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At least 1,657 records · Page 92
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Understanding Global Model Systematic Shortwave Radiation Errors in Subtropical Marine Boundary Layer Cloud Regimes

Abstract Global numerical weather prediction and climate models are subject to long‐standing systematic shortwave radiation errors due to deficiencies in the representation of boundary layer clouds over the ocean. In the subtropics, clouds are typically too reflective in the cumulus regime and not reflective enough in the stratocumulus regime. Potential sources of error include cloud cover, liquid water path, effective radius, and subgrid heterogeneity, but diagnosing the absolute contributions of each to the radiation bias is hampered by uncertainties and sometimes contradictory information from different observational products. This paper draws on a set of ship‐based observations of boundary layer clouds obtained during the ARM MAGIC campaign along a northeast Pacific Ocean transect, crossing both stratocumulus and shallow cumulus cloud regimes. The surface‐based observations of cloud properties are compared with various satellite products, taking account of the diurnal cycle, to provide an improved quantitative assessment of the deficiencies in the European Centre for Medium‐Range Weather Forecasts global numerical weather prediction model. A series of off‐line radiation calculations are then performed to assess the impact on the shortwave radiation bias of correcting each of the model's deficiencies in cloud characteristics along the transect. A reduction in the bias is achieved by improving the agreement between modeled and observed in‐cloud liquid water path frequency distributions. In the cumulus regime, this is accomplished primarily by reducing the all‐sky water path, while for the stratocumulus regime, an underestimate of cloud cover and liquid water and an overestimate in effective radius and subgrid heterogeneity all contribute to a lack of reflected shortwave radiation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

Classical non-homologous end-joining pathway utilizes nascent RNA for error-free double-strand break repair of transcribed genes

DNA double-strand breaks (DSBs) leading to loss of nucleotides in the transcribed region can be lethal. Classical non-homologous end-joining (C-NHEJ) is the dominant pathway for DSB repair (DSBR) in adult mammalian cells. Here we report that during such DSBR, mammalian C-NHEJ proteins form a multiprotein complex with RNA polymerase II and preferentially associate with the transcribed genes after DSB induction. Depletion of C-NHEJ factors significantly abrogates DSBR in transcribed but not in non-transcribed genes. We hypothesized that nascent RNA can serve as a template for restoring the missing sequences, thus allowing error-free DSBR. We indeed found pre-mRNA in the C-NHEJ complex. Finally, when a DSB-containing plasmid with several nucleotides deleted within the E. coli lacZ gene was allowed time to repair in lacZ expressing mammalian cells, a functional lacZ plasmid could be recovered from control but not C-NHEJ factor-depleted cells, providing important mechanistic insights into C-NHEJ-mediated error-free DSBR of the transcribed genome.

Science & Technology - Other Topics↗
DOE OSTI2024

Enhancing detection of topological order by local error correction

The exploration of topologically-ordered states of matter is a long-standing goal at the interface of several subfields of the physical sciences. Such states feature intriguing physical properties such as long-range entanglement, emergent gauge fields and non-local correlations, and can aid in realization of scalable fault-tolerant quantum computation. However, these same features also make creation, detection, and characterization of topologically-ordered states particularly challenging. Motivated by recent experimental demonstrations, we introduce a paradigm for quantifying topological states—locally error-corrected decoration (LED)—by combining methods of error correction with ideas of renormalization-group flow. Our approach allows for efficient and robust identification of topological order, and is applicable in the presence of incoherent noise sources, making it particularly suitable for realistic experiments. We demonstrate the power of LED using numerical simulations of the toric code under a variety of perturbations. We subsequently apply it to an experimental realization, providing new insights into a quantum spin liquid created on a Rydberg-atom simulator. Finally, we extend LED to generic topological phases, including those with non-abelian order.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Transmon qubit readout fidelity at the threshold for quantum error correction without a quantum-limited amplifier

Abstract High-fidelity and rapid readout of a qubit state is key to quantum computing and communication, and it is a prerequisite for quantum error correction. We present a readout scheme for superconducting qubits that combines two microwave techniques: applying a shelving technique to the qubit that reduces the contribution of decay error during readout, and a two-tone excitation of the readout resonator to distinguish among qubit populations in higher energy levels. Using a machine-learning algorithm to post-process the two-tone measurement results further improves the qubit-state assignment fidelity. We perform single-shot frequency-multiplexed qubit readout, with a 140 ns readout time, and demonstrate 99.5% assignment fidelity for two-state readout and 96.9% for three-state readout–without using a quantum-limited amplifier.

Chen, Liangyu (ORCID:0000000250722445)↗
DOE OSTI2023

Detecting macroevolutionary genotype–phenotype associations using error-corrected rates of protein convergence

On macroevolutionary timescales, extensive mutations and phylogenetic uncertainty mask the signals of genotype–phenotype associations underlying convergent evolution. To overcome this problem, we extended the widely used framework of non-synonymous to synonymous substitution rate ratios and developed the novel metric ω C , which measures the error-corrected convergence rate of protein evolution. While ω C distinguishes natural selection from genetic noise and phylogenetic errors in simulation and real examples, its accuracy allows an exploratory genome-wide search of adaptive molecular convergence without phenotypic hypothesis or candidate genes. Using gene expression data, we explored over 20 million branch combinations in vertebrate genes and identified the joint convergence of expression patterns and protein sequences with amino acid substitutions in functionally important sites, providing hypotheses on undiscovered phenotypes. We further extended our method with a heuristic algorithm to detect highly repetitive convergence among computationally non-trivial higher-order phylogenetic combinations. Our approach allows bidirectional searches for genotype–phenotype associations, even in lineages that diverged for hundreds of millions of years.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Accelerating error correction in tomographic reconstruction

Abstract Spurred by recent advances in detector technology and X-ray optics, upgrades to scanning-probe-based tomographic imaging have led to an exponential growth in the amount and complexity of experimental data and have created a clear opportunity for tomographic imaging to approach single-atom sensitivity. The improved spatial resolution, however, is highly susceptible to systematic and random experimental errors, such as center of rotation drifts, which may lead to imaging artifacts and prevent reliable data extraction. Here, we present a model-based approach that simultaneously optimizes the reconstructed specimen and sinogram alignment as a single optimization problem for tomographic reconstruction with center of rotation error correction. Our algorithm utilizes an adaptive regularizer that is dynamically adjusted at each alternating iteration step. Furthermore, we describe its implementation in a software package targeting high-throughput workflows for execution on distributed-memory clusters. We demonstrate the performance of our solver on large-scale synthetic problems and show that it is robust to a wide range of noise and experimental drifts with near-ideal throughput.

Ali, Sajid (ORCID:0000000321864636)↗
DOE OSTI2016

Kohn–Sham calculations of NMR shifts for paramagnetic 3d metal complexes: protocols, delocalization error, and the curious amide proton shifts of a high-spin iron(ii) macrocycle complex

A theory for the nuclear chemical shifts of molecules in arbitrary spin states is applied to a set of paramagnetic organometallic complexes of 3d metals. Ligand chemical shifts are calculated and analyzed using Kohn–Sham (KS) density functional theory with and without relativistic corrections. The roles of the KS delocalization error, Gaussian-type versus Slater-type basis sets, relativistic effects (scalar and spin–orbit), and zero field splitting (ZFS) are investigated. A strong functional dependence of the chemical shifts is apparent and correlated with the delocalization error. Here, the functional dependence is between one and two orders of magnitude larger than variations of the NMR shifts due the other influences that are investigated. ZFS effects are negligible in the determination of the NMR chemical shifts of the complexes except at very low temperatures. The DFT calculated shifts agree reasonably well with experiment. A 73 ppm difference in the NMR shifts of the two protons in the amide groups of a high-spin Fe(II) macrocycle complex arises from selective O → Fe dative bonding that only involves the transfer of β spin density, along with orbital delocalization throughout the ligand bonding framework which electronically couples the coordinating oxygen lone pair orbitals directly to the amide trans proton.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Delocalization error poisons the density-functional many-body expansion

The many-body expansion is a fragment-based approach to large-scale quantum chemistry that partitions a single monolithic calculation into manageable subsystems. This technique is increasingly being used as a basis for fitting classical force fields to electronic structure data, especially for water and aqueous ions, and for machine learning. Here, we show that the many-body expansion based on semilocal density functional theory affords wild oscillations and runaway error accumulation for ion–water interactions, typified by F − (H 2 O) N with N ≳ 15. We attribute these oscillations to self-interaction error in the density-functional approximation. The effect is minor or negligible in small water clusters, explaining why it has not been noticed previously, but grows to catastrophic proportion in clusters that are only moderately larger. This behavior can be counteracted with hybrid functionals but only if the fraction of exact exchange is ≳50%, whereas modern meta-generalized gradient approximations including ωB97X-V, SCAN, and SCAN0 are insufficient to eliminate divergent behavior. Other mitigation strategies including counterpoise correction, density correction (i.e., exchange–correlation functionals evaluated atop Hartree–Fock densities), and dielectric continuum boundary conditions do little to curtail the problematic oscillations. In contrast, energy-based screening to cull unimportant subsystems can successfully forestall divergent behavior. These results suggest that extreme caution is warranted when the many-body expansion is combined with density functional theory.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Informed total-error-minimizing priors: Interpretable cosmological parameter constraints despite complex nuisance effects

While Bayesian inference techniques are standard in cosmological analyses, it is common to interpret resulting parameter constraints with a frequentist intuition. This intuition can fail, for example, when marginalizing high-dimensional parameter spaces onto subsets of parameters, because of what has come to be known as projection effects or prior volume effects. We present the method of informed total-error-minimizing (ITEM) priors to address this problem. An ITEM prior is a prior distribution on a set of nuisance parameters, such as those describing astrophysical or calibration systematics, intended to enforce the validity of a frequentist interpretation of the posterior constraints derived for a set of target parameters (e.g., cosmological parameters). Our method works as follows. For a set of plausible nuisance realizations, we generate target parameter posteriors using several different candidate priors for the nuisance parameters. We reject candidate priors that do not accomplish the minimum requirements of bias (of point estimates) and coverage (of confidence regions among a set of noisy realizations of the data) for the target parameters on one or more of the plausible nuisance realizations. Of the priors that survive this cut, we select the ITEM prior as the one that minimizes the total error of the marginalized posteriors of the target parameters. As a proof of concept, we applied our method to the density split statistics measured in Dark Energy Survey Year 1 data. We demonstrate that the ITEM priors substantially reduce prior volume effects that otherwise arise and that they allow for sharpened yet robust constraints on the parameters of interest.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2012

High-resolution Thomson scattering system on the COMPASS tokamak: Evaluation of plasma parameters and error analysis

The electron density and temperature profiles measured by the Thomson scattering diagnostic on the COMPASS tokamak are used for estimation of electron kinetic energy, energy confinement time, and effective charge number Z{sub eff}. Data are compared with the line-integrated electron density measured by a microwave interferometer in an ohmically heated plasma with a circular cross section. An error analysis of both electron temperature and density are performed by two methods-a constant chi-square boundaries method and a Monte Carlo simulation, determining asymmetrical error bars for the electron temperature.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2014

Quantum error correcting codes and 4-dimensional arithmetic hyperbolic manifolds

Using 4-dimensional arithmetic hyperbolic manifolds, we construct some new homological quantum error correcting codes. They are low density parity check codes with linear rate and distance n{sup ε}. Their rate is evaluated via Euler characteristic arguments and their distance using Z{sub 2}-systolic geometry. This construction answers a question of Zémor [“On Cayley graphs, surface codes, and the limits of homological coding for quantum error correction,” in Proceedings of Second International Workshop on Coding and Cryptology (IWCC), Lecture Notes in Computer Science Vol. 5557 (2009), pp. 259–273], who asked whether homological codes with such parameters could exist at all.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Density-functional errors in ionization potential with increasing system size

This work investigates the effects of molecular size on the accuracy of density-functional ionization potentials for a set of 28 hydrocarbons, including series of alkanes, alkenes, and oligoacenes. As the system size increases, delocalization error introduces a systematic underestimation of the ionization potential, which is rationalized by considering the fractional-charge behavior of the electronic energies. The computation of the ionization potential with many density-functional approximations is not size-extensive due to excessive delocalization of the incipient positive charge. While inclusion of exact exchange reduces the observed errors, system-specific tuning of long-range corrected functionals does not generally improve accuracy. These results emphasize that good performance of a functional for small molecules is not necessarily transferable to larger systems.

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

Three sources of errors in the Ehrenfest treatment of inelastic scattering and possible ways of resolving them

In order to identify the origin of possible errors in the mixed quantum/classical approach to inelastic scattering [A. Semenov and D. Babikov, J. Chem. Phys. 140, 044306 (2014) and A. Semenov, M.-L. Dubernet, and D. Babikov, J. Chem. Phys. 141, 114304 (2014)], a simplified model is considered that consists of one intermolecular degree of freedom and two intramolecular states, coupled by a simple potential. For this system, analytic derivations are carried out to determine (i) the exact quantum mechanical solution of the inelastic scattering problem, (ii) a simplified version of it with all oscillatory terms neglected, and (iii) the Ehrenfest solution in which the translational motion is described by the mean-field trajectory while the internal molecular motion is treated by the time-dependent Schrodinger equation. It is shown that the appropriate choice of velocity for the mean-field trajectory permits to enforce microscopic reversibility and gives results in excellent agreement with full-quantum results. The average velocity method of Billing is rigorously derived as a limiting case (of this more general approach), when reversibility is enforced locally, at the initial moment of time only. It is demonstrated that errors of state-to-state transition probabilities in the Ehrenfest approach occur at lower values of total energy E if the magnitudes of excitation energy ΔE, potential energy difference between the two states ΔV, and coupling of two states V12 are large. Possible ways of applying this concept to rotational transitions in real molecules are explored, using examples from CO + CO inelastic scattering.

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

Effective empirical corrections for basis set superposition error in the def2-SVPD basis: gCP and DFT-C

With the aim of mitigating the basis set error in density functional theory (DFT) calculations employing local basis sets, we herein develop two empirical corrections for basis set superposition error (BSSE) in the def2-SVPD basis, a basis which - when stripped of BSSE - is capable of providing near-complete-basis DFT results for non-covalent interactions. Specifically, we adapt the existing pairwise geometrical counterpoise (gCP) approach to the def2-SVPD basis, and we develop a beyond-pairwise approach, DFT-C, which we parameterize across a small set of intermolecular interactions. Both gCP and DFT-C are evaluated against the traditional Boys-Bernardi counterpoise correction across a set of 3402 non-covalent binding energies and isomerization energies. We find that the DFT-C method represents a significant improvement over gCP, particularly for non-covalently-interacting molecular clusters. Furthermore, DFT-C is transferable among density functionals and can be combined with existing functionals - such as B97M-V - to recover large-basis results at a fraction of the cost.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

A neoclassical drift-magnetohydrodynamical fluid model of the interaction of a magnetic island chain with a resonant error-field in a high temperature tokamak plasma

A two-fluid, neoclassical theory of the interaction of a single magnetic island chain with a resonant error-field in a quasi-cylindrical, low-β, tokamak plasma is presented. The plasmas typically found in large hot tokamaks lie in the so-called weak neoclassical flow-damping regime in which the neoclassical ion stress tensor is not the dominant term in the ion parallel equation of motion. Nevertheless, flow-damping in such plasmas dominates ion perpendicular viscosity, and is largely responsible for determining the phase velocity of a freely rotating island chain (which is in the ion diamagnetic direction relative to the local E × B frame at the rational surface). The critical vacuum island width required to lock the island chain is mostly determined by the ion neoclassical poloidal flow damping rate at the rational surface. The stabilizing effect of the average field-line curvature, as well as the destabilizing effect of the perturbed bootstrap current, is the same for a freely rotating, a non-uniformly rotating, and a locked island chain. The destabilizing effect of the error-field averages to zero when the chain is rotating and only manifests itself when the chain locks. The perturbed ion polarization current has a small destabilizing effect on a freely rotating island chain, but a large destabilizing effect on both a non-uniformly rotating and a locked island chain. Finally, this behavior may account for the experimentally observed fact that locked island chains are much more unstable than corresponding freely rotating chains.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2019

Subtlety of TiO 2 phase stability: Reliability of the density functional theory predictions and persistence of the self-interaction error

TiO 2 is an important material with broad applications that can exist in different phases with dramatically different properties. Theoretical prediction of their polymorph energetics is therefore critical for the material design and for identifying thermodynamically accessible structures. Determining TiO 2 relative phase stabilities remains challenging for first-principles methods, and density functional theory is the only approach available for studying phase stabilities at finite temperatures with acceptable computational efficiency. Here, we show that density functional theory using the recently developed efficient strongly constrained and appropriately normed (SCAN) [Sun et al., Phys. Rev. Lett. 115, 036402 (2015)] exchange-correlation functional for the first time predicts the phase stability in qualitative agreement with the experimental results at realistic conditions. Further analysis shows that the self-interaction error intrinsic in the density functional persists in the stability prediction. By correcting the self-interaction error through an empirical approach, SCAN predicts the relative stability as well as defect properties in excellent agreement with the experimental results.

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

Rates of adsorption and desorption: Entropic contributions and errors due to mean-field approximations

We have performed exact classical rate calculations to compute adsorption and desorption rate constants with a model representative of a real system. We compute the desorption rate using transition-state theory by taking the dividing-surface far from the surface of the solid. We find that using a mean-field assumption, i.e., applying potential of mean force to transition state theory, could lead to two orders-of-magnitude errors in the rate constant owing to large fluctuations in the desorption barrier. Furthermore, we compute the adsorption rate by including a dynamical factor which reflects the probability of sticking to the solid surface. We find that the sticking probability is highly sensitive to the coverage. Also, we find that the adsorption rate computed from the mean-field assumption is not very different from the exact adsorption rate. We also compute entropic contribution to desorption rates and compare it to that obtained from two limiting models of adsorption—2D ideal gas and 2D ideal lattice gas. We show that at high temperatures (700 K), the entropic contribution to desorption rates computed from the exact calculations is very close to that obtained from the 2D ideal gas model. However, for lower to intermediate temperatures from 200 K to 500 K, the entropic contributions cover a wide range which lies in between the two limiting models and could lead to over two-orders-of-magnitude errors in the rate coefficient.

Activation energies↗
DOE OSTI2019

The effect of self-interaction error on electrostatic dipoles calculated using density functional theory

Spurious electron self-interaction in density functional approximations (DFAs) can lead to inaccurate predictions of charge transfer in heteronuclear molecules that manifest as errors in calculated electrostatic dipoles. Here we show the magnitude of these errors on dipoles computed for a diverse set of 47 molecules taken from the recent benchmark study of Hait and Head-Gordon. We compare results of Perdew-Wang local spin density approximation (PW92), Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation (GGA), and strongly constrained and appropriatedly normed (SCAN) meta-GGA dipole calculations, along with those of their respective self-interaction-corrected (SIC) counterparts, to reference values from accurate wave function-based methods. The SIC calculations were carried out using the Fermi-Löwdin orbital (FLO-SIC) approach. We find that correcting for self-interaction generally increases the degree of charge transfer, thereby increasing the size of calculated dipole moments. The FLO-SIC-PW92 and FLO-SIC-PBE dipoles are in better agreement with reference values than their uncorrected DFA counterparts, particularly for strongly ionic molecules where significant improvement is seen. Applying FLO-SIC to SCAN does not improve dipole values overall. In addition, we show that removing self-interaction improves the description of the dipole for stretched-bond geometries and recovers the physically correct separated atom limit of zero dipole. Finally, we find that the best agreement between the FLO-SIC-DFA and reference dipoles occurs when the molecular geometries are optimized using the FLO-SIC-DFA.

74 ATOMIC AND MOLECULAR PHYSICS↗