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At least 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Protein Molecular Dynamics Simulations with Approximate QM: What Can We Learn?

Classical force fields are essential for computer simulations of proteins and are typically parameterized to reproduce secondary and tertiary structure of isolated proteins. However, while protein-protein interactions are ubiquitous in nature, they are not considered in parameterization efforts and are far less understood than isolated proteins. A better characterization of intermolecular interactions is widely recognized as a key to revolutionizing drug and therapeutic developments with high-throughput computational screening. Urgently needed is a critical assessment of the performance of modern protein force fields against first-principles electronic structure methods and experiments. In a daring step toward this goal, we here describe a comparison of peptide folding dynamics as predicted by a molecular mechanics force field on the one hand and by an approximate electronic structure quantum mechanical (QM) method based on density-functional tight-binding (DFTB) on the other. We further compare the dynamics from straightforward DFTB simulations with a near-linear scaling version of DFTB for massively parallel computation based on the fragment molecular orbital (FMO-DFTB) method. We illustrate differences between the phenomenology of the folding dynamics from these three methods for a small model peptide, as well as charge polarization and dynamic fluctuations, point out possible correlations and implications for force field developers, and discuss the lessons learned that might become applicable to future predictive high-throughput computer screening for personalized neoantigen cancer therapy.

Irle, Stephan↗
DOE OSTI2021

Real time evolution for ultracompact Hamiltonian eigenstates on quantum hardware

In this work we present a detailed analysis of variational quantum phase estimation (VQPE), a method based on real-time evolution for ground and excited state estimation on near-term hardware. We derive the theoretical ground on which the approach stands, and demonstrate that it provides one of the most compact variational expansions to date for solving strongly correlated Hamiltonians. At the center of VQPE lies a set of equations, with a simple geometrical interpretation, which provides conditions for the time evolution grid in order to decouple eigenstates out of the set of time evolved expansion states, and connects the method to the classical filter diagonalization algorithm. Further, we introduce what we call the unitary formulation of VQPE, in which the number of matrix elements that need to be measured scales linearly with the number of expansion states, and we provide an analysis of the effects of noise which substantially improves previous considerations. The unitary formulation allows for a direct comparison to iterative phase estimation. Our results mark VQPE as both a natural and highly efficient quantum algorithm for ground and excited state calculations of general many-body systems. We demonstrate a hardware implementation of VQPE for the transverse field Ising model. Further, we illustrate its power on a paradigmatic example of strong correlation (Cr2 in the SVP basis set), and show that it is possible to reach chemical accuracy with as few as ~50 timesteps.

Klymko, Katherine↗
DOE OSTI2021

A Computationally Efficient Algorithm for Computing Convex Hull Prices

Electricity markets worldwide allow participants to bid non-convex production offers. While non-convex offers can more accurately reflect a resource's capabilities, they create challenges for market clearing processes. For example, system operators may execute side payments when a participant’s cost is not covered through energy sale settlements from locational marginal pricing schemes, or when a participant incurs lost opportunity costs to follow the dispatch signal. Convex hull pricing minimizes these and other types of side payments while providing uniform (i.e., locationally and temporally consistent) prices. However, computing convex hull prices involves solving either a large-scale linear program - which in turn requires explicit descriptions of market participants’ convex hulls -or the Lagrangian dual of the corresponding non-convex scheduling problem. Here, we propose a computationally feasible and industrially scalable Benders decomposition approach to computing convex hull prices at least an order of magnitude faster than the current state-of-the-art while leveraging recent advances in convex hull formulations for thermal generating units.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2026

Dark Energy Survey Year 6 Results: MagLim++ Lens Sample Selection and Measurements of Galaxy Clustering

Galaxy clustering is a sensitive probe of the expansion history and growth of structure of the universe, and key degeneracies can be broken by combining these data with measurements of cosmic shear and galaxy-galaxy lensing (a so-called 3$\times$2pt analysis). The largest and least biased statistical samples of galaxies for use in clustering analyses can be collected photometrically through large imaging surveys. However, selecting clean photometric subsamples for cosmology are crucial for avoiding contamination that can bias cosmological constraints. Here we present the MagLim++ galaxy sample, selected to optimize for cosmological constraining power and incorporating an array of novel quality cuts to identify and remove residual contamination. This sample comes from the full six years of observations from the Dark Energy Survey. We present measurements of the two-point angular clustering ($w(θ)$) of 9,186,205 galaxies distributed over 4031 sq. degrees and in six tomographic redshift bins centered at $\bar{z}\approx$ [0.31, 0.44, 0.62, 0.78, 0.90, 1.01]. These measurements are used as part of the 3$\times$2pt and other DES Y6 legacy cosmological analyses in companion works. We describe the battery of null tests and mitigation schemes implemented to address observational, astrophysical, and methodological systematics in the analysis. The resulting $w(θ)$ measurements have a S/N = 149 (90.2 for linear scales only), which we use to place galaxy-clustering-only constraints on the matter density of the Universe, $Ω_m=0.311^{+0.023}_{-0.035}$, and amplitude of galaxy clustering in each redshift bin, $b_iσ_8=[1.16^{+0.04}_{-0.06},\ 1.40^{+0.04}_{-0.06},\ 1.57^{+0.04}_{-0.06},\ 1.59^{+0.04}_{-0.05},\ 1.50^{+0.04}_{-0.05},\ 1.74^{+0.06}_{-0.08}]$.

Weaverdyck, N. [BCCP, Berkeley; UC, Berkeley; LBL,↗
DOE OSTI2026

Universal monitored dynamics in multimode bosonic systems

We propose a route to study monitored many-body dynamics in multimode bosonic systems using circuit quantum electrodynamics. In this experimental setting, we construct several bosonic models comprising brickwork circuits built from beam-splitter gates, local parity measurements, and optional on-site Hubbard interactions, and diagnose their monitored dynamics via ancilla purification and a learnability-based probe. Under parity measurements, generic gate sets exhibit behavior that is largely consistent with a conventional measurement-induced phase transition, while a special class of beam-splitter circuits shows an apparent critical-like high-measurement regime in which purification times scale linearly with system size. We show that for realistic noise, gate, and measurement rates, these signatures are observable with near-term circuit QED hardware.

Patel, Shivam [Rutgers U., Piscataway]↗
DOE OSTI2025

ForestFlow: predicting the Lyman-α forest clustering from linear to nonlinear scales

On large scales, the Lyman-α forest provides insights into the expansion history of the Universe, while on small scales, it imposes strict constraints on the growth history, the nature of dark matter, and the sum of neutrino masses. This work introduces ForestFlow, a novel framework that bridges the gap between large- and small-scale analyses, which have traditionally relied on distinct modeling approaches. Using conditional normalizing flows, ForestFlow predicts the two Lyman-α linear biases (b δ and b η ) and six parameters describing small-scale deviations of the three-dimensional flux power spectrum (P 3D ) from linear theory as a function of cosmology and intergalactic medium physics. These are then combined with a Boltzmann solver to make consistent predictions, from arbitrarily large scales down to the nonlinear regime, for P 3D and any other statistics derived from it. Trained on a suite of 30 fixed-and-paired cosmological hydrodynamical simulations spanning redshifts from z = 2 to 4.5, ForestFlow achieves 3 and 1.5% precision in describing P 3D and the one-dimensional flux power spectrum (P 1D ) from linear scales to k = 5 Mpc −1 and k ∥ = 4 Mpc −1 , respectively. Thanks to its conditional parameterization, ForestFlow shows similar performance for ionization histories and two ΛCDM model extensions – massive neutrinos and curvature – even though none of these are included in the training set. This framework will enable full-scale cosmological analyses of Lyman-α forest measurements from the DESI survey.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1991

Sensitivity-based scaling for correlating structural response from different analytical models

A sensitivity-based linearly varying scale factor is described used to reconcile results from refined models for analysis of the same structure. The improved accuracy of the linear scale factor compared to a constant scale factor as well as the commonly used tangent approximation is demonstrated. A wing box structure is used as an example, with displacements, stresses, and frequencies correlated. The linear scale factor could permit the use of a simplified model in an optimization procedure during preliminary design to approximate the response given by a refined model over a considerable range of design changes.

Chang, Kwan J.↗
NASA NTRS1991

Sensitivity-based scaling for correlating structural response from different analytical models

This paper presents a sensitivity-based linearly varying scale factor used to reconcile results from simple and refined models for analysis of the same structure. The improved accuracy of the linear scale factor compared to a constant scale factor as well as the commonly used tangent approximation is demonstrated. A wing box structure is used as an example, with displacements, stresses and frequencies correlated. The linear scale factor could permit the use of a simplified model in an optimization procedure during preliminary design to approximate the response given by a refined model over a considerable range of design changes.

Chang, Kwan J.↗
NASA NTRS1992

Linear velocity fields in non-Gaussian models for large-scale structure

Linear velocity fields in two types of physically motivated non-Gaussian models are examined for large-scale structure: seed models, in which the density field is a convolution of a density profile with a distribution of points, and local non-Gaussian fields, derived from a local nonlinear transformation on a Gaussian field. The distribution of a single component of the velocity is derived for seed models with randomly distributed seeds, and these results are applied to the seeded hot dark matter model and the global texture model with cold dark matter. An expression for the distribution of a single component of the velocity in arbitrary local non-Gaussian models is given, and these results are applied to such fields with chi-squared and lognormal distributions. It is shown that all seed models with randomly distributed seeds and all local non-Guassian models have single-component velocity distributions with positive kurtosis.

Scherrer, Robert J.↗
DOE OSTI2022

Linear ion-scale microstability analysis of high and low-collisionality NSTX discharges and NSTX-U projections

Linear gyrokinetic simulations were conducted to investigate ion-gyroradius-scale micro-instability predictions for high-beta NSTX discharges and NSTX-U projections that span over an order of magnitude variation in collisionality. A complex mix of microtearing modes and hybrid trapped electron modes/kinetic ballooning modes (TEM/KBM) is predicted for all experimental or projected conditions. Ion temperature gradient (ITG) instabilities are typically stable in the NSTX discharges investigated, consistent with the observed neoclassical ion thermal transport. ITG thresholds inferred from the simulations are typically much higher than the experimental NSTX gradients, as well as the projected gradients in the NSTX-U scenario, which assumed ion temperatures limited by neoclassical transport only. The analysis suggests ITG instabilities are unlikely to contribute significant anomalous thermal losses in high-beta, lower collisionality NSTX-U scenarios. On the other hand, the NSTX experimental profiles and NSTX-U projections are predicted to be very close to the predicted onset of unstable KBM at most radii investigated. The proximity of the various discharges to the KBM instability threshold implies it may play an important role in setting profile shapes and limiting global energy confinement. Here, it remains to be understood and predicted how KBM contributes to multi-channel transport (thermal and particle transport, for both ions and electrons) in a way that is consistent with experimental inferences.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Linear and Nonlinear Solvers for Simulating Multiphase Flow within Large-Scale Engineered Subsurface Systems

Simulation of multiphase flow in the subsurface is well-known to be computationally challenging. While there have been many studies that have explored approaches to overcoming these challenges, they often utilize relatively simple case studies. In this paper, we focus on the unique numerical challenges posed by modeling large-scale engineered subsurface systems, characterized by discrete features embedded in a heterogeneous natural subsurface setting. The man-made features such as shafts, tunnels, and barriers often cause multiple challenges in modeling the domain for multiphase porous media flow. This flow scenario can have a wide range of applications such as nuclear waste repositories, enhanced recovery of a petroleum reservoir, geothermal engineering, and carbon sequestration. An example of these severe numerical challenges is the case of performance assessment (PA) for Waste Isolation Pilot Plant (WIPP), the only operating deep geological repository in the US, which simulates extreme material properties of bedded salt rock formation and extreme contrast due to open excavation next to the formation. The models have extremes not only of permeability and porosity but also of the constitutive models needed for multiphase flow; additionally, they have process models like salt creep closure reducing porosity over time, fracturing in clay and anhydrite interbeds of the bedded salt, gas generation from the waste materials, and unintentional human borehole intrusions in some scenarios. Numerical simulations require the solution of coupled systems of nonlinear PDEs; in our work, we use the open-source simulator PFLOTRAN which is based on Finite Volume discretization. The solution of the nonlinear equations requires use of the Newton-Raphson iteration at each time step, which entails the solution of the linearized Jacobian system at each iteration. The effects of all the processes (i.e., large number of unknowns, highly nonlinear constitutive relations, large contrasts in material properties in short distances) lead to an ill-conditioned Jacobian matrix that severely challenges traditional linear solver, i.e., stabilized biconjugate gradient with block Jacobi incomplete LU preconditioner (BCGS-ILU) leading to non-convergence for traditional Newton-Raphson nonlinear solver causing unacceptably long computation time for each model. This paper presents linear solvers such as constrained pressure residual (CPR) two-stage preconditioner with alternate-block-factorization (ABF) and quasi- implicit pressure and explicit saturation (QIMPES) decouplers and flexible generalized residual solver (FGMRES). The new general-purpose nonlinear solver, Newton trust-region dogleg Cauchy (NTRDC), is also introduced to resolve extreme nonlinearities in the models. We demonstrate the effectiveness of each method relative to the default BCGS-Newton solver. The two best cases had nearly 50 times speed-up and achieved completion of a simulation in 14 hours that never completed due to non-convergence with the default solver. We also investigate the strong scalability of each method and discuss some of the deficiencies found for Block Jacobi preconditioner using parallel domain decomposition, and node packing effects of modern processor architecture.

Preconditioner, Nonlinear, Porous media, Multiphas↗
DOE OSTI2024

Sparse Linear Solvers for Large-scale Electromagnetic Transient Simulations

Linear solvers form the basis for electromagnetic transient (EMT) simulations. There is a need to speed up EMT simulations as larger regions are analyzed using EMT simulations. For the same, the performance of linear solvers plays an important role. Exploiting the sparsity of the matrices generated in EMT simulations could assist with speed-up. Scalability is also crucial as power grids expand, demanding solutions capable of accommodating the increasing system size. Recent studies from the North American Electric Reliability Corporation (NERC) increasingly emphasize that EMT simulation models of the power grid will grow larger with the inclusion of power electronics components. Parallelisms in sparsity patterns exploit modern central processing units (CPUs), multi-core CPUs, and graphics processing units (GPUs) architectures in sparse solver designs. Therefore, this paper explores publicly available existing linear solvers and investigates their efficiency in large-scale power grid simulations. A large-scale power grid is developed by increasing the size of the IEEE 39 bus test system to up to 39000 bus systems.

Hsu, Kuan-Chieh↗
DOE OSTI2020

Temperature scaling behavior of the linear magnetoresistance observed in high-temperature superconductors

An analytical model invoking variations in the charge-carrier density is used to generate magnetoresistance curves that are almost indistinguishable from those produced by sophisticated numerical models. This demonstrates that, though disorder is pivotal in causing linear magnetoresistance, the form of the magnetoresistance thus generated is insensitive to details of the disorder. Additionally, taken in conjunction with the temperature (T) dependence of the zero-field resistivity, realistic levels of disorder are shown to be sufficient to explain the linear magnetoresistance and field-T resistance scaling observed in high-temperature pnictide and cuprate superconductors. Hence, though the T-linear zero-field resistance is a definite signature of the “strange metal” state of high-temperature superconductors, their linear magnetoresistance and its scaling is unlikely to be so.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Large-Scale Optimization with Linear Equality Constraints Using Reduced Compact Representation

For optimization problems with linear equality constraints, we prove that the (1,1) block of the inverse KKT matrix remains unchanged when projected onto the nullspace of the constraint matrix. In this work, we develop reduced compact representations of the limited-memory inverse BFGS Hessian to compute search directions efficiently when the constraint Jacobian is sparse. Orthogonal projections are implemented by a sparse QR factorization or a preconditioned LSQR iteration. In numerical experiments two proposed trust-region algorithms improve in computation times, often significantly, compared to previous implementations of related algorithms and compared to IPOPT.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS2005

Scaling the Non-linear Impact Response of Flat and Curved Composite Panels

The application of scaling laws to thin flat and curved composite panels exhibiting nonlinear response when subjected to low-velocity transverse impact is investigated. Previous research has shown that the elastic impact response of structural configurations exhibiting geometrically linear response can be effectively scaled. In the present paper, a preliminary experimental study is presented to assess the applicability of the scaling laws to structural configurations exhibiting geometrically nonlinear deformations. The effect of damage on the scalability of the structural response characteristics, and the effect of scale on damage development are also investigated. Damage is evaluated using conventional methods including C-scan, specimen de-plying and visual inspection of the impacted panels. Coefficient of restitution and normalized contact duration are also used to assess the extent of damage. The results confirm the validity of the scaling parameters for elastic impacts. However, for the panels considered in the study, the extent and manifestation of damage do not scale according to the scaling laws. Furthermore, the results indicate that even though the damage does not scale, the overall panel response characteristics, as indicated by contact force profiles, do scale for some levels of damage.

Ambur, Damodar R.↗
NASA NTRS2004

Fast Query-Optimized Kernel-Machine Classification

A recently developed algorithm performs kernel-machine classification via incremental approximate nearest support vectors. The algorithm implements support-vector machines (SVMs) at speeds 10 to 100 times those attainable by use of conventional SVM algorithms. The algorithm offers potential benefits for classification of images, recognition of speech, recognition of handwriting, and diverse other applications in which there are requirements to discern patterns in large sets of data. SVMs constitute a subset of kernel machines (KMs), which have become popular as models for machine learning and, more specifically, for automated classification of input data on the basis of labeled training data. While similar in many ways to k-nearest-neighbors (k-NN) models and artificial neural networks (ANNs), SVMs tend to be more accurate. Using representations that scale only linearly in the numbers of training examples, while exploring nonlinear (kernelized) feature spaces that are exponentially larger than the original input dimensionality, KMs elegantly and practically overcome the classic curse of dimensionality. However, the price that one must pay for the power of KMs is that query-time complexity scales linearly with the number of training examples, making KMs often orders of magnitude more computationally expensive than are ANNs, decision trees, and other popular machine learning alternatives. The present algorithm treats an SVM classifier as a special form of a k-NN. The algorithm is based partly on an empirical observation that one can often achieve the same classification as that of an exact KM by using only small fraction of the nearest support vectors (SVs) of a query. The exact KM output is a weighted sum over the kernel values between the query and the SVs. In this algorithm, the KM output is approximated with a k-NN classifier, the output of which is a weighted sum only over the kernel values involving k selected SVs. Before query time, there are gathered statistics about how misleading the output of the k-NN model can be, relative to the outputs of the exact KM for a representative set of examples, for each possible k from 1 to the total number of SVs. From these statistics, there are derived upper and lower thresholds for each step k. These thresholds identify output levels for which the particular variant of the k-NN model already leans so strongly positively or negatively that a reversal in sign is unlikely, given the weaker SV neighbors still remaining. At query time, the partial output of each query is incrementally updated, stopping as soon as it exceeds the predetermined statistical thresholds of the current step. For an easy query, stopping can occur as early as step k = 1. For more difficult queries, stopping might not occur until nearly all SVs are touched. A key empirical observation is that this approach can tolerate very approximate nearest-neighbor orderings. In experiments, SVs and queries were projected to a subspace comprising the top few principal- component dimensions and neighbor orderings were computed in that subspace. This approach ensured that the overhead of the nearest-neighbor computations was insignificant, relative to that of the exact KM computation.

Mazzoni, Dominic↗