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The Pines method for trajectory integration is derived from the equations of two-body motion. The concept of the perturbation derivative is explained and a formal definition is presented. An algorithm for applying the Pines method to numerical integration of trajectories is included.
A computational method is proposed to obtain rotational transition probabilities in collisions between two diatomic molecules. The potential method of Rabitz and an exponential approximation are used to solve the semiclassical coupled equations without invoking any perturbational technique. The collision trajectory is determined in the classical modified-wave-number approximation. The method can treat systems involving strong interactions and provide probabilities for transitions even with a multiquantum jump. A simultaneous transition in the rotational states of both molecules, i.e., the rotational-rotational energy transfer, is taken into account. An application to the system N2 + N2 is presented.
Dysregulation of normal transcription factor activity is a common driver of disease. Therefore, the detection of aberrant transcription factor activity is important to understand disease pathogenesis. We have developed Priori, a method to predict transcription factor activity from RNA sequencing data. Priori has two key advantages over existing methods. First, Priori utilizes literature-supported regulatory information to identify transcription factor-target gene relationships. It then applies linear models to determine the impact of transcription factor regulation on the expression of its target genes. Second, results from a third-party benchmarking pipeline reveals that Priori detects aberrant activity from 124 single-gene perturbation experiments with higher sensitivity and specificity than 11 other methods. We applied Priori and other top-performing methods to predict transcription factor activity from two large primary patient datasets. Our work demonstrates that Priori uniquely discovered significant determinants of survival in breast cancer and identified mediators of drug response in leukemia.
In earlier papers, Doedel and the authors have developed a numerical method and derived error estimates for the computation of branches of heteroclinic orbits for a system of autonomous ordinary differential equations in R(exp n). The idea of the method is to reduce a boundary value problem on the real line to a boundary value problem on a finite interval by using a local (linear or higher order) approximation of the stable and unstable manifolds. A practical limitation for the computation of homoclinic and heteroclinic orbits has been the difficulty in obtaining starting orbits. Typically these were obtained from a closed form solution or via a homotopy from a known solution. Here we consider extensions of our algorithm which allow us to obtain starting orbits on the continuation branch in a more systematic way as well as make the continuation algorithm more flexible. In applications, we use the continuation software package AUTO in combination with some initial value software. The examples considered include computation of homoclinic orbits in a singular perturbation problem and in a turbulent fluid boundary layer in the wall region problem.
This article describes a method for calculating higher order or nonadiabatic corrections in Born–Oppenheimer theory and its interaction with the translational degrees of freedom. The method uses the Wigner–Weyl correspondence to map nuclear operators into functions on the classical phase space and the Moyal star product to represent operator multiplication on those functions. These are explained in the body of the paper. The result is a power series in κ 2 , where κ = (m/M)1/4 is the usual Born–Oppenheimer parameter. The lowest order term is the usual Born–Oppenheimer approximation, while higher order terms are nonadiabatic corrections. These are needed in calculations of electronic currents, momenta, and densities. The separation of nuclear and electronic degrees of freedom takes place in the context of the exact symmetries (for an isolated molecule) of translations and rotations, and these, especially translations, are explicitly incorporated into our discussion. This article presents an independent derivation of the Moyal expansion in molecular Born–Oppenheimer theory. Here, we show how electronic currents and momenta can be calculated within the framework of Moyal perturbation theory; we derive the transformation laws of the electronic Hamiltonian, the electronic eigenstates, and the derivative couplings under translations; we discuss in detail the rectilinear motion of the molecular center of mass in the Born–Oppenheimer representation; and we show how the elimination of the translational components of the derivative couplings leads to a unitary transformation that has the effect of exactly separating the translational degrees of freedom.
We propose a novel method for evaluating sensitivity coefficients of neutronics parameters to cross sections, so-called the reduced-order modeling technique ROM-Lasso. In this method, cross sections of interest are randomly sampled, and corresponding perturbed core analyses are performed. Then, the sensitivity coefficient vector of the higher-level model is expanded via the active subspace bases obtained with the lower-level model whose dimensional complexity is smaller than that of the higher-level model, and the expansion coefficients are estimated by the Lasso regression. A unique feature of the ROM-Lasso method allows the use of different bases optimized for each neutronics parameter. We conducted a verification calculation for an accelerator-driven system and demonstrated that the ROM-Lasso method can reproduce the sensitivity coefficients with a much smaller number of forward calculations than the direct method. The proposed method can be used to practically evaluate sensitivity coefficients. (authors)
The proposed paper presents a variety novel uses of Space-Filling-Curves (SFCs) for Cartesian mesh methods in 0. While these techniques will be demonstrated using non-body-fitted Cartesian meshes, most are applicable on general body-fitted meshes -both structured and unstructured. We demonstrate the use of single O(N log N) SFC-based reordering to produce single-pass (O(N)) algorithms for mesh partitioning, multigrid coarsening, and inter-mesh interpolation. The intermesh interpolation operator has many practical applications including warm starts on modified geometry, or as an inter-grid transfer operator on remeshed regions in moving-body simulations. Exploiting the compact construction of these operators, we further show that these algorithms are highly amenable to parallelization. Examples using the SFC-based mesh partitioner show nearly linear speedup to 512 CPUs even when using multigrid as a smoother. Partition statistics are presented showing that the SFC partitions are, on-average, within 10% of ideal even with only around 50,000 cells in each subdomain. The inter-mesh interpolation operator also has linear asymptotic complexity and can be used to map a solution with N unknowns to another mesh with M unknowns with O(max(M,N)) operations. This capability is demonstrated both on moving-body simulations and in mapping solutions to perturbed meshes for finite-difference-based gradient design methods.
Two major advancements of an aerodynamic optimization method with two design variables are described. The first is represnted by an improved flow prediction method that uses the third-order accurate discretization of the Euler equations. This method makes it possible to predict the flowfield of a perturbed shape which generates shocks and other large gradients without intermediate CFD analysis. The second advancement is the use of every surface grid point as a design variable in the aerodynamic shape optimization problem. The improved algorithm is demonstrated by optimizing the ramp shape of a scramjet-afterbody configuration for maximum axial thrust. It is concluded that the improved flow-field prediction method eliminates most of the flow analysis and a priori guessing of all possible shapes from which the optimum is to be selected.
The aerospace industry has a need for new metallic alloys that are lightweight and have high strength at elevated temperatures. The BFS (Bozzolo, Ferrante, and Smith) method is a new, computationally efficient and physically sound quantum semi-perturbative approach for describing metals and their defects. Based on a simple interpretation of the alloy formation process that identifies strain and chemical contributions to the energy of the alloy, the method provides an atom-by-atom description of an alloy. Its implementation requires little more than algebra and the solution of transcendental equations. At the NASA Lewis Research Center, we have demonstrated that BFS can investigate the properties of a large number of alloys with a minimum computational effort on low-level computers. This screening allows the selection of the best alloy candidates for a particular application and, therefore, promises large cost savings over current approaches.
The propagation of charged particles through interstellar and interplanetary space has often been described as a random process in which the particles are scattered by ambient electromagnetic turbulence. In general, this changes both the magnitude and direction of the particles' momentum. Some situations for which scattering in direction (pitch angle) is of primary interest were studied. A perturbed orbit, resonant scattering theory for pitch-angle diffusion in magnetostatic turbulence was slightly generalized and then utilized to compute the diffusion coefficient for spatial propagation parallel to the mean magnetic field, Kappa. All divergences inherent in the quasilinear formalism when the power spectrum of the fluctuation field falls off as K to the minus Q power (Q less than 2) were removed. Various methods of computing Kappa were compared and limits on the validity of the theory discussed. For Q less than 1 or 2, the various methods give roughly comparable values of Kappa, but use of perturbed orbits systematically results in a somewhat smaller Kappa than can be obtained from quasilinear theory.
The use of Green's function has played a fundamental role in transport calculations for high-charge high-energy (HZE) ions. Two recent developments have greatly advanced the practical aspects of implementation of these methods. The first was the formulation of a closed-form solution as a multiple fragmentation perturbation series. The second was the effective summation of the closed-form solution through nonperturbative techniques. The nonperturbative methods have been recently extended to an inhomogeneous, two-layer transport media to simulate the lead scattering foil present in the Lawrence Berkeley Laboratories (LBL) biomedical beam line used for cancer therapy. Such inhomogeneous codes are necessary for astronaut shielding in space. The transport codes utilize the Langley Research Center atomic and nuclear database. Transport code and database evaluation are performed by comparison with experiments performed at the LBL Bevalac facility using 670 A MeV 20Ne and 600 A MeV 56Fe ion beams. The comparison with a time-of-flight and delta E detector measurement for the 20Ne beam and the plastic nuclear track detectors for 56Fe show agreement up to 35%-40% in water and aluminium targets, respectively.
Angular cosmological correlators are infamously difficult to compute due to the highly oscillatory nature of the projection integrals. Motivated by recent development on analytic approaches to cosmological perturbation theory, in this paper we present an efficient method for computing cosmological four-point correlations in angular space, generalizing previous works on lower-point functions. This builds on the FFTLog algorithm that approximates the matter power spectrum as a sum over power-law functions, which makes certain momentum integrals analytically solvable. The computational complexity is drastically reduced for correlators in a "separable" form—we define a suitable notion of separability for cosmological trispectra, and derive formulas for angular correlators of different separability classes. As an application of our formalism, we compute the angular galaxy trispectrum at tree level, with and without primordial non-Gaussianity. This includes effects of redshift space distortion and bias parameters up to cubic order. We also compute the non-Gaussian covariance of the angular matter power spectrum due to the connected four-point function, beyond the Limber approximation. Finally, we demonstrate that, in contrast to the standard lore, the Limber approximation can fail for the non-Gaussian covariance computation even for large multipoles.
A parallel algorithm for the efficient solution of nonlinear time-dependent convection-diffusion equations with small parameter on the diffusion term is presented. The method is based on a physically motivated domain decomposition that is dictated by singular perturbation analysis. The analysis is used to determine regions where certain reduced equations may be solved in place of the full equation. The method is suitable for the solution of problems arising in the simulation of fluid dynamics. Experimental results for a nonlinear equation in two-dimensions are presented.
An external 3D magnetic perturbation typically drives a resonant response at the rational surfaces from the core to the edge of tokamak plasmas, due to strong mode coupling and amplification. In this paper, we present a method to isolate the edge from core resonant fields using the ideal perturbed equilibrium code and to design an edge-localized resonant magnetic perturbation (RMP) for effective edge localized mode (ELM) control. A robust feature of the edge-localized RMP is the curtailed response to the field at the low-field-side (LFS) midplane, as opposed to typical RMPs which strongly resonate with the LFS fields. This emphasizes the importance of off-midplane coils to improve ELM control without provoking a large core response that could lead to devastating instabilities. The conceptual design of new ELM control coils based on the edge-localized RMP in KSTAR shows how this new insight can be utilized to enhance the efficiency of our ELM suppression capabilities. Simple window-pane coils matching the edge-localized resonant mode structure substantially expand in the ELM suppression window beyond the existing coil. Further optimization using the flexible optimized coils using space-curves code leads to additional enhancement in the edge-localized control.
The development of high-order accurate numerical discretization techniques for irregular domains and meshes is often cited as one of the remaining challenges facing the field of computational fluid dynamics. In structural mechanics, the advantages of high-order finite element approximation are widely recognized. This is especially true when high-order element approximation is combined with element refinement (h-p refinement). In computational fluid dynamics, high-order discretization methods are infrequently used in the computation of compressible fluid flow. The hyperbolic nature of the governing equations and the presence of solution discontinuities makes high-order accuracy difficult to achieve. Consequently, second-order accurate methods are still predominately used in industrial applications even though evidence suggests that high-order methods may offer a way to significantly improve the resolution and accuracy for these calculations. To address this important topic, a special course was jointly organized by the Applied Vehicle Technology Panel of NATO's Research and Technology Organization (RTO), the von Karman Institute for Fluid Dynamics, and the Numerical Aerospace Simulation Division at the NASA Ames Research Center. The NATO RTO sponsored course entitled "Higher Order Discretization Methods in Computational Fluid Dynamics" was held September 14-18, 1998 at the von Karman Institute for Fluid Dynamics in Belgium and September 21-25, 1998 at the NASA Ames Research Center in the United States. During this special course, lecturers from Europe and the United States gave a series of comprehensive lectures on advanced topics related to the high-order numerical discretization of partial differential equations with primary emphasis given to computational fluid dynamics (CFD). Additional consideration was given to topics in computational physics such as the high-order discretization of the Hamilton-Jacobi, Helmholtz, and elasticity equations. This volume consists of five articles prepared by the special course lecturers. These articles should be of particular relevance to those readers with an interest in numerical discretization techniques which generalize to very high-order accuracy. The articles of Professors Abgrall and Shu consider the mathematical formulation of high-order accurate finite volume schemes utilizing essentially non-oscillatory (ENO) and weighted essentially non-oscillatory (WENO) reconstruction together with upwind flux evaluation. These formulations are particularly effective in computing numerical solutions of conservation laws containing solution discontinuities. Careful attention is given by the authors to implementational issues and techniques for improving the overall efficiency of these methods. The article of Professor Cockburn discusses the discontinuous Galerkin finite element method. This method naturally extends to high-order accuracy and has an interpretation as a finite volume method. Cockburn addresses two important issues associated with the discontinuous Galerkin method: controlling spurious extrema near solution discontinuities via "limiting" and the extension to second order advective-diffusive equations (joint work with Shu). The articles of Dr. Henderson and Professor Schwab consider the mathematical formulation and implementation of the h-p finite element methods using hierarchical basis functions and adaptive mesh refinement. These methods are particularly useful in computing high-order accurate solutions containing perturbative layers and corner singularities. Additional flexibility is obtained using a mortar FEM technique whereby nonconforming elements are interfaced together. Numerous examples are given by Henderson applying the h-p FEM method to the simulation of turbulence and turbulence transition.
The tropical upper troposphere and lower stratosphere (UTLS) region is dominated by aerosols and clouds affecting Earth’s radiation budget and climate. Thus, satellites’ continuous monitoring and identification of these layers is crucial for quantifying their radiative impact. However, distinguishing between aerosols and clouds is challenging, especially under the perturbed UTLS conditions during post-volcanic eruptions and wildfire events. Aerosol-cloud discrimination is primarily based on their disparate wavelength-dependent scattering and absorption properties. In this study, we use aerosol extinction observations in the tropical (15°N-15°S) UTLS from June 2017 to February 2021, available from the latest generation of the Stratospheric Aerosol and Gas Experiment (SAGE) instrument-SAGE III onboard the International Space Station (ISS) to study aerosols and clouds. During this period, the SAGE III/ISS provided better coverage over the tropics at additional wavelength channels (relative to previous SAGE missions) and witnessed several volcanic and wildfire events that perturbed the tropical UTLS. We explore the advantage of having an extinction coefficient at an additional wavelength channel (1550 nm) from the SAGE III/ISS in aerosol-cloud discrimination using a method based on thresholds of two extinction coefficient ratios, R1R1 (520 nm/1020 nm) and R2R2 (1020 nm/1550 nm). This method was proposed earlier by Kent et al. [Appl. Opt. 36, 8639 (1997) [CrossRef] ] for the SAGE III-Meteor-3M but was never tested for the tropical region under volcanically perturbed conditions. We call this method the Extinction Color Ratio (ECR) method. The ECR method is applied to the SAGE III/ISS aerosol extinction data to obtain cloud-filtered aerosol extinction coefficients, cloud-top altitude, and seasonal cloud occurrence frequency during the entire study period. Cloud-filtered aerosol extinction coefficient obtained using the ECR method revealed the presence of enhanced aerosols in the UTLS following volcanic eruptions and wildfire events consistent with the Ozone Mapping and Profiler Suite (OMPS) and space-borne lidar-Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP). The cloud-top altitude obtained from the SAGE III/ISS is within 1 km of the nearly co-located observations from OMPS and CALIOP. In general, the seasonal mean cloud-top altitude from the SAGE III/ISS events peaks during the December, January, and February months, with sunset events showing higher cloud tops than the sunrise events, indicating the seasonal and diurnal variation of the tropical convection. The seasonal altitude distribution of cloud occurrence frequency obtained from the SAGE III/ISS also agrees well with CALIOP observations within 10%. We show that the ECR method is a simple approach that relies on thresholds independent of the sampling period, providing cloud-filtered aerosol extinction coefficients uniformly for climate studies irrespective of the UTLS conditions. However, since the predecessor of SAGE III did not include a 1550 nm channel, the usefulness of this approach is limited to short-term climate studies after 2017.
An analysis of instability dynamics in a stochastic magnetic field is presented for the tractable case of the resistive interchange. Externally prescribed static magnetic perturbations convert the eigenmode problem to a stochastic differential equation, which is solved by the method of averaging. The dynamics are rendered multi-scale, due to the size disparity between the test mode and magnetic perturbations. Maintaining quasi-neutrality at all orders requires that small-scale convective cell turbulence be driven by disparate scale interaction. Here, the cells in turn produce turbulent mixing of vorticity and pressure, which is calculated by fluctuation-dissipation type analyses, and are relevant to pump-out phenomena. The development of correlation between the ambient magnetic perturbations and the cells is demonstrated, showing that turbulence will 'lock on' to ambient stochasticity. Magnetic perturbations are shown to produce a magnetic braking effect on vorticity generation at large scale. Detailed testable predictions are presented. The relations of these findings to the results of available simulations and recent experiments are discussed.
In this work, we introduce a differentiable implementation of the local natural orbital coupled cluster (LNO-CC) method within the automatic differentiation framework of the PySCFAD package. The implementation is comprehensively tuned for enhanced performance, which enables the calculation of first-order static response properties on medium-sized molecular systems using coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. We evaluate the accuracy of our method by benchmarking it against the canonical CCSD(T) reference for nuclear gradients, dipole moments, and geometry optimizations. In addition, we demonstrate the possibility of property calculations for chemically interesting systems through the computation of bond orders and Mössbauer spectroscopy parameters for a [NiFe]-hydrogenase active site model, along with the simulation of infrared spectra via ab initio LNO-CC molecular dynamics for a protonated water hexamer.