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At least 559 records · Page 31

Multi-level methods and approximating distribution functions

Biochemical reaction networks are often modelled using discrete-state, continuous-time Markov chains. System statistics of these Markov chains usually cannot be calculated analytically and therefore estimates must be generated via simulation techniques. There is a well documented class of simulation techniques known as exact stochastic simulation algorithms, an example of which is Gillespie’s direct method. These algorithms often come with high computational costs, therefore approximate stochastic simulation algorithms such as the tau-leap method are used. However, in order to minimise the bias in the estimates generated using them, a relatively small value of tau is needed, rendering the computational costs comparable to Gillespie’s direct method. The multi-level Monte Carlo method (Anderson and Higham, Multiscale Model. Simul. 10:146–179, 2012) provides a reduction in computational costs whilst minimising or even eliminating the bias in the estimates of system statistics. This is achieved by first crudely approximating required statistics with many sample paths of low accuracy. Then correction terms are added until a required level of accuracy is reached. Recent literature has primarily focussed on implementing the multi-level method efficiently to estimate a single system statistic. However, it is clearly also of interest to be able to approximate entire probability distributions of species counts. We present two novel methods that combine known techniques for distribution reconstruction with the multi-level method. We demonstrate the potential of our methods using a number of examples.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Application of a low order panel method to complex three-dimensional internal flow problems

An evaluation of the ability of a low order panel method to predict complex three-dimensional internal flow fields was made. The computer code VSAERO was used as a basis for the evaluation. Guidelines for modeling internal flow geometries were determined and the effects of varying the boundary conditions and the use of numerical approximations on the solutions accuracy were studied. Several test cases were run and the results were compared with theoretical or experimental results. Modeling an internal flow geometry as a closed box with normal velocities specified on an inlet and exit face provided accurate results and gave the user control over the boundary conditions. The values of the boundary conditions greatly influenced the amount of leakage an internal flow geometry suffered and could be adjusted to eliminate leakage. The use of the far-field approximation to reduce computation time influenced the accuracy of a solution and was coupled with the values of the boundary conditions needed to eliminate leakage. The error induced in the influence coefficients by using the far-field approximation was found to be dependent on the type of influence coefficient, the far-field radius, and the aspect ratio of the panels.

Ashby, D. L.↗

BGRID: A block-structured grid generation code for wing sections

The operation of the BGRID computer program is described for generating block-structured grids. Examples are provided to illustrate the code input and output. The application of a fully implicit AF (approximation factorization)-based computer code, called TWINGB (Transonic WING), for solving the 3D transonic full potential equation in conservation form on block-structured grids is also discussed.

Chen, H. C.↗

Microscopic Theory of Nuclear Fission: A Review

This paper reviews how nuclear fission is described within nuclear density functional theory. A distinction should be made between spontaneous fission, where half-lives are the main observables and quantum tunnelling the essential concept, and induced fission, where the focus is on fragment properties and explicitly time-dependent approaches are often invoked. Overall, the cornerstone of the density functional theory approach to fission is the energy density functional formalism. The basic tenets of this method, including some well-known tools such as the Hartree–Fock–Bogoliubov (HFB) theory, effective two-body nuclear potentials such as the Skyrme and Gogny force, finite-temperature extensions and beyond mean-field corrections, are presented succinctly. The energy density functional approach is often combined with the hypothesis that the time-scale of the large amplitude collective motion driving the system to fission is slow compared to typical time-scales of nucleons inside the nucleus. In practice, this hypothesis of adiabaticity is implemented by introducing (a few) collective variables and mapping out the many-body Schrödinger equation into a collective Schrödinger-like equation for the nuclear wave-packet. The region of the collective space where the system transitions from one nucleus to two (or more) fragments defines what are called the scission configurations. The inertia tensor that enters the kinetic energy term of the collective Schrödinger-like equation is one of the most essential ingredients of the theory, since it includes the response of the system to small changes in the collective variables. For this reason, the two main approximations used to compute this inertia tensor, the adiabatic time-dependent HFB and the generator coordinate method, are presented in detail, both in their general formulation and in their most common approximations. The collective inertia tensor enters also the Wentzel–Kramers–Brillouin (WKB) formula used to extract spontaneous fission half-lives from multi-dimensional quantum tunnelling probabilities (For the sake of completeness, other approaches to tunnelling based on functional integrals are also briefly discussed, although there are very few applications.) It is also an important component of some of the time-dependent methods that have been used in fission studies. Concerning the latter, both the semi-classical approaches to time-dependent nuclear dynamics and more microscopic theories involving explicit quantum-many-body methods are presented. One of the hallmarks of the microscopic theory of fission is the tremendous amount of computing needed for practical applications. In particular, the successful implementation of the theories presented in this article requires a very precise numerical resolution of the HFB equations for large values of the collective variables. This aspect is often overlooked, and several sections are devoted to discussing the resolution of the HFB equations, especially in the context of very deformed nuclear shapes. In particular, the numerical precision and iterative methods employed to obtain the HFB solution are documented in detail. Finally, a selection of the most recent and representative results obtained for both spontaneous and induced fission is presented, with the goal of emphasizing the coherence of the microscopic approaches employed. In conclusion, although impressive progress has been achieved over the last two decades to understand fission microscopically, much work remains to be done. Several possible lines of research are outlined in the conclusion.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Spatially Local Surrogate Modeling of Subgrid-Scale Effects in Idealized Atmospheric Flows: A Deep Learned Approach Using High-Resolution Simulation Data

Abstract We introduce a machine learned surrogate model from high-resolution simulation data to capture the subgrid-scale effects in dry, stratified atmospheric flows. We use deep neural networks (NNs) to model the spatially local state differences between a coarse-resolution simulation and a high-resolution simulation. The setup enables the capture of both dissipative and antidissipative effects in the state differences. The NN model is able to accurately capture the state differences in offline tests outside the training regime. In online tests intended for production use, the NN-coupled coarse simulation has higher accuracy over a significant period of time compared to the coarse-resolution simulation without any correction. We provide evidence of the capability of the NN model to accurately capture high-gradient regions in the flow field. With the accumulation of the errors, the NN-coupled simulation becomes computationally unstable after approximately 90 coarse simulation time steps. Insights gained from these surrogate models further pave the way for formulating stable, complex, physics-based spatially local NN models which are driven by traditional subgrid-scale turbulence closure models. Significance Statement Flows in the atmosphere are highly chaotic and turbulent, comprising flow structures of broad scales. For effective computational modeling of atmospheric flows, the effects of the small- and large-scale structures need to be captured by the simulations. Capturing the small-scale structures requires fine-resolution simulations. Even with the current state-of-the-art supercomputers, it can be prohibitively expensive to simulate these flows when computed for the entire earth over climate time scales. Thus, it is necessary to focus on the larger-scale structures using a coarse-resolution simulation while capturing the effects of the smaller-scale structures using some parameterization (approximation) scheme and incorporating it into the coarse-resolution simulation. We use machine learning to model the effects of the small-scale structures (subgrid-scale effects) in atmospheric flows. Data from a fine-resolution simulation is used to compute the missing subgrid-scale effects in coarse-resolution simulations. We then use machine learning models to approximate these differences between the coarse- and fine-resolution simulations. We see improved accuracy for the coarse-resolution simulations when corrected using these machine learned models.

54 ENVIRONMENTAL SCIENCES↗

Applications of a General Finite-Difference Method for Calculating Bending Deformations of Solid Plates

This paper reports the findings of an investigation of a finite - difference method directly applicable to calculating static or simple harmonic flexures of solid plates and potentially useful in other problems of structural analysis. The method, which was proposed in doctoral thesis by John C. Houbolt, is based on linear theory and incorporates the principle of minimum potential energy. Full realization of its advantages requires use of high-speed computing equipment. After a review of Houbolt's method, results of some applications are presented and discussed. The applications consisted of calculations of the natural modes and frequencies of several uniform-thickness cantilever plates and, as a special case of interest, calculations of the modes and frequencies of the uniform free-free beam. Computed frequencies and nodal patterns for the first five or six modes of each plate are compared with existing experiments, and those for one plate are compared with another approximate theory. Beam computations are compared with exact theory. On the basis of the comparisons it is concluded that the method is accurate and general in predicting plate flexures, and additional applications are suggested. An appendix is devoted t o computing procedures which evolved in the progress of the applications and which facilitate use of the method in conjunction with high-speed computing equipment.

Walton, William C., Jr.↗

A useful approximation for the flat surface impulse response

The flat surface impulse response (FSIR) is a very useful quantity in computing the mean return power for near-nadir-oriented short-pulse radar altimeters. However, for very small antenna beamwidths and relatively large pointing angles, previous analytical descriptions become very difficult to compute accurately. An asymptotic approximation is developed to overcome these computational problems. Since accuracy is of key importance, a condition is developed under which this solution is within 2 percent of the exact answer. The asymptotic solution is shown to be in functional agreement with a conventional clutter power result and gives a 1.25-dB correction to this formula to account properly for the antenna-pattern variation over the illuminated area.

Brown, Gary S.↗

Correlated pair ansatz with a binary tree structure

We develop an efficient algorithm to implement the recently introduced binary tree state (BTS) ansatz on a classical computer. BTS allows a simple approximation to permanents arising from the computationally intractable antisymmetric product of interacting geminals and respects size-consistency. We show how to compute BTS overlap and reduced density matrices efficiently. We also explore two routes for developing correlated BTS approaches: Jastrow coupled cluster on BTS and linear combinations of BT states. Here, the resulting methods show great promise in benchmark applications to the reduced Bardeen–Cooper–Schrieffer Hamiltonian and the one-dimensional XXZ Heisenberg Hamiltonian.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A forward method for optimal stochastic nonlinear and adaptive control

A computational approach is taken to solve the optimal nonlinear stochastic control problem. The approach is to systematically solve the stochastic dynamic programming equations forward in time, using a nested stochastic approximation technique. Although computationally intensive, this provides a straightforward numerical solution for this class of problems and provides an alternative to the usual dimensionality problem associated with solving the dynamic programming equations backward in time. It is shown that the cost degrades monotonically as the complexity of the algorithm is reduced. This provides a strategy for suboptimal control with clear performance/computation tradeoffs. A numerical study focusing on a generic optimal stochastic adaptive control example is included to demonstrate the feasibility of the method.

Bayard, David S.↗

A New Look at Aubrites: Investigating 3D Modal Mineralogy with X-Ray Computed Tomography

The aubrites (approximately 30 known meteorites) are a unique group of differentiated meteorites that formed on asteroids with oxygen fugacities (ƒO2) from approximately 2 to approximately 6 log units below the iron-wustite buffer. At these highly reduced conditions, elements deviate from the geochemical behavior exhibited at terrestrial ƒO2, forming FeO-poor silicates and exotic sulfides. While previous studies have described the petrology and 2D modal abundances of aubrites, this work investigates the 3D modal mineralogies of silicate, metal, and sulfide phases in aubrite samples, which are then compared to the available 2D data. In addition to 3D modal mineralogies, we have examined the geochemistry of fourteen aubrites, including mineral major-element compositions, bulk-rock compositions, and oxygen isotopic compositions to understand their formation and evolution at extreme ƒO2 conditions. We utilize X-ray computed tomography (XCT) to non-destructively analyze the distribution and abundances of mineral phases in aubrites and locate composite clasts of sulfide grains for future analytical study. In order to better constrain elemental behavior under reduced conditions, we specifically target minerals phases that comprise moderately volatile elements (i.e. oldhamite [CaS], caswellsilverite [NaCrS2] and djerfisherite [K6Na(Fe,Cu,Ni)25S26Cl]) as it has been shown that their geochemical behavior changes as a function of ƒO2. Currently, we have produced 3D scans of the Norton County aubrite. The results of the XCT data have allowed for the determination of the abundances of silicate groundmass (i.e., enstatite, forsterite, albite, and diopside), light (based on electron density) sulfides (i.e. alabandite [MnS] and daubréelite [FeCr2S4]), heavy (based on electron density) sulfides (i.e., troilite [FeS]), and Fe,Ni metal by segmenting a density histogram in Volume Graphics Studio software. XCT scans of additional aubrites are underway. By combining the 3D representation of the exotic phases found in aubrites with existing 2D characterizations, we are able to better determine modal abundances. By integrating 3D and 2D modal abundances and geochemistry, we can ultimately better constrain aubrite petrogenesis and elemental partitioning under reduced conditions. Furthermore, application of this new 3D approach offers the opportunity to identify and select clasts for future study prior to cutting the sample, which will minimize sample loss of this precious material.

Wilbur, Zoe↗

Charge Exchange of Highly Charged Ne and Mg Ions with H and He

Cross sections for single electron capture (SEC), or charge exchange (CX), in collisions of Ne{sup (8–10)+} and Mg{sup (8–12)+} with H and He, are computed using an approximate multichannel Landau–Zener (MCLZ) formalism. Final-state-resolved cross sections for the principal (n), orbital angular momentum (ℓ), and where appropriate, total spin angular momentum (S) quantum numbers are explicitly computed, except for the incident bare ions Ne{sup 10+} and Mg{sup 12+}. In the latter two cases, nℓ-resolution is obtained from analytical ℓ-distribution functions applied to n-resolved MCLZ cross sections. In all cases, the cross sections are computed over the collision energy range 1 meV/u to 50 keV/u with LZ parameters estimated from atomic energies obtained from experiment, theory, or, in the case of high-lying Rydberg levels, estimated with a quantum defect approach. Errors in the energy differences in the adiabatic potentials at the avoided crossing distances give the largest contribution to the uncertainties in the cross sections, which are expected to increase with decreasing cross section magnitude. The energy differences are deduced here with the Olson–Salop–Tauljberg radial coupling model. Proper selection of an ℓ-distribution function for bare ion collisions introduces another level of uncertainty into the results. Comparison is made to existing experimental or theoretical results when available, but such data are absent for most considered collision systems. The nℓS-resolved SEC cross sections are used in an optically thin cascade simulation to predict X-ray spectra and line ratios that will aid in modeling the X-ray emission in environments where CX is an important mechanism. Details on a MCLZ computational package, Stueckelberg, are also provided.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

A hybrid Monte Carlo, discontinuous Galerkin method for linear kinetic transport equations

Here we present a hybrid method for time-dependent particle transport problems that combines Monte Carlo (MC) estimation with deterministic solutions based on discrete ordinates. For spatial discretizations, the MC algorithm computes a piecewise constant solution and the discrete ordinates use bilinear discontinuous finite elements. From the hybridization of the problem, the resulting problem solved by Monte Carlo is scattering free, resulting in a simple, efficient solution procedure. Between time steps, we use a projection approach to “relabel” collided particles as uncollided particles. In conclusion, from a series of standard 2-D Cartesian test problems we observe that our hybrid method has improved accuracy and reduction in computational complexity of approximately an order of magnitude relative to standard discrete ordinates solutions.

97 MATHEMATICS AND COMPUTING↗

An approximate Kalman filter for ocean data assimilation: An example with an idealized Gulf Stream model

A practical method of data assimilation for use with large, nonlinear, ocean general circulation models is explored. A Kalman filter based on approximation of the state error covariance matrix is presented, employing a reduction of the effective model dimension, the error's asymptotic steady state limit, and a time-invariant linearization of the dynamic model for the error integration. The approximations lead to dramatic computational savings in applying estimation theory to large complex systems. We examine the utility of the approximate filter in assimilating different measurement types using a twin experiment of an idealized Gulf Stream. A nonlinear primitive equation model of an unstable east-west jet is studied with a state dimension exceeding 170,000 elements. Assimilation of various pseudomeasurements are examined, including velocity, density, and volume transport at localized arrays and realistic distributions of satellite altimetry and acoustic tomography observations. Results are compared in terms of their effects on the accuracies of the estimation. The approximate filter is shown to outperform an empirical nudging scheme used in a previous study. The examples demonstrate that useful approximate estimation errors can be computed in a practical manner for general circulation models.

Fukumori, Ichiro↗

An Approximate Kalman Filter for Ocean Data Assimilation; An Example with an Idealized Gulf Stream Model

A practical method of data assimilation for use with large, nonlinear, ocean general circulation models is explored. A Kalman filter based on approximations of the state error covariance matrix is presented, employing a reduction of the effective model dimension, the error's asymptotic steady-state limit, and a time-invariant linearization of the dynamic model for the error integration. The approximations lead to dramatic computational savings in applying estimation theory to large complex systems. We examine the utility of the approximate filter in assimilating different measurement types using a twin experiment of an idealized Gulf Stream. A nonlinear primitive equation model of an unstable east-west jet is studied with a state dimension exceeding 170,000 elements. Assimilation of various pseudo measurements is examined, including velocity, density, and volume transport at localized arrays, and realistic distributions of satellite altimetry and acoustic tomography observations. Results are compared in terms of their effects on the accuracies of the estimation. The approximate filter is shown to outperform a previous study that used an empirical nudging scheme. The examples demonstrate that useful approximate estimation errors can be computed in a practical manner for general circulation models.

['Kalman↗

Rational RBF-based partition of unity method for efficiently and accurately approximating 3D objects

We consider the problem of reconstructing 3D objects via meshfree interpolation methods. In this framework, we usually deal with large data sets and thus develop an efficient local scheme via the well-known partition of unity method. The main contribution in this paper consists in constructing the local interpolants for the implicit interpolation by means of rational radial basis functions. Numerical experiments, devoted to test the accuracy of the scheme, confirm that the proposed method is particularly performing when 3D objects, or more in general implicit functions defined by scattered points, need to be approximated.

97 MATHEMATICS AND COMPUTING↗

Basis adaptive sample efficient polynomial chaos (BASE-PC)

For a large class of orthogonal basis functions, there has been a recent identification of expansion methods for computing accurate, stable approximations of a quantity of interest. Here this paper presents, within the context of uncertainty quantification, a practical implementation using basis adaptation, and coherence motivated sampling, which under assumptions has satisfying guarantees. This implementation is referred to as Basis Adaptive Sample Efficient Polynomial Chaos (BASE-PC). A key component of this is the use of anisotropic polynomial order which admits evolving global bases for approximation in an efficient manner, leading to consistently stable approximation for a practical class of smooth functionals. This fully adaptive, non-intrusive method, requires no a priori information of the solution, and has satisfying theoretical guarantees of recovery. A key contribution to stability is the use of a presented correction sampling for coherence-optimal sampling in order to improve stability and accuracy within the adaptive basis scheme. Theoretically, the method may dramatically reduce the impact of dimensionality in function approximation, and numerically the method is demonstrated to perform well on problems with dimension up to 1000.

97 MATHEMATICS AND COMPUTING↗

FINETUNA: fine-tuning accelerated molecular simulations

Abstract Progress towards the energy breakthroughs needed to combat climate change can be significantly accelerated through the efficient simulation of atomistic systems. However, simulation techniques based on first principles, such as density functional theory (DFT), are limited in their practical use due to their high computational expense. Machine learning approaches have the potential to approximate DFT in a computationally efficient manner, which could dramatically increase the impact of computational simulations on real-world problems. However, they are limited by their accuracy and the cost of generating labeled data. Here, we present an online active learning framework for accelerating the simulation of atomic systems efficiently and accurately by incorporating prior physical information learned by large-scale pre-trained graph neural network models from the Open Catalyst Project. Accelerating these simulations enables useful data to be generated more cheaply, allowing better models to be trained and more atomistic systems to be screened. We also present a method of comparing local optimization techniques on the basis of both their speed and accuracy. Experiments on 30 benchmark adsorbate-catalyst systems show that our method of transfer learning to incorporate prior information from pre-trained models accelerates simulations by reducing the number of DFT calculations by 91%, while meeting an accuracy threshold of 0.02 eV 93% of the time. Finally, we demonstrate a technique for leveraging the interactive functionality built in to Vienna ab initio Simulation Package (VASP) to efficiently compute single point calculations within our online active learning framework without the significant startup costs. This allows VASP to work in tandem with our framework while requiring 75% fewer self-consistent cycles than conventional single point calculations. The online active learning implementation, and examples using the VASP interactive code, are available in the open source FINETUNA package on Github.

97 MATHEMATICS AND COMPUTING↗