Radiation Magnetohydrodynamics: Analysis for Model Problems and Efficient 3d-Simulations for the Full System

The Chemical Master Equation is a standard approach to model biochemical reaction networks. It consists of a system of linear differential equations, in which each state corresponds to a possible configuration of the reaction system, and the solution describes a time-dependent probability distribution over all configurations. The Stochastic Simulation Algorithm (SSA) is a method to simulate sample paths from this stochastic process. Both approaches are only applicable for small systems, characterized by few reactions and small numbers of molecules. For larger systems, the CME is computationally intractable due to a large number of possible configurations, and the SSA suffers from large reaction propensities. In our study, we focus on catalytic reaction systems, in which substrates are converted by catalytic molecules. We present an alternative description of these systems, called SiCaSMA, in which the full system is subdivided into smaller subsystems with one catalyst molecule each. These single catalyst subsystems can be analyzed individually, and their solutions are concatenated to give the solution of the full system. We show the validity of our approach by applying it to two test-bed reaction systems, a reversible switch of a molecule and methyltransferase-mediated DNA methylation.

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3D Simulation-Based Acoustic Wave Resonator Analysis and Validation Using Novel Finite Element Method Software

Sensors ◽

10.3390/s21082715 ◽

2021 ◽

Vol 21 (8) ◽

pp. 2715

Author(s):

Ruth Yadira Vidana Morales ◽

Susana Ortega Cisneros ◽

Jose Rodrigo Camacho Perez ◽

Federico Sandoval Ibarra ◽

Ricardo Casas Carrillo

Keyword(s):

Finite Element ◽

High Performance ◽

Cloud Services ◽

3D Simulation ◽

3D Simulations ◽

Acoustic Resonators ◽

Analysis And Design ◽

Wave Resonator ◽

Film Bulk ◽

Simulation Results

This work illustrates the analysis of Film Bulk Acoustic Resonators (FBAR) using 3D Finite Element (FEM) simulations with the software OnScale in order to predict and improve resonator performance and quality before manufacturing. This kind of analysis minimizes manufacturing cycles by reducing design time with 3D simulations running on High-Performance Computing (HPC) cloud services. It also enables the identification of manufacturing effects on device performance. The simulation results are compared and validated with a manufactured FBAR device, previously reported, to further highlight the usefulness and advantages of the 3D simulations-based design process. In the 3D simulation results, some analysis challenges, like boundary condition definitions, mesh tuning, loss source tracing, and device quality estimations, were studied. Hence, it is possible to highlight that modern FEM solvers, like OnScale enable unprecedented FBAR analysis and design optimization.

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Accelerated Boundary Element Method for 3D Simulations of Bubble Cluster Dynamics in an Acoustic Field

Communications in Computer and Information Science - Parallel Computational Technologies ◽

10.1007/978-3-030-28163-2_24 ◽

2019 ◽

pp. 335-349 ◽

Cited By ~ 1

Author(s):

Yulia A. Pityuk ◽

Nail A. Gumerov ◽

Olga A. Abramova ◽

Ilnur A. Zarafutdinov ◽

Iskander S. Akhatov

Keyword(s):

Boundary Element Method ◽

Boundary Element ◽

Acoustic Field ◽

Bubble Cluster ◽

3D Simulations ◽

Element Method

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Application of a Differential Drag Controller to a Full System Simulation

The Journal of the Astronautical Sciences ◽

10.1007/s40295-014-0001-5 ◽

2012 ◽

Vol 59 (3) ◽

pp. 541-563

Author(s):

Annie Lum ◽

E. Glenn Lightsey

Keyword(s):

System Simulation ◽

Full System ◽

Differential Drag

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A Full-System Approach of the Elastohydrodynamic Line/Point Contact Problem

Journal of Tribology ◽

10.1115/1.2842246 ◽

2008 ◽

Vol 130 (2) ◽

Cited By ~ 61

Author(s):

W. Habchi ◽

D. Eyheramendy ◽

P. Vergne ◽

G. Morales-Espejel

Keyword(s):

Finite Element ◽

Nonlinear System ◽

System Approach ◽

Jacobian Matrix ◽

Point Contact ◽

System Of Equations ◽

Nonlinear System Of Equations ◽

Full System ◽

Element Discretization ◽

Fully Coupled

The solution of the elastohydrodynamic lubrication (EHL) problem involves the simultaneous resolution of the hydrodynamic (Reynolds equation) and elastic problems (elastic deformation of the contacting surfaces). Up to now, most of the numerical works dealing with the modeling of the isothermal EHL problem were based on a weak coupling resolution of the Reynolds and elasticity equations (semi-system approach). The latter were solved separately using iterative schemes and a finite difference discretization. Very few authors attempted to solve the problem in a fully coupled way, thus solving both equations simultaneously (full-system approach). These attempts suffered from a major drawback which is the almost full Jacobian matrix of the nonlinear system of equations. This work presents a new approach for solving the fully coupled isothermal elastohydrodynamic problem using a finite element discretization of the corresponding equations. The use of the finite element method allows the use of variable unstructured meshing and different types of elements within the same model which leads to a reduced size of the problem. The nonlinear system of equations is solved using a Newton procedure which provides faster convergence rates. Suitable stabilization techniques are used to extend the solution to the case of highly loaded contacts. The complexity is the same as for classical algorithms, but an improved convergence rate, a reduced size of the problem and a sparse Jacobian matrix are obtained. Thus, the computational effort, time and memory usage are considerably reduced.

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