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An automated analysis workflow for optimization of force-field parameters using neutron scattering data
Graphical abstract: - Highlights: • An automated workflow to optimize force-field parameters. • Used the workflow to optimize force-field parameter for a system containing nanodiamond and tRNA. • The mechanism relies on molecular dynamics simulation and neutron scattering experimental data. • The workflow can be generalized to any other experimental and simulation techniques. - Abstract: Large-scale simulations and data analysis are often required to explain neutron scattering experiments to establish a connection between the fundamental physics at the nanoscale and data probed by neutrons. However, to perform simulations at experimental conditions it is critical to use correct force-field (FF) parameters which are unfortunately not available for most complex experimental systems. In this work, we have developed a workflow optimization technique to provide optimized FF parameters by comparing molecular dynamics (MD) to neutron scattering data. We describe the workflow in detail by using an example system consisting of tRNA and hydrophilic nanodiamonds in a deuterated water (D{sub 2}O) environment. Quasi-elastic neutron scattering (QENS) data show a faster motion of the tRNA in the presence of nanodiamond than without the ND. To compare the QENS and MD results quantitatively, a proper choice of FF parameters is necessary. We use an efficient workflow to optimize the FF parameters between the hydrophilic nanodiamond and water by comparing to the QENS data. Our results show that we can obtain accurate FF parameters by using this technique. The workflow can be generalized to other types of neutron data for FF optimization, such as vibrational spectroscopy and spin echo.
Systematic parameter inference in stochastic mesoscopic modeling
We propose a method to efficiently determine the optimal coarse-grained force field in mesoscopic stochastic simulations of Newtonian fluid and polymer melt systems modeled by dissipative particle dynamics (DPD) and energy conserving dissipative particle dynamics (eDPD). The response surfaces of various target properties (viscosity, diffusivity, pressure, etc.) with respect to model parameters are constructed based on the generalized polynomial chaos (gPC) expansion using simulation results on sampling points (e.g., individual parameter sets). To alleviate the computational cost to evaluate the target properties, we employ the compressive sensing method to compute the coefficients of the dominant gPC terms given the prior knowledge that the coefficients are “sparse”. The proposed method shows comparable accuracy with the standard probabilistic collocation method (PCM) while it imposes a much weaker restriction on the number of the simulation samples especially for systems with high dimensional parametric space. Fully access to the response surfaces within the confidence range enables us to infer the optimal force parameters given the desirable values of target properties at the macroscopic scale. Moreover, it enables us to investigate the intrinsic relationship between the model parameters, identify possible degeneracies in the parameter space, and optimize the model by eliminating model redundancies. The proposed method provides an efficient alternative approach for constructing mesoscopic models by inferring model parameters to recover target properties of the physics systems (e.g., from experimental measurements), where those force field parameters and formulation cannot be derived from the microscopic level in a straight forward way.
Machine Learning Based Network Parameter Estimation Using AMI Data
The expansion of distribution power system and the growing penetration of distributed energy resources present new challenges for situational awareness. Calibrating the extended system model with sensor measurements and maintaining the usability is critical for utilities. This paper presents a distribution network parameter estimation (DNPE) approach using machine learning (ML) and metering data that improve the quality of extended distribution power system modeling. The reliability model can improve the ability of endpoint data to be translated into network-level situational awareness in real time and help distribution system operators (DSOs) solve branch flow and voltage problems. In addition, a data analytic and automate processing scheme is proposed to improve the sensor data quality and prevent misleading information. The effectiveness of the proposed method is verified with actual advanced metering infrastructure (AMI) data on a real utility feeder model, while considering the higher penetration of photovoltaic power generation. The test of DNPE and study results are demonstrated in this paper.
VIC-Global Parameter Dataset Sensitivity with the Variable Infiltration Capacity Model: Evaluating the importance of dynamic land surface parameters when using the VIC-Global parameter dataset
Accurate prediction of runoff is essential to water resources management, flood risk assessment, and ecosystem protection. However, many hydrological models still have relatively substantial limitations when representing the influence of land use and land cover (LULC) on runoff generation and routing. Changes in LULC, such as deforestation, urban expansion, agricultural intensification, and wetland loss, have been shown to alter the water balance at the land surface through fundamental hydrologic processes (e.g., interception, infiltration, evapotranspiration, and soil storage). However, it remains an open question what the exact magnitude and timing of these impacts are for the spatial and temporal scales commonly used in engineering applications. In this analysis we focus on one aspect of recent LULC change for assessing human impacts, which is urbanization. Specifically we seek to determine the impacts of urbanization on the magnitude and timing of surface runoff and baseflow in HUC-12 basins in Clark County, Nevada which has experienced rapid urbanization. We use the Variable Infiltration Capacity (VIC) hydrology model with a widely used off-the-shelf dataset of land surface parameters, VIC-Global, both of which have been commonly used in the past for water and energy balance modeling for large scale hydrologic studies. We examine two scenarios where the first scenario removes all urbanized land cover and parameterizes those areas of the basins as barren or open shrubland. The second scenario tests the opposite case where all areas of the basins are classified as urban regardless of their present classification. The results from the VIC model show there is a low sensitivity for daily surface runoff between scenarios. The daily baseflow values indicate similar low sensitivity to the classification change during specific periods, but then have substantial differences during other period when large precipitation events are occurring. This is likely due to the assumed parameter values for the urban land cover classification made by the VIC-Global dataset. Using a static land cover parameterization is reasonable for large domain hydrology models that are being used for near-term planning horizons (<30 years). However, longer planning horizons where feedbacks between the atmosphere and land surface are important, especially in transient climate situations, considerations for how to update land surface parameters should be incorporated.
Dependence of nuclear quadrupole resonance transitions on the electric field gradient asymmetry parameter for nuclides with half-integer spins
Allowed transition energies and eigenstate expansions have been calculated and tabulated in numerical form as functions of the electric field gradient asymmetry parameter for the zero field Hamiltonian of quadrupolar nuclides with I=3/2,5/2,7/2, and 9/2. These results are essential to interpret nuclear quadrupole resonance (NQR) spectra and extract accurate values of the electric field gradient tensors. Applications of NQR methods to studies of electronic structure in heavy element systems are proposed.
Flow battery flow field having volume that is function of power parameter, time parameter and concentration parameter
A flow battery includes a cell that has first and second flow fields spaced apart from each other and an electrolyte separator layer. A supply/storage system is external of the cell and includes first and second vessels fluidly connected with the first and second flow fields, and first and second pumps configured to selectively move first and second fluid electrolytes between the vessels and the first and second flow fields. The flow fields each have an electrochemically active zone that is configured to receive flow of the fluid electrolytes. The electrochemically active zone has a total open volume that is a function of at least one of a power parameter of the flow battery, a time parameter of the pumps and a concentration parameter of the fluid electrolytes.
Sensitivity of Turbine-Height Wind Speeds to Parameters in Planetary Boundary-Layer and Surface-Layer Schemes in the Weather Research and Forecasting Model
We evaluate the sensitivity of simulated turbine-height winds to 26 parameters applied in a planetary boundary layer (PBL) scheme and a surface layer scheme of the Weather Research and Forecasting (WRF) model over an area of complex terrain during the Columbia Basin Wind Energy Study. An efficient sampling algorithm and a generalized linear model are used to explore the multiple-dimensional parameter space and quantify the parametric sensitivity of modeled turbine-height winds. The results indicate that most of the variability in the ensemble simulations is contributed by parameters related to the dissipation of the turbulence kinetic energy (TKE), Prandtl number, turbulence length scales, surface roughness, and the von Kármán constant. The relative contributions of individual parameters are found to be dependent on both the terrain slope and atmospheric stability. The parameter associated with the TKE dissipation rate is found to be the most important one, and a larger dissipation rate can produce larger hub-height winds. A larger Prandtl number results in weaker nighttime winds. Increasing surface roughness reduces the frequencies of both extremely weak and strong winds, implying a reduction in the variability of the wind speed. All of the above parameters can significantly affect the vertical profiles of wind speed, the altitude of the low-level jet and the magnitude of the wind shear strength. The wind direction is found to be modulated by the same subset of influential parameters. Remainder of abstract is in attachment.
A Short-Term and High-Resolution System Load Forecasting Approach Using Support Vector Regression with Hybrid Parameters Optimization
This work proposes an approach for distribution system load forecasting, which aims to provide highly accurate short-term load forecasting with high resolution utilizing a support vector regression (SVR) based forecaster and a two-step hybrid parameters optimization method. Specifically, because the load profiles in distribution systems contain abrupt deviations, a data normalization is designed as the pretreatment for the collected historical load data. Then an SVR model is trained by the load data to forecast the future load. For better performance of SVR, a two-step hybrid optimization algorithm is proposed to determine the best parameters. In the first step of the hybrid optimization algorithm, a designed grid traverse algorithm (GTA) is used to narrow the parameters searching area from a global to local space. In the second step, based on the result of the GTA, particle swarm optimization (PSO) is used to determine the best parameters in the local parameter space. After the best parameters are determined, the SVR model is used to forecast the short-term load deviation in the distribution system.
A Bayesian approach to calibrating hydrogen flame kinetics using many experiments and parameters
First-principles Markov Chain Monte Carlo sampling is used to investigate uncertainty quantification and uncertainty propagation in parameters describing hydrogen kinetics. Specifically, we sample the posterior distribution for thirty-one parameters focusing on the H 2 O 2 and HO 2 reactions resulting from conditioning on ninety-one experiments. Established literature values are used for the remaining parameters in the mechanism as well as other thermodynamic and transport data needed to specify fluid properties. The samples are computed using an affine invariant sampler starting with broad, noninformative priors. Autocorrelation analysis shows that O(1M) samples are sufficient to obtain a reasonable sampling of the posterior. The resulting distribution identifies strong positive and negative correlations and several non-Gaussian characteristics. Using samples drawn from the posterior, we investigate the impact of parameter uncertainty on the prediction of two more complex flames: a 2D premixed flame kernel and the ignition of a hydrogen jet issuing into a heated chamber. The former represents a combustion regime similar to the target experiments used to calibrate the mechanism and the latter represents a different combustion regime. For the premixed flame, the net amount of product after a given time interval has a standard deviation of less than 2% whereas the standard deviation of the ignition time for the jet is more than 10%. The samples used for these studies are posted online. These results indicate the degree to which parameters consistent with the target experiments constrain predicted behavior in different combustion regimes. Finally, this process provides a framework for both identifying reactions for further study from candidate mechanisms as well as combining uncertainty quantification and propagation to, ultimately, tie uncertainty in laboratory flame experiments to uncertainty in end-use numerical predictions of more complicated scenarios.
Parameter Reduction of Composite Load Model Using Active Subspace Method
Over the past decades, the increasing penetration of distributed energy resources (DERs) has dramatically changed the power load composition in the distribution networks. The traditional static and dynamic load models can hardly capture the dynamic behavior of modern loads especially for fault-induced delayed voltage recovery (FIDVR) events. Thus, a more comprehensive composite load model with combination of static load, different types of induction motors, single-phase A/C motor, electronic load and DERs has been proposed by Western Electricity Coordinating Council (WECC). However, due to the large number of parameters and model complexity, the WECC composite load model (WECC CMLD) raises new challenges to power system studies. To overcome these challenges, in this paper, a cutting-edge parameter reduction (PR) approach for WECC CMLD based on active subspace method (ASM) is proposed. Firstly, the WECC CMLD is parameterized in a discrete-time manner for the application of the proposed method. Then, parameter sensitivities are calculated by discovering the active subspace, which is a lower-dimensional linear subspace of the parameter space of WECC CMLD in which the dynamic response is most sensitive. The interdependency among parameters can be taken into consideration by our approach. Finally, the numerical experiments validate the effectiveness and advantages of the proposed approach for WECC CMLD model.
A Comparison of Cosmological Parameters Determined from CMB Temperature Power Spectra from the South Pole Telescope and the Planck Satellite
The Planck cosmic microwave background temperature data are best fit with a Lambda CDM model that mildly contradicts constraints from other cosmological probes. The South Pole Telescope (SPT) 2540 deg(2) SPT-SZ survey offers measurements on sub-degree angular scales (multipoles 650 <= l <= 2500) with sufficient precision to use as an independent check of the Planck data. Here we build on the recent joint analysis of the SPT-SZ and Planck data in Hou et al. by comparing Lambda CDM parameter estimates using the temperature power spectrum from both data sets in the SPT-SZ survey region. We also restrict the multipole range used in parameter fitting to focus on modes measured well by both SPT and Planck, thereby greatly reducing sample variance as a driver of parameter differences and creating a stringent test for systematic errors. We find no evidence of systematic errors from these tests. When we expand the maximum multipole of SPT data used, we see low-significance shifts in the angular scale of the sound horizon and the physical baryon and cold dark matter densities, with a resulting trend to higher Hubble constant. When we compare SPT and Planck data on the SPT-SZ sky patch to Planck full-sky data but keep the multipole range restricted, we find differences in the parameters n(s) and A(s)e(-2 tau). We perform further checks, investigating instrumental effects and modeling assumptions, and we find no evidence that the effects investigated are responsible for any of the parameter shifts. Taken together, these tests reveal no evidence for systematic errors in SPT or Planck data in the overlapping sky coverage and multipole range and at most weak evidence for a breakdown of Lambda CDM or systematic errors influencing either the Planck data outside the SPT-SZ survey area or the SPT data at l > 2000.
Inference of reaction rate parameters based on summary statistics from experiments
Here, we present the results of an application of Bayesian inference and maximum entropy methods for the estimation of the joint probability density for the Arrhenius rate para meters of the rate coefficient of the H 2 /O 2 -mechanism chain branching reaction H + O 2 → OH + O. Available published data is in the form of summary statistics in terms of nominal values and error bars of the rate coefficient of this reaction at a number of temperature values obtained from shock-tube experiments. Our approach relies on generating data, in this case OH concentration profiles, consistent with the given summary statistics, using Approximate Bayesian Computation methods and a Markov Chain Monte Carlo procedure. The approach permits the forward propagation of parametric uncertainty through the computational model in a manner that is consistent with the published statistics. A consensus joint posterior on the parameters is obtained by pooling the posterior parameter densities given each consistent data set. To expedite this process, we construct efficient surrogates for the OH concentration using a combination of Pad'e and polynomial approximants. These surrogate models adequately represent forward model observables and their dependence on input parameters and are computationally efficient to allow their use in the Bayesian inference procedure. We also utilize Gauss-Hermite quadrature with Gaussian proposal probability density functions for moment computation resulting in orders of magnitude speedup in data likelihood evaluation. Despite the strong non-linearity in the model, the consistent data sets all res ult in nearly Gaussian conditional parameter probability density functions. The technique also accounts for nuisance parameters in the form of Arrhenius parameters of other rate coefficients with prescribed uncertainty. The resulting pooled parameter probability density function is propagated through stoichiometric hydrogen-air auto-ignition computations to illustrate the need to account for correlation among the Arrhenius rate parameters of one reaction and across rate parameters of different reactions.
K-ε Turbulence Model Parameter Estimates Using an Approximate Self-similar Jet-in-Crossflow Solution
The k-ε turbulence model has been described as perhaps “the most widely used complete turbulence model.” This family of heuristic Reynolds Averaged Navier-Stokes (RANS) turbulence closures is supported by a suite of model parameters that have been estimated by demanding the satisfaction of well-established canonical flows such as homogeneous shear flow, log-law behavior, etc. While this procedure does yield a set of so-called nominal parameters, it is abundantly clear that they do not provide a universally satisfactory turbulence model that is capable of simulating complex flows. Recent work on the Bayesian calibration of the k-ε model using jet-in-crossflow wind tunnel data has yielded parameter estimates that are far more predictive than nominal parameter values. In this paper, we develop a self-similar asymptotic solution for axisymmetric jet-in-crossflow interactions and derive analytical estimates of the parameters that were inferred using Bayesian calibration. The self-similar method utilizes a near field approach to estimate the turbulence model parameters while retaining the classical far-field scaling to model flow field quantities. Our parameter values are seen to be far more predictive than the nominal values, as checked using RANS simulations and experimental measurements. They are also closer to the Bayesian estimates than the nominal parameters. A traditional simplified jet trajectory model is explicitly related to the turbulence model parameters and is shown to yield good agreement with measurement when utilizing the analytical derived turbulence model coefficients. Finally, the close agreement between the turbulence model coefficients obtained via Bayesian calibration and the analytically estimated coefficients derived in this paper is consistent with the contention that the Bayesian calibration approach is firmly rooted in the underlying physical description.
Consequences of CCD imperfections for cosmology determined by weak lensing surveys: from laboratory measurements to cosmological parameter bias
Weak gravitational lensing causes subtle changes in the apparent shapes of galaxies due to the bending of light by the gravity of foreground masses. By measuring the shapes of large numbers of galaxies (millions in recent surveys, up to tens of billions in future surveys) we can infer the parameters that determine cosmology. Imperfections in the detectors used to record images of the sky can introduce changes in the apparent shapes of galaxies, which in turn can bias the inferred cosmological parameters. In this paper we consider the effect of two widely discussed sensor imperfections: tree rings, due to impurity gradients that cause transverse electric fields in the charge-coupled devices (CCDs), and pixel size variation, due to periodic CCD fabrication errors. These imperfections can be observed when the detectors are subject to uniform illumination (flat-field images). We develop methods to determine the spurious shear and convergence (due to the imperfections) from the flat-field images. We calculate how the spurious shear when added to the lensing shear will bias the determination of cosmological parameters. We apply our methods to candidate sensors of the Large Synoptic Survey Telescope (LSST) as a timely and important example, analyzing flat-field images recorded with LSST prototype CCDs in the laboratory. We find that tree rings and periodic pixel size variation present in the LSST CCDs will introduce negligible bias to cosmological parameters determined from the lensing power spectrum, specifically w, Ω{sub m}, and σ{sub 8}.
Automated extraction of physical parameters from experimentally obtained thermal profiles using a machine learning approach
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