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The basic principles of the surface harmonics method are described. A one-dimensional problem is used to exemplify the specific features of the method and the algorithms for construction of finite-difference equations. The objective of this study is to popularize the surface harmonics method among specialists.
Systems biology models written in the BioNetGen language often contain parameters that must be fit based on experimental data. PyBioNetFit is a software tool designed to fit parameters of BioNetGen models. The user is expected to provide a BioNetGen model that contains unknown parameters, along with one or more text files containing experimental data. PyBioNetFit will perform a series of calls to the BioNetGen simulator using different parameter sets, to identify the parameter set that best fits the data. The parameter search is dictated by the user's choice of one of several metaheuristic optimization algorithms, including differential evolution, particle swarm optimization, scatter search, and simulated annealing. The software supports parallelized computing on multi-core computers and on computing clusters. We expect this software to be a useful tool for researchers designing BioNetGen models in collaboration with experimentalists.
Stan is a probabilistic programming language for specifying statistical models. A Stan program imperatively defines a log probability function over parameters conditioned on specified data and constants. As of version 2.14.0, Stan provides full Bayesian inference for continuous-variable models through Markov chain Monte Carlo methods such as the No-U-Turn sampler, an adaptive form of Hamiltonian Monte Carlo sampling. Penalized maximum likelihood estimates are calculated using optimization methods such as the limited memory Broyden-Fletcher-Goldfarb-Shanno algorithm. Stan is also a platform for computing log densities and their gradients and Hessians, which can be used in alternative algorithms such as variational Bayes, expectation propagation, and marginal inference using approximate integration. To this end, Stan is set up so that the densities, gradients, and Hessians, along with intermediate quantities of the algorithm such as acceptance probabilities, are easily accessible. Stan can also be called from the command line using the cmdstan package, through R using the rstan package, and through Python using the pystan package. All three interfaces support sampling and optimization-based inference with diagnostics and posterior analysis. rstan and pystan also provide access to log probabilities, gradients, Hessians, parameter transforms, and specialized plotting.
Work carried out under this grant addressed the need for improved materials and device characterization of solar cell designs. This experimental program aimed to develop joint electrical and optical studies of solar cells based on the group-II-VI semiconductor CdTe and the chalcogenide semiconductor Cu(InGa)Se 2 . Electrical measurements focused on temperature (T) and illumination intensity (I) dependence of the open-circuit voltage (VOC), a quantity that plays an important role in conversion efficiency. The VOC depends on temperature and illumination intensity through the energy gap and positions of the quasiFermi levels (QFLs). Optical measurements exploited the illumination and temperature dependence of absolute photoluminescence (PL) intensity (PL-I), a quantity that also depends on the QFL positions. The QFL splitting is a quantity that also depends on recombination rates within the solar cell, including radiative and non-radiative processes. Other factors affect the electrical and optical properties. These include band offsets at both the front and back interfaces of the device active region where electrical contacts are formed. Understanding, locating, and quantifying the recombination properties of the solar cells was the principal goal of this research. Custom simulations were developed to solve continuity and Poisson equations selfconsistently to obtain free-electron and free-hole concentrations. The measurements of temperature and intensity dependent VOC and PL-I allowed the extraction of a number of physical parameters including the conduction band offset, the shunt constant, and the effective capture coefficient for recombination centers, both within the absorber and at the absorber-buffer interface. In addition, the back-contact barrier height is determined from electrical properties. Each of these is discussed in the report. The illumination intensity dependence of VOC and PL-I do not overlap in experiments primarily because PL is not observed in the low-intensity regime where VOC is studied. Absolute PL-I measurements enabled development of an approach directly comparing it with VOC. This in turn allowed development of a simulation capability that would consistently use both measurements, as functions of T and I, for producing a minimization scheme using a differential evolution algorithm. The approach was applied to both CdTe and Cu(InGa)Se 2 solar cells each prepared under various conditions. Shunt conductivity, QFL splitting, recombination were measured. Also extensively studied are current-voltage and frequency-dependent capacitance voltage. Work completed under this grant included studies of magnesium zinc oxide (MZO) buffered CdTe solar cells including the effects of hydroiodic acid (HI) treatment. From these studies the recombination rates were quantified at the buffer/absorber (front) interface. The effect of back-contact barrier height was investigated. CdTe solar cells were prepared with CdSe and CdS buffer layers. Lower grain-boundary potential fluctuation, higher back-contact barrier height, and greater bulk recombination were observed in early devices with CdSe buffer layer. Investigations were also carried out into CdS/Cu(InGa)Se 2 solar cells. A metal-insulatorsemiconductor capacitance-voltage technique was developed to extract recombinationrelevant properties of the absorber interface. From this work the density of interface states D it , their capture cross-section σ, fixed charge at the interface Q f , and surface recombination velocity were all extracted.
The key to success in geothermal drilling is economic feasibility, and a major cost in the development of geothermal resources is the actual drilling of the wells. In this project, a real-time drilling optimization system for geothermal drilling was developed. The system couples three individual components while drilling. The first component is a drill stem vibration analysis model, the second is Mechanical Specific Energy (MSE) analyses, and the third is a detailed PDC Rate of Penetration (ROP) drill bit model for optimum RPM and WOB combinations. The benefit of the coupled system is that the range of WOB and RPM could be selected to avoid drill stem vibrations. Secondly, MSE is used as an efficiency measure and the detailed PDC drill bit model ensures the drill bit does not endure temperatures that exceed the temperature at which the PDC cutters experience accelerated wear. The new detailed PDC bit model is based on rock/bit interaction that physically tracks the PDC cutter wear flats as the bit drills ahead giving the capability to calculate the temperature being generated underneath the worn cutters to better advise on operational parameters to avoid accelerated cutter wear and failure and to ensure that operational parameters are applied so that overall ROP is maximized. By combining the drill stem vibrations and the detailed PDC bit cutter wear and “safe” non-accelerated cutter wear temperature and optimum ranges of operating parameters, it results in higher ROP and lower cost drilling. Single cutter PDC testing performed in different lithologies at Sandia was utilized to verify the PDC cutter forces and depth of cut for new and worn cutters. Based on single cutter PDC temperature modeling, verification using single cutter data from the testing done by National Oilwell Varco (NOV) was performed. Sandia’s Hard-Rock Drilling Facility (HRDF) was utilized to test different drill bit configurations with different cutter designs and wear status with different induced modes of vibration to obtain the critical bit RPM/WOB ranges resulting in ineffective drilling and low ROP. The collected test data were further used to verify and calibrate the full hole PDC ROP model that was developed based on single cutter interaction data. A full coupled drill stem vibration model was formulated and verified with geothermal field data from the Chocolate Mountain Aerial Gunnery Range (CMAGR). A graphical user interface (GUI) was developed using Tkinter library in the computer programming language Python, which integrates all the developed models in one system. The developed system consists mainly of the PDC ROP model, PDC bit wear model, PDC cutter temperature model, Mechanical Specific Energy (MSE) model, and drillstring vibration model integrated into one system. The developed system can be used for both, post well analysis and real-time optimization using different criteria such as ROP maximization or MSE minimization. The software uses Differential Evolution Algorithm (DEA) to find optimum values for operational parameters based on last foot drilled while avoiding the drillstring vibration and cutter temperature critical operating parameters.
In this paper, we explore methods for the identification of stellar flare events in irregularly sampled data of ground-based time domain surveys. In particular, we describe a new technique for identifying flaring stars, which we have implemented in a publicly available Python module called "PyVAN." The approach uses the Differential Evolution algorithm to optimize parameters of empirically derived light curve templates for different types of stars to fit a candidate light curve. The difference of the likelihoods that these best-fit templates produced the observed data is then used to delineate targets that are well-explained by a flare template but simultaneously poorly explained by templates of common contaminants. By testing on light curves of known identity and morphology, we show that our technique is capable of recovering flaring status in 69% of all light curves containing a flare event above thresholds drawn to include <1% of any contaminant population. By applying to Palomar Transient Factory data, we show consistency with prior samples of flaring stars, and identify a small selection of candidate flaring G-type stars for possible follow-up.
We fit the mass and radial profile of the Orphan–Chenab Stream's (OCS) dwarf-galaxy progenitor by using turnoff stars in the Sloan Digital Sky Survey and the Dark Energy Camera to constrain N-body simulations of the OCS progenitor falling into the Milky Way on the 1.5 PetaFLOPS MilkyWay@home distributed supercomputer. We infer the internal structure of the OCS's progenitor under the assumption that it was a spherically symmetric dwarf galaxy composed of a stellar system embedded in an extended dark matter halo. We optimize the evolution time, the baryonic and dark matter scale radii, and the baryonic and dark matter masses of the progenitor using a differential evolution algorithm. The likelihood score for each set of parameters is determined by comparing the simulated tidal stream to the angular distribution of OCS stars observed in the sky. We fit the total mass of the OCS's progenitor to (2.0 ± 0.3) × 10 7 M ⊙ with a mass-to-light ratio of γ = 73.5 ± 10.6 and (1.1 ± 0.2) × 10 6 M ⊙ within 300 pc of its center. Within the progenitor's half-light radius, we estimate a total mass of (4.0 ± 1.0) × 10 5 M ⊙ . We also fit the current sky position of the progenitor's remnant to be (α, δ) = ((166.0 ± 0.9)°, (–11.1 ± 2.5)°) and show that it is gravitationally unbound at the present time. The measured progenitor mass is on the low end of previous measurements and, if confirmed, lowers the mass range of ultrafaint dwarf galaxies. Our optimization assumes a fixed Milky Way potential, OCS orbit, and radial profile for the progenitor, ignoring the impact of the Large Magellanic Cloud.
Protection and control of nuclear fuels is paramount for nuclear security and safeguards; therefore, it is important to develop fast and robust controlling mechanisms to ensure the safety of nuclear fuels. Through both passive- and active-interrogation methods we can use fast-neutron detection to perform real-time measurements of fission neutrons for process monitoring. Active interrogation allows us to use different ranges of incident neutron energy to probe for different isotopes of uranium. With fast-neutron detectors, such as organic liquid scintillation detectors, we can detect the induced-fission neutrons and photons and work towards quantifying a sample’s mass and enrichment. Using MCNPX-PoliMi, a system was designed to measure induced-fission neutrons from U-235 and U-238. Measurements were then performed in the summer of 2010 at the Joint Research Centre in Ispra, Italy. Fissions were induced with an associated particle D-T generator and an isotopic Am-Li source. The fission neutrons, as well as neutrons from (n, 2n) and (n, 3n) reactions, were measured with five 5” by 5” EJ-309 organic liquid scintillators. The D-T neutron generator was available as part of a measurement campaign in place by Padova University. The measurement and data-acquisition systems were developed at the University of Michigan utilizing a CAEN V1720 digitizer and pulse-shape discrimination algorithms to differentiate neutron and photon detections. Low-enriched uranium samples of varying mass and enrichment were interrogated. Acquired time-of-flight curves and cross-correlation curves are currently analyzed to draw relationships between detected neutrons and sample mass and enrichment. In the full paper, the promise of active-interrogation measurements and fast-neutron detection will be assessed through the example of this proof-of-concept measurement campaign. Additionally, MCNPX-PoliMi simulation results will be compared to the measured data to validate the MCNPX-PoliMi code when used for active-interrogation simulations.
Geothermal energy is renewable, reliable and environmentally friendly source of energy. The major cost in the development of geothermal wells is the actual drilling of the wells. The main objective of this paper is to introduce a new real-time drilling optimization system designed for granite formation to reduce the overall drilling cost. In this study, a drilling optimization system is verified using drilling data from Utah-Forge well 58-32. The drilling optimization system used the Utah-Forge well 58-32 data to achieve real-time unconfined compressive strength (UCS). Based on the UCS value from the previous feet, the system simulates the ROP for the next drilling feet. The drilling optimization system utilizes the Differential Evolution Algorithm (DEA), which is a metaheuristic method to search the space of solution, to find the best operating parameters (i.e. WOB and RPM) for the next drilling foot. The optimization algorithm takes a maximum cutter temperature into account as a constraint and avoids the accelerated wear. The developed drilling optimization system improves ROP responses and reduces the drilling cost of geothermal wells. The simulated ROP results from the system show a good agreement with the ROP from Utah-Forge well 58-32 drilling data. The drilling time before and after optimization for both intervals were presented.
In the problem of inverse radiation transport, measurements of particle leakages from radioactive source/shield systems are used to infer unknown parameters within the systems. This reconstruction can be accomplished by finding the physical parameters of the unknown system that minimize the difference between calculated detector responses and measured detector responses. The inverse transport solver should also propagate uncertainties from the detector responses to the reconstructed parameter values. Recently, the Differential Evolution Adaptive Metropolis (DREAM) method was shown to be a robust method for uncertainty quantification in inverse problems. The DREAM method uses the differential evolution algorithm to choose efficient steps in a Markov chain Monte Carlo (MCMC) simulation. Although the DREAM method has been shown to be more efficient than traditional MCMC approaches, it still requires thousands of transport computations to accurately quantify uncertainty. For the simple ray-tracing model, it was possible to perform these calculations in a reasonable amount of time (under an hour). However, inverse transport problems that require computationally-intensive transport solvers will need prohibitively long run times when using the DREAM method. A way to overcome the computational burden of the DREAM method is to perform surrogate modeling using the polynomial chaos expansion (PCE) approach. It was recently shown that the PCE method provides both accurate and computationally inexpensive uncertainty quantification in forward radiation source/shield problems. PCE was also recently applied to an inverse problem in nonlinear point reactor kinetics within a standard MCMC approach. PCE was first used with the DREAM method where it was applied to inverse problems in groundwater modeling.
Purpose: Interior tomography has been recognized as one of the most effective approaches in computed tomography (CT) to reduce radiation dose rendered to patients. In this work, the authors propose and evaluate an imaging method of radial differential interior tomography.Methods: In interior tomography, an x-ray beam is collimated to only irradiate the region of interest (ROI) with suspected lesions while the surrounding area/volume of normal tissues/organs is spared. In the proposed imaging method of radial differential interior tomography, the outcome is a ROI image that has gone through a radial differential filtering. The image reconstruction algorithm for the radial differential interior tomography is kept in the fashion of differentiated backprojection and projection onto convex sets, but the required a priori knowledge in a small round area becomes zero and may be more readily available in practice.Results: Using the projection data simulated by computer and acquired by CT scanner, the authors evaluate and verify the performance of the proposed radial differential interior tomography method and its associated image reconstruction algorithm. The preliminary results show that the proposed imaging method can generate an image that is the radial differentiation of a conventional tomographic image and is robust over noise that inevitably exist in practice.Conclusions: It is believed that the proposed imaging method may find its utility in advanced clinical applications wherein a ROI-based image processing and analysis is required for lesion visualization, characterization, and diagnosis.
This paper presents the theory and implementation of a distributed algorithm for controlling differential power processing converters in photovoltaic (PV) applications. This distributed algorithm achieves true maximum power point tracking of series-connected PV submodules by relying only on local voltage measurements and neighbor-to-neighbor communication between the differential power converters. Compared to previous solutions, the proposed algorithm achieves reduced number of perturbations at each step and potentially faster tracking without adding extra hardware; all these features make this algorithm well-suited for long submodule strings. The formulation of the algorithm, discussion of its properties, as well as three case studies are presented. The performance of the distributed tracking algorithm has been verified via experiments, which yielded quantifiable improvements over other techniques that have been implemented in practice. Both simulations and hardware experiments have confirmed the effectiveness of the proposed distributed algorithm.
An algorithm for solving the linear Cauchy problem for large systems of ordinary differential equations is presented. The algorithm for systems of first-order differential equations is implemented in the EDELWEISS code with the possibility of parallel computations on supercomputers employing the MPI (Message Passing Interface) standard for the data exchange between parallel processes. The solution is represented by a series of orthogonal polynomials on the interval [0, 1]. The algorithm is characterized by simplicity and the possibility to solve nonlinear problems with a correction of the operator in accordance with the solution obtained in the previous iterative process.
Large machine learning models are revolutionary technologies of artificial intelligence whose bottlenecks include huge computational expenses, power, and time used both in the pre-training and fine-tuning process. In this work, we show that fault-tolerant quantum computing could possibly provide provably efficient resolutions for generic (stochastic) gradient descent algorithms, scaling as $\mathcal{O}$(T 2 x polylog($n$)), where n is the size of the models and T is the number of iterations in the training, as long as the models are both sufficiently dissipative and sparse, with small learning rates. Based on earlier efficient quantum algorithms for dissipative differential equations, we find and prove that similar algorithms work for (stochastic) gradient descent, the primary algorithm for machine learning. In practice, we benchmark instances of large machine learning models from 7 million to 103 million parameters. We find that, in the context of sparse training, a quantum enhancement is possible at the early stage of learning after model pruning, motivating a sparse parameter download and re-upload scheme. Our work shows solidly that fault-tolerant quantum algorithms could potentially contribute to most state-of-the-art, large-scale machine-learning problems.
This work explores the use of differentiable programming to integrate domain knowledge, in the form of domain specific software, into neural networks to develop scientific machine learning systems. We propose a differentiable vertex fitting algorithm that estimates the crossing point of multiple curves. In the high energy physics setting, these curves are defined by particle equations of motion and the crossing point represents the origin of particle production. This differentiable vertex fitting algorithm can be seamlessly integrated into neural networks, and we show its utility and efficacy in the high energy physics application of the classification of jets, i.e., collimated streams of particles in particle detectors whose originating parent particle we aim to classify. We demonstrate how differentiable vertex fitting can be integrated into larger transformer-based models for jet flavor tagging and show improvements in heavy flavor jet classification when compared to baseline models. Published by the American Physical Society 2024
We present a quantum algorithm for simulating the wave equation under Dirichlet and Neumann boundary conditions. The algorithm uses Hamiltonian simulation and quantum linear system algorithms as subroutines. It relies on factorizations of discretized Laplacian operators to allow for polynomially improved scaling in truncation errors and improved scaling for state preparation relative to general purpose quantum algorithms for solving linear differential equations. Relative to classical algorithms for simulating the D-dimensional wave equation, our quantum algorithm achieves exponential space savings and achieves a speedup which is polynomial for fixed D and exponential in D. Furthermore, we also consider using Hamiltonian simulation for Klein-Gordon equations and Maxwell's equations.
Recently developed quantum algorithms address computational challenges in numerical analysis by performing linear algebra in Hilbert space. Such algorithms can produce a quantum state proportional to the solution of a d-dimensional system of linear equations or linear differential equations with complexity poly(logd). While several of these algorithms approximate the solution to within ϵ with complexity poly(log(1/ϵ)), no such algorithm was previously known for differential equations with time-dependent coefficients. In this work, we develop a quantum algorithm for linear ordinary differential equations based on so-called spectral methods, an alternative to finite difference methods that approximates the solution globally. Using this approach, we give a quantum algorithm for time-dependent initial and boundary value problems with complexity poly(logd, log(1/ϵ)).
Large-scale pressure increases resulting from carbon dioxide (CO 2 ) injection in the subsurface can potentially impact caprock integrity, induce reactivation of critically stressed faults, and drive CO 2 or brine through conductive features into shallow groundwater. Pressure management involving the extraction of native fluids from storage formations can be used to reduce such pressure increases. However, dealing with large volumes of extracted brine can be technically challenging and expensive. Selection of optimal well locations and pumping rates are critical for maximizing CO 2 storage and minimizing brine extraction during geologic CO 2 sequestration (GCS). Robust and efficient computerized algorithms combining reservoir models and optimization methods are needed to make proper decisions on well placement and pumping rates. This work presents a constrained differential evolution (CDE) algorithm for solving global optimization problems involving pressure management of GCS projects. Application of the CDE optimization methodology was demonstrated for a hypothetical CO 2 storage scenario in a deep sandstone reservoir in the Southern San Joaquin Basin in California, USA. Industrial-scale storage of CO 2 would generate significant pressure buildup in this formation, which in turn would raise concerns about induced seismicity due to presence of multiple faults surrounding the injection site. Through the CDE optimization algorithm coupled to a vertically-averaged reservoir simulator, we successfully estimated optimal solutions for brine extraction wells in the reservoir that would limit the local pressure along the faults to a prescribed threshold. Multiple realizations of the reservoir permeability field were created to understand the impact of reservoir heterogeneity on optimization results. Our results indicate that the reservoir slope and heterogeneity have significant impact on optimum extraction rates. Reservoir heterogeneity is also a significant factor for extraction well locations, suggesting that in practice decisions about extraction well placement through optimization should be made at later project stages when data from a few years of CO 2 injection have allowed iterative updating and refining of the reservoir forward models. Although the study focused on optimization of brine extraction, the CDE optimization methodology presented in this paper has also potential to solve other complex optimization problems related to GCS, such as increasing storage efficiency by enhancing injectivity and capillary and dissolution trapping.