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At least 307 records · Page 17

solveME: fast and reliable solution of nonlinear ME models

Background Genome-scale models of metabolism and macromolecular expression (ME) significantly expand the scope and predictive capabilities of constraint-based modeling. ME models present considerable computational challenges: they are much (>30 times) larger than corresponding metabolic reconstructions (M models), are multiscale, and growth maximization is a nonlinear programming (NLP) problem, mainly due to macromolecule dilution constraints. Results Here, we address these computational challenges. We develop a fast and numerically reliable solution method for growth maximization in ME models using a quad-precision NLP solver (Quad MINOS). Our method was up to 45 % faster than binary search for six significant digits in growth rate. We also develop a fast, quad-precision flux variability analysis that is accelerated (up to 60× speedup) via solver warm-starts. Finally, we employ the tools developed to investigate growth-coupled succinate overproduction, accounting for proteome constraints. Conclusions Just as genome-scale metabolic reconstructions have become an invaluable tool for computational and systems biologists, we anticipate that these fast and numerically reliable ME solution methods will accelerate the wide-spread adoption of ME models for researchers in these fields.

Biochemistry & Molecular Biology↗

Maximum likelihood identification of aircraft stability and control derivatives

Application of a generalized identification method to flight test data analysis. The method is based on the maximum likelihood (ML) criterion and includes output error and equation error methods as special cases. Both the linear and nonlinear models with and without process noise are considered. The flight test data from lateral maneuvers of HL-10 and M2/F3 lifting bodies are processed to determine the lateral stability and control derivatives, instrumentation accuracies, and biases. A comparison is made between the results of the output error method and the ML method for M2/F3 data containing gusts. It is shown that better fits to time histories are obtained by using the ML method. The nonlinear model considered corresponds to the longitudinal equations of the X-22 VTOL aircraft. The data are obtained from a computer simulation and contain both process and measurement noise. The applicability of the ML method to nonlinear models with both process and measurement noise is demonstrated.

Mehra, R. K.↗

A reduced-order model for nonlinear radiative transfer problems based on moment equations and POD-Petrov-Galerkin projection of the normalized Boltzmann transport equation

A data-driven projection-based reduced-order model (ROM) for nonlinear thermal radiative transfer (TRT) problems is presented. The TRT ROM is formulated by (i) a hierarchy of low-order quasidiffusion (aka variable Eddington factor) equations for moments of the radiation intensity and (ii) the normalized Boltzmann transport equation (BTE). The multilevel system of moment equations is derived by projection of the BTE onto a sequence of subspaces which represent elements of the phase space of the problem. Exact closure for the moment equations is provided by the Eddington tensor. A Petrov-Galerkin (PG) projection of the normalized BTE is formulated using a proper orthogonal decomposition (POD) basis representing the normalized radiation intensity over the whole phase space and time. The Eddington tensor linearly depends on the solution of the normalized BTE. By linear superposition of the POD basis functions, a low-rank expansion of the Eddington tensor is constructed with coefficients defined by the PG projected normalized BTE. The material energy balance (MEB) equation is coupled with the effective gray low-order equations which exist on the same dimensional scale as the MEB equation. The resulting TRT ROM is structure and asymptotic preserving. A detailed analysis of the ROM is performed on the classical Fleck-Cummings (F-C) TRT multigroup test problem in 2D geometry. Numerical results are presented to demonstrate the ROM's effectiveness in the simulation of radiation wave phenomena. Importantly, the ROM is shown to produce solutions with sufficiently high accuracy while using low-rank approximation of the normalized BTE solution. Essential physical characteristics of supersonic radiation wave are preserved in the ROM solutions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Noise propagation in hybrid models of nonlinear systems: The Ginzburg–Landau equation

Every physical phenomenon can be described by multiple models with varying degrees of fidelity. The computational cost of higher fidelity models (e.g., molecular dynamics simulations) is invariably higher than that of their lower fidelity counterparts (e.g., a continuum model based on differential equations). While the former might not be suitable for large-scale simulations, the latter are not universally valid. Hybrid algorithms provide a compromise between the computational efficiency of a coarse-scale model and the representational accuracy of a fine-scale description. This is achieved by conducting a fine-scale computation in subdomains where it is absolutely required (e.g., due to a local breakdown of a continuum model) and coupling it with a coarse-scale computation in the rest of a computational domain. We analyze the effects of random fluctuations generated by the fine-scale component of a nonlinear hybrid on the hybrid's overall accuracy and stability. Two variants of the time-dependent Ginzburg–Landau equation (GLE) and their discrete representations provided by a nearest-neighbor Ising model serve as a computational testbed. Our analysis shows that coupling these descriptions in a one-dimensional simulation leads to erroneous results. Adding a random source term to the GLE provides accurate prediction of the mean behavior of the quantity of interest (magnetization). It also allows the two GLE variants to correctly capture the strength of the microscale fluctuations. Our work demonstrates the importance of fine-scale noise in hybrid simulations, and suggests the need for replacing an otherwise deterministic coarse-scale component of the hybrid with its stochastic counterpart.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Optimisation of confinement in a fusion reactor using a nonlinear turbulence model

We report the confinement of heat in the core of a magnetic fusion reactor is optimised using a multidimensional optimisation algorithm. For the first time in such a study, the loss of heat due to turbulence is modelled at every stage using first-principles nonlinear simulations which accurately capture the turbulent cascade and large-scale zonal flows. The simulations utilise a novel approach, with gyrofluid treatment of the small-scale drift waves and gyrokinetic treatment of the large-scale zonal flows. A simple near-circular equilibrium with standard parameters is chosen as the initial condition. The figure of merit, fusion power per unit volume, is calculated, and then two control parameters, the elongation and triangularity of the outer flux surface, are varied, with the algorithm seeking to optimise the chosen figure of merit. A twofold increase in the plasma power per unit volume is achieved by moving to higher elongation and strongly negative triangularity.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Application of triggered lightning numerical models to the F106B and extension to other aircraft

The goal of the F106B Thunderstorm Research Program is to characterize the lightning environment for aircraft in flight. This report describes the application of numerical electromagnetic models to this problem. Topics include: (1) Extensive application of linear triggered lightning to F106B data; (2) Electrostatic analysis of F106B field mill data; (3) Application of subgrid modeling to F106B nose region, including both static and nonlinear models; (4) Extension of F106B results to other aircraft of varying sizes and shapes; and (5) Application of nonlinear model to interaction of F106B with lightning leader-return stroke event.

Ng, Poh H.↗

Low-order nonlinear dynamic model of IC engine-variable pitch propeller system for general aviation aircraft

This paper presents a dynamic model of an internal combustion engine coupled to a variable pitch propeller. The low-order, nonlinear time-dependent model is useful for simulating the propulsion system of general aviation single-engine light aircraft. This model is suitable for investigating engine diagnostics and monitoring and for control design and development. Furthermore, the model may be extended to provide a tool for the study of engine emissions, fuel economy, component effects, alternative fuels, alternative engine cycles, flight simulators, sensors, and actuators. Results show that the model provides a reasonable representation of the propulsion system dynamics from zero to 10 Hertz.

Richard, Jacques C.↗

Fully explicit nonlinear optics model in a particle-in-cell framework

A numerical technique which incorporates the nonlinear optics of anisotropic crystals into a particle-in-cell framework is described. The model is useful for simulating interactions between crystals, ultra-short laser pulses, intense relativistic electron bunches, plasmas, or any combination thereof. The frequency content of the incident and scattered radiation is limited only by the resolution of the spatial and temporal grid. A numerical stability analysis indicates that the Courant condition is more stringent than in the vacuum case. Numerical experiments are carried out illustrating the electro-optic effect, soliton propagation, and the generation of fields in a crystal by a relativistic electron bunch.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

A Criterion to Control Nonlinear Error in the Mixed-Mode Bending Test

The mixed-mode bending test ha: been widely used to measure delamination toughness and was recently standardized by ASTM as Standard Test Method D6671-01. This simple test is a combination of the standard Mode I (opening) test and a Mode II (sliding) test. This test uses a unidirectional composite test specimen with an artificial delamination subjected to bending loads to characterize when a delamination will extend. When the displacements become large, the linear theory used to analyze the results of the test yields errors in the calcu1ated toughness values. The current standard places no limit on the specimen loading and therefore test data can be created using the standard that are significantly in error. A method of limiting the error that can be incurred in the calculated toughness values is needed. In this paper, nonlinear models of the MMB test are refined. One of the nonlinear models is then used to develop a simple criterion for prescribing conditions where thc nonlinear error will remain below 5%.

Reeder, James R.↗

Electric and magnetic black holes in a new nonlinear electrodynamics model

Highlights: • We introduce a new NED model which is comparable with the BI model in the weak-field limit. • We find an electric black hole solution in the context of Einstein’s gravity minimally coupled with the new NED model. • We study the thermal stability of the electric black hole solution. • Modified Smarr’s formula consistent with the first law of black hole thermodynamics is obtained. A new nonlinear electrodynamics (NED) model is introduced in the form of a nonpolynomial Lagrangian which admits static spherical and also plane wave solutions in a flat space. Upon coupling with gravity the electric field is finite and comparable with the Born–Infeld counterpart. The electric and magnetic black hole solutions in the Einstein’s gravity coupled with this NED model are presented. The solutions give both asymptotically and in the weak field limit Reissner–Nordström (RN) black hole and unlike the other known models our electric solution is expressed in terms of elementary functions in a closed form. We study the first law and derive the modified Smarr’s formula for the electric type extension of our model. Considerable rich structure, especially thermodynamic ones, ranging from first to the second order phase transitions are added to the RN black hole of linear electrodynamics with this NED model. Having the exact solution for the metric function at our disposal we investigate the stability of the electric black hole from both the thermodynamical and causal points of view.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

On the modeling and nonlinear dynamics of autonomous Silva-Young type chaotic oscillators with flat power spectrum

The nonlinear dynamics of fourth-order Silva-Young type chaotic oscillators with flat power spectrum recently introduced by Tamaseviciute and collaborators is considered. In this type of oscillators, a pair of semiconductor diodes in an anti-parallel connection acts as the nonlinear component necessary for generating chaotic oscillations. Based on the Shockley diode equation and an appropriate selection of the state variables, a smooth mathematical model (involving hyperbolic sine and cosine functions) is derived for a better description of both the regular and chaotic dynamics of the system. The complex behavior of the oscillator is characterized in terms of its parameters by using time series, bifurcation diagrams, Lyapunov exponents' plots, Poincaré sections, and frequency spectra. It is shown that the onset of chaos is achieved via the classical period-doubling and symmetry restoring crisis scenarios. Some PSPICE simulations of the nonlinear dynamics of the oscillator are presented in order to confirm the ability of the proposed mathematical model to accurately describe/predict both the regular and chaotic behaviors of the oscillator.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Modeling the Nonlinear, Strain Rate Dependent Deformation of Woven Ceramic Matrix Composites With Hydrostatic Stress Effects Included

An analysis method based on a deformation (as opposed to damage) approach has been developed to model the strain rate dependent, nonlinear deformation of woven ceramic matrix composites with a plain weave fiber architecture. In the developed model, the differences in the tension and compression response have also been considered. State variable based viscoplastic equations originally developed for metals have been modified to analyze the ceramic matrix composites. To account for the tension/compression asymmetry in the material, the effective stress and effective inelastic strain definitions have been modified. The equations have also been modified to account for the fact that in an orthotropic composite the in-plane shear stiffness is independent of the stiffness in the normal directions. The developed equations have been implemented into a commercially available transient dynamic finite element code, LS-DYNA, through the use of user defined subroutines (UMATs). The tensile, compressive, and shear deformation of a representative plain weave woven ceramic matrix composite are computed and compared to experimental results. The computed values correlate well to the experimental data, demonstrating the ability of the model to accurately compute the deformation response of woven ceramic matrix composites.

Goldberg, Robert K.↗

Nonlinear model-based controller for premixed charge compression ignition combustion timing in diesel engines

Advanced combustion modes, such as PCCI, operate near the system stability limits. In PCCI, the combustion event begins without a direct combustion trigger in contrast to traditional spark-ignited gasoline engines and direct-injected diesel engines. The lack of a direct combustion trigger encourages the usage of model-based controls to provide robust control of the combustion phasing. The nonlinear relationships between the control inputs and the combustion system response often limit the effectiveness of traditional, non-model-based controllers. Accurate knowledge of the system states and inputs is helpful for implementation of an effective nonlinear controller. A nonlinear controller is developed and implemented to control the engine combustion timing during diesel PCCI operation by targeting desired values of the in-cylinder oxygen concentration, pressure, and temperature during early fuel injection.

42 ENGINEERING↗

Acoustic field distribution of sawtooth wave with nonlinear SBE model

For precise prediction of the acoustic field distribution of extracorporeal shock wave lithotripsy with an ellipsoid transducer, the nonlinear spheroidal beam equations (SBE) are employed to model acoustic wave propagation in medium. To solve the SBE model with frequency domain algorithm, boundary conditions are obtained for monochromatic and sawtooth waves based on the phase compensation. In numerical analysis, the influence of sinusoidal wave and sawtooth wave on axial pressure distributions are investigated.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Modeling the Nonlinear, Strain Rate Dependent Deformation of Shuttle Leading Edge Materials with Hydrostatic Stress Effects Included

An analysis method based on a deformation (as opposed to damage) approach has been developed to model the strain rate dependent, nonlinear deformation of woven ceramic matrix composites, such as the Reinforced Carbon Carbon (RCC) material used on the leading edges of the Space Shuttle. In the developed model, the differences in the tension and compression deformation behaviors have also been accounted for. State variable viscoplastic equations originally developed for metals have been modified to analyze the ceramic matrix composites. To account for the tension/compression asymmetry in the material, the effective stress and effective inelastic strain definitions have been modified. The equations have also been modified to account for the fact that in an orthotropic composite the in-plane shear response is independent of the stiffness in the normal directions. The developed equations have been implemented into LS-DYNA through the use of user defined subroutines (UMATs). Several sample qualitative calculations have been conducted, which demonstrate the ability of the model to qualitatively capture the features of the deformation response present in woven ceramic matrix composites.

Goldberg, Robert K.↗

Linear and Nonlinear Constitutive Model for Piezoelectricity in ALEGRA-FE

This report develops and documents linear and nonlinear constitutive relations implemented in ALEGRA-FE (ferroelectric). A thermodynamic framework is created to describe the electromechanical system in the form of a free energy functional. Constitutive relations are derived by taking series expansions of the free energy functional with respect to the independent fields. First order expansion terms yield linear constitutive relations and higher order expansion terms yield non-linear constitutive relations. This document serves as supplement to Section 4 of Sandia Report SAND2013-7363, Rev 3. Methods for implementation of kinematic relations of piezoelectric models and rotation of material principal axes are covered in the supplemented report. Additional discussion on phase velocity calculation is also presented.

30 DIRECT ENERGY CONVERSION↗