A concurrent multiscale micromorphic molecular dynamics
International Nuclear Information System (INIS)
Li, Shaofan; Tong, Qi
2015-01-01
In this work, we have derived a multiscale micromorphic molecular dynamics (MMMD) from first principle to extend the (Andersen)-Parrinello-Rahman molecular dynamics to mesoscale and continuum scale. The multiscale micromorphic molecular dynamics is a con-current three-scale dynamics that couples a fine scale molecular dynamics, a mesoscale micromorphic dynamics, and a macroscale nonlocal particle dynamics together. By choosing proper statistical closure conditions, we have shown that the original Andersen-Parrinello-Rahman molecular dynamics is the homogeneous and equilibrium case of the proposed multiscale micromorphic molecular dynamics. In specific, we have shown that the Andersen-Parrinello-Rahman molecular dynamics can be rigorously formulated and justified from first principle, and its general inhomogeneous case, i.e., the three scale con-current multiscale micromorphic molecular dynamics can take into account of macroscale continuum mechanics boundary condition without the limitation of atomistic boundary condition or periodic boundary conditions. The discovered multiscale scale structure and the corresponding multiscale dynamics reveal a seamless transition from atomistic scale to continuum scale and the intrinsic coupling mechanism among them based on first principle formulation
Multiscale Universal Interface: A concurrent framework for coupling heterogeneous solvers
Energy Technology Data Exchange (ETDEWEB)
Tang, Yu-Hang, E-mail: yuhang_tang@brown.edu [Division of Applied Mathematics, Brown University, Providence, RI (United States); Kudo, Shuhei, E-mail: shuhei-kudo@outlook.jp [Graduate School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501 (Japan); Bian, Xin, E-mail: xin_bian@brown.edu [Division of Applied Mathematics, Brown University, Providence, RI (United States); Li, Zhen, E-mail: zhen_li@brown.edu [Division of Applied Mathematics, Brown University, Providence, RI (United States); Karniadakis, George Em, E-mail: george_karniadakis@brown.edu [Division of Applied Mathematics, Brown University, Providence, RI (United States); Collaboratory on Mathematics for Mesoscopic Modeling of Materials, Pacific Northwest National Laboratory, Richland, WA 99354 (United States)
2015-09-15
Graphical abstract: - Abstract: Concurrently coupled numerical simulations using heterogeneous solvers are powerful tools for modeling multiscale phenomena. However, major modifications to existing codes are often required to enable such simulations, posing significant difficulties in practice. In this paper we present a C++ library, i.e. the Multiscale Universal Interface (MUI), which is capable of facilitating the coupling effort for a wide range of multiscale simulations. The library adopts a header-only form with minimal external dependency and hence can be easily dropped into existing codes. A data sampler concept is introduced, combined with a hybrid dynamic/static typing mechanism, to create an easily customizable framework for solver-independent data interpretation. The library integrates MPI MPMD support and an asynchronous communication protocol to handle inter-solver information exchange irrespective of the solvers' own MPI awareness. Template metaprogramming is heavily employed to simultaneously improve runtime performance and code flexibility. We validated the library by solving three different multiscale problems, which also serve to demonstrate the flexibility of the framework in handling heterogeneous models and solvers. In the first example, a Couette flow was simulated using two concurrently coupled Smoothed Particle Hydrodynamics (SPH) simulations of different spatial resolutions. In the second example, we coupled the deterministic SPH method with the stochastic Dissipative Particle Dynamics (DPD) method to study the effect of surface grafting on the hydrodynamics properties on the surface. In the third example, we consider conjugate heat transfer between a solid domain and a fluid domain by coupling the particle-based energy-conserving DPD (eDPD) method with the Finite Element Method (FEM)
Multiscale Simulations Using Particles
DEFF Research Database (Denmark)
Walther, Jens Honore
vortex methods for problems in continuum fluid dynamics, dissipative particle dynamics for flow at the meso scale, and atomistic molecular dynamics simulations of nanofluidic systems. We employ multiscale techniques to breach the atomistic and continuum scales to study fundamental problems in fluid...... dynamics. Recent work on the thermophoretic motion of water nanodroplets confined inside carbon nanotubes, and multiscale techniques for polar liquids will be discussed in detail at the symposium....
The Adaptive Multi-scale Simulation Infrastructure
Energy Technology Data Exchange (ETDEWEB)
Tobin, William R. [Rensselaer Polytechnic Inst., Troy, NY (United States)
2015-09-01
The Adaptive Multi-scale Simulation Infrastructure (AMSI) is a set of libraries and tools developed to support the development, implementation, and execution of general multimodel simulations. Using a minimal set of simulation meta-data AMSI allows for minimally intrusive work to adapt existent single-scale simulations for use in multi-scale simulations. Support for dynamic runtime operations such as single- and multi-scale adaptive properties is a key focus of AMSI. Particular focus has been spent on the development on scale-sensitive load balancing operations to allow single-scale simulations incorporated into a multi-scale simulation using AMSI to use standard load-balancing operations without affecting the integrity of the overall multi-scale simulation.
The Multiscale Material Point Method for Simulating Transient Responses
Chen, Zhen; Su, Yu-Chen; Zhang, Hetao; Jiang, Shan; Sewell, Thomas
2015-06-01
To effectively simulate multiscale transient responses such as impact and penetration without invoking master/slave treatment, the multiscale material point method (Multi-MPM) is being developed in which molecular dynamics at nanoscale and dissipative particle dynamics at mesoscale might be concurrently handled within the framework of the original MPM at microscale (continuum level). The proposed numerical scheme for concurrently linking different scales is described in this paper with simple examples for demonstration. It is shown from the preliminary study that the mapping and re-mapping procedure used in the original MPM could coarse-grain the information at fine scale and that the proposed interfacial scheme could provide a smooth link between different scales. Since the original MPM is an extension from computational fluid dynamics to solid dynamics, the proposed Multi-MPM might also become robust for dealing with multiphase interactions involving failure evolution. This work is supported in part by DTRA and NSFC.
Deductive multiscale simulation using order parameters
Ortoleva, Peter J.
2017-05-16
Illustrative embodiments of systems and methods for the deductive multiscale simulation of macromolecules are disclosed. In one illustrative embodiment, a deductive multiscale simulation method may include (i) constructing a set of order parameters that model one or more structural characteristics of a macromolecule, (ii) simulating an ensemble of atomistic configurations for the macromolecule using instantaneous values of the set of order parameters, (iii) simulating thermal-average forces and diffusivities for the ensemble of atomistic configurations, and (iv) evolving the set of order parameters via Langevin dynamics using the thermal-average forces and diffusivities.
Alleman, Coleman N.; Foulk, James W.; Mota, Alejandro; Lim, Hojun; Littlewood, David J.
2018-02-01
The heterogeneity in mechanical fields introduced by microstructure plays a critical role in the localization of deformation. To resolve this incipient stage of failure, it is therefore necessary to incorporate microstructure with sufficient resolution. On the other hand, computational limitations make it infeasible to represent the microstructure in the entire domain at the component scale. In this study, the authors demonstrate the use of concurrent multiscale modeling to incorporate explicit, finely resolved microstructure in a critical region while resolving the smoother mechanical fields outside this region with a coarser discretization to limit computational cost. The microstructural physics is modeled with a high-fidelity model that incorporates anisotropic crystal elasticity and rate-dependent crystal plasticity to simulate the behavior of a stainless steel alloy. The component-scale material behavior is treated with a lower fidelity model incorporating isotropic linear elasticity and rate-independent J2 plasticity. The microstructural and component scale subdomains are modeled concurrently, with coupling via the Schwarz alternating method, which solves boundary-value problems in each subdomain separately and transfers solution information between subdomains via Dirichlet boundary conditions. In this study, the framework is applied to model incipient localization in tensile specimens during necking.
Zavadlav, Julija; Marrink, Siewert J; Praprotnik, Matej
The adaptive resolution scheme (AdResS) is a multiscale molecular dynamics simulation approach that can concurrently couple atomistic (AT) and coarse-grained (CG) resolution regions, i.e., the molecules can freely adapt their resolution according to their current position in the system. Coupling to
Multiscale simulation of protein hydration using the SWINGER dynamical clustering algorithm
Zavadlav, Julija; Marrink, Siewert J; Praprotnik, Matej
To perform computationally efficient concurrent multiscale simulations of biological macromolecules in solution, where the all-atom (AT) models are coupled to supramolecular coarse-grained (SCG) solvent models, previous studies resorted to a modified AT water models, such as the bundled-SPC models,
An Overview of the State of the Art in Atomistic and Multiscale Simulation of Fracture
Saether, Erik; Yamakov, Vesselin; Phillips, Dawn R.; Glaessgen, Edward H.
2009-01-01
The emerging field of nanomechanics is providing a new focus in the study of the mechanics of materials, particularly in simulating fundamental atomic mechanisms involved in the initiation and evolution of damage. Simulating fundamental material processes using first principles in physics strongly motivates the formulation of computational multiscale methods to link macroscopic failure to the underlying atomic processes from which all material behavior originates. This report gives an overview of the state of the art in applying concurrent and sequential multiscale methods to analyze damage and failure mechanisms across length scales.
Multiscale Simulation Framework for Coupled Fluid Flow and Mechanical Deformation
Energy Technology Data Exchange (ETDEWEB)
Hou, Thomas [California Inst. of Technology (CalTech), Pasadena, CA (United States); Efendiev, Yalchin [Stanford Univ., CA (United States); Tchelepi, Hamdi [Texas A & M Univ., College Station, TX (United States); Durlofsky, Louis [Stanford Univ., CA (United States)
2016-05-24
Our work in this project is aimed at making fundamental advances in multiscale methods for flow and transport in highly heterogeneous porous media. The main thrust of this research is to develop a systematic multiscale analysis and efficient coarse-scale models that can capture global effects and extend existing multiscale approaches to problems with additional physics and uncertainties. A key emphasis is on problems without an apparent scale separation. Multiscale solution methods are currently under active investigation for the simulation of subsurface flow in heterogeneous formations. These procedures capture the effects of fine-scale permeability variations through the calculation of specialized coarse-scale basis functions. Most of the multiscale techniques presented to date employ localization approximations in the calculation of these basis functions. For some highly correlated (e.g., channelized) formations, however, global effects are important and these may need to be incorporated into the multiscale basis functions. Other challenging issues facing multiscale simulations are the extension of existing multiscale techniques to problems with additional physics, such as compressibility, capillary effects, etc. In our project, we explore the improvement of multiscale methods through the incorporation of additional (single-phase flow) information and the development of a general multiscale framework for flows in the presence of uncertainties, compressible flow and heterogeneous transport, and geomechanics. We have considered (1) adaptive local-global multiscale methods, (2) multiscale methods for the transport equation, (3) operator-based multiscale methods and solvers, (4) multiscale methods in the presence of uncertainties and applications, (5) multiscale finite element methods for high contrast porous media and their generalizations, and (6) multiscale methods for geomechanics.
International Nuclear Information System (INIS)
Yu Xiao-Xiang; Wang Chong-Yu
2013-01-01
An effective multiscale simulation which concurrently couples the quantum-mechanical and molecular-mechanical calculations based on the position continuity of atoms is presented. By an iterative procedure, the structure of the dislocation core in face-centered cubic metal is obtained by first-principles calculation and the long-range stress is released by molecular dynamics relaxation. Compared to earlier multiscale methods, the present work couples the long-range strain to the local displacements of the dislocation core in a simpler way with the same accuracy. (condensed matter: electronic structure, electrical, magnetic, and optical properties)
Multiscale simulation approach for battery production systems
Schönemann, Malte
2017-01-01
Addressing the challenge of improving battery quality while reducing high costs and environmental impacts of the production, this book presents a multiscale simulation approach for battery production systems along with a software environment and an application procedure. Battery systems are among the most important technologies of the 21st century since they are enablers for the market success of electric vehicles and stationary energy storage solutions. However, the performance of batteries so far has limited possible applications. Addressing this challenge requires an interdisciplinary understanding of dynamic cause-effect relationships between processes, equipment, materials, and environmental conditions. The approach in this book supports the integrated evaluation of improvement measures and is usable for different planning horizons. It is applied to an exemplary battery cell production and module assembly in order to demonstrate the effectiveness and potential benefits of the simulation.
Parallel multiscale simulations of a brain aneurysm
Energy Technology Data Exchange (ETDEWEB)
Grinberg, Leopold [Division of Applied Mathematics, Brown University, Providence, RI 02912 (United States); Fedosov, Dmitry A. [Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, Jülich 52425 (Germany); Karniadakis, George Em, E-mail: george_karniadakis@brown.edu [Division of Applied Mathematics, Brown University, Providence, RI 02912 (United States)
2013-07-01
Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multiscale simulations of platelet depositions on the wall of a brain aneurysm. The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier–Stokes solver NεκTαr. The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers (NεκTαr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300 K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in
Parallel multiscale simulations of a brain aneurysm
International Nuclear Information System (INIS)
Grinberg, Leopold; Fedosov, Dmitry A.; Karniadakis, George Em
2013-01-01
Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multiscale simulations of platelet depositions on the wall of a brain aneurysm. The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier–Stokes solver NεκTαr. The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers (NεκTαr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300 K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in
Computational simulation of concurrent engineering for aerospace propulsion systems
Chamis, C. C.; Singhal, S. N.
1992-01-01
Results are summarized of an investigation to assess the infrastructure available and the technology readiness in order to develop computational simulation methods/software for concurrent engineering. These results demonstrate that development of computational simulations methods for concurrent engineering is timely. Extensive infrastructure, in terms of multi-discipline simulation, component-specific simulation, system simulators, fabrication process simulation, and simulation of uncertainties - fundamental in developing such methods, is available. An approach is recommended which can be used to develop computational simulation methods for concurrent engineering for propulsion systems and systems in general. Benefits and facets needing early attention in the development are outlined.
Computational simulation for concurrent engineering of aerospace propulsion systems
Chamis, C. C.; Singhal, S. N.
1993-01-01
Results are summarized for an investigation to assess the infrastructure available and the technology readiness in order to develop computational simulation methods/software for concurrent engineering. These results demonstrate that development of computational simulation methods for concurrent engineering is timely. Extensive infrastructure, in terms of multi-discipline simulation, component-specific simulation, system simulators, fabrication process simulation, and simulation of uncertainties--fundamental to develop such methods, is available. An approach is recommended which can be used to develop computational simulation methods for concurrent engineering of propulsion systems and systems in general. Benefits and issues needing early attention in the development are outlined.
Multi-Scale Simulation of High Energy Density Ionic Liquids
National Research Council Canada - National Science Library
Voth, Gregory A
2007-01-01
The focus of this AFOSR project was the molecular dynamics (MD) simulation of ionic liquid structure, dynamics, and interfacial properties, as well as multi-scale descriptions of these novel liquids (e.g...
Energy Technology Data Exchange (ETDEWEB)
Foulk, James W. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Alleman, Coleman N. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Mota, Alejandro [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Lim, Hojun [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Littlewood, David John [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Bergel, Guy Leshem [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Popova, Evdokia [Georgia Inst. of Technology, Atlanta, GA (United States). Woodruff School of Mechanical Engineering; Montes de Oca Zapiain, David [Georgia Inst. of Technology, Atlanta, GA (United States). Woodruff School of Mechanical Engineering; Kalidindi, Suryanarayana Raju [Georgia Inst. of Technology, Atlanta, GA (United States). Woodruff School of Mechanical Engineering; Ernst, Corey [Elemental Technologies, Provo, UT (United States)
2017-09-01
The heterogeneity in mechanical fields introduced by microstructure plays a critical role in the localization of deformation. To resolve this incipient stage of failure, it is therefore necessary to incorporate microstructure with sufficient resolution. On the other hand, computational limitations make it infeasible to represent the microstructure in the entire domain at the component scale. In this study, the authors demonstrate the use of concurrent multi- scale modeling to incorporate explicit, finely resolved microstructure in a critical region while resolving the smoother mechanical fields outside this region with a coarser discretization to limit computational cost. The microstructural physics is modeled with a high-fidelity model that incorporates anisotropic crystal elasticity and rate-dependent crystal plasticity to simulate the behavior of a stainless steel alloy. The component-scale material behavior is treated with a lower fidelity model incorporating isotropic linear elasticity and rate-independent J 2 plas- ticity. The microstructural and component scale subdomains are modeled concurrently, with coupling via the Schwarz alternating method, which solves boundary-value problems in each subdomain separately and transfers solution information between subdomains via Dirichlet boundary conditions. Beyond cases studies in concurrent multiscale, we explore progress in crystal plastic- ity through modular designs, solution methodologies, model verification, and extensions to Sierra/SM and manycore applications. Advances in conformal microstructures having both hexahedral and tetrahedral workflows in Sculpt and Cubit are highlighted. A structure-property case study in two-phase metallic composites applies the Materials Knowledge System to local metrics for void evolution. Discussion includes lessons learned, future work, and a summary of funded efforts and proposed work. Finally, an appendix illustrates the need for two-way coupling through a single degree of
Multiscale Simulation of Breaking Wave Impacts
DEFF Research Database (Denmark)
Lindberg, Ole
compare reasonably well. The incompressible and inviscid ALE-WLS model is coupled with the potential flow model of Engsig-Karup et al. [2009], to perform multiscale calculation of breaking wave impacts on a vertical breakwater. The potential flow model provides accurate calculation of the wave...... with a potential flow model to provide multiscale calculation of forces from breaking wave impacts on structures....
Multiscale simulation of molecular processes in cellular environments.
Chiricotto, Mara; Sterpone, Fabio; Derreumaux, Philippe; Melchionna, Simone
2016-11-13
We describe the recent advances in studying biological systems via multiscale simulations. Our scheme is based on a coarse-grained representation of the macromolecules and a mesoscopic description of the solvent. The dual technique handles particles, the aqueous solvent and their mutual exchange of forces resulting in a stable and accurate methodology allowing biosystems of unprecedented size to be simulated.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'. © 2016 The Author(s).
Multiscale simulation of water flow past a C540 fullerene
DEFF Research Database (Denmark)
Walther, Jens Honore; Praprotnik, Matej; Kotsalis, Evangelos M.
2012-01-01
We present a novel, three-dimensional, multiscale algorithm for simulations of water flow past a fullerene. We employ the Schwarz alternating overlapping domain method to couple molecular dynamics (MD) of liquid water around the C540 buckyball with a Lattice–Boltzmann (LB) description for the Nav......We present a novel, three-dimensional, multiscale algorithm for simulations of water flow past a fullerene. We employ the Schwarz alternating overlapping domain method to couple molecular dynamics (MD) of liquid water around the C540 buckyball with a Lattice–Boltzmann (LB) description...
Multiscale modeling and simulation of brain blood flow
Energy Technology Data Exchange (ETDEWEB)
Perdikaris, Paris, E-mail: parisp@mit.edu [Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States); Grinberg, Leopold, E-mail: leopoldgrinberg@us.ibm.com [IBM T.J Watson Research Center, 1 Rogers St, Cambridge, Massachusetts 02142 (United States); Karniadakis, George Em, E-mail: george-karniadakis@brown.edu [Division of Applied Mathematics, Brown University, Providence, Rhode Island 02912 (United States)
2016-02-15
The aim of this work is to present an overview of recent advances in multi-scale modeling of brain blood flow. In particular, we present some approaches that enable the in silico study of multi-scale and multi-physics phenomena in the cerebral vasculature. We discuss the formulation of continuum and atomistic modeling approaches, present a consistent framework for their concurrent coupling, and list some of the challenges that one needs to overcome in achieving a seamless and scalable integration of heterogeneous numerical solvers. The effectiveness of the proposed framework is demonstrated in a realistic case involving modeling the thrombus formation process taking place on the wall of a patient-specific cerebral aneurysm. This highlights the ability of multi-scale algorithms to resolve important biophysical processes that span several spatial and temporal scales, potentially yielding new insight into the key aspects of brain blood flow in health and disease. Finally, we discuss open questions in multi-scale modeling and emerging topics of future research.
Adaptive Multiscale Finite Element Method for Subsurface Flow Simulation
Van Esch, J.M.
2010-01-01
Natural geological formations generally show multiscale structural and functional heterogeneity evolving over many orders of magnitude in space and time. In subsurface hydrological simulations the geological model focuses on the structural hierarchy of physical sub units and the flow model addresses
Fast 2D Simulation of Superconductors: a Multiscale Approach
DEFF Research Database (Denmark)
Rodriguez Zermeno, Victor Manuel; Sørensen, Mads Peter; Pedersen, Niels Falsig
2009-01-01
This work presents a method to calculate AC losses in thin conductors such as the commercially available second generation superconducting wires through a multiscale meshing technique. The main idea is to use large aspect ratio elements to accurately simulate thin material layers. For a single thin...
Control algorithm for multiscale flow simulations of water
DEFF Research Database (Denmark)
Kotsalis, E. M.; Walther, Jens Honore; Kaxiras, E.
2009-01-01
We present a multiscale algorithm to couple atomistic water models with continuum incompressible flow simulations via a Schwarz domain decomposition approach. The coupling introduces an inhomogeneity in the description of the atomistic domain and prevents the use of periodic boundary conditions...
Final Technical Report "Multiscale Simulation Algorithms for Biochemical Systems"
Energy Technology Data Exchange (ETDEWEB)
Petzold, Linda R.
2012-10-25
Biochemical systems are inherently multiscale and stochastic. In microscopic systems formed by living cells, the small numbers of reactant molecules can result in dynamical behavior that is discrete and stochastic rather than continuous and deterministic. An analysis tool that respects these dynamical characteristics is the stochastic simulation algorithm (SSA, Gillespie, 1976), a numerical simulation procedure that is essentially exact for chemical systems that are spatially homogeneous or well stirred. Despite recent improvements, as a procedure that simulates every reaction event, the SSA is necessarily inefficient for most realistic problems. There are two main reasons for this, both arising from the multiscale nature of the underlying problem: (1) stiffness, i.e. the presence of multiple timescales, the fastest of which are stable; and (2) the need to include in the simulation both species that are present in relatively small quantities and should be modeled by a discrete stochastic process, and species that are present in larger quantities and are more efficiently modeled by a deterministic differential equation (or at some scale in between). This project has focused on the development of fast and adaptive algorithms, and the fun- damental theory upon which they must be based, for the multiscale simulation of biochemical systems. Areas addressed by this project include: (1) Theoretical and practical foundations for ac- celerated discrete stochastic simulation (tau-leaping); (2) Dealing with stiffness (fast reactions) in an efficient and well-justified manner in discrete stochastic simulation; (3) Development of adaptive multiscale algorithms for spatially homogeneous discrete stochastic simulation; (4) Development of high-performance SSA algorithms.
Formalizing Knowledge in Multi-Scale Agent-Based Simulations.
Somogyi, Endre; Sluka, James P; Glazier, James A
2016-10-01
Multi-scale, agent-based simulations of cellular and tissue biology are increasingly common. These simulations combine and integrate a range of components from different domains. Simulations continuously create, destroy and reorganize constituent elements causing their interactions to dynamically change. For example, the multi-cellular tissue development process coordinates molecular, cellular and tissue scale objects with biochemical, biomechanical, spatial and behavioral processes to form a dynamic network. Different domain specific languages can describe these components in isolation, but cannot describe their interactions. No current programming language is designed to represent in human readable and reusable form the domain specific knowledge contained in these components and interactions. We present a new hybrid programming language paradigm that naturally expresses the complex multi-scale objects and dynamic interactions in a unified way and allows domain knowledge to be captured, searched, formalized, extracted and reused.
Numerical Simulations of a Multiscale Model of Stratified Langmuir Circulation
Malecha, Ziemowit; Chini, Gregory; Julien, Keith
2012-11-01
Langmuir circulation (LC), a prominent form of wind and surface-wave driven shear turbulence in the ocean surface boundary layer (BL), is commonly modeled using the Craik-Leibovich (CL) equations, a phase-averaged variant of the Navier-Stokes (NS) equations. Although surface-wave filtering renders the CL equations more amenable to simulation than are the instantaneous NS equations, simulations in wide domains, hundreds of times the BL depth, currently earn the ``grand challenge'' designation. To facilitate simulations of LC in such spatially-extended domains, we have derived multiscale CL equations by exploiting the scale separation between submesoscale and BL flows in the upper ocean. The numerical algorithm for simulating this multiscale model resembles super-parameterization schemes used in meteorology, but retains a firm mathematical basis. We have validated our algorithm and here use it to perform multiscale simulations of the interaction between LC and upper ocean density stratification. ZMM, GPC, KJ gratefully acknowledge funding from NSF CMG Award 0934827.
Multiscale eddy simulation for moist atmospheric convection: Preliminary investigation
Energy Technology Data Exchange (ETDEWEB)
Stechmann, Samuel N., E-mail: stechmann@wisc.edu [Department of Mathematics, University of Wisconsin-Madison (United States); Department of Atmospheric and Oceanic Sciences, University of Wisconsin-Madison (United States)
2014-08-15
A multiscale computational framework is designed for simulating atmospheric convection and clouds. In this multiscale framework, large eddy simulation (LES) is used to model the coarse scales of 100 m and larger, and a stochastic, one-dimensional turbulence (ODT) model is used to represent the fine scales of 100 m and smaller. Coupled and evolving together, these two components provide a multiscale eddy simulation (MES). Through its fine-scale turbulence and moist thermodynamics, MES allows coarse grid cells to be partially cloudy and to encompass cloudy–clear air mixing on scales down to 1 m; in contrast, in typical LES such fine-scale processes are not represented or are parameterized using bulk deterministic closures. To illustrate MES and investigate its multiscale dynamics, a shallow cumulus cloud field is simulated. The fine-scale variability is seen to take a plausible form, with partially cloudy grid cells prominent near cloud edges and cloud top. From earlier theoretical work, this mixing of cloudy and clear air is believed to have an important impact on buoyancy. However, contrary to expectations based on earlier theoretical studies, the mean statistics of the bulk cloud field are essentially the same in MES and LES; possible reasons for this are discussed, including possible limitations in the present formulation of MES. One difference between LES and MES is seen in the coarse-scale turbulent kinetic energy, which appears to grow slowly in time due to incoherent stochastic fluctuations in the buoyancy. This and other considerations suggest the need for some type of spatial and/or temporal filtering to attenuate undersampling of the stochastic fine-scale processes.
Multiscale eddy simulation for moist atmospheric convection: Preliminary investigation
International Nuclear Information System (INIS)
Stechmann, Samuel N.
2014-01-01
A multiscale computational framework is designed for simulating atmospheric convection and clouds. In this multiscale framework, large eddy simulation (LES) is used to model the coarse scales of 100 m and larger, and a stochastic, one-dimensional turbulence (ODT) model is used to represent the fine scales of 100 m and smaller. Coupled and evolving together, these two components provide a multiscale eddy simulation (MES). Through its fine-scale turbulence and moist thermodynamics, MES allows coarse grid cells to be partially cloudy and to encompass cloudy–clear air mixing on scales down to 1 m; in contrast, in typical LES such fine-scale processes are not represented or are parameterized using bulk deterministic closures. To illustrate MES and investigate its multiscale dynamics, a shallow cumulus cloud field is simulated. The fine-scale variability is seen to take a plausible form, with partially cloudy grid cells prominent near cloud edges and cloud top. From earlier theoretical work, this mixing of cloudy and clear air is believed to have an important impact on buoyancy. However, contrary to expectations based on earlier theoretical studies, the mean statistics of the bulk cloud field are essentially the same in MES and LES; possible reasons for this are discussed, including possible limitations in the present formulation of MES. One difference between LES and MES is seen in the coarse-scale turbulent kinetic energy, which appears to grow slowly in time due to incoherent stochastic fluctuations in the buoyancy. This and other considerations suggest the need for some type of spatial and/or temporal filtering to attenuate undersampling of the stochastic fine-scale processes
Growth of nitrogen-doped graphene on copper: Multiscale simulations
Gaillard, P.; Schoenhalz, A. L.; Moskovkin, P.; Lucas, S.; Henrard, L.
2016-02-01
We used multiscale simulations to model the growth of nitrogen-doped graphene on a copper substrate by chemical vapour deposition (CVD). Our simulations are based on ab-initio calculations of energy barriers for surface diffusion, which are complemented by larger scale Kinetic Monte Carlo (KMC) simulations. Our results indicate that the shape of grown doped graphene flakes depends on the temperature and deposition flux they are submitted during the process, but we found no significant effect of nitrogen doping on this shape. However, we show that nitrogen atoms have a preference for pyridine-like sites compared to graphite-like sites, as observed experimentally.
Multi-scale simulation for homogenization of cement media
International Nuclear Information System (INIS)
Abballe, T.
2011-01-01
To solve diffusion problems on cement media, two scales must be taken into account: a fine scale, which describes the micrometers wide microstructures present in the media, and a work scale, which is usually a few meters long. Direct numerical simulations are almost impossible because of the huge computational resources (memory, CPU time) required to assess both scales at the same time. To overcome this problem, we present in this thesis multi-scale resolution methods using both Finite Volumes and Finite Elements, along with their efficient implementations. More precisely, we developed a multi-scale simulation tool which uses the SALOME platform to mesh domains and post-process data, and the parallel calculation code MPCube to solve problems. This SALOME/MPCube tool can solve automatically and efficiently multi-scale simulations. Parallel structure of computer clusters can be use to dispatch the more time-consuming tasks. We optimized most functions to account for cement media specificities. We presents numerical experiments on various cement media samples, e.g. mortar and cement paste. From these results, we manage to compute a numerical effective diffusivity of our cement media and to reconstruct a fine scale solution. (author) [fr
Coupled multiscale simulation and optimization in nanoelectronics
2015-01-01
Designing complex integrated circuits relies heavily on mathematical methods and calls for suitable simulation and optimization tools. The current design approach involves simulations and optimizations in different physical domains (device, circuit, thermal, electromagnetic) and in a range of electrical engineering disciplines (logic, timing, power, crosstalk, signal integrity, system functionality). COMSON was a Marie Curie Research Training Network created to meet these new scientific and training challenges by (a) developing new descriptive models that take these mutual dependencies into account, (b) combining these models with existing circuit descriptions in new simulation strategies, and (c) developing new optimization techniques that will accommodate new designs. The book presents the main project results in the fields of PDAE modeling and simulation, model order reduction techniques and optimization, based on merging the know-how of three major European semiconductor companies with the combined expe...
Multiscale Modeling and Simulation of Material Processing
2006-07-01
challenge is how to develop methods that permit simulation of a process with a fewer number of atoms (for e.g. 106 instead of 1014 atoms in a cube) or...rreula bakgrundmes to ea wih poblms n-here. In dynamic simulations, the mass and momentum volving rapidly varying stress, such as stress field near a...significant, as indicated by numerical examples that will follow. We next summarize the coupling scheme with the aid of flowchart Fig. 8. The material
A multiscale quantum mechanics/electromagnetics method for device simulations.
Yam, ChiYung; Meng, Lingyi; Zhang, Yu; Chen, GuanHua
2015-04-07
Multiscale modeling has become a popular tool for research applying to different areas including materials science, microelectronics, biology, chemistry, etc. In this tutorial review, we describe a newly developed multiscale computational method, incorporating quantum mechanics into electronic device modeling with the electromagnetic environment included through classical electrodynamics. In the quantum mechanics/electromagnetics (QM/EM) method, the regions of the system where active electron scattering processes take place are treated quantum mechanically, while the surroundings are described by Maxwell's equations and a semiclassical drift-diffusion model. The QM model and the EM model are solved, respectively, in different regions of the system in a self-consistent manner. Potential distributions and current densities at the interface between QM and EM regions are employed as the boundary conditions for the quantum mechanical and electromagnetic simulations, respectively. The method is illustrated in the simulation of several realistic systems. In the case of junctionless field-effect transistors, transfer characteristics are obtained and a good agreement between experiments and simulations is achieved. Optical properties of a tandem photovoltaic cell are studied and the simulations demonstrate that multiple QM regions are coupled through the classical EM model. Finally, the study of a carbon nanotube-based molecular device shows the accuracy and efficiency of the QM/EM method.
Multiscale Simulations of Magnetic Island Coalescence
Dorelli, John C.
2010-01-01
We describe a new interactive parallel Adaptive Mesh Refinement (AMR) framework written in the Python programming language. This new framework, PyAMR, hides the details of parallel AMR data structures and algorithms (e.g., domain decomposition, grid partition, and inter-process communication), allowing the user to focus on the development of algorithms for advancing the solution of a systems of partial differential equations on a single uniform mesh. We demonstrate the use of PyAMR by simulating the pairwise coalescence of magnetic islands using the resistive Hall MHD equations. Techniques for coupling different physics models on different levels of the AMR grid hierarchy are discussed.
Integrated multi-scale modelling and simulation of nuclear fuels
International Nuclear Information System (INIS)
Valot, C.; Bertolus, M.; Masson, R.; Malerba, L.; Rachid, J.; Besmann, T.; Phillpot, S.; Stan, M.
2015-01-01
This chapter aims at discussing the objectives, implementation and integration of multi-scale modelling approaches applied to nuclear fuel materials. We will first show why the multi-scale modelling approach is required, due to the nature of the materials and by the phenomena involved under irradiation. We will then present the multiple facets of multi-scale modelling approach, while giving some recommendations with regard to its application. We will also show that multi-scale modelling must be coupled with appropriate multi-scale experiments and characterisation. Finally, we will demonstrate how multi-scale modelling can contribute to solving technology issues. (authors)
Hybrid numerical methods for multiscale simulations of subsurface biogeochemical processes
International Nuclear Information System (INIS)
Scheibe, T D; Tartakovsky, A M; Tartakovsky, D M; Redden, G D; Meakin, P
2007-01-01
Many subsurface flow and transport problems of importance today involve coupled non-linear flow, transport, and reaction in media exhibiting complex heterogeneity. In particular, problems involving biological mediation of reactions fall into this class of problems. Recent experimental research has revealed important details about the physical, chemical, and biological mechanisms involved in these processes at a variety of scales ranging from molecular to laboratory scales. However, it has not been practical or possible to translate detailed knowledge at small scales into reliable predictions of field-scale phenomena important for environmental management applications. A large assortment of numerical simulation tools have been developed, each with its own characteristic scale. Important examples include 1. molecular simulations (e.g., molecular dynamics); 2. simulation of microbial processes at the cell level (e.g., cellular automata or particle individual-based models); 3. pore-scale simulations (e.g., lattice-Boltzmann, pore network models, and discrete particle methods such as smoothed particle hydrodynamics); and 4. macroscopic continuum-scale simulations (e.g., traditional partial differential equations solved by finite difference or finite element methods). While many problems can be effectively addressed by one of these models at a single scale, some problems may require explicit integration of models across multiple scales. We are developing a hybrid multi-scale subsurface reactive transport modeling framework that integrates models with diverse representations of physics, chemistry and biology at different scales (sub-pore, pore and continuum). The modeling framework is being designed to take advantage of advanced computational technologies including parallel code components using the Common Component Architecture, parallel solvers, gridding, data and workflow management, and visualization. This paper describes the specific methods/codes being used at each
Distributed multiscale computing
Borgdorff, J.
2014-01-01
Multiscale models combine knowledge, data, and hypotheses from different scales. Simulating a multiscale model often requires extensive computation. This thesis evaluates distributing these computations, an approach termed distributed multiscale computing (DMC). First, the process of multiscale
MULTISCALE SPARSE APPEARANCE MODELING AND SIMULATION OF PATHOLOGICAL DEFORMATIONS
Directory of Open Access Journals (Sweden)
Rami Zewail
2017-08-01
Full Text Available Machine learning and statistical modeling techniques has drawn much interest within the medical imaging research community. However, clinically-relevant modeling of anatomical structures continues to be a challenging task. This paper presents a novel method for multiscale sparse appearance modeling in medical images with application to simulation of pathological deformations in X-ray images of human spine. The proposed appearance model benefits from the non-linear approximation power of Contourlets and its ability to capture higher order singularities to achieve a sparse representation while preserving the accuracy of the statistical model. Independent Component Analysis is used to extract statistical independent modes of variations from the sparse Contourlet-based domain. The new model is then used to simulate clinically-relevant pathological deformations in radiographic images.
Multiscale Lattice Boltzmann method for flow simulations in highly heterogenous porous media
Li, Jun; Brown, Donald; Calo, Victor M.; Efendiev, Yalchin R.; Illiev, Oleg
2013-01-01
.g., water and oil) are modeled using cohesive or repulsive forces, respectively. The relative permeability can be computed using pore-scale simulations and seamlessly applied for intermediate and Darcy-scale simulations. A multiscale LBM that can reduce
Fast spot-based multiscale simulations of granular drainage
Energy Technology Data Exchange (ETDEWEB)
Rycroft, Chris H.; Wong, Yee Lok; Bazant, Martin Z.
2009-05-22
We develop a multiscale simulation method for dense granular drainage, based on the recently proposed spot model, where the particle packing flows by local collective displacements in response to diffusing"spots'" of interstitial free volume. By comparing with discrete-element method (DEM) simulations of 55,000 spheres in a rectangular silo, we show that the spot simulation is able to approximately capture many features of drainage, such as packing statistics, particle mixing, and flow profiles. The spot simulation runs two to three orders of magnitude faster than DEM, making it an appropriate method for real-time control or optimization. We demonstrateextensions for modeling particle heaping and avalanching at the free surface, and for simulating the boundary layers of slower flow near walls. We show that the spot simulations are robust and flexible, by demonstrating that they can be used in both event-driven and fixed timestep approaches, and showing that the elastic relaxation step used in the model can be applied much less frequently and still create good results.
Fast Multiscale Reservoir Simulations using POD-DEIM Model Reduction
Ghasemi, Mohammadreza
2015-02-23
In this paper, we present a global-local model reduction for fast multiscale reservoir simulations in highly heterogeneous porous media with applications to optimization and history matching. Our proposed approach identifies a low dimensional structure of the solution space. We introduce an auxiliary variable (the velocity field) in our model reduction that allows achieving a high degree of model reduction. The latter is due to the fact that the velocity field is conservative for any low-order reduced model in our framework. Because a typical global model reduction based on POD is a Galerkin finite element method, and thus it can not guarantee local mass conservation. This can be observed in numerical simulations that use finite volume based approaches. Discrete Empirical Interpolation Method (DEIM) is used to approximate the nonlinear functions of fine-grid functions in Newton iterations. This approach allows achieving the computational cost that is independent of the fine grid dimension. POD snapshots are inexpensively computed using local model reduction techniques based on Generalized Multiscale Finite Element Method (GMsFEM) which provides (1) a hierarchical approximation of snapshot vectors (2) adaptive computations by using coarse grids (3) inexpensive global POD operations in a small dimensional spaces on a coarse grid. By balancing the errors of the global and local reduced-order models, our new methodology can provide an error bound in simulations. Our numerical results, utilizing a two-phase immiscible flow, show a substantial speed-up and we compare our results to the standard POD-DEIM in finite volume setup.
A framework for WRF to WRF-IBM grid nesting to enable multiscale simulations
Energy Technology Data Exchange (ETDEWEB)
Wiersema, David John [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Univ. of California, Berkeley, CA (United States); Lundquist, Katherine A. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Chow, Fotini Katapodes [Univ. of California, Berkeley, CA (United States)
2016-09-29
With advances in computational power, mesoscale models, such as the Weather Research and Forecasting (WRF) model, are often pushed to higher resolutions. As the model’s horizontal resolution is refined, the maximum resolved terrain slope will increase. Because WRF uses a terrain-following coordinate, this increase in resolved terrain slopes introduces additional grid skewness. At high resolutions and over complex terrain, this grid skewness can introduce large numerical errors that require methods, such as the immersed boundary method, to keep the model accurate and stable. Our implementation of the immersed boundary method in the WRF model, WRF-IBM, has proven effective at microscale simulations over complex terrain. WRF-IBM uses a non-conforming grid that extends beneath the model’s terrain. Boundary conditions at the immersed boundary, the terrain, are enforced by introducing a body force term to the governing equations at points directly beneath the immersed boundary. Nesting between a WRF parent grid and a WRF-IBM child grid requires a new framework for initialization and forcing of the child WRF-IBM grid. This framework will enable concurrent multi-scale simulations within the WRF model, improving the accuracy of high-resolution simulations and enabling simulations across a wide range of scales.
Development of porous structure simulator for multi-scale simulation of irregular porous catalysts
International Nuclear Information System (INIS)
Koyama, Michihisa; Suzuki, Ai; Sahnoun, Riadh; Tsuboi, Hideyuki; Hatakeyama, Nozomu; Endou, Akira; Takaba, Hiromitsu; Kubo, Momoji; Del Carpio, Carlos A.; Miyamoto, Akira
2008-01-01
Efficient development of highly functional porous materials, used as catalysts in the automobile industry, demands a meticulous knowledge of the nano-scale interface at the electronic and atomistic scale. However, it is often difficult to correlate the microscopic interfacial interactions with macroscopic characteristics of the materials; for instance, the interaction between a precious metal and its support oxide with long-term sintering properties of the catalyst. Multi-scale computational chemistry approaches can contribute to bridge the gap between micro- and macroscopic characteristics of these materials; however this type of multi-scale simulations has been difficult to apply especially to porous materials. To overcome this problem, we have developed a novel mesoscopic approach based on a porous structure simulator. This simulator can construct automatically irregular porous structures on a computer, enabling simulations with complex meso-scale structures. Moreover, in this work we have developed a new method to simulate long-term sintering properties of metal particles on porous catalysts. Finally, we have applied the method to the simulation of sintering properties of Pt on alumina support. This newly developed method has enabled us to propose a multi-scale simulation approach for porous catalysts
Multiscale modeling and simulation of microtubule-motor-protein assemblies
Gao, Tong; Blackwell, Robert; Glaser, Matthew A.; Betterton, M. D.; Shelley, Michael J.
2015-12-01
Microtubules and motor proteins self-organize into biologically important assemblies including the mitotic spindle and the centrosomal microtubule array. Outside of cells, microtubule-motor mixtures can form novel active liquid-crystalline materials driven out of equilibrium by adenosine triphosphate-consuming motor proteins. Microscopic motor activity causes polarity-dependent interactions between motor proteins and microtubules, but how these interactions yield larger-scale dynamical behavior such as complex flows and defect dynamics is not well understood. We develop a multiscale theory for microtubule-motor systems in which Brownian dynamics simulations of polar microtubules driven by motors are used to study microscopic organization and stresses created by motor-mediated microtubule interactions. We identify polarity-sorting and crosslink tether relaxation as two polar-specific sources of active destabilizing stress. We then develop a continuum Doi-Onsager model that captures polarity sorting and the hydrodynamic flows generated by these polar-specific active stresses. In simulations of active nematic flows on immersed surfaces, the active stresses drive turbulent flow dynamics and continuous generation and annihilation of disclination defects. The dynamics follow from two instabilities, and accounting for the immersed nature of the experiment yields unambiguous characteristic length and time scales. When turning off the hydrodynamics in the Doi-Onsager model, we capture formation of polar lanes as observed in the Brownian dynamics simulation.
Multiscale Data Assimilation for Large-Eddy Simulations
Li, Z.; Cheng, X.; Gustafson, W. I., Jr.; Xiao, H.; Vogelmann, A. M.; Endo, S.; Toto, T.
2017-12-01
Large-eddy simulation (LES) is a powerful tool for understanding atmospheric turbulence, boundary layer physics and cloud development, and there is a great need for developing data assimilation methodologies that can constrain LES models. The U.S. Department of Energy Atmospheric Radiation Measurement (ARM) User Facility has been developing the capability to routinely generate ensembles of LES. The LES ARM Symbiotic Simulation and Observation (LASSO) project (https://www.arm.gov/capabilities/modeling/lasso) is generating simulations for shallow convection days at the ARM Southern Great Plains site in Oklahoma. One of major objectives of LASSO is to develop the capability to observationally constrain LES using a hierarchy of ARM observations. We have implemented a multiscale data assimilation (MSDA) scheme, which allows data assimilation to be implemented separately for distinct spatial scales, so that the localized observations can be effectively assimilated to constrain the mesoscale fields in the LES area of about 15 km in width. The MSDA analysis is used to produce forcing data that drive LES. With such LES workflow we have examined 13 days with shallow convection selected from the period May-August 2016. We will describe the implementation of MSDA, present LES results, and address challenges and opportunities for applying data assimilation to LES studies.
Multiscale modeling and simulation of microtubule–motor-protein assemblies
Gao, Tong; Blackwell, Robert; Glaser, Matthew A.; Betterton, M. D.; Shelley, Michael J.
2016-01-01
Microtubules and motor proteins self-organize into biologically important assemblies including the mitotic spindle and the centrosomal microtubule array. Outside of cells, microtubule-motor mixtures can form novel active liquid-crystalline materials driven out of equilibrium by adenosine triphosphate–consuming motor proteins. Microscopic motor activity causes polarity-dependent interactions between motor proteins and microtubules, but how these interactions yield larger-scale dynamical behavior such as complex flows and defect dynamics is not well understood. We develop a multiscale theory for microtubule-motor systems in which Brownian dynamics simulations of polar microtubules driven by motors are used to study microscopic organization and stresses created by motor-mediated microtubule interactions. We identify polarity-sorting and crosslink tether relaxation as two polar-specific sources of active destabilizing stress. We then develop a continuum Doi-Onsager model that captures polarity sorting and the hydrodynamic flows generated by these polar-specific active stresses. In simulations of active nematic flows on immersed surfaces, the active stresses drive turbulent flow dynamics and continuous generation and annihilation of disclination defects. The dynamics follow from two instabilities, and accounting for the immersed nature of the experiment yields unambiguous characteristic length and time scales. When turning off the hydrodynamics in the Doi-Onsager model, we capture formation of polar lanes as observed in the Brownian dynamics simulation. PMID:26764729
Multiscale modeling and simulation of microtubule-motor-protein assemblies.
Gao, Tong; Blackwell, Robert; Glaser, Matthew A; Betterton, M D; Shelley, Michael J
2015-01-01
Microtubules and motor proteins self-organize into biologically important assemblies including the mitotic spindle and the centrosomal microtubule array. Outside of cells, microtubule-motor mixtures can form novel active liquid-crystalline materials driven out of equilibrium by adenosine triphosphate-consuming motor proteins. Microscopic motor activity causes polarity-dependent interactions between motor proteins and microtubules, but how these interactions yield larger-scale dynamical behavior such as complex flows and defect dynamics is not well understood. We develop a multiscale theory for microtubule-motor systems in which Brownian dynamics simulations of polar microtubules driven by motors are used to study microscopic organization and stresses created by motor-mediated microtubule interactions. We identify polarity-sorting and crosslink tether relaxation as two polar-specific sources of active destabilizing stress. We then develop a continuum Doi-Onsager model that captures polarity sorting and the hydrodynamic flows generated by these polar-specific active stresses. In simulations of active nematic flows on immersed surfaces, the active stresses drive turbulent flow dynamics and continuous generation and annihilation of disclination defects. The dynamics follow from two instabilities, and accounting for the immersed nature of the experiment yields unambiguous characteristic length and time scales. When turning off the hydrodynamics in the Doi-Onsager model, we capture formation of polar lanes as observed in the Brownian dynamics simulation.
Multiscale Quantum Mechanics/Molecular Mechanics Simulations with Neural Networks.
Shen, Lin; Wu, Jingheng; Yang, Weitao
2016-10-11
Molecular dynamics simulation with multiscale quantum mechanics/molecular mechanics (QM/MM) methods is a very powerful tool for understanding the mechanism of chemical and biological processes in solution or enzymes. However, its computational cost can be too high for many biochemical systems because of the large number of ab initio QM calculations. Semiempirical QM/MM simulations have much higher efficiency. Its accuracy can be improved with a correction to reach the ab initio QM/MM level. The computational cost on the ab initio calculation for the correction determines the efficiency. In this paper we developed a neural network method for QM/MM calculation as an extension of the neural-network representation reported by Behler and Parrinello. With this approach, the potential energy of any configuration along the reaction path for a given QM/MM system can be predicted at the ab initio QM/MM level based on the semiempirical QM/MM simulations. We further applied this method to three reactions in water to calculate the free energy changes. The free-energy profile obtained from the semiempirical QM/MM simulation is corrected to the ab initio QM/MM level with the potential energies predicted with the constructed neural network. The results are in excellent accordance with the reference data that are obtained from the ab initio QM/MM molecular dynamics simulation or corrected with direct ab initio QM/MM potential energies. Compared with the correction using direct ab initio QM/MM potential energies, our method shows a speed-up of 1 or 2 orders of magnitude. It demonstrates that the neural network method combined with the semiempirical QM/MM calculation can be an efficient and reliable strategy for chemical reaction simulations.
A constrained approach to multiscale stochastic simulation of chemically reacting systems
Cotter, Simon L.; Zygalakis, Konstantinos C.; Kevrekidis, Ioannis G.; Erban, Radek
2011-01-01
Stochastic simulation of coupled chemical reactions is often computationally intensive, especially if a chemical system contains reactions occurring on different time scales. In this paper, we introduce a multiscale methodology suitable to address
Atomistic to Continuum Multiscale and Multiphysics Simulation of NiTi Shape Memory Alloy
Gur, Sourav
(transformation temperature, phase fraction evolution kinetics due to temperature) are also demonstrated herein. Next, to couple and transfer the statistical information of length scale dependent phase transformation process, multiscale/ multiphysics methods are used. Here, the computational difficulty from the fact that the representative governing equations (i.e. different sub-methods such as molecular dynamics simulations, phase field simulations and continuum level constitutive/ material models) are only valid or can be implemented over a range of spatiotemporal scales. Therefore, in the present study, a wavelet based multiscale coupling method is used, where simulation results (phase fraction evolution kinetics) from different sub-methods are linked via concurrent multiscale coupling fashion. Finally, these multiscale/ multiphysics simulation results are used to develop/ modify the macro/ continuum scale thermo-mechanical constitutive relations for NiTi SMA. Finally, the improved material model is used to model new devices, such as thermal diodes and smart dampers.
Chung, Eric
2015-12-11
In this paper, we develop a mass conservative multiscale method for coupled flow and transport in heterogeneous porous media. We consider a coupled system consisting of a convection-dominated transport equation and a flow equation. We construct a coarse grid solver based on the Generalized Multiscale Finite Element Method (GMsFEM) for a coupled system. In particular, multiscale basis functions are constructed based on some snapshot spaces for the pressure and the concentration equations and some local spectral decompositions in the snapshot spaces. The resulting approach uses a few multiscale basis functions in each coarse block (for both the pressure and the concentration) to solve the coupled system. We use the mixed framework, which allows mass conservation. Our main contributions are: (1) the development of a mass conservative GMsFEM for the coupled flow and transport; (2) the development of a robust multiscale method for convection-dominated transport problems by choosing appropriate test and trial spaces within Petrov-Galerkin mixed formulation. We present numerical results and consider several heterogeneous permeability fields. Our numerical results show that with only a few basis functions per coarse block, we can achieve a good approximation.
Chung, Eric; Efendiev, Yalchin R.; Leung, Wing; Ren, Jun
2015-01-01
In this paper, we develop a mass conservative multiscale method for coupled flow and transport in heterogeneous porous media. We consider a coupled system consisting of a convection-dominated transport equation and a flow equation. We construct a coarse grid solver based on the Generalized Multiscale Finite Element Method (GMsFEM) for a coupled system. In particular, multiscale basis functions are constructed based on some snapshot spaces for the pressure and the concentration equations and some local spectral decompositions in the snapshot spaces. The resulting approach uses a few multiscale basis functions in each coarse block (for both the pressure and the concentration) to solve the coupled system. We use the mixed framework, which allows mass conservation. Our main contributions are: (1) the development of a mass conservative GMsFEM for the coupled flow and transport; (2) the development of a robust multiscale method for convection-dominated transport problems by choosing appropriate test and trial spaces within Petrov-Galerkin mixed formulation. We present numerical results and consider several heterogeneous permeability fields. Our numerical results show that with only a few basis functions per coarse block, we can achieve a good approximation.
Multiscale Hy3S: Hybrid stochastic simulation for supercomputers
Directory of Open Access Journals (Sweden)
Kaznessis Yiannis N
2006-02-01
Full Text Available Abstract Background Stochastic simulation has become a useful tool to both study natural biological systems and design new synthetic ones. By capturing the intrinsic molecular fluctuations of "small" systems, these simulations produce a more accurate picture of single cell dynamics, including interesting phenomena missed by deterministic methods, such as noise-induced oscillations and transitions between stable states. However, the computational cost of the original stochastic simulation algorithm can be high, motivating the use of hybrid stochastic methods. Hybrid stochastic methods partition the system into multiple subsets and describe each subset as a different representation, such as a jump Markov, Poisson, continuous Markov, or deterministic process. By applying valid approximations and self-consistently merging disparate descriptions, a method can be considerably faster, while retaining accuracy. In this paper, we describe Hy3S, a collection of multiscale simulation programs. Results Building on our previous work on developing novel hybrid stochastic algorithms, we have created the Hy3S software package to enable scientists and engineers to both study and design extremely large well-mixed biological systems with many thousands of reactions and chemical species. We have added adaptive stochastic numerical integrators to permit the robust simulation of dynamically stiff biological systems. In addition, Hy3S has many useful features, including embarrassingly parallelized simulations with MPI; special discrete events, such as transcriptional and translation elongation and cell division; mid-simulation perturbations in both the number of molecules of species and reaction kinetic parameters; combinatorial variation of both initial conditions and kinetic parameters to enable sensitivity analysis; use of NetCDF optimized binary format to quickly read and write large datasets; and a simple graphical user interface, written in Matlab, to help users
MATHEMATICAL SIMULATION OF CONCURRENT TWO-SIDED LENS PROCESSING
Directory of Open Access Journals (Sweden)
A. S. Kozeruk
2015-01-01
Full Text Available The purpose of the paper is to modernize technology for obtaining high-accuracy lenses with fine centre. Presently their operating surfaces are fixed to an accessory with the help of adhesive substance that leads to elastic deformation in glass and causes local errors in lens parts.A mathematical model for concurrent two-sided processing of high-accuracy optical parts with spherical surfaces has been developed in the paper. The paper presents analytical expressions that permit to calculate sliding speed at any point on the processed spherical surface depending on type and value of technological equipment settings. Calculation of parameter Q = Pv in a diametric section of the convexo-concave lens has been carried out while using these expressions together with functional dependence of pressure on contact zone еarea of tool and part bedding surfaces.Theoretical and experimental investigations have been carried out with the purpose to study changes in Q parameter according to the processed lens surface for various setting parameters of the technological equipment and their optimum values ensuring preferential stock removal in the central or boundary part zone or uniform distribution of the removal along the whole processed surface have been determined in the paper.The paper proposes a machine tool scheme for concurrent two-sided grinding and polishing of lenses while fixing their side (cylindrical surface. Machine tool kinematics makes it possible flexibly and within wide limits to change its setting parameters that significantly facilitates the control of form-building process of parts with highly-precise spherical surfaces.Methodology for investigations presupposes the following: mathematical simulation of highly-precise spherical surface form-building process under conditions of forced closing, execution of numerical and experimental studies.
Multi-Scale Initial Conditions For Cosmological Simulations
Energy Technology Data Exchange (ETDEWEB)
Hahn, Oliver; /KIPAC, Menlo Park; Abel, Tom; /KIPAC, Menlo Park /ZAH, Heidelberg /HITS, Heidelberg
2011-11-04
We discuss a new algorithm to generate multi-scale initial conditions with multiple levels of refinements for cosmological 'zoom-in' simulations. The method uses an adaptive convolution of Gaussian white noise with a real-space transfer function kernel together with an adaptive multi-grid Poisson solver to generate displacements and velocities following first- (1LPT) or second-order Lagrangian perturbation theory (2LPT). The new algorithm achieves rms relative errors of the order of 10{sup -4} for displacements and velocities in the refinement region and thus improves in terms of errors by about two orders of magnitude over previous approaches. In addition, errors are localized at coarse-fine boundaries and do not suffer from Fourier-space-induced interference ringing. An optional hybrid multi-grid and Fast Fourier Transform (FFT) based scheme is introduced which has identical Fourier-space behaviour as traditional approaches. Using a suite of re-simulations of a galaxy cluster halo our real-space-based approach is found to reproduce correlation functions, density profiles, key halo properties and subhalo abundances with per cent level accuracy. Finally, we generalize our approach for two-component baryon and dark-matter simulations and demonstrate that the power spectrum evolution is in excellent agreement with linear perturbation theory. For initial baryon density fields, it is suggested to use the local Lagrangian approximation in order to generate a density field for mesh-based codes that is consistent with the Lagrangian perturbation theory instead of the current practice of using the Eulerian linearly scaled densities.
A New Multiscale Technique for Time-Accurate Geophysics Simulations
Omelchenko, Y. A.; Karimabadi, H.
2006-12-01
Large-scale geophysics systems are frequently described by multiscale reactive flow models (e.g., wildfire and climate models, multiphase flows in porous rocks, etc.). Accurate and robust simulations of such systems by traditional time-stepping techniques face a formidable computational challenge. Explicit time integration suffers from global (CFL and accuracy) timestep restrictions due to inhomogeneous convective and diffusion processes, as well as closely coupled physical and chemical reactions. Application of adaptive mesh refinement (AMR) to such systems may not be always sufficient since its success critically depends on a careful choice of domain refinement strategy. On the other hand, implicit and timestep-splitting integrations may result in a considerable loss of accuracy when fast transients in the solution become important. To address this issue, we developed an alternative explicit approach to time-accurate integration of such systems: Discrete-Event Simulation (DES). DES enables asynchronous computation by automatically adjusting the CPU resources in accordance with local timescales. This is done by encapsulating flux- conservative updates of numerical variables in the form of events, whose execution and synchronization is explicitly controlled by imposing accuracy and causality constraints. As a result, at each time step DES self- adaptively updates only a fraction of the global system state, which eliminates unnecessary computation of inactive elements. DES can be naturally combined with various mesh generation techniques. The event-driven paradigm results in robust and fast simulation codes, which can be efficiently parallelized via a new preemptive event processing (PEP) technique. We discuss applications of this novel technology to time-dependent diffusion-advection-reaction and CFD models representative of various geophysics applications.
Fast Multiscale Reservoir Simulations using POD-DEIM Model Reduction
Ghasemi, Mohammadreza; Yang, Yanfang; Gildin, Eduardo; Efendiev, Yalchin R.; Calo, Victor M.
2015-01-01
snapshots are inexpensively computed using local model reduction techniques based on Generalized Multiscale Finite Element Method (GMsFEM) which provides (1) a hierarchical approximation of snapshot vectors (2) adaptive computations by using coarse grids (3
Implementation of Grid-computing Framework for Simulation in Multi-scale Structural Analysis
Directory of Open Access Journals (Sweden)
Data Iranata
2010-05-01
Full Text Available A new grid-computing framework for simulation in multi-scale structural analysis is presented. Two levels of parallel processing will be involved in this framework: multiple local distributed computing environments connected by local network to form a grid-based cluster-to-cluster distributed computing environment. To successfully perform the simulation, a large-scale structural system task is decomposed into the simulations of a simplified global model and several detailed component models using various scales. These correlated multi-scale structural system tasks are distributed among clusters and connected together in a multi-level hierarchy and then coordinated over the internet. The software framework for supporting the multi-scale structural simulation approach is also presented. The program architecture design allows the integration of several multi-scale models as clients and servers under a single platform. To check its feasibility, a prototype software system has been designed and implemented to perform the proposed concept. The simulation results show that the software framework can increase the speedup performance of the structural analysis. Based on this result, the proposed grid-computing framework is suitable to perform the simulation of the multi-scale structural analysis.
Multiscale simulations of ligand adsorption and exchange on gold nanoparticles.
Gao, Hui-Min; Liu, Hong; Qian, Hu-Jun; Jiao, Gui-Sheng; Lu, Zhong-Yuan
2018-01-17
We have developed a multiscale model that combines first-principles methods with atomistic and mesoscopic simulations to explore the molecular structures and packing density of the ligands present on the gold nanoparticle (AuNP) surface, as well as the adsorption/exchange reaction kinetics of cetyltrimethylammonium bromide (CTAB)/PEG-SH ligands on different facets of gold, namely, Au(111), Au(100), and Au(110). Our model predicts that on clean gold surfaces, CTAB adsorption is diffusion limited. Specifically, CTAB has the preferentially higher adsorption rate and coverage density on Au(100) and Au(110) surfaces, forming a more compact layer with respect to that on the Au(111) surface, which could result in greater growth of gold nanoparticles along the (111) direction. As opposed to CTAB adsorption, the exchange reaction between PEG-SH with CTAB shows no selectivity to different crystal faces, and the reaction process follows Langmuir diffusion kinetics. Kinetic analysis reveals that, in water, the exchange reaction is zeroth order with respect to the concentration of an incoming PEG-SH, indicative of a dissociative exchange mechanism. The observed rate constant decreases exponentially with the PEG-SH chain length, consistent with a diffusion process for the free PEG-SH in water. In particular, we show that the exchange efficiency increases as the chain rigidness and size of the incoming ligand and/or steric bulk of the initial protecting ligand shell are decreased. Our objectives are to provide a model to assess the kinetics and thermodynamics of the adsorption/exchange reaction process, and we expect that these findings will have important implications for routine surface characterization of AuNPs.
Chun, Chan; Haohua, Wen; Lanyuan, Lu; Jun, Fan
2016-01-01
Membrane curvature is no longer thought of as a passive property of the membrane; rather, it is considered as an active, regulated state that serves various purposes in the cell such as between cells and organelle definition. While transport is usually mediated by tiny membrane bubbles known as vesicles or membrane tubules, such communication requires complex interplay between the lipid bilayers and cytosolic proteins such as members of the Bin/Amphiphysin/Rvs (BAR) superfamily of proteins. With rapid developments in novel experimental techniques, membrane remodeling has become a rapidly emerging new field in recent years. Molecular dynamics (MD) simulations are important tools for obtaining atomistic information regarding the structural and dynamic aspects of biological systems and for understanding the physics-related aspects. The availability of more sophisticated experimental data poses challenges to the theoretical community for developing novel theoretical and computational techniques that can be used to better interpret the experimental results to obtain further functional insights. In this review, we summarize the general mechanisms underlying membrane remodeling controlled or mediated by proteins. While studies combining experiments and molecular dynamics simulations recall existing mechanistic models, concurrently, they extend the role of different BAR domain proteins during membrane remodeling processes. We review these recent findings, focusing on how multiscale molecular dynamics simulations aid in understanding the physical basis of BAR domain proteins, as a representative of membrane-remodeling proteins. Project supported by the National Natural Science Foundation of China (Grant No. 21403182) and the Research Grants Council of Hong Kong, China (Grant No. CityU 21300014).
Towards Faster FEM Simulation of Thin Film Superconductors: A Multiscale Approach
DEFF Research Database (Denmark)
Rodriguez Zermeno, Victor Manuel; Mijatovic, Nenad; Træholt, Chresten
2011-01-01
This work presents a method to simulate the electromagnetic properties of superconductors with high aspect ratio such as the commercially available second generation superconducting YBCO tapes. The method is based on a multiscale representation for both thickness and width of the superconducting...... at considerable lower computational time. Several test cases were simulated including transport current, externally applied magnetic field and a combination of both. The results are in good agreement with recently published numerical simulations. The computational time to solve the present multiscale approach...
A hybrid multiscale kinetic Monte Carlo method for simulation of copper electrodeposition
International Nuclear Information System (INIS)
Zheng Zheming; Stephens, Ryan M.; Braatz, Richard D.; Alkire, Richard C.; Petzold, Linda R.
2008-01-01
A hybrid multiscale kinetic Monte Carlo (HMKMC) method for speeding up the simulation of copper electrodeposition is presented. The fast diffusion events are simulated deterministically with a heterogeneous diffusion model which considers site-blocking effects of additives. Chemical reactions are simulated by an accelerated (tau-leaping) method for discrete stochastic simulation which adaptively selects exact discrete stochastic simulation for the appropriate reaction whenever that is necessary. The HMKMC method is seen to be accurate and highly efficient
Multi-scale imaging and elastic simulation of carbonates
Faisal, Titly Farhana; Awedalkarim, Ahmed; Jouini, Mohamed Soufiane; Jouiad, Mustapha; Chevalier, Sylvie; Sassi, Mohamed
2016-05-01
for this current unresolved phase is important. In this work we take a multi-scale imaging approach by first extracting a smaller 0.5" core and scanning at approx 13 Âµm, then further extracting a 5mm diameter core scanned at 5 μm. From this last scale, region of interests (containing unresolved areas) are identified for scanning at higher resolutions using Focalised Ion Beam (FIB/SEM) scanning technique reaching 50 nm resolution. Numerical simulation is run on such a small unresolved section to obtain a better estimate of the effective moduli which is then used as input for simulations performed using CT-images. Results are compared with expeirmental acoustic test moduli obtained also at two scales: 1.5" and 0.5" diameter cores.
On a multiscale approach for filter efficiency simulations
Iliev, Oleg
2014-07-01
Filtration in general, and the dead end depth filtration of solid particles out of fluid in particular, is intrinsic multiscale problem. The deposition (capturing of particles) essentially depends on local velocity, on microgeometry (pore scale geometry) of the filtering medium and on the diameter distribution of the particles. The deposited (captured) particles change the microstructure of the porous media what leads to change of permeability. The changed permeability directly influences the velocity field and pressure distribution inside the filter element. To close the loop, we mention that the velocity influences the transport and deposition of particles. In certain cases one can evaluate the filtration efficiency considering only microscale or only macroscale models, but in general an accurate prediction of the filtration efficiency requires multiscale models and algorithms. This paper discusses the single scale and the multiscale models, and presents a fractional time step discretization algorithm for the multiscale problem. The velocity within the filter element is computed at macroscale, and is used as input for the solution of microscale problems at selected locations of the porous medium. The microscale problem is solved with respect to transport and capturing of individual particles, and its solution is postprocessed to provide permeability values for macroscale computations. Results from computational experiments with an oil filter are presented and discussed.
Multiscale correlations in highly resolved Large Eddy Simulations
Biferale, Luca; Buzzicotti, Michele; Linkmann, Moritz
2017-11-01
Understanding multiscale turbulent statistics is one of the key challenges for many modern applied and fundamental problems in fluid dynamics. One of the main obstacles is the existence of anomalously strong non Gaussian fluctuations, which become more and more important with increasing Reynolds number. In order to assess the performance of LES models in reproducing these extreme events with reasonable accuracy, it is helpful to further understand the statistical properties of the coupling between the resolved and the subgrid scales. We present analytical and numerical results focussing on the multiscale correlations between the subgrid stress and the resolved velocity field obtained both from LES and filtered DNS data. Furthermore, a comparison is carried out between LES and DNS results concerning the scaling behaviour of higher-order structure functions using both Smagorinsky or self-similar Fourier sub-grid models. ERC AdG Grant No 339032 NewTURB.
Sensitivity of the scale partition for variational multiscale large-eddy simulation of channel flow
Holmen, J.; Hughes, T.J.R.; Oberai, A.A.; Wells, G.N.
2004-01-01
The variational multiscale method has been shown to perform well for large-eddy simulation (LES) of turbulent flows. The method relies upon a partition of the resolved velocity field into large- and small-scale components. The subgrid model then acts only on the small scales of motion, unlike
Multi-scale simulation of droplet-droplet interactions and coalescence
CSIR Research Space (South Africa)
Musehane, Ndivhuwo M
2016-10-01
Full Text Available Conference on Computational and Applied Mechanics Potchefstroom 3–5 October 2016 Multi-scale simulation of droplet-droplet interactions and coalescence 1,2Ndivhuwo M. Musehane?, 1Oliver F. Oxtoby and 2Daya B. Reddy 1. Aeronautic Systems, Council... topology changes that result when droplets interact. This work endeavours to eliminate the need to use empirical correlations based on phenomenological models by developing a multi-scale model that predicts the outcome of a collision between droplets from...
Vijaykumar, Adithya; Ouldridge, Thomas E.; ten Wolde, Pieter Rein; Bolhuis, Peter G.
2017-03-01
The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic Brownian, Langevin, or deterministic molecular dynamics to treat reactants at the microscopic scale [A. Vijaykumar, P. G. Bolhuis, and P. R. ten Wolde, J. Chem. Phys. 143, 214102 (2015)]. Here we extend this multiscale MD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems. We present the novel algorithm focusing on Brownian dynamics only, although the methodology is generic. We illustrate the novel algorithm using a simple patchy particle model. After validation of the algorithm, we discuss its performance. The rotational Brownian dynamics MD-GFRD multiscale method will open up the possibility for large scale simulations of protein signalling networks.
Anatomy and Physiology of Multiscale Modeling and Simulation in Systems Medicine.
Mizeranschi, Alexandru; Groen, Derek; Borgdorff, Joris; Hoekstra, Alfons G; Chopard, Bastien; Dubitzky, Werner
2016-01-01
Systems medicine is the application of systems biology concepts, methods, and tools to medical research and practice. It aims to integrate data and knowledge from different disciplines into biomedical models and simulations for the understanding, prevention, cure, and management of complex diseases. Complex diseases arise from the interactions among disease-influencing factors across multiple levels of biological organization from the environment to molecules. To tackle the enormous challenges posed by complex diseases, we need a modeling and simulation framework capable of capturing and integrating information originating from multiple spatiotemporal and organizational scales. Multiscale modeling and simulation in systems medicine is an emerging methodology and discipline that has already demonstrated its potential in becoming this framework. The aim of this chapter is to present some of the main concepts, requirements, and challenges of multiscale modeling and simulation in systems medicine.
Analyzing and designing object-oriented missile simulations with concurrency
Randorf, Jeffrey Allen
2000-11-01
A software object model for the six degree-of-freedom missile modeling domain is presented. As a precursor, a domain analysis of the missile modeling domain was started, based on the Feature-Oriented Domain Analysis (FODA) technique described by the Software Engineering Institute (SEI). It was subsequently determined the FODA methodology is functionally equivalent to the Object Modeling Technique. The analysis used legacy software documentation and code from the ENDOSIM, KDEC, and TFrames 6-DOF modeling tools, including other technical literature. The SEI Object Connection Architecture (OCA) was the template for designing the object model. Three variants of the OCA were considered---a reference structure, a recursive structure, and a reference structure with augmentation for flight vehicle modeling. The reference OCA design option was chosen for maintaining simplicity while not compromising the expressive power of the OMT model. The missile architecture was then analyzed for potential areas of concurrent computing. It was shown how protected objects could be used for data passing between OCA object managers, allowing concurrent access without changing the OCA reference design intent or structure. The implementation language was the 1995 release of Ada. OCA software components were shown how to be expressed as Ada child packages. While acceleration of several low level and other high operations level are possible on proper hardware, there was a 33% degradation of 4th order Runge-Kutta integrator performance of two simultaneous ordinary differential equations using Ada tasking on a single processor machine. The Defense Department's High Level Architecture was introduced and explained in context with the OCA. It was shown the HLA and OCA were not mutually exclusive architectures, but complimentary. HLA was shown as an interoperability solution, with the OCA as an architectural vehicle for software reuse. Further directions for implementing a 6-DOF missile modeling
Efficient Integration of Coupled Electrical-chemical Systems in Multiscale Neuronal Simulations
Directory of Open Access Journals (Sweden)
Ekaterina Brocke
2016-09-01
Full Text Available Multiscale modeling and simulations in neuroscience is gaining scientific attention due to its growing importance and unexplored capabilities. For instance, it can help to acquire better understanding of biological phenomena that have important features at multiple scales of time and space. This includes synaptic plasticity, memory formation and modulation, homeostasis. There are several ways to organize multiscale simulations depending on the scientific problem and the system to be modeled. One of the possibilities is to simulate different components of a multiscale system simultaneously and exchange data when required. The latter may become a challenging task for several reasons. One of them is that the components of a multiscale system usually span different spatial and temporal scales, such that rigorous analysis of possible coupling solutions is required. For certain classes of problems a number of coupling mechanisms have been proposed and successfully used. However, a strict mathematical theory is missing in many cases. Recent work in the field has not so far investigated artifacts that may arise during coupled integration of different approximation methods. Moreover, the coupling of widely used numerical fixed step size solvers may lead to unexpected inefficiency. In this paper we address the question of possible numerical artifacts that can arise during the integration of a coupled system. We develop an efficient strategy to couple the components of a multiscale test system. We introduce an efficient coupling method based on the second-order backward differentiation formula numerical approximation. The method uses an adaptive step size integration with an error estimation proposed by Skelboe (2000. The method shows a significant advantage over conventional fixed step size solvers used for similar problems. We explore different coupling strategies that define the organization of computations between system components. We study the
Kikuchi, Hideaki; Kalia, Rajiv; Nakano, Aiichiro; Vashishta, Priya; Iyetomi, Hiroshi; Ogata, Shuji; Kouno, Takahisa; Shimojo, Fuyuki; Tsuruta, Kanji; Saini, Subhash;
2002-01-01
A multidisciplinary, collaborative simulation has been performed on a Grid of geographically distributed PC clusters. The multiscale simulation approach seamlessly combines i) atomistic simulation backed on the molecular dynamics (MD) method and ii) quantum mechanical (QM) calculation based on the density functional theory (DFT), so that accurate but less scalable computations are performed only where they are needed. The multiscale MD/QM simulation code has been Grid-enabled using i) a modular, additive hybridization scheme, ii) multiple QM clustering, and iii) computation/communication overlapping. The Gridified MD/QM simulation code has been used to study environmental effects of water molecules on fracture in silicon. A preliminary run of the code has achieved a parallel efficiency of 94% on 25 PCs distributed over 3 PC clusters in the US and Japan, and a larger test involving 154 processors on 5 distributed PC clusters is in progress.
Physical multiscale modeling and numerical simulation of electrochemical devices for energy conversion and storage from theory to engineering to practice
Franco, Alejandro A; Bessler, Wolfgang G
2015-01-01
This book reviews the use of innovative physical multiscale modeling methods to deeply understand the electrochemical mechanisms and numerically simulate the structure and properties of electrochemical devices for energy storage and conversion.
Simulated shift work in rats perturbs multiscale regulation of locomotor activity
Hsieh, Wan-Hsin; Escobar, Carolina; Yugay, Tatiana; Lo, Men-Tzung; Pittman-Polletta, Benjamin; Salgado-Delgado, Roberto; Scheer, Frank A. J. L.; Shea, Steven A.; Buijs, Ruud M.; Hu, Kun
2014-01-01
Motor activity possesses a multiscale regulation that is characterized by fractal activity fluctuations with similar structure across a wide range of timescales spanning minutes to hours. Fractal activity patterns are disturbed in animals after ablating the master circadian pacemaker (suprachiasmatic nucleus, SCN) and in humans with SCN dysfunction as occurs with aging and in dementia, suggesting the crucial role of the circadian system in the multiscale activity regulation. We hypothesized that the normal synchronization between behavioural cycles and the SCN-generated circadian rhythms is required for multiscale activity regulation. To test the hypothesis, we studied activity fluctuations of rats in a simulated shift work protocol that was designed to force animals to be active during the habitual resting phase of the circadian/daily cycle. We found that these animals had gradually decreased mean activity level and reduced 24-h activity rhythm amplitude, indicating disturbed circadian and behavioural cycles. Moreover, these animals had disrupted fractal activity patterns as characterized by more random activity fluctuations at multiple timescales from 4 to 12 h. Intriguingly, these activity disturbances exacerbated when the shift work schedule lasted longer and persisted even in the normal days (without forced activity) following the shift work. The disrupted circadian and fractal patterns resemble those of SCN-lesioned animals and of human patients with dementia, suggesting a detrimental impact of shift work on multiscale activity regulation. PMID:24829282
Screening wells by multi-scale grids for multi-stage Markov Chain Monte Carlo simulation
DEFF Research Database (Denmark)
Akbari, Hani; Engsig-Karup, Allan Peter
2018-01-01
/production wells, aiming at accurate breakthrough capturing as well as above mentioned efficiency goals. However this short time simulation needs fine-scale structure of the geological model around wells and running a fine-scale model is not as cheap as necessary for screening steps. On the other hand applying...... it on a coarse-scale model declines important data around wells and causes inaccurate results, particularly accurate breakthrough capturing which is important for prediction applications. Therefore we propose a multi-scale grid which preserves the fine-scale model around wells (as well as high permeable regions...... and fractures) and coarsens rest of the field and keeps efficiency and accuracy for the screening well stage and coarse-scale simulation, as well. A discrete wavelet transform is used as a powerful tool to generate the desired unstructured multi-scale grid efficiently. Finally an accepted proposal on coarse...
A constrained approach to multiscale stochastic simulation of chemically reacting systems
Cotter, Simon L.
2011-01-01
Stochastic simulation of coupled chemical reactions is often computationally intensive, especially if a chemical system contains reactions occurring on different time scales. In this paper, we introduce a multiscale methodology suitable to address this problem, assuming that the evolution of the slow species in the system is well approximated by a Langevin process. It is based on the conditional stochastic simulation algorithm (CSSA) which samples from the conditional distribution of the suitably defined fast variables, given values for the slow variables. In the constrained multiscale algorithm (CMA) a single realization of the CSSA is then used for each value of the slow variable to approximate the effective drift and diffusion terms, in a similar manner to the constrained mean-force computations in other applications such as molecular dynamics. We then show how using the ensuing Fokker-Planck equation approximation, we can in turn approximate average switching times in stochastic chemical systems. © 2011 American Institute of Physics.
Multiscale Simulation of Gas Film Lubrication During Liquid Droplet Collision
Chen, Xiaodong; Khare, Prashant; Ma, Dongjun; Yang, Vigor
2012-02-01
Droplet collision plays an elementary role in dense spray combustion process. When two droplets approach each other, a gas film forms in between. The pressure generated within the film prevents motion of approaching droplets. This fluid mechanics is fluid film lubrication that occurs when opposing bearing surfaces are completely separated by fluid film. The lubrication flow in gas film decides the collision outcome, coalescence or bouncing. Present study focuses on gas film drainage process over a wide range of Weber numbers during equal- and unequal-sized droplet collision. The formulation is based on complete set of conservation equations for both liquid and surrounding gas phases. An improved volume-of-fluid technique, augmented by an adaptive mesh refinement algorithm, is used to track liquid/gas interfaces. A unique thickness-based refinement algorithm based on topology of interfacial flow is developed and implemented to efficiently resolve the multiscale problem. The grid size on interface is up O(10-4) of droplet size with a max resolution of 0.015 μm. An advanced visualization technique using the Ray-tracing methodology is used to gain direct insights to detailed physics. Theories are established by analyzing the characteristics of shape changing and flow evolution.
An open source platform for multi-scale spatially distributed simulations of microbial ecosystems
Energy Technology Data Exchange (ETDEWEB)
Segre, Daniel [Boston Univ., MA (United States)
2014-08-14
The goal of this project was to develop a tool for facilitating simulation, validation and discovery of multiscale dynamical processes in microbial ecosystems. This led to the development of an open-source software platform for Computation Of Microbial Ecosystems in Time and Space (COMETS). COMETS performs spatially distributed time-dependent flux balance based simulations of microbial metabolism. Our plan involved building the software platform itself, calibrating and testing it through comparison with experimental data, and integrating simulations and experiments to address important open questions on the evolution and dynamics of cross-feeding interactions between microbial species.
Concurrent Probabilistic Simulation of High Temperature Composite Structural Response
Abdi, Frank
1996-01-01
A computational structural/material analysis and design tool which would meet industry's future demand for expedience and reduced cost is presented. This unique software 'GENOA' is dedicated to parallel and high speed analysis to perform probabilistic evaluation of high temperature composite response of aerospace systems. The development is based on detailed integration and modification of diverse fields of specialized analysis techniques and mathematical models to combine their latest innovative capabilities into a commercially viable software package. The technique is specifically designed to exploit the availability of processors to perform computationally intense probabilistic analysis assessing uncertainties in structural reliability analysis and composite micromechanics. The primary objectives which were achieved in performing the development were: (1) Utilization of the power of parallel processing and static/dynamic load balancing optimization to make the complex simulation of structure, material and processing of high temperature composite affordable; (2) Computational integration and synchronization of probabilistic mathematics, structural/material mechanics and parallel computing; (3) Implementation of an innovative multi-level domain decomposition technique to identify the inherent parallelism, and increasing convergence rates through high- and low-level processor assignment; (4) Creating the framework for Portable Paralleled architecture for the machine independent Multi Instruction Multi Data, (MIMD), Single Instruction Multi Data (SIMD), hybrid and distributed workstation type of computers; and (5) Market evaluation. The results of Phase-2 effort provides a good basis for continuation and warrants Phase-3 government, and industry partnership.
International Nuclear Information System (INIS)
Sen, Oishik; Davis, Sean; Jacobs, Gustaaf; Udaykumar, H.S.
2015-01-01
The effectiveness of several metamodeling techniques, viz. the Polynomial Stochastic Collocation method, Adaptive Stochastic Collocation method, a Radial Basis Function Neural Network, a Kriging Method and a Dynamic Kriging Method is evaluated. This is done with the express purpose of using metamodels to bridge scales between micro- and macro-scale models in a multi-scale multimaterial simulation. The rate of convergence of the error when used to reconstruct hypersurfaces of known functions is studied. For sufficiently large number of training points, Stochastic Collocation methods generally converge faster than the other metamodeling techniques, while the DKG method converges faster when the number of input points is less than 100 in a two-dimensional parameter space. Because the input points correspond to computationally expensive micro/meso-scale computations, the DKG is favored for bridging scales in a multi-scale solver
Probabilistic Simulation of Multi-Scale Composite Behavior
Chamis, Christos C.
2012-01-01
A methodology is developed to computationally assess the non-deterministic composite response at all composite scales (from micro to structural) due to the uncertainties in the constituent (fiber and matrix) properties, in the fabrication process and in structural variables (primitive variables). The methodology is computationally efficient for simulating the probability distributions of composite behavior, such as material properties, laminate and structural responses. Bi-products of the methodology are probabilistic sensitivities of the composite primitive variables. The methodology has been implemented into the computer codes PICAN (Probabilistic Integrated Composite ANalyzer) and IPACS (Integrated Probabilistic Assessment of Composite Structures). The accuracy and efficiency of this methodology are demonstrated by simulating the uncertainties in composite typical laminates and comparing the results with the Monte Carlo simulation method. Available experimental data of composite laminate behavior at all scales fall within the scatters predicted by PICAN. Multi-scaling is extended to simulate probabilistic thermo-mechanical fatigue and to simulate the probabilistic design of a composite redome in order to illustrate its versatility. Results show that probabilistic fatigue can be simulated for different temperature amplitudes and for different cyclic stress magnitudes. Results also show that laminate configurations can be selected to increase the redome reliability by several orders of magnitude without increasing the laminate thickness--a unique feature of structural composites. The old reference denotes that nothing fundamental has been done since that time.
Multiscale simulation of yield strength in reduced-activation ferritic/martensitic steel
Energy Technology Data Exchange (ETDEWEB)
Wang, Chen Chong; Zhang, Chi; Yang, Zhigang [Key Laboratory of Advanced Materials of Ministry of Education, School of Materials Science and Engineering, Tsinghua University, Beijing (China); Zhao, Ji Jun [State Key Laboratory of Materials Modification by Laser, Electron, and Ion Beams, School of Physics and Optoelectronic Technology and College of Advanced Science and Technology, Dalian University of Technology, Dalian (China)
2017-04-15
One of the important requirements for the application of reduced-activation ferritic/martensitic (RAFM) steel is to retain proper mechanical properties under irradiation and high-temperature conditions. To simulate the yield strength and stress-strain curve of steels during high-temperature and irradiation conditions, a multiscale simulation method consisting of both microstructure and strengthening simulations was established. The simulation results of microstructure parameters were added to a superposition strengthening model, which consisted of constitutive models of different strengthening methods. Based on the simulation results, the strength contribution for different strengthening methods at both room temperature and high-temperature conditions was analyzed. The simulation results of the yield strength in irradiation and high-temperature conditions were mainly consistent with the experimental results. The optimal application field of this multiscale model was 9Cr series (7–9 wt.%Cr) RAFM steels in a condition characterized by 0.1–5 dpa (or 0 dpa) and a temperature range of 25–500°C.
Multiscale simulation of mechanical properties of TiNb alloy
Nikonov, A. Yu.
2017-12-01
The article presents a numerical simulation of the mechanical properties of a Ti-Nb β-alloy on three different scales. The ab-initio approach is used to estimate the concentrations of the Ti alloy with required elastic properties. On the basis of molecular dynamics simulation, we calculate the adhesive force between individual particles of the alloy. The calculated dependence is implemented within the movable cellular automata method to determine the mechanical properties of Ti-Nb depending on the interparticle free space.
Multiscale Lattice Boltzmann method for flow simulations in highly heterogenous porous media
Li, Jun
2013-01-01
A lattice Boltzmann method (LBM) for flow simulations in highly heterogeneous porous media at both pore and Darcy scales is proposed in the paper. In the pore scale simulations, flow of two phases (e.g., oil and gas) or two immiscible fluids (e.g., water and oil) are modeled using cohesive or repulsive forces, respectively. The relative permeability can be computed using pore-scale simulations and seamlessly applied for intermediate and Darcy-scale simulations. A multiscale LBM that can reduce the computational complexity of existing LBM and transfer the information between different scales is implemented. The results of coarse-grid, reduced-order, simulations agree very well with the averaged results obtained using fine grid.
DEFF Research Database (Denmark)
Vermesi, Izabella; Rein, Guillermo; Colella, Francesco
2017-01-01
Multiscale modelling of tunnel fires that uses a coupled 3D (fire area) and 1D (the rest of the tunnel) model is seen as the solution to the numerical problem of the large domains associated with long tunnels. The present study demonstrates the feasibility of the implementation of this method...... in FDS version 6.0, a widely used fire-specific, open source CFD software. Furthermore, it compares the reduction in simulation time given by multiscale modelling with the one given by the use of multiple processor calculation. This was done using a 1200m long tunnel with a rectangular cross......-section as a demonstration case. The multiscale implementation consisted of placing a 30MW fire in the centre of a 400m long 3D domain, along with two 400m long 1D ducts on each side of it, that were again bounded by two nodes each. A fixed volume flow was defined in the upstream duct and the two models were coupled...
Parallel Multiscale Algorithms for Astrophysical Fluid Dynamics Simulations
Norman, Michael L.
1997-01-01
Our goal is to develop software libraries and applications for astrophysical fluid dynamics simulations in multidimensions that will enable us to resolve the large spatial and temporal variations that inevitably arise due to gravity, fronts and microphysical phenomena. The software must run efficiently on parallel computers and be general enough to allow the incorporation of a wide variety of physics. Cosmological structure formation with realistic gas physics is the primary application driver in this work. Accurate simulations of e.g. galaxy formation require a spatial dynamic range (i.e., ratio of system scale to smallest resolved feature) of 104 or more in three dimensions in arbitrary topologies. We take this as our technical requirement. We have achieved, and in fact, surpassed these goals.
Simulation of left atrial function using a multi-scale model of the cardiovascular system.
Directory of Open Access Journals (Sweden)
Antoine Pironet
Full Text Available During a full cardiac cycle, the left atrium successively behaves as a reservoir, a conduit and a pump. This complex behavior makes it unrealistic to apply the time-varying elastance theory to characterize the left atrium, first, because this theory has known limitations, and second, because it is still uncertain whether the load independence hypothesis holds. In this study, we aim to bypass this uncertainty by relying on another kind of mathematical model of the cardiac chambers. In the present work, we describe both the left atrium and the left ventricle with a multi-scale model. The multi-scale property of this model comes from the fact that pressure inside a cardiac chamber is derived from a model of the sarcomere behavior. Macroscopic model parameters are identified from reference dog hemodynamic data. The multi-scale model of the cardiovascular system including the left atrium is then simulated to show that the physiological roles of the left atrium are correctly reproduced. This include a biphasic pressure wave and an eight-shaped pressure-volume loop. We also test the validity of our model in non basal conditions by reproducing a preload reduction experiment by inferior vena cava occlusion with the model. We compute the variation of eight indices before and after this experiment and obtain the same variation as experimentally observed for seven out of the eight indices. In summary, the multi-scale mathematical model presented in this work is able to correctly account for the three roles of the left atrium and also exhibits a realistic left atrial pressure-volume loop. Furthermore, the model has been previously presented and validated for the left ventricle. This makes it a proper alternative to the time-varying elastance theory if the focus is set on precisely representing the left atrial and left ventricular behaviors.
Simulation of Concurrent Precipitation of Two Strengthening Phases in Magnesium Alloys
Sun, Weihua; Zhang, Chuan; Klarner, Andrew D.; Cao, Weisheng; Luo, Alan A.
The precipitation kinetics and microtructure in Mg-Sn binary and Mg-Al-Sn ternary alloys are simulated using PanPrecipitation coupled with Mg thermodynamic database and a newly established mobility database of the Mg-Al-Sn ternary system. Both Mg2Sn and Mg17Al12 precipitates are considered in this work. The obtained kinetic parameters for these two precipitates can be used in the simulation of both individual and concurrent precipitations of Mg17Al12 and Mg2Sn in Mg-Al-Sn alloys. The simulated microstructure evolution, such as the particle size and number density, are in agreement with experimental data.
Directory of Open Access Journals (Sweden)
Xuewei Yan
2018-02-01
Full Text Available Liquid metal cooling (LMC process as a powerful directional solidification (DS technique is prospectively used to manufacture single crystal (SC turbine blades. An understanding of the temperature distribution and microstructure evolution in LMC process is required in order to improve the properties of the blades. For this reason, a multi-scale model coupling with the temperature field, grain growth and solute diffusion was established. The temperature distribution and mushy zone evolution of the hollow blade was simulated and discussed. According to the simulation results, the mushy zone might be convex and ahead of the ceramic beads at a lower withdrawal rate, while it will be concave and laggard at a higher withdrawal rate, and a uniform and horizontal mushy zone will be formed at a medium withdrawal rate. Grain growth of the blade at different withdrawal rates was also investigated. Single crystal structures were all selected out at three different withdrawal rates. Moreover, mis-orientation of the grains at 8 mm/min reached ~30°, while it was ~5° and ~15° at 10 mm/min and 12 mm/min, respectively. The model for predicting dendritic morphology was verified by corresponding experiment. Large scale for 2D dendritic distribution in the whole sections was investigated by experiment and simulation, and they presented a well agreement with each other. Keywords: Hollow blade, Single crystal, Multi-scale simulation, Liquid metal cooling
Multiscale Molecular Dynamics Simulations of Beta-Amyloid Interactions with Neurons
Qiu, Liming; Vaughn, Mark; Cheng, Kelvin
2012-10-01
Early events of human beta-amyloid protein interactions with cholesterol-containing membranes are critical to understanding the pathogenesis of Alzheimer's disease (AD) and to exploring new therapeutic interventions of AD. Atomistic molecular dynamics (AMD) simulations have been extensively used to study the protein-lipid interaction at high atomic resolutions. However, traditional MD simulations are not efficient in sampling the phase space of complex lipid/protein systems with rugged free energy landscapes. Meanwhile, coarse-grained MD (CGD) simulations are efficient in the phase space sampling but suffered from low spatial resolutions and from the fact that the energy landscapes are not identical to those of the AMD. Here, a multiscale approach was employed to simulate the protein-lipid interactions of beta-amyloid upon its release from proteolysis residing in the neuronal membranes. We utilized a forward (AMD to CGD) and reverse (CGD-AMD) strategy to explore new transmembrane and surface protein configuration and evaluate the stabilization mechanisms by measuring the residue-specific protein-lipid or protein conformations. The detailed molecular interactions revealed in this multiscale MD approach will provide new insights into understanding the early molecular events leading to the pathogenesis of AD.
International Nuclear Information System (INIS)
Yang, L H; Tang, M; Moriarty, J A
2001-01-01
Plastic deformation in bcc metals at low temperatures and high-strain rates is controlled by the motion of a/2 screw dislocations, and understanding the fundamental atomistic processes of this motion is essential to develop predictive multiscale models of crystal plasticity. The multiscale modeling approach presented here for bcc Ta is based on information passing, where results of simulations at the atomic scale are used in simulations of plastic deformation at mesoscopic length scales via dislocation dynamics (DD). The relevant core properties of a/2 screw dislocations in Ta have been obtained using quantum-based interatomic potentials derived from model generalized pseudopotential theory and an ab-initio data base together with an accurate Green's-function simulation method that implements flexible boundary conditions. In particular, the stress-dependent activation enthalpy for the lowest-energy kink-pair mechanism has been calculated and fitted to a revealing analytic form. This is the critical quantity determining dislocation mobility in the DD simulations, and the present activation enthalpy is found to be in good agreement with the previous empirical form used to explain the temperature dependence of the yield stress
A Framework for Parallel Numerical Simulations on Multi-Scale Geometries
Varduhn, Vasco
2012-06-01
In this paper, an approach on performing numerical multi-scale simulations on fine detailed geometries is presented. In particular, the focus lies on the generation of sufficient fine mesh representations, whereas a resolution of dozens of millions of voxels is inevitable in order to sufficiently represent the geometry. Furthermore, the propagation of boundary conditions is investigated by using simulation results on the coarser simulation scale as input boundary conditions on the next finer scale. Finally, the applicability of our approach is shown on a two-phase simulation for flooding scenarios in urban structures running from a city wide scale to a fine detailed in-door scale on feature rich building geometries. © 2012 IEEE.
Directory of Open Access Journals (Sweden)
Shengwei Li
2017-01-01
Full Text Available To study the micro/mesomechanical behaviors of heterogeneous geomaterials, a multiscale simulation method that combines molecular simulation at the microscale, a mesoscale analysis of polished slices, and finite element numerical simulation is proposed. By processing the mesostructure images obtained from analyzing the polished slices of heterogeneous geomaterials and mapping them onto finite element meshes, a numerical model that more accurately reflects the mesostructures of heterogeneous geomaterials was established by combining the results with the microscale mechanical properties of geomaterials obtained from the molecular simulation. This model was then used to analyze the mechanical behaviors of heterogeneous materials. Because kernstone is a typical heterogeneous material that comprises many types of mineral crystals, it was used for the micro/mesoscale mechanical behavior analysis in this paper using the proposed method. The results suggest that the proposed method can be used to accurately and effectively study the mechanical behaviors of heterogeneous geomaterials at the micro/mesoscales.
Energy Technology Data Exchange (ETDEWEB)
Choi, Yong Hee; Joo, Han Gyu, E-mail: joohan@snu.ac.kr
2013-10-15
Highlights: • A multiscale defect simulation system tailored for neutron damage estimation is introduced. • The new recoil spectrum code can use the most recent ENDF-B/VII nuclear data. • The high energy cascades are broken into subcascades using the INCAS model. • OKMC simulation provides data for shear stress estimation using dislocation dynamics formula. • Demonstration is made with a fusion blanket design having different spectral shifters. -- Abstract: A multiscale material defect simulation established to evaluate neutron induced damages on metals is applied to an estimation of material degradation in helium cooled molten lithium blankets in which four different spectral shifter materials are examined as a means of maximizing the tritium breeding ratio through proper shaping of the neutron spectrum. The multiscale system consists of a Monte Carlo neutron transport code, a recoil spectrum generation code, a molecular dynamics code, a high energy cascade breakup model, an object kinetic Monte Carlo code, and a simple formula as the shear stress estimator. The average recoil energy of the primary knock-on atoms, the total concentration of the defects, average defect sizes, and the increase in shear stress after a certain irradiation time are calculated for each spectral shifter. Among the four proposed materials of B4C, Be, Graphite and TiC, B4C reveals the best shielding performance in terms of neutron radiation hardening. The result for the increase in shear stress after 100 days of irradiation indicates that the increased shear stress is 1.5 GPa for B4C which is about 40% less than that of the worst one, the graphite spectral shifter. The other damage indicators show consistent trends.
Multiscale simulation of DC corona discharge and ozone generation from nanostructures
Wang, Pengxiang
Atmospheric direct current (dc) corona discharge from micro-sized objects has been widely used as an ion source in many devices, such as photocopiers, laser printers, and electronic air cleaners. Shrinking the size of the discharge electrode to the nanometer range (e.g., through the use of carbon nanotubes or CNTs) is expected to lead to a significant reduction in power consumption and detrimental ozone production in these devices. The objectives of this study are to unveil the fundamental physics of the nanoscale corona discharge and to evaluate its performance and ozone production through numerical models. The extremely small size of CNTs presents considerable complexity and challenges in modeling CNT corona discharges. A hybrid multiscale model, which combines a kinetic particle-in-cell plus Monte Carlo collision (PIC-MCC) model and a continuum model, is developed to simulate the corona discharge from nanostructures. The multiscale model is developed in several steps. First, a pure PIC-MCC model is developed and PIC-MCC simulations of corona plasma from micro-sized electrode with same boundary conditions as prior model are performed to validate the PIC-MCC scheme. The agreement between the PIC-MCC model and the prior continuum model indicates the validity of the PIC-MCC scheme. The validated PIC-MCC scheme is then coupled with a continuum model to simulate the corona discharge from a micro-sized electrode. Unlike the prior continuum model which only predicts the corona plasma region, the hybrid model successfully predicts the self-consistent discharge process in the entire corona discharge gap that includes both corona plasma region and unipolar ion region. The voltage-current density curves obtained by the hybrid model agree well with analytical prediction and experimental results. The hybrid modeling approach, which combines the accuracy of a kinetic model and the efficiency of a continuum model, is thus validated for modeling dc corona discharges. For
Simulating multi-scale oceanic processes around Taiwan on unstructured grids
Yu, Hao-Cheng; Zhang, Yinglong J.; Yu, Jason C. S.; Terng, C.; Sun, Weiling; Ye, Fei; Wang, Harry V.; Wang, Zhengui; Huang, Hai
2017-11-01
We validate a 3D unstructured-grid (UG) model for simulating multi-scale processes as occurred in Northwestern Pacific around Taiwan using recently developed new techniques (Zhang et al., Ocean Modeling, 102, 64-81, 2016) that require no bathymetry smoothing even for this region with prevalent steep bottom slopes and many islands. The focus is on short-term forecast for several months instead of long-term variability. Compared with satellite products, the errors for the simulated Sea-surface Height (SSH) and Sea-surface Temperature (SST) are similar to a reference data-assimilated global model. In the nearshore region, comparison with 34 tide gauges located around Taiwan indicates an average RMSE of 13 cm for the tidal elevation. The average RMSE for SST at 6 coastal buoys is 1.2 °C. The mean transport and eddy kinetic energy compare reasonably with previously published values and the reference model used to provide boundary and initial conditions. The model suggests ∼2-day interruption of Kuroshio east of Taiwan during a typhoon period. The effect of tidal mixing is shown to be significant nearshore. The multi-scale model is easily extendable to target regions of interest due to its UG framework and a flexible vertical gridding system, which is shown to be superior to terrain-following coordinates.
Multi-scale modelling and numerical simulation of electronic kinetic transport
International Nuclear Information System (INIS)
Duclous, R.
2009-11-01
This research thesis which is at the interface between numerical analysis, plasma physics and applied mathematics, deals with the kinetic modelling and numerical simulations of the electron energy transport and deposition in laser-produced plasmas, having in view the processes of fuel assembly to temperature and density conditions necessary to ignite fusion reactions. After a brief review of the processes at play in the collisional kinetic theory of plasmas, with a focus on basic models and methods to implement, couple and validate them, the author focuses on the collective aspect related to the free-streaming electron transport equation in the non-relativistic limit as well as in the relativistic regime. He discusses the numerical development and analysis of the scheme for the Vlasov-Maxwell system, and the selection of a validation procedure and numerical tests. Then, he investigates more specific aspects of the collective transport: the multi-specie transport, submitted to phase-space discontinuities. Dealing with the multi-scale physics of electron transport with collision source terms, he validates the accuracy of a fast Monte Carlo multi-grid solver for the Fokker-Planck-Landau electron-electron collision operator. He reports realistic simulations for the kinetic electron transport in the frame of the shock ignition scheme, the development and validation of a reduced electron transport angular model. He finally explores the relative importance of the processes involving electron-electron collisions at high energy by means a multi-scale reduced model with relativistic Boltzmann terms
A nuclear training simulator implementing a capability for multiple, concurrent-training sessions
International Nuclear Information System (INIS)
Groeneveld, B.J.; Nannister, D.G.; Estes, K.R.; Johnsen, M.R.
1996-01-01
The Advanced Test Reactor (ATR) Simulator at the Test Reactor Area of the Idaho National Engineering Laboratory (INEL) has recently been upgraded to reflect plant installation of a distributed control system (DCS). The ATR Simulator re-design implements traditional needs for software extensibility and plant installation prototyping, but the driving force behind its new design was an instruction requirement for multiple, concurrent-training sessions. Support is provided for up to three concurrent, independent or interacting, training sessions of reactor, balance of plant, and experiment loop operators. This capability has been achieved by modifying the existing design to consistently apply client-server, parent-child, and peer-to-peer processing technologies, and then to encapsulate concurrency software into all interfaces. When the resulting component-oriented design is linked with build and runtime flexibility in a distributed computing environment, traditional needs for extensibility and parallel software and scenario development are satisfied with minimal additional effort. Sensible configuration management practices coupled with the ability to perform piecewise system builds also greatly facilitate prototyping of plant changes prior to installation
Toward multi-scale simulation of reconnection phenomena in space plasma
Den, M.; Horiuchi, R.; Usami, S.; Tanaka, T.; Ogawa, T.; Ohtani, H.
2013-12-01
Magnetic reconnection is considered to play an important role in space phenomena such as substorm in the Earth's magnetosphere. It is well known that magnetic reconnection is controlled by microscopic kinetic mechanism. Frozen-in condition is broken due to particle kinetic effects and collisionless reconnection is triggered when current sheet is compressed as thin as ion kinetic scales under the influence of external driving flow. On the other hand configuration of the magnetic field leading to formation of diffusion region is determined in macroscopic scale and topological change after reconnection is also expressed in macroscopic scale. Thus magnetic reconnection is typical multi-scale phenomenon and microscopic and macroscopic physics are strongly coupled. Recently Horiuchi et al. developed an effective resistivity model based on particle-in-cell (PIC) simulation results obtained in study of collisionless driven reconnection and applied to a global magnetohydrodynamics (MHD) simulation of substorm in the Earth's magnetosphere. They showed reproduction of global behavior in substrom such as dipolarization and flux rope formation by global three dimensional MHD simulation. Usami et al. developed multi-hierarchy simulation model, in which macroscopic and microscopic physics are solved self-consistently and simultaneously. Based on the domain decomposition method, this model consists of three parts: a MHD algorithm for macroscopic global dynamics, a PIC algorithm for microscopic kinetic physics, and an interface algorithm to interlock macro and micro hierarchies. They verified the interface algorithm by simulation of plasma injection flow. In their latest work, this model was applied to collisionless reconnection in an open system and magnetic reconnection was successfully found. In this paper, we describe our approach to clarify multi-scale phenomena and report the current status. Our recent study about extension of the MHD domain to global system is presented. We
Modeling Coronal Mass Ejections with the Multi-Scale Fluid-Kinetic Simulation Suite
International Nuclear Information System (INIS)
Pogorelov, N. V.; Borovikov, S. N.; Wu, S. T.; Yalim, M. S.; Kryukov, I. A.; Colella, P. C.; Van Straalen, B.
2017-01-01
The solar eruptions and interacting solar wind streams are key drivers of geomagnetic storms and various related space weather disturbances that may have hazardous effects on the space-borne and ground-based technological systems as well as on human health. Coronal mass ejections (CMEs) and their interplanetary counterparts, interplanetary CMEs (ICMEs), belong to the strongest disturbances and therefore are of great importance for the space weather predictions. In this paper we show a few examples of how adaptive mesh refinement makes it possible to resolve the complex CME structure and its evolution in time while a CME propagates from the inner boundary to Earth. Simulations are performed with the Multi-Scale Fluid-Kinetic Simulation Suite (MS-FLUKSS). (paper)
Collaborative Multi-Scale 3d City and Infrastructure Modeling and Simulation
Breunig, M.; Borrmann, A.; Rank, E.; Hinz, S.; Kolbe, T.; Schilcher, M.; Mundani, R.-P.; Jubierre, J. R.; Flurl, M.; Thomsen, A.; Donaubauer, A.; Ji, Y.; Urban, S.; Laun, S.; Vilgertshofer, S.; Willenborg, B.; Menninghaus, M.; Steuer, H.; Wursthorn, S.; Leitloff, J.; Al-Doori, M.; Mazroobsemnani, N.
2017-09-01
Computer-aided collaborative and multi-scale 3D planning are challenges for complex railway and subway track infrastructure projects in the built environment. Many legal, economic, environmental, and structural requirements have to be taken into account. The stringent use of 3D models in the different phases of the planning process facilitates communication and collaboration between the stake holders such as civil engineers, geological engineers, and decision makers. This paper presents concepts, developments, and experiences gained by an interdisciplinary research group coming from civil engineering informatics and geo-informatics banding together skills of both, the Building Information Modeling and the 3D GIS world. New approaches including the development of a collaborative platform and 3D multi-scale modelling are proposed for collaborative planning and simulation to improve the digital 3D planning of subway tracks and other infrastructures. Experiences during this research and lessons learned are presented as well as an outlook on future research focusing on Building Information Modeling and 3D GIS applications for cities of the future.
COLLABORATIVE MULTI-SCALE 3D CITY AND INFRASTRUCTURE MODELING AND SIMULATION
Directory of Open Access Journals (Sweden)
M. Breunig
2017-09-01
Full Text Available Computer-aided collaborative and multi-scale 3D planning are challenges for complex railway and subway track infrastructure projects in the built environment. Many legal, economic, environmental, and structural requirements have to be taken into account. The stringent use of 3D models in the different phases of the planning process facilitates communication and collaboration between the stake holders such as civil engineers, geological engineers, and decision makers. This paper presents concepts, developments, and experiences gained by an interdisciplinary research group coming from civil engineering informatics and geo-informatics banding together skills of both, the Building Information Modeling and the 3D GIS world. New approaches including the development of a collaborative platform and 3D multi-scale modelling are proposed for collaborative planning and simulation to improve the digital 3D planning of subway tracks and other infrastructures. Experiences during this research and lessons learned are presented as well as an outlook on future research focusing on Building Information Modeling and 3D GIS applications for cities of the future.
Chierici, A.; Chirco, L.; Da Vià, R.; Manservisi, S.; Scardovelli, R.
2017-11-01
Nowadays the rapidly-increasing computational power allows scientists and engineers to perform numerical simulations of complex systems that can involve many scales and several different physical phenomena. In order to perform such simulations, two main strategies can be adopted: one may develop a new numerical code where all the physical phenomena of interest are modelled or one may couple existing validated codes. With the latter option, the creation of a huge and complex numerical code is avoided but efficient methods for data exchange are required since the performance of the simulation is highly influenced by its coupling techniques. In this work we propose a new algorithm that can be used for volume and/or boundary coupling purposes for both multiscale and multiphysics numerical simulations. The proposed algorithm is used for a multiscale simulation involving several CFD domains and monodimensional loops. We adopt the overlapping domain strategy, so the entire flow domain is simulated with the system code. We correct the system code solution by matching averaged inlet and outlet fields located at the boundaries of the CFD domains that overlap parts of the monodimensional loop. In particular we correct pressure losses and enthalpy values with source-sink terms that are imposed in the system code equations. The 1D-CFD coupling is a defective one since the CFD code requires point-wise values on the coupling interfaces and the system code provides only averaged quantities. In particular we impose, as inlet boundary conditions for the CFD domains, the mass flux and the mean enthalpy that are calculated by the system code. With this method the mass balance is preserved at every time step of the simulation. The coupling between consecutive CFD domains is not a defective one since with the proposed algorithm we can interpolate the field solutions on the boundary interfaces. We use the MED data structure as the base structure where all the field operations are
A general concurrent algorithm for plasma particle-in-cell simulation codes
International Nuclear Information System (INIS)
Liewer, P.C.; Decyk, V.K.
1989-01-01
We have developed a new algorithm for implementing plasma particle-in-cell (PIC) simulation codes on concurrent processors with distributed memory. This algorithm, named the general concurrent PIC algorithm (GCPIC), has been used to implement an electrostatic PIC code on the 33-node JPL Mark III Hypercube parallel computer. To decompose at PIC code using the GCPIC algorithm, the physical domain of the particle simulation is divided into sub-domains, equal in number to the number of processors, such that all sub-domains have roughly equal numbers of particles. For problems with non-uniform particle densities, these sub-domains will be of unequal physical size. Each processor is assigned a sub-domain and is responsible for updating the particles in its sub-domain. This algorithm has led to a a very efficient parallel implementation of a well-benchmarked 1-dimensional PIC code. The dominant portion of the code, updating the particle positions and velocities, is nearly 100% efficient when the number of particles is increased linearly with the number of hypercube processors used so that the number of particles per processor is constant. For example, the increase in time spent updating particles in going from a problem with 11,264 particles run on 1 processor to 360,448 particles on 32 processors was only 3% (parallel efficiency of 97%). Although implemented on a hypercube concurrent computer, this algorithm should also be efficient for PIC codes on other parallel architectures and for large PIC codes on sequential computers where part of the data must reside on external disks. copyright 1989 Academic Press, Inc
Multiscale simulations of the early stages of the growth of graphene on copper
Gaillard, P.; Chanier, T.; Henrard, L.; Moskovkin, P.; Lucas, S.
2015-07-01
We have performed multiscale simulations of the growth of graphene on defect-free copper (111) in order to model the nucleation and growth of graphene flakes during chemical vapour deposition and potentially guide future experimental work. Basic activation energies for atomic surface diffusion were determined by ab initio calculations. Larger scale growth was obtained within a kinetic Monte Carlo approach (KMC) with parameters based on the ab initio results. The KMC approach counts the first and second neighbours to determine the probability of surface diffusion. We report qualitative results on the size and shape of the graphene islands as a function of deposition flux. The dominance of graphene zigzag edges for low deposition flux, also observed experimentally, is explained by its larger dynamical stability that the present model fully reproduced.
Barajas-Solano, D. A.; Tartakovsky, A. M.
2017-12-01
We present a multiresolution method for the numerical simulation of flow and reactive transport in porous, heterogeneous media, based on the hybrid Multiscale Finite Volume (h-MsFV) algorithm. The h-MsFV algorithm allows us to couple high-resolution (fine scale) flow and transport models with lower resolution (coarse) models to locally refine both spatial resolution and transport models. The fine scale problem is decomposed into various "local'' problems solved independently in parallel and coordinated via a "global'' problem. This global problem is then coupled with the coarse model to strictly ensure domain-wide coarse-scale mass conservation. The proposed method provides an alternative to adaptive mesh refinement (AMR), due to its capacity to rapidly refine spatial resolution beyond what's possible with state-of-the-art AMR techniques, and the capability to locally swap transport models. We illustrate our method by applying it to groundwater flow and reactive transport of multiple species.
Yang, Shengfeng; Chen, Youping
2015-03-08
In this paper, we present the development of a concurrent atomistic-continuum (CAC) methodology for simulation of the grain boundary (GB) structures and their interaction with other defects in ionic materials. Simulation results show that the CAC simulation allows a smooth passage of cracks through the atomistic-continuum interface without the need for additional constitutive rules or special numerical treatment; both the atomic-scale structures and the energies of the four different [001] tilt GBs in bi-crystal strontium titanate obtained by CAC compare well with those obtained by existing experiments and density function theory calculations. Although 98.4% of the degrees of freedom of the simulated atomistic system have been eliminated in a coarsely meshed finite-element region, the CAC results, including the stress-strain responses, the GB-crack interaction mechanisms and the effect of the interaction on the fracture strength, are comparable with that of all-atom molecular dynamics simulation results. In addition, CAC simulation results show that the GB-crack interaction has a significant effect on the fracture behaviour of bi-crystal strontium titanate; not only the misorientation angle but also the atomic-level details of the GB structure influence the effect of the GB on impeding crack propagation.
Energy Technology Data Exchange (ETDEWEB)
Guedes, Solange da Silva
1998-07-01
Advances in petroleum reservoir descriptions have provided an amount of data that can not be handled directly during numerical simulations. This detailed geological information must be incorporated into a coarser model during multiphase fluid flow simulations by means of some upscaling technique. the most used approach is the pseudo relative permeabilities and the more widely used is the Kyte and Berry method (1975). In this work, it is proposed a multi-scale computational model for multiphase flow that implicitly treats the upscaling without using pseudo functions. By solving a sequence of local problems on subdomains of the refined scale it is possible to achieve results with a coarser grid without expensive computations of a fine grid model. The main advantage of this new procedure is to treat the upscaling step implicitly in the solution process, overcoming some practical difficulties related the use of traditional pseudo functions. results of bidimensional two phase flow simulations considering homogeneous porous media are presented. Some examples compare the results of this approach and the commercial upscaling program PSEUDO, a module of the reservoir simulation software ECLIPSE. (author)
Towards an integrated multiscale simulation of turbulent clouds on PetaScale computers
International Nuclear Information System (INIS)
Wang Lianping; Ayala, Orlando; Parishani, Hossein; Gao, Guang R; Kambhamettu, Chandra; Li Xiaoming; Rossi, Louis; Orozco, Daniel; Torres, Claudio; Grabowski, Wojciech W; Wyszogrodzki, Andrzej A; Piotrowski, Zbigniew
2011-01-01
The development of precipitating warm clouds is affected by several effects of small-scale air turbulence including enhancement of droplet-droplet collision rate by turbulence, entrainment and mixing at the cloud edges, and coupling of mechanical and thermal energies at various scales. Large-scale computation is a viable research tool for quantifying these multiscale processes. Specifically, top-down large-eddy simulations (LES) of shallow convective clouds typically resolve scales of turbulent energy-containing eddies while the effects of turbulent cascade toward viscous dissipation are parameterized. Bottom-up hybrid direct numerical simulations (HDNS) of cloud microphysical processes resolve fully the dissipation-range flow scales but only partially the inertial subrange scales. it is desirable to systematically decrease the grid length in LES and increase the domain size in HDNS so that they can be better integrated to address the full range of scales and their coupling. In this paper, we discuss computational issues and physical modeling questions in expanding the ranges of scales realizable in LES and HDNS, and in bridging LES and HDNS. We review our on-going efforts in transforming our simulation codes towards PetaScale computing, in improving physical representations in LES and HDNS, and in developing better methods to analyze and interpret the simulation results.
Multiscale Computing with the Multiscale Modeling Library and Runtime Environment
Borgdorff, J.; Mamonski, M.; Bosak, B.; Groen, D.; Ben Belgacem, M.; Kurowski, K.; Hoekstra, A.G.
2013-01-01
We introduce a software tool to simulate multiscale models: the Multiscale Coupling Library and Environment 2 (MUSCLE 2). MUSCLE 2 is a component-based modeling tool inspired by the multiscale modeling and simulation framework, with an easy-to-use API which supports Java, C++, C, and Fortran. We
Multiscale simulation of thermal disruption in resistance switching process in amorphous carbon
International Nuclear Information System (INIS)
Popov, A M; Nikishin, N G; Shumkin, G N
2015-01-01
The switching of material atomic structure and electric conductivity is used in novel technologies of making memory on the base of phase change. The possibility of making memory on the base of amorphous carbon is shown in experiment [1]. Present work is directed to simulation of experimentally observed effects. Ab initio quantum calculations were used for simulation of atomic structure changes in amorphous carbon [2]. These simulations showed that the resistance change is connected with thermally induced effects. The temperature was supposed to be the function of time. In present paper we propose a new multiscale, self-consistent model which combines three levels of simulation scales and takes into account the space and time dependencies of the temperature. On the first level of quantum molecular dynamic we provide the calculations of phase change in atomic structure with space and time dependence of the temperature. Nose-Hover thermostats are used for MD simulations to reproduce space dependency of the temperature. It is shown that atomic structure is localized near graphitic layers in conducting dot. Structure parameter is used then on the next levels of the modeling. Modified Ehrenfest Molecular Dynamics is used on the second level. Switching evolution of electronic subsystem is obtained. In macroscopic scale level the heat conductivity equation for continuous media is used for calculation space-time dependence of the temperature. Joule heat source depends on structure parameter and electric conductivity profiles obtained on previous levels of modeling. Iterative procedure is self-consistently repeated combining three levels of simulation. Space localization of Joule heat source leads to the thermal disruption. Obtained results allow us to explain S-form of the Volt-Ampere characteristic observed in experiment. Simulations were performed on IBM Blue Gene/P supercomputer at Moscow State University. (paper)
Multiscale numerical simulations of magnetoconvection at low magnetic Prandtl and Rossby numbers.
Maffei, S.; Calkins, M. A.; Julien, K. A.; Marti, P.
2017-12-01
The dynamics of the Earth's outer core is characterized by low values of the Rossby (Ro), Ekman and magnetic Prandtl numbers. These values indicate the large spectra of temporal and spatial scales that need to be accounted for in realistic numerical simulations of the system. Current direct numerical simulation are not capable of reaching this extreme regime, suggesting that a new class of models is required to account for the rich dynamics expected in the natural system. Here we present results from a quasi-geostrophic, multiscale model based on the scale separation implied by the low Ro typical of rapidly rotating systems. We investigate a plane layer geometry where convection is driven by an imposed temperature gradient and the hydrodynamic equations are modified by a large scale magnetic field. Analytical investigation shows that at values of thermal and magnetic Prandtl numbers relevant for liquid metals, the energetic requirements for the onset of convection is not significantly altered even in the presence of strong magnetic fields. Results from strongly forced nonlinear numerical simulations show the presence of an inverse cascade, typical of 2-D turbulence, when no or weak magnetic field is applied. For higher values of the magnetic field the inverse cascade is quenched.
A Novel Multi-scale Simulation Strategy for Turbulent Reacting Flows
Energy Technology Data Exchange (ETDEWEB)
James, Sutherland [University of Utah
2018-04-12
Abstract In this project, a new methodology was proposed to bridge the gap between Direct Numerical Simulation (DNS) and Large Eddy Simulation (LES). This novel methodology, titled Lattice-Based Multiscale Simulation (LBMS), creates a lattice structure of One-Dimensional Turbulence (ODT) models. This model has been shown to capture turbulent combustion with high fidelity by fully resolving interactions between turbulence and diffusion. By creating a lattice of ODT models, which are then coupled, LBMS overcomes the shortcomings of ODT, which are its inability to capture large scale three dimensional flow structures. However, by spacing these lattices significantly apart, LBMS can avoid the curse of dimensionality that creates untenable computational costs associated with DNS. This project has shown that LBMS is capable of reproducing statistics of isotropic turbulent flows while coarsening the spacing between lines significantly. It also investigates and resolves issues that arise when coupling ODT lines, such as flux reconstruction perpendicular to a given ODT line, preservation of conserved quantities when eddies cross a course cell volume and boundary condition application. Robust parallelization is also investigated.
Computational approach on PEB process in EUV resist: multi-scale simulation
Kim, Muyoung; Moon, Junghwan; Choi, Joonmyung; Lee, Byunghoon; Jeong, Changyoung; Kim, Heebom; Cho, Maenghyo
2017-03-01
For decades, downsizing has been a key issue for high performance and low cost of semiconductor, and extreme ultraviolet lithography is one of the promising candidates to achieve the goal. As a predominant process in extreme ultraviolet lithography on determining resolution and sensitivity, post exposure bake has been mainly studied by experimental groups, but development of its photoresist is at the breaking point because of the lack of unveiled mechanism during the process. Herein, we provide theoretical approach to investigate underlying mechanism on the post exposure bake process in chemically amplified resist, and it covers three important reactions during the process: acid generation by photo-acid generator dissociation, acid diffusion, and deprotection. Density functional theory calculation (quantum mechanical simulation) was conducted to quantitatively predict activation energy and probability of the chemical reactions, and they were applied to molecular dynamics simulation for constructing reliable computational model. Then, overall chemical reactions were simulated in the molecular dynamics unit cell, and final configuration of the photoresist was used to predict the line edge roughness. The presented multiscale model unifies the phenomena of both quantum and atomic scales during the post exposure bake process, and it will be helpful to understand critical factors affecting the performance of the resulting photoresist and design the next-generation material.
Simulations of ecosystem hydrological processes using a unified multi-scale model
Energy Technology Data Exchange (ETDEWEB)
Yang, Xiaofan; Liu, Chongxuan; Fang, Yilin; Hinkle, Ross; Li, Hong-Yi; Bailey, Vanessa; Bond-Lamberty, Ben
2015-01-01
This paper presents a unified multi-scale model (UMSM) that we developed to simulate hydrological processes in an ecosystem containing both surface water and groundwater. The UMSM approach modifies the Navier–Stokes equation by adding a Darcy force term to formulate a single set of equations to describe fluid momentum and uses a generalized equation to describe fluid mass balance. The advantage of the approach is that the single set of the equations can describe hydrological processes in both surface water and groundwater where different models are traditionally required to simulate fluid flow. This feature of the UMSM significantly facilitates modelling of hydrological processes in ecosystems, especially at locations where soil/sediment may be frequently inundated and drained in response to precipitation, regional hydrological and climate changes. In this paper, the UMSM was benchmarked using WASH123D, a model commonly used for simulating coupled surface water and groundwater flow. Disney Wilderness Preserve (DWP) site at the Kissimmee, Florida, where active field monitoring and measurements are ongoing to understand hydrological and biogeochemical processes, was then used as an example to illustrate the UMSM modelling approach. The simulations results demonstrated that the DWP site is subject to the frequent changes in soil saturation, the geometry and volume of surface water bodies, and groundwater and surface water exchange. All the hydrological phenomena in surface water and groundwater components including inundation and draining, river bank flow, groundwater table change, soil saturation, hydrological interactions between groundwater and surface water, and the migration of surface water and groundwater interfaces can be simultaneously simulated using the UMSM. Overall, the UMSM offers a cross-scale approach that is particularly suitable to simulate coupled surface and ground water flow in ecosystems with strong surface water and groundwater interactions.
Bolhuis, Peter
Important reaction-diffusion processes, such as biochemical networks in living cells, or self-assembling soft matter, span many orders in length and time scales. In these systems, the reactants' spatial dynamics at mesoscopic length and time scales of microns and seconds is coupled to the reactions between the molecules at microscopic length and time scales of nanometers and milliseconds. This wide range of length and time scales makes these systems notoriously difficult to simulate. While mean-field rate equations cannot describe such processes, the mesoscopic Green's Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. The recently developed multiscale Molecular Dynamics Green's Function Reaction Dynamics (MD-GFRD) approach combines GFRD for simulating the system at the mesocopic scale where particles are far apart, with microscopic Molecular (or Brownian) Dynamics, for simulating the system at the microscopic scale where reactants are in close proximity. The association and dissociation of particles are treated with rare event path sampling techniques. I will illustrate the efficiency of this method for patchy particle systems. Replacing the microscopic regime with a Markov State Model avoids the microscopic regime completely. The MSM is then pre-computed using advanced path-sampling techniques such as multistate transition interface sampling. I illustrate this approach on patchy particle systems that show multiple modes of binding. MD-GFRD is generic, and can be used to efficiently simulate reaction-diffusion systems at the particle level, including the orientational dynamics, opening up the possibility for large-scale simulations of e.g. protein signaling networks.
A voxel-based multiscale model to simulate the radiation response of hypoxic tumors.
Espinoza, I; Peschke, P; Karger, C P
2015-01-01
In radiotherapy, it is important to predict the response of tumors to irradiation prior to the treatment. This is especially important for hypoxic tumors, which are known to be highly radioresistant. Mathematical modeling based on the dose distribution, biological parameters, and medical images may help to improve this prediction and to optimize the treatment plan. A voxel-based multiscale tumor response model for simulating the radiation response of hypoxic tumors was developed. It considers viable and dead tumor cells, capillary and normal cells, as well as the most relevant biological processes such as (i) proliferation of tumor cells, (ii) hypoxia-induced angiogenesis, (iii) spatial exchange of cells leading to tumor growth, (iv) oxygen-dependent cell survival after irradiation, (v) resorption of dead cells, and (vi) spatial exchange of cells leading to tumor shrinkage. Oxygenation is described on a microscopic scale using a previously published tumor oxygenation model, which calculates the oxygen distribution for each voxel using the vascular fraction as the most important input parameter. To demonstrate the capabilities of the model, the dependence of the oxygen distribution on tumor growth and radiation-induced shrinkage is investigated. In addition, the impact of three different reoxygenation processes is compared and tumor control probability (TCP) curves for a squamous cells carcinoma of the head and neck (HNSSC) are simulated under normoxic and hypoxic conditions. The model describes the spatiotemporal behavior of the tumor on three different scales: (i) on the macroscopic scale, it describes tumor growth and shrinkage during radiation treatment, (ii) on a mesoscopic scale, it provides the cell density and vascular fraction for each voxel, and (iii) on the microscopic scale, the oxygen distribution may be obtained in terms of oxygen histograms. With increasing tumor size, the simulated tumors develop a hypoxic core. Within the model, tumor shrinkage was
A voxel-based multiscale model to simulate the radiation response of hypoxic tumors
International Nuclear Information System (INIS)
Espinoza, I.; Peschke, P.; Karger, C. P.
2015-01-01
Purpose: In radiotherapy, it is important to predict the response of tumors to irradiation prior to the treatment. This is especially important for hypoxic tumors, which are known to be highly radioresistant. Mathematical modeling based on the dose distribution, biological parameters, and medical images may help to improve this prediction and to optimize the treatment plan. Methods: A voxel-based multiscale tumor response model for simulating the radiation response of hypoxic tumors was developed. It considers viable and dead tumor cells, capillary and normal cells, as well as the most relevant biological processes such as (i) proliferation of tumor cells, (ii) hypoxia-induced angiogenesis, (iii) spatial exchange of cells leading to tumor growth, (iv) oxygen-dependent cell survival after irradiation, (v) resorption of dead cells, and (vi) spatial exchange of cells leading to tumor shrinkage. Oxygenation is described on a microscopic scale using a previously published tumor oxygenation model, which calculates the oxygen distribution for each voxel using the vascular fraction as the most important input parameter. To demonstrate the capabilities of the model, the dependence of the oxygen distribution on tumor growth and radiation-induced shrinkage is investigated. In addition, the impact of three different reoxygenation processes is compared and tumor control probability (TCP) curves for a squamous cells carcinoma of the head and neck (HNSSC) are simulated under normoxic and hypoxic conditions. Results: The model describes the spatiotemporal behavior of the tumor on three different scales: (i) on the macroscopic scale, it describes tumor growth and shrinkage during radiation treatment, (ii) on a mesoscopic scale, it provides the cell density and vascular fraction for each voxel, and (iii) on the microscopic scale, the oxygen distribution may be obtained in terms of oxygen histograms. With increasing tumor size, the simulated tumors develop a hypoxic core. Within the
Carmeliet, J.; Descamps, F.; Houvenaghel, G.
1999-01-01
A multiscale network model is presented to model unsaturated moisture transfer in hygroscopic capillary-porous materials showing a broad pore-size distribution. Both capillary effects and water sorption phenomena, water vapour and liquid water transfer are considered. The multiscale approach is
Modeling and Simulation of Electromutagenic Processes for Multiscale Modification of Concrete
Directory of Open Access Journals (Sweden)
Daniela S. Mainardi
2009-04-01
Full Text Available Concrete contains numerous pores that allow degradation when chloride ions migrate through these paths and make contact with the steel reinforcement in a structure. Chlorides come mainly from the sea or de-icing salts. To keep the reinforcement from being exposed to chlorides, it is possible to electrokinetically force nanoparticles into the pores, blocking access. This procedure is called electrokinetic nanoparticle treatment. When the particles used are reactive in nature, the process becomes both structural and chemical in nature. We use the term electromutagenic processing to describe such extensive electrochemical remodeling. Filling the pores in a block of concrete with solid materials or nanoparticles tends to improve the strength significantly. In this paper, results obtained from modeling and simulation were aimed at multi-scale porosity reduction of concrete. Since nanoparticles and pores were modeled with spheres and cylinders having different sizes, the results were compared with traditional sphere packing problems in mathematics. There were significant differences observed related to the sizes of spheres and allowable boundary conditions. From traditional sphere packing analysis the highest porosity reduction anticipated was 74%. In contrast, the highest pore reduction obtained in this work was approximately 50%, which matched results from actual electrokinetic nanoparticle treatments. This work also compared the analytical and simulation methods used for several sizes of nanoparticles and pores.
Development of a multi-scale simulation model of tube hydroforming for superconducting RF cavities
Energy Technology Data Exchange (ETDEWEB)
Kim, H.S. [Department of Materials Science and Engineering, The Ohio State University, Columbus, OH (United States); Sumption, M.D., E-mail: sumption.3@osu.edu [Department of Materials Science and Engineering, The Ohio State University, Columbus, OH (United States); Bong, H.J. [Department of Materials Science and Engineering, The Ohio State University, Columbus, OH (United States); Lim, H. [Sandia National Laboratories, Albuquerque, NM (United States); Collings, E.W. [Department of Materials Science and Engineering, The Ohio State University, Columbus, OH (United States)
2017-01-02
This work focuses on finite element modeling of the hydroforming process for niobium tubes intended for use in superconducting radio frequency (SRF) cavities. The hydroforming of tubular samples into SRF-relevant shapes involves the complex geometries and loading conditions which develop during the deformation, as well as anisotropic materials properties. Numerical description of the process entails relatively complex numerical simulations. A crystal plasticity (CP) model was constructed that included the evolution of crystallographic orientation during deformation as well as the anisotropy of tubes in all directions and loading conditions. In this work we demonstrate a multi-scale simulation approach which uses both microscopic CP and macroscopic continuum models. In this approach a CP model (developed and implemented into ABAQUS using UMAT) was used for determining the flow stress curve only under bi-axial loading in order to reduce the computing time. The texture of the materials obtained using orientation imaging microscopy (OIM) and tensile test data were inputs for this model. Continuum FE analysis of tube hydroforming using the obtained constitutive equation from the CP modeling was then performed and compared to the results of hydraulic bulge testing. The results show that high quality predictions of the deformation under hydroforming of Nb tubes can be obtained using CP-FEM based on their known texture and the results of tensile tests. The importance of the CP-FEM based approach is that it reduces the need for hydraulic bulge testing, using a relatively simple computational approach.
Self-Adaptive Event-Driven Simulation of Multi-Scale Plasma Systems
Omelchenko, Yuri; Karimabadi, Homayoun
2005-10-01
Multi-scale plasmas pose a formidable computational challenge. The explicit time-stepping models suffer from the global CFL restriction. Efficient application of adaptive mesh refinement (AMR) to systems with irregular dynamics (e.g. turbulence, diffusion-convection-reaction, particle acceleration etc.) may be problematic. To address these issues, we developed an alternative approach to time stepping: self-adaptive discrete-event simulation (DES). DES has origin in operations research, war games and telecommunications. We combine finite-difference and particle-in-cell techniques with this methodology by assuming two caveats: (1) a local time increment, dt for a discrete quantity f can be expressed in terms of a physically meaningful quantum value, df; (2) f is considered to be modified only when its change exceeds df. Event-driven time integration is self-adaptive as it makes use of causality rules rather than parametric time dependencies. This technique enables asynchronous flux-conservative update of solution in accordance with local temporal scales, removes the curse of the global CFL condition, eliminates unnecessary computation in inactive spatial regions and results in robust and fast parallelizable codes. It can be naturally combined with various mesh refinement techniques. We discuss applications of this novel technology to diffusion-convection-reaction systems and hybrid simulations of magnetosonic shocks.
Development of a multi-scale simulation model of tube hydroforming for superconducting RF cavities
International Nuclear Information System (INIS)
Kim, H.S.; Sumption, M.D.; Bong, H.J.; Lim, H.; Collings, E.W.
2017-01-01
This work focuses on finite element modeling of the hydroforming process for niobium tubes intended for use in superconducting radio frequency (SRF) cavities. The hydroforming of tubular samples into SRF-relevant shapes involves the complex geometries and loading conditions which develop during the deformation, as well as anisotropic materials properties. Numerical description of the process entails relatively complex numerical simulations. A crystal plasticity (CP) model was constructed that included the evolution of crystallographic orientation during deformation as well as the anisotropy of tubes in all directions and loading conditions. In this work we demonstrate a multi-scale simulation approach which uses both microscopic CP and macroscopic continuum models. In this approach a CP model (developed and implemented into ABAQUS using UMAT) was used for determining the flow stress curve only under bi-axial loading in order to reduce the computing time. The texture of the materials obtained using orientation imaging microscopy (OIM) and tensile test data were inputs for this model. Continuum FE analysis of tube hydroforming using the obtained constitutive equation from the CP modeling was then performed and compared to the results of hydraulic bulge testing. The results show that high quality predictions of the deformation under hydroforming of Nb tubes can be obtained using CP-FEM based on their known texture and the results of tensile tests. The importance of the CP-FEM based approach is that it reduces the need for hydraulic bulge testing, using a relatively simple computational approach.
International Nuclear Information System (INIS)
NiewieczerzaŁ, Daniel; Oleksy, CzesŁaw; Szczepkowicz, Andrzej
2012-01-01
Multi-scale simulations of field ion microscopy images of faceted and hemispherical samples are performed using a 3D model. It is shown that faceted crystals have compressed images even in cases with no shank. The presence of the shank increases the compression of images of faceted crystals quantitatively in the same way as for hemispherical samples. It is hereby proven that the shank does not influence significantly the local, relative variations of the magnification caused by the atomic-scale structure of the sample. -- Highlights: ► Multi-scale simulations of field ion microscopy images. ► Faceted and hemispherical samples with and without shank. ► Shank causes overall compression, but does not influence local magnification effects. ► Image compression linearly increases with the shank angle. ► Shank changes compression of image of faceted tip in the same way as for smooth sample.
Vision 2040: A Roadmap for Integrated, Multiscale Modeling and Simulation of Materials and Systems
Liu, Xuan; Furrer, David; Kosters, Jared; Holmes, Jack
2018-01-01
Over the last few decades, advances in high-performance computing, new materials characterization methods, and, more recently, an emphasis on integrated computational materials engineering (ICME) and additive manufacturing have been a catalyst for multiscale modeling and simulation-based design of materials and structures in the aerospace industry. While these advances have driven significant progress in the development of aerospace components and systems, that progress has been limited by persistent technology and infrastructure challenges that must be overcome to realize the full potential of integrated materials and systems design and simulation modeling throughout the supply chain. As a result, NASA's Transformational Tools and Technology (TTT) Project sponsored a study (performed by a diverse team led by Pratt & Whitney) to define the potential 25-year future state required for integrated multiscale modeling of materials and systems (e.g., load-bearing structures) to accelerate the pace and reduce the expense of innovation in future aerospace and aeronautical systems. This report describes the findings of this 2040 Vision study (e.g., the 2040 vision state; the required interdependent core technical work areas, Key Element (KE); identified gaps and actions to close those gaps; and major recommendations) which constitutes a community consensus document as it is a result of over 450 professionals input obtain via: 1) four society workshops (AIAA, NAFEMS, and two TMS), 2) community-wide survey, and 3) the establishment of 9 expert panels (one per KE) consisting on average of 10 non-team members from academia, government and industry to review, update content, and prioritize gaps and actions. The study envisions the development of a cyber-physical-social ecosystem comprised of experimentally verified and validated computational models, tools, and techniques, along with the associated digital tapestry, that impacts the entire supply chain to enable cost
Lardeau, Sylvain; Ferrari, Simone; Rossi, Lionel
2008-12-01
Three-dimensional (3D) direct numerical simulations of a flow driven by multiscale electromagnetic forcing are performed in order to reproduce with maximum accuracy the quasi-two-dimensional (2D) flow generated by the same multiscale forcing in the laboratory. The method presented is based on a 3D description of the flow and the electromagnetic forcing. Very good agreements between our simulations and the experiments are found both on velocity and acceleration field, this last comparison being, to our knowledge, done for the first time. Such agreement requires that both experiments and simulations are carefully performed and, more importantly, that the underlying simplification to model the experiments and the multiscale electromagnetic forcing do not introduce significant errors. The results presented in this paper differ significantly from previous 2D direct numerical simulation in which a classical linear Rayleigh friction modeling term was used to mimic the effect of the wall-normal friction. Indeed, purely 2D simulations are found to underestimate the Reynolds number and, due to the dominance of nonhomogeneous bottom friction, lead to the wrong physical mechanism. For the range of conditions presented in this paper, the Reynolds number, defined by the ratio between acceleration and viscous terms, remains the order of unity, and the Hartmann number, defined by the ratio between electromagnetic force terms and viscous terms, is about 2. The main conclusion is that 3D simulations are required to model the (3D) electromagnetic forces and the wall-normal shear. Indeed, even if the flow is quasi-2D in terms of energy, a full 3D approach is required to simulate these shallow layer flows driven by multiscale electromagnetic forcing. In the range of forcing intensity investigated in this paper, these multiscale flows remain quasi-2D, with negligible energy in the wall-normal velocity component. It is also shown that the driving terms are the electromagnetic forcing and
Ható, Zoltán; Valiskó, Mónika; Kristóf, Tamás; Gillespie, Dirk; Boda, Dezsö
2017-07-21
In a multiscale modeling approach, we present computer simulation results for a rectifying bipolar nanopore at two modeling levels. In an all-atom model, we use explicit water to simulate ion transport directly with the molecular dynamics technique. In a reduced model, we use implicit water and apply the Local Equilibrium Monte Carlo method together with the Nernst-Planck transport equation. This hybrid method makes the fast calculation of ion transport possible at the price of lost details. We show that the implicit-water model is an appropriate representation of the explicit-water model when we look at the system at the device (i.e., input vs. output) level. The two models produce qualitatively similar behavior of the electrical current for different voltages and model parameters. Looking at the details of concentration and potential profiles, we find profound differences between the two models. These differences, however, do not influence the basic behavior of the model as a device because they do not influence the z-dependence of the concentration profiles which are the main determinants of current. These results then address an old paradox: how do reduced models, whose assumptions should break down in a nanoscale device, predict experimental data? Our simulations show that reduced models can still capture the overall device physics correctly, even though they get some important aspects of the molecular-scale physics quite wrong; reduced models work because they include the physics that is necessary from the point of view of device function. Therefore, reduced models can suffice for general device understanding and device design, but more detailed models might be needed for molecular level understanding.
Multiscale Simulation of Porous Ceramics Based on Movable Cellular Automaton Method
Smolin, A.; Smolin, I.; Eremina, G.; Smolina, I.
2017-10-01
The paper presents a model for simulating mechanical behaviour of multiscale porous ceramics based on movable cellular automaton method, which is a novel particle method in computational mechanics of solid. The initial scale of the proposed approach corresponds to the characteristic size of the smallest pores in the ceramics. At this scale, we model uniaxial compression of several representative samples with an explicit account of pores of the same size but with the random unique position in space. As a result, we get the average values of Young’s modulus and strength, as well as the parameters of the Weibull distribution of these properties at the current scale level. These data allow us to describe the material behaviour at the next scale level were only the larger pores are considered explicitly, while the influence of small pores is included via the effective properties determined at the previous scale level. If the pore size distribution function of the material has N maxima we need to perform computations for N - 1 levels in order to get the properties from the lowest scale up to the macroscale step by step. The proposed approach was applied to modelling zirconia ceramics with bimodal pore size distribution. The obtained results show correct behaviour of the model sample at the macroscale.
The Cea multi-scale and multi-physics simulation project for nuclear applications
International Nuclear Information System (INIS)
Ledermann, P.; Chauliac, C.; Thomas, J.B.
2005-01-01
Full text of publication follows. Today numerical modelling is everywhere recognized as an essential tool of capitalization, integration and share of knowledge. For this reason, it becomes the central tool of research. Until now, the Cea developed a set of scientific software allowing to model, in each situation, the operation of whole or part of a nuclear installation and these codes are largely used in nuclear industry. However, for the future, it is essential to aim for a better accuracy, a better control of uncertainties and better performance in computing times. The objective is to obtain validated models allowing accurate predictive calculations for actual complex nuclear problems such as fuel behaviour in accidental situation. This demands to master a large and interactive set of phenomena ranging from nuclear reaction to heat transfer. To this end, Cea, with industrial partners (EDF, Framatome-ANP, ANDRA) has designed an integrated platform of calculation, devoted to the study of nuclear systems, and intended at the same time for industries and scientists. The development of this platform is under way with the start in 2005 of the integrated project NURESIM, with 18 European partners. Improvement is coming not only through a multi-scale description of all phenomena but also through an innovative design approach requiring deep functional analysis which is upstream from the development of the simulation platform itself. In addition, the studies of future nuclear systems are increasingly multidisciplinary (simultaneous modelling of core physics, thermal-hydraulics and fuel behaviour). These multi-physics and multi-scale aspects make mandatory to pay very careful attention to software architecture issues. A global platform is thus developed integrating dedicated specialized platforms: DESCARTES for core physics, NEPTUNE for thermal-hydraulics, PLEIADES for fuel behaviour, SINERGY for materials behaviour under irradiation, ALLIANCES for the performance
International Nuclear Information System (INIS)
Bestion, D.
2010-01-01
A multi-scale analysis of water-cooled reactor thermal hydraulics can be used to take advantage of increased computer power and improved simulation tools, including Direct Numerical Simulation (DNS), Computational Fluid Dynamics (CFD) (in both open and porous mediums), and system thermalhydraulic codes. This paper presents a general strategy for this procedure for various thermalhydraulic scales. A short state of the art is given for each scale, and the role of the scale in the overall multi-scale analysis process is defined. System thermalhydraulic codes will remain a privileged tool for many investigations related to safety. CFD in porous medium is already being frequently used for core thermal hydraulics, either in 3D modules of system codes or in component codes. CFD in open medium allows zooming on some reactor components in specific situations, and may be coupled to the system and component scales. Various modeling approaches exist in the domain from DNS to CFD which may be used to improve the understanding of flow processes, and as a basis for developing more physically based models for macroscopic tools. A few examples are given to illustrate the multi-scale approach. Perspectives for the future are drawn from the present state of the art and directions for future research and development are given
The Study of Non-Linear Acceleration of Particles during Substorms Using Multi-Scale Simulations
International Nuclear Information System (INIS)
Ashour-Abdalla, Maha
2011-01-01
To understand particle acceleration during magnetospheric substorms we must consider the problem on multple scales ranging from the large scale changes in the entire magnetosphere to the microphysics of wave particle interactions. In this paper we present two examples that demonstrate the complexity of substorm particle acceleration and its multi-scale nature. The first substorm provided us with an excellent example of ion acceleration. On March 1, 2008 four THEMIS spacecraft were in a line extending from 8 R E to 23 R E in the magnetotail during a very large substorm during which ions were accelerated to >500 keV. We used a combination of a global magnetohydrodynamic and large scale kinetic simulations to model the ion acceleration and found that the ions gained energy by non-adiabatic trajectories across the substorm electric field in a narrow region extending across the magnetotail between x = -10 R E and x = -15 R E . In this strip called the 'wall region' the ions move rapidly in azimuth and gain 100s of keV. In the second example we studied the acceleration of electrons associated with a pair of dipolarization fronts during a substorm on February 15, 2008. During this substorm three THEMIS spacecraft were grouped in the near-Earth magnetotail (x ∼-10 R E ) and observed electron acceleration of >100 keV accompanied by intense plasma waves. We used the MHD simulations and analytic theory to show that adiabatic motion (betatron and Fermi acceleration) was insufficient to account for the electron acceleration and that kinetic processes associated with the plasma waves were important.
Multiscale Simulation and Modeling of Multilayer Heteroepitactic Growth of C60 on Pentacene.
Acevedo, Yaset M; Cantrell, Rebecca A; Berard, Philip G; Koch, Donald L; Clancy, Paulette
2016-03-29
We apply multiscale methods to describe the strained growth of multiple layers of C60 on a thin film of pentacene. We study this growth in the presence of a monolayer pentacene step to compare our simulations to recent experimental studies by Breuer and Witte of submonolayer growth in the presence of monolayer steps. The molecular-level details of this organic semiconductor interface have ramifications on the macroscale structural and electronic behavior of this system and allow us to describe several unexplained experimental observations for this system. The growth of a C60 thin film on a pentacene surface is complicated by the differing crystal habits of the two component species, leading to heteroepitactical growth. In order to probe this growth, we use three computational methods that offer different approaches to coarse-graining the system and differing degrees of computational efficiency. We present a new, efficient reaction-diffusion continuum model for 2D systems whose results compare well with mesoscale kinetic Monte Carlo (KMC) results for submonolayer growth. KMC extends our ability to simulate multiple layers but requires a library of predefined rates for event transitions. Coarse-grained molecular dynamics (CGMD) circumvents KMC's need for predefined lattices, allowing defects and grain boundaries to provide a more realistic thin film morphology. For multilayer growth, in this particularly suitable candidate for coarse-graining, CGMD is a preferable approach to KMC. Combining the results from these three methods, we show that the lattice strain induced by heteroepitactical growth promotes 3D growth and the creation of defects in the first monolayer. The CGMD results are consistent with experimental results on the same system by Conrad et al. and by Breuer and Witte in which C60 aggregates change from a 2D structure at low temperature to 3D clusters along the pentacene step edges at higher temperatures.
Multiscale computing in the exascale era
Alowayyed, S.; Groen, D.; Coveney, P.V.; Hoekstra, A.G.
We expect that multiscale simulations will be one of the main high performance computing workloads in the exascale era. We propose multiscale computing patterns as a generic vehicle to realise load balanced, fault tolerant and energy aware high performance multiscale computing. Multiscale computing
International Nuclear Information System (INIS)
Cruz, Roberto de la; Guerrero, Pilar; Calvo, Juan; Alarcón, Tomás
2017-01-01
of front, which cannot be accounted for by the coarse-grained model. Such fluctuations have non-trivial effects on the wave velocity. Beyond the development of a new hybrid method, we thus conclude that birth-rate fluctuations are central to a quantitatively accurate description of invasive phenomena such as tumour growth. - Highlights: • A hybrid method for stochastic multi-scale models of cells populations that extends existing hybrid methods for reaction–diffusion system. • Our analysis unveils non-trivial macroscopic effects triggered by noise at the level of structuring variables. • Our hybrid method hugely speeds up age-structured SSA simulations while preserving stochastic effects.
Energy Technology Data Exchange (ETDEWEB)
Dombroski, M; Melius, C; Edmunds, T; Banks, L E; Bates, T; Wheeler, R
2008-09-24
This study uses the Multi-scale Epidemiologic Simulation and Analysis (MESA) system developed for foreign animal diseases to assess consequences of nationwide human infectious disease outbreaks. A literature review identified the state of the art in both small-scale regional models and large-scale nationwide models and characterized key aspects of a nationwide epidemiological model. The MESA system offers computational advantages over existing epidemiological models and enables a broader array of stochastic analyses of model runs to be conducted because of those computational advantages. However, it has only been demonstrated on foreign animal diseases. This paper applied the MESA modeling methodology to human epidemiology. The methodology divided 2000 US Census data at the census tract level into school-bound children, work-bound workers, elderly, and stay at home individuals. The model simulated mixing among these groups by incorporating schools, workplaces, households, and long-distance travel via airports. A baseline scenario with fixed input parameters was run for a nationwide influenza outbreak using relatively simple social distancing countermeasures. Analysis from the baseline scenario showed one of three possible results: (1) the outbreak burned itself out before it had a chance to spread regionally, (2) the outbreak spread regionally and lasted a relatively long time, although constrained geography enabled it to eventually be contained without affecting a disproportionately large number of people, or (3) the outbreak spread through air travel and lasted a long time with unconstrained geography, becoming a nationwide pandemic. These results are consistent with empirical influenza outbreak data. The results showed that simply scaling up a regional small-scale model is unlikely to account for all the complex variables and their interactions involved in a nationwide outbreak. There are several limitations of the methodology that should be explored in future
Toward Multi-scale Modeling and simulation of conduction in heterogeneous materials
Energy Technology Data Exchange (ETDEWEB)
Lechman, Jeremy B. [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Battaile, Corbett Chandler. [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Bolintineanu, Dan [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Cooper, Marcia A. [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Erikson, William W. [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Foiles, Stephen M. [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Kay, Jeffrey J [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Phinney, Leslie M. [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Piekos, Edward S. [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Specht, Paul Elliott [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Wixom, Ryan R. [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Yarrington, Cole [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States)
2015-01-01
This report summarizes a project in which the authors sought to develop and deploy: (i) experimental techniques to elucidate the complex, multiscale nature of thermal transport in particle-based materials; and (ii) modeling approaches to address current challenges in predicting performance variability of materials (e.g., identifying and characterizing physical- chemical processes and their couplings across multiple length and time scales, modeling information transfer between scales, and statically and dynamically resolving material structure and its evolution during manufacturing and device performance). Experimentally, several capabilities were successfully advanced. As discussed in Chapter 2 a flash diffusivity capability for measuring homogeneous thermal conductivity of pyrotechnic powders (and beyond) was advanced; leading to enhanced characterization of pyrotechnic materials and properties impacting component development. Chapter 4 describes success for the first time, although preliminary, in resolving thermal fields at speeds and spatial scales relevant to energetic components. Chapter 7 summarizes the first ever (as far as the authors know) application of TDTR to actual pyrotechnic materials. This is the first attempt to actually characterize these materials at the interfacial scale. On the modeling side, new capabilities in image processing of experimental microstructures and direct numerical simulation on complicated structures were advanced (see Chapters 3 and 5). In addition, modeling work described in Chapter 8 led to improved prediction of interface thermal conductance from first principles calculations. Toward the second point, for a model system of packed particles, significant headway was made in implementing numerical algorithms and collecting data to justify the approach in terms of highlighting the phenomena at play and pointing the way forward in developing and informing the kind of modeling approach originally envisioned (see Chapter 6). In
Integrated multiscale simulation of combined heat and power based district heating system
International Nuclear Information System (INIS)
Li, Peifeng; Nord, Natasa; Ertesvåg, Ivar Ståle; Ge, Zhihua; Yang, Zhiping; Yang, Yongping
2015-01-01
Highlights: • Simulation of power plant, district heating network and heat users in detail and integrated. • Coupled calculation and analysis of the heat and pressure losses of the district heating network. • District heating is not preferable for very low heat load due to relatively high heat loss. • Lower design supply temperatures of the district heating network give higher system efficiency. - Abstract: Many studies have been carried out separately on combined heat and power and district heating. However, little work has been done considering the heat source, the district heating network and the heat users simultaneously, especially when it comes to the heating system with large-scale combined heat and power plant. For the purpose of energy conservation, it is very important to know well the system performance of the integrated heating system from the very primary fuel input to the terminal heat users. This paper set up a model of 300 MW electric power rated air-cooled combined heat and power plant using Ebsilon software, which was validated according to the design data from the turbine manufacturer. Then, the model of heating network and heat users were developed based on the fundamental theories of fluid mechanics and heat transfer. Finally the combined heat and power based district heating system was obtained and the system performances within multiscale scope of the system were analyzed using the developed Ebsilon model. Topics with regard to the heat loss, the pressure drop, the pump power consumption and the supply temperatures of the district heating network were discussed. Besides, the operational issues of the integrated system were also researched. Several useful conclusions were drawn. It was found that a lower design primary supply temperature of the district heating network would give a higher seasonal energy efficiency of the integrated system throughout the whole heating season. Moreover, it was not always right to relate low design
Xiao, Li; Luo, Ray
2017-12-07
We explored a multi-scale algorithm for the Poisson-Boltzmann continuum solvent model for more robust simulations of biomolecules. In this method, the continuum solvent/solute interface is explicitly simulated with a numerical fluid dynamics procedure, which is tightly coupled to the solute molecular dynamics simulation. There are multiple benefits to adopt such a strategy as presented below. At this stage of the development, only nonelectrostatic interactions, i.e., van der Waals and hydrophobic interactions, are included in the algorithm to assess the quality of the solvent-solute interface generated by the new method. Nevertheless, numerical challenges exist in accurately interpolating the highly nonlinear van der Waals term when solving the finite-difference fluid dynamics equations. We were able to bypass the challenge rigorously by merging the van der Waals potential and pressure together when solving the fluid dynamics equations and by considering its contribution in the free-boundary condition analytically. The multi-scale simulation method was first validated by reproducing the solute-solvent interface of a single atom with analytical solution. Next, we performed the relaxation simulation of a restrained symmetrical monomer and observed a symmetrical solvent interface at equilibrium with detailed surface features resembling those found on the solvent excluded surface. Four typical small molecular complexes were then tested, both volume and force balancing analyses showing that these simple complexes can reach equilibrium within the simulation time window. Finally, we studied the quality of the multi-scale solute-solvent interfaces for the four tested dimer complexes and found that they agree well with the boundaries as sampled in the explicit water simulations.
Modeling and simulation of high dimensional stochastic multiscale PDE systems at the exascale
Energy Technology Data Exchange (ETDEWEB)
Zabaras, Nicolas J. [Cornell Univ., Ithaca, NY (United States)
2016-11-08
Predictive Modeling of multiscale and Multiphysics systems requires accurate data driven characterization of the input uncertainties, and understanding of how they propagate across scales and alter the final solution. This project develops a rigorous mathematical framework and scalable uncertainty quantification algorithms to efficiently construct realistic low dimensional input models, and surrogate low complexity systems for the analysis, design, and control of physical systems represented by multiscale stochastic PDEs. The work can be applied to many areas including physical and biological processes, from climate modeling to systems biology.
Runge, Keith; Muralidharan, Krishna
2016-01-01
This book presents cutting-edge concepts, paradigms, and research highlights in the field of computational materials science and engineering, and provides a fresh, up-to-date perspective on solving present and future materials challenges. The chapters are written by not only pioneers in the fields of computational materials chemistry and materials science, but also experts in multi-scale modeling and simulation as applied to materials engineering. Pedagogical introductions to the different topics and continuity between the chapters are provided to ensure the appeal to a broad audience and to address the applicability of integrated computational materials science and engineering for solving real-world problems.
Energy Technology Data Exchange (ETDEWEB)
Hammond, Glenn Edward; Yang, Xiaofan; Song, Xuehang; Song, Hyun-Seob; Hou, Zhangshuan; Chen, Xingyuan; Liu, Yuanyuan; Scheibe, Tim
2017-03-01
The groundwater-surface water interaction zone (GSIZ) plays an important role in riverine and watershed ecosystems as the exchange of waters of variable composition and temperature (hydrologic exchange flows) stimulate microbial activity and associated biogeochemical reactions. Variable temporal and spatial scales of hydrologic exchange flows, heterogeneity of the subsurface environment, and complexity of biogeochemical reaction networks in the GSIZ present challenges to incorporation of fundamental process representations and model parameterization across a range of spatial scales (e.g. from pore-scale to field scale). This paper presents a novel hybrid multiscale simulation approach that couples hydrologic-biogeochemical (HBGC) processes between two distinct length scales of interest.
International Nuclear Information System (INIS)
Takei, Toshifumi; Doi, Shun; Matsumoto, Hideki; Muramatsu, Kazuhiro
2000-01-01
We have developed a concurrent visualization system RVSLIB (Real-time Visual Simulation Library). This paper shows the effectiveness of the system when it is applied to large-scale unsteady simulations, for which the conventional post-processing approach may no longer work, on high-performance parallel vector supercomputers. The system performs almost all of the visualization tasks on a computation server and uses compressed visualized image data for efficient communication between the server and the user terminal. We have introduced several techniques, including vectorization and parallelization, into the system to minimize the computational costs of the visualization tools. The performance of RVSLIB was evaluated by using an actual CFD code on an NEC SX-4. The computational time increase due to the concurrent visualization was at most 3% for a smaller (1.6 million) grid and less than 1% for a larger (6.2 million) one. (author)
Predictive Maturity of Multi-Scale Simulation Models for Fuel Performance
International Nuclear Information System (INIS)
Atamturktur, Sez; Unal, Cetin; Hemez, Francois; Williams, Brian; Tome, Carlos
2015-01-01
The project proposed to provide a Predictive Maturity Framework with its companion metrics that (1) introduce a formalized, quantitative means to communicate information between interested parties, (2) provide scientifically dependable means to claim completion of Validation and Uncertainty Quantification (VU) activities, and (3) guide the decision makers in the allocation of Nuclear Energy's resources for code development and physical experiments. The project team proposed to develop this framework based on two complimentary criteria: (1) the extent of experimental evidence available for the calibration of simulation models and (2) the sophistication of the physics incorporated in simulation models. The proposed framework is capable of quantifying the interaction between the required number of physical experiments and degree of physics sophistication. The project team has developed this framework and implemented it with a multi-scale model for simulating creep of a core reactor cladding. The multi-scale model is composed of the viscoplastic self-consistent (VPSC) code at the meso-scale, which represents the visco-plastic behavior and changing properties of a highly anisotropic material and a Finite Element (FE) code at the macro-scale to represent the elastic behavior and apply the loading. The framework developed takes advantage of the transparency provided by partitioned analysis, where independent constituent codes are coupled in an iterative manner. This transparency allows model developers to better understand and remedy the source of biases and uncertainties, whether they stem from the constituents or the coupling interface by exploiting separate-effect experiments conducted within the constituent domain and integral-effect experiments conducted within the full-system domain. The project team has implemented this procedure with the multi- scale VPSC-FE model and demonstrated its ability to improve the predictive capability of the model. Within this
Predictive Maturity of Multi-Scale Simulation Models for Fuel Performance
Energy Technology Data Exchange (ETDEWEB)
Atamturktur, Sez [Clemson Univ., SC (United States); Unal, Cetin [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Hemez, Francois [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Williams, Brian [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Tome, Carlos [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
2015-03-16
The project proposed to provide a Predictive Maturity Framework with its companion metrics that (1) introduce a formalized, quantitative means to communicate information between interested parties, (2) provide scientifically dependable means to claim completion of Validation and Uncertainty Quantification (VU) activities, and (3) guide the decision makers in the allocation of Nuclear Energy’s resources for code development and physical experiments. The project team proposed to develop this framework based on two complimentary criteria: (1) the extent of experimental evidence available for the calibration of simulation models and (2) the sophistication of the physics incorporated in simulation models. The proposed framework is capable of quantifying the interaction between the required number of physical experiments and degree of physics sophistication. The project team has developed this framework and implemented it with a multi-scale model for simulating creep of a core reactor cladding. The multi-scale model is composed of the viscoplastic self-consistent (VPSC) code at the meso-scale, which represents the visco-plastic behavior and changing properties of a highly anisotropic material and a Finite Element (FE) code at the macro-scale to represent the elastic behavior and apply the loading. The framework developed takes advantage of the transparency provided by partitioned analysis, where independent constituent codes are coupled in an iterative manner. This transparency allows model developers to better understand and remedy the source of biases and uncertainties, whether they stem from the constituents or the coupling interface by exploiting separate-effect experiments conducted within the constituent domain and integral-effect experiments conducted within the full-system domain. The project team has implemented this procedure with the multi- scale VPSC-FE model and demonstrated its ability to improve the predictive capability of the model. Within this
Directory of Open Access Journals (Sweden)
Yan Yu
2018-05-01
Full Text Available Urban agglomeration has become the predominant form of urbanization in China. In this process, spatial interaction evidently played a significant role in promoting the collaborative development of these correlated cities. The traditional urban model’s focus on individual cities should be transformed to an urban system model. In this study, a multi-scale simulation model has been proposed to simulate the agglomeration development process of the Wuhan urban agglomeration area by embedding the multi-scale spatial interaction into the transition rule system of cellular automata (CA. A system dynamic model was used to predict the demand for new urban land at an aggregated urban agglomeration area scale. A data field approach was adopted to measuring the interaction of intercity at city scale. Neighborhood interaction was interpreted with a logistic regression method at the land parcel scale. Land use data from 1995, 2005, and 2015 were used to calibrate and evaluate the model. The simulation results show that there has been continuing urban growth in the Wuhan urban agglomeration area from 1995 to 2020. Although extension-sprawl was the predominant pattern of urban spatial expansion, the trend of extensive growth to intensive growth is clear during the entire period. The spatial interaction among these cities has been reinforced, which guided the collaborative development and formed the regional urban system network.
Colloca, M.; Blanchard, R.; Hellmich, C.; Ito, K.; Rietbergen, van B.
2014-01-01
Bone is a dynamic and hierarchical porous material whose spatial and temporal mechanical properties can vary considerably due to differences in its microstructure and due to remodeling. Hence, a multiscale analytical approach, which combines bone structural information at multiple scales to the
Vijaykumar, A.; Ouldridge, T.E.; ten Wolde, P.R.; Bolhuis, P.G.
2017-01-01
The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic
Fuchs, Andreas; Steinbrecher, Thomas; Mommer, Mario S; Nagata, Yuki; Elstner, Marcus; Lennartz, Christian
2012-03-28
In order to determine the molecular origin of the difference in electron and hole mobilities of amorphous thin films of Alq(3) (meridional Alq(3) (tris(8-hydroxyquinoline) aluminium)) we performed multiscale simulations covering quantum mechanics, molecular mechanics and lattice models. The study includes realistic disordered morphologies, polarized site energies to describe diagonal disorder, quantum chemically calculated transfer integrals for the off-diagonal disorder, inner sphere reorganization energies and an approximative scheme for outer sphere reorganization energies. Intermolecular transfer rates were calculated via Marcus-theory and mobilities were simulated via kinetic Monte Carlo simulations and by a Master Equation approach. The difference in electron and hole mobility originates from the different localization of charge density in the radical anion (more delocalized) compared to the radical cation (more confined). This results in higher diagonal disorder for holes and less favourable overlap properties for the hole transfer integrals leading to an overall higher electron mobility.
Partridge, Roland W; Brown, Fraser S; Brennan, Paul M; Hennessey, Iain A M; Hughes, Mark A
2016-02-01
To assess the potential of the LEAP™ infrared motion tracking device to map laparoscopic instrument movement in a simulated environment. Simulator training is optimized when augmented by objective performance feedback. We explore the potential LEAP has to provide this in a way compatible with affordable take-home simulators. LEAP and the previously validated InsTrac visual tracking tool mapped expert and novice performances of a standardized simulated laparoscopic task. Ability to distinguish between the 2 groups (construct validity) and correlation between techniques (concurrent validity) were the primary outcome measures. Forty-three expert and 38 novice performances demonstrated significant differences in LEAP-derived metrics for instrument path distance (P device is able to track the movement of hands using instruments in a laparoscopic box simulator. Construct validity is demonstrated by its ability to distinguish novice from expert performances. Only time and instrument path distance demonstrated concurrent validity with an existing tracking method however. A number of limitations to the tracking method used by LEAP have been identified. These need to be addressed before it can be considered an alternative to visual tracking for the delivery of objective performance metrics in take-home laparoscopic simulators. © The Author(s) 2015.
Warnke, Tom; Reinhardt, Oliver; Klabunde, Anna; Willekens, Frans; Uhrmacher, Adelinde M
2017-10-01
Individuals' decision processes play a central role in understanding modern migration phenomena and other demographic processes. Their integration into agent-based computational demography depends largely on suitable support by a modelling language. We are developing the Modelling Language for Linked Lives (ML3) to describe the diverse decision processes of linked lives succinctly in continuous time. The context of individuals is modelled by networks the individual is part of, such as family ties and other social networks. Central concepts, such as behaviour conditional on agent attributes, age-dependent behaviour, and stochastic waiting times, are tightly integrated in the language. Thereby, alternative decisions are modelled by concurrent processes that compete by stochastic race. Using a migration model, we demonstrate how this allows for compact description of complex decisions, here based on the Theory of Planned Behaviour. We describe the challenges for the simulation algorithm posed by stochastic race between multiple concurrent complex decisions.
Bazile , Alban; Hachem , Elie; Larroya-Huguet , Juan-Carlos; Mesri , Youssef
2018-01-01
International audience; In this work, we present a new a posteriori error estimator based on the Variational Multiscale method for anisotropic adaptive fluid mechanics problems. The general idea is to combine the large scale error based on the solved part of the solution with the sub-mesh scale error based on the unresolved part of the solution. We compute the latter with two different methods: one using the stabilizing parameters and the other using bubble functions. We propose two different...
Towards a physically-based multi-scale ecohydrological simulator for semi-arid regions
Caviedes-Voullième, Daniel; Josefik, Zoltan; Hinz, Christoph
2017-04-01
The use of numerical models as tools for describing and understanding complex ecohydrological systems has enabled to test hypothesis and propose fundamental, process-based explanations of the system system behaviour as a whole as well as its internal dynamics. Reaction-diffusion equations have been used to describe and generate organized pattern such as bands, spots, and labyrinths using simple feedback mechanisms and boundary conditions. Alternatively, pattern-matching cellular automaton models have been used to generate vegetation self-organization in arid and semi-arid regions also using simple description of surface hydrological processes. A key question is: How much physical realism is needed in order to adequately capture the pattern formation processes in semi-arid regions while reliably representing the water balance dynamics at the relevant time scales? In fact, redistribution of water by surface runoff at the hillslope scale occurs at temporal resolution of minutes while the vegetation development requires much lower temporal resolution and longer times spans. This generates a fundamental spatio-temporal multi-scale problem to be solved, for which high resolution rainfall and surface topography are required. Accordingly, the objective of this contribution is to provide proof-of-concept that governing processes can be described numerically at those multiple scales. The requirements for a simulating ecohydrological processes and pattern formation with increased physical realism are, amongst others: i. high resolution rainfall that adequately captures the triggers of growth as vegetation dynamics of arid regions respond as pulsed systems. ii. complex, natural topography in order to accurately model drainage patterns, as surface water redistribution is highly sensitive to topographic features. iii. microtopography and hydraulic roughness, as small scale variations do impact on large scale hillslope behaviour iv. moisture dependent infiltration as temporal
International Nuclear Information System (INIS)
Kyu Cho, Hyoung; Cho, Yun Je; Yoon, Han Young
2014-01-01
Graphical abstract: - Highlights: • PAFS is designed to replace a conventional active auxiliary feedwater system. • Multi-D T/H analysis code, CUPID was coupled with the 1-D system analysis code MARS. • The coupled CUPID and MARS was applied for the multi-scale analysis of the PAFS test facility. • The simulation result showed that the coupled code can reproduce important phenomena in PAFS. - Abstract: For the analysis of transient two-phase flows in nuclear reactor components, a three-dimensional thermal hydraulics code, named CUPID, has been developed. In the present study, the CUPID code was coupled with a system analysis code MARS in order to apply it for the multi-scale thermal-hydraulic analysis of the passive auxiliary feedwater system (PAFS). The PAFS is one of the advanced safety features adopted in the Advanced Power Reactor Plus (APR+), which is intended to completely replace the conventional active auxiliary feedwater system. For verification of the coupling and validation of the coupled code, the PASCAL test facility was simulated, which was constructed with an aim of validating the cooling and operational performance of the PAFS. The two-phase flow phenomena of the steam supply system including the condensation inside the heat exchanger tube were calculated by MARS while the natural circulation and the boil-off in the large water pool that contains the heat exchanger tube were simulated by CUPID. This paper presents the description of the PASCAL facility, the coupling method and the simulation results using the coupled code
A Generalized Hybrid Multiscale Modeling Approach for Flow and Reactive Transport in Porous Media
Yang, X.; Meng, X.; Tang, Y. H.; Guo, Z.; Karniadakis, G. E.
2017-12-01
Using emerging understanding of biological and environmental processes at fundamental scales to advance predictions of the larger system behavior requires the development of multiscale approaches, and there is strong interest in coupling models at different scales together in a hybrid multiscale simulation framework. A limited number of hybrid multiscale simulation methods have been developed for subsurface applications, mostly using application-specific approaches for model coupling. The proposed generalized hybrid multiscale approach is designed with minimal intrusiveness to the at-scale simulators (pre-selected) and provides a set of lightweight C++ scripts to manage a complex multiscale workflow utilizing a concurrent coupling approach. The workflow includes at-scale simulators (using the lattice-Boltzmann method, LBM, at the pore and Darcy scale, respectively), scripts for boundary treatment (coupling and kriging), and a multiscale universal interface (MUI) for data exchange. The current study aims to apply the generalized hybrid multiscale modeling approach to couple pore- and Darcy-scale models for flow and mixing-controlled reaction with precipitation/dissolution in heterogeneous porous media. The model domain is packed heterogeneously that the mixing front geometry is more complex and not known a priori. To address those challenges, the generalized hybrid multiscale modeling approach is further developed to 1) adaptively define the locations of pore-scale subdomains, 2) provide a suite of physical boundary coupling schemes and 3) consider the dynamic change of the pore structures due to mineral precipitation/dissolution. The results are validated and evaluated by comparing with single-scale simulations in terms of velocities, reactive concentrations and computing cost.
International Nuclear Information System (INIS)
Angeli, P.-E.
2011-01-01
The present work is devoted to a multi-scale numerical simulation of an assembly of fast neutron reactor. In spite of the rapid growth of the computer power, the fine complete CFD of a such system remains out of reach in a context of research and development. After the determination of the thermalhydraulic behaviour of the assembly at the macroscopic scale, we propose to carry out a local reconstruction of the fine scale information. The complete approach will require a much lower CPU time than the CFD of the entire structure. The macro-scale description is obtained using either the volume averaging formalism in porous media, or an alternative modeling historically developed for the study of fast neutron reactor assemblies. It provides some information used as constraint of a down-scaling problem, through a penalization technique of the local conservation equations. This problem lean on the periodic nature of the structure by integrating periodic boundary conditions for the required microscale fields or their spatial deviation. After validating the methodologies on some model applications, we undertake to perform them on 'industrial' configurations which demonstrate the viability of this multi-scale approach. (author) [fr
Energy Technology Data Exchange (ETDEWEB)
Hadad, Kamal; Esmaeili-Sanjavanmareh, Mansour [Shiraz Univ., Shiraz (Iran, Islamic Republic of). Dept. of Nuclear Engineering
2017-05-15
PCTRAN capability to simulate a large break loss of coolant accident concurrent with the loss of offsite power in Bushehr Nuclear Power Plant is enhanced and investigated. Following the correction of the accident scenario for Bushehr nuclear power plant in PCTRAN, simulation results are compared with the final safety assessment report of that plant. As a result, the primary loop thermal hydraulics parameters including pressure, total flow rates, leakage flow rates and reactor power are in a good agreement with the reference data. Hot and cold leg temperature variations have the same trends as reference data but have a maximum of 80 C disagreement at the transient initiation. The reason for this disagreement is explained and its adjustment is discussed. Improvements of PCTRAN simulator are mainly due to enhancing user control for atmospheric steam dump valve, containment pressure and emergency core cooling systems which are thoroughly described in this paper.
Ghaffari Motlagh, Yousef; Ahn, Hyungtaek; Hughes, Thomas Jr R; Calo, Victor M.
2013-01-01
We present an application of the residual-based variational multiscale modeling methodology to the computation of laminar and turbulent concentric annular pipe flows. Isogeometric analysis is utilized for higher-order approximation of the solution using Non-Uniform Rational B-Splines (NURBS). The ability of NURBS to exactly represent curved geometries makes NURBS-based isogeometric analysis attractive for the application to the flow through annular channels. We demonstrate the applicability of the methodology to both laminar and turbulent flow regimes. © 2012 Elsevier Ltd.
Macklin, Paul; Cristini, Vittorio
2013-01-01
Simulating cancer behavior across multiple biological scales in space and time, i.e., multiscale cancer modeling, is increasingly being recognized as a powerful tool to refine hypotheses, focus experiments, and enable more accurate predictions. A growing number of examples illustrate the value of this approach in providing quantitative insight on the initiation, progression, and treatment of cancer. In this review, we introduce the most recent and important multiscale cancer modeling works that have successfully established a mechanistic link between different biological scales. Biophysical, biochemical, and biomechanical factors are considered in these models. We also discuss innovative, cutting-edge modeling methods that are moving predictive multiscale cancer modeling toward clinical application. Furthermore, because the development of multiscale cancer models requires a new level of collaboration among scientists from a variety of fields such as biology, medicine, physics, mathematics, engineering, and computer science, an innovative Web-based infrastructure is needed to support this growing community. PMID:21529163
Liu, Yushi; Poh, Hee Joo
2014-11-01
The Computational Fluid Dynamics analysis has become increasingly important in modern urban planning in order to create highly livable city. This paper presents a multi-scale modeling methodology which couples Weather Research and Forecasting (WRF) Model with open source CFD simulation tool, OpenFOAM. This coupling enables the simulation of the wind flow and pollutant dispersion in urban built-up area with high resolution mesh. In this methodology meso-scale model WRF provides the boundary condition for the micro-scale CFD model OpenFOAM. The advantage is that the realistic weather condition is taken into account in the CFD simulation and complexity of building layout can be handled with ease by meshing utility of OpenFOAM. The result is validated against the Joint Urban 2003 Tracer Field Tests in Oklahoma City and there is reasonably good agreement between the CFD simulation and field observation. The coupling of WRF- OpenFOAM provide urban planners with reliable environmental modeling tool in actual urban built-up area; and it can be further extended with consideration of future weather conditions for the scenario studies on climate change impact.
Multi-scale high-performance fluid flow: Simulations through porous media
Perović, Nevena
2016-08-03
Computational fluid dynamic (CFD) calculations on geometrically complex domains such as porous media require high geometric discretisation for accurately capturing the tested physical phenomena. Moreover, when considering a large area and analysing local effects, it is necessary to deploy a multi-scale approach that is both memory-intensive and time-consuming. Hence, this type of analysis must be conducted on a high-performance parallel computing infrastructure. In this paper, the coupling of two different scales based on the Navier–Stokes equations and Darcy\\'s law is described followed by the generation of complex geometries, and their discretisation and numerical treatment. Subsequently, the necessary parallelisation techniques and a rather specific tool, which is capable of retrieving data from the supercomputing servers and visualising them during the computation runtime (i.e. in situ) are described. All advantages and possible drawbacks of this approach, together with the preliminary results and sensitivity analyses are discussed in detail.
Modeling and Simulation of High Dimensional Stochastic Multiscale PDE Systems at the Exascale
Energy Technology Data Exchange (ETDEWEB)
Kevrekidis, Ioannis [Princeton Univ., NJ (United States)
2017-03-22
The thrust of the proposal was to exploit modern data-mining tools in a way that will create a systematic, computer-assisted approach to the representation of random media -- and also to the representation of the solutions of an array of important physicochemical processes that take place in/on such media. A parsimonious representation/parametrization of the random media links directly (via uncertainty quantification tools) to good sampling of the distribution of random media realizations. It also links directly to modern multiscale computational algorithms (like the equation-free approach that has been developed in our group) and plays a crucial role in accelerating the scientific computation of solutions of nonlinear PDE models (deterministic or stochastic) in such media – both solutions in particular realizations of the random media, and estimation of the statistics of the solutions over multiple realizations (e.g. expectations).
Multi-scale high-performance fluid flow: Simulations through porous media
Perović, Nevena; Frisch, Jé rô me; Salama, Amgad; Sun, Shuyu; Rank, Ernst; Mundani, Ralf Peter
2016-01-01
Computational fluid dynamic (CFD) calculations on geometrically complex domains such as porous media require high geometric discretisation for accurately capturing the tested physical phenomena. Moreover, when considering a large area and analysing local effects, it is necessary to deploy a multi-scale approach that is both memory-intensive and time-consuming. Hence, this type of analysis must be conducted on a high-performance parallel computing infrastructure. In this paper, the coupling of two different scales based on the Navier–Stokes equations and Darcy's law is described followed by the generation of complex geometries, and their discretisation and numerical treatment. Subsequently, the necessary parallelisation techniques and a rather specific tool, which is capable of retrieving data from the supercomputing servers and visualising them during the computation runtime (i.e. in situ) are described. All advantages and possible drawbacks of this approach, together with the preliminary results and sensitivity analyses are discussed in detail.
Individual-specific multi-scale finite element simulation of cortical bone of human proximal femur
International Nuclear Information System (INIS)
Ascenzi, Maria-Grazia; Kawas, Neal P.; Lutz, Andre; Kardas, Dieter; Nackenhorst, Udo; Keyak, Joyce H.
2013-01-01
We present an innovative method to perform multi-scale finite element analyses of the cortical component of the femur using the individual’s (1) computed tomography scan; and (2) a bone specimen obtained in conjunction with orthopedic surgery. The method enables study of micro-structural characteristics regulating strains and stresses under physiological loading conditions. The analysis of the micro-structural scenarios that cause variation of strain and stress is the first step in understanding the elevated strains and stresses in bone tissue, which are indicative of higher likelihood of micro-crack formation in bone, implicated in consequent remodeling or macroscopic bone fracture. Evidence that micro-structure varies with clinical history and contributes in significant, but poorly understood, ways to bone function, motivates the method’s development, as does need for software tools to investigate relationships between macroscopic loading and micro-structure. Three applications – varying region of interest, bone mineral density, and orientation of collagen type I, illustrate the method. We show, in comparison between physiological loading and simple compression of a patient’s femur, that strains computed at the multi-scale model’s micro-level: (i) differ; and (ii) depend on local collagen-apatite orientation and degree of calcification. Our findings confirm the strain concentration role of osteocyte lacunae, important for mechano-transduction. We hypothesize occurrence of micro-crack formation, leading either to remodeling or macroscopic fracture, when the computed strains exceed the elastic range observed in micro-structural testing
Individual-specific multi-scale finite element simulation of cortical bone of human proximal femur
Energy Technology Data Exchange (ETDEWEB)
Ascenzi, Maria-Grazia, E-mail: mgascenzi@mednet.ucla.edu [UCLA/Orthopaedic Hospital, Department of Orthopaedic Surgery, Rehabilitation Bldg, Room 22-69, 1000 Veteran Avenue, University of California, Los Angeles, CA 90095 (United States); Kawas, Neal P., E-mail: nealkawas@ucla.edu [UCLA/Orthopaedic Hospital, Department of Orthopaedic Surgery, Rehabilitation Bldg, Room 22-69, 1000 Veteran Avenue, University of California, Los Angeles, CA 90095 (United States); Lutz, Andre, E-mail: andre.lutz@hotmail.de [Institute of Biomechanics and Numerical Mechanics, Leibniz University Hannover, 30167 Hannover (Germany); Kardas, Dieter, E-mail: kardas@ibnm.uni-hannover.de [ContiTech Vibration Control, Jaedekamp 30 None, 30419 Hannover (Germany); Nackenhorst, Udo, E-mail: nackenhorst@ibnm.uni-hannover.de [Institute of Biomechanics and Numerical Mechanics, Leibniz University Hannover, 30167 Hannover (Germany); Keyak, Joyce H., E-mail: jhkeyak@uci.edu [Department of Radiological Sciences, Medical Sciences I, Bldg 811, Room B140, University of California, Irvine, CA 92697-5000 (United States)
2013-07-01
We present an innovative method to perform multi-scale finite element analyses of the cortical component of the femur using the individual’s (1) computed tomography scan; and (2) a bone specimen obtained in conjunction with orthopedic surgery. The method enables study of micro-structural characteristics regulating strains and stresses under physiological loading conditions. The analysis of the micro-structural scenarios that cause variation of strain and stress is the first step in understanding the elevated strains and stresses in bone tissue, which are indicative of higher likelihood of micro-crack formation in bone, implicated in consequent remodeling or macroscopic bone fracture. Evidence that micro-structure varies with clinical history and contributes in significant, but poorly understood, ways to bone function, motivates the method’s development, as does need for software tools to investigate relationships between macroscopic loading and micro-structure. Three applications – varying region of interest, bone mineral density, and orientation of collagen type I, illustrate the method. We show, in comparison between physiological loading and simple compression of a patient’s femur, that strains computed at the multi-scale model’s micro-level: (i) differ; and (ii) depend on local collagen-apatite orientation and degree of calcification. Our findings confirm the strain concentration role of osteocyte lacunae, important for mechano-transduction. We hypothesize occurrence of micro-crack formation, leading either to remodeling or macroscopic fracture, when the computed strains exceed the elastic range observed in micro-structural testing.
Concurrent heterogeneous neural model simulation on real-time neuromimetic hardware.
Rast, Alexander; Galluppi, Francesco; Davies, Sergio; Plana, Luis; Patterson, Cameron; Sharp, Thomas; Lester, David; Furber, Steve
2011-11-01
Dedicated hardware is becoming increasingly essential to simulate emerging very-large-scale neural models. Equally, however, it needs to be able to support multiple models of the neural dynamics, possibly operating simultaneously within the same system. This may be necessary either to simulate large models with heterogeneous neural types, or to simplify simulation and analysis of detailed, complex models in a large simulation by isolating the new model to a small subpopulation of a larger overall network. The SpiNNaker neuromimetic chip is a dedicated neural processor able to support such heterogeneous simulations. Implementing these models on-chip uses an integrated library-based tool chain incorporating the emerging PyNN interface that allows a modeller to input a high-level description and use an automated process to generate an on-chip simulation. Simulations using both LIF and Izhikevich models demonstrate the ability of the SpiNNaker system to generate and simulate heterogeneous networks on-chip, while illustrating, through the network-scale effects of wavefront synchronisation and burst gating, methods that can provide effective behavioural abstractions for large-scale hardware modelling. SpiNNaker's asynchronous virtual architecture permits greater scope for model exploration, with scalable levels of functional and temporal abstraction, than conventional (or neuromorphic) computing platforms. The complete system illustrates a potential path to understanding the neural model of computation, by building (and breaking) neural models at various scales, connecting the blocks, then comparing them against the biology: computational cognitive neuroscience. Copyright © 2011 Elsevier Ltd. All rights reserved.
Leiner, Claude; Nemitz, Wolfgang; Schweitzer, Susanne; Kuna, Ladislav; Wenzl, Franz P; Hartmann, Paul; Satzinger, Valentin; Sommer, Christian
2016-03-20
We show that with an appropriate combination of two optical simulation techniques-classical ray-tracing and the finite difference time domain method-an optical device containing multiple diffractive and refractive optical elements can be accurately simulated in an iterative simulation approach. We compare the simulation results with experimental measurements of the device to discuss the applicability and accuracy of our iterative simulation procedure.
Directory of Open Access Journals (Sweden)
Thomas eEissing
2011-02-01
Full Text Available Today, in silico studies and trial simulations already complement experimental approaches in pharmaceutical R&D and have become indispensable tools for decision making and communication with regulatory agencies. While biology is multi-scale by nature, project work and software tools usually focus on isolated aspects of drug action, such as pharmacokinetics at the organism scale or pharmacodynamic interaction on the molecular level. We present a modeling and simulation software platform consisting of PK-Sim® and MoBi® capable of building and simulating models that integrate across biological scales. A prototypical multiscale model for the progression of a pancreatic tumor and its response to pharmacotherapy is constructed and virtual patients are treated with a prodrug activated by hepatic metabolization. Tumor growth is driven by signal transduction leading to cell cycle transition and proliferation. Free tumor concentrations of the active metabolite inhibit Raf kinase in the signaling cascade and thereby cell cycle progression. In a virtual clinical study, the individual therapeutic outcome of the chemotherapeutic intervention is simulated for a large population with heterogeneous genomic background. Thereby, the platform allows efficient model building and integration of biological knowledge and prior data from all biological scales. Experimental in vitro model systems can be linked with observations in animal experiments and clinical trials. The interplay between patients, diseases, and drugs and topics with high clinical relevance such as the role of pharmacogenomics, drug-drug or drug-metabolite interactions can be addressed using this mechanistic, insight driven multiscale modeling approach.
Directory of Open Access Journals (Sweden)
Shufen Pan
2014-01-01
Full Text Available There is a critical need to monitor and predict terrestrial primary production, the key indicator of ecosystem functioning, in a changing global environment. Here we provide a brief review of three major approaches to monitoring and predicting terrestrial primary production: (1 ground-based field measurements, (2 satellite-based observations, and (3 process-based ecosystem modelling. Much uncertainty exists in the multi-approach estimations of terrestrial gross primary production (GPP and net primary production (NPP. To improve the capacity of model simulation and prediction, it is essential to evaluate ecosystem models against ground and satellite-based measurements and observations. As a case, we have shown the performance of the dynamic land ecosystem model (DLEM at various scales from site to region to global. We also discuss how terrestrial primary production might respond to climate change and increasing atmospheric CO2 and uncertainties associated with model and data. Further progress in monitoring and predicting terrestrial primary production requires a multiscale synthesis of observations and model simulations. In the Anthropocene era in which human activity has indeed changed the Earth’s biosphere, therefore, it is essential to incorporate the socioeconomic component into terrestrial ecosystem models for accurately estimating and predicting terrestrial primary production in a changing global environment.
Liu, Lei; Wade, Rebecca C; Heermann, Dieter W
2015-09-01
The conformational properties of unbound multi-Cys2 His2 (mC2H2) zinc finger proteins, in which zinc finger domains are connected by flexible linkers, are studied by a multiscale approach. Three methods on different length scales are utilized. First, atomic detail molecular dynamics simulations of one zinc finger and its adjacent flexible linker confirmed that the zinc finger is more rigid than the flexible linker. Second, the end-to-end distance distributions of mC2H2 zinc finger proteins are computed using an efficient atomistic pivoting algorithm, which only takes excluded volume interactions into consideration. The end-to-end distance distribution gradually changes its profile, from left-tailed to right-tailed, as the number of zinc fingers increases. This is explained by using a worm-like chain model. For proteins of a few zinc fingers, an effective bending constraint favors an extended conformation. Only for proteins containing more than nine zinc fingers, is a somewhat compacted conformation preferred. Third, a mesoscale model is modified to study both the local and the global conformational properties of multi-C2H2 zinc finger proteins. Simulations of the CCCTC-binding factor (CTCF), an important mC2H2 zinc finger protein for genome spatial organization, are presented. © 2015 Wiley Periodicals, Inc.
Naik, Shivangi; Hancock, Bruno; Abramov, Yuriy; Yu, Weili; Rowland, Martin; Huang, Zhonghui; Chaudhuri, Bodhisattwa
2016-04-01
Pharmaceutical powders are very prone to electrostatic charging by colliding and sliding contacts. In pharmaceutical formulation processes, particle charging is often a nuisance and can cause problems in the manufacture of products, such as affecting powder flow, fill, and dose uniformity. For a fundamental understanding of the powder triboelectrification, it is essential to study charge transfer under well-defined conditions. Hence, all experiments in the present study were conducted in a V-blender located inside a glove box with a controlled humidity of 20%. To understand tribocharging, different contact surfaces, namely aluminum, Teflon, poly methyl methacrylate, and nylon were used along with 2 pharmaceutical excipients and 2 drug substances. For the pharmaceutical materials, the work function values were estimated using MOPAC, a semiempirical molecular orbital package which has been previously used for the solid-state studies and molecular structure predictions. For a mechanistic understanding of tribocharging, a discrete element model incorporating charge transfer and electrostatic forces was developed. An effort was made to correlate tribocharging of pharmaceutical powders to properties such as cohesive energy density and surface energy. The multiscale model used is restricted as it considers only spherical particles with smooth surfaces. It should be used judiciously for other experimental assemblies because it does not represent a full validation of a tightly integrated model. Copyright © 2016 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.
Station black out concurrent with PORV failure using a Generic Pressurized Water Reactor simulator
International Nuclear Information System (INIS)
Zubair, Muhammad; Ababneh, Ahmad; Ishag, Ahmed
2017-01-01
Highlights: •SBO accident simulation by using a GPWR simulator. •Normal SBO, and SBO with additional failure of Pilot Operated Relief Valve. •The research results will provide help in future for better understanding of accidents in APR 1400 reactors. -- Abstract: Station Black Out (SBO) is an accident situation that refers to the total loss of offsite power, along with the unavailability of onsite power, which results from the failure of all Diesel Generators (DG). Probabilistic Safety Assessment (PSA) spans a number of methods that include modeling of event-trees and simulation of accidents scenarios, aimed to quantify risk and ensure safety in nuclear power plants. PSA also deals with prediction of future accidents and calculation of failure probabilities that has been done in this study. A SBO accident was simulated using a Generic Pressurized Water Reactor (GPWR) simulator from KEYMASTER™. The accident scenario consists of two stages; the first stage belongs to normal SBO, in second stage SBO accident with additional failure of Pilot Operated Relief Valve (PORV) opens and it stuck open has been considered for the pressurizer. A comparison of the two stages was made by plotting variables on the same graph. The research has been carried out to analyze the hot and cold leg temperatures, Steam Generator (SG) pressure, SG Narrow Range (NR) level, SG water-level-percentage (PCT), Pressurizer pressure, Fuel Temperature, and containment pressure. Simulation results suggest that failure in closing PORV has negligible impact on hot and cold leg temperatures, results in an overall less pressure in SGs, but higher pressure in the pressurizer. Additionally, containment pressure did not exceed the maximum approved pressure of 8.7 kg/cm 2 , but was approaching the Advanced Pressurized Water Reactor’s (APR-1400) design pressure of 4.218 kg/cm 2 . Finally, nuclear fuel temperature exceeded Probabilistic Risk Assessment (PRA) limit of 726.7 °C for both scenarios. The
Energy Technology Data Exchange (ETDEWEB)
Emery, John M. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Coffin, Peter [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Robbins, Brian A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Carroll, Jay [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Field, Richard V. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Jeremy Yoo, Yung Suk [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Kacher, Josh [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
2017-09-01
Microstructural variabilities are among the predominant sources of uncertainty in structural performance and reliability. We seek to develop efficient algorithms for multiscale calcu- lations for polycrystalline alloys such as aluminum alloy 6061-T6 in environments where ductile fracture is the dominant failure mode. Our approach employs concurrent multiscale methods, but does not focus on their development. They are a necessary but not sufficient ingredient to multiscale reliability predictions. We have focused on how to efficiently use concurrent models for forward propagation because practical applications cannot include fine-scale details throughout the problem domain due to exorbitant computational demand. Our approach begins with a low-fidelity prediction at the engineering scale that is sub- sequently refined with multiscale simulation. The results presented in this report focus on plasticity and damage at the meso-scale, efforts to expedite Monte Carlo simulation with mi- crostructural considerations, modeling aspects regarding geometric representation of grains and second-phase particles, and contrasting algorithms for scale coupling.
Lee, Cheng-Kuang
2014-12-10
© 2014 American Chemical Society. The nanomorphologies of the bulk heterojunction (BHJ) layer of polymer solar cells are extremely sensitive to the electrode materials and thermal annealing conditions. In this work, the correlations of electrode materials, thermal annealing sequences, and resultant BHJ nanomorphological details of P3HT:PCBM BHJ polymer solar cell are studied by a series of large-scale, coarse-grained (CG) molecular simulations of system comprised of PEDOT:PSS/P3HT:PCBM/Al layers. Simulations are performed for various configurations of electrode materials as well as processing temperature. The complex CG molecular data are characterized using a novel extension of our graph-based framework to quantify morphology and establish a link between morphology and processing conditions. Our analysis indicates that vertical phase segregation of P3HT:PCBM blend strongly depends on the electrode material and thermal annealing schedule. A thin P3HT-rich film is formed on the top, regardless of bottom electrode material, when the BHJ layer is exposed to the free surface during thermal annealing. In addition, preferential segregation of P3HT chains and PCBM molecules toward PEDOT:PSS and Al electrodes, respectively, is observed. Detailed morphology analysis indicated that, surprisingly, vertical phase segregation does not affect the connectivity of donor/acceptor domains with respective electrodes. However, the formation of P3HT/PCBM depletion zones next to the P3HT/PCBM-rich zones can be a potential bottleneck for electron/hole transport due to increase in transport pathway length. Analysis in terms of fraction of intra- and interchain charge transports revealed that processing schedule affects the average vertical orientation of polymer chains, which may be crucial for enhanced charge transport, nongeminate recombination, and charge collection. The present study establishes a more detailed link between processing and morphology by combining multiscale molecular
Chang, Kyungsik
2012-09-01
We report on the isogeometric residual-based variational multiscale (VMS) large eddy simulation of a fully developed turbulent flow over a wavy wall. To assess the predictive capability of the VMS modeling framework, we compare its predictions against the results from direct numerical simulation (DNS) and large eddy simulation (LES) and, when available, against experimental measurements. We use C 1 quadratic B-spline basis functions to represent the smooth geometry of the sinusoidal lower wall and the solution variables. The Reynolds numbers of the flows considered are 6760 and 30,000 based on the bulk velocity and average channel height. The ratio of amplitude to wavelength (α/λ) of the sinusoidal wavy surface is set to 0.05. The computational domain is 2λ×1.05λ×λ in the streamwise, wall-normal and spanwise directions, respectively. For the Re=6760 case, mean averaged quantities, including velocity and pressure profiles, and the separation/reattachment points in the recirculation region, are compared with DNS and experimental data. The turbulent kinetic energy and Reynolds stress are in good agreement with benchmark data. Coherent structures over the wavy wall are observed in isosurfaces of the Q-criterion and show similar features to those previously reported in the literature. Comparable accuracy to DNS solutions is obtained with at least one order of magnitude fewer degrees of freedom. For the Re=30,000 case, good agreement was obtained for mean wall shear stress and velocity profiles compared with available LES results reported in the literature. © 2012 Elsevier Ltd.
Chang, Kyungsik; Hughes, Thomas Jr R; Calo, Victor M.
2012-01-01
We report on the isogeometric residual-based variational multiscale (VMS) large eddy simulation of a fully developed turbulent flow over a wavy wall. To assess the predictive capability of the VMS modeling framework, we compare its predictions against the results from direct numerical simulation (DNS) and large eddy simulation (LES) and, when available, against experimental measurements. We use C 1 quadratic B-spline basis functions to represent the smooth geometry of the sinusoidal lower wall and the solution variables. The Reynolds numbers of the flows considered are 6760 and 30,000 based on the bulk velocity and average channel height. The ratio of amplitude to wavelength (α/λ) of the sinusoidal wavy surface is set to 0.05. The computational domain is 2λ×1.05λ×λ in the streamwise, wall-normal and spanwise directions, respectively. For the Re=6760 case, mean averaged quantities, including velocity and pressure profiles, and the separation/reattachment points in the recirculation region, are compared with DNS and experimental data. The turbulent kinetic energy and Reynolds stress are in good agreement with benchmark data. Coherent structures over the wavy wall are observed in isosurfaces of the Q-criterion and show similar features to those previously reported in the literature. Comparable accuracy to DNS solutions is obtained with at least one order of magnitude fewer degrees of freedom. For the Re=30,000 case, good agreement was obtained for mean wall shear stress and velocity profiles compared with available LES results reported in the literature. © 2012 Elsevier Ltd.
Matichuk, Rebecca; Tonnesen, Gail; Luecken, Deborah; Gilliam, Rob; Napelenok, Sergey L.; Baker, Kirk R.; Schwede, Donna; Murphy, Ben; Helmig, Detlev; Lyman, Seth N.; Roselle, Shawn
2017-12-01
The Weather Research and Forecasting (WRF) and Community Multiscale Air Quality (CMAQ) models were used to simulate a 10 day high-ozone episode observed during the 2013 Uinta Basin Winter Ozone Study (UBWOS). The baseline model had a large negative bias when compared to ozone (O3) and volatile organic compound (VOC) measurements across the basin. Contrary to other wintertime Uinta Basin studies, predicted nitrogen oxides (NOx) were typically low compared to measurements. Increases to oil and gas VOC emissions resulted in O3 predictions closer to observations, and nighttime O3 improved when reducing the deposition velocity for all chemical species. Vertical structures of these pollutants were similar to observations on multiple days. However, the predicted surface layer VOC mixing ratios were generally found to be underestimated during the day and overestimated at night. While temperature profiles compared well to observations, WRF was found to have a warm temperature bias and too low nighttime mixing heights. Analyses of more realistic snow heat capacity in WRF to account for the warm bias and vertical mixing resulted in improved temperature profiles, although the improved temperature profiles seldom resulted in improved O3 profiles. While additional work is needed to investigate meteorological impacts, results suggest that the uncertainty in the oil and gas emissions contributes more to the underestimation of O3. Further, model adjustments based on a single site may not be suitable across all sites within the basin.
Comer, Joanne; Indiana Olbert, Agnieszka; Nash, Stephen; Hartnett, Michael
2017-02-01
Urban developments in coastal zones are often exposed to natural hazards such as flooding. In this research, a state-of-the-art, multi-scale nested flood (MSN_Flood) model is applied to simulate complex coastal-fluvial urban flooding due to combined effects of tides, surges and river discharges. Cork city on Ireland's southwest coast is a study case. The flood modelling system comprises a cascade of four dynamically linked models that resolve the hydrodynamics of Cork Harbour and/or its sub-region at four scales: 90, 30, 6 and 2 m. Results demonstrate that the internalization of the nested boundary through the use of ghost cells combined with a tailored adaptive interpolation technique creates a highly dynamic moving boundary that permits flooding and drying of the nested boundary. This novel feature of MSN_Flood provides a high degree of choice regarding the location of the boundaries to the nested domain and therefore flexibility in model application. The nested MSN_Flood model through dynamic downscaling facilitates significant improvements in accuracy of model output without incurring the computational expense of high spatial resolution over the entire model domain. The urban flood model provides full characteristics of water levels and flow regimes necessary for flood hazard identification and flood risk assessment.
Multiscale Simulations of Lamellar PS–PEO Block Copolymers Doped with LiPF6 Ions
Sethuraman, Vaidyanathan; Mogurampelly, Santosh; Ganesan, Venkat
2017-01-01
We report the results of atomistic simulations of the structural equilibrium properties of PS–PEO block copolymer (BCP) melt in the ordered lamellar phase doped with LiPF6 salt. A hybrid simulation strategy, consisting of steps of coarse
Energy Technology Data Exchange (ETDEWEB)
Gamble, K. A. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Hales, J. D. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Zhang, Y. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Andersson, D. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Capolungo, L. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Wirth, B. D. [Univ. of Tennessee, Knoxville, TN (United States)
2017-07-26
Since the events at the Fukushima-Daiichi nuclear power plant in March 2011 significant research has unfolded at national laboratories, universities and other institutions into alternative materials that have potential enhanced ac- cident tolerance when compared to traditional UO2 fuel zircaloy clad fuel rods. One of the potential replacement claddings are iron-chromium-alunimum (FeCrAl) alloys due to their increased oxidation resistance [1–4] and higher strength [1, 2]. While the oxidation characteristics of FeCrAl are a benefit for accident tolerance, the thermal neu- tron absorption cross section of FeCrAl is about ten times that of Zircaloy. This neutronic penalty necessitates thinner cladding. This allows for slightly larger pellets to give the same cold gap width in the rod. However, the slight increase in pellet diameter is not sufficient to compensate for the neutronic penalty and enriching the fuel beyond the current 5% limit appears to be necessary [5]. Current estimates indicate that this neutronic penalty will impose an increase in fuel cost of 15-35% [1, 2]. In addition to the neutronic disadvantage, it is anticipated that tritium release to the coolant will be larger because the permeability of hydrogen in FeCrAl is about 100 times higher than in Zircaloy [6]. Also, radiation-induced hardening and embrittlement of FeCrAl need to be fully characterized experimentally [7]. Due to the aggressive development schedule for inserting some of the potential materials into lead test assemblies or rods by 2022 [8] multiscale multiphysics modeling approaches have been used to provide insight into these the use of FeCrAl as a cladding material. The purpose of this letter report is to highlight the multiscale modeling effort for iron-chromium-alunimum (FeCrAl) cladding alloys as part of the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program through its Accident Tolerant Fuel (ATF) High Impact Problem (HIP). The approach taken throughout the HIP is to
International Nuclear Information System (INIS)
Honorio-De-Faria, Tulio
2015-01-01
The accurate prediction of the long and short-term behaviour of concrete structures in the nuclear domain is essential to ensure optimal performances (integrity, containment properties) during their service life. In the particular case of massive concrete structures, at early age the heat produced by hydration reactions cannot be evacuated fast enough so that high temperatures may be reached and the resulting gradients of temperature might lead to cracking according to the external and internal restraints to which the structures are subjected. The goals of this study are (1) to perform numerical simulations in order to describe and predict the thermo-chemo-mechanical behaviour at early-age of a massive concrete structure devoted to nuclear waste disposal on surface, and (2) to develop and apply up-scaling tools to estimate rigorously the key properties of concrete needed in an early-age analysis from the composition of the material. Firstly, a chemo-thermal analysis aims at determining the influence of convection, solar radiation, re-radiation and hydration heat on the thermal response of the structure. Practical recommendations regarding concreting temperatures are provided in order to limit the maximum temperature reached within the structure. Then, by means of a mechanical analysis, simplified and more complex (i.e. accounting for coupled creep and damage) modelling strategies are used to assess scenarios involving different boundary conditions defined from the previous chemo-thermal analysis. Secondly, a study accounting for the multi-scale character of concrete is performed. A simplified model of cement hydration kinetics is proposed. The evolution of the different phases at the cement paste level can be estimated. Then, analytical and numerical tools to upscale the ageing properties are presented and applied to estimate the mechanical and thermal properties of cement based materials. Finally, the input data used in the structural analysis are compared with
Concurrent particle-in-cell plasma simulation on a multi-transputer parallel computer
International Nuclear Information System (INIS)
Khare, A.N.; Jethra, A.; Patel, Kartik
1992-01-01
This report describes the parallelization of a Particle-in-Cell (PIC) plasma simulation code on a multi-transputer parallel computer. The algorithm used in the parallelization of the PIC method is described. The decomposition schemes related to the distribution of the particles among the processors are discussed. The implementation of the algorithm on a transputer network connected as a torus is presented. The solutions of the problems related to global communication of data are presented in the form of a set of generalized communication functions. The performance of the program as a function of data size and the number of transputers show that the implementation is scalable and represents an effective way of achieving high performance at acceptable cost. (author). 11 refs., 4 figs., 2 tabs., appendices
International Nuclear Information System (INIS)
Paszynski, Maciej; Gurgul, Piotr; Sieniek, Marcin; Pardo, David
2010-01-01
In the first part of the paper we present the multi-scale simulation of the Step-and-Flash Imprint Lithography (SFIL), a modern patterning process. The simulation utilizes the hp adaptive Finite Element Method (hp-FEM) coupled with Molecular Statics (MS) model. Thus, we consider the multi-scale problem, with molecular statics applied in the areas of the mesh where the highest accuracy is required, and the continuous linear elasticity with thermal expansion coefficient applied in the remaining part of the domain. The degrees of freedom from macro-scale element's nodes located on the macro-scale side of the interface have been identified with particles from nano-scale elements located on the nano-scale side of the interface. In the second part of the paper we present Unified Modeling Language (UML) description of the resulting multi-scale application (hp-FEM coupled with MS). We investigated classical, procedural codes from the point of view of the object-oriented (O-O) programming paradigm. The discovered hierarchical structure of classes and algorithms makes the UML project as independent on the spatial dimension of the problem as possible. The O-O UML project was defined at an abstract level, independent on the programming language used.
Multi-scale modelling of supercapacitors: From molecular simulations to a transmission line model
Pean, C.; Rotenberg, B.; Simon, P.; Salanne, M.
2016-09-01
We perform molecular dynamics simulations of a typical nanoporous-carbon based supercapacitor. The organic electrolyte consists in 1-ethyl-3-methylimidazolium and hexafluorophosphate ions dissolved in acetonitrile. We simulate systems at equilibrium, for various applied voltages. This allows us to determine the relevant thermodynamic (capacitance) and transport (in-pore resistivities) properties. These quantities are then injected in a transmission line model for testing its ability to predict the charging properties of the device. The results from this macroscopic model are in good agreement with non-equilibrium molecular dynamics simulations, which validates its use for interpreting electrochemical impedance experiments.
Parker, Jeffrey B.; LoDestro, Lynda L.; Told, Daniel; Merlo, Gabriele; Ricketson, Lee F.; Campos, Alejandro; Jenko, Frank; Hittinger, Jeffrey A. F.
2018-05-01
The vast separation dividing the characteristic times of energy confinement and turbulence in the core of toroidal plasmas makes first-principles prediction on long timescales extremely challenging. Here we report the demonstration of a multiple-timescale method that enables coupling global gyrokinetic simulations with a transport solver to calculate the evolution of the self-consistent temperature profile. This method, which exhibits resiliency to the intrinsic fluctuations arising in turbulence simulations, holds potential for integrating nonlocal gyrokinetic turbulence simulations into predictive, whole-device models.
High Fidelity Multi-Scale Regolith Simulation Tool for ISRU, Phase II
National Aeronautics and Space Administration — NASA has serious unmet needs for simulation tools capable of predicting the behavior of lunar regolith in proposed excavation, transport and handling systems....
Parker, Jeffrey; Lodestro, Lynda; Told, Daniel; Merlo, Gabriele; Ricketson, Lee; Campos, Alejandro; Jenko, Frank; Hittinger, Jeffrey
2017-10-01
Predictive whole-device simulation models will play an increasingly important role in ensuring the success of fusion experiments and accelerating the development of fusion energy. In the core of tokamak plasmas, a separation of timescales between turbulence and transport makes a single direct simulation of both processes computationally expensive. We present the first demonstration of a multiple-timescale method coupling global gyrokinetic simulations with a transport solver to calculate the self-consistent, steady-state temperature profile. Initial results are highly encouraging, with the coupling method appearing robust to the difficult problem of turbulent fluctuations. The method holds potential for integrating first-principles turbulence simulations into whole-device models and advancing the understanding of global plasma behavior. Work supported by US DOE under Contract DE-AC52-07NA27344 and the Exascale Computing Project (17-SC-20-SC).
Multiscale Simulation of Thermo-mechanical Processes in Irradiated Fission-reactor Materials
International Nuclear Information System (INIS)
Phillpot, Simon R.
2012-01-01
The work funded from this project has been published in six papers, with two more in draft form, with submission planned for the near future. The papers are: (1) Kinetically-Evolving Irradiation-Induced Point-Defect Clusters in UO 2 by Molecular-Dynamics Simulation; (2) Kinetically driven point-defect clustering in irradiated MgO by molecular-dynamics simulation; (3) Grain-Boundary Source/Sink Behavior for Point Defect: An Atomistic Simulation Study; (4) Energetics of intrinsic point defects in uranium dioxide from electronic structure calculations; (5) Thermodynamics of fission products in UO 2±x ; and (6) Atomistic study of grain boundary sink strength under prolonged electron irradiation. The other two pieces of work that are currently being written-up for publication are: (1) Effect of Pores and He Bubbles on the Thermal Transport Properties of UO2 by Molecular Dynamics Simulation; and (2) Segregation of Ruthenium to Edge Dislocations in Uranium Dioxide.
Measurement-Based Hybrid Fluid-Flow Models for Fast Multi-Scale Simulation and Control
National Research Council Canada - National Science Library
Sohraby, Khosrow
2004-01-01
.... We point out that traditional queuing models are intractable or provide poor fit to real-life networks, while discrete-event simulation at the packet level can consume prohibitive amounts of CPU times...
Multi-scale Modeling of Compressible Single-phase Flow in Porous Media using Molecular Simulation
Saad, Ahmed Mohamed
2016-05-01
In this study, an efficient coupling between Monte Carlo (MC) molecular simulation and Darcy-scale flow in porous media is presented. The cell-centered finite difference method with a non-uniform rectangular mesh were used to discretize the simulation domain and solve the governing equations. To speed up the MC simulations, we implemented a recently developed scheme that quickly generates MC Markov chains out of pre-computed ones, based on the reweighting and reconstruction algorithm. This method astonishingly reduces the required computational time by MC simulations from hours to seconds. In addition, the reweighting and reconstruction scheme, which was originally designed to work with the LJ potential model, is extended to work with a potential model that accounts for the molecular quadrupole moment of fluids with non-spherical molecules such as CO2. The potential model was used to simulate the thermodynamic equilibrium properties for single-phase and two-phase systems using the canonical ensemble and the Gibbs ensemble, respectively. Comparing the simulation results with the experimental data showed that the implemented model has an excellent fit outperforming the standard LJ model. To demonstrate the strength of the proposed coupling in terms of computational time efficiency and numerical accuracy in fluid properties, various numerical experiments covering different compressible single-phase flow scenarios were conducted. The novelty in the introduced scheme is in allowing an efficient coupling of the molecular scale and Darcy scale in reservoir simulators. This leads to an accurate description of the thermodynamic behavior of the simulated reservoir fluids; consequently enhancing the confidence in the flow predictions in porous media.
Directory of Open Access Journals (Sweden)
Amanda Buyan
2016-07-01
Full Text Available Dok7 is a peripheral membrane protein that is associated with the MuSK receptor tyrosine kinase. Formation of the Dok7/MuSK/membrane complex is required for the activation of MuSK. This is a key step in the complex exchange of signals between neuron and muscle, which lead to neuromuscular junction formation, dysfunction of which is associated with congenital myasthenic syndromes. The Dok7 structure consists of a Pleckstrin Homology (PH domain and a Phosphotyrosine Binding (PTB domain. The mechanism of the Dok7 association with the membrane remains largely unknown. Using multi-scale molecular dynamics simulations we have explored the formation of the Dok7 PH/membrane complex. Our simulations indicate that the PH domain of Dok7 associates with membranes containing phosphatidylinositol phosphates (PIPs via interactions of the β1/β2, β3/β4, and β5/β6 loops, which together form a positively charged surface on the PH domain and interact with the negatively charged headgroups of PIP molecules. The initial encounter of the Dok7 PH domain is followed by formation of additional interactions with the lipid bilayer, and especially with PIP molecules, which stabilizes the Dok7 PH/membrane complex. We have quantified the binding of the PH domain to the model bilayers by calculating a density landscape for protein/membrane interactions. Detailed analysis of the PH/PIP interactions reveal both a canonical and an atypical site to be occupied by the anionic lipid. PH domain binding leads to local clustering of PIP molecules in the bilayer. Association of the Dok7 PH domain with PIP lipids is therefore seen as a key step in localization of Dok7 to the membrane and formation of a complex with MuSK.
Energy Technology Data Exchange (ETDEWEB)
Priese, L
1983-07-01
The author presents a precise notion of a realization (or simulation) of one concurrent system by another, and studies the relations of modular concurrent systems and non-persistent (i.e. With conflicts) concurrent systems in an automata theoretical style. He introduces a conception of realization that obeys three requirements: it allows for proper hierarchies in certain classes of concurrent systems; it allows for normal-form theorems, and the standard constructions of the literature remain realizations in formal concept; and it clarifies some counterintuitive examples. Further, although this realization conception is developed to translate the computational aspects of concurrent systems, it also gives a formal tool for the handling of synchronization problems. 38 references.
de Groot, Stefan; de Winter, Joost C F; López García, José Manuel; Mulder, Max; Wieringa, Peter A
2011-02-01
The aim of this study was to investigate whether concurrent bandwidth feedback improves learning of the lane-keeping task in a driving simulator. Previous research suggests that bandwidth feedback improves learning and that off-target feedback is superior to on-target feedback. This study aimed to extend these findings for the lane-keeping task. Participants without a driver's license drove five 8-min lane-keeping sessions in a driver training simulator: three practice sessions, an immediate retention session, and a delayed retention session I day later. There were four experimental groups (n=15 per group): (a) on-target, receiving seat vibrations when the center of the car was within 0.5 m of the lane center; (b) off-target, receiving seat vibrations when the center of the car was more than 0.5 m away from the lane center; (c) control, receiving no vibrations; and (d) realistic, receiving seat vibrations depending on engine speed. During retention, all groups were provided with the realistic vibrations. During practice, on-target and off-target groups had better lane-keeping performance than the nonaugmented groups, but this difference diminished in the retention phase. Furthermore, during late practice and retention, the off-target group outperformed the on-target group.The off-target group had a higher rate of steering reversal and higher steering entropy than the nonaugmented groups, whereas no clear group differences were found regarding mean speed, mental workload, or self-reported measures. Off-target feedback is superior to on-target feedback for learning the lane-keeping task. This research provides knowledge to researchers and designers of training systems about the value of feedback in simulator-based training of vehicular control.
Xiao, Li; Cai, Qin; Li, Zhilin; Zhao, Hongkai; Luo, Ray
2014-11-25
A multi-scale framework is proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent. This article reports our initial efforts to formulate the physical concepts necessary for coupling the two mechanics and develop a 3D numerical algorithm to simulate the solvent fluid via the Navier-Stokes equation. The numerical algorithm was validated with multiple test cases. The validation shows that the algorithm is effective and stable, with observed accuracy consistent with our design.
Knightes, C D; Golden, H E; Journey, C A; Davis, G M; Conrads, P A; Marvin-DiPasquale, M; Brigham, M E; Bradley, P M
2014-04-01
Mercury is a ubiquitous global environmental toxicant responsible for most US fish advisories. Processes governing mercury concentrations in rivers and streams are not well understood, particularly at multiple spatial scales. We investigate how insights gained from reach-scale mercury data and model simulations can be applied at broader watershed scales using a spatially and temporally explicit watershed hydrology and biogeochemical cycling model, VELMA. We simulate fate and transport using reach-scale (0.1 km(2)) study data and evaluate applications to multiple watershed scales. Reach-scale VELMA parameterization was applied to two nested sub-watersheds (28 km(2) and 25 km(2)) and the encompassing watershed (79 km(2)). Results demonstrate that simulated flow and total mercury concentrations compare reasonably to observations at different scales, but simulated methylmercury concentrations are out-of-phase with observations. These findings suggest that intricacies of methylmercury biogeochemical cycling and transport are under-represented in VELMA and underscore the complexity of simulating mercury fate and transport. Published by Elsevier Ltd.
International Nuclear Information System (INIS)
Miyamoto, Akira; Sato, Etsuko; Sato, Ryo; Inaba, Kenji; Hatakeyama, Nozomu
2014-01-01
In collaboration with experimental experts we have reported in the present conference (Hatakeyama, N. et al., “Experiment-integrated multi-scale, multi-physics computational chemistry simulation applied to corrosion behaviour of BWR structural materials”) the results of multi-scale multi-physics computational chemistry simulations applied to the corrosion behaviour of BWR structural materials. In macro-scale, a macroscopic simulator of anode polarization curve was developed to solve the spatially one-dimensional electrochemical equations on the material surface in continuum level in order to understand the corrosion behaviour of typical BWR structural material, SUS304. The experimental anode polarization behaviours of each pure metal were reproduced by fitting all the rates of electrochemical reactions and then the anode polarization curve of SUS304 was calculated by using the same parameters and found to reproduce the experimental behaviour successfully. In meso-scale, a kinetic Monte Carlo (KMC) simulator was applied to an actual-time simulation of the morphological corrosion behaviour under the influence of an applied voltage. In micro-scale, an ultra-accelerated quantum chemical molecular dynamics (UA-QCMD) code was applied to various metallic oxide surfaces of Fe 2 O 3 , Fe 3 O 4 , Cr 2 O 3 modelled as same as water molecules and dissolved metallic ions on the surfaces, then the dissolution and segregation behaviours were successfully simulated dynamically by using UA-QCMD. In this paper we describe details of the multi-scale, multi-physics computational chemistry method especially the UA-QCMD method. This method is approximately 10,000,000 times faster than conventional first-principles molecular dynamics methods based on density-functional theory (DFT), and the accuracy was also validated for various metals and metal oxides compared with DFT results. To assure multi-scale multi-physics computational chemistry simulation based on the UA-QCMD method for
Multiscale Simulation of Thermo-mechancial Processes in Irradiated Fission-reactor Materials.
Energy Technology Data Exchange (ETDEWEB)
Simon R. Phillpot
2012-06-08
The work funded from this project has been published in six papers, with two more in draft form, with submission planned for the near future. The papers are: (1) Kinetically-Evolving Irradiation-Induced Point-Defect Clusters in UO{sub 2} by Molecular-Dynamics Simulation; (2) Kinetically driven point-defect clustering in irradiated MgO by molecular-dynamics simulation; (3) Grain-Boundary Source/Sink Behavior for Point Defect: An Atomistic Simulation Study; (4) Energetics of intrinsic point defects in uranium dioxide from electronic structure calculations; (5) Thermodynamics of fission products in UO{sub 2{+-}x}; and (6) Atomistic study of grain boundary sink strength under prolonged electron irradiation. The other two pieces of work that are currently being written-up for publication are: (1) Effect of Pores and He Bubbles on the Thermal Transport Properties of UO2 by Molecular Dynamics Simulation; and (2) Segregation of Ruthenium to Edge Dislocations in Uranium Dioxide.
Multi-scale Modeling of Compressible Single-phase Flow in Porous Media using Molecular Simulation
Saad, Ahmed Mohamed
2016-01-01
potential model that accounts for the molecular quadrupole moment of fluids with non-spherical molecules such as CO2. The potential model was used to simulate the thermodynamic equilibrium properties for single-phase and two-phase systems using the canonical
Energy Technology Data Exchange (ETDEWEB)
Guerrier, C. [Applied Mathematics and Computational Biology, IBENS, Ecole Normale Supérieure, 46 rue d' Ulm, 75005 Paris (France); Holcman, D., E-mail: david.holcman@ens.fr [Applied Mathematics and Computational Biology, IBENS, Ecole Normale Supérieure, 46 rue d' Ulm, 75005 Paris (France); Mathematical Institute, Oxford OX2 6GG, Newton Institute (United Kingdom)
2017-07-01
The main difficulty in simulating diffusion processes at a molecular level in cell microdomains is due to the multiple scales involving nano- to micrometers. Few to many particles have to be simulated and simultaneously tracked while there are exploring a large portion of the space for binding small targets, such as buffers or active sites. Bridging the small and large spatial scales is achieved by rare events representing Brownian particles finding small targets and characterized by long-time distribution. These rare events are the bottleneck of numerical simulations. A naive stochastic simulation requires running many Brownian particles together, which is computationally greedy and inefficient. Solving the associated partial differential equations is also difficult due to the time dependent boundary conditions, narrow passages and mixed boundary conditions at small windows. We present here two reduced modeling approaches for a fast computation of diffusing fluxes in microdomains. The first approach is based on a Markov mass-action law equations coupled to a Markov chain. The second is a Gillespie's method based on the narrow escape theory for coarse-graining the geometry of the domain into Poissonian rates. The main application concerns diffusion in cellular biology, where we compute as an example the distribution of arrival times of calcium ions to small hidden targets to trigger vesicular release.
Anatomy and Physiology of Multiscale Modeling and Simulation in Systems Medicine
Mizeranschi, A.; Groen, D.; Borgdorff, J.; Hoekstra, A.G.; Chopard, B.; Dubitzky, W.; Schmitz, U; Wolkenhauer, O.
2016-01-01
Systems medicine is the application of systems biology concepts, methods, and tools to medical research and practice. It aims to integrate data and knowledge from different disciplines into biomedical models and simulations for the understanding, prevention, cure, and management of complex diseases.
International Nuclear Information System (INIS)
Tonks, Michael R.; Millett, Paul C.; Nerikar, Pankaj; Du, Shiyu; Andersson, David; Stanek, Christopher R.; Gaston, Derek; Andrs, David; Williamson, Richard
2013-01-01
Fission gas production and evolution significantly impact the fuel performance, causing swelling, a reduction in the thermal conductivity and fission gas release. However, typical empirical models of fuel properties treat each of these effects separately and uncoupled. Here, we couple a fission gas release model to a model of the impact of fission gas on the fuel thermal conductivity. To quantify the specific impact of grain boundary (GB) bubbles on the thermal conductivity, we use atomistic and mesoscale simulations. Atomistic molecular dynamic simulations were employed to determine the GB thermal resistance. These values were then used in mesoscale heat conduction simulations to develop a mechanistic expression for the effective GB thermal resistance of a GB containing gas bubbles, as a function of the percentage of the GB covered by fission gas. The coupled fission gas release and thermal conductivity model was implemented in Idaho National Laboratory’s BISON fuel performance code to model the behavior of a 10-pellet LWR fuel rodlet, showing how the fission gas impacts the UO 2 thermal conductivity. Furthermore, additional BISON simulations were conducted to demonstrate the impact of average grain size on both the fuel thermal conductivity and the fission gas release
International Nuclear Information System (INIS)
Guerrier, C.; Holcman, D.
2017-01-01
The main difficulty in simulating diffusion processes at a molecular level in cell microdomains is due to the multiple scales involving nano- to micrometers. Few to many particles have to be simulated and simultaneously tracked while there are exploring a large portion of the space for binding small targets, such as buffers or active sites. Bridging the small and large spatial scales is achieved by rare events representing Brownian particles finding small targets and characterized by long-time distribution. These rare events are the bottleneck of numerical simulations. A naive stochastic simulation requires running many Brownian particles together, which is computationally greedy and inefficient. Solving the associated partial differential equations is also difficult due to the time dependent boundary conditions, narrow passages and mixed boundary conditions at small windows. We present here two reduced modeling approaches for a fast computation of diffusing fluxes in microdomains. The first approach is based on a Markov mass-action law equations coupled to a Markov chain. The second is a Gillespie's method based on the narrow escape theory for coarse-graining the geometry of the domain into Poissonian rates. The main application concerns diffusion in cellular biology, where we compute as an example the distribution of arrival times of calcium ions to small hidden targets to trigger vesicular release.
Chen, J Y C; Terrence, P I
2009-08-01
This study investigated the performance and workload of the combined position of gunner and robotics operator in a simulated military multitasking environment. Specifically, the study investigated how aided target recognition (AiTR) capabilities for the gunnery task with imperfect reliability (false-alarm-prone vs. miss-prone) might affect the concurrent robotics and communication tasks. Additionally, the study examined whether performance was affected by individual differences in spatial ability and attentional control. Results showed that when the robotics task was simply monitoring the video, participants had the best performance in their gunnery and communication tasks and the lowest perceived workload, compared with the other robotics tasking conditions. There was a strong interaction between the type of AiTR unreliability and participants' perceived attentional control. Overall, for participants with higher perceived attentional control, false-alarm-prone alerts were more detrimental; for low attentional control participants, conversely, miss-prone automation was more harmful. Low spatial ability participants preferred visual cueing and high spatial ability participants favoured tactile cueing. Potential applications of the findings include personnel selection for robotics operation, robotics user interface designs and training development. The present results will provide further understanding of the interplays among automation reliability, multitasking performance and individual differences in military tasking environments. These results will also facilitate the implementation of robots in military settings and will provide useful data to military system designs.
Multiscale image-based modeling and simulation of gas flow and particle transport in the human lungs
Tawhai, Merryn H; Hoffman, Eric A
2013-01-01
Improved understanding of structure and function relationships in the human lungs in individuals and sub-populations is fundamentally important to the future of pulmonary medicine. Image-based measures of the lungs can provide sensitive indicators of localized features, however to provide a better prediction of lung response to disease, treatment and environment, it is desirable to integrate quantifiable regional features from imaging with associated value-added high-level modeling. With this objective in mind, recent advances in computational fluid dynamics (CFD) of the bronchial airways - from a single bifurcation symmetric model to a multiscale image-based subject-specific lung model - will be reviewed. The interaction of CFD models with local parenchymal tissue expansion - assessed by image registration - allows new understanding of the interplay between environment, hot spots where inhaled aerosols could accumulate, and inflammation. To bridge ventilation function with image-derived central airway structure in CFD, an airway geometrical modeling method that spans from the model ‘entrance’ to the terminal bronchioles will be introduced. Finally, the effects of turbulent flows and CFD turbulence models on aerosol transport and deposition will be discussed. CFD simulation of airflow and particle transport in the human lung has been pursued by a number of research groups, whose interest has been in studying flow physics and airways resistance, improving drug delivery, or investigating which populations are most susceptible to inhaled pollutants. The three most important factors that need to be considered in airway CFD studies are lung structure, regional lung function, and flow characteristics. Their correct treatment is important because the transport of therapeutic or pollutant particles is dependent on the characteristics of the flow by which they are transported; and the airflow in the lungs is dependent on the geometry of the airways and how ventilation
Multi-scale and multi-physics simulations using the multi-fluid plasma model
2017-04-25
small The simulation uses 512 second-order elements Bz = 1.0, Te = Ti = 0.01, ui = ue = 0 ne = ni = 1.0 + e−10(x−6) 2 Baboolal, Math . and Comp. Sim. 55...DISTRIBUTION Clearance No. 17211 23 / 31 SUMMARY The blended finite element method (BFEM) is presented DG spatial discretization with explicit Runge...Kutta (i+, n) CG spatial discretization with implicit Crank-Nicolson (e−, fileds) DG captures shocks and discontinuities CG is efficient and robust for
2015-12-02
of completely new nonlinear Malliavin calculus . This type of calculus is important for the analysis and simulation of stationary and/or “causal...been limited by the fact that it requires the solution of an optimization problem with noisy gradients . When using deterministic optimization schemes...under uncertainty. We tested new developments on nonlinear Malliavin calculus , combining reduced basis methods with ANOVA, model validation, on
Simulation of macromolecule self-assembly in solution: A multiscale approach
Energy Technology Data Exchange (ETDEWEB)
Lavino, Alessio D., E-mail: alessiodomenico.lavino@studenti.polito.it; Barresi, Antonello A., E-mail: antonello.barresi@polito.it; Marchisio, Daniele L., E-mail: daniele.marchisio@polito.it [Dipartimento di Scienza Applicata e Tecnologia, Istituto di Ingegneria Chimica, Politecnico di Torino, C.so Duca degli Abruzzi 24, 10129 Torino (Italy); Pasquale, Nicodemo di, E-mail: nicodemo.dipasquale@manchester.ac.uk [School of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, UnitedKingdom (United Kingdom); Carbone, Paola, E-mail: paola.carbone@manchester.ac.uk [School of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, UnitedKingdom (United Kingdom)
2015-12-17
One of the most common processes to produce polymer nanoparticles is to induce self-assembly by using the solvent-displacement method, in which the polymer is dissolved in a “good” solvent and the solution is then mixed with an “anti-solvent”. The polymer ability to self-assemble in solution is therefore determined by its structural and transport properties in solutions of the pure solvents and at the intermediate compositions. In this work, we focus on poly-ε-caprolactone (PCL) which is a biocompatible polymer that finds widespread application in the pharmaceutical and biomedical fields, performing simulation at three different scales using three different computational tools: full atomistic molecular dynamics (MD), population balance modeling (PBM) and computational fluid dynamics (CFD). Simulations consider PCL chains of different molecular weight in solution of pure acetone (good solvent), of pure water (anti-solvent) and their mixtures, and mixing at different rates and initial concentrations in a confined impinging jets mixer (CIJM). Our MD simulations reveal that the nano-structuring of one of the solvents in the mixture leads to an unexpected identical polymer structure irrespectively of the concentration of the two solvents. In particular, although in pure solvents the behavior of the polymer is, as expected, very different, at intermediate compositions, the PCL chain shows properties very similar to those found in pure acetone as a result of the clustering of the acetone molecules in the vicinity of the polymer chain. We derive an analytical expression to predict the polymer structural properties in solution at different solvent compositions and use it to formulate an aggregation kernel to describe the self-assembly in the CIJM via PBM and CFD. Simulations are eventually validated against experiments.
Understanding Creep Mechanisms in Graphite with Experiments, Multiscale Simulations, and Modeling
International Nuclear Information System (INIS)
2014-01-01
Disordering mechanisms in graphite have a long history with conflicting viewpoints. Using Raman and x-ray photon spectroscopy, electron microscopy, x-ray diffraction experiments and atomistic modeling and simulations, the current project has developed a fundamental understanding of early-to-late state radiation damage mechanisms in nuclear reactor grade graphite (NBG-18 and PCEA). We show that the topological defects in graphite play an important role under neutron and ion irradiation.
Understanding Creep Mechanisms in Graphite with Experiments, Multiscale Simulations, and Modeling
Energy Technology Data Exchange (ETDEWEB)
Eapen, Jacob [North Carolina State Univ., Raleigh, NC (United States); Murty, Korukonda [North Carolina State Univ., Raleigh, NC (United States); Burchell, Timothy [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
2014-06-02
Disordering mechanisms in graphite have a long history with conflicting viewpoints. Using Raman and x-ray photon spectroscopy, electron microscopy, x-ray diffraction experiments and atomistic modeling and simulations, the current project has developed a fundamental understanding of early-to-late state radiation damage mechanisms in nuclear reactor grade graphite (NBG-18 and PCEA). We show that the topological defects in graphite play an important role under neutron and ion irradiation.
Modeling and Simulation of Multi-scale Environmental Systems with Generalized Hybrid Petri Nets
Directory of Open Access Journals (Sweden)
Mostafa eHerajy
2015-07-01
Full Text Available Predicting and studying the dynamics and properties of environmental systems necessitates the construction and simulation of mathematical models entailing different levels of complexities. Such type of computational experiments often require the combination of discrete and continuous variables as well as processes operating at different time scales. Furthermore, the iterative steps of constructing and analyzing environmental models might involve researchers with different background. Hybrid Petri nets may contribute in overcoming such challenges as they facilitate the implementation of systems integrating discrete and continuous dynamics. Additionally, the visual depiction of model components will inevitably help to bridge the gap between scientists with distinct expertise working on the same problem. Thus, modeling environmental systems with hybrid Petri nets enables the construction of complex processes while keeping the models comprehensible for researchers working on the same project with significantly divergent education path. In this paper we propose the utilization of a special class of hybrid Petri nets, Generalized Hybrid Petri Nets (GHPN, to model and simulate environmental systems exposing processes interacting at different time-scales. GHPN integrate stochastic and deterministic semantics as well as other types of special basic events. Moreover, a case study is presented to illustrate the use of GHPN in constructing and simulating multi-timescale environmental scenarios.
Multi-scale simulations of droplets in generic time-dependent flows
Milan, Felix; Biferale, Luca; Sbragaglia, Mauro; Toschi, Federico
2017-11-01
We study the deformation and dynamics of droplets in time-dependent flows using a diffuse interface model for two immiscible fluids. The numerical simulations are at first benchmarked against analytical results of steady droplet deformation, and further extended to the more interesting case of time-dependent flows. The results of these time-dependent numerical simulations are compared against analytical models available in the literature, which assume the droplet shape to be an ellipsoid at all times, with time-dependent major and minor axis. In particular we investigate the time-dependent deformation of a confined droplet in an oscillating Couette flow for the entire capillary range until droplet break-up. In this way these multi component simulations prove to be a useful tool to establish from ``first principles'' the dynamics of droplets in complex flows involving multiple scales. European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No 642069. & European Research Council under the European Community's Seventh Framework Program, ERC Grant Agreement No 339032.
Multiscale combination of climate model simulations and proxy records over the last millennium
Chen, Xin; Xing, Pei; Luo, Yong; Nie, Suping; Zhao, Zongci; Huang, Jianbin; Tian, Qinhua
2018-05-01
To highlight the compatibility of climate model simulation and proxy reconstruction at different timescales, a timescale separation merging method combining proxy records and climate model simulations is presented. Annual mean surface temperature anomalies for the last millennium (851-2005 AD) at various scales over the land of the Northern Hemisphere were reconstructed with 2° × 2° spatial resolution, using an optimal interpolation (OI) algorithm. All target series were decomposed using an ensemble empirical mode decomposition method followed by power spectral analysis. Four typical components were obtained at inter-annual, decadal, multidecadal, and centennial timescales. A total of 323 temperature-sensitive proxy chronologies were incorporated after screening for each component. By scaling the proxy components using variance matching and applying a localized OI algorithm to all four components point by point, we obtained merged surface temperatures. Independent validation indicates that the most significant improvement was for components at the inter-annual scale, but this became less evident with increasing timescales. In mid-latitude land areas, 10-30% of grids were significantly corrected at the inter-annual scale. By assimilating the proxy records, the merged results reduced the gap in response to volcanic forcing between a pure reconstruction and simulation. Difficulty remained in verifying the centennial information and quantifying corresponding uncertainties, so additional effort should be devoted to this aspect in future research.
Predicting Silk Fiber Mechanical Properties through Multiscale Simulation and Protein Design.
Rim, Nae-Gyune; Roberts, Erin G; Ebrahimi, Davoud; Dinjaski, Nina; Jacobsen, Matthew M; Martín-Moldes, Zaira; Buehler, Markus J; Kaplan, David L; Wong, Joyce Y
2017-08-14
Silk is a promising material for biomedical applications, and much research is focused on how application-specific, mechanical properties of silk can be designed synthetically through proper amino acid sequences and processing parameters. This protocol describes an iterative process between research disciplines that combines simulation, genetic synthesis, and fiber analysis to better design silk fibers with specific mechanical properties. Computational methods are used to assess the protein polymer structure as it forms an interconnected fiber network through shearing and how this process affects fiber mechanical properties. Model outcomes are validated experimentally with the genetic design of protein polymers that match the simulation structures, fiber fabrication from these polymers, and mechanical testing of these fibers. Through iterative feedback between computation, genetic synthesis, and fiber mechanical testing, this protocol will enable a priori prediction capability of recombinant material mechanical properties via insights from the resulting molecular architecture of the fiber network based entirely on the initial protein monomer composition. This style of protocol may be applied to other fields where a research team seeks to design a biomaterial with biomedical application-specific properties. This protocol highlights when and how the three research groups (simulation, synthesis, and engineering) should be interacting to arrive at the most effective method for predictive design of their material.
International Nuclear Information System (INIS)
Tognevi, Amen
2012-01-01
The concrete structures of nuclear power plants can be subjected to moderate thermo-hydric loadings characterized by temperatures of the order of hundred of degrees in service conditions as well as in accidental ones. These loadings can be at the origin of important disorders, in particular cracking which accelerate hydric transfers in the structure. In the framework of the study of durability of these structures, a coupled thermo-hydro-mechanical model denoted THMs has been developed at Laboratoire d'Etude du Comportement des Betons et des Argiles (LECBA) of CEA Saclay in order to perform simulations of the concrete behavior submitted to such loadings. In this work, we focus on the improvement in the model THMs in one hand of the assessment of the mechanical and hydro-mechanical parameters of the unsaturated micro-cracked material and in the other hand of the description of cracking in terms of opening and propagation. The first part is devoted to the development of a model based on a multi-scale description of cement-based materials starting from the scale of the main hydrated products (portlandite, ettringite, C-S-H etc.) to the macroscopic scale of the cracked material. The investigated parameters are obtained at each scale of the description by applying analytical homogenization techniques. The second part concerns a fine numerical description of cracking. To this end, we choose to use combined finite element and discrete element methods. This procedure is presented and illustrated through a series of mechanical tests in order to show the feasibility of the method and to proceed to its validation. Finally, we apply the procedure to a heated wall and the proposed method for estimating the permeability shows the interest to take into account an anisotropic permeability tensor when dealing with mass transfers in cracked concrete structures. (author) [fr
Multiscale simulations of PS-SiO2 nanocomposites: from melt to glassy state.
Mathioudakis, I G; Vogiatzis, G G; Tzoumanekas, C; Theodorou, D N
2016-09-28
The interaction energetics, molecular packing, entanglement network properties, segmental dynamics, and elastic constants of atactic polystyrene-amorphous silica nanocomposites in the molten and the glassy state are studied via molecular simulations using two interconnected levels of representation: (a) a coarse-grained one, wherein each polystyrene repeat unit is mapped onto a single "superatom" and the silica nanoparticle is viewed as a solid sphere. Equilibration at all length scales at this level is achieved via connectivity-altering Monte Carlo simulations. (b) A united-atom (UA) level, wherein the polymer chains are represented in terms of a united-atom forcefield and the silica nanoparticle is represented in terms of a simplified, fully atomistic model. Initial configurations for UA molecular dynamics (MD) simulations are obtained by reverse mapping well-equilibrated coarse-grained configurations. By analysing microcanonical UA MD trajectories, the polymer density profile is studied and the polymer is found to exhibit layering in the vicinity of the nanoparticle surface. An estimate of the enthalpy of mixing between polymer and nanoparticles, derived from the UA simulations, compares favourably against available experimental values. The dynamical behaviour of polystyrene (in neat and filled melt systems) is characterized in terms of bond orientation and dihedral angle time autocorrelation functions. At low concentration in the molten polymer matrix, silica nanoparticles are found to cause a slight deceleration of the segmental dynamics close to their surface compared to the bulk polymer. Well-equilibrated coarse-grained long-chain configurations are reduced to entanglement networks via topological analysis with the CReTA algorithm, yielding a slightly lower density of entanglements in the filled than in the neat systems. UA melt configurations are glassified by MD cooling. The elastic moduli of the resulting glassy nanocomposites are computed through an
Modeling and simulation of multi-physics multi-scale transport phenomenain bio-medical applications
International Nuclear Information System (INIS)
Kenjereš, Saša
2014-01-01
We present a short overview of some of our most recent work that combines the mathematical modeling, advanced computer simulations and state-of-the-art experimental techniques of physical transport phenomena in various bio-medical applications. In the first example, we tackle predictions of complex blood flow patterns in the patient-specific vascular system (carotid artery bifurcation) and transfer of the so-called 'bad' cholesterol (low-density lipoprotein, LDL) within the multi-layered artery wall. This two-way coupling between the blood flow and corresponding mass transfer of LDL within the artery wall is essential for predictions of regions where atherosclerosis can develop. It is demonstrated that a recently developed mathematical model, which takes into account the complex multi-layer arterial-wall structure, produced LDL profiles within the artery wall in good agreement with in-vivo experiments in rabbits, and it can be used for predictions of locations where the initial stage of development of atherosclerosis may take place. The second example includes a combination of pulsating blood flow and medical drug delivery and deposition controlled by external magnetic field gradients in the patient specific carotid artery bifurcation. The results of numerical simulations are compared with own PIV (Particle Image Velocimetry) and MRI (Magnetic Resonance Imaging) in the PDMS (silicon-based organic polymer) phantom. A very good agreement between simulations and experiments is obtained for different stages of the pulsating cycle. Application of the magnetic drug targeting resulted in an increase of up to ten fold in the efficiency of local deposition of the medical drug at desired locations. Finally, the LES (Large Eddy Simulation) of the aerosol distribution within the human respiratory system that includes up to eight bronchial generations is performed. A very good agreement between simulations and MRV (Magnetic Resonance Velocimetry) measurements is
Modeling and simulation of multi-physics multi-scale transport phenomenain bio-medical applications
Kenjereš, Saša
2014-08-01
We present a short overview of some of our most recent work that combines the mathematical modeling, advanced computer simulations and state-of-the-art experimental techniques of physical transport phenomena in various bio-medical applications. In the first example, we tackle predictions of complex blood flow patterns in the patient-specific vascular system (carotid artery bifurcation) and transfer of the so-called "bad" cholesterol (low-density lipoprotein, LDL) within the multi-layered artery wall. This two-way coupling between the blood flow and corresponding mass transfer of LDL within the artery wall is essential for predictions of regions where atherosclerosis can develop. It is demonstrated that a recently developed mathematical model, which takes into account the complex multi-layer arterial-wall structure, produced LDL profiles within the artery wall in good agreement with in-vivo experiments in rabbits, and it can be used for predictions of locations where the initial stage of development of atherosclerosis may take place. The second example includes a combination of pulsating blood flow and medical drug delivery and deposition controlled by external magnetic field gradients in the patient specific carotid artery bifurcation. The results of numerical simulations are compared with own PIV (Particle Image Velocimetry) and MRI (Magnetic Resonance Imaging) in the PDMS (silicon-based organic polymer) phantom. A very good agreement between simulations and experiments is obtained for different stages of the pulsating cycle. Application of the magnetic drug targeting resulted in an increase of up to ten fold in the efficiency of local deposition of the medical drug at desired locations. Finally, the LES (Large Eddy Simulation) of the aerosol distribution within the human respiratory system that includes up to eight bronchial generations is performed. A very good agreement between simulations and MRV (Magnetic Resonance Velocimetry) measurements is obtained
International Nuclear Information System (INIS)
Buldum, A.; Clemons, C.B.; Dill, L.H.; Kreider, K.L.; Young, G.W.; Zheng, X.; Evans, E.A.; Zhang, G.; Hariharan, S.I.
2005-01-01
This work is Part II of an integrated experimental/modeling investigation of a procedure to coat nanofibers and core-clad nanostructures with thin-film materials using plasma-enhanced physical vapor deposition. In the experimental effort, electrospun polymer nanofibers are coated with aluminum materials under different operating conditions to observe changes in the coating morphology. This procedure begins with the sputtering of the coating material from a target. Part I [J. Appl. Phys. 98, 044303 (2005)] focused on the sputtering aspect and transport of the sputtered material through the reactor. That reactor level model determines the concentration field of the coating material. This field serves as input into the present species transport and deposition model for the region surrounding an individual nanofiber. The interrelationships among processing factors for the transport and deposition are investigated here from a detailed modeling approach that includes the salient physical and chemical phenomena. Solution strategies that couple continuum and atomistic models are used. At the continuum scale, transport dynamics near the nanofiber are described. At the atomic level, molecular dynamics (MD) simulations are used to study the deposition and sputtering mechanisms at the coating surface. Ion kinetic energies and fluxes are passed from the continuum sheath model to the MD simulations. These simulations calculate sputtering and sticking probabilities that in turn are used to calculate parameters for the continuum transport model. The continuum transport model leads to the definition of an evolution equation for the coating-free surface. This equation is solved using boundary perturbation and level set methods to determine the coating morphology as a function of operating conditions
Multiscale molecular dynamics simulation approaches to the structure and dynamics of viruses.
Huber, Roland G; Marzinek, Jan K; Holdbrook, Daniel A; Bond, Peter J
2017-09-01
Viral pathogens are a significant source of human morbidity and mortality, and have a major impact on societies and economies around the world. One of the challenges inherent in targeting these pathogens with drugs is the tight integration of the viral life cycle with the host's cellular machinery. However, the reliance of the virus on the host cell replication machinery is also an opportunity for therapeutic targeting, as successful entry- and exit-inhibitors have demonstrated. An understanding of the extracellular and intracellular structure and dynamics of the virion - as well as of the entry and exit pathways in host and vector cells - is therefore crucial to the advancement of novel antivirals. In recent years, advances in computing architecture and algorithms have begun to allow us to use simulations to study the structure and dynamics of viral ultrastructures at various stages of their life cycle in atomistic or near-atomistic detail. In this review, we outline specific challenges and solutions that have emerged to allow for structurally detailed modelling of viruses in silico. We focus on the history and state of the art of atomistic and coarse-grained approaches to simulate the dynamics of the large, macromolecular structures associated with viral infection, and on their usefulness in explaining and expanding upon experimental data. We discuss the types of interactions that need to be modeled to describe major components of the virus particle and advances in modelling techniques that allow for the treatment of these systems, highlighting recent key simulation studies. Copyright © 2016 Elsevier Ltd. All rights reserved.
Directory of Open Access Journals (Sweden)
L. Yao
2011-03-01
Full Text Available Relations between mineralization and certain geological processes are established mostly by geologist's knowledge of field observations. However, these relations are descriptive and a quantitative model of how certain geological processes strengthen or hinder mineralization is not clear, that is to say, the mechanism of the interactions between mineralization and the geological framework has not been thoroughly studied. The dynamics behind these interactions are key in the understanding of fractal or multifractal formations caused by mineralization, among which singularities arise due to anomalous concentration of metals in narrow space. From a statistical point of view, we think that cascade dynamics play an important role in mineralization and studying them can reveal the nature of the various interactions throughout the process. We have constructed a multiplicative cascade model to simulate these dynamics. The probabilities of mineral deposit occurrences are used to represent direct results of mineralization. Multifractal simulation of probabilities of mineral potential based on our model is exemplified by a case study dealing with hydrothermal gold deposits in southern Nova Scotia, Canada. The extent of the impacts of certain geological processes on gold mineralization is related to the scale of the cascade process, especially to the maximum cascade division number n_{max}. Our research helps to understand how the singularity occurs during mineralization, which remains unanswered up to now, and the simulation may provide a more accurate distribution of mineral deposit occurrences that can be used to improve the results of the weights of evidence model in mapping mineral potential.
Molecular dynamics simulations of stratum corneum lipid mixtures: A multiscale perspective.
Moore, Timothy C; Iacovella, Christopher R; Leonhard, Anne C; Bunge, Annette L; McCabe, Clare
2018-03-29
The lipid matrix of the stratum corneum (SC) layer of skin is essential for human survival; it acts as a barrier to prevent rapid dehydration while keeping potentially hazardous material outside the body. While the composition of the SC lipid matrix is known, the molecular-level details of its organization are difficult to infer experimentally, hindering the discovery of structure-property relationships. To this end, molecular dynamics simulations, which give molecular-level resolution, have begun to play an increasingly important role in understanding these relationships. However, most simulation studies of SC lipids have focused on preassembled bilayer configurations, which, owing to the slow dynamics of the lipids, may influence the final structure and hence the calculated properties. Self-assembled structures would avoid this dependence on the initial configuration, however, the size and length scales involved make self-assembly impractical to study with atomistic models. Here, we report on the development of coarse-grained models of SC lipids designed to study self-assembly. Building on previous work, we present the interactions between the headgroups of ceramide and free fatty acid developed using the multistate iterative Boltzmann inversion method. Validation of the new interactions is performed with simulations of preassembled bilayers and good agreement between the atomistic and coarse-grained models is found for structural properties. The self-assembly of mixtures of ceramide and free fatty acid is investigated and both bilayer and multilayer structures are found to form. This work therefore represents a necessary step in studying SC lipid systems on multiple time and length scales. Copyright © 2017 Elsevier Inc. All rights reserved.
International Nuclear Information System (INIS)
Gomez Torres, Armando Miguel
2011-01-01
This doctoral thesis describes the methodological development of coupled neutron-kinetics/thermal-hydraulics codes for the design and safety analysis of reactor systems taking into account the feedback mechanisms on the fuel rod level, according to different approaches. A central part of this thesis is the development and validation of a high fidelity simulation tool, DYNSUB, which results from the ''two-way-coupling'' of DYN3D-SP3 and SUBCHANFLOW. It allows the determination of local safety parameters through a detailed description of the core behavior under stationary and transient conditions at fuel rod level.
A multi-scale experimental and simulation approach for fractured subsurface systems
Viswanathan, H. S.; Carey, J. W.; Frash, L.; Karra, S.; Hyman, J.; Kang, Q.; Rougier, E.; Srinivasan, G.
2017-12-01
Fractured systems play an important role in numerous subsurface applications including hydraulic fracturing, carbon sequestration, geothermal energy and underground nuclear test detection. Fractures that range in scale from microns to meters and their structure control the behavior of these systems which provide over 85% of our energy and 50% of US drinking water. Determining the key mechanisms in subsurface fractured systems has been impeded due to the lack of sophisticated experimental methods to measure fracture aperture and connectivity, multiphase permeability, and chemical exchange capacities at the high temperature, pressure, and stresses present in the subsurface. In this study, we developed and use microfluidic and triaxial core flood experiments required to reveal the fundamental dynamics of fracture-fluid interactions. In addition we have developed high fidelity fracture propagation and discrete fracture network flow models to simulate these fractured systems. We also have developed reduced order models of these fracture simulators in order to conduct uncertainty quantification for these systems. We demonstrate an integrated experimental/modeling approach that allows for a comprehensive characterization of fractured systems and develop models that can be used to optimize the reservoir operating conditions over a range of subsurface conditions.
Shang, Barry Z; Voulgarakis, Nikolaos K; Chu, Jhih-Wei
2012-07-28
This work illustrates that fluctuating hydrodynamics (FHD) simulations can be used to capture the thermodynamic and hydrodynamic responses of molecular fluids at the nanoscale, including those associated with energy and heat transfer. Using all-atom molecular dynamics (MD) trajectories as the reference data, the atomistic coordinates of each snapshot are mapped onto mass, momentum, and energy density fields on Eulerian grids to generate a corresponding field trajectory. The molecular length-scale associated with finite molecule size is explicitly imposed during this coarse-graining by requiring that the variances of density fields scale inversely with the grid volume. From the fluctuations of field variables, the response functions and transport coefficients encoded in the all-atom MD trajectory are computed. By using the extracted fluid properties in FHD simulations, we show that the fluctuations and relaxation of hydrodynamic fields quantitatively match with those observed in the reference all-atom MD trajectory, hence establishing compatibility between the atomistic and field representations. We also show that inclusion of energy transfer in the FHD equations can more accurately capture the thermodynamic and hydrodynamic responses of molecular fluids. The results indicate that the proposed MD-to-FHD mapping with explicit consideration of finite molecule size provides a robust framework for coarse-graining the solution phase of complex molecular systems.
Illuminating the star clusters and satellite galaxies with multi-scale baryonic simulations
Maji, Moupiya; Zhu, Qirong; Li, Yuexing; Marinacci, Federico; Charlton, Jane; Hernquist, Lars; Knebe, Alexander
2018-01-01
Over the past decade, advances in computational architecture have made it possible for the first time to investigate some of the fundamental questions around the formation, evolution and assembly of the building blocks of the universe; star clusters and galaxies. In this talk, I will focus on two major questions: What is the origin of the observed universal lognormal mass function in globular clusters? What is the statistical distribution of the properties of satellite planes in a large sample of satellite systems?Observations of globular clusters show that they have universal lognormal mass functions with a characteristic peak at 2X105 MSun, although the origin of this peaked distribution is unclear. We investigate the formation of star clusters in interacting galaxies using baryonic simulations and found that massive clusters preferentially form in extremely high pressure gas clouds which reside in highly shocked regions produced by galaxy interactions. These massive clusters have quasi-lognormal initial mass functions with a peak around ~106MSun which may survive dynamical evolution and slowly evolve into the universal lognormal profiles observed today.The classical Milky Way (MW) satellites are observed to be distributed in a highly-flattened plane, called Disk of Satellites (DoS). However the significance, coherence and origin of DoS is highly debated. To understand this, we first analyze all MW satellites and find that a small sample size can artificially produce a highly anisotropic spatial distribution and a strong clustering of their angular momentum. Comparing a baryonic simulation of a MW-sized galaxy with its N-body counterpart we find that an anisotropic DoS can originate from baryonic processes. Furthermore, we explore the statistical distribution of DoS properties by analyzing 2591 satellite systems in the cosmological hydrodynamic simulation Illustris. We find that the DoS becomes more isotropic with increasing sample sizes and most (~90%) satellite
Understanding the catalytic activity of gold nanoparticles through multi-scale simulations
DEFF Research Database (Denmark)
Brodersen, Simon Hedegaard; Vej-Hansen, Ulrik Grønbjerg; Larsen, Britt Hvolbæk
2011-01-01
We investigate how the chemical reactivity of gold nanoparticles depends on the cluster size and shape using a combination of simulation techniques at different length scales, enabling us to model at the atomic level the shapes of clusters in the size range relevant for catalysis. The detailed......-coordinated active sites is found, and their reactivities are extracted from models based on Density Functional Theory calculations. This enables us to determine the chemical activity of clusters in the same range of particle sizes that is accessible experimentally. The variation of reactivity with particle size...... is in excellent agreement with experiments, and we conclude that the experimentally observed trends are mostly explained by the high reactivity of under-coordinated corner atoms on the gold clusters. Other effects, such as the effect of the substrate, may influence the reactivities significantly, but the presence...
Multiscale Simulations of Lamellar PS–PEO Block Copolymers Doped with LiPF6 Ions
Sethuraman, Vaidyanathan
2017-06-02
We report the results of atomistic simulations of the structural equilibrium properties of PS–PEO block copolymer (BCP) melt in the ordered lamellar phase doped with LiPF6 salt. A hybrid simulation strategy, consisting of steps of coarse-graining and inverse coarse-graining, was employed to equilibrate the melt at an atomistic resolution in the ordered phase. We characterize the structural distributions between different atoms/ions and compare the features arising in BCPs against the corresponding behavior in PEO homopolymers for different salt concentrations. In addition, the local structural distributions are characterized in the lamellar phase as a function of distance from the interface. The cation–anion radial distribution functions (RDF) display stronger coordination in the block copolymer melts at high salt concentrations, whereas the trends are reversed for low salt concentrations. Radial distribution functions isolated in the PEO and PS domains demonstrate that the stronger coordination seen in BCPs arises from the influence of both the higher fraction of ions segregated in the PS phase and the influence of interactions in the PS domain. Such a behavior also manifests in the cation–anion clusters, which show a larger fraction of free ions in the BCP. While the average number of free anions (cations) decreases with increasing salt concentration, higher order aggregates of LiPF6 increase with increasing salt concentration. Further, the cation–anion RDFs display spatial heterogeneity, with a stronger cation–anion binding in the interfacial region compared to bulk of the PEO domain.
Nebgen, Benjamin T; Magurudeniya, Harsha D; Kwock, Kevin W C; Ringstrand, Bryan S; Ahmed, Towfiq; Seifert, Sönke; Zhu, Jian-Xin; Tretiak, Sergei; Firestone, Millicent A
2017-12-14
Molecular dynamics simulations (up to the nanoscale) were performed on the 3-methyl-1-pentylimidazolium ionic liquid cation paired with three anions; chloride, nitrate, and thiocyanate as aqueous mixtures, using the effective fragment potential (EFP) method, a computationally inexpensive way of modeling intermolecular interactions. The simulations provided insight (preferred geometries, radial distribution functions and theoretical proton NMR resonances) into the interactions within the ionic domain and are validated against 1 H NMR spectroscopy and small- and wide-angle X-ray scattering experiments on 1-decyl-3-methylimidazolium. Ionic liquids containing thiocyanate typically resist gelation and form poorly ordered lamellar structures upon mixing with water. Conversely, chloride, a strongly coordinating anion, normally forms strong physical gels and produces well-ordered nanostructures adopting a variety of structural motifs over a very wide range of water compositions. Nitrate is intermediate in character, whereby upon dispersal in water it displays a range of viscosities and self-assembles into nanostructures with considerable variability in the fidelity of ordering and symmetry, as a function of water content in the binary mixtures. The observed changes in the macro and nanoscale characteristics were directly correlated to ionic domain structures and intermolecular interactions as theoretically predicted by the analysis of MD trajectories and calculated RDFs. Specifically, both chloride and nitrate are positioned in the plane of the cation. Anion to cation proximity is dependent on water content. Thiocyanate is more susceptible to water insertion into the second solvent shell. Experimental 1 H NMR chemical shifts monitor the site-specific competition dependence with water content in the binary mixtures. Thiocyanate preferentially sits above and below the aromatic ring plane, a state disallowing interaction with the protons on the imidazolium ring.
Jung, Jaewoon; Mori, Takaharu; Kobayashi, Chigusa; Matsunaga, Yasuhiro; Yoda, Takao; Feig, Michael; Sugita, Yuji
2015-07-01
GENESIS (Generalized-Ensemble Simulation System) is a new software package for molecular dynamics (MD) simulations of macromolecules. It has two MD simulators, called ATDYN and SPDYN. ATDYN is parallelized based on an atomic decomposition algorithm for the simulations of all-atom force-field models as well as coarse-grained Go-like models. SPDYN is highly parallelized based on a domain decomposition scheme, allowing large-scale MD simulations on supercomputers. Hybrid schemes combining OpenMP and MPI are used in both simulators to target modern multicore computer architectures. Key advantages of GENESIS are (1) the highly parallel performance of SPDYN for very large biological systems consisting of more than one million atoms and (2) the availability of various REMD algorithms (T-REMD, REUS, multi-dimensional REMD for both all-atom and Go-like models under the NVT, NPT, NPAT, and NPγT ensembles). The former is achieved by a combination of the midpoint cell method and the efficient three-dimensional Fast Fourier Transform algorithm, where the domain decomposition space is shared in real-space and reciprocal-space calculations. Other features in SPDYN, such as avoiding concurrent memory access, reducing communication times, and usage of parallel input/output files, also contribute to the performance. We show the REMD simulation results of a mixed (POPC/DMPC) lipid bilayer as a real application using GENESIS. GENESIS is released as free software under the GPLv2 licence and can be easily modified for the development of new algorithms and molecular models. WIREs Comput Mol Sci 2015, 5:310-323. doi: 10.1002/wcms.1220.
Breaking the power law: Multiscale simulations of self-ion irradiated tungsten
Jin, Miaomiao; Permann, Cody; Short, Michael P.
2018-06-01
The initial stage of radiation defect creation has often been shown to follow a power law distribution at short time scales, recently so with tungsten, following many self-organizing patterns found in nature. The evolution of this damage, however, is dominated by interactions between defect clusters, as the coalescence of smaller defects into clusters depends on the balance between transport, absorption, and emission to/from existing clusters. The long-time evolution of radiation-induced defects in tungsten is studied with cluster dynamics parameterized with lower length scale simulations, and is shown to deviate from a power law size distribution. The effects of parameters such as dose rate and total dose, as parameters affecting the strength of the driving force for defect evolution, are also analyzed. Excellent agreement is achieved with regards to an experimentally measured defect size distribution at 30 K. This study provides another satisfactory explanation for experimental observations in addition to that of primary radiation damage, which should be reconciled with additional validation data.
Directory of Open Access Journals (Sweden)
S. F. Mueller
2011-01-01
Full Text Available The Community Multiscale Air Quality (CMAQ model version 4.6 has been revised with regard to the representation of chlorine (HCl, ClNO_{2} and sulfur (dimethylsulfide, or DMS, and H_{2}S, and evaluated against observations and earlier published models. Chemistry parameterizations were based on published reaction kinetic data and a recently developed cloud chemistry model that includes heterogeneous reactions of organic sulfur compounds. Evaluation of the revised model was conducted using a recently enhanced data base of natural emissions that includes ocean and continental sources of DMS, H_{2}S, chlorinated gases and lightning NO_{x} for the continental United States and surrounding regions. Results using 2002 meteorology and emissions indicated that most simulated "natural" (plus background chemical and aerosol species exhibit the expected seasonal variations at the surface. Ozone exhibits a winter and early spring maximum consistent with ozone data and an earlier published model. Ozone distributions reflect the influences of atmospheric dynamics and pollutant background levels imposed on the CMAQ simulation by boundary conditions derived from a global model. A series of model experiments reveals that the consideration of gas-phase organic sulfur chemistry leads to sulfate aerosol increases over most of the continental United States. Cloud chemistry parameterization changes result in widespread decreases in SO_{2} across the modeling domain and both increases and decreases in sulfate. Most cloud-mediated sulfate increases occurred mainly over the Pacific Ocean (up to about 0.1 μg m^{−3} but also over and downwind from the Gulf of Mexico (including parts of the eastern US. Geographic variations in simulated SO_{2} and sulfate are due to the link between DMS/H_{2}S and their byproduct SO_{2}, the heterogeneity of cloud cover and precipitation (precipitating clouds act as
DEFF Research Database (Denmark)
Solov'yov, Ilia; Yakubovich, Alexander V.; Nikolaev, Pavel V.
2012-01-01
it significantly different from the existing codes, is its universality and applicability to the description of a broad range of problems involving different molecular systems. Most of the existing codes are developed for particular classes of molecular systems and do not permit multiscale approach while MBN...
Collaborating for Multi-Scale Chemical Science
Energy Technology Data Exchange (ETDEWEB)
William H. Green
2006-07-14
Advanced model reduction methods were developed and integrated into the CMCS multiscale chemical science simulation software. The new technologies were used to simulate HCCI engines and burner flames with exceptional fidelity.
Ganguli, Supriya B.; Gavrishchaka, Valeriy V.
1999-01-01
Multiscale transverse structures in the magnetic-field-aligned flows have been frequently observed in the auroral region by FAST and Freja satellites. A number of multiscale processes, such as broadband low-frequency oscillations and various cross-field transport effects are well correlated with these structures. To study these effects, we have used our three-dimensional multifluid model with multiscale transverse inhomogeneities in the initial velocity profile. Self-consistent-frequency mode driven by local transverse gradients in the generation of the low field-aligned ion flow and associated transport processes were simulated. Effects of particle interaction with the self-consistent time-dependent three-dimensional wave potential have been modeled using a distribution of test particles. For typical polar wind conditions it has been found that even large-scale (approximately 50 - 100 km) transverse inhomogeneities in the flow can generate low-frequency oscillations that lead to significant flow modifications, cross-field particle diffusion, and other transport effects. It has also been shown that even small-amplitude (approximately 10 - 20%) short-scale (approximately 10 km) modulations of the original large-scale flow profile significantly increases low-frequency mode generation and associated cross-field transport, not only at the local spatial scales imposed by the modulations but also on global scales. Note that this wave-induced cross-field transport is not included in any of the global numerical models of the ionosphere, ionosphere-thermosphere, or ionosphere-polar wind. The simulation results indicate that the wave-induced cross-field transport not only affects the ion outflow rates but also leads to a significant broadening of particle phase-space distribution and transverse particle diffusion.
Directory of Open Access Journals (Sweden)
Tetsuya Ishida
2018-03-01
Full Text Available In November 2011, the Japanese government resolved to build “Revival Roads” in the Tohoku region to accelerate the recovery from the Great East Japan Earthquake of March 2011. Because the Tohoku region experiences such cold and snowy weather in winter, complex degradation from a combination of frost damage, chloride attack from de-icing agents, alkali–silica reaction, cracking and fatigue is anticipated. Thus, to enhance the durability performance of road structures, particularly reinforced concrete (RC bridge decks, multiple countermeasures are proposed: a low water-to-cement ratio in the mix, mineral admixtures such as ground granulated blast furnace slag and/or fly ash to mitigate the risks of chloride attack and alkali–silica reaction, anticorrosion rebar and 6% entrained air for frost damage. It should be noted here that such high durability specifications may conversely increase the risk of early age cracking caused by temperature and shrinkage due to the large amounts of cement and the use of mineral admixtures. Against this background, this paper presents a numerical simulation of early age deformation and cracking of RC bridge decks with full 3D multiscale and multi-chemo-physical integrated analysis. First, a multiscale constitutive model of solidifying cementitious materials is briefly introduced based on systematic knowledge coupling microscopic thermodynamic phenomena and microscopic structural mechanics. With the aim to assess the early age thermal and shrinkage-induced cracks on real bridge deck, the study began with extensive model validations by applying the multiscale and multi-physical integrated analysis system to small specimens and mock-up RC bridge deck specimens. Then, through the application of the current computational system, factors that affect the generation and propagation of early age thermal and shrinkage-induced cracks are identified via experimental validation and full-scale numerical simulation on real
Rasthofer, U.; Wall, W. A.; Gravemeier, V.
2018-04-01
A novel and comprehensive computational method, referred to as the eXtended Algebraic Variational Multiscale-Multigrid-Multifractal Method (XAVM4), is proposed for large-eddy simulation of the particularly challenging problem of turbulent two-phase flow. The XAVM4 involves multifractal subgrid-scale modeling as well as a Nitsche-type extended finite element method as an approach for two-phase flow. The application of an advanced structural subgrid-scale modeling approach in conjunction with a sharp representation of the discontinuities at the interface between two bulk fluids promise high-fidelity large-eddy simulation of turbulent two-phase flow. The high potential of the XAVM4 is demonstrated for large-eddy simulation of turbulent two-phase bubbly channel flow, that is, turbulent channel flow carrying a single large bubble of the size of the channel half-width in this particular application.
Directory of Open Access Journals (Sweden)
J. T. Kelly
2010-04-01
Full Text Available Chemical processing of sea-salt particles in coastal environments significantly impacts concentrations of particle components and gas-phase species and has implications for human exposure to particulate matter and nitrogen deposition to sensitive ecosystems. Emission of sea-salt particles from the coastal surf zone is known to be elevated compared to that from the open ocean. Despite the importance of sea-salt emissions and chemical processing, the US EPA's Community Multiscale Air Quality (CMAQ model has traditionally treated coarse sea-salt particles as chemically inert and has not accounted for enhanced surf-zone emissions. In this article, updates to CMAQ are described that enhance sea-salt emissions from the coastal surf zone and allow dynamic transfer of HNO_{3}, H_{2}SO_{4}, HCl, and NH_{3} between coarse particles and the gas phase. Predictions of updated CMAQ models and the previous release version, CMAQv4.6, are evaluated using observations from three coastal sites during the Bay Regional Atmospheric Chemistry Experiment (BRACE in Tampa, FL in May 2002. Model updates improve predictions of NO_{3}^{−}, SO_{4}^{2−}, NH_{4}^{+}, Na^{+}, and Cl^{−} concentrations at these sites with only a 8% increase in run time. In particular, the chemically interactive coarse particle mode dramatically improves predictions of nitrate concentration and size distributions as well as the fraction of total nitrate in the particle phase. Also, the surf-zone emission parameterization improves predictions of total sodium and chloride concentration. Results of a separate study indicate that the model updates reduce the mean absolute error of nitrate predictions at coastal CASTNET and SEARCH sites in the eastern US. Although the new model features improve performance relative to CMAQv4.6, some persistent differences exist between observations and predictions
Evolution of Radiation Induced Defects in SiC: A Multiscale Simulation Approach
Jiang, Hao
Because of various excellent properties, SiC has been proposed for many applications in nuclear reactors including cladding layers in fuel rod, fission products container in TRISO fuel, and first wall/blanket in magnetic controlled fusion reactors. Upon exposure to high energy radiation environments, point defects and defect clusters are generated in materials in amounts significantly exceeding their equilibrium concentrations. The accumulation of defects can lead to undesired consequences such as crystalline-to-amorphous transformation1, swelling, and embrittlement, and these phenomena can adversely affect the lifetime of SiC based components in nuclear reactors. It is of great importance to understand the accumulation process of these defects in order to estimate change in properties of this material and to design components with superior ability to withstand radiation damages. Defect clusters are widely in SiC irradiated at the operation temperatures of various reactors. These clusters are believed to cause more than half of the overall swelling of irradiated SiC and can potentially lead to lowered thermal conductivity and mechanical strength. It is critical to understand the formation and growth of these clusters. Diffusion of these clusters is one importance piece to determine the growth rate of clusters; however it is unclear so far due to the challenges in simulating rare events. Using a combination of kinetic Activation Relaxation Technique with empirical potential and ab initio based climbing image nudged elastic band method, I performed an extensive search of the migration paths of the most stable carbon tri-interstitial cluster in SiC. This research reveals paths with the lowest energy barriers to migration, rotation, and dissociation of the most stable cluster. Based on these energy barriers, I concluded defect clusters are thermally immobile at temperatures lower than 1500 K and can dissociate into smaller clusters and single interstitials at
Directory of Open Access Journals (Sweden)
Ana Belén Petro
2014-04-01
Full Text Available While the retinex theory aimed at explaining human color perception, its derivations have led to efficient algorithms enhancing local image contrast, thus permitting among other features, to "see in the shadows". Among these derived algorithms, Multiscale Retinex is probably the most successful center-surround image filter. In this paper, we offer an analysis and implementation of Multiscale Retinex. We point out and resolve some ambiguities of the method. In particular, we show that the important color correction final step of the method can be seriously improved. This analysis permits to come up with an automatic implementation of Multiscale Retinex which is as faithful as possible to the one described in the original paper. Overall, this implementation delivers excellent results and confirms the validity of Multiscale Retinex for image color restoration and contrast enhancement. Nevertheless, while the method parameters can be fixed, we show that a crucial choice must be left to the user, depending on the lightning condition of the image: the method must either be applied to each color independently if a color balance is required, or to the luminance only if the goal is to achieve local contrast enhancement. Thus, we propose two slightly different algorithms to deal with both cases.
Lagardère, Louis; Jolly, Luc-Henri; Lipparini, Filippo; Aviat, Félix; Stamm, Benjamin; Jing, Zhifeng F; Harger, Matthew; Torabifard, Hedieh; Cisneros, G Andrés; Schnieders, Michael J; Gresh, Nohad; Maday, Yvon; Ren, Pengyu Y; Ponder, Jay W; Piquemal, Jean-Philip
2018-01-28
We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) encompassing distributed multipoles electrostatics. Tinker-HP is an evolution of the popular Tinker package code that conserves its simplicity of use and its reference double precision implementation for CPUs. Grounded on interdisciplinary efforts with applied mathematics, Tinker-HP allows for long polarizable MD simulations on large systems up to millions of atoms. We detail in the paper the newly developed extension of massively parallel 3D spatial decomposition to point dipole polarizable models as well as their coupling to efficient Krylov iterative and non-iterative polarization solvers. The design of the code allows the use of various computer systems ranging from laboratory workstations to modern petascale supercomputers with thousands of cores. Tinker-HP proposes therefore the first high-performance scalable CPU computing environment for the development of next generation point dipole PFFs and for production simulations. Strategies linking Tinker-HP to Quantum Mechanics (QM) in the framework of multiscale polarizable self-consistent QM/MD simulations are also provided. The possibilities, performances and scalability of the software are demonstrated via benchmarks calculations using the polarizable AMOEBA force field on systems ranging from large water boxes of increasing size and ionic liquids to (very) large biosystems encompassing several proteins as well as the complete satellite tobacco mosaic virus and ribosome structures. For small systems, Tinker-HP appears to be competitive with the Tinker-OpenMM GPU implementation of Tinker. As the system size grows, Tinker-HP remains operational thanks to its access to distributed memory and takes advantage of its new algorithmic enabling for stable long timescale polarizable simulations. Overall, a several thousand-fold acceleration over
Directory of Open Access Journals (Sweden)
Scott C Sibole
Full Text Available Cells of the musculoskeletal system are known to respond to mechanical loading and chondrocytes within the cartilage are not an exception. However, understanding how joint level loads relate to cell level deformations, e.g. in the cartilage, is not a straightforward task. In this study, a multi-scale analysis pipeline was implemented to post-process the results of a macro-scale finite element (FE tibiofemoral joint model to provide joint mechanics based displacement boundary conditions to micro-scale cellular FE models of the cartilage, for the purpose of characterizing chondrocyte deformations in relation to tibiofemoral joint loading. It was possible to identify the load distribution within the knee among its tissue structures and ultimately within the cartilage among its extracellular matrix, pericellular environment and resident chondrocytes. Various cellular deformation metrics (aspect ratio change, volumetric strain, cellular effective strain and maximum shear strain were calculated. To illustrate further utility of this multi-scale modeling pipeline, two micro-scale cartilage constructs were considered: an idealized single cell at the centroid of a 100×100×100 μm block commonly used in past research studies, and an anatomically based (11 cell model of the same volume representation of the middle zone of tibiofemoral cartilage. In both cases, chondrocytes experienced amplified deformations compared to those at the macro-scale, predicted by simulating one body weight compressive loading on the tibiofemoral joint. In the 11 cell case, all cells experienced less deformation than the single cell case, and also exhibited a larger variance in deformation compared to other cells residing in the same block. The coupling method proved to be highly scalable due to micro-scale model independence that allowed for exploitation of distributed memory computing architecture. The method's generalized nature also allows for substitution of any macro
Sibole, Scott C.; Erdemir, Ahmet
2012-01-01
Cells of the musculoskeletal system are known to respond to mechanical loading and chondrocytes within the cartilage are not an exception. However, understanding how joint level loads relate to cell level deformations, e.g. in the cartilage, is not a straightforward task. In this study, a multi-scale analysis pipeline was implemented to post-process the results of a macro-scale finite element (FE) tibiofemoral joint model to provide joint mechanics based displacement boundary conditions to micro-scale cellular FE models of the cartilage, for the purpose of characterizing chondrocyte deformations in relation to tibiofemoral joint loading. It was possible to identify the load distribution within the knee among its tissue structures and ultimately within the cartilage among its extracellular matrix, pericellular environment and resident chondrocytes. Various cellular deformation metrics (aspect ratio change, volumetric strain, cellular effective strain and maximum shear strain) were calculated. To illustrate further utility of this multi-scale modeling pipeline, two micro-scale cartilage constructs were considered: an idealized single cell at the centroid of a 100×100×100 μm block commonly used in past research studies, and an anatomically based (11 cell model of the same volume) representation of the middle zone of tibiofemoral cartilage. In both cases, chondrocytes experienced amplified deformations compared to those at the macro-scale, predicted by simulating one body weight compressive loading on the tibiofemoral joint. In the 11 cell case, all cells experienced less deformation than the single cell case, and also exhibited a larger variance in deformation compared to other cells residing in the same block. The coupling method proved to be highly scalable due to micro-scale model independence that allowed for exploitation of distributed memory computing architecture. The method’s generalized nature also allows for substitution of any macro-scale and/or micro
J. T. Kelly; P. V. Bhave; C. G. Nolte; U. Shankar; K. M. Foley
2009-01-01
Chemical processing of sea-salt particles in coastal environments significantly impacts concentrations of particle components and gas-phase species and has implications for human exposure to particulate matter and nitrogen deposition to sensitive ecosystems. Emission of sea-salt particles from the coastal surf zone is known to be elevated compared to that from the open ocean. Despite the importance of sea-salt emissions and chemical processing, the US EPA's Community Multiscale Air Quality (C...
International Nuclear Information System (INIS)
Rhodes, T.L.; Doyle, E.J.; Hillesheim, J.C.; Peebles, W.A.; Schmitz, L.; Holland, C.; Smith, S.P.; Burrell, K.H.; Candy, J.; DeBoo, J.C.; Kinsey, J.E.; Petty, C.C.; Prater, R.; Staebler, G.M.; Waltz, R.E.; White, A.E.; McKee, G.R.; Mikkelsen, D.; Parker, S.; Chen, Y.
2011-01-01
A series of carefully designed experiments on DIII-D have taken advantage of a broad set of turbulence and profile diagnostics to rigorously test gyrokinetic turbulence simulations. In this paper the goals, tools and experiments performed in these validation studies are reviewed and specific examples presented. It is found that predictions of transport and fluctuation levels in the mid-core region (0.4 < ρ < 0.75) are in better agreement with experiment than those in the outer region (ρ ≥ 0.75) where edge coupling effects may become increasingly important and multiscale simulations may also be necessary. Validation studies such as these are crucial in developing confidence in a first-principles based predictive capability for ITER.
de la Cruz, Roberto; Guerrero, Pilar; Calvo, Juan; Alarcón, Tomás
2017-12-01
The development of hybrid methodologies is of current interest in both multi-scale modelling and stochastic reaction-diffusion systems regarding their applications to biology. We formulate a hybrid method for stochastic multi-scale models of cells populations that extends the remit of existing hybrid methods for reaction-diffusion systems. Such method is developed for a stochastic multi-scale model of tumour growth, i.e. population-dynamical models which account for the effects of intrinsic noise affecting both the number of cells and the intracellular dynamics. In order to formulate this method, we develop a coarse-grained approximation for both the full stochastic model and its mean-field limit. Such approximation involves averaging out the age-structure (which accounts for the multi-scale nature of the model) by assuming that the age distribution of the population settles onto equilibrium very fast. We then couple the coarse-grained mean-field model to the full stochastic multi-scale model. By doing so, within the mean-field region, we are neglecting noise in both cell numbers (population) and their birth rates (structure). This implies that, in addition to the issues that arise in stochastic-reaction diffusion systems, we need to account for the age-structure of the population when attempting to couple both descriptions. We exploit our coarse-graining model so that, within the mean-field region, the age-distribution is in equilibrium and we know its explicit form. This allows us to couple both domains consistently, as upon transference of cells from the mean-field to the stochastic region, we sample the equilibrium age distribution. Furthermore, our method allows us to investigate the effects of intracellular noise, i.e. fluctuations of the birth rate, on collective properties such as travelling wave velocity. We show that the combination of population and birth-rate noise gives rise to large fluctuations of the birth rate in the region at the leading edge of
Chen, Hai; Liang, Xiaoying; Li, Rui
2013-01-01
Multi-Agent Systems (MAS) offer a conceptual approach to include multi-actor decision making into models of land use change. Through the simulation based on the MAS, this paper tries to show the application of MAS in the micro scale LUCC, and reveal the transformation mechanism of difference scale. This paper starts with a description of the context of MAS research. Then, it adopts the Nested Spatial Choice (NSC) method to construct the multi-scale LUCC decision-making model. And a case study for Mengcha village, Mizhi County, Shaanxi Province is reported. Finally, the potentials and drawbacks of the following approach is discussed and concluded. From our design and implementation of the MAS in multi-scale model, a number of observations and conclusions can be drawn on the implementation and future research directions. (1) The use of the LUCC decision-making and multi-scale transformation framework provides, according to us, a more realistic modeling of multi-scale decision making process. (2) By using continuous function, rather than discrete function, to construct the decision-making of the households is more realistic to reflect the effect. (3) In this paper, attempts have been made to give a quantitative analysis to research the household interaction. And it provides the premise and foundation for researching the communication and learning among the households. (4) The scale transformation architecture constructed in this paper helps to accumulate theory and experience for the interaction research between the micro land use decision-making and the macro land use landscape pattern. Our future research work will focus on: (1) how to rational use risk aversion principle, and put the rule on rotation between household parcels into model. (2) Exploring the methods aiming at researching the household decision-making over a long period, it allows us to find the bridge between the long-term LUCC data and the short-term household decision-making. (3) Researching the
Budimlić, Zoran; Burke, Michael; Cavé, Vincent; Knobe, Kathleen; Lowney, Geoff; Newton, Ryan; Palsberg, Jens; Peixotto, David; Sarkar, Vivek; Schlimbach, Frank; Taşırlar, Sağnak
2010-01-01
We introduce the Concurrent Collections (CnC) programming model. CnC supports flexible combinations of task and data parallelism while retaining determinism. CnC is implicitly parallel, with the user providing high-level operations along with semantic ordering constraints that together form a CnC graph. We formally describe the execution semantics of CnC and prove that the model guarantees deterministic computation. We evaluate the performance of CnC implementations on several applications an...
May, Christian P; Kolokotroni, Eleni; Stamatakos, Georgios S; Büchler, Philippe
2011-10-01
Modeling of tumor growth has been performed according to various approaches addressing different biocomplexity levels and spatiotemporal scales. Mathematical treatments range from partial differential equation based diffusion models to rule-based cellular level simulators, aiming at both improving our quantitative understanding of the underlying biological processes and, in the mid- and long term, constructing reliable multi-scale predictive platforms to support patient-individualized treatment planning and optimization. The aim of this paper is to establish a multi-scale and multi-physics approach to tumor modeling taking into account both the cellular and the macroscopic mechanical level. Therefore, an already developed biomodel of clinical tumor growth and response to treatment is self-consistently coupled with a biomechanical model. Results are presented for the free growth case of the imageable component of an initially point-like glioblastoma multiforme tumor. The composite model leads to significant tumor shape corrections that are achieved through the utilization of environmental pressure information and the application of biomechanical principles. Using the ratio of smallest to largest moment of inertia of the tumor material to quantify the effect of our coupled approach, we have found a tumor shape correction of 20% by coupling biomechanics to the cellular simulator as compared to a cellular simulation without preferred growth directions. We conclude that the integration of the two models provides additional morphological insight into realistic tumor growth behavior. Therefore, it might be used for the development of an advanced oncosimulator focusing on tumor types for which morphology plays an important role in surgical and/or radio-therapeutic treatment planning. Copyright © 2011 Elsevier Ltd. All rights reserved.
Multiscale analysis and computation for flows in heterogeneous media
Energy Technology Data Exchange (ETDEWEB)
Efendiev, Yalchin [Texas A & M Univ., College Station, TX (United States); Hou, T. Y. [California Inst. of Technology (CalTech), Pasadena, CA (United States); Durlofsky, L. J. [Stanford Univ., CA (United States); Tchelepi, H. [Stanford Univ., CA (United States)
2016-08-04
Our work in this project is aimed at making fundamental advances in multiscale methods for flow and transport in highly heterogeneous porous media. The main thrust of this research is to develop a systematic multiscale analysis and efficient coarse-scale models that can capture global effects and extend existing multiscale approaches to problems with additional physics and uncertainties. A key emphasis is on problems without an apparent scale separation. Multiscale solution methods are currently under active investigation for the simulation of subsurface flow in heterogeneous formations. These procedures capture the effects of fine-scale permeability variations through the calculation of specialized coarse-scale basis functions. Most of the multiscale techniques presented to date employ localization approximations in the calculation of these basis functions. For some highly correlated (e.g., channelized) formations, however, global effects are important and these may need to be incorporated into the multiscale basis functions. Other challenging issues facing multiscale simulations are the extension of existing multiscale techniques to problems with additional physics, such as compressibility, capillary effects, etc. In our project, we explore the improvement of multiscale methods through the incorporation of additional (single-phase flow) information and the development of a general multiscale framework for flows in the presence of uncertainties, compressible flow and heterogeneous transport, and geomechanics. We have considered (1) adaptive local-global multiscale methods, (2) multiscale methods for the transport equation, (3) operator-based multiscale methods and solvers, (4) multiscale methods in the presence of uncertainties and applications, (5) multiscale finite element methods for high contrast porous media and their generalizations, and (6) multiscale methods for geomechanics. Below, we present a brief overview of each of these contributions.
Multifunctional multiscale composites: Processing, modeling and characterization
Qiu, Jingjing
Carbon nanotubes (CNTs) demonstrate extraordinary properties and show great promise in enhancing out-of-plane properties of traditional polymer/fiber composites and enabling functionality. However, current manufacturing challenges hinder the realization of their potential. In the dissertation research, both experimental and computational efforts have been conducted to investigate effective manufacturing techniques of CNT integrated multiscale composites. The fabricated composites demonstrated significant improvements in physical properties, such as tensile strength, tensile modulus, inter-laminar shear strength, thermal dimension stability and electrical conductivity. Such multiscale composites were truly multifunctional with the addition of CNTs. Furthermore, a novel hierarchical multiscale modeling method was developed in this research. Molecular dynamic (MD) simulation offered reasonable explanation of CNTs dispersion and their motion in polymer solution. Bi-mode finite-extensible-nonlinear-elastic (FENE) dumbbell simulation was used to analyze the influence of CNT length distribution on the stress tensor and shear-rate-dependent viscosity. Based on the simulated viscosity profile and empirical equations from experiments, a macroscale flow simulation model on the finite element method (FEM) method was developed and validated to predict resin flow behavior in the processing of CNT-enhanced multiscale composites. The proposed multiscale modeling method provided a comprehensive understanding of micro/nano flow in both atomistic details and mesoscale. The simulation model can be used to optimize process design and control of the mold-filling process in multiscale composite manufacturing. This research provided systematic investigations into the CNT-based multiscale composites. The results from this study may be used to leverage the benefits of CNTs and open up new application opportunities for high-performance multifunctional multiscale composites. Keywords. Carbon
Multivariate refined composite multiscale entropy analysis
International Nuclear Information System (INIS)
Humeau-Heurtier, Anne
2016-01-01
Multiscale entropy (MSE) has become a prevailing method to quantify signals complexity. MSE relies on sample entropy. However, MSE may yield imprecise complexity estimation at large scales, because sample entropy does not give precise estimation of entropy when short signals are processed. A refined composite multiscale entropy (RCMSE) has therefore recently been proposed. Nevertheless, RCMSE is for univariate signals only. The simultaneous analysis of multi-channel (multivariate) data often over-performs studies based on univariate signals. We therefore introduce an extension of RCMSE to multivariate data. Applications of multivariate RCMSE to simulated processes reveal its better performances over the standard multivariate MSE. - Highlights: • Multiscale entropy quantifies data complexity but may be inaccurate at large scale. • A refined composite multiscale entropy (RCMSE) has therefore recently been proposed. • Nevertheless, RCMSE is adapted to univariate time series only. • We herein introduce an extension of RCMSE to multivariate data. • It shows better performances than the standard multivariate multiscale entropy.
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Becchetti, M; Tian, X; Segars, P; Samei, E [Clinical Imaging Physics Group, Department of Radiology, Duke University Me, Durham, NC (United States)
2015-06-15
Purpose: To develop an accurate and fast Monte Carlo (MC) method of simulating CT that is capable of correlating dose with image quality using voxelized phantoms. Methods: A realistic voxelized phantom based on patient CT data, XCAT, was used with a GPU accelerated MC code for helical MDCT. Simulations were done with both uniform density organs and with textured organs. The organ doses were validated using previous experimentally validated simulations of the same phantom under the same conditions. Images acquired by tracking photons through the phantom with MC require lengthy computation times due to the large number of photon histories necessary for accurate representation of noise. A substantial speed up of the process was attained by using a low number of photon histories with kernel denoising of the projections from the scattered photons. These FBP reconstructed images were validated against those that were acquired in simulations using many photon histories by ensuring a minimal normalized root mean square error. Results: Organ doses simulated in the XCAT phantom are within 10% of the reference values. Corresponding images attained using projection kernel smoothing were attained with 3 orders of magnitude less computation time compared to a reference simulation using many photon histories. Conclusion: Combining GPU acceleration with kernel denoising of scattered photon projections in MC simulations allows organ dose and corresponding image quality to be attained with reasonable accuracy and substantially reduced computation time than is possible with standard simulation approaches.
International Nuclear Information System (INIS)
Becchetti, M; Tian, X; Segars, P; Samei, E
2015-01-01
Purpose: To develop an accurate and fast Monte Carlo (MC) method of simulating CT that is capable of correlating dose with image quality using voxelized phantoms. Methods: A realistic voxelized phantom based on patient CT data, XCAT, was used with a GPU accelerated MC code for helical MDCT. Simulations were done with both uniform density organs and with textured organs. The organ doses were validated using previous experimentally validated simulations of the same phantom under the same conditions. Images acquired by tracking photons through the phantom with MC require lengthy computation times due to the large number of photon histories necessary for accurate representation of noise. A substantial speed up of the process was attained by using a low number of photon histories with kernel denoising of the projections from the scattered photons. These FBP reconstructed images were validated against those that were acquired in simulations using many photon histories by ensuring a minimal normalized root mean square error. Results: Organ doses simulated in the XCAT phantom are within 10% of the reference values. Corresponding images attained using projection kernel smoothing were attained with 3 orders of magnitude less computation time compared to a reference simulation using many photon histories. Conclusion: Combining GPU acceleration with kernel denoising of scattered photon projections in MC simulations allows organ dose and corresponding image quality to be attained with reasonable accuracy and substantially reduced computation time than is possible with standard simulation approaches
Linkmann, Moritz; Buzzicotti, Michele; Biferale, Luca
2018-06-01
We provide analytical and numerical results concerning multi-scale correlations between the resolved velocity field and the subgrid-scale (SGS) stress-tensor in large eddy simulations (LES). Following previous studies for Navier-Stokes equations, we derive the exact hierarchy of LES equations governing the spatio-temporal evolution of velocity structure functions of any order. The aim is to assess the influence of the subgrid model on the inertial range intermittency. We provide a series of predictions, within the multifractal theory, for the scaling of correlation involving the SGS stress and we compare them against numerical results from high-resolution Smagorinsky LES and from a-priori filtered data generated from direct numerical simulations (DNS). We find that LES data generally agree very well with filtered DNS results and with the multifractal prediction for all leading terms in the balance equations. Discrepancies are measured for some of the sub-leading terms involving cross-correlation between resolved velocity increments and the SGS tensor or the SGS energy transfer, suggesting that there must be room to improve the SGS modelisation to further extend the inertial range properties for any fixed LES resolution.
International Nuclear Information System (INIS)
Völker, Benjamin; Landis, Chad M; Kamlah, Marc
2012-01-01
Within a knowledge-based multiscale simulation approach for ferroelectric materials, the atomic level can be linked to the mesoscale by transferring results from first-principles calculations into a phase-field model. A recently presented routine (Völker et al 2011 Contin. Mech. Thermodyn. 23 435–51) for adjusting the Helmholtz free energy coefficients to intrinsic and extrinsic ferroelectric material properties obtained by DFT calculations and atomistic simulations was subject to certain limitations: caused by too small available degrees of freedom, an independent adjustment of the spontaneous strains and piezoelectric coefficients was not possible, and the elastic properties could only be considered in cubic instead of tetragonal symmetry. In this work we overcome such restrictions by expanding the formulation of the free energy function, i.e. by motivating and introducing new higher-order terms that have not appeared in the literature before. Subsequently we present an improved version of the adjustment procedure for the free energy coefficients that is solely based on input parameters from first-principles calculations performed by Marton and Elsässer, as documented in Völker et al (2011 Contin. Mech. Thermodyn. 23 435–51). Full sets of adjusted free energy coefficients for PbTiO 3 and tetragonal Pb(Zr,Ti)O 3 are presented, and the benefits of the newly introduced higher-order free energy terms are discussed. (paper)
International Nuclear Information System (INIS)
Mahalov, Alex
2014-01-01
Multiscale modeling and high resolution three-dimensional simulations of nonequilibrium ionospheric dynamics are major frontiers in the field of space sciences. The latest developments in fast computational algorithms and novel numerical methods have advanced reliable forecasting of ionospheric environments at fine scales. These new capabilities include improved physics-based predictive modeling, nesting and implicit relaxation techniques that are designed to integrate models of disparate scales. A range of scales, from mesoscale to ionospheric microscale, are included in a 3D modeling framework. Analyses and simulations of primary and secondary Rayleigh–Taylor instabilities in the equatorial spread F (ESF), the response of the plasma density to the neutral turbulent dynamics, and wave breaking in the lower region of the ionosphere and nonequilibrium layer dynamics at fine scales are presented for coupled systems (ions, electrons and neutral winds), thus enabling studies of mesoscale/microscale dynamics for a range of altitudes that encompass the ionospheric E and F layers. We examine the organizing mixing patterns for plasma flows, which occur due to polarized gravity wave excitations in the neutral field, using Lagrangian coherent structures (LCS). LCS objectively depict the flow topology and the extracted scintillation-producing irregularities that indicate a generation of ionospheric density gradients, due to the accumulation of plasma. The scintillation effects in propagation, through strongly inhomogeneous ionospheric media, are induced by trapping electromagnetic (EM) waves in parabolic cavities, which are created by the refractive index gradients along the propagation paths. (paper)
International Nuclear Information System (INIS)
Chauliac, Christian; Bestion, Dominique; Crouzet, Nicolas; Aragones, Jose-Maria; Cacuci, Dan Gabriel; Weiss, Frank-Peter; Zimmermann, Martin A.
2010-01-01
The NURESIM project, the numerical simulation platform, is developed in the frame of the NURISP European Collaborative Project (FP7), which includes 22 organizations from 14 European countries. NURESIM intends to be a reference platform providing high quality software tools, physical models, generic functions and assessment results. The NURESIM platform provides an accurate representation of the physical phenomena by promoting and incorporating the latest advances in core physics, two-phase thermal-hydraulics and fuel modelling. It includes multi-scale and multi-physics features, especially for coupling core physics and thermal-hydraulics models for reactor safety. Easy coupling of the different codes and solvers is provided through the use of a common data structure and generic functions (e.g., for interpolation between non-conforming meshes). More generally, the platform includes generic pre-processing, post-processing and supervision functions through the open-source SALOME software, in order to make the codes more user-friendly. The platform also provides the informatics environment for testing and comparing different codes. The contribution summarizes the achievements and ongoing developments of the simulation platform in core physics, thermal-hydraulics, multi-physics, uncertainties and code integration
Multi-Scale Coupling Between Monte Carlo Molecular Simulation and Darcy-Scale Flow in Porous Media
Saad, Ahmed Mohamed; Kadoura, Ahmad Salim; Sun, Shuyu
2016-01-01
In this work, an efficient coupling between Monte Carlo (MC) molecular simulation and Darcy-scale flow in porous media is presented. The cell centered finite difference method with non-uniform rectangular mesh were used to discretize the simulation
Energy Technology Data Exchange (ETDEWEB)
Liu, Z.; Bessa, M. A.; Liu, W.K.
2017-10-25
A predictive computational theory is shown for modeling complex, hierarchical materials ranging from metal alloys to polymer nanocomposites. The theory can capture complex mechanisms such as plasticity and failure that span across multiple length scales. This general multiscale material modeling theory relies on sound principles of mathematics and mechanics, and a cutting-edge reduced order modeling method named self-consistent clustering analysis (SCA) [Zeliang Liu, M.A. Bessa, Wing Kam Liu, “Self-consistent clustering analysis: An efficient multi-scale scheme for inelastic heterogeneous materials,” Comput. Methods Appl. Mech. Engrg. 306 (2016) 319–341]. SCA reduces by several orders of magnitude the computational cost of micromechanical and concurrent multiscale simulations, while retaining the microstructure information. This remarkable increase in efficiency is achieved with a data-driven clustering method. Computationally expensive operations are performed in the so-called offline stage, where degrees of freedom (DOFs) are agglomerated into clusters. The interaction tensor of these clusters is computed. In the online or predictive stage, the Lippmann-Schwinger integral equation is solved cluster-wise using a self-consistent scheme to ensure solution accuracy and avoid path dependence. To construct a concurrent multiscale model, this scheme is applied at each material point in a macroscale structure, replacing a conventional constitutive model with the average response computed from the microscale model using just the SCA online stage. A regularized damage theory is incorporated in the microscale that avoids the mesh and RVE size dependence that commonly plagues microscale damage calculations. The SCA method is illustrated with two cases: a carbon fiber reinforced polymer (CFRP) structure with the concurrent multiscale model and an application to fatigue prediction for additively manufactured metals. For the CFRP problem, a speed up estimated to be about
Directory of Open Access Journals (Sweden)
Mainka Julia
2016-01-01
Full Text Available Our recently developed multi-scale form of Terzaghi’s effective stress principle for unsaturated swelling clays that was rigorously derived by periodic homogenization starting from micro- and nano-mechanical analyses is applied to numerically simulate one-dimensional swelling pressure tests of compacted bentonites during hydration. The total macroscopic stress captures the coupling between disjoining forces at the nanoscopic scale of clay platelets and capillary effects at the microscopic scale of clay aggregates over the entire water content range. The numerical results allow to draw conclusions on the water transfer mechanism between inter- and intra-aggregate pores during hydration and consequently on the evolution of the external swelling pressure resulting from the competition between capillary and disjoining forces. In addition, such application highlights the abilities and the limits of the electrical double-layer theory to compute the disjoining pressure in the nano-pores. For large platelet distances, in the range of osmotic swelling, the nature of the disjoining pressure is electro-chemical and can be computed from Poisson-Boltzmann theory. Conversely, at small distances, in the crystalline swelling, a solvation component has to be added to account for the molecular nature of the solvent. As a first improvement of the nano-scale description the solvent is treated as a hard sphere fluid using Density Functional Theory.
Zhang, Y.; Yang, W.; Zhang, R.; Zhang, Z.; Lyu, S.; Yu, J.; Wang, Y.; Wang, G.; Wang, X.
2017-12-01
Isoprene, the most abundant non-methane hydrocarbon emitted from plants, directly and indirectly affects atmospheric photochemistry and radiative forcing, yet narrowing its emission uncertainties is a continuous challenge. Comparison of observed and modelled isoprene on large spatiotemporal scales would help recognize factors that control isoprene variability, systematic field observation data are however quite lacking. Here we collected ambient air samples with 1 L silonite-treated stainless steel canisters simultaneously at 20 sites over China on every Wednesday at approximately 14:00 pm Beijing time from 2012 to 2014, and analyzed isoprene mixing ratios by preconcentrator-GC-MSD/FID. Observed isoprene mixing ratios were also compared with that simulated by coupling MEGAN 2.0 (Guenther et al., 2006) with a 3-D Regional chEmical trAnsport Model (REAM) (Zhang et al., 2017). Similar seasonal variations between observation and model simulation were obtained for most of sampling sites, but overall the average isoprene mixing ratios during growing months (May to October) was 0.37 ± 0.08 ppbv from model simulation, about 32% lower than that of 0.54 ± 0.20 ppbv based on ground-based observation, and this discrepancy was particularly significant in north China during wintertime. Further investigation demonstrated that emission of biogenic isoprene in northwest China might be underestimated and non-biogenic emission, such burning biomass/biofuel, might contribute to the elevated levels of isoprene during winter time. The observation-based empirical formulas for changing isoprene emission with solar radiation and temperature were also derived for different regions of China.
Buscheck, T.; Glascoe, L.; Sun, Y.; Gansemer, J.; Lee, K.
2003-12-01
For the proposed Yucca Mountain geologic repository for high-level nuclear waste, the planned method of disposal involves the emplacement of cylindrical packages containing the waste inside horizontal tunnels, called emplacement drifts, bored several hundred meters below the ground surface. The emplacement drifts reside in highly fractured, partially saturated volcanic tuff. An important phenomenological consideration for the licensing of the proposed repository at Yucca Mountain is the generation of decay heat by the emplaced waste and the consequences of this decay heat. Changes in temperature will affect the hydrologic and chemical environment at Yucca Mountain. A thermohydrologic-modeling tool is necessary to support the performance assessment of the Engineered Barrier System (EBS) of the proposed repository. This modeling tool must simultaneously account for processes occurring at a scale of a few tens of centimeters around individual waste packages, for processes occurring around the emplacement drifts themselves, and for processes occurring at the multi-kilometer scale of the mountain. Additionally, many other features must be considered including non-isothermal, multiphase-flow in fractured porous rock of variable liquid-phase saturation and thermal radiation and convection in open cavities. The Multiscale Thermohydrologic Model (MSTHM) calculates the following thermohydrologic (TH) variables: temperature, relative humidity, liquid-phase saturation, evaporation rate, air-mass fraction, gas-phase pressure, capillary pressure, and liquid- and gas-phase fluxes. The TH variables are determined as a function of position along each of the emplacement drifts in the repository and as a function of waste-package (WP) type. These variables are determined at various generic locations within the emplacement drifts, including the waste package and drip-shield surfaces and in the invert; they are also determined at various generic locations in the adjoining host rock
Lee, Cheng-Kuang; Wodo, Olga; Ganapathysubramanian, Baskar; Pao, Chun-Wei
2014-01-01
. Simulations are performed for various configurations of electrode materials as well as processing temperature. The complex CG molecular data are characterized using a novel extension of our graph-based framework to quantify morphology and establish a link
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Yu Zou
2013-07-01
Full Text Available Reconciling competing desires to build urban models that can be simple and complicated is something of a grand challenge for urban simulation. It also prompts difficulties in many urban policy situations, such as urban sprawl, where simple, actionable ideas may need to be considered in the context of the messily complex and complicated urban processes and phenomena that work within cities. In this paper, we present a novel architecture for achieving both simple and complicated realizations of urban sprawl in simulation. Fine-scale simulations of sprawl geography are run using geographic automata to represent the geographical drivers of sprawl in intricate detail and over fine resolutions of space and time. We use Equation-Free computing to deploy population as a coarse observable of sprawl, which can be leveraged to run automata-based models as short-burst experiments within a meta-simulation framework.
Multiscale modelling in immunology: a review.
Cappuccio, Antonio; Tieri, Paolo; Castiglione, Filippo
2016-05-01
One of the greatest challenges in biomedicine is to get a unified view of observations made from the molecular up to the organism scale. Towards this goal, multiscale models have been highly instrumental in contexts such as the cardiovascular field, angiogenesis, neurosciences and tumour biology. More recently, such models are becoming an increasingly important resource to address immunological questions as well. Systematic mining of the literature in multiscale modelling led us to identify three main fields of immunological applications: host-virus interactions, inflammatory diseases and their treatment and development of multiscale simulation platforms for immunological research and for educational purposes. Here, we review the current developments in these directions, which illustrate that multiscale models can consistently integrate immunological data generated at several scales, and can be used to describe and optimize therapeutic treatments of complex immune diseases. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.
Multi-Scale Coupling Between Monte Carlo Molecular Simulation and Darcy-Scale Flow in Porous Media
Saad, Ahmed Mohamed
2016-06-01
In this work, an efficient coupling between Monte Carlo (MC) molecular simulation and Darcy-scale flow in porous media is presented. The cell centered finite difference method with non-uniform rectangular mesh were used to discretize the simulation domain and solve the governing equations. To speed up the MC simulations, we implemented a recently developed scheme that quickly generates MC Markov chains out of pre-computed ones, based on the reweighting and reconstruction algorithm. This method astonishingly reduces the required computational times by MC simulations from hours to seconds. To demonstrate the strength of the proposed coupling in terms of computational time efficiency and numerical accuracy in fluid properties, various numerical experiments covering different compressible single-phase flow scenarios were conducted. The novelty in the introduced scheme is in allowing an efficient coupling of the molecular scale and the Darcy\\'s one in reservoir simulators. This leads to an accurate description of thermodynamic behavior of the simulated reservoir fluids; consequently enhancing the confidence in the flow predictions in porous media.
Houtenbos, M; de Winter, J C F; Hale, A R; Wieringa, P A; Hagenzieker, M P
2017-04-01
A large portion of road traffic crashes occur at intersections for the reason that drivers lack necessary visual information. This research examined the effects of an audio-visual display that provides real-time sonification and visualization of the speed and direction of another car approaching the crossroads on an intersecting road. The location of red blinking lights (left vs. right on the speedometer) and the lateral input direction of beeps (left vs. right ear in headphones) corresponded to the direction from where the other car approached, and the blink and beep rates were a function of the approaching car's speed. Two driving simulators were linked so that the participant and the experimenter drove in the same virtual world. Participants (N = 25) completed four sessions (two with the audio-visual display on, two with the audio-visual display off), each session consisting of 22 intersections at which the experimenter approached from the left or right and either maintained speed or slowed down. Compared to driving with the display off, the audio-visual display resulted in enhanced traffic efficiency (i.e., greater mean speed, less coasting) while not compromising safety (i.e., the time gap between the two vehicles was equivalent). A post-experiment questionnaire showed that the beeps were regarded as more useful than the lights. It is argued that the audio-visual display is a promising means of supporting drivers until fully automated driving is technically feasible. Copyright © 2016. Published by Elsevier Ltd.
Towards practical multiscale approach for analysis of reinforced concrete structures
Moyeda, Arturo; Fish, Jacob
2017-12-01
We present a novel multiscale approach for analysis of reinforced concrete structural elements that overcomes two major hurdles in utilization of multiscale technologies in practice: (1) coupling between material and structural scales due to consideration of large representative volume elements (RVE), and (2) computational complexity of solving complex nonlinear multiscale problems. The former is accomplished using a variant of computational continua framework that accounts for sizeable reinforced concrete RVEs by adjusting the location of quadrature points. The latter is accomplished by means of reduced order homogenization customized for structural elements. The proposed multiscale approach has been verified against direct numerical simulations and validated against experimental results.
CTF/DYN3D multi-scale coupled simulation of a rod ejection transient on the NURESIM platform
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Yann Périn
2017-09-01
Full Text Available In the framework of the EU funded project NURESAFE, the subchannel code CTF and the neutronics code DYN3D were integrated and coupled on the NURESIM platform. The developments achieved during this 3-year project include assembly-level and pin-by-pin multiphysics thermal hydraulics/neutron kinetics coupling. In order to test this coupling, a PWR rod ejection transient was simulated on a MOX/UOX minicore. The transient is simulated using two different models of the minicore. In the first simulation, both codes model the core with an assembly-wise resolution. In the second simulation, a pin-by-pin fuel-centered model is used in CTF for the central assembly, and a pin power reconstruction method is applied in DYN3D. The analysis shows the influence of the different models on global parameters, such as the power and the average fuel temperature, but also on local parameters such as the maximum fuel temperature.
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Albert De Graaf
2015-10-01
Full Text Available Background: To empower patients to optimize lifestyle factors and compliance in intervention strategies, predictive personalised simulation models such as developed in the framework of the Virtual Physiological Human initiative (http://www.vph-institute.org/ are a potential important asset. Aim:The FP7 EU project MISSION-T2D aims to develop and validate a computer model incorporating genetic, metabolic, and nutritional data for the simulation and prediction of the onset and progression of T2D. The model should include immunological/inflammatory processes contributing to insulin resistance and beta cell function loss, functionally interacting with energy intake/expenditure-associated metabolic regulatory mechanisms. Methods: The overall architecture of the model interconnects and integrates an already established immune system simulator with newly developed and/or adapted discrete and continuous mathematical simulation models for relevant processes as detailed below. The model is programmed in ANSI/C. Results: Model sections are as follows: 1 GUT MICROBIOTA: predicts how different dietary components affect the relative abundance of important gut bacteria, thus influencing butyrate production, and thereby modulating TNF, IL-6 and IL-1β; 2 PANCREATIC BETA CELL employs mTOR signaling as a central mechanism and predicts the beta cell survival and –functionality as a function of concentration of macrophages, acivated macrophages, and beta cell antigenic proteins; 3 WHOLE BODY METABOLISM describes seven tissue compartments: brain, heart, liver, gastrointestinal tract, skeletal muscle, and adipose tissue, by dynamic mass balances for major cellular metabolic reactions involving glucose, lactate, pyruvate, alanine, free fatty acids, triglycerides, glycerol and ATP as driven by macronutrient meal intake and hormonal control by insulin, glucagon and epinphrine; 4 PHYSICAL ACTIVITY predicts epinephrine concentration and IL-6 as a function of exercise
Lépinoux, J.; Sigli, C.
2018-01-01
In a recent paper, the authors showed how the clusters free energies are constrained by the coagulation probability, and explained various anomalies observed during the precipitation kinetics in concentrated alloys. This coagulation probability appeared to be a too complex function to be accurately predicted knowing only the cluster distribution in Cluster Dynamics (CD). Using atomistic Monte Carlo (MC) simulations, it is shown that during a transformation at constant temperature, after a short transient regime, the transformation occurs at quasi-equilibrium. It is proposed to use MC simulations until the system quasi-equilibrates then to switch to CD which is mean field but not limited by a box size like MC. In this paper, we explain how to take into account the information available before the quasi-equilibrium state to establish guidelines to safely predict the cluster free energies.
Energy Technology Data Exchange (ETDEWEB)
Naserifar, Saber [Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211 (United States); Materials and Process Simulation Center, California Institute of Technology, Pasadena, California 91125 (United States); Goddard, William A. [Materials and Process Simulation Center, California Institute of Technology, Pasadena, California 91125 (United States); Tsotsis, Theodore T.; Sahimi, Muhammad, E-mail: moe@usc.edu [Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211 (United States)
2015-05-07
Progress has recently been made in developing reactive force fields to describe chemical reactions in systems too large for quantum mechanical (QM) methods. In particular, ReaxFF, a force field with parameters that are obtained solely from fitting QM reaction data, has been used to predict structures and properties of many materials. Important applications require, however, determination of the final structures produced by such complex processes as chemical vapor deposition, atomic layer deposition, and formation of ceramic films by pyrolysis of polymers. This requires the force field to properly describe the formation of other products of the process, in addition to yielding the final structure of the material. We describe a strategy for accomplishing this and present an example of its use for forming amorphous SiC films that have a wide variety of applications. Extensive reactive molecular dynamics (MD) simulations have been carried out to simulate the pyrolysis of hydridopolycarbosilane. The reaction products all agree with the experimental data. After removing the reaction products, the system is cooled down to room temperature at which it produces amorphous SiC film, for which the computed radial distribution function, x-ray diffraction pattern, and the equation of state describing the three main SiC polytypes agree with the data and with the QM calculations. Extensive MD simulations have also been carried out to compute other structural properties, as well the effective diffusivities of light gases in the amorphous SiC film.
Matichuk, R.; Tonnesen, G.; Luecken, D.; Roselle, S. J.; Napelenok, S. L.; Baker, K. R.; Gilliam, R. C.; Misenis, C.; Murphy, B.; Schwede, D. B.
2015-12-01
The western United States is an important source of domestic energy resources. One of the primary environmental impacts associated with oil and natural gas production is related to air emission releases of a number of air pollutants. Some of these pollutants are important precursors to the formation of ground-level ozone. To better understand ozone impacts and other air quality issues, photochemical air quality models are used to simulate the changes in pollutant concentrations in the atmosphere on local, regional, and national spatial scales. These models are important for air quality management because they assist in identifying source contributions to air quality problems and designing effective strategies to reduce harmful air pollutants. The success of predicting oil and natural gas air quality impacts depends on the accuracy of the input information, including emissions inventories, meteorological information, and boundary conditions. The treatment of chemical and physical processes within these models is equally important. However, given the limited amount of data collected for oil and natural gas production emissions in the past and the complex terrain and meteorological conditions in western states, the ability of these models to accurately predict pollution concentrations from these sources is uncertain. Therefore, this presentation will focus on understanding the Community Multiscale Air Quality (CMAQ) model's ability to predict air quality impacts associated with oil and natural gas production and its sensitivity to input uncertainties. The results will focus on winter ozone issues in the Uinta Basin, Utah and identify the factors contributing to model performance issues. The results of this study will help support future air quality model development, policy and regulatory decisions for the oil and gas sector.
Debussche, A.; Dubois, T.; Temam, R.
1993-01-01
Using results of Direct Numerical Simulation (DNS) in the case of two-dimensional homogeneous isotropic flows, the behavior of the small and large scales of Kolmogorov like flows at moderate Reynolds numbers are first analyzed in detail. Several estimates on the time variations of the small eddies and the nonlinear interaction terms were derived; those terms play the role of the Reynolds stress tensor in the case of LES. Since the time step of a numerical scheme is determined as a function of the energy-containing eddies of the flow, the variations of the small scales and of the nonlinear interaction terms over one iteration can become negligible by comparison with the accuracy of the computation. Based on this remark, a multilevel scheme which treats differently the small and the large eddies was proposed. Using mathematical developments, estimates of all the parameters involved in the algorithm, which then becomes a completely self-adaptive procedure were derived. Finally, realistic simulations of (Kolmorov like) flows over several eddy-turnover times were performed. The results are analyzed in detail and a parametric study of the nonlinear Galerkin method is performed.
Directory of Open Access Journals (Sweden)
Li Zhen
2008-05-01
Full Text Available Abstract Background Bioactivity profiling using high-throughput in vitro assays can reduce the cost and time required for toxicological screening of environmental chemicals and can also reduce the need for animal testing. Several public efforts are aimed at discovering patterns or classifiers in high-dimensional bioactivity space that predict tissue, organ or whole animal toxicological endpoints. Supervised machine learning is a powerful approach to discover combinatorial relationships in complex in vitro/in vivo datasets. We present a novel model to simulate complex chemical-toxicology data sets and use this model to evaluate the relative performance of different machine learning (ML methods. Results The classification performance of Artificial Neural Networks (ANN, K-Nearest Neighbors (KNN, Linear Discriminant Analysis (LDA, Naïve Bayes (NB, Recursive Partitioning and Regression Trees (RPART, and Support Vector Machines (SVM in the presence and absence of filter-based feature selection was analyzed using K-way cross-validation testing and independent validation on simulated in vitro assay data sets with varying levels of model complexity, number of irrelevant features and measurement noise. While the prediction accuracy of all ML methods decreased as non-causal (irrelevant features were added, some ML methods performed better than others. In the limit of using a large number of features, ANN and SVM were always in the top performing set of methods while RPART and KNN (k = 5 were always in the poorest performing set. The addition of measurement noise and irrelevant features decreased the classification accuracy of all ML methods, with LDA suffering the greatest performance degradation. LDA performance is especially sensitive to the use of feature selection. Filter-based feature selection generally improved performance, most strikingly for LDA. Conclusion We have developed a novel simulation model to evaluate machine learning methods for the
Energy Technology Data Exchange (ETDEWEB)
Liu, Yongming [Arizona State Univ., Tempe, AZ (United States). School for Engineering of Matter, Transport and Energy; Oskay, Caglar [Vanderbilt Univ., Nashville, TN (United States). Dept. of Civil and Environmental Engineering
2017-04-30
This report outlines the research activities that were carried out for the integrated experimental and simulation investigation of creep-fatigue damage mechanism and life prediction of Nickel-based alloy, Inconel 617 at high temperatures (950° and 850°). First, a novel experimental design using a hybrid control technique is proposed. The newly developed experimental technique can generate different combinations of creep and fatigue damage by changing the experimental design parameters. Next, detailed imaging analysis and statistical data analysis are performed to quantify the failure mechanisms of the creep fatigue of alloy 617 at high temperatures. It is observed that the creep damage is directly associated with the internal voids at the grain boundaries and the fatigue damage is directly related to the surface cracking. It is also observed that the classical time fraction approach does not has a good correlation with the experimental observed damage features. An effective time fraction parameter is seen to have an excellent correlation with the material microstructural damage. Thus, a new empirical damage interaction diagram is proposed based on the experimental observations. Following this, a macro level viscoplastic model coupled with damage is developed to simulate the stress/strain response under creep fatigue loadings. A damage rate function based on the hysteresis energy and creep energy is proposed to capture the softening behavior of the material and a good correlation with life prediction and material hysteresis behavior is observed. The simulation work is extended to include the microstructural heterogeneity. A crystal plasticity finite element model considering isothermal and large deformation conditions at the microstructural scale has been developed for fatigue, creep-fatigue as well as creep deformation and rupture at high temperature. The model considers collective dislocation glide and climb of the grains and progressive damage accumulation of
Sreekanth, J.; Moore, Catherine
2018-04-01
The application of global sensitivity and uncertainty analysis techniques to groundwater models of deep sedimentary basins are typically challenged by large computational burdens combined with associated numerical stability issues. The highly parameterized approaches required for exploring the predictive uncertainty associated with the heterogeneous hydraulic characteristics of multiple aquifers and aquitards in these sedimentary basins exacerbate these issues. A novel Patch Modelling Methodology is proposed for improving the computational feasibility of stochastic modelling analysis of large-scale and complex groundwater models. The method incorporates a nested groundwater modelling framework that enables efficient simulation of groundwater flow and transport across multiple spatial and temporal scales. The method also allows different processes to be simulated within different model scales. Existing nested model methodologies are extended by employing 'joining predictions' for extrapolating prediction-salient information from one model scale to the next. This establishes a feedback mechanism supporting the transfer of information from child models to parent models as well as parent models to child models in a computationally efficient manner. This feedback mechanism is simple and flexible and ensures that while the salient small scale features influencing larger scale prediction are transferred back to the larger scale, this does not require the live coupling of models. This method allows the modelling of multiple groundwater flow and transport processes using separate groundwater models that are built for the appropriate spatial and temporal scales, within a stochastic framework, while also removing the computational burden associated with live model coupling. The utility of the method is demonstrated by application to an actual large scale aquifer injection scheme in Australia.
Marsh, C.; Pomeroy, J. W.; Wheater, H. S.
2017-12-01
Accurate management of water resources is necessary for social, economic, and environmental sustainability worldwide. In locations with seasonal snowcovers, the accurate prediction of these water resources is further complicated due to frozen soils, solid-phase precipitation, blowing snow transport, and snowcover-vegetation-atmosphere interactions. Complex process interactions and feedbacks are a key feature of hydrological systems and may result in emergent phenomena, i.e., the arising of novel and unexpected properties within a complex system. One example is the feedback associated with blowing snow redistribution, which can lead to drifts that cause locally-increased soil moisture, thus increasing plant growth that in turn subsequently impacts snow redistribution, creating larger drifts. Attempting to simulate these emergent behaviours is a significant challenge, however, and there is concern that process conceptualizations within current models are too incomplete to represent the needed interactions. An improved understanding of the role of emergence in hydrological systems often requires high resolution distributed numerical hydrological models that incorporate the relevant process dynamics. The Canadian Hydrological Model (CHM) provides a novel tool for examining cold region hydrological systems. Key features include efficient terrain representation, allowing simulations at various spatial scales, reduced computational overhead, and a modular process representation allowing for an alternative-hypothesis framework. Using both physics-based and conceptual process representations sourced from long term process studies and the current cold regions literature allows for comparison of process representations and importantly, their ability to produce emergent behaviours. Examining the system in a holistic, process-based manner can hopefully derive important insights and aid in development of improved process representations.
Directory of Open Access Journals (Sweden)
Christos eLamprakis
2015-07-01
Full Text Available We used multiple sets of simulations both at the atomistic and coarse-grained level of resolution, to investigate interaction and binding of α-tochoperol transfer protein (α-TTP to phosphatidylinositol phosphate lipids (PIPs. Our calculations indicate that enrichment of membranes with such lipids facilitate membrane anchoring. Atomistic models suggest that PIP can be incorporated into the binding cavity of α-TTP and therefore confirm that such protein can work as lipid exchanger between the endosome and the plasma membrane. Comparison of the atomistic models of the α-TTP / PIPs complex with membrane-bound α-TTP revealed different roles for the various basic residues composing the basic patch that is key for the protein / ligand interaction. Such residues are of critical importance as several point mutations at their position lead to severe forms of ataxia with vitamin E deficiency (AVED phenotypes. Specifically, R221 is main residue responsible for the stabilisation of the complex. R68 and R192 exchange strong interactions in the protein or in the membrane complex only, suggesting that the two residues alternate contact formation, thus facilitating lipid flipping from the membrane into the protein cavity during the lipid exchange process. Finally, R59 shows weaker interactions with PIPs anyway with a clear preference for specific phosphorylation positions, hinting a role in early membrane selectivity for the protein. Altogether, our simulations reveal significant aspects at the atomistic scale of interactions of α-TTP with the plasma membrane and with PIP, providing clarifications on the mechanism of intracellular vitamin E trafficking and helping establishing the role of key residue for the functionality of α-TTP.
Ghatage, Dhairyasheel; Chatterji, Apratim
2013-10-01
We introduce a method to obtain steady-state uniaxial exponential-stretching flow of a fluid (akin to extensional flow) in the incompressible limit, which enables us to study the response of suspended macromolecules to the flow by computer simulations. The flow field in this flow is defined by v(x) = εx, where v(x) is the velocity of the fluid and ε is the stretch flow gradient. To eliminate the effect of confining boundaries, we produce the flow in a channel of uniform square cross section with periodic boundary conditions in directions perpendicular to the flow, but simultaneously maintain uniform density of fluid along the length of the tube. In experiments a perfect elongational flow is obtained only along the axis of symmetry in a four-roll geometry or a filament-stretching rheometer. We can reproduce flow conditions very similar to extensional flow near the axis of symmetry by exponential-stretching flow; we do this by adding the right amounts of fluid along the length of the flow in our simulations. The fluid particles added along the length of the tube are the same fluid particles which exit the channel due to the flow; thus mass conservation is maintained in our model by default. We also suggest a scheme for possible realization of exponential-stretching flow in experiments. To establish our method as a useful tool to study various soft matter systems in extensional flow, we embed (i) spherical colloids with excluded volume interactions (modeled by the Weeks-Chandler potential) as well as (ii) a bead-spring model of star polymers in the fluid to study their responses to the exponential-stretched flow and show that the responses of macromolecules in the two flows are very similar. We demonstrate that the variation of number density of the suspended colloids along the direction of flow is in tune with our expectations. We also conclude from our study of the deformation of star polymers with different numbers of arms f that the critical flow gradient ε
Directory of Open Access Journals (Sweden)
Frederic Zubler
Full Text Available Current models of embryological development focus on intracellular processes such as gene expression and protein networks, rather than on the complex relationship between subcellular processes and the collective cellular organization these processes support. We have explored this collective behavior in the context of neocortical development, by modeling the expansion of a small number of progenitor cells into a laminated cortex with layer and cell type specific projections. The developmental process is steered by a formal language analogous to genomic instructions, and takes place in a physically realistic three-dimensional environment. A common genome inserted into individual cells control their individual behaviors, and thereby gives rise to collective developmental sequences in a biologically plausible manner. The simulation begins with a single progenitor cell containing the artificial genome. This progenitor then gives rise through a lineage of offspring to distinct populations of neuronal precursors that migrate to form the cortical laminae. The precursors differentiate by extending dendrites and axons, which reproduce the experimentally determined branching patterns of a number of different neuronal cell types observed in the cat visual cortex. This result is the first comprehensive demonstration of the principles of self-construction whereby the cortical architecture develops. In addition, our model makes several testable predictions concerning cell migration and branching mechanisms.
International Nuclear Information System (INIS)
Mallet, J.
2012-01-01
This research thesis stands at the crossroad of plasma physics, numerical analysis and applied mathematics. After an introduction presenting the problematic and previous works, the author recalls some basis of classical kinetic models for plasma physics (collisionless kinetic theory and Vlasov equation, collisional kinetic theory with the non-relativistic Maxwell-Fokker-Plansk system) and describes the fundamental properties of the collision operators such as conservation laws, entropy dissipation, and so on. He reports the improvement of a deterministic numerical method to solve the non-relativistic Vlasov-Maxwell system coupled with Fokker-Planck-Landau type operators. The efficiency of each high order scheme is compared. The evolution of the hot spot is studied in the case of thermonuclear reactions in the centre of the pellet in a weakly collisional regime. The author focuses on the simulation of the kinetic electron collisional transport in inertial confinement fusion (ICF) between the laser absorption zone and the ablation front. A new approach is then introduced to reduce the huge computation time obtained with kinetic models. In a last chapter, the kinetic continuous equation in spherical domain is described and a new model is chosen for collisions in order to preserve collision properties
DEFF Research Database (Denmark)
Xue, Bingtian; Larsen, Kim Guldstrand; Mardare, Radu Iulian
2015-01-01
We introduce Concurrent Weighted Logic (CWL), a multimodal logic for concurrent labeled weighted transition systems (LWSs). The synchronization of LWSs is described using dedicated functions that, in various concurrency paradigms, allow us to encode the compositionality of LWSs. To reflect these......-completeness results for this logic. To complete these proofs we involve advanced topological techniques from Model Theory....
Data refinement for true concurrency
Directory of Open Access Journals (Sweden)
Brijesh Dongol
2013-05-01
Full Text Available The majority of modern systems exhibit sophisticated concurrent behaviour, where several system components modify and observe the system state with fine-grained atomicity. Many systems (e.g., multi-core processors, real-time controllers also exhibit truly concurrent behaviour, where multiple events can occur simultaneously. This paper presents data refinement defined in terms of an interval-based framework, which includes high-level operators that capture non-deterministic expression evaluation. By modifying the type of an interval, our theory may be specialised to cover data refinement of both discrete and continuous systems. We present an interval-based encoding of forward simulation, then prove that our forward simulation rule is sound with respect to our data refinement definition. A number of rules for decomposing forward simulation proofs over both sequential and parallel composition are developed.
Evaluation of a multi-scale WRF-CAM5 simulation during the 2010 East Asian Summer Monsoon
Energy Technology Data Exchange (ETDEWEB)
Campbell, Patrick; Zhang, Yang; Wang, Kai; Leung, Ruby; Fan, Jiwen; Zheng, Bo; Zhang, Qiang; He, Kebin
2017-11-01
The Weather Research and Forecasting model with Chemistry (WRF-Chem) with the physics package of the Community Atmosphere Model Version 5 (CAM5) has been applied at multiple scales over Eastern China (EC) and the Yangtze River Delta (YRD) to evaluate how increased horizontal resolution with physics designed for a coarser resolution climate model impacts aerosols and clouds, and the resulting precipitation characteristics and performance during the 2010 East Asian Summer Monsoon (EASM). Despite large underpredictions in surface aerosol concentrations and aerosol optical depth, there is good spatial agreement with surface observations of chemical predictions, and increasing spatial resolution tends to improve performance. Model bias and normalized root mean square values for precipitation predictions are relatively small, but there are significant differences when comparing modeled and observed probability density functions for precipitation in EC and YRD. Increasing model horizontal resolution tends to reduce model bias and error for precipitation predictions. The surface and column aerosol loading is maximized between about 32N and 42N in early to mid-May during the 2010 EASM, and then shifts north while decreasing in magnitude during July and August. Changing model resolution moderately changes the spatiotemporal relationships between aerosols, cloud properties, and precipitation during the EASM, thus demonstrating the importance of model grid resolution in simulating EASM circulation and rainfall patterns over EC and the YRD. Results from this work demonstrate the capability and limitations in the aerosol, cloud, and precipitation representation of WRF-CAM5 for regional-scale applications down to relatively fine horizontal resolutions. Further WRF-CAM5 model development and application in this area is needed.
Measuring and modelling concurrency
Sawers, Larry
2013-01-01
This article explores three critical topics discussed in the recent debate over concurrency (overlapping sexual partnerships): measurement of the prevalence of concurrency, mathematical modelling of concurrency and HIV epidemic dynamics, and measuring the correlation between HIV and concurrency. The focus of the article is the concurrency hypothesis – the proposition that presumed high prevalence of concurrency explains sub-Saharan Africa's exceptionally high HIV prevalence. Recent surveys using improved questionnaire design show reported concurrency ranging from 0.8% to 7.6% in the region. Even after adjusting for plausible levels of reporting errors, appropriately parameterized sexual network models of HIV epidemics do not generate sustainable epidemic trajectories (avoid epidemic extinction) at levels of concurrency found in recent surveys in sub-Saharan Africa. Efforts to support the concurrency hypothesis with a statistical correlation between HIV incidence and concurrency prevalence are not yet successful. Two decades of efforts to find evidence in support of the concurrency hypothesis have failed to build a convincing case. PMID:23406964
Multiscale Lyapunov exponent for 2-microlocal functions
International Nuclear Information System (INIS)
Dhifaoui, Zouhaier; Kortas, Hedi; Ammou, Samir Ben
2009-01-01
The Lyapunov exponent is an important indicator of chaotic dynamics. Using wavelet analysis, we define a multiscale representation of this exponent which we demonstrate the scale-wise dependence for functions belonging to C x 0 s,s ' spaces. An empirical study involving simulated processes and financial time series corroborates the theoretical findings.
Multiscale phenomenology of the cosmic web
Aragón-Calvo, Miguel A.; van de Weygaert, Rien; Jones, Bernard J. T.
2010-01-01
We analyse the structure and connectivity of the distinct morphologies that define the cosmic web. With the help of our multiscale morphology filter (MMF), we dissect the matter distribution of a cosmological Lambda cold dark matter N-body computer simulation into cluster, filaments and walls. The
Multiscale modeling of complex materials phenomenological, theoretical and computational aspects
Trovalusci, Patrizia
2014-01-01
The papers in this volume deal with materials science, theoretical mechanics and experimental and computational techniques at multiple scales, providing a sound base and a framework for many applications which are hitherto treated in a phenomenological sense. The basic principles are formulated of multiscale modeling strategies towards modern complex multiphase materials subjected to various types of mechanical, thermal loadings and environmental effects. The focus is on problems where mechanics is highly coupled with other concurrent physical phenomena. Attention is also focused on the historical origins of multiscale modeling and foundations of continuum mechanics currently adopted to model non-classical continua with substructure, for which internal length scales play a crucial role.
Multiscale Modeling of Ceramic Matrix Composites
Bednarcyk, Brett A.; Mital, Subodh K.; Pineda, Evan J.; Arnold, Steven M.
2015-01-01
Results of multiscale modeling simulations of the nonlinear response of SiC/SiC ceramic matrix composites are reported, wherein the microstructure of the ceramic matrix is captured. This micro scale architecture, which contains free Si material as well as the SiC ceramic, is responsible for residual stresses that play an important role in the subsequent thermo-mechanical behavior of the SiC/SiC composite. Using the novel Multiscale Generalized Method of Cells recursive micromechanics theory, the microstructure of the matrix, as well as the microstructure of the composite (fiber and matrix) can be captured.
Differential Geometry Based Multiscale Models
Wei, Guo-Wei
2010-01-01
Large chemical and biological systems such as fuel cells, ion channels, molecular motors, and viruses are of great importance to the scientific community and public health. Typically, these complex systems in conjunction with their aquatic environment pose a fabulous challenge to theoretical description, simulation, and prediction. In this work, we propose a differential geometry based multiscale paradigm to model complex macromolecular systems, and to put macroscopic and microscopic descriptions on an equal footing. In our approach, the differential geometry theory of surfaces and geometric measure theory are employed as a natural means to couple the macroscopic continuum mechanical description of the aquatic environment with the microscopic discrete atom-istic description of the macromolecule. Multiscale free energy functionals, or multiscale action functionals are constructed as a unified framework to derive the governing equations for the dynamics of different scales and different descriptions. Two types of aqueous macromolecular complexes, ones that are near equilibrium and others that are far from equilibrium, are considered in our formulations. We show that generalized Navier–Stokes equations for the fluid dynamics, generalized Poisson equations or generalized Poisson–Boltzmann equations for electrostatic interactions, and Newton's equation for the molecular dynamics can be derived by the least action principle. These equations are coupled through the continuum-discrete interface whose dynamics is governed by potential driven geometric flows. Comparison is given to classical descriptions of the fluid and electrostatic interactions without geometric flow based micro-macro interfaces. The detailed balance of forces is emphasized in the present work. We further extend the proposed multiscale paradigm to micro-macro analysis of electrohydrodynamics, electrophoresis, fuel cells, and ion channels. We derive generalized Poisson–Nernst–Planck equations that
Differential geometry based multiscale models.
Wei, Guo-Wei
2010-08-01
Large chemical and biological systems such as fuel cells, ion channels, molecular motors, and viruses are of great importance to the scientific community and public health. Typically, these complex systems in conjunction with their aquatic environment pose a fabulous challenge to theoretical description, simulation, and prediction. In this work, we propose a differential geometry based multiscale paradigm to model complex macromolecular systems, and to put macroscopic and microscopic descriptions on an equal footing. In our approach, the differential geometry theory of surfaces and geometric measure theory are employed as a natural means to couple the macroscopic continuum mechanical description of the aquatic environment with the microscopic discrete atomistic description of the macromolecule. Multiscale free energy functionals, or multiscale action functionals are constructed as a unified framework to derive the governing equations for the dynamics of different scales and different descriptions. Two types of aqueous macromolecular complexes, ones that are near equilibrium and others that are far from equilibrium, are considered in our formulations. We show that generalized Navier-Stokes equations for the fluid dynamics, generalized Poisson equations or generalized Poisson-Boltzmann equations for electrostatic interactions, and Newton's equation for the molecular dynamics can be derived by the least action principle. These equations are coupled through the continuum-discrete interface whose dynamics is governed by potential driven geometric flows. Comparison is given to classical descriptions of the fluid and electrostatic interactions without geometric flow based micro-macro interfaces. The detailed balance of forces is emphasized in the present work. We further extend the proposed multiscale paradigm to micro-macro analysis of electrohydrodynamics, electrophoresis, fuel cells, and ion channels. We derive generalized Poisson-Nernst-Planck equations that are
Generalization of concurrence vectors
International Nuclear Information System (INIS)
Yu Changshui; Song Heshan
2004-01-01
In this Letter, based on the generalization of concurrence vectors for bipartite pure state with respect to employing tensor product of generators of the corresponding rotation groups, we generalize concurrence vectors to the case of mixed states; a new criterion of separability of multipartite pure states is given out, for which we define a concurrence vector; we generalize the vector to the case of multipartite mixed state and give out a good measure of free entanglement
Temporal Concurrent Constraint Programming
DEFF Research Database (Denmark)
Nielsen, Mogens; Valencia Posso, Frank Dan
2002-01-01
The ntcc calculus is a model of non-deterministic temporal concurrent constraint programming. In this paper we study behavioral notions for this calculus. In the underlying computational model, concurrent constraint processes are executed in discrete time intervals. The behavioral notions studied...... reflect the reactive interactions between concurrent constraint processes and their environment, as well as internal interactions between individual processes. Relationships between the suggested notions are studied, and they are all proved to be decidable for a substantial fragment of the calculus...
Building Safe Concurrency Abstractions
DEFF Research Database (Denmark)
Madsen, Ole Lehrmann
2014-01-01
Concurrent object-oriented programming in Beta is based on semaphores and coroutines and the ability to define high-level concurrency abstractions like monitors, and rendezvous-based communication, and their associated schedulers. The coroutine mechanism of SIMULA has been generalized into the no......Concurrent object-oriented programming in Beta is based on semaphores and coroutines and the ability to define high-level concurrency abstractions like monitors, and rendezvous-based communication, and their associated schedulers. The coroutine mechanism of SIMULA has been generalized...
Energy Technology Data Exchange (ETDEWEB)
Graham, Samuel Jr. (; .); Wong, C. C.; Piekos, Edward Stanley
2004-02-01
A concurrent computational and experimental investigation of thermal transport is performed with the goal of improving understanding of, and predictive capability for, thermal transport in microdevices. The computational component involves Monte Carlo simulation of phonon transport. In these simulations, all acoustic modes are included and their properties are drawn from a realistic dispersion relation. Phonon-phonon and phonon-boundary scattering events are treated independently. A new set of phonon-phonon scattering coefficients are proposed that reflect the elimination of assumptions present in earlier analytical work from the simulation. The experimental component involves steady-state measurement of thermal conductivity on silicon films as thin as 340nm at a range of temperatures. Agreement between the experiment and simulation on single-crystal silicon thin films is excellent, Agreement for polycrystalline films is promising, but significant work remains to be done before predictions can be made confidently. Knowledge gained from these efforts was used to construct improved semiclassical models with the goal of representing microscale effects in existing macroscale codes in a computationally efficient manner.
Multiscale Representations Phase II
National Research Council Canada - National Science Library
Bar-Yam, Yaneer
2004-01-01
.... Multiscale analysis provides an analytic tool that can be applied to evaluating force capabilities as well as the relevance of designs for technological innovations to support force structures and their modernization...
1990-02-21
LIDS-P-1953 Multiscale System Theory Albert Benveniste IRISA-INRIA, Campus de Beaulieu 35042 RENNES CEDEX, FRANCE Ramine Nikoukhah INRIA...TITLE AND SUBTITLE Multiscale System Theory 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e...the development of a corresponding system theory and a theory of stochastic processes and their estimation. The research presented in this and several
Memmesheimer, M.; Jakobs, H. J.; Wurzler, S.; Friese, E.; Piekorz, G.; Ebel, A.
2009-04-01
The Rhine-Ruhr area is a strongly industrialized region with about 10 Million inhabitants. It is one of the regions in Europe, which has the characteristics of a megacity with respect to population density, traffic, industry and environmental issues. The main centre of European steel production and the biggest inland port of the world is located in Duisburg, one of the major cities in the Rhine-Ruhr area. Together with the nearby urban agglomerations in the Benelux area including Brussels, Amsterdam and in particular Rotterdam as one of the most important sea-harbours of the world together with Singapore and Shanghai, it forms one of the regions in Europe heavily loaded with air pollutants as ozone, NO2 and particulate matter. Ammonia emissions outside the urban agglomerations but within the domain are also on a quite high level due to intense agricultural usage in Benelux, North-Rhine-Westphalia and lower Saxony. Therefore this area acts also as an important source region for gaseous precursors contributing to the formation of secondary particles in the atmosphere. The Benelux/Rhine-Ruhr area therefore has been selected within the framework of the recently established FP7 research project CityZen as one hot spot for detailed investigations of the past and current status of air pollution and its future development on different spatial and temporal scales. Some examples from numerical simulations with the regional multi-scale chemistry transport model EURAD for Central Europe and the Rhine-Ruhr area will be presented. The model calculates the transport, chemical transformations and deposition of trace constituents in the troposphere from the surface up to about 16 km using MM5 as meteorological driver, the RACM-MIM gas-phase chemistry and MADE-SORGAM for the treatment of particulate matter. Horizontal grid sizes are in the range of 100 km down to 1 km for heavily polluted urbanized areas within Benelux/Rhine-Ruhr. The planetary boundary layer is resolved by 15
Temporal Concurrent Constraint Programming
DEFF Research Database (Denmark)
Nielsen, Mogens; Palamidessi, Catuscia; Valencia, Frank Dan
2002-01-01
The ntcc calculus is a model of non-deterministic temporal concurrent constraint programming. In this paper we study behavioral notions for this calculus. In the underlying computational model, concurrent constraint processes are executed in discrete time intervals. The behavioral notions studied...
Impredicative concurrent abstract predicates
DEFF Research Database (Denmark)
Svendsen, Kasper; Birkedal, Lars
2014-01-01
We present impredicative concurrent abstract predicates { iCAP { a program logic for modular reasoning about concurrent, higher- order, reentrant, imperative code. Building on earlier work, iCAP uses protocols to reason about shared mutable state. A key novel feature of iCAP is the ability to dene...
2015-01-01
The reliability of free energy simulations (FES) is limited by two factors: (a) the need for correct sampling and (b) the accuracy of the computational method employed. Classical methods (e.g., force fields) are typically used for FES and present a myriad of challenges, with parametrization being a principle one. On the other hand, parameter-free quantum mechanical (QM) methods tend to be too computationally expensive for adequate sampling. One widely used approach is a combination of methods, where the free energy difference between the two end states is computed by, e.g., molecular mechanics (MM), and the end states are corrected by more accurate methods, such as QM or hybrid QM/MM techniques. Here we report two new approaches that significantly improve the aforementioned scheme; with a focus on how to compute corrections between, e.g., the MM and the more accurate QM calculations. First, a molecular dynamics trajectory that properly samples relevant conformational degrees of freedom is generated. Next, potential energies of each trajectory frame are generated with a QM or QM/MM Hamiltonian. Free energy differences are then calculated based on the QM or QM/MM energies using either a non-Boltzmann Bennett approach (QM-NBB) or non-Boltzmann free energy perturbation (NB-FEP). Both approaches are applied to calculate relative and absolute solvation free energies in explicit and implicit solvent environments. Solvation free energy differences (relative and absolute) between ethane and methanol in explicit solvent are used as the initial test case for QM-NBB. Next, implicit solvent methods are employed in conjunction with both QM-NBB and NB-FEP to compute absolute solvation free energies for 21 compounds. These compounds range from small molecules such as ethane and methanol to fairly large, flexible solutes, such as triacetyl glycerol. Several technical aspects were investigated. Ultimately some best practices are suggested for improving methods that seek to connect
Xiao, Jie
Polymer nanocomposites have a great potential to be a dominant coating material in a wide range of applications in the automotive, aerospace, ship-making, construction, and pharmaceutical industries. However, how to realize design sustainability of this type of nanostructured materials and how to ensure the true optimality of the product quality and process performance in coating manufacturing remain as a mountaintop area. The major challenges arise from the intrinsic multiscale nature of the material-process-product system and the need to manipulate the high levels of complexity and uncertainty in design and manufacturing processes. This research centers on the development of a comprehensive multiscale computational methodology and a computer-aided tool set that can facilitate multifunctional nanocoating design and application from novel function envisioning and idea refinement, to knowledge discovery and design solution derivation, and further to performance testing in industrial applications and life cycle analysis. The principal idea is to achieve exceptional system performance through concurrent characterization and optimization of materials, product and associated manufacturing processes covering a wide range of length and time scales. Multiscale modeling and simulation techniques ranging from microscopic molecular modeling to classical continuum modeling are seamlessly coupled. The tight integration of different methods and theories at individual scales allows the prediction of macroscopic coating performance from the fundamental molecular behavior. Goal-oriented design is also pursued by integrating additional methods for bio-inspired dynamic optimization and computational task management that can be implemented in a hierarchical computing architecture. Furthermore, multiscale systems methodologies are developed to achieve the best possible material application towards sustainable manufacturing. Automotive coating manufacturing, that involves paint spay and
Multiscale modelling of DNA mechanics
International Nuclear Information System (INIS)
Dršata, Tomáš; Lankaš, Filip
2015-01-01
Mechanical properties of DNA are important not only in a wide range of biological processes but also in the emerging field of DNA nanotechnology. We review some of the recent developments in modeling these properties, emphasizing the multiscale nature of the problem. Modern atomic resolution, explicit solvent molecular dynamics simulations have contributed to our understanding of DNA fine structure and conformational polymorphism. These simulations may serve as data sources to parameterize rigid base models which themselves have undergone major development. A consistent buildup of larger entities involving multiple rigid bases enables us to describe DNA at more global scales. Free energy methods to impose large strains on DNA, as well as bead models and other approaches, are also briefly discussed. (topical review)
Peridynamic Multiscale Finite Element Methods
Energy Technology Data Exchange (ETDEWEB)
Costa, Timothy [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Bond, Stephen D. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Littlewood, David John [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Moore, Stan Gerald [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
2015-12-01
art of local models with the flexibility and accuracy of the nonlocal peridynamic model. In the mixed locality method this coupling occurs across scales, so that the nonlocal model can be used to communicate material heterogeneity at scales inappropriate to local partial differential equation models. Additionally, the computational burden of the weak form of the peridynamic model is reduced dramatically by only requiring that the model be solved on local patches of the simulation domain which may be computed in parallel, taking advantage of the heterogeneous nature of next generation computing platforms. Addition- ally, we present a novel Galerkin framework, the 'Ambulant Galerkin Method', which represents a first step towards a unified mathematical analysis of local and nonlocal multiscale finite element methods, and whose future extension will allow the analysis of multiscale finite element methods that mix models across scales under certain assumptions of the consistency of those models.
DEFF Research Database (Denmark)
Dai, Gaoming; Mishnaevsky, Leon, Jr.
2014-01-01
3D numerical simulations of fatigue damage of multiscale fiber reinforced polymer composites with secondary nanoclay reinforcement are carried out. Macro–micro FE models of the multiscale composites are generated automatically using Python based software. The effect of the nanoclay reinforcement....... Multiscale composites with exfoliated nanoreinforcement and aligned nanoplatelets ensure the better fatigue resistance than those with intercalated/clustered and randomly oriented nanoreinforcement....
Multiscale Modeling of Poromechanics in Geologic Media
Castelletto, N.; Hajibeygi, H.; Klevtsov, S.; Tchelepi, H.
2017-12-01
We describe a hybrid MultiScale Finite Element-Finite Volume (h-MSFE-FV) framework for the simulation of single-phase Darcy flow through deformable porous media that exhibit highly heterogeneous poromechanical properties over a wide range of length scales. In such systems, high resolution characterizations are a key requirement to obtain reliable modeling predictions and motivate the development of multiscale solution strategies to cope with the computational burden. A coupled two-field fine-scale mixed FE-FV discretization of the governing equations, namely conservation laws of linear momentum and mass, is first implemented based on a displacement-pressure formulation. After imposing a coarse-scale grid on the given fine-scale problem, for the MSFE displacement stage, the coarse-scale basis functions are obtained by solving local equilibrium problems within coarse elements. Such MSFE stage is then coupled with the MSFV method for flow, in which a dual-coarse grid is introduced to obtain approximate but conservative multiscale solutions. Robustness and accuracy of the proposed multiscale framework is demonstrated using a variety of challenging test problems.
Jiang, Lijian; Efendiev, Yalchin; Mishev, IIya
2009-01-01
The use of limited global information in multiscale simulations is needed when there is no scale separation. Previous approaches entail fine-scale simulations in the computation of the global information. The computation of the global information
Multiscale Mathematics for Biomass Conversion to Renewable Hydrogen
Energy Technology Data Exchange (ETDEWEB)
Plechac, Petr [Univ. of Tennessee, Knoxville, TN (United States). Dept. of Mathematics; Univ. of Delaware, Newark, DE (United States). Dept. of Mathematics; Vlachos, Dionisios [Univ. of Delaware, Newark, DE (United States). Dept. of Chemical and Biomolecular Engineering; Katsoulakis, Markos [Univ. of Massachusetts, Amherst, MA (United States). Dept. of Mathematics
2013-09-05
The overall objective of this project is to develop multiscale models for understanding and eventually designing complex processes for renewables. To the best of our knowledge, our work is the first attempt at modeling complex reacting systems, whose performance relies on underlying multiscale mathematics. Our specific application lies at the heart of biofuels initiatives of DOE and entails modeling of catalytic systems, to enable economic, environmentally benign, and efficient conversion of biomass into either hydrogen or valuable chemicals. Specific goals include: (i) Development of rigorous spatio-temporal coarse-grained kinetic Monte Carlo (KMC) mathematics and simulation for microscopic processes encountered in biomass transformation. (ii) Development of hybrid multiscale simulation that links stochastic simulation to a deterministic partial differential equation (PDE) model for an entire reactor. (iii) Development of hybrid multiscale simulation that links KMC simulation with quantum density functional theory (DFT) calculations. (iv) Development of parallelization of models of (i)-(iii) to take advantage of Petaflop computing and enable real world applications of complex, multiscale models. In this NCE period, we continued addressing these objectives and completed the proposed work. Main initiatives, key results, and activities are outlined.
Energy Technology Data Exchange (ETDEWEB)
Gamble, K. A. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Hales, J. D. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Miao, Y. [Argonne National Lab. (ANL), Argonne, IL (United States); Andersson, D. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Zhang, Y. [Idaho National Lab. (INL), Idaho Falls, ID (United States)
2017-07-26
Since the events at the Fukushima-Daiichi nuclear power plant in March 2011 significant research has unfolded at national laboratories, universities and other institutions into alternative materials that have potential enhanced accident tolerance when compared to traditional \\uo~fuel zircaloy clad fuel rods. One of the potential replacement fuels is uranium silicide (\\usi) for its higher thermal conductivity and uranium density. The lower melting temperature is of potential concern during postulated accident conditions. Another disadvantage for \\usi~ is the lack of experimental data under power reactor conditions. Due to the aggressive development schedule for inserting some of the potential materials into lead test assemblies or rods by 2022~\\cite{bragg-sitton_2014} multiscale multiphysics modeling approaches have been used to provide insight into these materials. \\\\ \
Kovalenko, Andriy; Gusarov, Sergey
2018-01-31
In this work, we will address different aspects of self-consistent field coupling of computational chemistry methods at different time and length scales in modern materials and biomolecular science. Multiscale methods framework yields dramatically improved accuracy, efficiency, and applicability by coupling models and methods on different scales. This field benefits many areas of research and applications by providing fundamental understanding and predictions. It could also play a particular role in commercialization by guiding new developments and by allowing quick evaluation of prospective research projects. We employ molecular theory of solvation which allows us to accurately introduce the effect of the environment on complex nano-, macro-, and biomolecular systems. The uniqueness of this method is that it can be naturally coupled with the whole range of computational chemistry approaches, including QM, MM, and coarse graining.
The Caltech Concurrent Computation Program - Project description
Fox, G.; Otto, S.; Lyzenga, G.; Rogstad, D.
1985-01-01
The Caltech Concurrent Computation Program wwhich studies basic issues in computational science is described. The research builds on initial work where novel concurrent hardware, the necessary systems software to use it and twenty significant scientific implementations running on the initial 32, 64, and 128 node hypercube machines have been constructed. A major goal of the program will be to extend this work into new disciplines and more complex algorithms including general packages that decompose arbitrary problems in major application areas. New high-performance concurrent processors with up to 1024-nodes, over a gigabyte of memory and multigigaflop performance are being constructed. The implementations cover a wide range of problems in areas such as high energy and astrophysics, condensed matter, chemical reactions, plasma physics, applied mathematics, geophysics, simulation, CAD for VLSI, graphics and image processing. The products of the research program include the concurrent algorithms, hardware, systems software, and complete program implementations.
Toward the multiscale nature of stress corrosion cracking
Directory of Open Access Journals (Sweden)
Xiaolong Liu
2018-02-01
Full Text Available This article reviews the multiscale nature of stress corrosion cracking (SCC observed by high-resolution characterizations in austenite stainless steels and Ni-base superalloys in light water reactors (including boiling water reactors, pressurized water reactors, and supercritical water reactors with related opinions. A new statistical summary and comparison of observed degradation phenomena at different length scales is included. The intrinsic causes of this multiscale nature of SCC are discussed based on existing evidence and related opinions, ranging from materials theory to practical processing technologies. Questions of interest are then discussed to improve bottom-up understanding of the intrinsic causes. Last, a multiscale modeling and simulation methodology is proposed as a promising interdisciplinary solution to understand the intrinsic causes of the multiscale nature of SCC in light water reactors, based on a review of related supporting application evidence.
A multiscale approach to Brownian motors
International Nuclear Information System (INIS)
Pavliotis, G.A.
2005-01-01
The problem of Brownian motion in a periodic potential, under the influence of external forcing, which is either random or periodic in time, is studied in this Letter. Multiscale techniques are used to derive general formulae for the steady state particle current and the effective diffusion tensor. These formulae are then applied to calculate the effective diffusion coefficient for a Brownian particle in a periodic potential driven simultaneously by additive Gaussian white and colored noise. Our theoretical findings are supported by numerical simulations
Pregeljc, Domen; Jug, Urška; Mavri, Janez; Stare, Jernej
2018-02-07
This work investigates the Y326I point mutation effect on the kinetics of oxidative deamination of phenylethylamine (PEA) catalyzed by the monoamine oxidase B (MAO B) enzyme. PEA is a neuromodulator capable of affecting the plasticity of the brain and is responsible for the mood enhancing effect caused by physical exercise. Due to a similar functionality, PEA is often regarded as an endogenous amphetamine. The rate limiting step of the deamination was simulated at the multiscale level, employing the Empirical Valence Bond approach for the quantum treatment of the involved valence states, whereas the environment (solvated protein) was represented with a classical force field. A comparison of the reaction free energy profiles delivered by simulation of the reaction in the wild type MAO B and its Y326I mutant yields an increase in the barrier by 1.06 kcal mol -1 upon mutation, corresponding to a roughly 6-fold decrease in the reaction rate. This is in excellent agreement with the experimental kinetic studies. Inspection of simulation trajectories reveals possible sources of the point mutation effect, namely vanishing favorable electrostatic interactions between PEA and a Tyr326 side chain and an increased amount of water molecules at the active site due to the replacement of tyrosine by a less spacious isoleucine residue, thereby increasing the dielectric shielding of the catalytic environment provided by the enzyme.
Multiscale Biological Materials
DEFF Research Database (Denmark)
Frølich, Simon
of multiscale biological systems have been investigated and new research methods for automated Rietveld refinement and diffraction scattering computed tomography developed. The composite nature of biological materials was investigated at the atomic scale by looking at the consequences of interactions between...
An approach to multiscale modelling with graph grammars.
Ong, Yongzhi; Streit, Katarína; Henke, Michael; Kurth, Winfried
2014-09-01
Functional-structural plant models (FSPMs) simulate biological processes at different spatial scales. Methods exist for multiscale data representation and modification, but the advantages of using multiple scales in the dynamic aspects of FSPMs remain unclear. Results from multiscale models in various other areas of science that share fundamental modelling issues with FSPMs suggest that potential advantages do exist, and this study therefore aims to introduce an approach to multiscale modelling in FSPMs. A three-part graph data structure and grammar is revisited, and presented with a conceptual framework for multiscale modelling. The framework is used for identifying roles, categorizing and describing scale-to-scale interactions, thus allowing alternative approaches to model development as opposed to correlation-based modelling at a single scale. Reverse information flow (from macro- to micro-scale) is catered for in the framework. The methods are implemented within the programming language XL. Three example models are implemented using the proposed multiscale graph model and framework. The first illustrates the fundamental usage of the graph data structure and grammar, the second uses probabilistic modelling for organs at the fine scale in order to derive crown growth, and the third combines multiscale plant topology with ozone trends and metabolic network simulations in order to model juvenile beech stands under exposure to a toxic trace gas. The graph data structure supports data representation and grammar operations at multiple scales. The results demonstrate that multiscale modelling is a viable method in FSPM and an alternative to correlation-based modelling. Advantages and disadvantages of multiscale modelling are illustrated by comparisons with single-scale implementations, leading to motivations for further research in sensitivity analysis and run-time efficiency for these models.
Multiscale modeling of pedestrian dynamics
Cristiani, Emiliano; Tosin, Andrea
2014-01-01
This book presents mathematical models and numerical simulations of crowd dynamics. The core topic is the development of a new multiscale paradigm, which bridges the microscopic and macroscopic scales taking the most from each of them for capturing the relevant clues of complexity of crowds. The background idea is indeed that most of the complex trends exhibited by crowds are due to an intrinsic interplay between individual and collective behaviors. The modeling approach promoted in this book pursues actively this intuition and profits from it for designing general mathematical structures susceptible of application also in fields different from the inspiring original one. The book considers also the two most traditional points of view: the microscopic one, in which pedestrians are tracked individually, and the macroscopic one, in which pedestrians are assimilated to a continuum. Selected existing models are critically analyzed. The work is addressed to researchers and graduate students.
Channel's Concurrence and Quantum Teleportation
Institute of Scientific and Technical Information of China (English)
LING Yin-Sheng
2005-01-01
Concurrence can measure the entanglement property of a system. If the channel is a pure state, positive concurrence state can afford the good performance in the teleportation process. If the channel ia a mixed state, positive concurrence state cannot assure the good performance in the teleportation. The conditions of the positive concurrence and the quantum teleportation in the Heisenberg spin ring is derived.
Multiscale modeling of mucosal immune responses
2015-01-01
Computational modeling techniques are playing increasingly important roles in advancing a systems-level mechanistic understanding of biological processes. Computer simulations guide and underpin experimental and clinical efforts. This study presents ENteric Immune Simulator (ENISI), a multiscale modeling tool for modeling the mucosal immune responses. ENISI's modeling environment can simulate in silico experiments from molecular signaling pathways to tissue level events such as tissue lesion formation. ENISI's architecture integrates multiple modeling technologies including ABM (agent-based modeling), ODE (ordinary differential equations), SDE (stochastic modeling equations), and PDE (partial differential equations). This paper focuses on the implementation and developmental challenges of ENISI. A multiscale model of mucosal immune responses during colonic inflammation, including CD4+ T cell differentiation and tissue level cell-cell interactions was developed to illustrate the capabilities, power and scope of ENISI MSM. Background Computational techniques are becoming increasingly powerful and modeling tools for biological systems are of greater needs. Biological systems are inherently multiscale, from molecules to tissues and from nano-seconds to a lifespan of several years or decades. ENISI MSM integrates multiple modeling technologies to understand immunological processes from signaling pathways within cells to lesion formation at the tissue level. This paper examines and summarizes the technical details of ENISI, from its initial version to its latest cutting-edge implementation. Implementation Object-oriented programming approach is adopted to develop a suite of tools based on ENISI. Multiple modeling technologies are integrated to visualize tissues, cells as well as proteins; furthermore, performance matching between the scales is addressed. Conclusion We used ENISI MSM for developing predictive multiscale models of the mucosal immune system during gut
Multiscale modeling of mucosal immune responses.
Mei, Yongguo; Abedi, Vida; Carbo, Adria; Zhang, Xiaoying; Lu, Pinyi; Philipson, Casandra; Hontecillas, Raquel; Hoops, Stefan; Liles, Nathan; Bassaganya-Riera, Josep
2015-01-01
Computational techniques are becoming increasingly powerful and modeling tools for biological systems are of greater needs. Biological systems are inherently multiscale, from molecules to tissues and from nano-seconds to a lifespan of several years or decades. ENISI MSM integrates multiple modeling technologies to understand immunological processes from signaling pathways within cells to lesion formation at the tissue level. This paper examines and summarizes the technical details of ENISI, from its initial version to its latest cutting-edge implementation. Object-oriented programming approach is adopted to develop a suite of tools based on ENISI. Multiple modeling technologies are integrated to visualize tissues, cells as well as proteins; furthermore, performance matching between the scales is addressed. We used ENISI MSM for developing predictive multiscale models of the mucosal immune system during gut inflammation. Our modeling predictions dissect the mechanisms by which effector CD4+ T cell responses contribute to tissue damage in the gut mucosa following immune dysregulation.Computational modeling techniques are playing increasingly important roles in advancing a systems-level mechanistic understanding of biological processes. Computer simulations guide and underpin experimental and clinical efforts. This study presents ENteric Immune Simulator (ENISI), a multiscale modeling tool for modeling the mucosal immune responses. ENISI's modeling environment can simulate in silico experiments from molecular signaling pathways to tissue level events such as tissue lesion formation. ENISI's architecture integrates multiple modeling technologies including ABM (agent-based modeling), ODE (ordinary differential equations), SDE (stochastic modeling equations), and PDE (partial differential equations). This paper focuses on the implementation and developmental challenges of ENISI. A multiscale model of mucosal immune responses during colonic inflammation, including CD4+ T
Algebraic topology and concurrency
DEFF Research Database (Denmark)
Fajstrup, Lisbeth; Raussen, Martin; Goubault, Eric
2006-01-01
We show in this article that some concepts from homotopy theory, in algebraic topology,are relevant for studying concurrent programs. We exhibit a natural semantics of semaphore programs, based on partially ordered topological spaces, which are studied up to “elastic deformation” or homotopy...... differences between ordinary and directed homotopy through examples. We also relate the topological view to a combinatorial view of concurrent programs closer to transition systems, through the notion of a cubical set. Finally we apply some of these concepts to the proof of the safeness of a two...
DEFF Research Database (Denmark)
Birkedal, Lars; Sieczkowski, Filip; Thamsborg, Jacob Junker
2012-01-01
We present a logical relation for showing the correctness of program transformations based on a new type-and-eﬀect system for a concurrent extension of an ML-like language with higher-order functions, higher-order store and dynamic memory allocation. We show how to use our model to verify a number....... To the best of our knowledge, this is the ﬁrst such result for a concurrent higher-order language with higher-order store and dynamic memory allocation....
Towards distributed multiscale computing for the VPH
Hoekstra, A.G.; Coveney, P.
2010-01-01
Multiscale modeling is fundamental to the Virtual Physiological Human (VPH) initiative. Most detailed three-dimensional multiscale models lead to prohibitive computational demands. As a possible solution we present MAPPER, a computational science infrastructure for Distributed Multiscale Computing
Coalgebra, concurrency and control
J.J.M.M. Rutten (Jan)
1999-01-01
textabstractCoalgebra is used to generalize notions and techniques from concurrency theory, in order to apply them to problems concerning the supervisory control of discrete event systems. The main ingredients of this approach are the characterization of controllability in terms of (a variant of)
Correctness of concurrent processes
E.R. Olderog (Ernst-Rüdiger)
1989-01-01
textabstractA new notion of correctness for concurrent processes is introduced and investigated. It is a relationship P sat S between process terms P built up from operators of CCS [Mi 80], CSP [Ho 85] and COSY [LTS 79] and logical formulas S specifying sets of finite communication sequences as in
Lambropoulos, Nicholas A; Reimers, Jeffrey R; Crossley, Maxwell J; Hush, Noel S; Silverbrook, Kia
2013-12-20
A general method useful in molecular electronics design is developed that integrates modelling on the nano-scale (using quantum-chemical software) and on the micro-scale (using finite-element methods). It is applied to the design of an n-bit shift register memory that could conceivably be built using accessible technologies. To achieve this, the entire complex structure of the device would be built to atomic precision using feedback-controlled lithography to provide atomic-level control of silicon devices, controlled wet-chemical synthesis of molecular insulating pillars above the silicon, and controlled wet-chemical self-assembly of modular molecular devices to these pillars that connect to external metal electrodes (leads). The shift register consists of n connected cells that read data from an input electrode, pass it sequentially between the cells under the control of two external clock electrodes, and deliver it finally to an output device. The proposed cells are trimeric oligoporphyrin units whose internal states are manipulated to provide functionality, covalently connected to other cells via dipeptide linkages. Signals from the clock electrodes are conveyed by oligoporphyrin molecular wires, and μ-oxo porphyrin insulating columns are used as the supporting pillars. The developed multiscale modelling technique is applied to determine the characteristics of this molecular device, with in particular utilization of the inverted region for molecular electron-transfer processes shown to facilitate latching and control using exceptionally low energy costs per logic operation compared to standard CMOS shift register technology.
International Nuclear Information System (INIS)
Lambropoulos, Nicholas A; Reimers, Jeffrey R; Crossley, Maxwell J; Hush, Noel S; Silverbrook, Kia
2013-01-01
A general method useful in molecular electronics design is developed that integrates modelling on the nano-scale (using quantum-chemical software) and on the micro-scale (using finite-element methods). It is applied to the design of an n-bit shift register memory that could conceivably be built using accessible technologies. To achieve this, the entire complex structure of the device would be built to atomic precision using feedback-controlled lithography to provide atomic-level control of silicon devices, controlled wet-chemical synthesis of molecular insulating pillars above the silicon, and controlled wet-chemical self-assembly of modular molecular devices to these pillars that connect to external metal electrodes (leads). The shift register consists of n connected cells that read data from an input electrode, pass it sequentially between the cells under the control of two external clock electrodes, and deliver it finally to an output device. The proposed cells are trimeric oligoporphyrin units whose internal states are manipulated to provide functionality, covalently connected to other cells via dipeptide linkages. Signals from the clock electrodes are conveyed by oligoporphyrin molecular wires, and μ-oxo porphyrin insulating columns are used as the supporting pillars. The developed multiscale modelling technique is applied to determine the characteristics of this molecular device, with in particular utilization of the inverted region for molecular electron-transfer processes shown to facilitate latching and control using exceptionally low energy costs per logic operation compared to standard CMOS shift register technology. (paper)
Lambropoulos, Nicholas A.; Reimers, Jeffrey R.; Crossley, Maxwell J.; Hush, Noel S.; Silverbrook, Kia
2013-12-01
A general method useful in molecular electronics design is developed that integrates modelling on the nano-scale (using quantum-chemical software) and on the micro-scale (using finite-element methods). It is applied to the design of an n-bit shift register memory that could conceivably be built using accessible technologies. To achieve this, the entire complex structure of the device would be built to atomic precision using feedback-controlled lithography to provide atomic-level control of silicon devices, controlled wet-chemical synthesis of molecular insulating pillars above the silicon, and controlled wet-chemical self-assembly of modular molecular devices to these pillars that connect to external metal electrodes (leads). The shift register consists of n connected cells that read data from an input electrode, pass it sequentially between the cells under the control of two external clock electrodes, and deliver it finally to an output device. The proposed cells are trimeric oligoporphyrin units whose internal states are manipulated to provide functionality, covalently connected to other cells via dipeptide linkages. Signals from the clock electrodes are conveyed by oligoporphyrin molecular wires, and μ-oxo porphyrin insulating columns are used as the supporting pillars. The developed multiscale modelling technique is applied to determine the characteristics of this molecular device, with in particular utilization of the inverted region for molecular electron-transfer processes shown to facilitate latching and control using exceptionally low energy costs per logic operation compared to standard CMOS shift register technology.
Zhang, Hongliang; Chen, Gang; Hu, Jianlin; Chen, Shu-Hua; Wiedinmyer, Christine; Kleeman, Michael; Ying, Qi
2014-03-01
The performance of the Weather Research and Forecasting (WRF)/Community Multi-scale Air Quality (CMAQ) system in the eastern United States is analyzed based on results from a seven-year modeling study with a 4-km spatial resolution. For 2-m temperature, the monthly averaged mean bias (MB) and gross error (GE) values are generally within the recommended performance criteria, although temperature is over-predicted with MB values up to 2K. Water vapor at 2-m is well-predicted but significant biases (>2 g kg(-1)) were observed in wintertime. Predictions for wind speed are satisfactory but biased towards over-prediction with 0nitrate and sulfate concentrations are also well reproduced. The other unresolved PM2.5 components (OTHER) are significantly overestimated by more than a factor of two. No conclusive explanations can be made regarding the possible cause of this universal overestimation, which warrants a follow-up study to better understand this problem. Copyright © 2013 Elsevier B.V. All rights reserved.
The Goddard multi-scale modeling system with unified physics
Directory of Open Access Journals (Sweden)
W.-K. Tao
2009-08-01
Full Text Available Recently, a multi-scale modeling system with unified physics was developed at NASA Goddard. It consists of (1 a cloud-resolving model (CRM, (2 a regional-scale model, the NASA unified Weather Research and Forecasting Model (WRF, and (3 a coupled CRM-GCM (general circulation model, known as the Goddard Multi-scale Modeling Framework or MMF. The same cloud-microphysical processes, long- and short-wave radiative transfer and land-surface processes are applied in all of the models to study explicit cloud-radiation and cloud-surface interactive processes in this multi-scale modeling system. This modeling system has been coupled with a multi-satellite simulator for comparison and validation with NASA high-resolution satellite data.
This paper reviews the development and presents some applications of the multi-scale modeling system, including results from using the multi-scale modeling system to study the interactions between clouds, precipitation, and aerosols. In addition, use of the multi-satellite simulator to identify the strengths and weaknesses of the model-simulated precipitation processes will be discussed as well as future model developments and applications.
Concurrency meets probability: theory and practice (abstract)
Katoen, Joost P.
Treating random phenomena in concurrency theory has a long tradition. Petri nets [18, 10] and process algebras [14] have been extended with probabilities. The same applies to behavioural semantics such as strong and weak (bi)simulation [1], and testing pre-orders [5]. Beautiful connections between
DEFF Research Database (Denmark)
Somchaipeng, Kerawit; Sporring, Jon; Johansen, Peter
2007-01-01
We propose MultiScale Singularity Trees (MSSTs) as a structure to represent images, and we propose an algorithm for image comparison based on comparing MSSTs. The algorithm is tested on 3 public image databases and compared to 2 state-of-theart methods. We conclude that the computational complexity...... of our algorithm only allows for the comparison of small trees, and that the results of our method are comparable with state-of-the-art using much fewer parameters for image representation....
Multiscale modelling of nanostructures
International Nuclear Information System (INIS)
Vvedensky, Dimitri D
2004-01-01
Most materials phenomena are manifestations of processes that are operative over a vast range of length and time scales. A complete understanding of the behaviour of materials thereby requires theoretical and computational tools that span the atomic-scale detail of first-principles methods and the more coarse-grained description provided by continuum equations. Recent efforts have focused on combining traditional methodologies-density functional theory, molecular dynamics, Monte Carlo methods and continuum descriptions-within a unified multiscale framework. This review covers the techniques that have been developed to model various aspects of materials behaviour with the ultimate aim of systematically coupling the atomistic to the continuum descriptions. The approaches described typically have been motivated by particular applications but can often be applied in wider contexts. The self-assembly of quantum dot ensembles will be used as a case study for the issues that arise and the methods used for all nanostructures. Although quantum dots can be obtained with all the standard growth methods and for a variety of material systems, their appearance is a quite selective process, involving the competition between equilibrium and kinetic effects, and the interplay between atomistic and long-range interactions. Most theoretical models have addressed particular aspects of the ordering kinetics of quantum dot ensembles, with far fewer attempts at a comprehensive synthesis of this inherently multiscale phenomenon. We conclude with an assessment of the current status of multiscale modelling strategies and highlight the main outstanding issues. (topical review)
Multiscale approach to the physics of radiation damage with ions
International Nuclear Information System (INIS)
Surdutovich, E.; Solov'yov, A.
2014-01-01
The multiscale approach to the assessment of bio-damage resulting upon irradiation of biological media with ions is reviewed, explained and compared to other approaches. The processes of ion propagation in the medium concurrent with ionization and excitation of molecules, transport of secondary products, dynamics of the medium, and biological damage take place on a number of different temporal, spatial and energy scales. The multiscale approach, a physical phenomenon-based analysis of the scenario that leads to radiation damage, has been designed to consider all relevant effects on a variety of scales and develop an approach to the quantitative assessment of biological damage as a result of irradiation with ions. Presently, physical and chemical effects are included in the scenario while the biological effects such as DNA repair are only mentioned. This paper explains the scenario of radiation damage with ions, overviews its major parts, and applies the multiscale approach to different experimental conditions. On the basis of this experience, the recipe for application of the multiscale approach is formulated. The recipe leads to the calculation of relative biological effectiveness. (authors)
Hybrid continuum–molecular modelling of multiscale internal gas flows
International Nuclear Information System (INIS)
Patronis, Alexander; Lockerby, Duncan A.; Borg, Matthew K.; Reese, Jason M.
2013-01-01
We develop and apply an efficient multiscale method for simulating a large class of low-speed internal rarefied gas flows. The method is an extension of the hybrid atomistic–continuum approach proposed by Borg et al. (2013) [28] for the simulation of micro/nano flows of high-aspect ratio. The major new extensions are: (1) incorporation of fluid compressibility; (2) implementation using the direct simulation Monte Carlo (DSMC) method for dilute rarefied gas flows, and (3) application to a broader range of geometries, including periodic, non-periodic, pressure-driven, gravity-driven and shear-driven internal flows. The multiscale method is applied to micro-scale gas flows through a periodic converging–diverging channel (driven by an external acceleration) and a non-periodic channel with a bend (driven by a pressure difference), as well as the flow between two eccentric cylinders (with the inner rotating relative to the outer). In all these cases there exists a wide variation of Knudsen number within the geometries, as well as substantial compressibility despite the Mach number being very low. For validation purposes, our multiscale simulation results are compared to those obtained from full-scale DSMC simulations: very close agreement is obtained in all cases for all flow variables considered. Our multiscale simulation is an order of magnitude more computationally efficient than the full-scale DSMC for the first and second test cases, and two orders of magnitude more efficient for the third case
Concurrent credit portfolio losses.
Sicking, Joachim; Guhr, Thomas; Schäfer, Rudi
2018-01-01
We consider the problem of concurrent portfolio losses in two non-overlapping credit portfolios. In order to explore the full statistical dependence structure of such portfolio losses, we estimate their empirical pairwise copulas. Instead of a Gaussian dependence, we typically find a strong asymmetry in the copulas. Concurrent large portfolio losses are much more likely than small ones. Studying the dependences of these losses as a function of portfolio size, we moreover reveal that not only large portfolios of thousands of contracts, but also medium-sized and small ones with only a few dozens of contracts exhibit notable portfolio loss correlations. Anticipated idiosyncratic effects turn out to be negligible. These are troublesome insights not only for investors in structured fixed-income products, but particularly for the stability of the financial sector. JEL codes: C32, F34, G21, G32, H81.
Temporal Concurrent Constraint Programming
DEFF Research Database (Denmark)
Valencia, Frank Dan
Concurrent constraint programming (ccp) is a formalism for concurrency in which agents interact with one another by telling (adding) and asking (reading) information in a shared medium. Temporal ccp extends ccp by allowing agents to be constrained by time conditions. This dissertation studies...... temporal ccp by developing a process calculus called ntcc. The ntcc calculus generalizes the tcc model, the latter being a temporal ccp model for deterministic and synchronouss timed reactive systems. The calculus is built upon few basic ideas but it captures several aspects of timed systems. As tcc, ntcc...... structures, robotic devises, multi-agent systems and music applications. The calculus is provided with a denotational semantics that captures the reactive computations of processes in the presence of arbitrary environments. The denotation is proven to be fully-abstract for a substantial fragment...
Concurrent radiotherapy and chemotherapy
International Nuclear Information System (INIS)
Fu, K.K.
1985-01-01
The principal objective of combining chemotherapy with radiotherapy (XRT) for the treatment of advanced head and neck cancer is to improve the therapeutic ratio through the enhancement of local control and reduction of distant metastases without excessively enhancing normal tissue effects. Improved tumour control can result from sole additivity of either therapy or direct interactions between drug and radiation leading to increased tumour cell kill. Chemotherapy may sensitize the cells to radiation, interfere with repair of sublethal or potentially lethal radiation damage, induce cell synchrony, and reduce tumour mass leading to reoxygenation and decreased fraction of resistant hypoxic cells. Radiation may improve drug accessibility to tumour cells and reduce tumour volume leading to increased cell proliferation and chemosensitivity. If the enhanced effects of combined therapy are purely additive, then the two modalities can be administered either sequentially or concurrently with the same results. However, if the enhanced effects result from the direct interaction between drug and radiation, it is necessary that the two modalities be administered concurrently and in close temporal proximity. This review summarizes the results of clinical studies in which chemotherapy was administered concurrently during the course of radiotherapy for patients with previously untreated advanced squamous cell carcinoma in the head and neck
Microphysics in Multi-scale Modeling System with Unified Physics
Tao, Wei-Kuo
2012-01-01
Recently, a multi-scale modeling system with unified physics was developed at NASA Goddard. It consists of (1) a cloud-resolving model (Goddard Cumulus Ensemble model, GCE model), (2) a regional scale model (a NASA unified weather research and forecast, WRF), (3) a coupled CRM and global model (Goddard Multi-scale Modeling Framework, MMF), and (4) a land modeling system. The same microphysical processes, long and short wave radiative transfer and land processes and the explicit cloud-radiation, and cloud-land surface interactive processes are applied in this multi-scale modeling system. This modeling system has been coupled with a multi-satellite simulator to use NASA high-resolution satellite data to identify the strengths and weaknesses of cloud and precipitation processes simulated by the model. In this talk, a review of developments and applications of the multi-scale modeling system will be presented. In particular, the microphysics development and its performance for the multi-scale modeling system will be presented.
Multivariate multiscale entropy of financial markets
Lu, Yunfan; Wang, Jun
2017-11-01
In current process of quantifying the dynamical properties of the complex phenomena in financial market system, the multivariate financial time series are widely concerned. In this work, considering the shortcomings and limitations of univariate multiscale entropy in analyzing the multivariate time series, the multivariate multiscale sample entropy (MMSE), which can evaluate the complexity in multiple data channels over different timescales, is applied to quantify the complexity of financial markets. Its effectiveness and advantages have been detected with numerical simulations with two well-known synthetic noise signals. For the first time, the complexity of four generated trivariate return series for each stock trading hour in China stock markets is quantified thanks to the interdisciplinary application of this method. We find that the complexity of trivariate return series in each hour show a significant decreasing trend with the stock trading time progressing. Further, the shuffled multivariate return series and the absolute multivariate return series are also analyzed. As another new attempt, quantifying the complexity of global stock markets (Asia, Europe and America) is carried out by analyzing the multivariate returns from them. Finally we utilize the multivariate multiscale entropy to assess the relative complexity of normalized multivariate return volatility series with different degrees.
Multiscale Signal Analysis and Modeling
Zayed, Ahmed
2013-01-01
Multiscale Signal Analysis and Modeling presents recent advances in multiscale analysis and modeling using wavelets and other systems. This book also presents applications in digital signal processing using sampling theory and techniques from various function spaces, filter design, feature extraction and classification, signal and image representation/transmission, coding, nonparametric statistical signal processing, and statistical learning theory. This book also: Discusses recently developed signal modeling techniques, such as the multiscale method for complex time series modeling, multiscale positive density estimations, Bayesian Shrinkage Strategies, and algorithms for data adaptive statistics Introduces new sampling algorithms for multidimensional signal processing Provides comprehensive coverage of wavelets with presentations on waveform design and modeling, wavelet analysis of ECG signals and wavelet filters Reviews features extraction and classification algorithms for multiscale signal and image proce...
The adaptation of the Community Multiscale Air Quality (CMAQ) modeling system to simulate O3, particulate matter, and related precursor distributions over the northern hemisphere is presented. Hemispheric simulations with CMAQ and the Weather Research and Forecasting (...
Energy Technology Data Exchange (ETDEWEB)
Moskvin, V; Tsiamas, P; Axente, M; Farr, J [St. Jude Children’s Research Hospital, Memphis, TN (United States); Stewart, R [University of Washington, Seattle, WA. (United States)
2015-06-15
Purpose: One of the more critical initiating events for reproductive cell death is the creation of a DNA double strand break (DSB). In this study, we present a computationally efficient way to determine spatial variations in the relative biological effectiveness (RBE) of proton therapy beams within the FLUKA Monte Carlo (MC) code. Methods: We used the independently tested Monte Carlo Damage Simulation (MCDS) developed by Stewart and colleagues (Radiat. Res. 176, 587–602 2011) to estimate the RBE for DSB induction of monoenergetic protons, tritium, deuterium, hellium-3, hellium-4 ions and delta-electrons. The dose-weighted (RBE) coefficients were incorporated into FLUKA to determine the equivalent {sup 6}°60Co γ-ray dose for representative proton beams incident on cells in an aerobic and anoxic environment. Results: We found that the proton beam RBE for DSB induction at the tip of the Bragg peak, including primary and secondary particles, is close to 1.2. Furthermore, the RBE increases laterally to the beam axis at the area of Bragg peak. At the distal edge, the RBE is in the range from 1.3–1.4 for cells irradiated under aerobic conditions and may be as large as 1.5–1.8 for cells irradiated under anoxic conditions. Across the plateau region, the recorded RBE for DSB induction is 1.02 for aerobic cells and 1.05 for cells irradiated under anoxic conditions. The contribution to total effective dose from secondary heavy ions decreases with depth and is higher at shallow depths (e.g., at the surface of the skin). Conclusion: Multiscale simulation of the RBE for DSB induction provides useful insights into spatial variations in proton RBE within pristine Bragg peaks. This methodology is potentially useful for the biological optimization of proton therapy for the treatment of cancer. The study highlights the need to incorporate spatial variations in proton RBE into proton therapy treatment plans.
Concurrency in product realization
Kelly, Michael J.
1994-03-01
Technology per se does not provide a competitive advantage. Timely exploitation of technology is what gives the competitive edge, and this demands a major shift in the product development process and management of the industrial enterprise. `Teaming to win' is more than a management theme; it is the disciplined engineering practice that is essential to success in today's global marketplace. Teaming supports the concurrent engineering practices required to integrate the activities of people responsible for product realization through achievement of shorter development cycles, lower costs, and defect-free products.
DEFF Research Database (Denmark)
Nygaard, Mikkel
and associated comonads, it highlights the role of linearity in concurrent computation. Two choices of comonad yield two expressive metalanguages for higher-order processes, both arising from canonical constructions in the model. Their denotational semantics are fully abstract with respect to contextual...... equivalence. One language, called HOPLA for Higher-Order Process LAnguage, derives from an exponential of linear logic. It can be viewed as an extension of the simply-typed lambda calculus with CCS-like nondeterministic sum and prefix operations, in which types express the form of computation path of which...
Kozyra, Nathan
2014-01-01
A practical approach covering everything you need to know to get up and running with Go, starting with the basics and imparting increasingly more detail as the examples and topics become more complicated. The book utilizes a casual, conversational style, rife with actual code and historical anecdotes for perspective, as well as usable and extensible example applications. This book is intended for systems developers and programmers with some experience in either Go and/or concurrent programming who wish to become fluent in building high-performance applications that scale by leveraging single-c
DEFF Research Database (Denmark)
Wisniewski, Rafal
2003-01-01
The work is intended to provide some insight about concurrency theory using ideas from geometry and algebraic topology. We define a topological space containing all traces of execution of the computer program and the information about how time flows. This is the main difference with standard...... topological reasoning in which there is no information about relation "in time" among points. The main task is to define equivalence of paths reflecting execution of a program. We use the notion of homotopy history equivalence relation. The model space considered in this work is a differentiable manifold...
Multiscale analysis of structure development in expanded starch snacks
van der Sman, R. G. M.; Broeze, J.
2014-11-01
In this paper we perform a multiscale analysis of the food structuring process of the expansion of starchy snack foods like keropok, which obtains a solid foam structure. In particular, we want to investigate the validity of the hypothesis of Kokini and coworkers, that expansion is optimal at the moisture content, where the glass transition and the boiling line intersect. In our analysis we make use of several tools, (1) time scale analysis from the field of physical transport phenomena, (2) the scale separation map (SSM) developed within a multiscale simulation framework of complex automata, (3) the supplemented state diagram (SSD), depicting phase transition and glass transition lines, and (4) a multiscale simulation model for the bubble expansion. Results of the time scale analysis are plotted in the SSD, and give insight into the dominant physical processes involved in expansion. Furthermore, the results of the time scale analysis are used to construct the SSM, which has aided us in the construction of the multiscale simulation model. Simulation results are plotted in the SSD. This clearly shows that the hypothesis of Kokini is qualitatively true, but has to be refined. Our results show that bubble expansion is optimal for moisture content, where the boiling line for gas pressure of 4 bars intersects the isoviscosity line of the critical viscosity 106 Pa.s, which runs parallel to the glass transition line.
Multiscale equation-free algorithms for molecular dynamics
Abi Mansour, Andrew
Molecular dynamics is a physics-based computational tool that has been widely employed to study the dynamics and structure of macromolecules and their assemblies at the atomic scale. However, the efficiency of molecular dynamics simulation is limited because of the broad spectrum of timescales involved. To overcome this limitation, an equation-free algorithm is presented for simulating these systems using a multiscale model cast in terms of atomistic and coarse-grained variables. Both variables are evolved in time in such a way that the cross-talk between short and long scales is preserved. In this way, the coarse-grained variables guide the evolution of the atom-resolved states, while the latter provide the Newtonian physics for the former. While the atomistic variables are evolved using short molecular dynamics runs, time advancement at the coarse-grained level is achieved with a scheme that uses information from past and future states of the system while accounting for both the stochastic and deterministic features of the coarse-grained dynamics. To complete the multiscale cycle, an atom-resolved state consistent with the updated coarse-grained variables is recovered using algorithms from mathematical optimization. This multiscale paradigm is extended to nanofluidics using concepts from hydrodynamics, and it is demonstrated for macromolecular and nanofluidic systems. A toolkit is developed for prototyping these algorithms, which are then implemented within the GROMACS simulation package and released as an open source multiscale simulator.
Sadi, Toufik; Mehonic, Adnan; Montesi, Luca; Buckwell, Mark; Kenyon, Anthony; Asenov, Asen
2018-02-01
We employ an advanced three-dimensional (3D) electro-thermal simulator to explore the physics and potential of oxide-based resistive random-access memory (RRAM) cells. The physical simulation model has been developed recently, and couples a kinetic Monte Carlo study of electron and ionic transport to the self-heating phenomenon while accounting carefully for the physics of vacancy generation and recombination, and trapping mechanisms. The simulation framework successfully captures resistance switching, including the electroforming, set and reset processes, by modeling the dynamics of conductive filaments in the 3D space. This work focuses on the promising yet less studied RRAM structures based on silicon-rich silica (SiO x ) RRAMs. We explain the intrinsic nature of resistance switching of the SiO x layer, analyze the effect of self-heating on device performance, highlight the role of the initial vacancy distributions acting as precursors for switching, and also stress the importance of using 3D physics-based models to capture accurately the switching processes. The simulation work is backed by experimental studies. The simulator is useful for improving our understanding of the little-known physics of SiO x resistive memory devices, as well as other oxide-based RRAM systems (e.g. transition metal oxide RRAMs), offering design and optimization capabilities with regard to the reliability and variability of memory cells.
Sadi, Toufik; Mehonic, Adnan; Montesi, Luca; Buckwell, Mark; Kenyon, Anthony; Asenov, Asen
2018-02-28
We employ an advanced three-dimensional (3D) electro-thermal simulator to explore the physics and potential of oxide-based resistive random-access memory (RRAM) cells. The physical simulation model has been developed recently, and couples a kinetic Monte Carlo study of electron and ionic transport to the self-heating phenomenon while accounting carefully for the physics of vacancy generation and recombination, and trapping mechanisms. The simulation framework successfully captures resistance switching, including the electroforming, set and reset processes, by modeling the dynamics of conductive filaments in the 3D space. This work focuses on the promising yet less studied RRAM structures based on silicon-rich silica (SiO x ) RRAMs. We explain the intrinsic nature of resistance switching of the SiO x layer, analyze the effect of self-heating on device performance, highlight the role of the initial vacancy distributions acting as precursors for switching, and also stress the importance of using 3D physics-based models to capture accurately the switching processes. The simulation work is backed by experimental studies. The simulator is useful for improving our understanding of the little-known physics of SiO x resistive memory devices, as well as other oxide-based RRAM systems (e.g. transition metal oxide RRAMs), offering design and optimization capabilities with regard to the reliability and variability of memory cells.
Multiscale principal component analysis
International Nuclear Information System (INIS)
Akinduko, A A; Gorban, A N
2014-01-01
Principal component analysis (PCA) is an important tool in exploring data. The conventional approach to PCA leads to a solution which favours the structures with large variances. This is sensitive to outliers and could obfuscate interesting underlying structures. One of the equivalent definitions of PCA is that it seeks the subspaces that maximize the sum of squared pairwise distances between data projections. This definition opens up more flexibility in the analysis of principal components which is useful in enhancing PCA. In this paper we introduce scales into PCA by maximizing only the sum of pairwise distances between projections for pairs of datapoints with distances within a chosen interval of values [l,u]. The resulting principal component decompositions in Multiscale PCA depend on point (l,u) on the plane and for each point we define projectors onto principal components. Cluster analysis of these projectors reveals the structures in the data at various scales. Each structure is described by the eigenvectors at the medoid point of the cluster which represent the structure. We also use the distortion of projections as a criterion for choosing an appropriate scale especially for data with outliers. This method was tested on both artificial distribution of data and real data. For data with multiscale structures, the method was able to reveal the different structures of the data and also to reduce the effect of outliers in the principal component analysis
Multiscale Modeling in the Clinic: Drug Design and Development
Energy Technology Data Exchange (ETDEWEB)
Clancy, Colleen E.; An, Gary; Cannon, William R.; Liu, Yaling; May, Elebeoba E.; Ortoleva, Peter; Popel, Aleksander S.; Sluka, James P.; Su, Jing; Vicini, Paolo; Zhou, Xiaobo; Eckmann, David M.
2016-02-17
A wide range of length and time scales are relevant to pharmacology, especially in drug development, drug design and drug delivery. Therefore, multi-scale computational modeling and simulation methods and paradigms that advance the linkage of phenomena occurring at these multiple scales have become increasingly important. Multi-scale approaches present in silico opportunities to advance laboratory research to bedside clinical applications in pharmaceuticals research. This is achievable through the capability of modeling to reveal phenomena occurring across multiple spatial and temporal scales, which are not otherwise readily accessible to experimentation. The resultant models, when validated, are capable of making testable predictions to guide drug design and delivery. In this review we describe the goals, methods, and opportunities of multi-scale modeling in drug design and development. We demonstrate the impact of multiple scales of modeling in this field. We indicate the common mathematical techniques employed for multi-scale modeling approaches used in pharmacology and present several examples illustrating the current state-of-the-art regarding drug development for: Excitable Systems (Heart); Cancer (Metastasis and Differentiation); Cancer (Angiogenesis and Drug Targeting); Metabolic Disorders; and Inflammation and Sepsis. We conclude with a focus on barriers to successful clinical translation of drug development, drug design and drug delivery multi-scale models.
Generalized multiscale finite element method. Symmetric interior penalty coupling
Efendiev, Yalchin R.; Galvis, Juan; Lazarov, Raytcho D.; Moon, M.; Sarkis, Marcus V.
2013-01-01
Motivated by applications to numerical simulations of flows in highly heterogeneous porous media, we develop multiscale finite element methods for second order elliptic equations. We discuss a multiscale model reduction technique in the framework of the discontinuous Galerkin finite element method. We propose two different finite element spaces on the coarse mesh. The first space is based on a local eigenvalue problem that uses an interior weighted L2-norm and a boundary weighted L2-norm for computing the "mass" matrix. The second choice is based on generation of a snapshot space and subsequent selection of a subspace of a reduced dimension. The approximation with these multiscale spaces is based on the discontinuous Galerkin finite element method framework. We investigate the stability and derive error estimates for the methods and further experimentally study their performance on a representative number of numerical examples. © 2013 Elsevier Inc.
Generalized multiscale finite element method. Symmetric interior penalty coupling
Efendiev, Yalchin R.
2013-12-01
Motivated by applications to numerical simulations of flows in highly heterogeneous porous media, we develop multiscale finite element methods for second order elliptic equations. We discuss a multiscale model reduction technique in the framework of the discontinuous Galerkin finite element method. We propose two different finite element spaces on the coarse mesh. The first space is based on a local eigenvalue problem that uses an interior weighted L2-norm and a boundary weighted L2-norm for computing the "mass" matrix. The second choice is based on generation of a snapshot space and subsequent selection of a subspace of a reduced dimension. The approximation with these multiscale spaces is based on the discontinuous Galerkin finite element method framework. We investigate the stability and derive error estimates for the methods and further experimentally study their performance on a representative number of numerical examples. © 2013 Elsevier Inc.
Integrated multiscale biomaterials experiment and modelling: a perspective
Buehler, Markus J.; Genin, Guy M.
2016-01-01
Advances in multiscale models and computational power have enabled a broad toolset to predict how molecules, cells, tissues and organs behave and develop. A key theme in biological systems is the emergence of macroscale behaviour from collective behaviours across a range of length and timescales, and a key element of these models is therefore hierarchical simulation. However, this predictive capacity has far outstripped our ability to validate predictions experimentally, particularly when multiple hierarchical levels are involved. The state of the art represents careful integration of multiscale experiment and modelling, and yields not only validation, but also insights into deformation and relaxation mechanisms across scales. We present here a sampling of key results that highlight both challenges and opportunities for integrated multiscale experiment and modelling in biological systems. PMID:28981126
Kenjeres, S.
2015-01-01
We present a short overview of some of our most recent work that combines the mathematical modeling, advanced computer simulations and state-of-the-art experimental techniques of physical transport phenomena in various bio-medical applications. In the first example, we tackle predictions of complex
Kenjeres, S.
2016-01-01
We present a short overview of some of our most recent work that combines the mathematical modeling, advanced computer simulations and state-of-the-art experimental techniques of physical transport phenomena in various bio-medical applications. In the first example, we tackle predictions of complex
International Nuclear Information System (INIS)
Tome, Carlos N.; Caro, J.A.; Lebensohn, R.A.; Unal, Cetin; Arsenlis, A.; Marian, J.; Pasamehmetoglu, K.
2010-01-01
Advancing the performance of Light Water Reactors, Advanced Nuclear Fuel Cycles, and Advanced Reactors, such as the Next Generation Nuclear Power Plants, requires enhancing our fundamental understanding of fuel and materials behavior under irradiation. The capability to accurately model the nuclear fuel systems to develop predictive tools is critical. Not only are fabrication and performance models needed to understand specific aspects of the nuclear fuel, fully coupled fuel simulation codes are required to achieve licensing of specific nuclear fuel designs for operation. The backbone of these codes, models, and simulations is a fundamental understanding and predictive capability for simulating the phase and microstructural behavior of the nuclear fuel system materials and matrices. In this paper we review the current status of the advanced modeling and simulation of nuclear reactor cladding, with emphasis on what is available and what is to be developed in each scale of the project, how we propose to pass information from one scale to the next, and what experimental information is required for benchmarking and advancing the modeling at each scale level.
Multiscale Processes in Magnetic Reconnection
Surjalal Sharma, A.; Jain, Neeraj
The characteristic scales of the plasma processes in magnetic reconnection range from the elec-tron skin-depth to the magnetohydrodynamic (MHD) scale, and cross-scale coupling among them play a key role. Modeling these processes requires different physical models, viz. kinetic, electron-magnetohydrodynamics (EMHD), Hall-MHD, and MHD. The shortest scale processes are at the electron scale and these are modeled using an EMHD code, which provides many features of the multiscale behavior. In simulations using initial conditions consisting of pertur-bations with many scale sizes the reconnection takes place at many sites and the plasma flows from these interact with each other. This leads to thin current sheets with length less than 10 electron skin depths. The plasma flows also generate current sheets with multiple peaks, as observed by Cluster. The quadrupole structure of the magnetic field during reconnection starts on the electron scale and the interaction of inflow to the secondary sites and outflow from the dominant site generates a nested structure. In the outflow regions, the interaction of the electron outflows generated at the neighboring sites lead to the development of electron vortices. A signature of the nested structure of the Hall field is seen in Cluster observations, and more details of these features are expected from MMS.
Multiscale study of metal nanoparticles
Lee, Byeongchan
Extremely small structures with reduced dimensionality have emerged as a scientific motif for their interesting properties. In particular, metal nanoparticles have been identified as a fundamental material in many catalytic activities; as a consequence, a better understanding of structure-function relationship of nanoparticles has become crucial. The functional analysis of nanoparticles, reactivity for example, requires an accurate method at the electronic structure level, whereas the structural analysis to find energetically stable local minima is beyond the scope of quantum mechanical methods as the computational cost becomes prohibitingly high. The challenge is that the inherent length scale and accuracy associated with any single method hardly covers the broad scale range spanned by both structural and functional analyses. In order to address this, and effectively explore the energetics and reactivity of metal nanoparticles, a hierarchical multiscale modeling is developed, where methodologies of different length scales, i.e. first principles density functional theory, atomistic calculations, and continuum modeling, are utilized in a sequential fashion. This work has focused on identifying the essential information that bridges two different methods so that a successive use of different methods is seamless. The bond characteristics of low coordination systems have been obtained with first principles calculations, and incorporated into the atomistic simulation. This also rectifies the deficiency of conventional interatomic potentials fitted to bulk properties, and improves the accuracy of atomistic calculations for nanoparticles. For the systematic shape selection of nanoparticles, we have improved the Wulff-type construction using a semi-continuum approach, in which atomistic surface energetics and crystallinity of materials are added on to the continuum framework. The developed multiscale modeling scheme is applied to the rational design of platinum
On multiscale moving contact line theory.
Li, Shaofan; Fan, Houfu
2015-07-08
In this paper, a multiscale moving contact line (MMCL) theory is presented and employed to simulate liquid droplet spreading and capillary motion. The proposed MMCL theory combines a coarse-grained adhesive contact model with a fluid interface membrane theory, so that it can couple molecular scale adhesive interaction and surface tension with hydrodynamics of microscale flow. By doing so, the intermolecular force, the van der Waals or double layer force, separates and levitates the liquid droplet from the supporting solid substrate, which avoids the shear stress singularity caused by the no-slip condition in conventional hydrodynamics theory of moving contact line. Thus, the MMCL allows the difference of the surface energies and surface stresses to drive droplet spreading naturally. To validate the proposed MMCL theory, we have employed it to simulate droplet spreading over various elastic substrates. The numerical simulation results obtained by using MMCL are in good agreement with the molecular dynamics results reported in the literature.
Adaptive resolution simulation of salt solutions
International Nuclear Information System (INIS)
Bevc, Staš; Praprotnik, Matej; Junghans, Christoph; Kremer, Kurt
2013-01-01
We present an adaptive resolution simulation of aqueous salt (NaCl) solutions at ambient conditions using the adaptive resolution scheme. Our multiscale approach concurrently couples the atomistic and coarse-grained models of the aqueous NaCl, where water molecules and ions change their resolution while moving from one resolution domain to the other. We employ standard extended simple point charge (SPC/E) and simple point charge (SPC) water models in combination with AMBER and GROMOS force fields for ion interactions in the atomistic domain. Electrostatics in our model are described by the generalized reaction field method. The effective interactions for water–water and water–ion interactions in the coarse-grained model are derived using structure-based coarse-graining approach while the Coulomb interactions between ions are appropriately screened. To ensure an even distribution of water molecules and ions across the simulation box we employ thermodynamic forces. We demonstrate that the equilibrium structural, e.g. radial distribution functions and density distributions of all the species, and dynamical properties are correctly reproduced by our adaptive resolution method. Our multiscale approach, which is general and can be used for any classical non-polarizable force-field and/or types of ions, will significantly speed up biomolecular simulation involving aqueous salt. (paper)
Rethinking serializable multiversion concurrency control
Faleiro, Jose M.; Abadi, Daniel J.
2014-01-01
Multi-versioned database systems have the potential to significantly increase the amount of concurrency in transaction processing because they can avoid read-write conflicts. Unfortunately, the increase in concurrency usually comes at the cost of transaction serializability. If a database user requests full serializability, modern multi-versioned systems significantly constrain read-write concurrency among conflicting transactions and employ expensive synchronization patterns in their design....
Quantify entanglement by concurrence hierarchy
Fan, Heng; Matsumoto, Keiji; Imai, Hiroshi
2002-01-01
We define the concurrence hierarchy as d-1 independent invariants under local unitary transformations in d-level quantum system. The first one is the original concurrence defined by Wootters et al in 2-level quantum system and generalized to d-level pure quantum states case. We propose to use this concurrence hierarchy as measurement of entanglement. This measurement does not increase under local quantum operations and classical communication.
Concurrent Models for Object Execution
Diertens, Bob
2012-01-01
In previous work we developed a framework of computational models for the concurrent execution of functions on different levels of abstraction. It shows that the traditional sequential execution of function is just a possible implementation of an abstract computational model that allows for the concurrent execution of functions. We use this framework as base for the development of abstract computational models that allow for the concurrent execution of objects.
Multiscale sampling model for motion integration.
Sherbakov, Lena; Yazdanbakhsh, Arash
2013-09-30
Biologically plausible strategies for visual scene integration across spatial and temporal domains continues to be a challenging topic. The fundamental question we address is whether classical problems in motion integration, such as the aperture problem, can be solved in a model that samples the visual scene at multiple spatial and temporal scales in parallel. We hypothesize that fast interareal connections that allow feedback of information between cortical layers are the key processes that disambiguate motion direction. We developed a neural model showing how the aperture problem can be solved using different spatial sampling scales between LGN, V1 layer 4, V1 layer 6, and area MT. Our results suggest that multiscale sampling, rather than feedback explicitly, is the key process that gives rise to end-stopped cells in V1 and enables area MT to solve the aperture problem without the need for calculating intersecting constraints or crafting intricate patterns of spatiotemporal receptive fields. Furthermore, the model explains why end-stopped cells no longer emerge in the absence of V1 layer 6 activity (Bolz & Gilbert, 1986), why V1 layer 4 cells are significantly more end-stopped than V1 layer 6 cells (Pack, Livingstone, Duffy, & Born, 2003), and how it is possible to have a solution to the aperture problem in area MT with no solution in V1 in the presence of driving feedback. In summary, while much research in the field focuses on how a laminar architecture can give rise to complicated spatiotemporal receptive fields to solve problems in the motion domain, we show that one can reframe motion integration as an emergent property of multiscale sampling achieved concurrently within lamina and across multiple visual areas.
Economic explanations for concurrent sourcing
DEFF Research Database (Denmark)
Mols, Niels Peter
2010-01-01
Concurrent sourcing is a phenomenon where firms simultaneously make and buy the same good, i.e. they simultaneously use the governance modes of market and hierarchy. Though concurrent sourcing seems to be widespread, few studies of sourcing have focused on this phenomenon. This paper reviews...... different economic explanations for why firms use concurrent sourcing. The distinctive features of the explanations are compared, and it is discussed how they may serve as a springboard for research on concurrent sourcing. Managerial implications are also offered....
Concurrency Control for Transactional Drago
Patiño-Martinez, Marta; Jiménez-Peris, Ricardo; Kienzle, Jörg; Arévalo, Sergio
2002-01-01
The granularity of concurrency control has a big impact on the performance of transactional systems. Concurrency control granu- larity and data granularity (data size) are usually the same. The e ect of this coupling is that if a coarse granularity is used, the overhead of data access (number of disk accesses) is reduced, but also the degree of concurrency. On the other hand, if a ne granularity is chosen to achieve a higher degree of concurrency (there are less con icts), the cost of data ac...
Czech Academy of Sciences Publication Activity Database
Janeček, Ivan; Naar, P.; Stachoň, M.; Gadéa, F. X.; Kalus, R.
2017-01-01
Roč. 19, č. 4 (2017), s. 2778-2790 ISSN 1463-9076 R&D Projects: GA MŠk ED2.1.00/03.0082; GA MŠk(CZ) LO1406 Institutional support: RVO:68145535 Keywords : atom ic clusters * molecular physics * computer simulations Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Atom ic, molecular and chemical physics (physics of atom s and molecules including collision, interaction with radiation, magnetic resonances, Mössbauer effect) Impact factor: 4.123, year: 2016 http://pubs.rsc.org/en/content/articlelanding/2017/cp/c6cp07479k#!divAbstract
Czech Academy of Sciences Publication Activity Database
Janeček, Ivan; Naar, P.; Stachoň, M.; Gadéa, F. X.; Kalus, R.
2017-01-01
Roč. 19, č. 4 (2017), s. 2778-2790 ISSN 1463-9076 R&D Projects: GA MŠk ED2.1.00/03.0082; GA MŠk(CZ) LO1406 Institutional support: RVO:68145535 Keywords : atomic clusters * molecular physics * computer simulations Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Atomic, molecular and chemical physics ( physics of atoms and molecules including collision, interaction with radiation, magnetic resonances, Mössbauer effect) Impact factor: 4.123, year: 2016 http://pubs.rsc.org/en/content/articlelanding/2017/cp/c6cp07479k#!divAbstract
Neural network based multiscale image restoration approach
de Castro, Ana Paula A.; da Silva, José D. S.
2007-02-01
This paper describes a neural network based multiscale image restoration approach. Multilayer perceptrons are trained with artificial images of degraded gray level circles, in an attempt to make the neural network learn inherent space relations of the degraded pixels. The present approach simulates the degradation by a low pass Gaussian filter blurring operation and the addition of noise to the pixels at pre-established rates. The training process considers the degraded image as input and the non-degraded image as output for the supervised learning process. The neural network thus performs an inverse operation by recovering a quasi non-degraded image in terms of least squared. The main difference of the approach to existing ones relies on the fact that the space relations are taken from different scales, thus providing relational space data to the neural network. The approach is an attempt to come up with a simple method that leads to an optimum solution to the problem. Considering different window sizes around a pixel simulates the multiscale operation. In the generalization phase the neural network is exposed to indoor, outdoor, and satellite degraded images following the same steps use for the artificial circle image.
Development and application of a multiscale model for the magnetic fusion edge plasma region
International Nuclear Information System (INIS)
Hasenbeck, Felix Martin Michael
2016-01-01
Plasma edge particle and energy transport perpendicular to the magnetic field plays a decisive role for the performance and lifetime of a magnetic fusion reactor. For the particles, classical and neoclassical theories underestimate the associated radial transport by at least an order of magnitude. Drift fluid models, including mesoscale processes on scales down to tenths of millimeters and microseconds, account for the experimentally found level of radial transport; however, numerical simulations for typical reactor scales (of the order of seconds and centimeters) are computationally very expensive. Large scale code simulations are less costly but usually lack an adequate model for the radial transport. The multiscale model presented in this work aims at improving the description of radial particle transport in large scale codes by including the effects of averaged local drift fluid dynamics on the macroscale profiles. The multiscale balances are derived from a generic multiscale model for a fluid, using the Braginskii closure for a collisional, magnetized plasma, and the assumptions of the B2 code model (macroscale balances) and the model of the local version of the drift fluid code ATTEMPT (mesoscale balances). A combined concurrent-sequential coupling procedure is developed for the implementation of the multiscale model within a coupled code system. An algorithm for the determination of statistically stationary states and adequate averaging intervals for the mesoscale data is outlined and tested, proving that it works consistently and efficiently. The general relation between mesoscale and macroscale dynamics is investigated exemplarily by means of a passive scalar system. While mesoscale processes are convective in this system, earlier studies for small Kubo numbers K<<1 have shown that the macroscale behavior is diffusive. In this work it is demonstrated by numerical experiments that also in the regime of large Kubo numbers K<<1 the macroscale transport
Development and application of a multiscale model for the magnetic fusion edge plasma region
Energy Technology Data Exchange (ETDEWEB)
Hasenbeck, Felix Martin Michael
2016-07-01
Plasma edge particle and energy transport perpendicular to the magnetic field plays a decisive role for the performance and lifetime of a magnetic fusion reactor. For the particles, classical and neoclassical theories underestimate the associated radial transport by at least an order of magnitude. Drift fluid models, including mesoscale processes on scales down to tenths of millimeters and microseconds, account for the experimentally found level of radial transport; however, numerical simulations for typical reactor scales (of the order of seconds and centimeters) are computationally very expensive. Large scale code simulations are less costly but usually lack an adequate model for the radial transport. The multiscale model presented in this work aims at improving the description of radial particle transport in large scale codes by including the effects of averaged local drift fluid dynamics on the macroscale profiles. The multiscale balances are derived from a generic multiscale model for a fluid, using the Braginskii closure for a collisional, magnetized plasma, and the assumptions of the B2 code model (macroscale balances) and the model of the local version of the drift fluid code ATTEMPT (mesoscale balances). A combined concurrent-sequential coupling procedure is developed for the implementation of the multiscale model within a coupled code system. An algorithm for the determination of statistically stationary states and adequate averaging intervals for the mesoscale data is outlined and tested, proving that it works consistently and efficiently. The general relation between mesoscale and macroscale dynamics is investigated exemplarily by means of a passive scalar system. While mesoscale processes are convective in this system, earlier studies for small Kubo numbers K<<1 have shown that the macroscale behavior is diffusive. In this work it is demonstrated by numerical experiments that also in the regime of large Kubo numbers K<<1 the macroscale transport
Li, Zhongwu; Huang, Jinquan; Zeng, Guangming; Nie, Xiaodong; Ma, Wenming; Yu, Wei; Guo, Wang; Zhang, Jiachao
2013-01-01
The effects of water erosion (including long-term historical erosion and single erosion event) on soil properties and productivity in different farming systems were investigated. A typical sloping cropland with homogeneous soil properties was designed in 2009 and then protected from other external disturbances except natural water erosion. In 2012, this cropland was divided in three equally sized blocks. Three treatments were performed on these blocks with different simulated rainfall intensities and farming methods: (1) high rainfall intensity (1.5 - 1.7 mm min−1), no-tillage operation; (2) low rainfall intensity (0.5 - 0.7 mm min−1), no-tillage operation; and (3) low rainfall intensity, tillage operation. All of the blocks were divided in five equally sized subplots along the slope to characterize the three-year effects of historical erosion quantitatively. Redundancy analysis showed that the effects of long-term historical erosion significantly caused most of the variations in soil productivity in no-tillage and low rainfall erosion intensity systems. The intensities of the simulated rainfall did not exhibit significant effects on soil productivity in no-tillage systems. By contrast, different farming operations induced a statistical difference in soil productivity at the same single erosion intensity. Soil organic carbon (SOC) was the major limiting variable that influenced soil productivity. Most explanations of long-term historical erosion for the variation in soil productivity arose from its sharing with SOC. SOC, total nitrogen, and total phosphorus were found as the regressors of soil productivity because of tillage operation. In general, this study provided strong evidence that single erosion event could also impose significant constraints on soil productivity by integrating with tillage operation, although single erosion is not the dominant effect relative to the long-term historical erosion. Our study demonstrated that an effective management of
Hybrid stochastic simplifications for multiscale gene networks
Directory of Open Access Journals (Sweden)
Debussche Arnaud
2009-09-01
Full Text Available Abstract Background Stochastic simulation of gene networks by Markov processes has important applications in molecular biology. The complexity of exact simulation algorithms scales with the number of discrete jumps to be performed. Approximate schemes reduce the computational time by reducing the number of simulated discrete events. Also, answering important questions about the relation between network topology and intrinsic noise generation and propagation should be based on general mathematical results. These general results are difficult to obtain for exact models. Results We propose a unified framework for hybrid simplifications of Markov models of multiscale stochastic gene networks dynamics. We discuss several possible hybrid simplifications, and provide algorithms to obtain them from pure jump processes. In hybrid simplifications, some components are discrete and evolve by jumps, while other components are continuous. Hybrid simplifications are obtained by partial Kramers-Moyal expansion 123 which is equivalent to the application of the central limit theorem to a sub-model. By averaging and variable aggregation we drastically reduce simulation time and eliminate non-critical reactions. Hybrid and averaged simplifications can be used for more effective simulation algorithms and for obtaining general design principles relating noise to topology and time scales. The simplified models reproduce with good accuracy the stochastic properties of the gene networks, including waiting times in intermittence phenomena, fluctuation amplitudes and stationary distributions. The methods are illustrated on several gene network examples. Conclusion Hybrid simplifications can be used for onion-like (multi-layered approaches to multi-scale biochemical systems, in which various descriptions are used at various scales. Sets of discrete and continuous variables are treated with different methods and are coupled together in a physically justified approach.
Generalized multiscale finite element methods (GMsFEM)
Efendiev, Yalchin R.; Galvis, Juan; Hou, Thomasyizhao
2013-01-01
In this paper, we propose a general approach called Generalized Multiscale Finite Element Method (GMsFEM) for performing multiscale simulations for problems without scale separation over a complex input space. As in multiscale finite element methods (MsFEMs), the main idea of the proposed approach is to construct a small dimensional local solution space that can be used to generate an efficient and accurate approximation to the multiscale solution with a potentially high dimensional input parameter space. In the proposed approach, we present a general procedure to construct the offline space that is used for a systematic enrichment of the coarse solution space in the online stage. The enrichment in the online stage is performed based on a spectral decomposition of the offline space. In the online stage, for any input parameter, a multiscale space is constructed to solve the global problem on a coarse grid. The online space is constructed via a spectral decomposition of the offline space and by choosing the eigenvectors corresponding to the largest eigenvalues. The computational saving is due to the fact that the construction of the online multiscale space for any input parameter is fast and this space can be re-used for solving the forward problem with any forcing and boundary condition. Compared with the other approaches where global snapshots are used, the local approach that we present in this paper allows us to eliminate unnecessary degrees of freedom on a coarse-grid level. We present various examples in the paper and some numerical results to demonstrate the effectiveness of our method. © 2013 Elsevier Inc.
Generalized multiscale finite element methods (GMsFEM)
Efendiev, Yalchin R.
2013-10-01
In this paper, we propose a general approach called Generalized Multiscale Finite Element Method (GMsFEM) for performing multiscale simulations for problems without scale separation over a complex input space. As in multiscale finite element methods (MsFEMs), the main idea of the proposed approach is to construct a small dimensional local solution space that can be used to generate an efficient and accurate approximation to the multiscale solution with a potentially high dimensional input parameter space. In the proposed approach, we present a general procedure to construct the offline space that is used for a systematic enrichment of the coarse solution space in the online stage. The enrichment in the online stage is performed based on a spectral decomposition of the offline space. In the online stage, for any input parameter, a multiscale space is constructed to solve the global problem on a coarse grid. The online space is constructed via a spectral decomposition of the offline space and by choosing the eigenvectors corresponding to the largest eigenvalues. The computational saving is due to the fact that the construction of the online multiscale space for any input parameter is fast and this space can be re-used for solving the forward problem with any forcing and boundary condition. Compared with the other approaches where global snapshots are used, the local approach that we present in this paper allows us to eliminate unnecessary degrees of freedom on a coarse-grid level. We present various examples in the paper and some numerical results to demonstrate the effectiveness of our method. © 2013 Elsevier Inc.
Multiscale Finite Element Methods for Flows on Rough Surfaces
Efendiev, Yalchin
2013-01-01
In this paper, we present the Multiscale Finite Element Method (MsFEM) for problems on rough heterogeneous surfaces. We consider the diffusion equation on oscillatory surfaces. Our objective is to represent small-scale features of the solution via multiscale basis functions described on a coarse grid. This problem arises in many applications where processes occur on surfaces or thin layers. We present a unified multiscale finite element framework that entails the use of transformations that map the reference surface to the deformed surface. The main ingredients of MsFEM are (1) the construction of multiscale basis functions and (2) a global coupling of these basis functions. For the construction of multiscale basis functions, our approach uses the transformation of the reference surface to a deformed surface. On the deformed surface, multiscale basis functions are defined where reduced (1D) problems are solved along the edges of coarse-grid blocks to calculate nodalmultiscale basis functions. Furthermore, these basis functions are transformed back to the reference configuration. We discuss the use of appropriate transformation operators that improve the accuracy of the method. The method has an optimal convergence if the transformed surface is smooth and the image of the coarse partition in the reference configuration forms a quasiuniform partition. In this paper, we consider such transformations based on harmonic coordinates (following H. Owhadi and L. Zhang [Comm. Pure and Applied Math., LX(2007), pp. 675-723]) and discuss gridding issues in the reference configuration. Numerical results are presented where we compare the MsFEM when two types of deformations are used formultiscale basis construction. The first deformation employs local information and the second deformation employs a global information. Our numerical results showthat one can improve the accuracy of the simulations when a global information is used. © 2013 Global-Science Press.
The Feasibility of Multiscale Modeling of Tunnel Fires Using FDS 6
DEFF Research Database (Denmark)
Vermesi, Izabella; Colella, Francesco; Rein, Guillermo
2014-01-01
The HVAC component of FDS 6 was used to divide a 1.2km tunnel into a 3D near fire area and a 1D area further away from the fire in order to investigate the feasibility of multiscale modeling of tunnel fires with this new feature in FDS. The two sub-models were coupled directly. The results were...... compared with reference works on multiscale modeling and the outcome is considered positive, with a deviation of less than 5% in magnitude of relevant parameters, yet with a significant reduction of the simulation runtime. As such, the multiscale method is deemed feasible for simulating tunnel fires in FDS......6. However, the simplifications that are made in this work require further investigation in order to take full advantage of the potential of this computational method. INTRODUCTION Multiscale modeling for tunnel flows and fires has previously been studied using RANS general purpose CFD software...
Liu, Da-Jiang; Evans, James W.
2013-12-01
A realistic molecular-level description of catalytic reactions on single-crystal metal surfaces can be provided by stochastic multisite lattice-gas (msLG) models. This approach has general applicability, although in this report, we will focus on the example of CO-oxidation on the unreconstructed fcc metal (1 0 0) or M(1 0 0) surfaces of common catalyst metals M = Pd, Rh, Pt and Ir (i.e., avoiding regimes where Pt and Ir reconstruct). These models can capture the thermodynamics and kinetics of adsorbed layers for the individual reactants species, such as CO/M(1 0 0) and O/M(1 0 0), as well as the interaction and reaction between different reactant species in mixed adlayers, such as (CO + O)/M(1 0 0). The msLG models allow population of any of hollow, bridge, and top sites. This enables a more flexible and realistic description of adsorption and adlayer ordering, as well as of reaction configurations and configuration-dependent barriers. Adspecies adsorption and interaction energies, as well as barriers for various processes, constitute key model input. The choice of these energies is guided by experimental observations, as well as by extensive Density Functional Theory analysis. Model behavior is assessed via Kinetic Monte Carlo (KMC) simulation. We also address the simulation challenges and theoretical ramifications associated with very rapid diffusion and local equilibration of reactant adspecies such as CO. These msLG models are applied to describe adsorption, ordering, and temperature programmed desorption (TPD) for individual CO/M(1 0 0) and O/M(1 0 0) reactant adlayers. In addition, they are also applied to predict mixed (CO + O)/M(1 0 0) adlayer structure on the nanoscale, the complete bifurcation diagram for reactive steady-states under continuous flow conditions, temperature programmed reaction (TPR) spectra, and titration reactions for the CO-oxidation reaction. Extensive and reasonably successful comparison of model predictions is made with experimental
Plant management in concurrent engineering
International Nuclear Information System (INIS)
Haubensack, D.; Malvache, P.; Valleix, P.
1997-01-01
The ImagIn project consist in a method and a set of computer tools apt to bring perceptible and assessable improvements in the operational safety of a nuclear plant. Its aim is to design an information system that would maintain a highly detailed computerised representation of a nuclear plant, in its initial state and throughout its in-service life. It is not a tool to drive or help driving the nuclear plant, but a tool that manages concurrent operations that modify the plant configuration in a very general way (maintenance for example). The configuration of the plant, as well as rules and constraints about it, are described in a object-oriented, knowledge database, which is built using a generic ImagIn meta-model based on the semantical network theory. An inference engine works on this database and is connected to reality through interfaces to operators and captors on the installation; it verifies constantly in real-time the consistency of the database according to its inner rules, and reports eventual problems to concerned operators. A special effort is made on interfaces to provide natural and intuitive tools (using virtual reality, natural language, voice recognition and synthesis). A laboratory application on a fictive but realistic installation already exist and is used to simulate various test and scenari. A real application is being constructed on SILOE, an experimental reactor of the CEA. (authors)
Measuring coherence with entanglement concurrence
Qi, Xianfei; Gao, Ting; Yan, Fengli
2017-07-01
Quantum coherence is a fundamental manifestation of the quantum superposition principle. Recently, Baumgratz et al (2014 Phys. Rev. Lett. 113 140401) presented a rigorous framework to quantify coherence from the view of theory of physical resource. Here we propose a new valid quantum coherence measure which is a convex roof measure, for a quantum system of arbitrary dimension, essentially using the generalized Gell-Mann matrices. Rigorous proof shows that the proposed coherence measure, coherence concurrence, fulfills all the requirements dictated by the resource theory of quantum coherence measures. Moreover, strong links between the resource frameworks of coherence concurrence and entanglement concurrence is derived, which shows that any degree of coherence with respect to some reference basis can be converted to entanglement via incoherent operations. Our work provides a clear quantitative and operational connection between coherence and entanglement based on two kinds of concurrence. This new coherence measure, coherence concurrence, may also be beneficial to the study of quantum coherence.
ProtoMD: A prototyping toolkit for multiscale molecular dynamics
Somogyi, Endre; Mansour, Andrew Abi; Ortoleva, Peter J.
2016-05-01
ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales, such as the atomic to the mesoscopic scale, via coevolving microscopic and coarse-grained (CG) variables. ProtoMD can be also be used to calibrate parameters needed in traditional CG-MD methods. The toolkit integrates 'GROMACS wrapper' to initiate MD simulations, and 'MDAnalysis' to analyze and manipulate trajectory files. It facilitates experimentation with a spectrum of coarse-grained variables, prototyping rare events (such as chemical reactions), or simulating nanocharacterization experiments such as terahertz spectroscopy, AFM, nanopore, and time-of-flight mass spectroscopy. ProtoMD is written in python and is freely available under the GNU General Public License from github.com/CTCNano/proto_md.
International Nuclear Information System (INIS)
Toti, A.; Vierendeels, J.; Belloni, F.
2017-01-01
Highlights: • A system thermal-hydraulic/CFD coupling methodology is proposed for high-fidelity transient flow analyses. • The method is based on domain decomposition and implicit numerical scheme. • A novel interface Quasi-Newton algorithm is implemented to improve stability and convergence rate. • Preliminary validation analyses on the TALL-3D experiment. - Abstract: The paper describes the development and validation of a coupling methodology between the best-estimate system thermal-hydraulic code RELAP5-3D and the CFD code FLUENT, conceived for high fidelity plant-scale safety analyses of pool-type reactors. The computational tool is developed to assess the impact of three-dimensional phenomena occurring in accidental transients such as loss of flow (LOF) in the research reactor MYRRHA, currently in the design phase at the Belgian Nuclear Research Centre, SCK• CEN. A partitioned, implicit domain decomposition coupling algorithm is implemented, in which the coupled domains exchange thermal-hydraulics variables at coupling boundary interfaces. Numerical stability and interface convergence rates are improved by a novel interface Quasi-Newton algorithm, which is compared in this paper with previously tested numerical schemes. The developed computational method has been assessed for validation purposes against the experiment performed at the test facility TALL-3D, operated by the Royal Institute of Technology (KTH) in Sweden. This paper details the results of the simulation of a loss of forced convection test, showing the capability of the developed methodology to predict transients influenced by local three-dimensional phenomena.
Directory of Open Access Journals (Sweden)
Peter Michael Kekenes-Huskey
Full Text Available Troponin C (TnC is implicated in the initiation of myocyte contraction via binding of cytosolic Ca²⁺ and subsequent recognition of the Troponin I switch peptide. Mutations of the cardiac TnC N-terminal regulatory domain have been shown to alter both calcium binding and myofilament force generation. We have performed molecular dynamics simulations of engineered TnC variants that increase or decrease Ca²⁺ sensitivity, in order to understand the structural basis of their impact on TnC function. We will use the distinction for mutants that are associated with increased Ca²⁺ affinity and for those mutants with reduced affinity. Our studies demonstrate that for GOF mutants V44Q and L48Q, the structure of the physiologically-active site II Ca²⁺ binding site in the Ca²⁺-free (apo state closely resembled the Ca²⁺-bound (holo state. In contrast, site II is very labile for LOF mutants E40A and V79Q in the apo form and bears little resemblance with the holo conformation. We hypothesize that these phenomena contribute to the increased association rate, k(on, for the GOF mutants relative to LOF. Furthermore, we observe significant positive and negative positional correlations between helices in the GOF holo mutants that are not found in the LOF mutants. We anticipate these correlations may contribute either directly to Ca²⁺ affinity or indirectly through TnI association. Our observations based on the structure and dynamics of mutant TnC provide rationale for binding trends observed in GOF and LOF mutants and will guide the development of inotropic drugs that target TnC.
A Concurrent Distributed System for Aircraft Tactical Decision Generation
McManus, John W.
1990-01-01
A research program investigating the use of artificial intelligence (AI) techniques to aid in the development of a Tactical Decision Generator (TDG) for Within Visual Range (WVR) air combat engagements is discussed. The application of AI programming and problem solving methods in the development and implementation of a concurrent version of the Computerized Logic For Air-to-Air Warfare Simulations (CLAWS) program, a second generation TDG, is presented. Concurrent computing environments and programming approaches are discussed and the design and performance of a prototype concurrent TDG system are presented.
The Magnetospheric Multiscale Magnetometers
Russell, C. T.; Anderson, B. J.; Baumjohann, W.; Bromund, K. R.; Dearborn, D.; Fischer, D.; Le, G.; Leinweber, H. K.; Leneman, D.; Magnes, W.;
2014-01-01
The success of the Magnetospheric Multiscale mission depends on the accurate measurement of the magnetic field on all four spacecraft. To ensure this success, two independently designed and built fluxgate magnetometers were developed, avoiding single-point failures. The magnetometers were dubbed the digital fluxgate (DFG), which uses an ASIC implementation and was supplied by the Space Research Institute of the Austrian Academy of Sciences and the analogue magnetometer (AFG) with a more traditional circuit board design supplied by the University of California, Los Angeles. A stringent magnetic cleanliness program was executed under the supervision of the Johns Hopkins University,s Applied Physics Laboratory. To achieve mission objectives, the calibration determined on the ground will be refined in space to ensure all eight magnetometers are precisely inter-calibrated. Near real-time data plays a key role in the transmission of high-resolution observations stored onboard so rapid processing of the low-resolution data is required. This article describes these instruments, the magnetic cleanliness program, and the instrument pre-launch calibrations, the planned in-flight calibration program, and the information flow that provides the data on the rapid time scale needed for mission success.
Institute for Multiscale Modeling of Biological Interactions
Energy Technology Data Exchange (ETDEWEB)
Paulaitis, Michael E; Garcia-Moreno, Bertrand; Lenhoff, Abraham
2009-12-26
The Institute for Multiscale Modeling of Biological Interactions (IMMBI) has two primary goals: Foster interdisciplinary collaborations among faculty and their research laboratories that will lead to novel applications of multiscale simulation and modeling methods in the biological sciences and engineering; and Building on the unique biophysical/biology-based engineering foundations of the participating faculty, train scientists and engineers to apply computational methods that collectively span multiple time and length scales of biological organization. The success of IMMBI will be defined by the following: Size and quality of the applicant pool for pre-doctoral and post-doctoral fellows; Academic performance; Quality of the pre-doctoral and post-doctoral research; Impact of the research broadly and to the DOE (ASCR program) mission; Distinction of the next career step for pre-doctoral and post-doctoral fellows; and Faculty collaborations that result from IMMBI activities. Specific details about accomplishments during the three years of DOE support for IMMBI have been documented in Annual Progress Reports (April 2005, June 2006, and March 2007) and a Report for a National Academy of Sciences Review (October 2005) that were submitted to DOE on the dates indicated. An overview of these accomplishments is provided.
El-Amin, Mohamed F.; Kou, Jisheng; Sun, Shuyu
2017-01-01
This paper is devoted to study the problem of nonisothermal two-phase flow with nanoparticles transport in heterogenous porous media, numerically. For this purpose, we introduce a multiscale adapted time-splitting technique to simulate the problem
Concurrent LISP and its interpreter
Energy Technology Data Exchange (ETDEWEB)
Tabata, K; Sugimoto, S; Ohno, Y
1981-01-01
In the research field of artificial intelligence many languages have been developed based on LISP, such as Planner, Conniver and so on. They have been developed to give users many useful facilities, especially for describing flexible control structures. Backtracking and coroutine facilities are typical ones introduced into these languages. Compared with backtracking and coroutine facilities, multi-process description facilities are considered to be a better alternative for writing well-structured programs. This paper describes concurrent LISP, a new concurrent programming language based on LISP. Concurrent LISP is designed to provide simple and flexible facilities for multi-process description without changing the original language features of LISP. This paper also describes the concurrent LISP interpreter which has been implemented on a FACOM M-200 at the Data Processing Center of Kyoto University. 19 references.
Reference Capabilities for Concurrency Control
Castegren, Elias; Wrigstad, Tobias
2016-01-01
The proliferation of shared mutable state in object-oriented programming complicates software development as two seemingly unrelated operations may interact via an alias and produce unexpected results. In concurrent programming this manifests itself as data-races. Concurrent object-oriented programming further suffers from the fact that code that warrants synchronisation cannot easily be distinguished from code that does not. The burden is placed solely on the programmer to reason ab...
Multiscale Modeling of Composites: Toward Virtual Testing … and Beyond
LLorca, J.; González, C.; Molina-Aldareguía, J. M.; Lópes, C. S.
2013-02-01
Recent developments in the area of multiscale modeling of fiber-reinforced polymers are presented. The overall strategy takes advantage of the separation of length scales between different entities (ply, laminate, and component) found in composite structures. This allows us to carry out multiscale modeling by computing the properties of one entity (e.g., individual plies) at the relevant length scale, homogenizing the results into a constitutive model, and passing this information to the next length scale to determine the mechanical behavior of the larger entity (e.g., laminate). As a result, high-fidelity numerical simulations of the mechanical behavior of composite coupons and small components are nowadays feasible starting from the matrix, fiber, and interface properties and spatial distribution. Finally, the roadmap is outlined for extending the current strategy to include functional properties and processing into the simulation scheme.
Multiscale Modeling and Uncertainty Quantification for Nuclear Fuel Performance
Energy Technology Data Exchange (ETDEWEB)
Estep, Donald [Colorado State Univ., Fort Collins, CO (United States); El-Azab, Anter [Florida State Univ., Tallahassee, FL (United States); Pernice, Michael [Idaho National Lab. (INL), Idaho Falls, ID (United States); Peterson, John W. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Polyakov, Peter [Univ. of Wyoming, Laramie, WY (United States); Tavener, Simon [Colorado State Univ., Fort Collins, CO (United States); Xiu, Dongbin [Purdue Univ., West Lafayette, IN (United States); Univ. of Utah, Salt Lake City, UT (United States)
2017-03-23
In this project, we will address the challenges associated with constructing high fidelity multiscale models of nuclear fuel performance. We (*) propose a novel approach for coupling mesoscale and macroscale models, (*) devise efficient numerical methods for simulating the coupled system, and (*) devise and analyze effective numerical approaches for error and uncertainty quantification for the coupled multiscale system. As an integral part of the project, we will carry out analysis of the effects of upscaling and downscaling, investigate efficient methods for stochastic sensitivity analysis of the individual macroscale and mesoscale models, and carry out a posteriori error analysis for computed results. We will pursue development and implementation of solutions in software used at Idaho National Laboratories on models of interest to the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program.
International Nuclear Information System (INIS)
Tang Shaojie; Tang Xiangyang
2012-01-01
Purposes: The suppression of noise in x-ray computed tomography (CT) imaging is of clinical relevance for diagnostic image quality and the potential for radiation dose saving. Toward this purpose, statistical noise reduction methods in either the image or projection domain have been proposed, which employ a multiscale decomposition to enhance the performance of noise suppression while maintaining image sharpness. Recognizing the advantages of noise suppression in the projection domain, the authors propose a projection domain multiscale penalized weighted least squares (PWLS) method, in which the angular sampling rate is explicitly taken into consideration to account for the possible variation of interview sampling rate in advanced clinical or preclinical applications. Methods: The projection domain multiscale PWLS method is derived by converting an isotropic diffusion partial differential equation in the image domain into the projection domain, wherein a multiscale decomposition is carried out. With adoption of the Markov random field or soft thresholding objective function, the projection domain multiscale PWLS method deals with noise at each scale. To compensate for the degradation in image sharpness caused by the projection domain multiscale PWLS method, an edge enhancement is carried out following the noise reduction. The performance of the proposed method is experimentally evaluated and verified using the projection data simulated by computer and acquired by a CT scanner. Results: The preliminary results show that the proposed projection domain multiscale PWLS method outperforms the projection domain single-scale PWLS method and the image domain multiscale anisotropic diffusion method in noise reduction. In addition, the proposed method can preserve image sharpness very well while the occurrence of “salt-and-pepper” noise and mosaic artifacts can be avoided. Conclusions: Since the interview sampling rate is taken into account in the projection domain
Concurrent engineering: effective deployment strategies
Directory of Open Access Journals (Sweden)
Unny Menon
1996-12-01
Full Text Available This paper provides a comprehensive insight into current trends and developments in Concurrent Engineering for integrated development of products and processes with the goal of completing the entire cycle in a shorter time, at lower overall cost and with fewer engineering design changes after product release. The evolution and definition of Concurrent Engineering are addressed first, followed by a concise review of the following elements of the concurrent engineering approach to product development: Concept Development: The Front-End Process, identifying Customer Needs and Quality Function Deployment, Establishing Product Specifications, Concept Selection, Product Architecture, Design for Manufacturing, Effective Rapid Prototyping, and The Economics of Product Development. An outline of a computer-based tutorial developed by the authors and other graduate students funded by NASA ( accessible via the world-wide-web . is provided in this paper. A brief discussion of teamwork for successful concurrent engineering is included, t'ase histories of concurrent engineering implementation at North American and European companies are outlined with references to textbooks authored by Professor Menon and other writers. A comprehensive bibliography on concurrent engineering is included in the paper.
Managing Asynchronous Data in ATLAS's Concurrent Framework
Baines, John; The ATLAS collaboration
2016-01-01
In order to be able to make effective use of emerging hardware, where the amount of memory available to any CPU is rapidly decreasing as the core count continues to rise, ATLAS has begun a migration to a concurrent, multi-threaded software framework, known as AthenaMT. Significant progress has been made in implementing AthenaMT - we can currently run realistic Geant4 simulations on massively concurrent machines. the migration of realistic prototypes of reconstruction workflows is more difficult, given the large amounts of legacy code and the complexity and challenges of reconstruction software. These types of workflows, however, are the types that will most benefit from the memory reduction features of a multi-threaded framework. One of the challenges that we will report on in this paper is the re-design and implementation of several key asynchronous technologies whose behaviour is radically different in a concurrent environment than in a serial one, namely the management of Conditions data and the Detector D...
Multiscale Methods for Accurate, Efficient, and Scale-Aware Models
Energy Technology Data Exchange (ETDEWEB)
Larson, Vincent [Univ. of Wisconsin, Milwaukee, WI (United States)
2017-07-14
The goal of UWM’s portion of the Multiscale project was to develop a unified cloud parameterization that could simulate all cloud types --- including stratocumulus, shallow cumulus, and deep cumulus --- using the single equation set implemented in CLUBB. An advantage of a unified parameterization methodology is that it avoids the difficult task of interfacing different cloud parameterizations for different cloud types. To interface CLUBB’s clouds to the microphysics, a Monte Carlo interface, SILHS, was further developed.
Lattice Boltzmann accelerated direct simulation Monte Carlo for dilute gas flow simulations.
Di Staso, G; Clercx, H J H; Succi, S; Toschi, F
2016-11-13
Hybrid particle-continuum computational frameworks permit the simulation of gas flows by locally adjusting the resolution to the degree of non-equilibrium displayed by the flow in different regions of space and time. In this work, we present a new scheme that couples the direct simulation Monte Carlo (DSMC) with the lattice Boltzmann (LB) method in the limit of isothermal flows. The former handles strong non-equilibrium effects, as they typically occur in the vicinity of solid boundaries, whereas the latter is in charge of the bulk flow, where non-equilibrium can be dealt with perturbatively, i.e. according to Navier-Stokes hydrodynamics. The proposed concurrent multiscale method is applied to the dilute gas Couette flow, showing major computational gains when compared with the full DSMC scenarios. In addition, it is shown that the coupling with LB in the bulk flow can speed up the DSMC treatment of the Knudsen layer with respect to the full DSMC case. In other words, LB acts as a DSMC accelerator.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'. © 2016 The Author(s).
Multiscale simulations of star polymer melts
Liu, L.
2014-01-01
Depending on the architecture, polymers are observed to show different dynamical and rheological properties. The results obtained from this work will not only contribute to a fundamental understanding of the character of star polymeric systems, but also possibly help to design industrial
Relaxed Operational Semantics of Concurrent Programming Languages
Directory of Open Access Journals (Sweden)
Gustavo Petri
2012-08-01
Full Text Available We propose a novel, operational framework to formally describe the semantics of concurrent programs running within the context of a relaxed memory model. Our framework features a "temporary store" where the memory operations issued by the threads are recorded, in program order. A memory model then specifies the conditions under which a pending operation from this sequence is allowed to be globally performed, possibly out of order. The memory model also involves a "write grain," accounting for architectures where a thread may read a write that is not yet globally visible. Our formal model is supported by a software simulator, allowing us to run litmus tests in our semantics.
Multiscale scenarios for nature futures
CSIR Research Space (South Africa)
Rosa, IMD
2017-09-01
Full Text Available & Evolution, vol. 1: 1416-1419 Multiscale scenarios for nature futures Rosa IMD Pereira HM Ferrier S Alkemade R Acosta LA Akcakaya HR den Belder E Fazel AM Fujimori S Sitas NE ABSTRACT: Targets for human development are increasingly...
Multiscale mechanics of dynamical metamaterials
Geers, M.G.D.; Kouznetsova, V.; Sridhar, A.; Krushynska, A.; Kleiber, M.; Burczynski, T.; Wilde, K.; Gorski, J.; Winkelmann, K.; Smakosz, L.
2016-01-01
This contribution focuses on the computational multi-scale solution of wave propagation phenomena in dynamic metamaterials. Taking the Bloch-Floquet solution for the standard elastic case as a point of departure, an extended scheme is presented to solve for heterogeneous visco-elastic materials. The
Concurrency-Induced Transitions in Epidemic Dynamics on Temporal Networks.
Onaga, Tomokatsu; Gleeson, James P; Masuda, Naoki
2017-09-08
Social contact networks underlying epidemic processes in humans and animals are highly dynamic. The spreading of infections on such temporal networks can differ dramatically from spreading on static networks. We theoretically investigate the effects of concurrency, the number of neighbors that a node has at a given time point, on the epidemic threshold in the stochastic susceptible-infected-susceptible dynamics on temporal network models. We show that network dynamics can suppress epidemics (i.e., yield a higher epidemic threshold) when the node's concurrency is low, but can also enhance epidemics when the concurrency is high. We analytically determine different phases of this concurrency-induced transition, and confirm our results with numerical simulations.
Concurrency-Induced Transitions in Epidemic Dynamics on Temporal Networks
Onaga, Tomokatsu; Gleeson, James P.; Masuda, Naoki
2017-09-01
Social contact networks underlying epidemic processes in humans and animals are highly dynamic. The spreading of infections on such temporal networks can differ dramatically from spreading on static networks. We theoretically investigate the effects of concurrency, the number of neighbors that a node has at a given time point, on the epidemic threshold in the stochastic susceptible-infected-susceptible dynamics on temporal network models. We show that network dynamics can suppress epidemics (i.e., yield a higher epidemic threshold) when the node's concurrency is low, but can also enhance epidemics when the concurrency is high. We analytically determine different phases of this concurrency-induced transition, and confirm our results with numerical simulations.
MUSIC: MUlti-Scale Initial Conditions
Hahn, Oliver; Abel, Tom
2013-11-01
MUSIC generates multi-scale initial conditions with multiple levels of refinements for cosmological ‘zoom-in’ simulations. The code uses an adaptive convolution of Gaussian white noise with a real-space transfer function kernel together with an adaptive multi-grid Poisson solver to generate displacements and velocities following first- (1LPT) or second-order Lagrangian perturbation theory (2LPT). MUSIC achieves rms relative errors of the order of 10-4 for displacements and velocities in the refinement region and thus improves in terms of errors by about two orders of magnitude over previous approaches. In addition, errors are localized at coarse-fine boundaries and do not suffer from Fourier space-induced interference ringing.
Multiscale Thermohydrologic Model
Energy Technology Data Exchange (ETDEWEB)
T. Buscheck
2004-10-12
The purpose of the multiscale thermohydrologic model (MSTHM) is to predict the possible range of thermal-hydrologic conditions, resulting from uncertainty and variability, in the repository emplacement drifts, including the invert, and in the adjoining host rock for the repository at Yucca Mountain. Thus, the goal is to predict the range of possible thermal-hydrologic conditions across the repository; this is quite different from predicting a single expected thermal-hydrologic response. The MSTHM calculates the following thermal-hydrologic parameters: temperature, relative humidity, liquid-phase saturation, evaporation rate, air-mass fraction, gas-phase pressure, capillary pressure, and liquid- and gas-phase fluxes (Table 1-1). These thermal-hydrologic parameters are required to support ''Total System Performance Assessment (TSPA) Model/Analysis for the License Application'' (BSC 2004 [DIRS 168504]). The thermal-hydrologic parameters are determined as a function of position along each of the emplacement drifts and as a function of waste package type. These parameters are determined at various reference locations within the emplacement drifts, including the waste package and drip-shield surfaces and in the invert. The parameters are also determined at various defined locations in the adjoining host rock. The MSTHM uses data obtained from the data tracking numbers (DTNs) listed in Table 4.1-1. The majority of those DTNs were generated from the following analyses and model reports: (1) ''UZ Flow Model and Submodels'' (BSC 2004 [DIRS 169861]); (2) ''Development of Numerical Grids for UZ Flow and Transport Modeling'' (BSC 2004); (3) ''Calibrated Properties Model'' (BSC 2004 [DIRS 169857]); (4) ''Thermal Conductivity of the Potential Repository Horizon'' (BSC 2004 [DIRS 169854]); (5) ''Thermal Conductivity of the Non-Repository Lithostratigraphic Layers
Multiscale Pressure-Balanced Structures in Three-dimensional Magnetohydrodynamic Turbulence
Energy Technology Data Exchange (ETDEWEB)
Yang, Liping; Zhang, Lei; Feng, Xueshang [SIGMA Weather Group, State Key Laboratory for Space Weather, National Space Science Center, Chinese Academy of Sciences, 100190, Beijing (China); He, Jiansen; Tu, Chuanyi; Wang, Linghua [School of Earth and Space Sciences, Peking University, 100871 Beijing (China); Li, Shengtai [Theoretical Division, MS B284, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Marsch, Eckart [Institute for Experimental and Applied Physics, Christian Albrechts University at Kiel, D-24118 Kiel (Germany); Wang, Xin, E-mail: jshept@gmail.com [School of Space and Environment, Beihang University, 100191 Beijing (China)
2017-02-10
Observations of solar wind turbulence indicate the existence of multiscale pressure-balanced structures (PBSs) in the solar wind. In this work, we conduct a numerical simulation to investigate multiscale PBSs and in particular their formation in compressive magnetohydrodynamic turbulence. By the use of the higher-order Godunov code Athena, a driven compressible turbulence with an imposed uniform guide field is simulated. The simulation results show that both the magnetic pressure and the thermal pressure exhibit a turbulent spectrum with a Kolmogorov-like power law, and that in many regions of the simulation domain they are anticorrelated. The computed wavelet cross-coherence spectra of the magnetic pressure and the thermal pressure, as well as their space series, indicate the existence of multiscale PBSs, with the small PBSs being embedded in the large ones. These multiscale PBSs are likely to be related to the highly oblique-propagating slow-mode waves, as the traced multiscale PBS is found to be traveling in a certain direction at a speed consistent with that predicted theoretically for a slow-mode wave propagating in the same direction.
A rate-dependent multi-scale crack model for concrete
Karamnejad, A.; Nguyen, V.P.; Sluys, L.J.
2013-01-01
A multi-scale numerical approach for modeling cracking in heterogeneous quasi-brittle materials under dynamic loading is presented. In the model, a discontinuous crack model is used at macro-scale to simulate fracture and a gradient-enhanced damage model has been used at meso-scale to simulate
Multiscale modeling of polyisoprene on graphite
International Nuclear Information System (INIS)
Pandey, Yogendra Narayan; Brayton, Alexander; Doxastakis, Manolis; Burkhart, Craig; Papakonstantopoulos, George J.
2014-01-01
The local dynamics and the conformational properties of polyisoprene next to a smooth graphite surface constructed by graphene layers are studied by a multiscale methodology. First, fully atomistic molecular dynamics simulations of oligomers next to the surface are performed. Subsequently, Monte Carlo simulations of a systematically derived coarse-grained model generate numerous uncorrelated structures for polymer systems. A new reverse backmapping strategy is presented that reintroduces atomistic detail. Finally, multiple extensive fully atomistic simulations with large systems of long macromolecules are employed to examine local dynamics in proximity to graphite. Polyisoprene repeat units arrange close to a parallel configuration with chains exhibiting a distribution of contact lengths. Efficient Monte Carlo algorithms with the coarse-grain model are capable of sampling these distributions for any molecular weight in quantitative agreement with predictions from atomistic models. Furthermore, molecular dynamics simulations with well-equilibrated systems at all length-scales support an increased dynamic heterogeneity that is emerging from both intermolecular interactions with the flat surface and intramolecular cooperativity. This study provides a detailed comprehensive picture of polyisoprene on a flat surface and consists of an effort to characterize such systems in atomistic detail
Modal abstractions of concurrent behavior
DEFF Research Database (Denmark)
Nielson, Flemming; Nanz, Sebastian; Nielson, Hanne Riis
2011-01-01
We present an effective algorithm for the automatic construction of finite modal transition systems as abstractions of potentially infinite concurrent processes. Modal transition systems are recognized as valuable abstractions for model checking because they allow for the validation as well...... as refutation of safety and liveness properties. However, the algorithmic construction of finite abstractions from potentially infinite concurrent processes is a missing link that prevents their more widespread usage for model checking of concurrent systems. Our algorithm is a worklist algorithm using concepts...... from abstract interpretation and operating upon mappings from sets to intervals in order to express simultaneous over- and underapprox-imations of the multisets of process actions available in a particular state. We obtain a finite abstraction that is 3-valued in both states and transitions...
Managing Complexity of Control Software through Concurrency
Hilderink, G.H.
2005-01-01
In this thesis, we are concerned with the development of concurrent software for embedded systems. The emphasis is on the development of control software. Embedded systems are concurrent systems whereby hardware and software communicate with the concurrent world. Concurrency is essential, which
MULTISCALE THERMOHYDROLOGIC MODEL
International Nuclear Information System (INIS)
T. Buscheck
2005-01-01
The intended purpose of the multiscale thermohydrologic model (MSTHM) is to predict the possible range of thermal-hydrologic conditions, resulting from uncertainty and variability, in the repository emplacement drifts, including the invert, and in the adjoining host rock for the repository at Yucca Mountain. The goal of the MSTHM is to predict a reasonable range of possible thermal-hydrologic conditions within the emplacement drift. To be reasonable, this range includes the influence of waste-package-to-waste-package heat output variability relevant to the license application design, as well as the influence of uncertainty and variability in the geologic and hydrologic conditions relevant to predicting the thermal-hydrologic response in emplacement drifts. This goal is quite different from the goal of a model to predict a single expected thermal-hydrologic response. As a result, the development and validation of the MSTHM and the associated analyses using this model are focused on the goal of predicting a reasonable range of thermal-hydrologic conditions resulting from parametric uncertainty and waste-package-to-waste-package heat-output variability. Thermal-hydrologic conditions within emplacement drifts depend primarily on thermal-hydrologic conditions in the host rock at the drift wall and on the temperature difference between the drift wall and the drip-shield and waste-package surfaces. Thus, the ability to predict a reasonable range of relevant in-drift MSTHM output parameters (e.g., temperature and relative humidity) is based on valid predictions of thermal-hydrologic processes in the host rock, as well as valid predictions of heat-transfer processes between the drift wall and the drip-shield and waste-package surfaces. Because the invert contains crushed gravel derived from the host rock, the invert is, in effect, an extension of the host rock, with thermal and hydrologic properties that have been modified by virtue of the crushing (and the resulting
The Magnetospheric Multiscale Mission
Burch, James
Magnetospheric Multiscale (MMS), a NASA four-spacecraft mission scheduled for launch in November 2014, will investigate magnetic reconnection in the boundary regions of the Earth’s magnetosphere, particularly along its dayside boundary with the solar wind and the neutral sheet in the magnetic tail. Among the important questions about reconnection that will be addressed are the following: Under what conditions can magnetic-field energy be converted to plasma energy by the annihilation of magnetic field through reconnection? How does reconnection vary with time, and what factors influence its temporal behavior? What microscale processes are responsible for reconnection? What determines the rate of reconnection? In order to accomplish its goals the MMS spacecraft must probe both those regions in which the magnetic fields are very nearly antiparallel and regions where a significant guide field exists. From previous missions we know the approximate speeds with which reconnection layers move through space to be from tens to hundreds of km/s. For electron skin depths of 5 to 10 km, the full 3D electron population (10 eV to above 20 keV) has to be sampled at rates greater than 10/s. The MMS Fast-Plasma Instrument (FPI) will sample electrons at greater than 30/s. Because the ion skin depth is larger, FPI will make full ion measurements at rates of greater than 6/s. 3D E-field measurements will be made by MMS once every ms. MMS will use an Active Spacecraft Potential Control device (ASPOC), which emits indium ions to neutralize the photoelectron current and keep the spacecraft from charging to more than +4 V. Because ion dynamics in Hall reconnection depend sensitively on ion mass, MMS includes a new-generation Hot Plasma Composition Analyzer (HPCA) that corrects problems with high proton fluxes that have prevented accurate ion-composition measurements near the dayside magnetospheric boundary. Finally, Energetic Particle Detector (EPD) measurements of electrons and
MULTISCALE THERMOHYDROLOGIC MODEL
Energy Technology Data Exchange (ETDEWEB)
T. Buscheck
2005-07-07
The intended purpose of the multiscale thermohydrologic model (MSTHM) is to predict the possible range of thermal-hydrologic conditions, resulting from uncertainty and variability, in the repository emplacement drifts, including the invert, and in the adjoining host rock for the repository at Yucca Mountain. The goal of the MSTHM is to predict a reasonable range of possible thermal-hydrologic conditions within the emplacement drift. To be reasonable, this range includes the influence of waste-package-to-waste-package heat output variability relevant to the license application design, as well as the influence of uncertainty and variability in the geologic and hydrologic conditions relevant to predicting the thermal-hydrologic response in emplacement drifts. This goal is quite different from the goal of a model to predict a single expected thermal-hydrologic response. As a result, the development and validation of the MSTHM and the associated analyses using this model are focused on the goal of predicting a reasonable range of thermal-hydrologic conditions resulting from parametric uncertainty and waste-package-to-waste-package heat-output variability. Thermal-hydrologic conditions within emplacement drifts depend primarily on thermal-hydrologic conditions in the host rock at the drift wall and on the temperature difference between the drift wall and the drip-shield and waste-package surfaces. Thus, the ability to predict a reasonable range of relevant in-drift MSTHM output parameters (e.g., temperature and relative humidity) is based on valid predictions of thermal-hydrologic processes in the host rock, as well as valid predictions of heat-transfer processes between the drift wall and the drip-shield and waste-package surfaces. Because the invert contains crushed gravel derived from the host rock, the invert is, in effect, an extension of the host rock, with thermal and hydrologic properties that have been modified by virtue of the crushing (and the resulting
Concurrency & Asynchrony in Declarative Workflows
DEFF Research Database (Denmark)
Debois, Søren; Hildebrandt, Thomas; Slaats, Tijs
2015-01-01
of concurrency in DCR Graphs admits asynchronous execution of declarative workflows both conceptually and by reporting on a prototype implementation of a distributed declarative workflow engine. Both the theoretical development and the implementation is supported by an extended example; moreover, the theoretical....... In this paper, we pro- pose a notion of concurrency for declarative process models, formulated in the context of Dynamic Condition Response (DCR) graphs, and exploiting the so-called “true concurrency” semantics of Labelled Asynchronous Transition Systems. We demonstrate how this semantic underpinning...
Multi-scale approximation of Vlasov equation
International Nuclear Information System (INIS)
Mouton, A.
2009-09-01
One of the most important difficulties of numerical simulation of magnetized plasmas is the existence of multiple time and space scales, which can be very different. In order to produce good simulations of these multi-scale phenomena, it is recommended to develop some models and numerical methods which are adapted to these problems. Nowadays, the two-scale convergence theory introduced by G. Nguetseng and G. Allaire is one of the tools which can be used to rigorously derive multi-scale limits and to obtain new limit models which can be discretized with a usual numerical method: this procedure is so-called a two-scale numerical method. The purpose of this thesis is to develop a two-scale semi-Lagrangian method and to apply it on a gyrokinetic Vlasov-like model in order to simulate a plasma submitted to a large external magnetic field. However, the physical phenomena we have to simulate are quite complex and there are many questions without answers about the behaviour of a two-scale numerical method, especially when such a method is applied on a nonlinear model. In a first part, we develop a two-scale finite volume method and we apply it on the weakly compressible 1D isentropic Euler equations. Even if this mathematical context is far from a Vlasov-like model, it is a relatively simple framework in order to study the behaviour of a two-scale numerical method in front of a nonlinear model. In a second part, we develop a two-scale semi-Lagrangian method for the two-scale model developed by E. Frenod, F. Salvarani et E. Sonnendrucker in order to simulate axisymmetric charged particle beams. Even if the studied physical phenomena are quite different from magnetic fusion experiments, the mathematical context of the one-dimensional paraxial Vlasov-Poisson model is very simple for establishing the basis of a two-scale semi-Lagrangian method. In a third part, we use the two-scale convergence theory in order to improve M. Bostan's weak-* convergence results about the finite
Introduction and application of the multiscale coefficient of variation analysis.
Abney, Drew H; Kello, Christopher T; Balasubramaniam, Ramesh
2017-10-01
Quantifying how patterns of behavior relate across multiple levels of measurement typically requires long time series for reliable parameter estimation. We describe a novel analysis that estimates patterns of variability across multiple scales of analysis suitable for time series of short duration. The multiscale coefficient of variation (MSCV) measures the distance between local coefficient of variation estimates within particular time windows and the overall coefficient of variation across all time samples. We first describe the MSCV analysis and provide an example analytical protocol with corresponding MATLAB implementation and code. Next, we present a simulation study testing the new analysis using time series generated by ARFIMA models that span white noise, short-term and long-term correlations. The MSCV analysis was observed to be sensitive to specific parameters of ARFIMA models varying in the type of temporal structure and time series length. We then apply the MSCV analysis to short time series of speech phrases and musical themes to show commonalities in multiscale structure. The simulation and application studies provide evidence that the MSCV analysis can discriminate between time series varying in multiscale structure and length.
Physics-based hybrid method for multiscale transport in porous media
Yousefzadeh, Mehrdad; Battiato, Ilenia
2017-09-01
Despite advancements in the development of multiscale models for flow and reactive transport in porous media, the accurate, efficient and physics-based coupling of multiple scales in hybrid models remains a major theoretical and computational challenge. Improving the predictivity of macroscale predictions by means of multiscale algorithms relative to classical at-scale models is the primary motivation for the development of multiscale simulators. Yet, very few are the quantitative studies that explicitly address the predictive capability of multiscale coupling algorithms as it is still generally not possible to have a priori estimates of the errors that are present when complex flow processes are modeled. We develop a nonintrusive pore-/continuum-scale hybrid model whose coupling error is bounded by the upscaling error, i.e. we build a predictive tightly coupled multiscale scheme. This is accomplished by slightly enlarging the subdomain where continuum-scale equations are locally invalid and analytically defining physics-based coupling conditions at the interfaces separating the two computational sub-domains, while enforcing state variable and flux continuity. The proposed multiscale coupling approach retains the advantages of domain decomposition approaches, including the use of existing solvers for each subdomain, while it gains flexibility in the choice of the numerical discretization method and maintains the coupling errors bounded by the upscaling error. We implement the coupling in finite volumes and test the proposed method by modeling flow and transport through a reactive channel and past an array of heterogeneously reactive cylinders.
MULTISCALE TENSOR ANISOTROPIC FILTERING OF FLUORESCENCE MICROSCOPY FOR DENOISING MICROVASCULATURE.
Prasath, V B S; Pelapur, R; Glinskii, O V; Glinsky, V V; Huxley, V H; Palaniappan, K
2015-04-01
Fluorescence microscopy images are contaminated by noise and improving image quality without blurring vascular structures by filtering is an important step in automatic image analysis. The application of interest here is to automatically extract the structural components of the microvascular system with accuracy from images acquired by fluorescence microscopy. A robust denoising process is necessary in order to extract accurate vascular morphology information. For this purpose, we propose a multiscale tensor with anisotropic diffusion model which progressively and adaptively updates the amount of smoothing while preserving vessel boundaries accurately. Based on a coherency enhancing flow with planar confidence measure and fused 3D structure information, our method integrates multiple scales for microvasculature preservation and noise removal membrane structures. Experimental results on simulated synthetic images and epifluorescence images show the advantage of our improvement over other related diffusion filters. We further show that the proposed multiscale integration approach improves denoising accuracy of different tensor diffusion methods to obtain better microvasculature segmentation.
Global sensitivity analysis of multiscale properties of porous materials
Um, Kimoon; Zhang, Xuan; Katsoulakis, Markos; Plechac, Petr; Tartakovsky, Daniel M.
2018-02-01
Ubiquitous uncertainty about pore geometry inevitably undermines the veracity of pore- and multi-scale simulations of transport phenomena in porous media. It raises two fundamental issues: sensitivity of effective material properties to pore-scale parameters and statistical parameterization of Darcy-scale models that accounts for pore-scale uncertainty. Homogenization-based maps of pore-scale parameters onto their Darcy-scale counterparts facilitate both sensitivity analysis (SA) and uncertainty quantification. We treat uncertain geometric characteristics of a hierarchical porous medium as random variables to conduct global SA and to derive probabilistic descriptors of effective diffusion coefficients and effective sorption rate. Our analysis is formulated in terms of solute transport diffusing through a fluid-filled pore space, while sorbing to the solid matrix. Yet it is sufficiently general to be applied to other multiscale porous media phenomena that are amenable to homogenization.
Multi-Scale Models for the Scale Interaction of Organized Tropical Convection
Yang, Qiu
Assessing the upscale impact of organized tropical convection from small spatial and temporal scales is a research imperative, not only for having a better understanding of the multi-scale structures of dynamical and convective fields in the tropics, but also for eventually helping in the design of new parameterization strategies to improve the next-generation global climate models. Here self-consistent multi-scale models are derived systematically by following the multi-scale asymptotic methods and used to describe the hierarchical structures of tropical atmospheric flows. The advantages of using these multi-scale models lie in isolating the essential components of multi-scale interaction and providing assessment of the upscale impact of the small-scale fluctuations onto the large-scale mean flow through eddy flux divergences of momentum and temperature in a transparent fashion. Specifically, this thesis includes three research projects about multi-scale interaction of organized tropical convection, involving tropical flows at different scaling regimes and utilizing different multi-scale models correspondingly. Inspired by the observed variability of tropical convection on multiple temporal scales, including daily and intraseasonal time scales, the goal of the first project is to assess the intraseasonal impact of the diurnal cycle on the planetary-scale circulation such as the Hadley cell. As an extension of the first project, the goal of the second project is to assess the intraseasonal impact of the diurnal cycle over the Maritime Continent on the Madden-Julian Oscillation. In the third project, the goals are to simulate the baroclinic aspects of the ITCZ breakdown and assess its upscale impact on the planetary-scale circulation over the eastern Pacific. These simple multi-scale models should be useful to understand the scale interaction of organized tropical convection and help improve the parameterization of unresolved processes in global climate models.
Multi-scale window specification over streaming trajectories
Directory of Open Access Journals (Sweden)
Kostas Patroumpas
2013-12-01
Full Text Available Enormous amounts of positional information are collected by monitoring applications in domains such as fleet management, cargo transport, wildlife protection, etc. With the advent of modern location-based services, processing such data mostly focuses on providing real-time response to a variety of user requests in continuous and scalable fashion. An important class of such queries concerns evolving trajectories that continuously trace the streaming locations of moving objects, like GPS-equipped vehicles, commodities with RFID's, people with smartphones etc. In this work, we propose an advanced windowing operator that enables online, incremental examination of recent motion paths at multiple resolutions for numerous point entities. When applied against incoming positions, this window can abstract trajectories at coarser representations towards the past, while retaining progressively finer features closer to the present. We explain the semantics of such multi-scale sliding windows through parameterized functions that reflect the sequential nature of trajectories and can effectively capture their spatiotemporal properties. Such window specification goes beyond its usual role for non-blocking processing of multiple concurrent queries. Actually, it can offer concrete subsequences from each trajectory, thus preserving continuity in time and contiguity in space along the respective segments. Further, we suggest language extensions in order to express characteristic spatiotemporal queries using windows. Finally, we discuss algorithms for nested maintenance of multi-scale windows and evaluate their efficiency against streaming positional data, offering empirical evidence of their benefits to online trajectory processing.
Multiscale Modeling using Molecular Dynamics and Dual Domain Material Point Method
Energy Technology Data Exchange (ETDEWEB)
Dhakal, Tilak Raj [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Theoretical Division. Fluid Dynamics and Solid Mechanics Group, T-3; Rice Univ., Houston, TX (United States)
2016-07-07
For problems involving large material deformation rate, the material deformation time scale can be shorter than the material takes to reach a thermodynamical equilibrium. For such problems, it is difficult to obtain a constitutive relation. History dependency become important because of thermodynamic non-equilibrium. Our goal is to build a multi-scale numerical method which can bypass the need for a constitutive relation. In conclusion, multi-scale simulation method is developed based on the dual domain material point (DDMP). Molecular dynamics (MD) simulation is performed to calculate stress. Since the communication among material points is not necessary, the computation can be done embarrassingly parallel in CPU-GPU platform.
A Model for Concurrent Objects
DEFF Research Database (Denmark)
Sørensen, Morten U.
1996-01-01
We present a model for concurrent objects where obejcts interact by taking part in common events that are closely matched to form call-response pairs, resulting in resulting in rendez-vous like communications. Objects are built from primitive objects by parallel composition, encapsulation...
Forward progress on GPU concurrency
Donaldson, A.F.; Ketema, J.; Sorensen, T.; Wickerson, J.
2017-01-01
The tutorial at CONCUR will provide a practical overview of work undertaken over the last six years in the Multicore Programming Group at Imperial College London, and with collaborators internationally, related to understanding and reasoning about concurrency in software designed for acceleration on
True Concurrency can be Traced
DEFF Research Database (Denmark)
Engberg, Uffe Henrik
1990-01-01
In this paper sets of labelled partial orders are employed as fundamental mathematical entities for modelling nondeterministic and concurrent processes thereby obtaining so-called noninterleaving semantics. Based on closures of sets of labelled partial orders, a simple algebraic language with ref...
Relationships between models of concurrency
DEFF Research Database (Denmark)
Nielsen, Mogens; Sassone, Vladimiro; Winskel, Glynn
1994-01-01
Models for concurrency can be classified with respect to the three relevant parameters: behaviour/system, interleaving/noninterleaving, linear/branching time. When modelling a process, a choice concerning such parameters corresponds to choosing the level of abstraction of the resulting semantics....
Sun, S.; Kou, J.; Yu, B.
2011-01-01
The temporal discretization scheme is one important ingredient of efficient simulator for two-phase flow in the fractured porous media. The application of single-scale temporal scheme is restricted by the rapid changes of the pressure and saturation in the fractured system with capillarity. In this paper, we propose a multi-scale time splitting strategy to simulate multi-scale multi-physics processes of two-phase flow in fractured porous media. We use the multi-scale time schemes for both the pressure and saturation equations; that is, a large time-step size is employed for the matrix domain, along with a small time-step size being applied in the fractures. The total time interval is partitioned into four temporal levels: the first level is used for the pressure in the entire domain, the second level matching rapid changes of the pressure in the fractures, the third level treating the response gap between the pressure and the saturation, and the fourth level applied for the saturation in the fractures. This method can reduce the computational cost arisen from the implicit solution of the pressure equation. Numerical examples are provided to demonstrate the efficiency of the proposed method.
Numerical Analysis of Multiscale Computations
Engquist, Björn; Tsai, Yen-Hsi R
2012-01-01
This book is a snapshot of current research in multiscale modeling, computations and applications. It covers fundamental mathematical theory, numerical algorithms as well as practical computational advice for analysing single and multiphysics models containing a variety of scales in time and space. Complex fluids, porous media flow and oscillatory dynamical systems are treated in some extra depth, as well as tools like analytical and numerical homogenization, and fast multipole method.
Multi-scale calculation based on dual domain material point method combined with molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
Dhakal, Tilak Raj [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
2017-02-27
This dissertation combines the dual domain material point method (DDMP) with molecular dynamics (MD) in an attempt to create a multi-scale numerical method to simulate materials undergoing large deformations with high strain rates. In these types of problems, the material is often in a thermodynamically non-equilibrium state, and conventional constitutive relations are often not available. In this method, the closure quantities, such as stress, at each material point are calculated from a MD simulation of a group of atoms surrounding the material point. Rather than restricting the multi-scale simulation in a small spatial region, such as phase interfaces, or crack tips, this multi-scale method can be used to consider non-equilibrium thermodynamic e ects in a macroscopic domain. This method takes advantage that the material points only communicate with mesh nodes, not among themselves; therefore MD simulations for material points can be performed independently in parallel. First, using a one-dimensional shock problem as an example, the numerical properties of the original material point method (MPM), the generalized interpolation material point (GIMP) method, the convected particle domain interpolation (CPDI) method, and the DDMP method are investigated. Among these methods, only the DDMP method converges as the number of particles increases, but the large number of particles needed for convergence makes the method very expensive especially in our multi-scale method where we calculate stress in each material point using MD simulation. To improve DDMP, the sub-point method is introduced in this dissertation, which provides high quality numerical solutions with a very small number of particles. The multi-scale method based on DDMP with sub-points is successfully implemented for a one dimensional problem of shock wave propagation in a cerium crystal. The MD simulation to calculate stress in each material point is performed in GPU using CUDA to accelerate the
Zanin, Massimiliano; Chorbev, Ivan; Stres, Blaz; Stalidzans, Egils; Vera, Julio; Tieri, Paolo; Castiglione, Filippo; Groen, Derek; Zheng, Huiru; Baumbach, Jan; Schmid, Johannes A; Basilio, José; Klimek, Peter; Debeljak, Nataša; Rozman, Damjana; Schmidt, Harald H H W
2017-12-05
Systems medicine holds many promises, but has so far provided only a limited number of proofs of principle. To address this road block, possible barriers and challenges of translating systems medicine into clinical practice need to be identified and addressed. The members of the European Cooperation in Science and Technology (COST) Action CA15120 Open Multiscale Systems Medicine (OpenMultiMed) wish to engage the scientific community of systems medicine and multiscale modelling, data science and computing, to provide their feedback in a structured manner. This will result in follow-up white papers and open access resources to accelerate the clinical translation of systems medicine. © The Author 2017. Published by Oxford University Press.
Multiscale Molecular Dynamics Model for Heterogeneous Charged Systems
Stanton, L. G.; Glosli, J. N.; Murillo, M. S.
2018-04-01
Modeling matter across large length scales and timescales using molecular dynamics simulations poses significant challenges. These challenges are typically addressed through the use of precomputed pair potentials that depend on thermodynamic properties like temperature and density; however, many scenarios of interest involve spatiotemporal variations in these properties, and such variations can violate assumptions made in constructing these potentials, thus precluding their use. In particular, when a system is strongly heterogeneous, most of the usual simplifying assumptions (e.g., spherical potentials) do not apply. Here, we present a multiscale approach to orbital-free density functional theory molecular dynamics (OFDFT-MD) simulations that bridges atomic, interionic, and continuum length scales to allow for variations in hydrodynamic quantities in a consistent way. Our multiscale approach enables simulations on the order of micron length scales and 10's of picosecond timescales, which exceeds current OFDFT-MD simulations by many orders of magnitude. This new capability is then used to study the heterogeneous, nonequilibrium dynamics of a heated interface characteristic of an inertial-confinement-fusion capsule containing a plastic ablator near a fuel layer composed of deuterium-tritium ice. At these scales, fundamental assumptions of continuum models are explored; features such as the separation of the momentum fields among the species and strong hydrogen jetting from the plastic into the fuel region are observed, which had previously not been seen in hydrodynamic simulations.
Multiscale Modeling of Mesoscale and Interfacial Phenomena
Petsev, Nikolai Dimitrov
With rapidly emerging technologies that feature interfaces modified at the nanoscale, traditional macroscopic models are pushed to their limits to explain phenomena where molecular processes can play a key role. Often, such problems appear to defy explanation when treated with coarse-grained continuum models alone, yet remain prohibitively expensive from a molecular simulation perspective. A prominent example is surface nanobubbles: nanoscopic gaseous domains typically found on hydrophobic surfaces that have puzzled researchers for over two decades due to their unusually long lifetimes. We show how an entirely macroscopic, non-equilibrium model explains many of their anomalous properties, including their stability and abnormally small gas-side contact angles. From this purely transport perspective, we investigate how factors such as temperature and saturation affect nanobubbles, providing numerous experimentally testable predictions. However, recent work also emphasizes the relevance of molecular-scale phenomena that cannot be described in terms of bulk phases or pristine interfaces. This is true for nanobubbles as well, whose nanoscale heights may require molecular detail to capture the relevant physics, in particular near the bubble three-phase contact line. Therefore, there is a clear need for general ways to link molecular granularity and behavior with large-scale continuum models in the treatment of many interfacial problems. In light of this, we have developed a general set of simulation strategies that couple mesoscale particle-based continuum models to molecular regions simulated through conventional molecular dynamics (MD). In addition, we derived a transport model for binary mixtures that opens the possibility for a wide range of applications in biological and drug delivery problems, and is readily reconciled with our hybrid MD-continuum techniques. Approaches that couple multiple length scales for fluid mixtures are largely absent in the literature, and
A generalized multiscale finite element method for elastic wave propagation in fractured media
Chung, Eric T.
2016-02-26
In this paper, we consider elastic wave propagation in fractured media applying a linear-slip model to represent the effects of fractures on the wavefield. Fractured media, typically, are highly heterogeneous due to multiple length scales. Direct numerical simulations for wave propagation in highly heterogeneous fractured media can be computationally expensive and require some type of model reduction. We develop a multiscale model reduction technique that captures the complex nature of the media (heterogeneities and fractures) in the coarse scale system. The proposed method is based on the generalized multiscale finite element method, where the multiscale basis functions are constructed to capture the fine-scale information of the heterogeneous, fractured media and effectively reduce the degrees of freedom. These multiscale basis functions are coupled via the interior penalty discontinuous Galerkin method, which provides a block-diagonal mass matrix. The latter is needed for fast computation in an explicit time discretization, which is used in our simulations. Numerical results are presented to show the performance of the presented multiscale method for fractured media. We consider several cases where fractured media contain fractures of multiple lengths. Our numerical results show that the proposed reduced-order models can provide accurate approximations for the fine-scale solution.
A generalized multiscale finite element method for elastic wave propagation in fractured media
Chung, Eric T.; Efendiev, Yalchin R.; Gibson, Richard L.; Vasilyeva, Maria
2016-01-01
In this paper, we consider elastic wave propagation in fractured media applying a linear-slip model to represent the effects of fractures on the wavefield. Fractured media, typically, are highly heterogeneous due to multiple length scales. Direct numerical simulations for wave propagation in highly heterogeneous fractured media can be computationally expensive and require some type of model reduction. We develop a multiscale model reduction technique that captures the complex nature of the media (heterogeneities and fractures) in the coarse scale system. The proposed method is based on the generalized multiscale finite element method, where the multiscale basis functions are constructed to capture the fine-scale information of the heterogeneous, fractured media and effectively reduce the degrees of freedom. These multiscale basis functions are coupled via the interior penalty discontinuous Galerkin method, which provides a block-diagonal mass matrix. The latter is needed for fast computation in an explicit time discretization, which is used in our simulations. Numerical results are presented to show the performance of the presented multiscale method for fractured media. We consider several cases where fractured media contain fractures of multiple lengths. Our numerical results show that the proposed reduced-order models can provide accurate approximations for the fine-scale solution.
Concurrent Product & Supply Chain Creation
DEFF Research Database (Denmark)
Gubi, Ebbe
it is a structural premise. We also know that logistics costs generally are estimated 15-20% of total product costs. Accordingly, it stands to reason that a company can reduce costs, and thereby gain an edge on its competitors, by tailoring the supply chain in question to an individual product or product family; i.......e. by creating Focused Supply Chains. At the same time, customer satisfaction can be increased. As a second means to achieving a better fit between product and supply chain, the firm can deploy Design for Logistics, the discipline of considering the supply chain during product creation. The thesis sets out...... and supply chains should be created concurrently and integrated. The concept of Concurrent Product & Supply Chain Creation is introduced, and the two main components Focused Supply Chains and Design For Logistics are explained and exemplified by use of Bang & Olufsen....
Adding Concurrency to Smart Contracts
Dickerson, Thomas; Gazzillo, Paul; Herlihy, Maurice; Koskinen, Eric
2017-01-01
Modern cryptocurrency systems, such as Ethereum, permit complex financial transactions through scripts called smart contracts. These smart contracts are executed many, many times, always without real concurrency. First, all smart contracts are serially executed by miners before appending them to the blockchain. Later, those contracts are serially re-executed by validators to verify that the smart contracts were executed correctly by miners. Serial execution limits system throughput and fails ...
Evaluation of concurrent peak responses
International Nuclear Information System (INIS)
Wang, P.C.; Curreri, J.; Reich, M.
1983-01-01
This report deals with the problem of combining two or more concurrent responses which are induced by dynamic loads acting on nuclear power plant structures. Specifically, the acceptability of using the square root of the sum of the squares (SRSS) value of peak values as the combined response is investigated. Emphasis is placed on the establishment of a simplified criterion that is convenient and relatively easy to use by design engineers
PyCSP - controlled concurrency
DEFF Research Database (Denmark)
Vinter, Brian; Friborg, Rune Møllegaard; Bjørndalen, John Markus
2010-01-01
Producing readable and correct programs while at the same time taking advantage of multi-core architectures is a challenge. PyCSP is an implementation of Communicating Sequential Processes algebra (CSP) for the Python programming language, that take advantage of CSP's formal and verifiable approach...... to controlling concurrency and the readability of Python source code. We describe PyCSP, demonstrate it through examples and demonstrate how PyCSP compares to Pthreads in a master-worker benchmark....
PyCSP - controlled concurrency
DEFF Research Database (Denmark)
Friborg, Rune Møllegaard; Vinter, Brian; Bjørndalen, John Markus
Producing readable and correct programs while at the same time taking advantage of multi-core architectures is a challenge. PyCSP is an implementation of Communicating Sequential Processes algebra (CSP) for the Python programming language, taking advantage of CSP’s formal and verifiable approach...... to controlling concurrency and the readability of Python source code. We describe PyCSP, demonstrate it through examples and demonstrate how PyCSP compares to Pthreads using a benchmark....
Multiscale methods in turbulent combustion: strategies and computational challenges
International Nuclear Information System (INIS)
Echekki, Tarek
2009-01-01
A principal challenge in modeling turbulent combustion flows is associated with their complex, multiscale nature. Traditional paradigms in the modeling of these flows have attempted to address this nature through different strategies, including exploiting the separation of turbulence and combustion scales and a reduced description of the composition space. The resulting moment-based methods often yield reasonable predictions of flow and reactive scalars' statistics under certain conditions. However, these methods must constantly evolve to address combustion at different regimes, modes or with dominant chemistries. In recent years, alternative multiscale strategies have emerged, which although in part inspired by the traditional approaches, also draw upon basic tools from computational science, applied mathematics and the increasing availability of powerful computational resources. This review presents a general overview of different strategies adopted for multiscale solutions of turbulent combustion flows. Within these strategies, some specific models are discussed or outlined to illustrate their capabilities and underlying assumptions. These strategies may be classified under four different classes, including (i) closure models for atomistic processes, (ii) multigrid and multiresolution strategies, (iii) flame-embedding strategies and (iv) hybrid large-eddy simulation-low-dimensional strategies. A combination of these strategies and models can potentially represent a robust alternative strategy to moment-based models; but a significant challenge remains in the development of computational frameworks for these approaches as well as their underlying theories. (topical review)
Integrated Multiscale Latent Variable Regression and Application to Distillation Columns
Directory of Open Access Journals (Sweden)
Muddu Madakyaru
2013-01-01
Full Text Available Proper control of distillation columns requires estimating some key variables that are challenging to measure online (such as compositions, which are usually estimated using inferential models. Commonly used inferential models include latent variable regression (LVR techniques, such as principal component regression (PCR, partial least squares (PLS, and regularized canonical correlation analysis (RCCA. Unfortunately, measured practical data are usually contaminated with errors, which degrade the prediction abilities of inferential models. Therefore, noisy measurements need to be filtered to enhance the prediction accuracy of these models. Multiscale filtering has been shown to be a powerful feature extraction tool. In this work, the advantages of multiscale filtering are utilized to enhance the prediction accuracy of LVR models by developing an integrated multiscale LVR (IMSLVR modeling algorithm that integrates modeling and feature extraction. The idea behind the IMSLVR modeling algorithm is to filter the process data at different decomposition levels, model the filtered data from each level, and then select the LVR model that optimizes a model selection criterion. The performance of the developed IMSLVR algorithm is illustrated using three examples, one using synthetic data, one using simulated distillation column data, and one using experimental packed bed distillation column data. All examples clearly demonstrate the effectiveness of the IMSLVR algorithm over the conventional methods.
A Multiscale Enrichment Procedure for Nonlinear Monotone Operators
Efendiev, Yalchin R.
2014-03-11
In this paper, multiscale finite element methods (MsFEMs) and domain decomposition techniques are developed for a class of nonlinear elliptic problems with high-contrast coefficients. In the process, existing work on linear problems [Y. Efendiev, J. Galvis, R. Lazarov, S. Margenov and J. Ren, Robust two-level domain decomposition preconditioners for high-contrast anisotropic flows in multiscale media. Submitted.; Y. Efendiev, J. Galvis and X. Wu, J. Comput. Phys. 230 (2011) 937–955; J. Galvis and Y. Efendiev, SIAM Multiscale Model. Simul. 8 (2010) 1461–1483.] is extended to treat a class of nonlinear elliptic operators. The proposed method requires the solutions of (small dimension and local) nonlinear eigenvalue problems in order to systematically enrich the coarse solution space. Convergence of the method is shown to relate to the dimension of the coarse space (due to the enrichment procedure) as well as the coarse mesh size. In addition, it is shown that the coarse mesh spaces can be effectively used in two-level domain decomposition preconditioners. A number of numerical results are presented to complement the analysis.
Multiscale modeling of radiation effects in nuclear reactor structural materials
Energy Technology Data Exchange (ETDEWEB)
Kwon, Junhyun [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)
2015-10-15
Most problems in irradiated materials originate from the atomic collision of high-energy particles and lattice atoms. This collision leads to displacement cascades through the energy transfer reaction and causes various types of defects such as vacancies, interstitials, and clusters. The behavior of the point defects created in the displacement cascades is important because these defects play a major role in a microstructural evolution and further affect the changes in material properties. Rapid advances have been made in the computational capabilities for a realistic simulation of complex physical phenomena, such as irradiation and aging effects. At the same time, progress has been made in understanding the effect of radiation in metals, especially iron-based alloys. In this work, we present some of our ongoing work in this area, which illustrates a multiscale modeling for evaluating a microstructural evolution and mechanical property changes during irradiation. Multiscale modeling approaches are briefly presented here in the following order: nuclear interaction, atomic-level interaction, atomistic modeling, microstructural evolution modeling and mechanical property modeling. This is one of many possible methods for classifying techniques. The effort in developing physical multiscale models applied to radiation damage has been focused on a single crystal or single-grain materials.
Energy Technology Data Exchange (ETDEWEB)
Chen, Li; He, Ya-Ling [Key Laboratory of Thermo-Fluid Science and Engineering of MOE, School of Energy and Power Engineering, Xi' an Jiaotong University, Xi' an, Shaanxi 710049 (China); Kang, Qinjun [Computational Earth Science Group (EES-16), Los Alamos National Laboratory, Los Alamos, NM (United States); Tao, Wen-Quan, E-mail: wqtao@mail.xjtu.edu.cn [Key Laboratory of Thermo-Fluid Science and Engineering of MOE, School of Energy and Power Engineering, Xi' an Jiaotong University, Xi' an, Shaanxi 710049 (China)
2013-12-15
A coupled (hybrid) simulation strategy spatially combining the finite volume method (FVM) and the lattice Boltzmann method (LBM), called CFVLBM, is developed to simulate coupled multi-scale multi-physicochemical processes. In the CFVLBM, computational domain of multi-scale problems is divided into two sub-domains, i.e., an open, free fluid region and a region filled with porous materials. The FVM and LBM are used for these two regions, respectively, with information exchanged at the interface between the two sub-domains. A general reconstruction operator (RO) is proposed to derive the distribution functions in the LBM from the corresponding macro scalar, the governing equation of which obeys the convection–diffusion equation. The CFVLBM and the RO are validated in several typical physicochemical problems and then are applied to simulate complex multi-scale coupled fluid flow, heat transfer, mass transport, and chemical reaction in a wall-coated micro reactor. The maximum ratio of the grid size between the FVM and LBM regions is explored and discussed. -- Highlights: •A coupled simulation strategy for simulating multi-scale phenomena is developed. •Finite volume method and lattice Boltzmann method are coupled. •A reconstruction operator is derived to transfer information at the sub-domains interface. •Coupled multi-scale multiple physicochemical processes in micro reactor are simulated. •Techniques to save computational resources and improve the efficiency are discussed.
Multiscale Modeling of UHTC: Thermal Conductivity
Lawson, John W.; Murry, Daw; Squire, Thomas; Bauschlicher, Charles W.
2012-01-01
We are developing a multiscale framework in computational modeling for the ultra high temperature ceramics (UHTC) ZrB2 and HfB2. These materials are characterized by high melting point, good strength, and reasonable oxidation resistance. They are candidate materials for a number of applications in extreme environments including sharp leading edges of hypersonic aircraft. In particular, we used a combination of ab initio methods, atomistic simulations and continuum computations to obtain insights into fundamental properties of these materials. Ab initio methods were used to compute basic structural, mechanical and thermal properties. From these results, a database was constructed to fit a Tersoff style interatomic potential suitable for atomistic simulations. These potentials were used to evaluate the lattice thermal conductivity of single crystals and the thermal resistance of simple grain boundaries. Finite element method (FEM) computations using atomistic results as inputs were performed with meshes constructed on SEM images thereby modeling the realistic microstructure. These continuum computations showed the reduction in thermal conductivity due to the grain boundary network.
Partnership duration, concurrency, and HIV in sub-Saharan Africa.
Sawers, Larry; Isaac, Alan
2017-07-01
A widely accepted explanation for the exceptionally high HIV prevalence in sub-Saharan Africa is the practice of long-term overlapping heterosexual partnering. This article shows that long-duration concurrent partnering can be protective against HIV transmission rather than promoting it. Monogamous partnering prevents sexual transmission to anyone outside the partnership and, in an initially concordant-seronegative partnership, prevents sexual acquisition of HIV by either partner. Those protections against transmission and acquisition last as long as the partnership persists without new outside partnerships. Correspondingly, these two protective effects characterise polygynous partnerships, whether or not the polygyny is formal or informal, until a partner initiates a new partnership. Stable and exclusive unions of any size protect against HIV transmission, and more durable unions provide a longer protective effect. Survey research provides little information on partnership duration in sub-Saharan Africa and sheds no light on the interaction of duration, concurrency, and HIV. This article shows how assumptions about partnership duration in individual-based sexual-network models affect the contours of simulated HIV epidemics. Longer mean partnership duration slows the pace at which simulated epidemics grow. With plausible assumptions about partnership duration and at levels of concurrency found in the region, simulated HIV epidemics grow slowly or not at all. Those results are consistent with the hypothesis that long-duration partnering is protective against HIV and inconsistent with the hypothesis that long-term concurrency drives the HIV epidemics in sub-Saharan Africa.
Generalization of mixed multiscale finite element methods with applications
Energy Technology Data Exchange (ETDEWEB)
Lee, C S [Texas A & M Univ., College Station, TX (United States)
2016-08-01
Many science and engineering problems exhibit scale disparity and high contrast. The small scale features cannot be omitted in the physical models because they can affect the macroscopic behavior of the problems. However, resolving all the scales in these problems can be prohibitively expensive. As a consequence, some types of model reduction techniques are required to design efficient solution algorithms. For practical purpose, we are interested in mixed finite element problems as they produce solutions with certain conservative properties. Existing multiscale methods for such problems include the mixed multiscale finite element methods. We show that for complicated problems, the mixed multiscale finite element methods may not be able to produce reliable approximations. This motivates the need of enrichment for coarse spaces. Two enrichment approaches are proposed, one is based on generalized multiscale finte element metthods (GMsFEM), while the other is based on spectral element-based algebraic multigrid (rAMGe). The former one, which is called mixed GMsFEM, is developed for both Darcy’s flow and linear elasticity. Application of the algorithm in two-phase flow simulations are demonstrated. For linear elasticity, the algorithm is subtly modified due to the symmetry requirement of the stress tensor. The latter enrichment approach is based on rAMGe. The algorithm differs from GMsFEM in that both of the velocity and pressure spaces are coarsened. Due the multigrid nature of the algorithm, recursive application is available, which results in an efficient multilevel construction of the coarse spaces. Stability, convergence analysis, and exhaustive numerical experiments are carried out to validate the proposed enrichment approaches. iii
Multiscale empirical interpolation for solving nonlinear PDEs
Calo, Victor M.
2014-12-01
In this paper, we propose a multiscale empirical interpolation method for solving nonlinear multiscale partial differential equations. The proposed method combines empirical interpolation techniques and local multiscale methods, such as the Generalized Multiscale Finite Element Method (GMsFEM). To solve nonlinear equations, the GMsFEM is used to represent the solution on a coarse grid with multiscale basis functions computed offline. Computing the GMsFEM solution involves calculating the system residuals and Jacobians on the fine grid. We use empirical interpolation concepts to evaluate these residuals and Jacobians of the multiscale system with a computational cost which is proportional to the size of the coarse-scale problem rather than the fully-resolved fine scale one. The empirical interpolation method uses basis functions which are built by sampling the nonlinear function we want to approximate a limited number of times. The coefficients needed for this approximation are computed in the offline stage by inverting an inexpensive linear system. The proposed multiscale empirical interpolation techniques: (1) divide computing the nonlinear function into coarse regions; (2) evaluate contributions of nonlinear functions in each coarse region taking advantage of a reduced-order representation of the solution; and (3) introduce multiscale proper-orthogonal-decomposition techniques to find appropriate interpolation vectors. We demonstrate the effectiveness of the proposed methods on several nonlinear multiscale PDEs that are solved with Newton\\'s methods and fully-implicit time marching schemes. Our numerical results show that the proposed methods provide a robust framework for solving nonlinear multiscale PDEs on a coarse grid with bounded error and significant computational cost reduction.
Concurrent chemoradiation for vaginal cancer.
Directory of Open Access Journals (Sweden)
David T Miyamoto
Full Text Available BACKGROUND: It is not known whether the addition of chemotherapy to radiation therapy improves outcomes in primary vaginal cancer. Here, we review clinical outcomes in patients with primary vaginal cancer treated with radiation therapy (RT or concurrent chemoradiation therapy (CRT. METHODS: Seventy-one patients with primary vaginal cancer treated with definitive RT with or without concurrent chemotherapy at a single institution were identified and their records reviewed. A total of 51 patients were treated with RT alone; 20 patients were treated with CRT. Recurrences were analyzed. Overall survival (OS and disease-free survival (DFS rates were estimated using the Kaplan-Meier method. Cox regression analysis was performed. RESULTS: The median age at diagnosis was 61 years (range, 18-92 years and the median follow-up time among survivors was 3.0 years. Kaplan-Meier estimates for OS and DFS differed significantly between the RT and CRT groups (3-yr OS = 56% vs. 79%, log-rank p = 0.037; 3-yr DFS = 43% vs. 73%, log-rank p = 0.011. Twenty-three patients (45% in the RT group had a relapse at any site compared to 3 (15% in the CRT group (p = 0.027. With regard to the sites of first relapse, 10 patients (14% had local only, 4 (6% had local and regional, 9 (13% had regional only, 1 (1% had regional and distant, and 2 (3% had distant only relapse. On univariate analysis, the use of concurrent chemotherapy, FIGO stage, tumor size, and date of diagnosis were significant predictors of DFS. On multivariate analysis, the use of concurrent chemotherapy remained a significant predictor of DFS (hazard ratio 0.31 (95% CI, 0.10-0.97; p = 0.04. CONCLUSIONS: Vaginal cancer results in poor outcomes. Adequate radiation dose is essential to ensure curative management. Concurrent chemotherapy should be considered for vaginal cancer patients.
Concurrence classes for general pure multipartite states
International Nuclear Information System (INIS)
Heydari, Hoshang
2005-01-01
We propose concurrence classes for general pure multipartite states based on an orthogonal complement of a positive operator-valued measure on quantum phase. In particular, we construct W m class, GHZ m , and GHZ m-1 class concurrences for general pure m-partite states. We give explicit expressions for W 3 and GHZ 3 class concurrences for general pure three-partite states and for W 4 , GHZ 4 and GHZ 3 class concurrences for general pure four-partite states
Simple concurrent garbage collection almost without synchronization
Hesselink, Wim H.; Lali, M.I.
We present two simple mark and sweep algorithms, A and B, for concurrent garbage collection by a single collector running concurrently with a number of mutators that concurrently modify shared data. Both algorithms are based on the ideas of Ben-Ari's classical algorithm for on-the-fly garbage
An Intensional Concurrent Faithful Encoding of Turing Machines
Directory of Open Access Journals (Sweden)
Thomas Given-Wilson
2014-10-01
Full Text Available The benchmark for computation is typically given as Turing computability; the ability for a computation to be performed by a Turing Machine. Many languages exploit (indirect encodings of Turing Machines to demonstrate their ability to support arbitrary computation. However, these encodings are usually by simulating the entire Turing Machine within the language, or by encoding a language that does an encoding or simulation itself. This second category is typical for process calculi that show an encoding of lambda-calculus (often with restrictions that in turn simulates a Turing Machine. Such approaches lead to indirect encodings of Turing Machines that are complex, unclear, and only weakly equivalent after computation. This paper presents an approach to encoding Turing Machines into intensional process calculi that is faithful, reduction preserving, and structurally equivalent. The encoding is demonstrated in a simple asymmetric concurrent pattern calculus before generalised to simplify infinite terms, and to show encodings into Concurrent Pattern Calculus and Psi Calculi.
Multi-scale modeling with cellular automata: The complex automata approach
Hoekstra, A.G.; Falcone, J.-L.; Caiazzo, A.; Chopard, B.
2008-01-01
Cellular Automata are commonly used to describe complex natural phenomena. In many cases it is required to capture the multi-scale nature of these phenomena. A single Cellular Automata model may not be able to efficiently simulate a wide range of spatial and temporal scales. It is our goal to
Advanced computational workflow for the multi-scale modeling of the bone metabolic processes.
Dao, Tien Tuan
2017-06-01
Multi-scale modeling of the musculoskeletal system plays an essential role in the deep understanding of complex mechanisms underlying the biological phenomena and processes such as bone metabolic processes. Current multi-scale models suffer from the isolation of sub-models at each anatomical scale. The objective of this present work was to develop a new fully integrated computational workflow for simulating bone metabolic processes at multi-scale levels. Organ-level model employs multi-body dynamics to estimate body boundary and loading conditions from body kinematics. Tissue-level model uses finite element method to estimate the tissue deformation and mechanical loading under body loading conditions. Finally, cell-level model includes bone remodeling mechanism through an agent-based simulation under tissue loading. A case study on the bone remodeling process located on the human jaw was performed and presented. The developed multi-scale model of the human jaw was validated using the literature-based data at each anatomical level. Simulation outcomes fall within the literature-based ranges of values for estimated muscle force, tissue loading and cell dynamics during bone remodeling process. This study opens perspectives for accurately simulating bone metabolic processes using a fully integrated computational workflow leading to a better understanding of the musculoskeletal system function from multiple length scales as well as to provide new informative data for clinical decision support and industrial applications.
Multiscale modelling of hydrogen behaviour on beryllium (0001 surface
Directory of Open Access Journals (Sweden)
Ch. Stihl
2016-12-01
Full Text Available Beryllium is proposed to be a neutron multiplier and plasma facing material in future fusion devices. Therefore, it is crucial to acquire an understanding of the microscopic mechanisms of tritium accumulation and release as a result of transmutation processes that Be undergoes under neutron irradiation. A multiscale simulation of ad- and desorption of hydrogen isotopes on the beryllium (0001 surface is developed. It consists of ab initio calculations of certain H adsorption configurations, a suitable cluster expansion approximating the energies of arbitrary configurations, and a kinetic Monte Carlo method for dynamic simulations of adsorption and desorption. The processes implemented in the kinetic Monte Carlo simulation are deduced from further ab initio calculations comprising both, static relaxation as well as molecular dynamics runs. The simulation is used to reproduce experimental data and the results are compared and discussed. Based on the observed results, proposals for a refined model are made.
Steps in Modular Specifications for Concurrent Modules
DEFF Research Database (Denmark)
Da Rocha Pinto, Pedro; Dinsdale-Young, Thomas; Gardner, Philippa
2015-01-01
The specification of a concurrent program module is a difficult problem. The specifications must be strong enough to enable reasoning about the intended clients without reference to the underlying module implementation. We survey a range of verification techniques for specifying concurrent module......, in particular highlighting four key concepts: auxiliary state, interference abstraction, resource ownership and atomicity. We show how these concepts combine to provide powerful approaches to specifying concurrent modules.......The specification of a concurrent program module is a difficult problem. The specifications must be strong enough to enable reasoning about the intended clients without reference to the underlying module implementation. We survey a range of verification techniques for specifying concurrent modules...
Tan, C.F.; Chen, W.; Rauterberg, G.W.M.
2009-01-01
In this paper, a study of the concurrent engineering design for the environmental friendly low cost aircraft cabin simulator is presented. The study describes the used of concurrent design technique in the design activity. The simulator is a testbed that was designed and built for research on
Multiscale modelling for tokamak pedestals
Abel, I. G.
2018-04-01
Pedestal modelling is crucial to predict the performance of future fusion devices. Current modelling efforts suffer either from a lack of kinetic physics, or an excess of computational complexity. To ameliorate these problems, we take a first-principles multiscale approach to the pedestal. We will present three separate sets of equations, covering the dynamics of edge localised modes (ELMs), the inter-ELM pedestal and pedestal turbulence, respectively. Precisely how these equations should be coupled to each other is covered in detail. This framework is completely self-consistent; it is derived from first principles by means of an asymptotic expansion of the fundamental Vlasov-Landau-Maxwell system in appropriate small parameters. The derivation exploits the narrowness of the pedestal region, the smallness of the thermal gyroradius and the low plasma (the ratio of thermal to magnetic pressures) typical of current pedestal operation to achieve its simplifications. The relationship between this framework and gyrokinetics is analysed, and possibilities to directly match our systems of equations onto multiscale gyrokinetics are explored. A detailed comparison between our model and other models in the literature is performed. Finally, the potential for matching this framework onto an open-field-line region is briefly discussed.
Specifying and Verifying Concurrent Programs.
1985-02-01
for Verification and Specification of Concurrent Systems, held in La - Colle - Sur - Loup , France in October, 1984. Work Supported in part by the National...Proc. ACM Symposium on Princi- 0 ples of Programming Languages, Las Vegas, (January 1980), 251-261. [7] J. V. Guttag and J. J. Horning. An Introduction...names in ’V(S). However, the two formulas behave differently under a renaming mapping p. In particu- lar. p(Vv :A( LA )) equals Vv :p(A(v)), so the
Multiprocessor systems and their concurrency
Energy Technology Data Exchange (ETDEWEB)
Starke, P H
1984-01-01
A multiprocessor system can be considered as a collection of finite automata which communicate over channels or shared memory units. The behaviour of such a system can be described by a semilanguage. This approach allows to define a numerical measure for the concurrency of multiprocessor systems and of distributed systems. This measure is characterized algebraically and the reconfiguration problem asking for an algorithm to construct an l-processor system which is equivalent to a given n-processor system is solved in the paper. 6 references.
Multi-Scale Modeling of Microstructural Evolution in Structural Metallic Systems
Zhao, Lei
Metallic alloys are a widely used class of structural materials, and the mechanical properties of these alloys are strongly dependent on the microstructure. Therefore, the scientific design of metallic materials with superior mechanical properties requires the understanding of the microstructural evolution. Computational models and simulations offer a number of advantages over experimental techniques in the prediction of microstructural evolution, because they can allow studies of microstructural evolution in situ, i.e., while the material is mechanically loaded (meso-scale simulations), and bring atomic-level insights into the microstructure (atomistic simulations). In this thesis, we applied a multi-scale modeling approach to study the microstructural evolution in several metallic systems, including polycrystalline materials and metallic glasses (MGs). Specifically, for polycrystalline materials, we developed a coupled finite element model that combines phase field method and crystal plasticity theory to study the plasticity effect on grain boundary (GB) migration. Our model is not only coupled strongly (i.e., we include plastic driving force on GB migration directly) and concurrently (i.e., coupled equations are solved simultaneously), but also it qualitatively captures such phenomena as the dislocation absorption by mobile GBs. The developed model provides a tool to study the microstructural evolution in plastically deformed metals and alloys. For MGs, we used molecular dynamics (MD) simulations to investigate the nucleation kinetics in the primary crystallization in Al-Sm system. We calculated the time-temperature-transformation curves for low Sm concentrations, from which the strong suppressing effect of Sm solute on Al nucleation and its influencing mechanism are revealed. Also, through the comparative analysis of both Al attachment and Al diffusion in MGs, it has been found that the nucleation kinetics is controlled by interfacial attachment of Al, and that
3D Multiscale Modelling of Angiogenesis and Vascular Tumour Growth
Perfahl, H.
2012-11-01
We present a three-dimensional, multiscale model of vascular tumour growth, which couples nutrient/growth factor transport, blood flow, angiogenesis, vascular remodelling, movement of and interactions between normal and tumour cells, and nutrient-dependent cell cycle dynamics within each cell. We present computational simulations which show how a vascular network may evolve and interact with tumour and healthy cells. We also demonstrate how our model may be combined with experimental data, to predict the spatio-temporal evolution of a vascular tumour.
Fast Decentralized Averaging via Multi-scale Gossip
Tsianos, Konstantinos I.; Rabbat, Michael G.
We are interested in the problem of computing the average consensus in a distributed fashion on random geometric graphs. We describe a new algorithm called Multi-scale Gossip which employs a hierarchical decomposition of the graph to partition the computation into tractable sub-problems. Using only pairwise messages of fixed size that travel at most O(n^{1/3}) hops, our algorithm is robust and has communication cost of O(n loglogn logɛ - 1) transmissions, which is order-optimal up to the logarithmic factor in n. Simulated experiments verify the good expected performance on graphs of many thousands of nodes.
3D Multiscale Modelling of Angiogenesis and Vascular Tumour Growth
Perfahl, H.; Byrne, H. M.; Chen, T.; Estrella, V.; Alarcó n, T.; Lapin, A.; Gatenby, R. A.; Gillies, R. J.; Lloyd, M. C.; Maini, P. K.; Reuss, M.; Owen, M. R.
2012-01-01
We present a three-dimensional, multiscale model of vascular tumour growth, which couples nutrient/growth factor transport, blood flow, angiogenesis, vascular remodelling, movement of and interactions between normal and tumour cells, and nutrient-dependent cell cycle dynamics within each cell. We present computational simulations which show how a vascular network may evolve and interact with tumour and healthy cells. We also demonstrate how our model may be combined with experimental data, to predict the spatio-temporal evolution of a vascular tumour.
Multi-scale modeling of spin transport in organic semiconductors
Hemmatiyan, Shayan; Souza, Amaury; Kordt, Pascal; McNellis, Erik; Andrienko, Denis; Sinova, Jairo
In this work, we present our theoretical framework to simulate simultaneously spin and charge transport in amorphous organic semiconductors. By combining several techniques e.g. molecular dynamics, density functional theory and kinetic Monte Carlo, we are be able to study spin transport in the presence of anisotropy, thermal effects, magnetic and electric field effects in a realistic morphologies of amorphous organic systems. We apply our multi-scale approach to investigate the spin transport in amorphous Alq3 (Tris(8-hydroxyquinolinato)aluminum) and address the underlying spin relaxation mechanism in this system as a function of temperature, bias voltage, magnetic field and sample thickness.
Expected Navigation Flight Performance for the Magnetospheric Multiscale (MMS) Mission
Olson, Corwin; Wright, Cinnamon; Long, Anne
2012-01-01
The Magnetospheric Multiscale (MMS) mission consists of four formation-flying spacecraft placed in highly eccentric elliptical orbits about the Earth. The primary scientific mission objective is to study magnetic reconnection within the Earth s magnetosphere. The baseline navigation concept is the independent estimation of each spacecraft state using GPS pseudorange measurements (referenced to an onboard Ultra Stable Oscillator) and accelerometer measurements during maneuvers. State estimation for the MMS spacecraft is performed onboard each vehicle using the Goddard Enhanced Onboard Navigation System, which is embedded in the Navigator GPS receiver. This paper describes the latest efforts to characterize expected navigation flight performance using upgraded simulation models derived from recent analyses.
Fast online generalized multiscale finite element method using constraint energy minimization
Chung, Eric T.; Efendiev, Yalchin; Leung, Wing Tat
2018-02-01
Local multiscale methods often construct multiscale basis functions in the offline stage without taking into account input parameters, such as source terms, boundary conditions, and so on. These basis functions are then used in the online stage with a specific input parameter to solve the global problem at a reduced computational cost. Recently, online approaches have been introduced, where multiscale basis functions are adaptively constructed in some regions to reduce the error significantly. In multiscale methods, it is desired to have only 1-2 iterations to reduce the error to a desired threshold. Using Generalized Multiscale Finite Element Framework [10], it was shown that by choosing sufficient number of offline basis functions, the error reduction can be made independent of physical parameters, such as scales and contrast. In this paper, our goal is to improve this. Using our recently proposed approach [4] and special online basis construction in oversampled regions, we show that the error reduction can be made sufficiently large by appropriately selecting oversampling regions. Our numerical results show that one can achieve a three order of magnitude error reduction, which is better than our previous methods. We also develop an adaptive algorithm and enrich in selected regions with large residuals. In our adaptive method, we show that the convergence rate can be determined by a user-defined parameter and we confirm this by numerical simulations. The analysis of the method is presented.
Lu, Zhao; Sun, Jing; Butts, Kenneth
2014-05-01
Support vector regression for approximating nonlinear dynamic systems is more delicate than the approximation of indicator functions in support vector classification, particularly for systems that involve multitudes of time scales in their sampled data. The kernel used for support vector learning determines the class of functions from which a support vector machine can draw its solution, and the choice of kernel significantly influences the performance of a support vector machine. In this paper, to bridge the gap between wavelet multiresolution analysis and kernel learning, the closed-form orthogonal wavelet is exploited to construct new multiscale asymmetric orthogonal wavelet kernels for linear programming support vector learning. The closed-form multiscale orthogonal wavelet kernel provides a systematic framework to implement multiscale kernel learning via dyadic dilations and also enables us to represent complex nonlinear dynamics effectively. To demonstrate the superiority of the proposed multiscale wavelet kernel in identifying complex nonlinear dynamic systems, two case studies are presented that aim at building parallel models on benchmark datasets. The development of parallel models that address the long-term/mid-term prediction issue is more intricate and challenging than the identification of series-parallel models where only one-step ahead prediction is required. Simulation results illustrate the effectiveness of the proposed multiscale kernel learning.
Ngada, Narcisse
2015-06-15
The complexity and cost of building and running high-power electrical systems make the use of simulations unavoidable. The simulations available today provide great understanding about how systems really operate. This paper helps the reader to gain an insight into simulation in the field of power converters for particle accelerators. Starting with the definition and basic principles of simulation, two simulation types, as well as their leading tools, are presented: analog and numerical simulations. Some practical applications of each simulation type are also considered. The final conclusion then summarizes the main important items to keep in mind before opting for a simulation tool or before performing a simulation.
CERN. Geneva
2017-01-01
High Energy and Nuclear Physics (HENP) libraries are now required to be increasingly multi-thread-safe, if not multi-thread-friendly and multi-threaded. This is usually done using the new constructs and library components offered by the C++11 and C++14 standards. These components are however quite low-level (threads, mutexes, locks, ...) and hard to use and compose, or easy to misuse. However, Go -- a somewhat new language -- provides a set of better building blocks for tackling concurrency: goroutines and channels. This language is now used by the cloud industry at large; docker/moby, rkt, Kubernetes, OpenShift, etc... are obvious flagships for Go. It is also used in other interesting places like SpaceX's telemetry monitoring system and in the New York Times', YouTube's or Disney's content delivery infrastructures. In this talk, we will describe the building blocks of Go and see how they are combined to easily create concurrent programs that grow with grace, are fast to compile and deploy, but also easy to...
Patients survey after concurrent chemoradiotherapy
International Nuclear Information System (INIS)
Shimane, Toshikazku; Egawa, Syunya; Mori, Tomoaki; Ono, Tomohiro; Monden, Tetsuya; Kobayashi, Sei; Sanbe, Takeyuki; Suzaki, Harumi
2010-01-01
Concurrent chemoradiotherapy for cancer of head and neck is becoming more popular as the treatment of choice. It is considered to maintain the quality of life (QOL) of patients better than operative treatments in terms of preserving the functions, organs, and figure, but recently we cannot necessarily say that it maintains the QOL of patients better than operative treatments because its complications after therapy disturb daily life. We report the results of a questionnaire survey about complications after therapy, problems during therapy, improvements, and satisfaction level directed at patients with cancer of the head and neck who received Concurrent chemoradiotherapy for the purpose of ascertaining if patients can actually maintain their QOL after therapy. As a result, the most controversial problem was mouth dryness, but the symptom improved as the follow-up duration got longer. As for the satisfaction level, 'very-satisfied' and 'almost-satisfied' were more than 90%, so we concluded that the QOL of patients is maintained after therapy, while there are still improvements to be made. We also concluded that we should continue to make improvement and try to improve the QOL of patients during and after therapy. (author)
Foundations for a multiscale collaborative Earth model
Afanasiev, M.; Peter, Daniel; Sager, K.; Simut, S.; Ermert, L.; Krischer, L.; Fichtner, A.
2015-01-01
. The CSEM as a computational framework is intended to help bridging the gap between local, regional and global tomography, and to contribute to the development of a global multiscale Earth model. While the current construction serves as a first proof
State-of-the-Art Report on Multi-scale Modelling of Nuclear Fuels
International Nuclear Information System (INIS)
Bartel, T.J.; Dingreville, R.; Littlewood, D.; Tikare, V.; Bertolus, M.; Blanc, V.; Bouineau, V.; Carlot, G.; Desgranges, C.; Dorado, B.; Dumas, J.C.; Freyss, M.; Garcia, P.; Gatt, J.M.; Gueneau, C.; Julien, J.; Maillard, S.; Martin, G.; Masson, R.; Michel, B.; Piron, J.P.; Sabathier, C.; Skorek, R.; Toffolon, C.; Valot, C.; Van Brutzel, L.; Besmann, Theodore M.; Chernatynskiy, A.; Clarno, K.; Gorti, S.B.; Radhakrishnan, B.; Devanathan, R.; Dumont, M.; Maugis, P.; El-Azab, A.; Iglesias, F.C.; Lewis, B.J.; Krack, M.; Yun, Y.; Kurata, M.; Kurosaki, K.; Largenton, R.; Lebensohn, R.A.; Malerba, L.; Oh, J.Y.; Phillpot, S.R.; Tulenko, J. S.; Rachid, J.; Stan, M.; Sundman, B.; Tonks, M.R.; Williamson, R.; Van Uffelen, P.; Welland, M.J.; Valot, Carole; Stan, Marius; Massara, Simone; Tarsi, Reka
2015-10-01
The Nuclear Science Committee (NSC) of the Nuclear Energy Agency (NEA) has undertaken an ambitious programme to document state-of-the-art of modelling for nuclear fuels and structural materials. The project is being performed under the Working Party on Multi-Scale Modelling of Fuels and Structural Material for Nuclear Systems (WPMM), which has been established to assess the scientific and engineering aspects of fuels and structural materials, describing multi-scale models and simulations as validated predictive tools for the design of nuclear systems, fuel fabrication and performance. The WPMM's objective is to promote the exchange of information on models and simulations of nuclear materials, theoretical and computational methods, experimental validation and related topics. It also provides member countries with up-to-date information, shared data, models, and expertise. The goal is also to assess needs for improvement and address them by initiating joint efforts. The WPMM reviews and evaluates multi-scale modelling and simulation techniques currently employed in the selection of materials used in nuclear systems. It serves to provide advice to the nuclear community on the developments needed to meet the requirements of modelling for the design of different nuclear systems. The original WPMM mandate had three components (Figure 1), with the first component currently completed, delivering a report on the state-of-the-art of modelling of structural materials. The work on modelling was performed by three expert groups, one each on Multi-Scale Modelling Methods (M3), Multi-Scale Modelling of Fuels (M2F) and Structural Materials Modelling (SMM). WPMM is now composed of three expert groups and two task forces providing contributions on multi-scale methods, modelling of fuels and modelling of structural materials. This structure will be retained, with the addition of task forces as new topics are developed. The mandate of the Expert Group on Multi-Scale Modelling of
All-Particle Multiscale Computation of Hypersonic Rarefied Flow
Jun, E.; Burt, J. M.; Boyd, I. D.
2011-05-01
This study examines a new hybrid particle scheme used as an alternative means of multiscale flow simulation. The hybrid particle scheme employs the direct simulation Monte Carlo (DSMC) method in rarefied flow regions and the low diffusion (LD) particle method in continuum flow regions. The numerical procedures of the low diffusion particle method are implemented within an existing DSMC algorithm. The performance of the LD-DSMC approach is assessed by studying Mach 10 nitrogen flow over a sphere with a global Knudsen number of 0.002. The hybrid scheme results show good overall agreement with results from standard DSMC and CFD computation. Subcell procedures are utilized to improve computational efficiency and reduce sensitivity to DSMC cell size in the hybrid scheme. This makes it possible to perform the LD-DSMC simulation on a much coarser mesh that leads to a significant reduction in computation time.
Multiscale Modeling of Wear Degradation
Moraes, Alvaro; Ruggeri, Fabrizio; Tempone, Raul; Vilanova, Pedro
2016-01-01
Cylinder liners of diesel engines used for marine propulsion are naturally subjected to a wear process, and may fail when their wear exceeds a specified limit. Since failures often represent high economical costs, it is utterly important to predict and avoid them. In this work [4], we model the wear process using a pure jump process. Therefore, the inference goal here is to estimate: the number of possible jumps, its sizes, the coefficients and the shapes of the jump intensities. We propose a multiscale approach for the inference problem that can be seen as an indirect inference scheme. We found that using a Gaussian approximation based on moment expansions, it is possible to accurately estimate the jump intensities and the jump amplitudes. We obtained results equivalent to the state of the art but using a simpler and less expensive approach.
Multiscale Modeling of Wear Degradation
Moraes, Alvaro; Ruggeri, Fabrizio; Tempone, Raul; Vilanova, Pedro
2015-01-01
Cylinder liners of diesel engines used for marine propulsion are naturally subjected to a wear process, and may fail when their wear exceeds a specified limit. Since failures often represent high economical costs, it is utterly important to predict and avoid them. In this work [4], we model the wear process using a pure jump process. Therefore, the inference goal here is to estimate: the number of possible jumps, its sizes, the coefficients and the shapes of the jump intensities. We propose a multiscale approach for the inference problem that can be seen as an indirect inference scheme. We found that using a Gaussian approximation based on moment expansions, it is possible to accurately estimate the jump intensities and the jump amplitudes. We obtained results equivalent to the state of the art but using a simpler and less expensive approach.
Multiscale Modeling of Wear Degradation
Moraes, Alvaro
2015-01-07
Cylinder liners of diesel engines used for marine propulsion are naturally subjected to a wear process, and may fail when their wear exceeds a specified limit. Since failures often represent high economical costs, it is utterly important to predict and avoid them. In this work [4], we model the wear process using a pure jump process. Therefore, the inference goal here is to estimate: the number of possible jumps, its sizes, the coefficients and the shapes of the jump intensities. We propose a multiscale approach for the inference problem that can be seen as an indirect inference scheme. We found that using a Gaussian approximation based on moment expansions, it is possible to accurately estimate the jump intensities and the jump amplitudes. We obtained results equivalent to the state of the art but using a simpler and less expensive approach.
Multiscale Modeling of Wear Degradation
Moraes, Alvaro
2014-01-06
Cylinder liners of diesel engines used for marine propulsion are naturally subjected to a wear process, and may fail when their wear exceeds a specified limit. Since failures often represent high economical costs, it is utterly important to predict and avoid them. In this work [4], we model the wear process using a pure jump process. Therefore, the inference goal here is to estimate: the number of possible jumps, its sizes, the coefficients and the shapes of the jump intensities. We propose a multiscale approach for the inference problem that can be seen as an indirect inference scheme. We found that using a Gaussian approximation based on moment expansions, it is possible to accurately estimate the jump intensities and the jump amplitudes. We obtained results equivalent to the state of the art but using a simpler and less expensive approach.
Multiscale Modeling of Wear Degradation
Moraes, Alvaro
2016-01-06
Cylinder liners of diesel engines used for marine propulsion are naturally subjected to a wear process, and may fail when their wear exceeds a specified limit. Since failures often represent high economical costs, it is utterly important to predict and avoid them. In this work [4], we model the wear process using a pure jump process. Therefore, the inference goal here is to estimate: the number of possible jumps, its sizes, the coefficients and the shapes of the jump intensities. We propose a multiscale approach for the inference problem that can be seen as an indirect inference scheme. We found that using a Gaussian approximation based on moment expansions, it is possible to accurately estimate the jump intensities and the jump amplitudes. We obtained results equivalent to the state of the art but using a simpler and less expensive approach.
Wavelets and multiscale signal processing
Cohen, Albert
1995-01-01
Since their appearance in mid-1980s, wavelets and, more generally, multiscale methods have become powerful tools in mathematical analysis and in applications to numerical analysis and signal processing. This book is based on "Ondelettes et Traitement Numerique du Signal" by Albert Cohen. It has been translated from French by Robert D. Ryan and extensively updated by both Cohen and Ryan. It studies the existing relations between filter banks and wavelet decompositions and shows how these relations can be exploited in the context of digital signal processing. Throughout, the book concentrates on the fundamentals. It begins with a chapter on the concept of multiresolution analysis, which contains complete proofs of the basic results. The description of filter banks that are related to wavelet bases is elaborated in both the orthogonal case (Chapter 2), and in the biorthogonal case (Chapter 4). The regularity of wavelets, how this is related to the properties of the filters and the importance of regularity for t...
Multiphysics/multiscale multifluid computations
International Nuclear Information System (INIS)
Yadigaroglu, George
2014-01-01
Regarding experimentation, interesting examples of multi-scale approaches are found: the small-scale experiments to understand the mechanisms of counter-current flow limitations (CCFL) such as the growth of instabilities on films, droplet entrainment, etc; meso-scale experiments to quantify the CCFL conditions in typical geometries such as tubes and gaps between parallel plates, and finally full-scale experimentation in a typical reactor geometry - the UPTF tests. Another example is the mixing of the atmosphere produced by plumes and jets in a reactor containment: one needs first basic turbulence information that can be obtained at the microscopic level; follow medium-scale experiments to understand the behaviour of jets and plumes; finally reactor-scale tests can be conducted in facilities such as PANDA at PSI, in Switzerland to study the phenomena at large scale
Concurrent systems and time synchronization
Burgin, Mark; Grathoff, Annette
2018-05-01
In the majority of scientific fields, system dynamics is described assuming existence of unique time for the whole system. However, it is established theoretically, for example, in relativity theory or in the system theory of time, and validated experimentally that there are different times and time scales in a variety of real systems - physical, chemical, biological, social, etc. In spite of this, there are no wide-ranging scientific approaches to exploration of such systems. Therefore, the goal of this paper is to study systems with this property. We call them concurrent systems because processes in them can go, events can happen and actions can be performed in different time scales. The problem of time synchronization is specifically explored.
Nutritional strategies to support concurrent training.
Perez-Schindler, Joaquin; Hamilton, D Lee; Moore, Daniel R; Baar, Keith; Philp, Andrew
2015-01-01
Concurrent training (the combination of endurance exercise to resistance training) is a common practice for athletes looking to maximise strength and endurance. Over 20 years ago, it was first observed that performing endurance exercise after resistance exercise could have detrimental effects on strength gains. At the cellular level, specific protein candidates have been suggested to mediate this training interference; however, at present, the physiological reason(s) behind the concurrent training effect remain largely unknown. Even less is known regarding the optimal nutritional strategies to support concurrent training and whether unique nutritional approaches are needed to support endurance and resistance exercise during concurrent training approaches. In this review, we will discuss the importance of protein supplementation for both endurance and resistance training adaptation and highlight additional nutritional strategies that may support concurrent training. Finally, we will attempt to synergise current understanding of the interaction between physiological responses and nutritional approaches into practical recommendations for concurrent training.
Integrated multiscale modeling of molecular computing devices
International Nuclear Information System (INIS)
Cummings, Peter T; Leng Yongsheng
2005-01-01
Molecular electronics, in which single organic molecules are designed to perform the functions of transistors, diodes, switches and other circuit elements used in current siliconbased microelecronics, is drawing wide interest as a potential replacement technology for conventional silicon-based lithographically etched microelectronic devices. In addition to their nanoscopic scale, the additional advantage of molecular electronics devices compared to silicon-based lithographically etched devices is the promise of being able to produce them cheaply on an industrial scale using wet chemistry methods (i.e., self-assembly from solution). The design of molecular electronics devices, and the processes to make them on an industrial scale, will require a thorough theoretical understanding of the molecular and higher level processes involved. Hence, the development of modeling techniques for molecular electronics devices is a high priority from both a basic science point of view (to understand the experimental studies in this field) and from an applied nanotechnology (manufacturing) point of view. Modeling molecular electronics devices requires computational methods at all length scales - electronic structure methods for calculating electron transport through organic molecules bonded to inorganic surfaces, molecular simulation methods for determining the structure of self-assembled films of organic molecules on inorganic surfaces, mesoscale methods to understand and predict the formation of mesoscale patterns on surfaces (including interconnect architecture), and macroscopic scale methods (including finite element methods) for simulating the behavior of molecular electronic circuit elements in a larger integrated device. Here we describe a large Department of Energy project involving six universities and one national laboratory aimed at developing integrated multiscale methods for modeling molecular electronics devices. The project is funded equally by the Office of Basic
Multi-scale MHD analysis of heliotron plasma in change of background field
International Nuclear Information System (INIS)
Ichiguchi, K.; Sakakibara, S.; Ohdachi, S.; Carreras, B.A.
2012-11-01
A partial collapse observed in the Large Helical Device (LHD) experiments shifting the magnetic axis inwardly with a real time control of the background field is analyzed with a magnetohydrodynamics (MHD) numerical simulation. The simulation is carried out with a multi-scale simulation scheme. In the simulation, the equilibrium also evolves including the change of the pressure and the rotational transform due to the perturbation dynamics. The simulation result agrees with the experiments qualitatively, which shows that the mechanism is attributed to the destabilization of an infernal-like mode. The destabilization is caused by the change of the background field through the enhancement of the magnetic hill. (author)
Rain VM: Portable Concurrency through Managing Code
Brown, Neil C.C.
2006-01-01
A long-running recent trend in computer programming is the growth in popularity of virtual machines. However, few have included good support for concurrency - a natural mechanism in the Rain programming language. This paper details the design and implementation of a secure virtual machine with support for concurrency, which enables portability of concurrent programs. Possible implementation ideas of many-to-many threading models for the virtual machine kernel are discussed, and initial benchm...
Multiscale Model Reduction with Generalized Multiscale Finite Element Methods in Geomathematics
Efendiev, Yalchin R.; Presho, Michael
2015-01-01
In this chapter, we discuss multiscale model reduction using Generalized Multiscale Finite Element Methods (GMsFEM) in a number of geomathematical applications. GMsFEM has been recently introduced (Efendiev et al. 2012) and applied to various problems. In the current chapter, we consider some of these applications and outline the basic methodological concepts.
Distributed multiscale computing with MUSCLE 2, the Multiscale Coupling Library and Environment
Borgdorff, J.; Mamonski, M.; Bosak, B.; Kurowski, K.; Ben Belgacem, M.; Chopard, B.; Groen, D.; Coveney, P.V.; Hoekstra, A.G.
2014-01-01
We present the Multiscale Coupling Library and Environment: MUSCLE 2. This multiscale component-based execution environment has a simple to use Java, C++, C, Python and Fortran API, compatible with MPI, OpenMP and threading codes. We demonstrate its local and distributed computing capabilities and
Borgdorff, J.; Bona-Casas, C.; Mamonski, M.; Kurowski, K.; Piontek, T.; Bosak, B.; Rycerz, K.; Ciepiela, E.; Gubala, T.; Harezlak, D.; Bubak, M.; Lorenz, E.; Hoekstra, A.G.
2012-01-01
Nature is observed at all scales; with multiscale modeling, scientists bring together several scales for a holistic analysis of a phenomenon. The models on these different scales may require significant but also heterogeneous computational resources, creating the need for distributed multiscale
Multiscale Model Reduction with Generalized Multiscale Finite Element Methods in Geomathematics
Efendiev, Yalchin R.
2015-09-02
In this chapter, we discuss multiscale model reduction using Generalized Multiscale Finite Element Methods (GMsFEM) in a number of geomathematical applications. GMsFEM has been recently introduced (Efendiev et al. 2012) and applied to various problems. In the current chapter, we consider some of these applications and outline the basic methodological concepts.
Concurrence of three Jaynes-Cummings systems
Qiang, Wen-Chao; Sun, Guo-Hua; Dong, Qian; Camacho-Nieto, Oscar; Dong, Shi-Hai
2018-04-01
We apply genuine multipartite concurrence to investigate entanglement properties of three Jaynes-Cummings systems. Three atoms are initially put in GHZ-like state and locally interact with three independent cavities, respectively. We present analytical concurrence expressions for various subsystems including three-atom, three-cavity and some atom-cavity mixed systems. We also examine the global system and illustrate the evolution of its concurrence. Except for the sudden death of entanglement, we find for some initial entanglement parameter θ , the concurrence of the global system may maintain unchanged in some time intervals.
How does concurrent sourcing affect performance?
DEFF Research Database (Denmark)
Mols, Niels Peter
2010-01-01
be modelled. The propositions and discussion offer researchers a starting-point for further research. Practical implications – The propositions that are developed suggest that managers should consider using concurrent sourcing when they face problems caused by volume uncertainty, technological uncertainty....../methodology/approach – Based on transaction cost, agency, neoclassical economic, knowledge-based, and resource-based theory, it is proposed to show how concurrent sourcing affects performance. Findings – The paper argues that concurrent sourcing improves performance when firms face a combination of volume uncertainty...... how concurrent sourcing affects performance of the market and the hierarchy....
A Reference Framework for Concurrent Engineering
Institute of Scientific and Technical Information of China (English)
无
2001-01-01
Considering the diversity of methods and tools offered to concurrent engineering, the aspects playing important roles in the concurrent engineering c ontext have been pinpointed as being four core elements which are Activity, Meth od, Object and Information. Based on these four elements, a reference framework called AMOI is proposed to be the guideline for the systematic concurrent produc t design. Using the AMOI reference framework, concurrent product development sys tem can be structured into four function models (including the activity model, m ethod model, object model and information model) which are interconnected with e ach other.
Simulation of atmospheric oxidation capacity in Houston, Texas
Air quality model simulations are performed and evaluated for Houston using the Community Multiscale Air Quality (CMAQ) model. The simulations use two different emissions estimates: the EPA 2005 National Emissions Inventory (NEI) and the Texas Commission on Environmental Quality ...
Energy Technology Data Exchange (ETDEWEB)
Muraglia, M.
2009-10-15
In a tokamak, it exists many kinds of instability at the origin of a damage of the confinement and worst of a lost of a confinement. This work presents a study of the dynamics of a magnetic island in presence of turbulence in magnetized plasmas. More precisely, the goal is to understand the multi-scales interaction between turbulence, generated by a pressure gradient and the magnetic field curvature, and a magnetic island formed thanks to a tearing mode. Thanks to the derivation of a 2-dimensional slab model taking into account both tearing and interchange instabilities, theoretical and numerical linear studies show the pressure effect on the magnetic island linear formation and show interchange modes are stabilized in presence of a strong magnetic field. Then, a numerical nonlinear study is presented in order to understand how the interchange mechanism affects the nonlinear dynamics of a magnetic island. It is shown that the pressure gradient and the magnetic field curvature affect strongly the nonlinear evolution of a magnetic island through dynamics bifurcations. The nature of these bifurcations should be characterized in function of the linear situation. Finally, the last part of this work is devoted to the study of the origin of the nonlinear poloidal rotation of the magnetic island. A model giving the different contributions to the rotation is derived. It is shown, thanks to the model and to the numerical studies, that the nonlinear rotation of the island is mainly governed by the ExB poloidal flow and/or by the nonlinear diamagnetic drift. (author)