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At least 1,369 records · Page 76

Quantification of Ebola virus replication kinetics in vitro

Mathematical modelling has successfully been used to provide quantitative descriptions of many viral infections, but for the Ebola virus, which requires biosafety level 4 facilities for experimentation, modelling can play a crucial role. Ebola virus modelling efforts have primarily focused on in vivo virus kinetics, e.g., in animal models, to aid the development of antivirals and vaccines. But, thus far, these studies have not yielded a detailed specification of the infection cycle, which could provide a foundational description of the virus kinetics and thus a deeper understanding of their clinical manifestation. Here, we obtain a diverse experimental data set of the Ebola virus infection in vitro, and then make use of Bayesian inference methods to fully identify parameters in a mathematical model of the infection. Our results provide insights into the distribution of time an infected cell spends in the eclipse phase (the period between infection and the start of virus production), as well as the rate at which infectious virions lose infectivity. We suggest how these results can be used in future models to describe co-infection with defective interfering particles, which are an emerging alternative therapeutic.

59 BASIC BIOLOGICAL SCIENCES↗

Selected Uses of TSUNAMI in Critical Experiment Design and Analysis

Validation in criticality safety is performed by comparing the results of critical experiments with the calculated results from models of the experiments using the computational method to be validated. Laboratory critical experiments are controlled systems that achieve a k eff of approximately 1 and enable investigation of the parameters at which such a critical condition is achieved. For the critical experiments used in a validation to capture the biases of the materials and neutron energy spectra of interest, those materials must be included in the experiment such that they influence k eff or another observable parameter with statistical significance. This paper discusses the use of sensitivity uncertainty (S/U) methods to develop critical experiments for various purposes. S/U techniques are useful for understanding the underlying components of nuclear data which affect the k eff or another parameter of a given configuration. S/U calculations are most commonly used to compare existing experiments to applications of interest; however, S/U techniques can also be used to identify, optimize, or assess features of proposed experiments so that they can better test specific portions of nuclear data or match an application of interest. The S/U techniques discussed here are from the TSUNAMI code system. The two primary codes discussed in this work are TSUNAMI-3D, which implements the KENO criticality code to calculate the sensitivity of k eff to nuclear data, and TSAR, which calculates the sensitivity of a reactivity difference between two configurations based on their TSUNAMI-3D generated sensitivity profiles. The methods used in these tools are discussed in more detail in the SCALE manual. This paper is one of a series on the development and use of TSUNAMI tools. The other papers address development of TSUNAMI methods and a review of TSUNAMI applications.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

GPU Acceleration of Mean Free Path Based Kernel Density Estimators for Monte Carlo Neutronics Simulations

Kernel Density Estimators (KDEs) are a non-parametric density estimation technique that has recently been applied to Monte Carlo radiation transport simulations. Kernel density estimators are an alternative to histogram tallies for obtaining global solutions in Monte Carlo tallies. With KDEs, a single event, either a collision or particle track, can contribute to the score at multiple tally points with the uncertainty at those points being independent of the desired resolution of the solution. Thus, KDEs show potential for obtaining estimates of a global solution with reduced variance when compared to a histogram. Previously, KDEs have been applied to neutronics for one-group reactor physics problems and fixed source shielding applications. However, little work was done to obtain reaction rates using KDEs. This paper introduces a new form of the MFP KDE that is capable of handling general geometries. Furthermore, extending the MFP KDE to 2-D problems in continuous energy introduces inaccuracies to the solution. An ad-hoc solution to these inaccuracies is introduced that produces errors smaller than 4% at material interfaces.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Formal methods for life-critical software

The use of computer software in life-critical applications, such as for civil air transports, demands the use of rigorous formal mathematical verification procedures. This paper demonstrates how to apply formal methods to the development and verification of software by leading the reader step-by-step through requirements analysis, design, implementation, and verification of an electronic phone book application. The current maturity and limitations of formal methods tools and techniques are then discussed, and a number of examples of the successful use of formal methods by industry are cited.

Butler, Ricky W.↗

Formal Methods for Life-Critical Software

The use of computer software in life-critical applications, such as for civil air transports, demands the use of rigorous formal mathematical verification procedures. This paper demonstrates how to apply formal methods to the development and verification of software by leading the reader step-by-step through requirements analysis, design, implementation, and verification of an electronic phone book application. The current maturity and limitations of formal methods tools and techniques are then discussed, and a number of examples of the successful use of formal methods by industry are cited.

Butler, Ricky W.↗

Computer Science Research Needs for Parallel Discrete Event Simulation (PDES)

Historically, scientific computing efforts have demonstrated the clear need for, and effective use of, supercomputing with traditional time-stepped simulations. Nevertheless, there are several areas in the mission spaces of the U.S. Department of Energy and other agencies waiting to tap advanced computing research using a different, discrete event style of modeling, simulation, and analysis. These span a wide spectrum of applications including energy grid resilience, urban planning and policy, transportation science, building technologies, emergency response and planning, environmental impact analysis, computational epidemiology, Internet communications, cyber security, and cyber-physical systems, to name only a few. Even within traditional scientific applications, the role of discrete event modes of execution is increasing in the form of new event-based mathematical solvers such as quantized state integration methods and discrete-continuous hybrid system solvers. Co-design of advanced supercomputing hardware systems is another area that exploits discrete event simulation at its core for effective analyses. Complex systems, entity behaviors and interconnections play a significant role in all these applications, which are mapped to large-scale models with discrete event formulations.

97 MATHEMATICS AND COMPUTING↗

Application of Monte Carlo techniques to optimization of high-energy beam transport in a stochastic environment

An algorithm employing a modified sequential random perturbation, or creeping random search, was applied to the problem of optimizing the parameters of a high-energy beam transport system. The stochastic solution of the mathematical model for first-order magnetic-field expansion allows the inclusion of state-variable constraints, and the inclusion of parameter constraints allowed by the method of algorithm application eliminates the possibility of infeasible solutions. The mathematical model and the algorithm were programmed for a real-time simulation facility; thus, two important features are provided to the beam designer: (1) a strong degree of man-machine communication (even to the extent of bypassing the algorithm and applying analog-matching techniques), and (2) extensive graphics for displaying information concerning both algorithm operation and transport-system behavior. Chromatic aberration was also included in the mathematical model and in the optimization process. Results presented show this method as yielding better solutions (in terms of resolutions) to the particular problem than those of a standard analog program as well as demonstrating flexibility, in terms of elements, constraints, and chromatic aberration, allowed by user interaction with both the algorithm and the stochastic model. Example of slit usage and a limited comparison of predicted results and actual results obtained with a 600 MeV cyclotron are given.

Parrish, R. V.↗

Accumulated approximation: A new method for structural optimization by iterative improvement

A new method for the solution of non-linear mathematical programming problems in the field of structural optimization is presented. It is an iterative scheme which for each iteration refines the approximation of objective and constraint functions by accumulating the function values of previously visited design points. The method has proven to be competitive for a number of well-known examples of which one is presented here. Furthermore because of the accumulation strategy, the method produces convergence even when the sensitivity analysis is inaccurate.

Rasmussen, John↗

Classifying photonic topology using the spectral localizer and numerical K -theory

Recently, the spectral localizer framework has emerged as an efficient approach for classifying topology in photonic systems featuring local nonlinearities and radiative environments. In nonlinear systems, this framework provides rigorous definitions for concepts such as topological solitons and topological dynamics, where a system’s occupation induces a local change in its topology due to nonlinearity. For systems embedded in radiative environments that do not possess a shared bulk spectral gap, this framework enables the identification of local topology and shows that local topological protection is preserved despite the lack of a common gap. However, as the spectral localizer framework is rooted in the mathematics of C*-algebras, and not vector bundles, understanding and using this framework requires developing intuition for a somewhat different set of underlying concepts than those that appear in traditional approaches for classifying material topology. In this tutorial, we introduce the spectral localizer framework from a ground-up perspective and provide physically motivated arguments for understanding its local topological markers and associated local measure of topological protection. In doing so, we provide numerous examples of the framework’s application to a variety of topological classes, including crystalline and higher-order topology. We then show how Maxwell’s equations can be reformulated to be compatible with the spectral localizer framework, including the possibility of radiative boundary conditions. To aid in this introduction, we also provide a physics-oriented introduction to multi-operator pseudospectral methods and numerical K-theory, two mathematical concepts that form the foundation for the spectral localizer framework. Finally, we provide some mathematically oriented comments on the C*-algebraic origins of this framework, including a discussion of real C*-algebras and graded C*-algebras that are necessary for incorporating physical symmetries. Looking forward, we hope that this tutorial will serve as an approachable starting point for learning the foundations of the spectral localizer framework.

97 MATHEMATICS AND COMPUTING↗

A relaxed two-step splitting iteration method for computing PageRank

In this paper, we extend the two-step matrix splitting iteration approach by introducing a new relaxation parameter. The main idea is based on the inner–outer iteration for solving the PageRank problems proposed by Gleich et al. (J Sci Comput 32(1): 349–371, 2010) and Bai (Numer Algebra Cont Optim 2(4): 855–862, 2012) and the two-step splitting iteration presented by Gu et al. (Appl Math Comput 271: 337–343, 2015). The theoretical analysis results show that the proposed method is efficient. Numerical experiments demonstrate that the convergence performances of the method are better than the existing methods.

97 MATHEMATICS AND COMPUTING↗

Dynamics of a split torque helicopter transmission

Split torque designs, proposed as alternatives to traditional planetary designs for helicopter main rotor transmissions, can save weight and be more reliable than traditional designs. This report presents the results of an analytical study of the system dynamics and performance of a split torque gearbox that uses a balance beam mechanism for load sharing. The Lagrange method was applied to develop a system of equations of motion. The mathematical model includes time-varying gear mesh stiffness, friction, and manufacturing errors. Cornell's method for calculating the stiffness of spur gear teeth was extended and applied to helical gears. The phenomenon of sidebands spaced at shaft frequencies about gear mesh fundamental frequencies was simulated by modeling total composite gear errors as sinusoid functions. Although the gearbox has symmetric geometry, the loads and motions of the two power paths differ. Friction must be considered to properly evaluate the balance beam mechanism. For the design studied, the balance beam is not an effective device for load sharing unless the coefficient of friction is less than 0.003. The complete system stiffness as represented by the stiffness matrix used in this analysis must be considered to precisely determine the optimal tooth indexing position.

Krantz, Timothy L.↗

Formulation analysis and computation of an optimization-based local-to-nonlocal coupling method

We present an optimization-based coupling method for local and nonlocal continuum models. Our approach couches the coupling of the models into a control problem where the states are the solutions of the nonlocal and local equations, the objective is to minimize their mismatch on the overlap of the local and nonlocal problem domains, and the virtual controls are the nonlocal volume constraint and the local boundary condition. We present the method in the context of Local-to-Nonlocal diffusion coupling. Numerical examples illustrate the theoretical properties of the approach.

97 MATHEMATICS AND COMPUTING↗

The solution of coupled Schroedinger equations using an extrapolation method

In this paper, extrapolation to the limit in a finite-difference method is applied to solve a system of coupled Schroedinger equations. This combination results in a method that only requires knowledge of the potential energy functions for the system. This numerical procedure has several distinct advantages over the more conventional methods. Namely, initial guesses for the term values are not needed; assumptions need be made about the behavior of the wavefunctions, such as the slope or magnitude in the nonclassical region; and the algorithm is easy to implement, has a firm mathematical foundation, and provides error estimates. Moreover, the method is less sensitive to round-off error than other methods since a small number of mesh points is used and it can be implemented on small computers. A comparison of the method with another numerical method shows results agreeing within 1 part in 10 exp 4.

Goorvitch, D.↗

A Review of TSUNAMI Applications

The TSUNAMI-1D and TSUNAMI-3D sequences for generating k eff sensitivity coefficients were first released in SCALE 5 in 2004. Several other tools were introduced in the same release, including primarily the TSUNAMI-IP code for uncertainty analysis and similarity assessments. The TSUNAMI sequences added capabilities for identifying important reactions and data for systems using sensitivity coefficients and also introduced new quantitative tools for rigorously assessing the similarity of systems. Over time, the capabilities of these tools have grown, and their use has expanded into other areas such as nuclear data assessment and nuclear covariance data testing. This paper discusses applications of the TSUNAMI tools for sensitivity calculations, sensitivity/uncertainty (S/U)-based validation, and nuclear data testing. This paper is one of a series of papers at this conference on the development and use of TSUNAMI tools. The other papers address the development of the TSUNAMI methods and the use of TSUNAMI for critical experiment design and optimization.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Results and Responses for the 2022 User Forum Survey [Slides]

This presentation discusses the results of a MCNP user survey. Example of questions asked include: "Which MCNP particle types do you typically use?," "What sort of simulations do you run most often?," "Do you build the code?," "Which variance reduction methods do you use?," "Opinions on HDF5," with frequent discussions regarding each question.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗