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At least 937 records · Page 52

Better together: Elements of successful scientific software development in a distributed collaborative community

Many scientific disciplines rely on computational methods for data analysis, model generation, and prediction. Implementing these methods is often accomplished by researchers with domain expertise but without formal training in software engineering or computer science. This arrangement has led to underappreciation of sustainability and maintainability of scientific software tools developed in academic environments. Some software tools have avoided this fate, including the scientific library Rosetta. We use this software and its community as a case study to show how modern software development can be accomplished successfully, irrespective of subject area. Rosetta is one of the largest software suites for macromolecular modeling, with 3.1 million lines of code and many state-of-the-art applications. Since the mid 1990s, the software has been developed collaboratively by the RosettaCommons, a community of academics from over 60 institutions worldwide with diverse backgrounds including chemistry, biology, physiology, physics, engineering, mathematics, and computer science. Developing this software suite has provided us with more than two decades of experience in how to effectively develop advanced scientific software in a global community with hundreds of contributors. Here we illustrate the functioning of this development community by addressing technical aspects (like version control, testing, and maintenance), community-building strategies, diversity efforts, software dissemination, and user support. We demonstrate how modern computational research can thrive in a distributed collaborative community. The practices described here are independent of subject area and can be readily adopted by other software development communities

97 MATHEMATICS AND COMPUTING↗

Hyper-Differential Sensitivity Analysis of Uncertain Parameters in PDE-Constrained Optimization

Many problems in engineering and sciences require the solution of large scale optimization constrained by partial differential equations (PDEs). Though PDE-constrained optimization is itself challenging, most applications pose additional complexity, namely, uncertain parameters in the PDEs. Uncertainty quantification (UQ) is necessary to characterize, prioritize, and study the influence of these uncertain parameters. Sensitivity analysis, a classical tool in UQ, is frequently used to study the sensitivity of a model to uncertain parameters. In this article, we introduce "hyper-differential sensitivity analysis" which considers the sensitivity of the solution of a PDE-constrained optimization problem to uncertain parameters. Our approach is a goal-oriented analysis which may be viewed as a tool to complement other UQ methods in the service of decision making and robust design. We formally define hyper-differential sensitivity indices and highlight their relationship to the existing optimization and sensitivity analysis literatures. Assuming the presence of low rank structure in the parameter space, computational efficiency is achieved by leveraging a generalized singular value decomposition in conjunction with a randomized solver which converts the computational bottleneck of the algorithm into an embarrassingly parallel loop. Two multi-physics examples, consisting of nonlinear steady state control and transient linear inversion, demonstrate efficient identification of the uncertain parameters which have the greatest influence on the optimal solution.

97 MATHEMATICS AND COMPUTING↗

Primitive numerical simulation of circular Couette flow - Carrousel wind tunnel nonturbulent solutions

The azimuthal-invariant, three-dimensional cylindrical, incompressible Navier-Stokes equations are solved to steady state for a finite-length, physically realistic model. The numerical method relies on an alternating-direction implicit scheme that is formally second-order accurate in space and first-order accurate in time. The equations are linearized and uncoupled by evaluating variable coefficients at the previous time iteration. Wall grid clustering is provided by a Roberts transformation in radial and axial directions. A vorticity-velocity formulation is found to be preferable to a vorticity-streamfunction approach. Subject to no-slip, Dirichlet boundary conditions, except for the inner cylinder rotation velocity (impulsive start-up) and zero-flow initial conditions, nonturbulent solutions are obtained for sub- and supercritical Reynolds numbers of 100 to 400 for a finite geometry where R(outer)/R(inner) = 1.5, H/R(inner) = 0.73, and H/Delta-R = 1.5. An axially-stretched model solution is shown to asymptotically approach the one-dimensional analytic Couette solution at the cylinder midheight. Flowfield change from laminar to Taylor-vortex flow is discussed as a function of Reynolds number. Three-dimensional velocities, vorticity, and streamfunction are presented via two-dimensional graphs and three-dimensional surface and contour plots.

Hasiuk, Jan↗

Stability of propagating modons for small-amplitude perturbations

A stability analysis based on Arnol'd-Liapunov arguments in a gauge-variable formalism is applied to a generalized form of propagating modons. The method was previously applied to the special case of Stern's modon in a quiescent background flow. The analysis presented here shows that propagating-modon solutions in the shallow-water equations are stable to small-amplitude perturbations, regardless of the sign of their translational speed, as long as this is much smaller in magnitude than the solid-rotation speed of the earth. Sufficient conditions for stability are that the given flow be quasigeostrophic, i.e., that the Rossby number be small, and that the associated Froude number be one order of magnitude smaller than the Rossby number.

Sakuma, H.↗

Slow-Neutron Scattering by Rotators. II

The methods developed in a previous paper for extending the neutron scattering formalism of Zemach and Glauber to any type of molecular rotator have been employed to derive generalized forms generalized forms of the differential cross sections for rotator scattering. A mass-ratio expansion for the treatment of the high-energy limit is illustrated on the classical cross section and then employed in the treatment of the more general quantum-mechanical expression for the differential cross section. The results apply to an arbitrarily asymmetric rotator. The very low energy approximation is carried out for the symmetric rotator, and the procedure is compared with the explicit summing of the partial cross sections for individual rotational transitions. The inelastic correction to the static approximation for interference scattering is calculated to an accuracy of first order in the mass ratios for the case of the symmetric rotator.

Volkin, Howard C.↗

Statistical analysis of direct-strike lightning data (1980 to 1982)

Electromagnetic measurements are being made during direct lightning strikes by NASA Langley Center using a specially instrumented F-106B aircraft. The research is to aid refinement, characterization, and understanding of the lightning-aircraft interaction process and the lightning hazards to aircraft. Statistical methods are applied to characterize some aspects of the lightning data obtained from 176 strikes to the aircraft. Specific attention is given to the problem of estimating the upper extreme quantiles of the distributions of peak-to-peak values for currents and rates of change in the magnetic and flux densities. A formal treatment via a general location-scale family of models allows the estimation method to be adapted to the realized shapes the distributions. The shapes are examined by probability plotting methods.

Lee, L. D.↗

Non-oscillatory flux correlation functions for efficient nonadiabatic rate theory

There is currently much interest in the development of improved trajectory-based methods for the simulation of nonadiabatic processes in complex systems. An important goal for such methods is the accurate calculation of the rate constant over a wide range of electronic coupling strengths and it is often the nonadiabatic, weak-coupling limit, which being far from the Born-Oppenheimer regime, provides the greatest challenge to current methods. We show that in this limit there is an inherent sign problem impeding further development which originates from the use of the usual quantum flux correlation functions, which can be very oscillatory at short times. From linear response theory, we derive a modified flux correlation function for the calculation of nonadiabatic reaction rates, which still rigorously gives the correct result in the long-time limit regardless of electronic coupling strength, but unlike the usual formalism is not oscillatory in the weak-coupling regime. In particular, a trajectory simulation of the modified correlation function is naturally initialized in a region localized about the crossing of the potential energy surfaces. In the weak-coupling limit, a simple link can be found between the dynamics initialized from this transition-state region and an generalized quantum golden-rule transition-state theory, which is equivalent to Marcus theory in the classical harmonic limit. This new correlation function formalism thus provides a platform on which a wide variety of dynamical simulation methods can be built aiding the development of accurate nonadiabatic rate theories applicable to complex systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A method of weighted residuals with trigonometric basis functions for sound transmission in circular ducts

The method of weighted residuals (MWR) in the form of a modified Galerkin method with trigonometric basis functions is used to compute the transmission of sound in an axisymmetric duct. The method is used to generate the axial wave number for uniform ducts. These are compared with exact solutions generated by a formal eigenvalue routine in the hard-wall case and a Runge-Kutta integration eigenvalue scheme in the soft-wall case. The method is applicable to both flow and no-flow cases.

Vo, P. T.↗

Example of Occupational Surveillance in a Telemedicine Setting: Application of Epidemiologic Methods at NASA Johnson Space Center

In 2010, NASA implemented Lifetime Surveillance of Astronaut Health, a formal occupational surveillance program for the U.S. astronaut corps. Because of the nature of the space environment, space medicine presents unique challenges and opportunities for epidemiologists. One such example is the use of telemedicine while crewmembers are in flight, where the primary source of information about crew health is verbal communication between physicians and their crewmembers. Due to restricted medical capabilities, the available health information is primarily crewmember report of signs and symptoms, rather than diagnoses. As epidemiologists at NASA, Johnson Space Center, we have shifted our paradigm from tracking diagnoses based on traditional terrestrial clinical practice to one in which we also incorporate reported symptomology as potential antecedents of disease. In this presentation we describe how characterization of reported signs and symptoms can be used to establish incidence rates for inflight immunologic events. We describe interdisciplinary data sources of information that are used in combination with medical information to analyze the data. We also delineate criteria for symptom classification inclusion. Finally, we present incidence tables and graphs to illustrate the final outcomes. Using signs and symptoms reported via telemedicine, the epidemiologists provide summary evidence regarding incidence of potential inflight medical conditions. These results inform our NASA physicians and scientists, and support evaluation of the occupational health risks associated with spaceflight.

Babiak-Vazquez, Adriana↗

Extension of Liouville Formalism to Postinstability Dynamics

A mathematical formalism has been developed for predicting the postinstability motions of a dynamic system governed by a system of nonlinear equations and subject to initial conditions. Previously, there was no general method for prediction and mathematical modeling of postinstability behaviors (e.g., chaos and turbulence) in such a system. The formalism of nonlinear dynamics does not afford means to discriminate between stable and unstable motions: an additional stability analysis is necessary for such discrimination. However, an additional stability analysis does not suggest any modifications of a mathematical model that would enable the model to describe postinstability motions efficiently. The most important type of instability that necessitates a postinstability description is associated with positive Lyapunov exponents. Such an instability leads to exponential growth of small errors in initial conditions or, equivalently, exponential divergence of neighboring trajectories. The development of the present formalism was undertaken in an effort to remove positive Lyapunov exponents. The means chosen to accomplish this is coupling of the governing dynamical equations with the corresponding Liouville equation that describes the evolution of the flow of error probability. The underlying idea is to suppress the divergences of different trajectories that correspond to different initial conditions, without affecting a target trajectory, which is one that starts with prescribed initial conditions.

Zak, Michail↗

Model reduction methods for nuclear emulators

The field of model order reduction (MOR) is growing in importance due to its ability to extract the key insights from complex simulations while discarding computationally burdensome and superfluous information. We provide an overview of MOR methods for the creation of fast & accurate emulators of memory- and compute-intensive nuclear systems, focusing on eigen-emulators and variational emulators. As an example, we describe how 'eigenvector continuation' is a special case of a much more general and well-studied MOR formalism for parameterized systems. We continue with an introduction to the Ritz and Galerkin projection methods that underpin many such emulators, while pointing to the relevant MOR theory and its successful applications along the way. Here, we believe that this guide will open the door to broader applications in nuclear physics and facilitate communication with practitioners in other fields.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

A Wigner Monte Carlo approach to density functional theory

In order to simulate quantum N-body systems, stationary and time-dependent density functional theories rely on the capacity of calculating the single-electron wave-functions of a system from which one obtains the total electron density (Kohn–Sham systems). In this paper, we introduce the use of the Wigner Monte Carlo method in ab-initio calculations. This approach allows time-dependent simulations of chemical systems in the presence of reflective and absorbing boundary conditions. It also enables an intuitive comprehension of chemical systems in terms of the Wigner formalism based on the concept of phase-space. Finally, being based on a Monte Carlo method, it scales very well on parallel machines paving the way towards the time-dependent simulation of very complex molecules. A validation is performed by studying the electron distribution of three different systems, a Lithium atom, a Boron atom and a hydrogenic molecule. For the sake of simplicity, we start from initial conditions not too far from equilibrium and show that the systems reach a stationary regime, as expected (despite no restriction is imposed in the choice of the initial conditions). We also show a good agreement with the standard density functional theory for the hydrogenic molecule. These results demonstrate that the combination of the Wigner Monte Carlo method and Kohn–Sham systems provides a reliable computational tool which could, eventually, be applied to more sophisticated problems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Studying generalised dark matter interactions with extended halo-independent methods

The interpretation of dark matter direct detection experiments is complicated by the fact that neither the astrophysical distribution of dark matter nor the properties of its particle physics interactions with nuclei are known in detail. To address both of these issues in a very general way we develop a new framework that combines the full formalism of non-relativistic effective interactions with state-of-the-art halo-independent methods. This approach makes it possible to analyse direct detection experiments for arbitrary dark matter interactions and quantify the goodness-of-fit independent of astrophysical uncertainties. We employ this method in order to demonstrate that the degeneracy between astrophysical uncertainties and particle physics unknowns is not complete. Certain models can be distinguished in a halo-independent way using a single ton-scale experiment based on liquid xenon, while other models are indistinguishable with a single experiment but can be separated using combined information from several target elements.

79 ASTRONOMY AND ASTROPHYSICS↗

TU-F-18C-05: Evaluation of a Method to Calculate Patient-Oriented MGD Coefficients Using Estimates of Glandular Tissue Distribution

Purpose: Evaluate mammographic mean glandular dose (MGD) coefficients for particular known tissue distributions using a novel formalism that incorporates the effect of the heterogeneous glandular tissue distribution, by comparing them with MGD coefficients derived from the corresponding anthropomorphic computer breast phantom. Methods: MGD coefficients were obtained using MCNP5 simulations with the currently used homogeneous assumption and the heterogeneously-layered breast (HLB) geometry and compared against those from the computer phantom (ground truth). The tissue distribution for the HLB geometry was estimated using glandularity map image pairs corrected for the presence of non-glandular fibrous tissue. Heterogeneity of tissue distribution was quantified using the glandular tissue distribution index, Idist. The phantom had 5 cm compressed breast thickness (MLO and CC views) and 29% whole breast glandular percentage. Results: Differences as high as 116% were found between the MGD coefficients with the homogeneous breast core assumption and those from the corresponding ground truth. Higher differences were found for cases with more heterogeneous distribution of glandular tissue. The Idist for all cases was in the [−0.8{sup −}+0.3] range. The use of the methods presented in this work results in better agreement with ground truth with an improvement as high as 105 pp. The decrease in difference across all phantom cases was in the [9{sup −}105] pp range, dependent on the distribution of glandular tissue and was larger for the cases with the highest Idist values. Conclusion: Our results suggest that the use of corrected glandularity image pairs, as well as the HLB geometry, improves the estimates of MGD conversion coefficients by accounting for the distribution of glandular tissue within the breast. The accuracy of this approach with respect to ground truth is highly dependent on the particular glandular tissue distribution studied. Predrag Bakic discloses current funding from NIH, NSF, and DoD, former funding from Real Time Tomography, LLC and a current research collaboration with Barco and Hologic.

60 APPLIED LIFE SCIENCES↗

Thermo Field Dynamics on a Quantum Computer

In this project we develop a quantum algorithm to realize finite temperature simulation on a quantum computer. As quantum computers use real-time evolution we did not use the imaginary time methods popular on classical algorithms. Instead, we implemented a real-time therom field dynamics formalism, which has the added benefit of being able to compute quantities that are both time-and temperature-dependent. To implement thermo field dynamics we apply a unitary transformation [1] to discrete quantum mechanical operators to make new Hamiltoni-ans with encoded temperature dependence. The method works normally for fermions, which have a finite representation, but needs some modification to work with bosons. These Hamilto-nians are then processed into a Pauli matrix representation in order to be used as input for IBM's Qiskit package [2]. We then use IBM's quantum simulator to calculate an approximation to the Hamiltonaian's ground state energy via the variational quantum eigensolver (VQE) algorithm [3]. This approximation is then compared to a classically calculated value for the exact energy. The thermo field dynamics quantum algorithm has general applications to material science, high-energy physics and nuclear physics, particularly in those situations involving realtime evolution at high temperature.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

General approaches for shear-correcting coordinate transformations in Bragg coherent diffraction imaging. Part I

This two-part article series provides a generalized description of the scattering geometry of Bragg coherent diffraction imaging (BCDI) experiments, the shear distortion effects inherent in the 3D image obtained from presently used methods and strategies to mitigate this distortion. Part I starts from fundamental considerations to present the general real-space coordinate transformation required to correct this shear, in a compact operator formulation that easily lends itself to implementation with available software packages. Such a transformation, applied as a final post-processing step following phase retrieval, is crucial for arriving at an undistorted, correctly oriented and physically meaningful image of the 3D crystalline scatterer. As the relevance of BCDI grows in the field of materials characterization, the available sparse literature that addresses the geometric theory of BCDI and the subsequent analysis methods are generalized here. This geometrical aspect, specific to coherent Bragg diffraction and absent in 2D transmission CDI experiments, gains particular importance when it comes to spatially resolved characterization of 3D crystalline materials in a reliable nondestructive manner. This series of articles describes this theory, from the diffraction in Bragg geometry to the corrections needed to obtain a properly rendered digital image of the 3D scatterer. Part I of this series provides the experimental BCDI community with the general form of the 3D real-space distortions in the phase-retrieved object, along with the necessary post-retrieval correction method. Part II builds upon the geometric theory developed in Part I with the formalism to correct the shear distortions directly on an orthogonal grid within the phase-retrieval algorithm itself, allowing more physically realistic constraints to be applied. Taken together, Parts I and II provide the X-ray science community with a set of generalized BCDI shear-correction techniques crucial to the final rendering of a 3D crystalline scatterer and for the development of new BCDI methods and experiments.

36 MATERIALS SCIENCE↗

Ultrafast nonequilibrium evolution of excitonic modes in semiconductors

We study the time evolution of excitonic states after photoexcitation in the one-dimensional spinless extended Falicov-Kimball model. Several numerical methods are employed and benchmarked against each other: time-dependent mean-field simulations, the second-Born approximation (2BA) within the Kadanoff-Baym formalism, the generalized Kadanoff-Baym ansatz (GKBA) implemented with the 2BA, and the infinite time-evolving block decimation (iTEBD) method. It is found that the GKBA gives the best agreement with iTEBD and captures the relevant physics. Excitations to the particle-hole continuum and resonant excitations of the equilibrium exciton result in a qualitatively different dynamics. In the former case, the exciton binding energy remains positive and the frequency of the corresponding coherent oscillations is smaller than the band gap. On the other hand, resonant excitations trigger a collective mode whose frequency is larger than the band gap. We discuss the origin of these different behaviors by evaluating the nonequilibrium susceptibility using the nonthermal distribution and a random phase approximation. We note the peculiar mode with frequency larger than the band gap is associated with a partial population inversion with a sharp energy cutoff. We also discuss the effects of the cooling by a phonon bath. We demonstrate the real-time development of coherence in the polarization, which indicates excitonic condensation out of equilibrium.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Unified theory of effective interaction

We present a unified description of effective interaction theories in both algebraic and graphic representations. In our previous work, we have presented the Rayleigh–Schrödinger and Bloch perturbation theories in a unified fashion by introducing the main frame expansion of the effective interaction. In this work, we start also from the main frame expansion, and present various nonperturbative theories in a coherent manner, which include generalizations of the Brandow, Brillouin–Wigner, and Bloch–Horowitz theories on the formal side, and the extended Krenciglowa–Kuo and the extended Lee–Suzuki methods on the practical side. We thus establish a coherent and comprehensive description of both perturbative and nonperturbative theories on the basis of the main frame expansion.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗