCG) to treat large changes in the geometry in an accurate, flexible, and robust manner. The current work extends the AMP algorithm developed in Banks et al. [1] for linearly elasticity to the case of nonlinear solids. To ensure stability for the case of light solids, the new AMP algorithm embeds an approximate solution of a nonlinear fluid–solid Riemann (FSR) problem into the interface treatment. The solution to the FSR problem is derived and shown to be of a similar form to that derived for linear solids: the state on the interface being fundamentally an impedance-weighted average of the fluid and solid states. Numerical simulations demonstrate that the AMP algorithm is stable even for light solids when added-mass effects are large. The accuracy and stability of the AMP scheme is verified by comparison to an exact solution using the method of analytical solutions and to a semi-analytical solution that is obtained for a rotating solid disk immersed in a fluid. The scheme is applied to the simulation of a planar shock impacting a light elliptical-shaped solid, and comparisons are made between solutions of the FSI problem for a neo-Hookean solid, a linearly elastic solid, and a rigid solid. The ability of the approach to handle large deformations is demonstrated for a problem of a high-speed flow past a light, thin, and flexible solid beam.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Correlated Anion Disorder in Heteroanionic Cubic TiOF 2

Resolving anion configurations in heteroanionic materials is crucial for understanding and controlling their properties. For anion-disordered oxyfluorides, conventional Bragg diffraction cannot fully resolve the anionic structure, necessitating alternative structure determination methods. We have investigated the anionic structure of anion-disordered cubic (ReO 3 -type) TiOF 2 using X-ray pair distribution function (PDF), 19 F MAS NMR analysis, density functional theory (DFT), cluster expansion modeling, and genetic-algorithm structure prediction. Our computational data predict short-range anion ordering in TiOF 2 , characterized by predominant cis-[O 2 F 4 ] titanium coordination, resulting in correlated anion disorder at longer ranges. To validate our predictions, we generated partially disordered supercells using genetic-algorithm structure prediction and computed simulated X-ray PDF data and 19 F MAS NMR spectra, which we compared directly to experimental data. To construct our simulated 19 F NMR spectra, we derived new transformation functions for mapping calculated magnetic shieldings to predicted magnetic chemical shifts in titanium (oxy)fluorides, obtained by fitting DFT-calculated magnetic shieldings to previously published experimental chemical shift data for TiF 4 . We find good agreement between our simulated and experimental data, which supports our computationally predicted structural model and demonstrates the effectiveness of complementary experimental and computational techniques in resolving anionic structure in anion-disordered oxyfluorides. From additional DFT calculations, we predict that increasing anion disorder makes lithium intercalation more favorable by, on average, up to 2 eV, highlighting the significant effect of variations in short-range order on the intercalation properties of anion-disordered materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Optimization of transformer ratio and beam loading in a plasma wakefield accelerator with a structure-exploiting algorithm

Plasma-based acceleration has emerged as a promising candidate as an accelerator technology for a future linear collider or a next-generation light source. We consider the plasma wakefield accelerator (PWFA) concept where a plasma wave wake is excited by a particle beam and a trailing beam surfs on the wake. For a linear collider, the energy transfer efficiency from the drive beam to the wake and from the wake to the trailing beam must be large, while the emittance and energy spread of the trailing bunch must be preserved. One way to simultaneously achieve this when accelerating electrons is to use longitudinally shaped bunches and nonlinear wakes. In the linear regime, there is an analytical formalism to obtain the optimal shapes. In the nonlinear regime, however, the optimal shape of the driver to maximize the energy transfer efficiency cannot be precisely obtained because currently no theory describes the wake structure and excitation process for all degrees of nonlinearity. In addition, the ion channel radius is not well defined at the front of the wake where the plasma electrons are not fully blown out by the drive beam. We present results using a novel optimization method to effectively determine a current profile for the drive and trailing beam in PWFA that provides low energy spread, low emittance, and high acceleration efficiency. We parameterize the longitudinal beam current profile as a piecewise-linear function and define optimization objectives. For the trailing beam, the algorithm converges quickly to a nearly inverse trapezoidal trailing beam current profile similar to that predicted by the ultrarelativistic limit of the nonlinear wakefield theory. For the drive beam, the beam profile found by the optimization in the nonlinear regime that maximizes the transformer ratio also resembles that predicted by linear theory. Furthermore, the current profiles found from the optimization method provide higher transformer ratios compared with the linear ramp predicted by the relativistic limit of the nonlinear theory.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Theoretical search for possible Li–Ni–B crystal structures using an adaptive genetic algorithm

The structural diversity of rare-earth and transition metal borides indicates that alkali-transition metal borides (A-T-B) show tremendous promise in exhibiting a variety of crystal structures with different dimensionalities of T-B frameworks. On the other hand, the A-T-B ternary systems are severely underexplored because of the synthetic challenges associated with their preparation. Accurate and efficient computational predictions of low-energy stable and metastable phases can identify the optimal compositions of the hypothetical compounds in the A-T-B systems to guide the synthesis. As such, in this work, we have computationally discovered several new phases in the Li–Ni–B ternary system. The newly discovered LiNiB, Li 2 Ni 3 B, and Li 2 NiB phases expand the existing theoretical database, and the convex-hull surface of Li–Ni–B has been re-constructed. The lowest energy structure of the LiNiB compound has been found by an adaptive genetic algorithm with layered motif, which matches with the experimentally determined structure. According to our electrochemical calculations, LiNiB and another predicted layered Li 2 NiB compounds have great potential as anode materials for lithium batteries. The Li 2 Ni 3 B compound with the space group P4 3 32 was predicted to crystallize in a cubic structure composed of distorted octahedral units of BNi 6 , which is isostructural to two noncentrosymmetric superconductors Li 2 Pd 3 B and Li 2 Pt 3 B. While we were unable to experimentally confirm the Li 2 Ni 3 B compound utilizing the hydride synthetic route, attempts to synthesize this compound by alternate methods remain highly desirable, considering its potential superconducting properties.

36 MATERIALS SCIENCE↗
DOE OSTI2016

An Adaptive Mesh Algorithm: Mesh Structure and Generation

The purpose of Adaptive Mesh Refinement is to minimize spatial errors over the computational space not to minimize the number of computational elements. The additional result of the technique is that it may reduce the number of computational elements needed to retain a given level of spatial accuracy. Adaptive mesh refinement is a computational technique used to dynamically select, over a region of space, a set of computational elements designed to minimize spatial error in the computational model of a physical process. The fundamental idea is to increase the mesh resolution in regions where the physical variables are represented by a broad spectrum of modes in k-space, hence increasing the effective global spectral coverage of those physical variables. In addition, the selection of the spatially distributed elements is done dynamically by cyclically adjusting the mesh to follow the spectral evolution of the system. Over the years three types of AMR schemes have evolved; block, patch and locally refined AMR. In block and patch AMR logical blocks of various grid sizes are overlaid to span the physical space of interest, whereas in locally refined AMR no logical blocks are employed but locally nested mesh levels are used to span the physical space. The distinction between block and patch AMR is that in block AMR the original blocks refine and coarsen entirely in time, whereas in patch AMR the patches change location and zone size with time. The type of AMR described herein is a locally refi ned AMR. In the algorithm described, at any point in physical space only one zone exists at whatever level of mesh that is appropriate for that physical location. The dynamic creation of a locally refi ned computational mesh is made practical by a judicious selection of mesh rules. With these rules the mesh is evolved via a mesh potential designed to concentrate the nest mesh in regions where the physics is modally dense, and coarsen zones in regions where the physics is modally sparse.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Next-Generation Optimization under Uncertainty: Structure-Oriented Algorithms

With the advent of the smart grid, renewable technologies, and carbon emission programs, a key concern is the coordination of national infrastructures such as the electricity, natural gas, and water supply network systems. Anticipating and mitigating uncertainty of weather, demands, and contingencies in a more integrated environment is necessary to maximize resource efficiency and prevent cascading failures that can ultimately lead to catastrophic shortages of supplies. This project developed scalable algorithms for stochastic optimization capable of addressing extreme-scale problems (motivated by challenges in the design and operation of national infrastructures). Specifically, the project developed a new family of algorithms to solve continuous stochastic problems to local and global optimality as well as algorithms to solve mixed-integer convex and nonconvex stochastic programs. We developed supporting local and global convergence theory for these algorithms and implemented the algorithms in open-source software packages that can leverage high-performance computing architectures.

24 POWER TRANSMISSION AND DISTRIBUTION↗